Starting search... Converting FASTA to Prosit input Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx4096M -cp "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertFastaToPrositCSV -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -o "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.csv" -defaultNCE 27 -defaultCharge 3 -minCharge 2 -maxCharge 3 -maxMissedCleavage 1 [09:48:36] Starting to build Prosit CSV: E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.csv [09:48:36] Reading standard formated FASTA database [09:48:41] Finished writing 1630648 peptides to Prosit CSV! [09:48:41] Finished conversion from FASTA to Prosit CSV Reading Prosit CSV input Requesting predictions from Prosit Requesting predictions from Prosit 4096 / 1630648 Requesting predictions from Prosit 8192 / 1630648 Requesting predictions from Prosit 12288 / 1630648 Requesting predictions from Prosit 16384 / 1630648 Requesting predictions from Prosit 20480 / 1630648 Requesting predictions from Prosit 24576 / 1630648 Requesting predictions from Prosit 28672 / 1630648 Requesting predictions from Prosit 32768 / 1630648 Requesting predictions from Prosit 36864 / 1630648 Requesting predictions from Prosit 40960 / 1630648 Requesting predictions from Prosit 45056 / 1630648 Requesting predictions from Prosit 49152 / 1630648 Requesting predictions from Prosit 53248 / 1630648 Requesting predictions from Prosit 57344 / 1630648 Requesting predictions from Prosit 61440 / 1630648 Requesting predictions from Prosit 65536 / 1630648 Requesting predictions from Prosit 69632 / 1630648 Requesting 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predictions from Prosit 626688 / 1141300 Requesting predictions from Prosit 630784 / 1141300 Requesting predictions from Prosit 634880 / 1141300 Requesting predictions from Prosit 638976 / 1141300 Requesting predictions from Prosit 643072 / 1141300 Requesting predictions from Prosit 647168 / 1141300 Requesting predictions from Prosit 651264 / 1141300 Requesting predictions from Prosit 655360 / 1141300 Requesting predictions from Prosit 659456 / 1141300 Requesting predictions from Prosit 663552 / 1141300 Requesting predictions from Prosit 667648 / 1141300 Requesting predictions from Prosit 671744 / 1141300 Requesting predictions from Prosit 675840 / 1141300 Requesting predictions from Prosit 679936 / 1141300 Requesting predictions from Prosit 684032 / 1141300 Requesting predictions from Prosit 688128 / 1141300 Requesting predictions from Prosit 692224 / 1141300 Requesting predictions from Prosit 696320 / 1141300 Requesting predictions from Prosit 700416 / 1141300 Requesting predictions from Prosit 704512 / 1141300 Requesting predictions from Prosit 708608 / 1141300 Requesting predictions from Prosit 712704 / 1141300 Requesting predictions from Prosit 716800 / 1141300 Requesting predictions from Prosit 720896 / 1141300 Requesting predictions from Prosit 724992 / 1141300 Requesting predictions from Prosit 729088 / 1141300 Requesting predictions from Prosit 733184 / 1141300 Requesting predictions from Prosit 737280 / 1141300 Requesting predictions from Prosit 741376 / 1141300 Requesting predictions from Prosit 745472 / 1141300 Requesting predictions from Prosit 749568 / 1141300 Requesting predictions from Prosit 753664 / 1141300 Requesting predictions from Prosit 757760 / 1141300 Requesting predictions from Prosit 761856 / 1141300 Requesting predictions from Prosit 765952 / 1141300 Requesting predictions from Prosit 770048 / 1141300 Requesting predictions from Prosit 774144 / 1141300 Requesting predictions from Prosit 778240 / 1141300 Requesting predictions from Prosit 782336 / 1141300 Requesting predictions from Prosit 786432 / 1141300 Requesting predictions from Prosit 790528 / 1141300 Requesting predictions from Prosit 794624 / 1141300 Requesting predictions from Prosit 798720 / 1141300 Requesting predictions from Prosit 802816 / 1141300 Requesting predictions from Prosit 806912 / 1141300 Requesting predictions from Prosit 811008 / 1141300 Requesting predictions from Prosit 815104 / 1141300 Requesting predictions from Prosit 819200 / 1141300 Requesting predictions from Prosit 823296 / 1141300 Requesting predictions from Prosit 827392 / 1141300 Requesting predictions from Prosit 831488 / 1141300 Requesting predictions from Prosit 835584 / 1141300 Requesting predictions from Prosit 839680 / 1141300 Requesting predictions from Prosit 843776 / 1141300 Requesting predictions from Prosit 847872 / 1141300 Requesting predictions from Prosit 851968 / 1141300 Requesting predictions from Prosit 856064 / 1141300 Requesting predictions from Prosit 860160 / 1141300 Requesting predictions from Prosit 864256 / 1141300 Requesting predictions from Prosit 868352 / 1141300 Requesting predictions from Prosit 872448 / 1141300 Requesting predictions from Prosit 876544 / 1141300 Requesting predictions from Prosit 880640 / 1141300 Requesting predictions from Prosit 884736 / 1141300 Requesting predictions from Prosit 888832 / 1141300 Requesting predictions from Prosit 892928 / 1141300 Requesting predictions from Prosit 897024 / 1141300 Requesting predictions from Prosit 901120 / 1141300 Requesting predictions from Prosit 905216 / 1141300 Requesting predictions from Prosit 909312 / 1141300 Requesting predictions from Prosit 913408 / 1141300 Requesting predictions from Prosit 917504 / 1141300 Requesting predictions from Prosit 921600 / 1141300 Requesting predictions from Prosit 925696 / 1141300 Requesting predictions from Prosit 929792 / 1141300 Requesting predictions from Prosit 933888 / 1141300 Requesting predictions from Prosit 937984 / 1141300 Requesting predictions from Prosit 942080 / 1141300 Requesting predictions from Prosit 946176 / 1141300 Requesting predictions from Prosit 950272 / 1141300 Requesting predictions from Prosit 954368 / 1141300 Requesting predictions from Prosit 958464 / 1141300 Requesting predictions from Prosit 962560 / 1141300 Requesting predictions from Prosit 966656 / 1141300 Requesting predictions from Prosit 970752 / 1141300 Requesting predictions from Prosit 974848 / 1141300 Requesting predictions from Prosit 978944 / 1141300 Requesting predictions from Prosit 983040 / 1141300 Requesting predictions from Prosit 987136 / 1141300 Requesting predictions from Prosit 991232 / 1141300 Requesting predictions from Prosit 995328 / 1141300 Requesting predictions from Prosit 999424 / 1141300 Requesting predictions from Prosit 1003520 / 1141300 Requesting predictions from Prosit 1007616 / 1141300 Requesting predictions from Prosit 1011712 / 1141300 Requesting predictions from Prosit 1015808 / 1141300 Requesting predictions from Prosit 1019904 / 1141300 Requesting predictions from Prosit 1024000 / 1141300 Requesting predictions from Prosit 1028096 / 1141300 Requesting predictions from Prosit 1032192 / 1141300 Requesting predictions from Prosit 1036288 / 1141300 Requesting predictions from Prosit 1040384 / 1141300 Requesting predictions from Prosit 1044480 / 1141300 Requesting predictions from Prosit 1048576 / 1141300 Requesting predictions from Prosit 1052672 / 1141300 Requesting predictions from Prosit 1056768 / 1141300 Requesting predictions from Prosit 1060864 / 1141300 Requesting predictions from Prosit 1064960 / 1141300 Requesting predictions from Prosit 1069056 / 1141300 Requesting predictions from Prosit 1073152 / 1141300 Requesting predictions from Prosit 1077248 / 1141300 Requesting predictions from Prosit 1081344 / 1141300 Requesting predictions from Prosit 1085440 / 1141300 Requesting predictions from Prosit 1089536 / 1141300 Requesting predictions from Prosit 1093632 / 1141300 Requesting predictions from Prosit 1097728 / 1141300 Requesting predictions from Prosit 1101824 / 1141300 Requesting predictions from Prosit 1105920 / 1141300 Requesting predictions from Prosit 1110016 / 1141300 Requesting predictions from Prosit 1114112 / 1141300 Requesting predictions from Prosit 1118208 / 1141300 Requesting predictions from Prosit 1122304 / 1141300 Requesting predictions from Prosit 1126400 / 1141300 Requesting predictions from Prosit 1130496 / 1141300 Requesting predictions from Prosit 1134592 / 1141300 Requesting predictions from Prosit 1137204 / 1141300 Requesting predictions from Prosit 1141300 / 1141300 Exporting Prosit spectra to BiblioSpec library Converting Prosit output to EncyclopeDIA library Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -cp "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit-6D6B1237AF66AD6DAEE5FB1EFBF2F9C3.blib" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -o "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [10:01:50] Indexing UP000005640_9606-z3_nce27-prosit-6D6B1237AF66AD6DAEE5FB1EFBF2F9C3.blib ... [10:01:52] Reading BLIB file [10:01:53] Starting alignment 1 with 1141300 data points [10:02:20] Reading Fasta file UP000005640_9606.fasta [10:02:20] Reading standard formated FASTA database [10:02:20] Constructing trie from library peptides [10:02:34] Accession count histogram: [10:02:34] 0 Acc 0 Counts [10:02:34] 1 Acc 1572023 Counts [10:02:34] 2 Acc 42056 Counts [10:02:34] 3 Acc 8400 Counts [10:02:34] 4 Acc 3051 Counts [10:02:34] 5 Acc 1505 Counts [10:02:34] 6 Acc 1095 Counts [10:02:34] 7 Acc 616 Counts [10:02:34] 8 Acc 352 Counts [10:02:34] 9 Acc 405 Counts [10:02:34] 10 Acc 184 Counts [10:02:34] 11 Acc 200 Counts [10:02:34] 12 Acc 126 Counts [10:02:34] 13 Acc 91 Counts [10:02:34] 14 Acc 74 Counts [10:02:34] 15 Acc 83 Counts [10:02:34] 16 Acc 42 Counts [10:02:34] 17 Acc 25 Counts [10:02:34] 18 Acc 34 Counts [10:02:34] 19 Acc 37 Counts [10:02:34] 20 Acc 249 Counts [10:02:46] 20278 distinct protein groups found. [10:02:46] Writing library file encyclopedia_5391619402095990951.elib [10:05:24] Finished reading UP000005640_9606-z3_nce27-prosit-6D6B1237AF66AD6DAEE5FB1EFBF2F9C3.blib Generating chromatogram library (1 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [10:05:28] EncyclopeDIA version 2.12.30 [10:05:29] Getting count of protein accessions... [10:05:29] Using EncyclopeDIA 2.X Scoring System [10:05:29] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML ... [10:05:29] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML ... [10:05:30] Parsed 1% [10:05:30] Parsed 2% [10:05:30] Parsed 3% [10:05:30] Parsed 4% [10:05:31] Parsed 5% [10:05:31] Parsed 6% [10:05:32] Parsed 7% [10:05:32] Parsed 8% [10:05:33] Parsed 9% [10:05:33] Parsed 10% [10:05:34] Parsed 11% [10:05:34] Parsed 12% [10:05:35] Parsed 13% [10:05:36] Parsed 14% [10:05:37] Parsed 15% [10:05:38] Parsed 16% [10:05:39] Parsed 17% [10:05:40] Parsed 18% [10:05:40] Parsed 19% [10:05:41] Parsed 20% [10:05:42] Parsed 21% [10:05:43] Parsed 22% [10:05:44] Parsed 23% [10:05:45] Parsed 24% [10:05:45] Parsed 25% [10:05:46] Parsed 26% [10:05:47] Parsed 27% [10:05:48] Parsed 28% [10:05:49] Parsed 29% [10:05:50] Parsed 30% [10:05:51] Parsed 31% [10:05:52] Parsed 32% [10:05:55] Parsed 33% [10:05:57] Parsed 34% [10:05:58] Parsed 35% [10:05:59] Parsed 36% [10:05:59] Parsed 37% [10:06:00] Parsed 38% [10:06:01] Parsed 39% [10:06:02] Parsed 40% [10:06:03] Parsed 41% [10:06:04] Parsed 42% [10:06:05] Parsed 43% [10:06:06] Parsed 44% [10:06:09] Parsed 45% [10:06:10] Parsed 46% [10:06:11] Parsed 47% [10:06:12] Parsed 48% [10:06:12] Parsed 49% [10:06:13] Parsed 50% [10:06:14] Parsed 51% [10:06:15] Parsed 52% [10:06:17] Parsed 53% [10:06:18] Parsed 54% [10:06:19] Parsed 55% [10:06:22] Parsed 56% [10:06:24] Parsed 57% [10:06:26] Parsed 58% [10:06:30] Parsed 59% [10:06:33] Parsed 60% [10:06:38] Parsed 61% [10:06:42] Parsed 62% [10:06:47] Parsed 63% [10:06:52] Parsed 64% [10:06:58] Parsed 65% [10:07:04] Parsed 66% [10:07:12] Parsed 67% [10:07:25] Parsed 68% [10:07:25] Parsed 69% [10:07:26] Parsed 70% [10:07:27] Parsed 71% [10:07:28] Parsed 72% [10:07:29] Parsed 73% [10:07:30] Parsed 74% [10:07:32] Parsed 75% [10:07:33] Parsed 76% [10:07:36] Parsed 77% [10:07:38] Parsed 78% [10:07:42] Parsed 79% [10:07:45] Parsed 80% [10:07:49] Parsed 81% [10:07:54] Parsed 82% [10:08:00] Parsed 83% [10:08:05] Parsed 84% [10:08:11] Parsed 85% [10:08:17] Parsed 86% [10:08:23] Parsed 87% [10:08:29] Parsed 88% [10:08:35] Parsed 89% [10:08:42] Parsed 90% [10:08:48] Parsed 91% [10:08:55] Parsed 92% [10:09:01] Parsed 93% [10:09:09] Parsed 94% [10:09:16] Parsed 95% [10:09:20] Parsed 96% [10:09:26] Parsed 97% [10:09:41] Parsed 98% [10:09:46] Parsed 99% [10:09:46] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.dia ... [10:09:47] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.dia! [10:09:47] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML [10:09:47] Library File: UP000005640_9606-z3_nce27-prosit.dlib [10:09:47] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.elib [10:09:47] Parameters: [10:09:47] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [10:09:47] Converting files... [10:09:47] Calculating features... [10:09:47] Processing precursors scans... [10:09:47] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:09:47] Processing 398.4 to 400.4 m/z, (3.9095361 second duty cycle) [10:09:49] 4957 peptides remaining for 398.4 to 400.4... [10:09:50] 4451 peptides remaining for 398.4 to 400.4... [10:09:50] 3868 peptides remaining for 398.4 to 400.4... [10:09:51] 3299 peptides remaining for 398.4 to 400.4... [10:09:51] 2736 peptides remaining for 398.4 to 400.4... [10:09:52] 2126 peptides remaining for 398.4 to 400.4... [10:09:52] 1520 peptides remaining for 398.4 to 400.4... [10:09:53] 918 peptides remaining for 398.4 to 400.4... [10:09:53] 338 peptides remaining for 398.4 to 400.4... [10:09:54] Processing 400.4 to 402.4 m/z, (1.9547969 second duty cycle) [10:09:56] 7357 peptides remaining for 400.4 to 402.4... [10:09:56] 6879 peptides remaining for 400.4 to 402.4... [10:09:57] 6376 peptides remaining for 400.4 to 402.4... [10:09:57] 5885 peptides remaining for 400.4 to 402.4... [10:09:58] 5390 peptides remaining for 400.4 to 402.4... [10:09:58] 4902 peptides remaining for 400.4 to 402.4... [10:09:59] 4419 peptides remaining for 400.4 to 402.4... [10:09:59] 3923 peptides remaining for 400.4 to 402.4... [10:10:00] 3432 peptides remaining for 400.4 to 402.4... [10:10:00] 2927 peptides remaining for 400.4 to 402.4... [10:10:01] 2441 peptides remaining for 400.4 to 402.4... [10:10:01] 1975 peptides remaining for 400.4 to 402.4... [10:10:02] 1475 peptides remaining for 400.4 to 402.4... [10:10:02] 956 peptides remaining for 400.4 to 402.4... [10:10:03] 438 peptides remaining for 400.4 to 402.4... [10:10:03] Processing 402.4 to 404.4 m/z, (1.9547969 second duty cycle) [10:10:05] 5839 peptides remaining for 402.4 to 404.4... [10:10:05] 5345 peptides remaining for 402.4 to 404.4... [10:10:06] 4845 peptides remaining for 402.4 to 404.4... [10:10:06] 4309 peptides remaining for 402.4 to 404.4... [10:10:07] 3815 peptides remaining for 402.4 to 404.4... [10:10:07] 3319 peptides remaining for 402.4 to 404.4... [10:10:08] 2818 peptides remaining for 402.4 to 404.4... [10:10:08] 2321 peptides remaining for 402.4 to 404.4... [10:10:09] 1818 peptides remaining for 402.4 to 404.4... [10:10:10] 1310 peptides remaining for 402.4 to 404.4... [10:10:10] 801 peptides remaining for 402.4 to 404.4... [10:10:11] 289 peptides remaining for 402.4 to 404.4... [10:10:11] Processing 404.4 to 406.4 m/z, (1.954797 second duty cycle) [10:10:13] 5518 peptides remaining for 404.4 to 406.4... [10:10:13] 5058 peptides remaining for 404.4 to 406.4... [10:10:14] 4572 peptides remaining for 404.4 to 406.4... [10:10:14] 4077 peptides remaining for 404.4 to 406.4... [10:10:15] 3578 peptides remaining for 404.4 to 406.4... [10:10:15] 3093 peptides remaining for 404.4 to 406.4... [10:10:16] 2604 peptides remaining for 404.4 to 406.4... [10:10:16] 2109 peptides remaining for 404.4 to 406.4... [10:10:17] 1612 peptides remaining for 404.4 to 406.4... [10:10:17] 1102 peptides remaining for 404.4 to 406.4... [10:10:18] 612 peptides remaining for 404.4 to 406.4... [10:10:18] 113 peptides remaining for 404.4 to 406.4... [10:10:19] Processing 406.4 to 408.4 m/z, (1.9547969 second duty cycle) [10:10:20] 6251 peptides remaining for 406.4 to 408.4... [10:10:21] 5778 peptides remaining for 406.4 to 408.4... [10:10:21] 5275 peptides remaining for 406.4 to 408.4... [10:10:22] 4762 peptides remaining for 406.4 to 408.4... [10:10:23] 4248 peptides remaining for 406.4 to 408.4... [10:10:23] 3756 peptides remaining for 406.4 to 408.4... [10:10:24] 3247 peptides remaining for 406.4 to 408.4... [10:10:24] 2751 peptides remaining for 406.4 to 408.4... [10:10:25] 2253 peptides remaining for 406.4 to 408.4... [10:10:25] 1747 peptides remaining for 406.4 to 408.4... [10:10:26] 1233 peptides remaining for 406.4 to 408.4... [10:10:26] 731 peptides remaining for 406.4 to 408.4... [10:10:27] 213 peptides remaining for 406.4 to 408.4... [10:10:27] Processing 408.4 to 410.4 m/z, (1.954797 second duty cycle) [10:10:29] 6835 peptides remaining for 408.4 to 410.4... [10:10:29] 6365 peptides remaining for 408.4 to 410.4... [10:10:30] 5847 peptides remaining for 408.4 to 410.4... [10:10:30] 5340 peptides remaining for 408.4 to 410.4... [10:10:31] 4856 peptides remaining for 408.4 to 410.4... [10:10:31] 4362 peptides remaining for 408.4 to 410.4... [10:10:32] 3864 peptides remaining for 408.4 to 410.4... [10:10:32] 3341 peptides remaining for 408.4 to 410.4... [10:10:33] 2834 peptides remaining for 408.4 to 410.4... [10:10:33] 2328 peptides remaining for 408.4 to 410.4... [10:10:34] 1819 peptides remaining for 408.4 to 410.4... [10:10:34] 1301 peptides remaining for 408.4 to 410.4... [10:10:35] 777 peptides remaining for 408.4 to 410.4... [10:10:35] 287 peptides remaining for 408.4 to 410.4... [10:10:36] Processing 410.4 to 412.4 m/z, (1.9547969 second duty cycle) [10:10:38] 6035 peptides remaining for 410.4 to 412.4... [10:10:38] 5549 peptides remaining for 410.4 to 412.4... [10:10:39] 5065 peptides remaining for 410.4 to 412.4... [10:10:39] 4568 peptides remaining for 410.4 to 412.4... [10:10:40] 4089 peptides remaining for 410.4 to 412.4... [10:10:40] 3630 peptides remaining for 410.4 to 412.4... [10:10:41] 3153 peptides remaining for 410.4 to 412.4... [10:10:41] 2659 peptides remaining for 410.4 to 412.4... [10:10:42] 2180 peptides remaining for 410.4 to 412.4... [10:10:42] 1715 peptides remaining for 410.4 to 412.4... [10:10:43] 1245 peptides remaining for 410.4 to 412.4... [10:10:43] 774 peptides remaining for 410.4 to 412.4... [10:10:44] 295 peptides remaining for 410.4 to 412.4... [10:10:44] Processing 412.4 to 414.4 m/z, (1.9547969 second duty cycle) [10:10:46] 5345 peptides remaining for 412.4 to 414.4... [10:10:46] 4860 peptides remaining for 412.4 to 414.4... [10:10:47] 4372 peptides remaining for 412.4 to 414.4... [10:10:47] 3899 peptides remaining for 412.4 to 414.4... [10:10:48] 3430 peptides remaining for 412.4 to 414.4... [10:10:48] 2945 peptides remaining for 412.4 to 414.4... [10:10:49] 2444 peptides remaining for 412.4 to 414.4... [10:10:50] 1942 peptides remaining for 412.4 to 414.4... [10:10:50] 1448 peptides remaining for 412.4 to 414.4... [10:10:51] 967 peptides remaining for 412.4 to 414.4... [10:10:51] 472 peptides remaining for 412.4 to 414.4... [10:10:52] 0 peptides remaining for 412.4 to 414.4... [10:10:52] Processing 414.4 to 416.4 m/z, (1.9547967 second duty cycle) [10:10:54] 7768 peptides remaining for 414.4 to 416.4... [10:10:55] 7485 peptides remaining for 414.4 to 416.4... [10:10:55] 7132 peptides remaining for 414.4 to 416.4... [10:10:56] 6765 peptides remaining for 414.4 to 416.4... [10:10:56] 6385 peptides remaining for 414.4 to 416.4... [10:10:57] 5983 peptides remaining for 414.4 to 416.4... [10:10:57] 5600 peptides remaining for 414.4 to 416.4... [10:10:58] 5216 peptides remaining for 414.4 to 416.4... [10:10:58] 4819 peptides remaining for 414.4 to 416.4... [10:10:59] 4439 peptides remaining for 414.4 to 416.4... [10:10:59] 4034 peptides remaining for 414.4 to 416.4... [10:11:00] 3586 peptides remaining for 414.4 to 416.4... [10:11:00] 3117 peptides remaining for 414.4 to 416.4... [10:11:01] 2647 peptides remaining for 414.4 to 416.4... [10:11:01] 2223 peptides remaining for 414.4 to 416.4... [10:11:02] 1785 peptides remaining for 414.4 to 416.4... [10:11:02] 1334 peptides remaining for 414.4 to 416.4... [10:11:03] 897 peptides remaining for 414.4 to 416.4... [10:11:03] 451 peptides remaining for 414.4 to 416.4... [10:11:04] 12 peptides remaining for 414.4 to 416.4... [10:11:04] Processing 416.4 to 418.4 m/z, (1.954797 second duty cycle) [10:11:06] 7308 peptides remaining for 416.4 to 418.4... [10:11:07] 6831 peptides remaining for 416.4 to 418.4... [10:11:07] 6354 peptides remaining for 416.4 to 418.4... [10:11:08] 5886 peptides remaining for 416.4 to 418.4... [10:11:08] 5420 peptides remaining for 416.4 to 418.4... [10:11:09] 4933 peptides remaining for 416.4 to 418.4... [10:11:09] 4439 peptides remaining for 416.4 to 418.4... [10:11:10] 3970 peptides remaining for 416.4 to 418.4... [10:11:10] 3499 peptides remaining for 416.4 to 418.4... [10:11:11] 3013 peptides remaining for 416.4 to 418.4... [10:11:11] 2534 peptides remaining for 416.4 to 418.4... [10:11:12] 2045 peptides remaining for 416.4 to 418.4... [10:11:12] 1553 peptides remaining for 416.4 to 418.4... [10:11:13] 1092 peptides remaining for 416.4 to 418.4... [10:11:13] 617 peptides remaining for 416.4 to 418.4... [10:11:14] 140 peptides remaining for 416.4 to 418.4... [10:11:14] Processing 418.4 to 420.4 m/z, (1.954797 second duty cycle) [10:11:16] 6531 peptides remaining for 418.4 to 420.4... [10:11:17] 6041 peptides remaining for 418.4 to 420.4... [10:11:17] 5575 peptides remaining for 418.4 to 420.4... [10:11:18] 5091 peptides remaining for 418.4 to 420.4... [10:11:18] 4619 peptides remaining for 418.4 to 420.4... [10:11:19] 4139 peptides remaining for 418.4 to 420.4... [10:11:19] 3652 peptides remaining for 418.4 to 420.4... [10:11:20] 3180 peptides remaining for 418.4 to 420.4... [10:11:20] 2696 peptides remaining for 418.4 to 420.4... [10:11:21] 2217 peptides remaining for 418.4 to 420.4... [10:11:21] 1727 peptides remaining for 418.4 to 420.4... [10:11:22] 1240 peptides remaining for 418.4 to 420.4... [10:11:22] 759 peptides remaining for 418.4 to 420.4... [10:11:23] 304 peptides remaining for 418.4 to 420.4... [10:11:23] Processing 420.4 to 422.4 m/z, (1.9547969 second duty cycle) [10:11:25] 7064 peptides remaining for 420.4 to 422.4... [10:11:26] 6577 peptides remaining for 420.4 to 422.4... [10:11:26] 6089 peptides remaining for 420.4 to 422.4... [10:11:27] 5587 peptides remaining for 420.4 to 422.4... [10:11:27] 5096 peptides remaining for 420.4 to 422.4... [10:11:28] 4595 peptides remaining for 420.4 to 422.4... [10:11:28] 4099 peptides remaining for 420.4 to 422.4... [10:11:29] 3633 peptides remaining for 420.4 to 422.4... [10:11:29] 3180 peptides remaining for 420.4 to 422.4... [10:11:30] 2710 peptides remaining for 420.4 to 422.4... [10:11:30] 2211 peptides remaining for 420.4 to 422.4... [10:11:31] 1723 peptides remaining for 420.4 to 422.4... [10:11:31] 1258 peptides remaining for 420.4 to 422.4... [10:11:32] 761 peptides remaining for 420.4 to 422.4... [10:11:32] 288 peptides remaining for 420.4 to 422.4... [10:11:33] Processing 422.4 to 424.4 m/z, (1.9547969 second duty cycle) [10:11:35] 7850 peptides remaining for 422.4 to 424.4... [10:11:35] 7351 peptides remaining for 422.4 to 424.4... [10:11:36] 6843 peptides remaining for 422.4 to 424.4... [10:11:36] 6351 peptides remaining for 422.4 to 424.4... [10:11:37] 5852 peptides remaining for 422.4 to 424.4... [10:11:37] 5363 peptides remaining for 422.4 to 424.4... [10:11:38] 4857 peptides remaining for 422.4 to 424.4... [10:11:38] 4348 peptides remaining for 422.4 to 424.4... [10:11:39] 3850 peptides remaining for 422.4 to 424.4... [10:11:39] 3320 peptides remaining for 422.4 to 424.4... [10:11:40] 2827 peptides remaining for 422.4 to 424.4... [10:11:40] 2334 peptides remaining for 422.4 to 424.4... [10:11:41] 1846 peptides remaining for 422.4 to 424.4... [10:11:41] 1363 peptides remaining for 422.4 to 424.4... [10:11:42] 886 peptides remaining for 422.4 to 424.4... [10:11:42] 404 peptides remaining for 422.4 to 424.4... [10:11:43] Processing 424.4 to 426.4 m/z, (1.9547971 second duty cycle) [10:11:45] 7287 peptides remaining for 424.4 to 426.4... [10:11:45] 6819 peptides remaining for 424.4 to 426.4... [10:11:46] 6326 peptides remaining for 424.4 to 426.4... [10:11:46] 5830 peptides remaining for 424.4 to 426.4... [10:11:47] 5343 peptides remaining for 424.4 to 426.4... [10:11:47] 4858 peptides remaining for 424.4 to 426.4... [10:11:48] 4345 peptides remaining for 424.4 to 426.4... [10:11:48] 3854 peptides remaining for 424.4 to 426.4... [10:11:49] 3342 peptides remaining for 424.4 to 426.4... [10:11:49] 2857 peptides remaining for 424.4 to 426.4... [10:11:50] 2375 peptides remaining for 424.4 to 426.4... [10:11:50] 1888 peptides remaining for 424.4 to 426.4... [10:11:51] 1417 peptides remaining for 424.4 to 426.4... [10:11:51] 960 peptides remaining for 424.4 to 426.4... [10:11:52] 492 peptides remaining for 424.4 to 426.4... [10:11:52] 15 peptides remaining for 424.4 to 426.4... [10:11:53] Processing 426.4 to 428.4 m/z, (1.954797 second duty cycle) [10:11:54] 6352 peptides remaining for 426.4 to 428.4... [10:11:55] 5871 peptides remaining for 426.4 to 428.4... [10:11:55] 5372 peptides remaining for 426.4 to 428.4... [10:11:56] 4907 peptides remaining for 426.4 to 428.4... [10:11:56] 4451 peptides remaining for 426.4 to 428.4... [10:11:57] 3983 peptides remaining for 426.4 to 428.4... [10:11:58] 3525 peptides remaining for 426.4 to 428.4... [10:11:58] 3060 peptides remaining for 426.4 to 428.4... [10:11:59] 2593 peptides remaining for 426.4 to 428.4... [10:11:59] 2103 peptides remaining for 426.4 to 428.4... [10:12:00] 1607 peptides remaining for 426.4 to 428.4... [10:12:00] 1112 peptides remaining for 426.4 to 428.4... [10:12:01] 639 peptides remaining for 426.4 to 428.4... [10:12:01] 150 peptides remaining for 426.4 to 428.4... [10:12:02] Processing 428.4 to 430.4 m/z, (1.954797 second duty cycle) [10:12:03] 8197 peptides remaining for 428.4 to 430.4... [10:12:04] 7739 peptides remaining for 428.4 to 430.4... [10:12:04] 7248 peptides remaining for 428.4 to 430.4... [10:12:05] 6771 peptides remaining for 428.4 to 430.4... [10:12:06] 6286 peptides remaining for 428.4 to 430.4... [10:12:06] 5794 peptides remaining for 428.4 to 430.4... [10:12:07] 5327 peptides remaining for 428.4 to 430.4... [10:12:07] 4824 peptides remaining for 428.4 to 430.4... [10:12:08] 4326 peptides remaining for 428.4 to 430.4... [10:12:08] 3842 peptides remaining for 428.4 to 430.4... [10:12:09] 3384 peptides remaining for 428.4 to 430.4... [10:12:09] 2906 peptides remaining for 428.4 to 430.4... [10:12:10] 2413 peptides remaining for 428.4 to 430.4... [10:12:10] 1934 peptides remaining for 428.4 to 430.4... [10:12:11] 1471 peptides remaining for 428.4 to 430.4... [10:12:11] 1001 peptides remaining for 428.4 to 430.4... [10:12:12] 544 peptides remaining for 428.4 to 430.4... [10:12:12] 57 peptides remaining for 428.4 to 430.4... [10:12:13] Processing 430.4 to 432.4 m/z, (1.9547969 second duty cycle) [10:12:15] 8325 peptides remaining for 430.4 to 432.4... [10:12:15] 7853 peptides remaining for 430.4 to 432.4... [10:12:16] 7377 peptides remaining for 430.4 to 432.4... [10:12:16] 6905 peptides remaining for 430.4 to 432.4... [10:12:17] 6435 peptides remaining for 430.4 to 432.4... [10:12:17] 5977 peptides remaining for 430.4 to 432.4... [10:12:18] 5487 peptides remaining for 430.4 to 432.4... [10:12:18] 5008 peptides remaining for 430.4 to 432.4... [10:12:19] 4531 peptides remaining for 430.4 to 432.4... [10:12:19] 4059 peptides remaining for 430.4 to 432.4... [10:12:20] 3575 peptides remaining for 430.4 to 432.4... [10:12:20] 3107 peptides remaining for 430.4 to 432.4... [10:12:21] 2621 peptides remaining for 430.4 to 432.4... [10:12:21] 2156 peptides remaining for 430.4 to 432.4... [10:12:22] 1673 peptides remaining for 430.4 to 432.4... [10:12:22] 1212 peptides remaining for 430.4 to 432.4... [10:12:23] 750 peptides remaining for 430.4 to 432.4... [10:12:23] 292 peptides remaining for 430.4 to 432.4... [10:12:24] Processing 432.4 to 434.4 m/z, (1.9547971 second duty cycle) [10:12:26] 6879 peptides remaining for 432.4 to 434.4... [10:12:26] 6404 peptides remaining for 432.4 to 434.4... [10:12:27] 5923 peptides remaining for 432.4 to 434.4... [10:12:27] 5446 peptides remaining for 432.4 to 434.4... [10:12:28] 4965 peptides remaining for 432.4 to 434.4... [10:12:28] 4475 peptides remaining for 432.4 to 434.4... [10:12:29] 3992 peptides remaining for 432.4 to 434.4... [10:12:29] 3514 peptides remaining for 432.4 to 434.4... [10:12:30] 3019 peptides remaining for 432.4 to 434.4... [10:12:30] 2541 peptides remaining for 432.4 to 434.4... [10:12:31] 2074 peptides remaining for 432.4 to 434.4... [10:12:32] 1601 peptides remaining for 432.4 to 434.4... [10:12:32] 1174 peptides remaining for 432.4 to 434.4... [10:12:33] 731 peptides remaining for 432.4 to 434.4... [10:12:33] 274 peptides remaining for 432.4 to 434.4... [10:12:34] Processing 434.4 to 436.4 m/z, (1.9547971 second duty cycle) [10:12:35] 7189 peptides remaining for 434.4 to 436.4... [10:12:36] 6725 peptides remaining for 434.4 to 436.4... [10:12:36] 6247 peptides remaining for 434.4 to 436.4... [10:12:37] 5774 peptides remaining for 434.4 to 436.4... [10:12:37] 5298 peptides remaining for 434.4 to 436.4... [10:12:38] 4813 peptides remaining for 434.4 to 436.4... [10:12:38] 4316 peptides remaining for 434.4 to 436.4... [10:12:39] 3832 peptides remaining for 434.4 to 436.4... [10:12:39] 3385 peptides remaining for 434.4 to 436.4... [10:12:40] 2906 peptides remaining for 434.4 to 436.4... [10:12:41] 2432 peptides remaining for 434.4 to 436.4... [10:12:41] 1932 peptides remaining for 434.4 to 436.4... [10:12:42] 1493 peptides remaining for 434.4 to 436.4... [10:12:42] 1028 peptides remaining for 434.4 to 436.4... [10:12:43] 591 peptides remaining for 434.4 to 436.4... [10:12:43] 124 peptides remaining for 434.4 to 436.4... [10:12:44] Processing 436.4 to 438.4 m/z, (1.954797 second duty cycle) [10:12:45] 8590 peptides remaining for 436.4 to 438.4... [10:12:46] 8114 peptides remaining for 436.4 to 438.4... [10:12:46] 7635 peptides remaining for 436.4 to 438.4... [10:12:47] 7151 peptides remaining for 436.4 to 438.4... [10:12:47] 6684 peptides remaining for 436.4 to 438.4... [10:12:48] 6195 peptides remaining for 436.4 to 438.4... [10:12:48] 5718 peptides remaining for 436.4 to 438.4... [10:12:49] 5237 peptides remaining for 436.4 to 438.4... [10:12:50] 4752 peptides remaining for 436.4 to 438.4... [10:12:50] 4262 peptides remaining for 436.4 to 438.4... [10:12:51] 3763 peptides remaining for 436.4 to 438.4... [10:12:51] 3282 peptides remaining for 436.4 to 438.4... [10:12:52] 2785 peptides remaining for 436.4 to 438.4... [10:12:52] 2314 peptides remaining for 436.4 to 438.4... [10:12:53] 1854 peptides remaining for 436.4 to 438.4... [10:12:53] 1393 peptides remaining for 436.4 to 438.4... [10:12:54] 916 peptides remaining for 436.4 to 438.4... [10:12:54] 453 peptides remaining for 436.4 to 438.4... [10:12:55] 0 peptides remaining for 436.4 to 438.4... [10:12:55] Processing 438.4 to 440.5 m/z, (1.954797 second duty cycle) [10:12:57] 7901 peptides remaining for 438.4 to 440.5... [10:12:57] 7453 peptides remaining for 438.4 to 440.5... [10:12:58] 6996 peptides remaining for 438.4 to 440.5... [10:12:58] 6527 peptides remaining for 438.4 to 440.5... [10:12:59] 6082 peptides remaining for 438.4 to 440.5... [10:12:59] 5606 peptides remaining for 438.4 to 440.5... [10:13:00] 5159 peptides remaining for 438.4 to 440.5... [10:13:01] 4700 peptides remaining for 438.4 to 440.5... [10:13:01] 4242 peptides remaining for 438.4 to 440.5... [10:13:02] 3767 peptides remaining for 438.4 to 440.5... [10:13:02] 3285 peptides remaining for 438.4 to 440.5... [10:13:03] 2822 peptides remaining for 438.4 to 440.5... [10:13:03] 2362 peptides remaining for 438.4 to 440.5... [10:13:04] 1893 peptides remaining for 438.4 to 440.5... [10:13:04] 1441 peptides remaining for 438.4 to 440.5... [10:13:05] 987 peptides remaining for 438.4 to 440.5... [10:13:05] 539 peptides remaining for 438.4 to 440.5... [10:13:06] 100 peptides remaining for 438.4 to 440.5... [10:13:06] Processing 440.5 to 442.5 m/z, (1.9547971 second duty cycle) [10:13:08] 6823 peptides remaining for 440.5 to 442.5... [10:13:08] 6358 peptides remaining for 440.5 to 442.5... [10:13:09] 5892 peptides remaining for 440.5 to 442.5... [10:13:10] 5410 peptides remaining for 440.5 to 442.5... [10:13:10] 4952 peptides remaining for 440.5 to 442.5... [10:13:11] 4474 peptides remaining for 440.5 to 442.5... [10:13:11] 4007 peptides remaining for 440.5 to 442.5... [10:13:12] 3537 peptides remaining for 440.5 to 442.5... [10:13:12] 3077 peptides remaining for 440.5 to 442.5... [10:13:13] 2603 peptides remaining for 440.5 to 442.5... [10:13:13] 2144 peptides remaining for 440.5 to 442.5... [10:13:14] 1680 peptides remaining for 440.5 to 442.5... [10:13:14] 1221 peptides remaining for 440.5 to 442.5... [10:13:15] 754 peptides remaining for 440.5 to 442.5... [10:13:15] 293 peptides remaining for 440.5 to 442.5... [10:13:16] Processing 442.5 to 444.5 m/z, (1.9547971 second duty cycle) [10:13:17] 7994 peptides remaining for 442.5 to 444.5... [10:13:18] 7517 peptides remaining for 442.5 to 444.5... [10:13:19] 7013 peptides remaining for 442.5 to 444.5... [10:13:19] 6525 peptides remaining for 442.5 to 444.5... [10:13:20] 6054 peptides remaining for 442.5 to 444.5... [10:13:20] 5558 peptides remaining for 442.5 to 444.5... [10:13:21] 5099 peptides remaining for 442.5 to 444.5... [10:13:21] 4629 peptides remaining for 442.5 to 444.5... [10:13:22] 4158 peptides remaining for 442.5 to 444.5... [10:13:22] 3678 peptides remaining for 442.5 to 444.5... [10:13:23] 3207 peptides remaining for 442.5 to 444.5... [10:13:23] 2746 peptides remaining for 442.5 to 444.5... [10:13:24] 2285 peptides remaining for 442.5 to 444.5... [10:13:24] 1812 peptides remaining for 442.5 to 444.5... [10:13:25] 1347 peptides remaining for 442.5 to 444.5... [10:13:25] 879 peptides remaining for 442.5 to 444.5... [10:13:26] 415 peptides remaining for 442.5 to 444.5... [10:13:26] Processing 444.5 to 446.5 m/z, (1.954797 second duty cycle) [10:13:28] 8333 peptides remaining for 444.5 to 446.5... [10:13:29] 7850 peptides remaining for 444.5 to 446.5... [10:13:29] 7370 peptides remaining for 444.5 to 446.5... [10:13:30] 6885 peptides remaining for 444.5 to 446.5... [10:13:30] 6411 peptides remaining for 444.5 to 446.5... [10:13:31] 5943 peptides remaining for 444.5 to 446.5... [10:13:31] 5465 peptides remaining for 444.5 to 446.5... [10:13:32] 4964 peptides remaining for 444.5 to 446.5... [10:13:32] 4492 peptides remaining for 444.5 to 446.5... [10:13:33] 4002 peptides remaining for 444.5 to 446.5... [10:13:33] 3544 peptides remaining for 444.5 to 446.5... [10:13:34] 3073 peptides remaining for 444.5 to 446.5... [10:13:34] 2617 peptides remaining for 444.5 to 446.5... [10:13:35] 2167 peptides remaining for 444.5 to 446.5... [10:13:35] 1703 peptides remaining for 444.5 to 446.5... [10:13:36] 1243 peptides remaining for 444.5 to 446.5... [10:13:36] 787 peptides remaining for 444.5 to 446.5... [10:13:37] 332 peptides remaining for 444.5 to 446.5... [10:13:37] Processing 446.5 to 448.5 m/z, (1.954797 second duty cycle) [10:13:39] 7311 peptides remaining for 446.5 to 448.5... [10:13:40] 6860 peptides remaining for 446.5 to 448.5... [10:13:40] 6394 peptides remaining for 446.5 to 448.5... [10:13:41] 5944 peptides remaining for 446.5 to 448.5... [10:13:41] 5477 peptides remaining for 446.5 to 448.5... [10:13:42] 5002 peptides remaining for 446.5 to 448.5... [10:13:42] 4532 peptides remaining for 446.5 to 448.5... [10:13:43] 4080 peptides remaining for 446.5 to 448.5... [10:13:43] 3599 peptides remaining for 446.5 to 448.5... [10:13:44] 3116 peptides remaining for 446.5 to 448.5... [10:13:44] 2658 peptides remaining for 446.5 to 448.5... [10:13:45] 2207 peptides remaining for 446.5 to 448.5... [10:13:45] 1754 peptides remaining for 446.5 to 448.5... [10:13:46] 1311 peptides remaining for 446.5 to 448.5... [10:13:46] 847 peptides remaining for 446.5 to 448.5... [10:13:47] 402 peptides remaining for 446.5 to 448.5... [10:13:47] 0 peptides remaining for 446.5 to 448.5... [10:13:48] Processing 448.5 to 450.5 m/z, (1.9547973 second duty cycle) [10:13:50] 7126 peptides remaining for 448.5 to 450.5... [10:13:50] 6681 peptides remaining for 448.5 to 450.5... [10:13:51] 6233 peptides remaining for 448.5 to 450.5... [10:13:51] 5784 peptides remaining for 448.5 to 450.5... [10:13:52] 5335 peptides remaining for 448.5 to 450.5... [10:13:52] 4867 peptides remaining for 448.5 to 450.5... [10:13:53] 4403 peptides remaining for 448.5 to 450.5... [10:13:53] 3955 peptides remaining for 448.5 to 450.5... [10:13:54] 3527 peptides remaining for 448.5 to 450.5... [10:13:54] 3077 peptides remaining for 448.5 to 450.5... [10:13:55] 2639 peptides remaining for 448.5 to 450.5... [10:13:55] 2180 peptides remaining for 448.5 to 450.5... [10:13:56] 1728 peptides remaining for 448.5 to 450.5... [10:13:56] 1268 peptides remaining for 448.5 to 450.5... [10:13:57] 815 peptides remaining for 448.5 to 450.5... [10:13:57] 354 peptides remaining for 448.5 to 450.5... [10:13:58] 159 peptides remaining for 448.5 to 450.5... [10:13:59] Processing 450.5 to 452.5 m/z, (1.9547971 second duty cycle) [10:14:00] 8203 peptides remaining for 450.5 to 452.5... [10:14:01] 7735 peptides remaining for 450.5 to 452.5... [10:14:01] 7258 peptides remaining for 450.5 to 452.5... [10:14:02] 6787 peptides remaining for 450.5 to 452.5... [10:14:02] 6313 peptides remaining for 450.5 to 452.5... [10:14:03] 5868 peptides remaining for 450.5 to 452.5... [10:14:03] 5400 peptides remaining for 450.5 to 452.5... [10:14:04] 4920 peptides remaining for 450.5 to 452.5... [10:14:05] 4435 peptides remaining for 450.5 to 452.5... [10:14:05] 3966 peptides remaining for 450.5 to 452.5... [10:14:06] 3517 peptides remaining for 450.5 to 452.5... [10:14:06] 3038 peptides remaining for 450.5 to 452.5... [10:14:07] 2573 peptides remaining for 450.5 to 452.5... [10:14:07] 2107 peptides remaining for 450.5 to 452.5... [10:14:08] 1633 peptides remaining for 450.5 to 452.5... [10:14:08] 1177 peptides remaining for 450.5 to 452.5... [10:14:09] 725 peptides remaining for 450.5 to 452.5... [10:14:09] 262 peptides remaining for 450.5 to 452.5... [10:14:10] Processing 452.5 to 454.5 m/z, (1.9547971 second duty cycle) [10:14:11] 8119 peptides remaining for 452.5 to 454.5... [10:14:12] 7661 peptides remaining for 452.5 to 454.5... [10:14:13] 7186 peptides remaining for 452.5 to 454.5... [10:14:13] 6700 peptides remaining for 452.5 to 454.5... [10:14:14] 6240 peptides remaining for 452.5 to 454.5... [10:14:14] 5785 peptides remaining for 452.5 to 454.5... [10:14:15] 5303 peptides remaining for 452.5 to 454.5... [10:14:15] 4846 peptides remaining for 452.5 to 454.5... [10:14:16] 4400 peptides remaining for 452.5 to 454.5... [10:14:16] 3929 peptides remaining for 452.5 to 454.5... [10:14:17] 3454 peptides remaining for 452.5 to 454.5... [10:14:17] 2988 peptides remaining for 452.5 to 454.5... [10:14:18] 2544 peptides remaining for 452.5 to 454.5... [10:14:18] 2102 peptides remaining for 452.5 to 454.5... [10:14:19] 1659 peptides remaining for 452.5 to 454.5... [10:14:19] 1213 peptides remaining for 452.5 to 454.5... [10:14:20] 780 peptides remaining for 452.5 to 454.5... [10:14:20] 324 peptides remaining for 452.5 to 454.5... [10:14:21] Processing 454.5 to 456.5 m/z, (1.9547971 second duty cycle) [10:14:23] 6881 peptides remaining for 454.5 to 456.5... [10:14:23] 6427 peptides remaining for 454.5 to 456.5... [10:14:24] 5974 peptides remaining for 454.5 to 456.5... [10:14:24] 5511 peptides remaining for 454.5 to 456.5... [10:14:25] 5030 peptides remaining for 454.5 to 456.5... [10:14:25] 4570 peptides remaining for 454.5 to 456.5... [10:14:26] 4114 peptides remaining for 454.5 to 456.5... [10:14:26] 3676 peptides remaining for 454.5 to 456.5... [10:14:27] 3242 peptides remaining for 454.5 to 456.5... [10:14:27] 2792 peptides remaining for 454.5 to 456.5... [10:14:28] 2329 peptides remaining for 454.5 to 456.5... [10:14:28] 1869 peptides remaining for 454.5 to 456.5... [10:14:29] 1424 peptides remaining for 454.5 to 456.5... [10:14:29] 985 peptides remaining for 454.5 to 456.5... [10:14:30] 544 peptides remaining for 454.5 to 456.5... [10:14:30] 108 peptides remaining for 454.5 to 456.5... [10:14:31] Processing 456.5 to 458.5 m/z, (1.9548858 second duty cycle) [10:14:33] 7496 peptides remaining for 456.5 to 458.5... [10:14:33] 7047 peptides remaining for 456.5 to 458.5... [10:14:34] 6603 peptides remaining for 456.5 to 458.5... [10:14:34] 6152 peptides remaining for 456.5 to 458.5... [10:14:35] 5705 peptides remaining for 456.5 to 458.5... [10:14:35] 5261 peptides remaining for 456.5 to 458.5... [10:14:36] 4819 peptides remaining for 456.5 to 458.5... [10:14:36] 4373 peptides remaining for 456.5 to 458.5... [10:14:37] 3915 peptides remaining for 456.5 to 458.5... [10:14:37] 3457 peptides remaining for 456.5 to 458.5... [10:14:38] 3014 peptides remaining for 456.5 to 458.5... [10:14:38] 2554 peptides remaining for 456.5 to 458.5... [10:14:39] 2100 peptides remaining for 456.5 to 458.5... [10:14:39] 1655 peptides remaining for 456.5 to 458.5... [10:14:40] 1218 peptides remaining for 456.5 to 458.5... [10:14:40] 775 peptides remaining for 456.5 to 458.5... [10:14:41] 314 peptides remaining for 456.5 to 458.5... [10:14:41] Processing 458.5 to 460.5 m/z, (1.9548858 second duty cycle) [10:14:43] 8297 peptides remaining for 458.5 to 460.5... [10:14:44] 7840 peptides remaining for 458.5 to 460.5... [10:14:44] 7382 peptides remaining for 458.5 to 460.5... [10:14:45] 6903 peptides remaining for 458.5 to 460.5... [10:14:45] 6429 peptides remaining for 458.5 to 460.5... [10:14:46] 5963 peptides remaining for 458.5 to 460.5... [10:14:46] 5513 peptides remaining for 458.5 to 460.5... [10:14:47] 5054 peptides remaining for 458.5 to 460.5... [10:14:47] 4609 peptides remaining for 458.5 to 460.5... [10:14:48] 4150 peptides remaining for 458.5 to 460.5... [10:14:48] 3700 peptides remaining for 458.5 to 460.5... [10:14:49] 3251 peptides remaining for 458.5 to 460.5... [10:14:49] 2803 peptides remaining for 458.5 to 460.5... [10:14:50] 2355 peptides remaining for 458.5 to 460.5... [10:14:50] 1925 peptides remaining for 458.5 to 460.5... [10:14:51] 1497 peptides remaining for 458.5 to 460.5... [10:14:51] 1063 peptides remaining for 458.5 to 460.5... [10:14:52] 628 peptides remaining for 458.5 to 460.5... [10:14:52] 171 peptides remaining for 458.5 to 460.5... [10:14:53] Processing 460.5 to 462.5 m/z, (1.9548856 second duty cycle) [10:14:55] 7322 peptides remaining for 460.5 to 462.5... [10:14:55] 6879 peptides remaining for 460.5 to 462.5... [10:14:56] 6430 peptides remaining for 460.5 to 462.5... [10:14:56] 5989 peptides remaining for 460.5 to 462.5... [10:14:57] 5530 peptides remaining for 460.5 to 462.5... [10:14:57] 5072 peptides remaining for 460.5 to 462.5... [10:14:58] 4617 peptides remaining for 460.5 to 462.5... [10:14:58] 4205 peptides remaining for 460.5 to 462.5... [10:14:59] 3823 peptides remaining for 460.5 to 462.5... [10:14:59] 3400 peptides remaining for 460.5 to 462.5... [10:15:00] 2981 peptides remaining for 460.5 to 462.5... [10:15:00] 2525 peptides remaining for 460.5 to 462.5... [10:15:01] 2069 peptides remaining for 460.5 to 462.5... [10:15:01] 1638 peptides remaining for 460.5 to 462.5... [10:15:02] 1209 peptides remaining for 460.5 to 462.5... [10:15:03] 778 peptides remaining for 460.5 to 462.5... [10:15:03] 348 peptides remaining for 460.5 to 462.5... [10:15:04] Processing 462.5 to 464.5 m/z, (1.9548856 second duty cycle) [10:15:05] 7081 peptides remaining for 462.5 to 464.5... [10:15:06] 6636 peptides remaining for 462.5 to 464.5... [10:15:06] 6195 peptides remaining for 462.5 to 464.5... [10:15:07] 5749 peptides remaining for 462.5 to 464.5... [10:15:07] 5299 peptides remaining for 462.5 to 464.5... [10:15:08] 4852 peptides remaining for 462.5 to 464.5... [10:15:08] 4409 peptides remaining for 462.5 to 464.5... [10:15:09] 3963 peptides remaining for 462.5 to 464.5... [10:15:09] 3515 peptides remaining for 462.5 to 464.5... [10:15:10] 3065 peptides remaining for 462.5 to 464.5... [10:15:10] 2637 peptides remaining for 462.5 to 464.5... [10:15:11] 2191 peptides remaining for 462.5 to 464.5... [10:15:11] 1765 peptides remaining for 462.5 to 464.5... [10:15:12] 1341 peptides remaining for 462.5 to 464.5... [10:15:12] 926 peptides remaining for 462.5 to 464.5... [10:15:13] 494 peptides remaining for 462.5 to 464.5... [10:15:13] 53 peptides remaining for 462.5 to 464.5... [10:15:14] Processing 464.5 to 466.5 m/z, (1.9548858 second duty cycle) [10:15:16] 7933 peptides remaining for 464.5 to 466.5... [10:15:16] 7478 peptides remaining for 464.5 to 466.5... [10:15:17] 7019 peptides remaining for 464.5 to 466.5... [10:15:17] 6557 peptides remaining for 464.5 to 466.5... [10:15:18] 6105 peptides remaining for 464.5 to 466.5... [10:15:18] 5648 peptides remaining for 464.5 to 466.5... [10:15:19] 5192 peptides remaining for 464.5 to 466.5... [10:15:19] 4722 peptides remaining for 464.5 to 466.5... [10:15:20] 4267 peptides remaining for 464.5 to 466.5... [10:15:20] 3807 peptides remaining for 464.5 to 466.5... [10:15:21] 3347 peptides remaining for 464.5 to 466.5... [10:15:21] 2887 peptides remaining for 464.5 to 466.5... [10:15:22] 2417 peptides remaining for 464.5 to 466.5... [10:15:22] 1962 peptides remaining for 464.5 to 466.5... [10:15:23] 1514 peptides remaining for 464.5 to 466.5... [10:15:24] 1071 peptides remaining for 464.5 to 466.5... [10:15:24] 604 peptides remaining for 464.5 to 466.5... [10:15:25] 153 peptides remaining for 464.5 to 466.5... [10:15:25] Processing 466.5 to 468.5 m/z, (1.9548858 second duty cycle) [10:15:27] 7783 peptides remaining for 466.5 to 468.5... [10:15:27] 7345 peptides remaining for 466.5 to 468.5... [10:15:28] 6895 peptides remaining for 466.5 to 468.5... [10:15:28] 6439 peptides remaining for 466.5 to 468.5... [10:15:29] 5998 peptides remaining for 466.5 to 468.5... [10:15:29] 5552 peptides remaining for 466.5 to 468.5... [10:15:30] 5113 peptides remaining for 466.5 to 468.5... [10:15:31] 4676 peptides remaining for 466.5 to 468.5... [10:15:31] 4239 peptides remaining for 466.5 to 468.5... [10:15:32] 3772 peptides remaining for 466.5 to 468.5... [10:15:32] 3329 peptides remaining for 466.5 to 468.5... [10:15:33] 2862 peptides remaining for 466.5 to 468.5... [10:15:33] 2425 peptides remaining for 466.5 to 468.5... [10:15:34] 1982 peptides remaining for 466.5 to 468.5... [10:15:34] 1536 peptides remaining for 466.5 to 468.5... [10:15:35] 1091 peptides remaining for 466.5 to 468.5... [10:15:35] 658 peptides remaining for 466.5 to 468.5... [10:15:36] 214 peptides remaining for 466.5 to 468.5... [10:15:36] Processing 468.5 to 470.5 m/z, (1.9548858 second duty cycle) [10:15:38] 6824 peptides remaining for 468.5 to 470.5... [10:15:39] 6696 peptides remaining for 468.5 to 470.5... [10:15:39] 6260 peptides remaining for 468.5 to 470.5... [10:15:40] 5801 peptides remaining for 468.5 to 470.5... [10:15:40] 5342 peptides remaining for 468.5 to 470.5... [10:15:41] 4912 peptides remaining for 468.5 to 470.5... [10:15:41] 4468 peptides remaining for 468.5 to 470.5... [10:15:42] 4030 peptides remaining for 468.5 to 470.5... [10:15:42] 3588 peptides remaining for 468.5 to 470.5... [10:15:43] 3124 peptides remaining for 468.5 to 470.5... [10:15:43] 2673 peptides remaining for 468.5 to 470.5... [10:15:44] 2237 peptides remaining for 468.5 to 470.5... [10:15:44] 1786 peptides remaining for 468.5 to 470.5... [10:15:45] 1323 peptides remaining for 468.5 to 470.5... [10:15:45] 884 peptides remaining for 468.5 to 470.5... [10:15:46] 447 peptides remaining for 468.5 to 470.5... [10:15:46] 15 peptides remaining for 468.5 to 470.5... [10:15:47] Processing 470.5 to 472.5 m/z, (1.9548858 second duty cycle) [10:15:49] 7004 peptides remaining for 470.5 to 472.5... [10:15:49] 6560 peptides remaining for 470.5 to 472.5... [10:15:50] 6120 peptides remaining for 470.5 to 472.5... [10:15:50] 5705 peptides remaining for 470.5 to 472.5... [10:15:51] 5256 peptides remaining for 470.5 to 472.5... [10:15:51] 4815 peptides remaining for 470.5 to 472.5... [10:15:52] 4384 peptides remaining for 470.5 to 472.5... [10:15:52] 3933 peptides remaining for 470.5 to 472.5... [10:15:53] 3484 peptides remaining for 470.5 to 472.5... [10:15:53] 3045 peptides remaining for 470.5 to 472.5... [10:15:54] 2601 peptides remaining for 470.5 to 472.5... [10:15:54] 2144 peptides remaining for 470.5 to 472.5... [10:15:55] 1700 peptides remaining for 470.5 to 472.5... [10:15:55] 1261 peptides remaining for 470.5 to 472.5... [10:15:56] 838 peptides remaining for 470.5 to 472.5... [10:15:56] 426 peptides remaining for 470.5 to 472.5... [10:15:57] 0 peptides remaining for 470.5 to 472.5... [10:15:57] Processing 472.5 to 474.5 m/z, (1.9548458 second duty cycle) [10:15:59] 8144 peptides remaining for 472.5 to 474.5... [10:16:00] 7731 peptides remaining for 472.5 to 474.5... [10:16:00] 7311 peptides remaining for 472.5 to 474.5... [10:16:01] 6873 peptides remaining for 472.5 to 474.5... [10:16:01] 6441 peptides remaining for 472.5 to 474.5... [10:16:02] 6003 peptides remaining for 472.5 to 474.5... [10:16:02] 5553 peptides remaining for 472.5 to 474.5... [10:16:03] 5129 peptides remaining for 472.5 to 474.5... [10:16:03] 4715 peptides remaining for 472.5 to 474.5... [10:16:04] 4263 peptides remaining for 472.5 to 474.5... [10:16:04] 3807 peptides remaining for 472.5 to 474.5... [10:16:05] 3369 peptides remaining for 472.5 to 474.5... [10:16:05] 2922 peptides remaining for 472.5 to 474.5... [10:16:06] 2492 peptides remaining for 472.5 to 474.5... [10:16:06] 2063 peptides remaining for 472.5 to 474.5... [10:16:07] 1622 peptides remaining for 472.5 to 474.5... [10:16:08] 1199 peptides remaining for 472.5 to 474.5... [10:16:08] 786 peptides remaining for 472.5 to 474.5... [10:16:09] 362 peptides remaining for 472.5 to 474.5... [10:16:09] Processing 474.5 to 476.5 m/z, (1.9548671 second duty cycle) [10:16:11] 7230 peptides remaining for 474.5 to 476.5... [10:16:11] 6801 peptides remaining for 474.5 to 476.5... [10:16:12] 6378 peptides remaining for 474.5 to 476.5... [10:16:12] 5946 peptides remaining for 474.5 to 476.5... [10:16:13] 5497 peptides remaining for 474.5 to 476.5... [10:16:13] 5056 peptides remaining for 474.5 to 476.5... [10:16:14] 4616 peptides remaining for 474.5 to 476.5... [10:16:14] 4158 peptides remaining for 474.5 to 476.5... [10:16:15] 3712 peptides remaining for 474.5 to 476.5... [10:16:15] 3276 peptides remaining for 474.5 to 476.5... [10:16:16] 2826 peptides remaining for 474.5 to 476.5... [10:16:16] 2390 peptides remaining for 474.5 to 476.5... [10:16:17] 1964 peptides remaining for 474.5 to 476.5... [10:16:18] 1530 peptides remaining for 474.5 to 476.5... [10:16:18] 1114 peptides remaining for 474.5 to 476.5... [10:16:19] 694 peptides remaining for 474.5 to 476.5... [10:16:19] 261 peptides remaining for 474.5 to 476.5... [10:16:20] Processing 476.5 to 478.5 m/z, (1.9548455 second duty cycle) [10:16:21] 6984 peptides remaining for 476.5 to 478.5... [10:16:22] 6561 peptides remaining for 476.5 to 478.5... [10:16:22] 6128 peptides remaining for 476.5 to 478.5... [10:16:23] 5688 peptides remaining for 476.5 to 478.5... [10:16:23] 5249 peptides remaining for 476.5 to 478.5... [10:16:24] 4823 peptides remaining for 476.5 to 478.5... [10:16:24] 4374 peptides remaining for 476.5 to 478.5... [10:16:25] 3938 peptides remaining for 476.5 to 478.5... [10:16:25] 3502 peptides remaining for 476.5 to 478.5... [10:16:26] 3064 peptides remaining for 476.5 to 478.5... [10:16:26] 2614 peptides remaining for 476.5 to 478.5... [10:16:27] 2175 peptides remaining for 476.5 to 478.5... [10:16:27] 1746 peptides remaining for 476.5 to 478.5... [10:16:28] 1340 peptides remaining for 476.5 to 478.5... [10:16:29] 917 peptides remaining for 476.5 to 478.5... [10:16:29] 496 peptides remaining for 476.5 to 478.5... [10:16:30] 67 peptides remaining for 476.5 to 478.5... [10:16:30] Processing 478.5 to 480.5 m/z, (1.9548671 second duty cycle) [10:16:32] 7600 peptides remaining for 478.5 to 480.5... [10:16:32] 7170 peptides remaining for 478.5 to 480.5... [10:16:33] 6713 peptides remaining for 478.5 to 480.5... [10:16:33] 6272 peptides remaining for 478.5 to 480.5... [10:16:34] 5827 peptides remaining for 478.5 to 480.5... [10:16:34] 5389 peptides remaining for 478.5 to 480.5... [10:16:35] 4946 peptides remaining for 478.5 to 480.5... [10:16:35] 4524 peptides remaining for 478.5 to 480.5... [10:16:36] 4075 peptides remaining for 478.5 to 480.5... [10:16:37] 3616 peptides remaining for 478.5 to 480.5... [10:16:37] 3174 peptides remaining for 478.5 to 480.5... [10:16:38] 2733 peptides remaining for 478.5 to 480.5... [10:16:38] 2284 peptides remaining for 478.5 to 480.5... [10:16:39] 1854 peptides remaining for 478.5 to 480.5... [10:16:39] 1415 peptides remaining for 478.5 to 480.5... [10:16:40] 968 peptides remaining for 478.5 to 480.5... [10:16:40] 556 peptides remaining for 478.5 to 480.5... [10:16:41] 116 peptides remaining for 478.5 to 480.5... [10:16:41] Processing 480.5 to 482.5 m/z, (1.9548455 second duty cycle) [10:16:43] 7787 peptides remaining for 480.5 to 482.5... [10:16:43] 7337 peptides remaining for 480.5 to 482.5... [10:16:44] 6899 peptides remaining for 480.5 to 482.5... [10:16:44] 6436 peptides remaining for 480.5 to 482.5... [10:16:45] 5981 peptides remaining for 480.5 to 482.5... [10:16:46] 5528 peptides remaining for 480.5 to 482.5... [10:16:46] 5106 peptides remaining for 480.5 to 482.5... [10:16:47] 4650 peptides remaining for 480.5 to 482.5... [10:16:47] 4211 peptides remaining for 480.5 to 482.5... [10:16:48] 3777 peptides remaining for 480.5 to 482.5... [10:16:48] 3338 peptides remaining for 480.5 to 482.5... [10:16:49] 2874 peptides remaining for 480.5 to 482.5... [10:16:49] 2435 peptides remaining for 480.5 to 482.5... [10:16:50] 2021 peptides remaining for 480.5 to 482.5... [10:16:50] 1596 peptides remaining for 480.5 to 482.5... [10:16:51] 1157 peptides remaining for 480.5 to 482.5... [10:16:51] 739 peptides remaining for 480.5 to 482.5... [10:16:52] 344 peptides remaining for 480.5 to 482.5... [10:16:52] Processing 482.5 to 484.5 m/z, (1.9548671 second duty cycle) [10:16:54] 7113 peptides remaining for 482.5 to 484.5... [10:16:54] 6675 peptides remaining for 482.5 to 484.5... [10:16:55] 6243 peptides remaining for 482.5 to 484.5... [10:16:56] 5800 peptides remaining for 482.5 to 484.5... [10:16:56] 5371 peptides remaining for 482.5 to 484.5... [10:16:57] 4937 peptides remaining for 482.5 to 484.5... [10:16:57] 4499 peptides remaining for 482.5 to 484.5... [10:16:58] 4040 peptides remaining for 482.5 to 484.5... [10:16:58] 3582 peptides remaining for 482.5 to 484.5... [10:16:59] 3147 peptides remaining for 482.5 to 484.5... [10:16:59] 2732 peptides remaining for 482.5 to 484.5... [10:17:00] 2304 peptides remaining for 482.5 to 484.5... [10:17:00] 1878 peptides remaining for 482.5 to 484.5... [10:17:01] 1464 peptides remaining for 482.5 to 484.5... [10:17:01] 1078 peptides remaining for 482.5 to 484.5... [10:17:02] 666 peptides remaining for 482.5 to 484.5... [10:17:02] 248 peptides remaining for 482.5 to 484.5... [10:17:03] Processing 484.5 to 486.5 m/z, (1.9548455 second duty cycle) [10:17:05] 6790 peptides remaining for 484.5 to 486.5... [10:17:05] 6357 peptides remaining for 484.5 to 486.5... [10:17:06] 5913 peptides remaining for 484.5 to 486.5... [10:17:06] 5473 peptides remaining for 484.5 to 486.5... [10:17:07] 5035 peptides remaining for 484.5 to 486.5... [10:17:07] 4612 peptides remaining for 484.5 to 486.5... [10:17:08] 4189 peptides remaining for 484.5 to 486.5... [10:17:08] 3751 peptides remaining for 484.5 to 486.5... [10:17:09] 3309 peptides remaining for 484.5 to 486.5... [10:17:09] 2856 peptides remaining for 484.5 to 486.5... [10:17:10] 2406 peptides remaining for 484.5 to 486.5... [10:17:10] 1973 peptides remaining for 484.5 to 486.5... [10:17:11] 1551 peptides remaining for 484.5 to 486.5... [10:17:11] 1139 peptides remaining for 484.5 to 486.5... [10:17:12] 730 peptides remaining for 484.5 to 486.5... [10:17:12] 297 peptides remaining for 484.5 to 486.5... [10:17:13] Processing 486.5 to 488.5 m/z, (1.9548671 second duty cycle) [10:17:15] 8077 peptides remaining for 486.5 to 488.5... [10:17:15] 7656 peptides remaining for 486.5 to 488.5... [10:17:16] 7215 peptides remaining for 486.5 to 488.5... [10:17:16] 6785 peptides remaining for 486.5 to 488.5... [10:17:17] 6351 peptides remaining for 486.5 to 488.5... [10:17:17] 5931 peptides remaining for 486.5 to 488.5... [10:17:18] 5505 peptides remaining for 486.5 to 488.5... [10:17:18] 5054 peptides remaining for 486.5 to 488.5... [10:17:19] 4595 peptides remaining for 486.5 to 488.5... [10:17:19] 4157 peptides remaining for 486.5 to 488.5... [10:17:20] 3722 peptides remaining for 486.5 to 488.5... [10:17:20] 3296 peptides remaining for 486.5 to 488.5... [10:17:21] 2875 peptides remaining for 486.5 to 488.5... [10:17:21] 2466 peptides remaining for 486.5 to 488.5... [10:17:22] 2052 peptides remaining for 486.5 to 488.5... [10:17:22] 1643 peptides remaining for 486.5 to 488.5... [10:17:23] 1218 peptides remaining for 486.5 to 488.5... [10:17:23] 789 peptides remaining for 486.5 to 488.5... [10:17:24] 395 peptides remaining for 486.5 to 488.5... [10:17:24] 0 peptides remaining for 486.5 to 488.5... [10:17:25] Processing 488.5 to 490.5 m/z, (1.9548458 second duty cycle) [10:17:27] 7086 peptides remaining for 488.5 to 490.5... [10:17:27] 6658 peptides remaining for 488.5 to 490.5... [10:17:28] 6233 peptides remaining for 488.5 to 490.5... [10:17:28] 5803 peptides remaining for 488.5 to 490.5... [10:17:29] 5381 peptides remaining for 488.5 to 490.5... [10:17:29] 4958 peptides remaining for 488.5 to 490.5... [10:17:30] 4528 peptides remaining for 488.5 to 490.5... [10:17:30] 4124 peptides remaining for 488.5 to 490.5... [10:17:31] 3706 peptides remaining for 488.5 to 490.5... [10:17:31] 3286 peptides remaining for 488.5 to 490.5... [10:17:32] 2870 peptides remaining for 488.5 to 490.5... [10:17:32] 2477 peptides remaining for 488.5 to 490.5... [10:17:33] 2039 peptides remaining for 488.5 to 490.5... [10:17:33] 1620 peptides remaining for 488.5 to 490.5... [10:17:34] 1198 peptides remaining for 488.5 to 490.5... [10:17:34] 795 peptides remaining for 488.5 to 490.5... [10:17:35] 379 peptides remaining for 488.5 to 490.5... [10:17:35] Processing 490.5 to 492.5 m/z, (1.9548671 second duty cycle) [10:17:37] 6835 peptides remaining for 490.5 to 492.5... [10:17:37] 6437 peptides remaining for 490.5 to 492.5... [10:17:38] 6024 peptides remaining for 490.5 to 492.5... [10:17:38] 5612 peptides remaining for 490.5 to 492.5... [10:17:39] 5185 peptides remaining for 490.5 to 492.5... [10:17:39] 4774 peptides remaining for 490.5 to 492.5... [10:17:40] 4357 peptides remaining for 490.5 to 492.5... [10:17:41] 3942 peptides remaining for 490.5 to 492.5... [10:17:41] 3511 peptides remaining for 490.5 to 492.5... [10:17:42] 3077 peptides remaining for 490.5 to 492.5... [10:17:42] 2670 peptides remaining for 490.5 to 492.5... [10:17:43] 2248 peptides remaining for 490.5 to 492.5... [10:17:43] 1833 peptides remaining for 490.5 to 492.5... [10:17:44] 1447 peptides remaining for 490.5 to 492.5... [10:17:44] 1056 peptides remaining for 490.5 to 492.5... [10:17:45] 653 peptides remaining for 490.5 to 492.5... [10:17:45] 251 peptides remaining for 490.5 to 492.5... [10:17:46] Processing 492.5 to 494.5 m/z, (1.9548455 second duty cycle) [10:17:48] 7397 peptides remaining for 492.5 to 494.5... [10:17:49] 6989 peptides remaining for 492.5 to 494.5... [10:17:49] 6548 peptides remaining for 492.5 to 494.5... [10:17:50] 6119 peptides remaining for 492.5 to 494.5... [10:17:50] 5677 peptides remaining for 492.5 to 494.5... [10:17:51] 5263 peptides remaining for 492.5 to 494.5... [10:17:51] 4822 peptides remaining for 492.5 to 494.5... [10:17:52] 4390 peptides remaining for 492.5 to 494.5... [10:17:52] 3962 peptides remaining for 492.5 to 494.5... [10:17:53] 3522 peptides remaining for 492.5 to 494.5... [10:17:53] 3100 peptides remaining for 492.5 to 494.5... [10:17:54] 2672 peptides remaining for 492.5 to 494.5... [10:17:54] 2267 peptides remaining for 492.5 to 494.5... [10:17:55] 1855 peptides remaining for 492.5 to 494.5... [10:17:55] 1422 peptides remaining for 492.5 to 494.5... [10:17:56] 1003 peptides remaining for 492.5 to 494.5... [10:17:57] 598 peptides remaining for 492.5 to 494.5... [10:17:57] 175 peptides remaining for 492.5 to 494.5... [10:17:58] Processing 494.5 to 496.5 m/z, (1.9548671 second duty cycle) [10:17:59] 7667 peptides remaining for 494.5 to 496.5... [10:18:00] 7232 peptides remaining for 494.5 to 496.5... [10:18:00] 6817 peptides remaining for 494.5 to 496.5... [10:18:01] 6369 peptides remaining for 494.5 to 496.5... [10:18:01] 5939 peptides remaining for 494.5 to 496.5... [10:18:02] 5549 peptides remaining for 494.5 to 496.5... [10:18:02] 5140 peptides remaining for 494.5 to 496.5... [10:18:03] 4725 peptides remaining for 494.5 to 496.5... [10:18:03] 4299 peptides remaining for 494.5 to 496.5... [10:18:04] 3872 peptides remaining for 494.5 to 496.5... [10:18:05] 3431 peptides remaining for 494.5 to 496.5... [10:18:05] 3006 peptides remaining for 494.5 to 496.5... [10:18:06] 2567 peptides remaining for 494.5 to 496.5... [10:18:06] 2144 peptides remaining for 494.5 to 496.5... [10:18:07] 1728 peptides remaining for 494.5 to 496.5... [10:18:07] 1314 peptides remaining for 494.5 to 496.5... [10:18:08] 907 peptides remaining for 494.5 to 496.5... [10:18:08] 503 peptides remaining for 494.5 to 496.5... [10:18:09] 90 peptides remaining for 494.5 to 496.5... [10:18:09] Processing 496.5 to 498.5 m/z, (1.9548459 second duty cycle) [10:18:11] 6957 peptides remaining for 496.5 to 498.5... [10:18:11] 6532 peptides remaining for 496.5 to 498.5... [10:18:12] 6105 peptides remaining for 496.5 to 498.5... [10:18:12] 5673 peptides remaining for 496.5 to 498.5... [10:18:13] 5243 peptides remaining for 496.5 to 498.5... [10:18:13] 4834 peptides remaining for 496.5 to 498.5... [10:18:14] 4398 peptides remaining for 496.5 to 498.5... [10:18:15] 3977 peptides remaining for 496.5 to 498.5... [10:18:15] 3543 peptides remaining for 496.5 to 498.5... [10:18:16] 3098 peptides remaining for 496.5 to 498.5... [10:18:16] 2676 peptides remaining for 496.5 to 498.5... [10:18:17] 2249 peptides remaining for 496.5 to 498.5... [10:18:17] 1810 peptides remaining for 496.5 to 498.5... [10:18:18] 1380 peptides remaining for 496.5 to 498.5... [10:18:18] 937 peptides remaining for 496.5 to 498.5... [10:18:19] 526 peptides remaining for 496.5 to 498.5... [10:18:19] 87 peptides remaining for 496.5 to 498.5... [10:18:20] Processing 498.5 to 500.5 m/z, (1.9548672 second duty cycle) [10:18:21] 6579 peptides remaining for 498.5 to 500.5... [10:18:22] 6146 peptides remaining for 498.5 to 500.5... [10:18:22] 5680 peptides remaining for 498.5 to 500.5... [10:18:23] 5268 peptides remaining for 498.5 to 500.5... [10:18:23] 4849 peptides remaining for 498.5 to 500.5... [10:18:24] 4503 peptides remaining for 498.5 to 500.5... [10:18:24] 4183 peptides remaining for 498.5 to 500.5... [10:18:25] 3827 peptides remaining for 498.5 to 500.5... [10:18:25] 3470 peptides remaining for 498.5 to 500.5... [10:18:26] 3132 peptides remaining for 498.5 to 500.5... [10:18:26] 2787 peptides remaining for 498.5 to 500.5... [10:18:27] 2439 peptides remaining for 498.5 to 500.5... [10:18:27] 2040 peptides remaining for 498.5 to 500.5... [10:18:28] 1636 peptides remaining for 498.5 to 500.5... [10:18:28] 1232 peptides remaining for 498.5 to 500.5... [10:18:29] 803 peptides remaining for 498.5 to 500.5... [10:18:30] 396 peptides remaining for 498.5 to 500.5... [10:18:30] 0 peptides remaining for 498.5 to 500.5... [10:18:31] Processing 500.5 to 502.5 m/z, (3.909591 second duty cycle) [10:18:32] 7642 peptides remaining for 500.5 to 502.5... [10:18:33] 6994 peptides remaining for 500.5 to 502.5... [10:18:33] 6334 peptides remaining for 500.5 to 502.5... [10:18:34] 5696 peptides remaining for 500.5 to 502.5... [10:18:34] 5054 peptides remaining for 500.5 to 502.5... [10:18:35] 4387 peptides remaining for 500.5 to 502.5... [10:18:35] 3749 peptides remaining for 500.5 to 502.5... [10:18:36] 3094 peptides remaining for 500.5 to 502.5... [10:18:36] 2446 peptides remaining for 500.5 to 502.5... [10:18:37] 1792 peptides remaining for 500.5 to 502.5... [10:18:37] 1114 peptides remaining for 500.5 to 502.5... [10:18:38] 479 peptides remaining for 500.5 to 502.5... [10:18:38] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:19:08] Sorted feature file in 29.76 seconds wall clock time [10:19:08] File size check: 550544096 vs 550544096 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:19:08] 1409236 total peptides processed. [10:19:08] Running Percolator... [10:19:08] Executing [cmd /c C:\Windows\Temp\tmp3979.java\Percolator-v3-01-3061136244333103433.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt] [10:19:09] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [10:19:09] Copyright (c) 2006-9 University of Washington. All rights reserved. [10:19:09] Written by Lukas Käll (lukall@u.washington.edu) in the [10:19:09] Department of Genome Sciences at the University of Washington. [10:19:09] Issued command: [10:19:09] C:\Windows\Temp\tmp3979.java\Percolator-v3-01-3061136244333103433.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:19:09] Started Wed Jul 17 10:19:09 2024 [10:19:09] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [10:19:09] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:19:09] Features: [10:19:09] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:19:17] Processing line 1000000 [10:19:20] Found 1409236 PSMs [10:19:20] Separate target and decoy search inputs detected, using mix-max method. [10:19:20] Train/test set contains 251566 positives and 248434 negatives, size ratio=1.01261 and pi0=1 [10:19:21] Selecting Cpos by cross-validation. [10:19:21] Selecting Cneg by cross-validation. [10:19:24] Split 1: Selected feature 22 as initial search direction. Could separate 694 training set positives in that direction. [10:19:28] Split 2: Selected feature 22 as initial search direction. Could separate 661 training set positives in that direction. [10:19:31] Split 3: Selected feature 2 as initial search direction. Could separate 741 training set positives in that direction. [10:19:31] Found 1132 test set positives with q<0.01 in initial direction [10:19:31] Reading in data and feature calculation took 22.179 cpu seconds or 22 seconds wall clock time. [10:19:31] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [10:19:53] Iteration 1: Estimated 2526 PSMs with q<0.01 [10:20:18] Iteration 2: Estimated 3088 PSMs with q<0.01 [10:20:44] Iteration 3: Estimated 3454 PSMs with q<0.01 [10:20:44] Learned normalized SVM weights for the 3 cross-validation splits: [10:20:44] Split1 Split2 Split3 FeatureName [10:20:44] 0.0148 0.1945 0.8263 primary [10:20:44] 0.0238 0.1724 0.4380 xCorrLib [10:20:44] 0.2507 0.0506 0.1000 xCorrModel [10:20:44] -0.5410 1.6008 -0.3213 dotProduct [10:20:44] 1.4864 -0.5528 0.6639 contrastAngle [10:20:44] -0.2128 0.3766 -0.1331 logit [10:20:44] 0.4987 0.8643 0.1194 sumOfSquaredErrors [10:20:44] 0.1322 -0.3541 -0.7177 numberOfMatchingPeaks [10:20:44] -0.0367 -0.1073 -0.0946 numberOfMatchingPeaksAboveThreshold [10:20:44] 0.0358 0.1976 -0.0543 averageFragmentDeltaMasses [10:20:44] 0.1940 0.2502 0.2681 isotopeDotProduct [10:20:44] 0.6434 0.3107 0.2754 averageParentDeltaMass [10:20:44] 0.0762 0.0912 0.0957 percentBlankOverMono [10:20:44] 0.4042 0.4508 0.1272 numberPrecursorMatch [10:20:44] -0.8089 -1.0450 -0.5736 lnSp [10:20:44] 0.6188 0.8257 0.4011 maxLadderLength [10:20:44] 0.1472 0.2387 0.1177 evalue [10:20:44] 0.2691 -0.0042 0.1265 correlationToGaussian [10:20:44] 0.3834 0.0500 0.1615 correlationToPrecursor [10:20:44] -0.3179 -0.2064 -0.1624 isIntegratedSignal [10:20:44] -0.4326 0.0717 -0.0676 isIntegratedPrecursor [10:20:44] 0.7495 1.1398 0.3552 numPeaksWithGoodCorrelation [10:20:44] -0.5809 -0.5620 -0.4805 numMissedCleavage [10:20:44] -0.8749 -0.7599 -0.3037 pepLength [10:20:44] 0.0000 0.0000 0.0000 charge1 [10:20:44] -0.8416 -0.8670 -0.6980 charge2 [10:20:44] 0.8416 0.8670 0.6980 charge3 [10:20:44] 0.0000 0.0000 0.0000 charge4 [10:20:44] 0.7515 0.8917 0.5032 precursorMz [10:20:44] -0.7816 -0.8422 -1.1429 precursorMass [10:20:44] -0.5076 -0.4771 -0.2771 RTinMin [10:20:44] -6.5740 -7.5486 -5.1178 m0 [10:20:44] Found 2923 test set PSMs with q<0.01. [10:20:45] Scoring full list of PSMs with trained SVMs. [10:20:45] Features: [10:20:45] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:20:53] Processing line 1000000 [10:20:57] Found 1409236 PSMs [10:20:57] Evaluated set contained 708567 positives and 700669 negatives. [10:20:59] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [10:21:02] Selecting pi_0=0.927267 [10:21:02] Calculating q values. [10:21:02] New pi_0 estimate on final list yields 9460 target peptides with q<0.01. [10:21:02] Calculating posterior error probabilities (PEPs). [10:21:04] Processing took 92.33 cpu seconds or 93 seconds wall clock time. [10:21:16] First pass: 9460 peptides identified at 1.0% FDR [10:21:17] Generating retention time mapping using 9466 points... [10:21:17] Enough data points (9466) to perform KDE alignment. [10:21:18] Enough data points (9314) to perform KDE alignment. [10:21:19] Enough data points (9466) to perform KDE alignment. [10:21:20] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:21:25] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:21:42] Sorted feature file in 16.97 seconds wall clock time [10:21:42] File size check: 323275216 vs 323275216 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:21:42] Executing [cmd /c C:\Windows\Temp\tmp3979.java\Percolator-v3-01-4303304390917093937.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt] [10:21:42] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [10:21:42] Copyright (c) 2006-9 University of Washington. All rights reserved. [10:21:42] Written by Lukas Käll (lukall@u.washington.edu) in the [10:21:42] Department of Genome Sciences at the University of Washington. [10:21:42] Issued command: [10:21:42] C:\Windows\Temp\tmp3979.java\Percolator-v3-01-4303304390917093937.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:21:42] Started Wed Jul 17 10:21:42 2024 [10:21:42] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [10:21:42] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [10:21:42] Features: [10:21:42] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:21:50] Found 772084 PSMs [10:21:50] Separate target and decoy search inputs detected, using mix-max method. [10:21:50] Train/test set contains 250074 positives and 249926 negatives, size ratio=1.00059 and pi0=1 [10:21:51] Selecting Cpos by cross-validation. [10:21:51] Selecting Cneg by cross-validation. [10:21:54] Split 1: Selected feature 2 as initial search direction. Could separate 1385 training set positives in that direction. [10:21:58] Split 2: Selected feature 2 as initial search direction. Could separate 1358 training set positives in that direction. [10:22:02] Split 3: Selected feature 2 as initial search direction. Could separate 1257 training set positives in that direction. [10:22:02] Found 1902 test set positives with q<0.01 in initial direction [10:22:02] Reading in data and feature calculation took 19.575 cpu seconds or 20 seconds wall clock time. [10:22:02] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [10:22:30] Iteration 1: Estimated 3830 PSMs with q<0.01 [10:22:59] Iteration 2: Estimated 4948 PSMs with q<0.01 [10:23:28] Iteration 3: Estimated 5553 PSMs with q<0.01 [10:23:57] Iteration 4: Estimated 5910 PSMs with q<0.01 [10:24:26] Iteration 5: Estimated 6177 PSMs with q<0.01 [10:24:56] Iteration 6: Estimated 6333 PSMs with q<0.01 [10:25:26] Iteration 7: Estimated 6444 PSMs with q<0.01 [10:25:55] Iteration 8: Estimated 6490 PSMs with q<0.01 [10:26:25] Iteration 9: Estimated 6562 PSMs with q<0.01 [10:26:55] Iteration 10: Estimated 6626 PSMs with q<0.01 [10:26:55] Learned normalized SVM weights for the 3 cross-validation splits: [10:26:55] Split1 Split2 Split3 FeatureName [10:26:55] 0.1832 -0.7520 0.0661 primary [10:26:55] 0.2081 0.2422 0.0791 xCorrLib [10:26:55] 0.0931 0.1540 0.1739 xCorrModel [10:26:55] 0.2963 1.5784 0.0565 dotProduct [10:26:55] 0.2355 0.3627 0.3350 contrastAngle [10:26:55] 0.2129 0.0649 0.1464 logit [10:26:55] 0.4643 1.0278 0.2216 sumOfSquaredErrors [10:26:55] 0.0044 0.9196 0.0145 numberOfMatchingPeaks [10:26:55] -0.1657 -0.1995 0.0265 numberOfMatchingPeaksAboveThreshold [10:26:55] 0.0002 -0.3034 -0.0093 averageFragmentDeltaMasses [10:26:55] -0.0223 0.3772 0.1282 isotopeDotProduct [10:26:55] 0.0103 0.2278 0.0349 averageParentDeltaMass [10:26:55] -0.1295 -0.1957 0.0341 percentBlankOverMono [10:26:55] 0.0995 0.0391 0.0802 numberPrecursorMatch [10:26:55] -0.7328 -1.2484 -0.6714 lnSp [10:26:55] 0.5836 0.9062 0.5791 maxLadderLength [10:26:55] 0.1825 0.2673 0.1951 evalue [10:26:55] 0.2044 0.5077 0.1811 correlationToGaussian [10:26:55] 0.0511 -0.1902 0.1486 correlationToPrecursor [10:26:55] -0.0978 0.3399 -0.0339 isIntegratedSignal [10:26:55] 0.0373 0.6301 0.0392 isIntegratedPrecursor [10:26:55] 0.5070 1.0303 0.4859 numPeaksWithGoodCorrelation [10:26:55] 0.0782 0.1826 0.0789 deltaRT [10:26:55] -0.0770 0.0456 -0.0022 ms1MassError [10:26:55] -0.0830 -0.2979 -0.1306 ms2MassError [10:26:55] -0.3451 -0.6702 -0.2163 numMissedCleavage [10:26:55] -0.4313 -0.0480 -0.4656 pepLength [10:26:55] 0.0000 0.0000 0.0000 charge1 [10:26:55] -0.3368 -0.2611 -0.2034 charge2 [10:26:55] 0.3368 0.2611 0.2034 charge3 [10:26:55] 0.0000 0.0000 0.0000 charge4 [10:26:55] 0.3390 0.4717 0.2544 precursorMz [10:26:55] -0.2268 -0.2716 -0.0934 precursorMass [10:26:55] -0.2028 -0.3535 -0.2553 RTinMin [10:26:55] -4.2706 -8.4473 -3.8179 m0 [10:26:55] Found 5932 test set PSMs with q<0.01. [10:26:55] Scoring full list of PSMs with trained SVMs. [10:26:55] Features: [10:26:55] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:27:03] Found 772084 PSMs [10:27:03] Evaluated set contained 386042 positives and 386042 negatives. [10:27:04] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [10:27:06] Selecting pi_0=0.930809 [10:27:06] Calculating q values. [10:27:06] New pi_0 estimate on final list yields 10072 target peptides with q<0.01. [10:27:06] Calculating posterior error probabilities (PEPs). [10:27:08] Processing took 306 cpu seconds or 306 seconds wall clock time. [10:27:21] Generating retention time mapping using 10081 points... [10:27:21] Enough data points (10081) to perform KDE alignment. [10:27:23] Enough data points (9890) to perform KDE alignment. [10:27:23] Enough data points (10081) to perform KDE alignment. [10:27:24] Writing elib result library... [10:27:25] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 10072 vs local peptides: 10072 [10:27:25] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML... [10:27:25] Extracting Spectral Data for 10072 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML... [10:27:25] Number of global peptides: 10072 vs local peptides: 10072 [10:27:28] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [10:27:28] Parsed features and scores for 10072 peptides. [10:27:28] Extracting 10072 peptides... [10:27:28] Quant Extracting 398.4 to 400.4 m/z (7.3527617 to 79.41267 min) [10:27:28] Quant Extracting 400.4 to 402.4 m/z (5.2905254 to 79.832504 min) [10:27:28] Quant Extracting 402.4 to 404.4 m/z (10.586303 to 80.35251 min) [10:27:28] Quant Extracting 404.4 to 406.4 m/z (7.15772 to 81.93882 min) [10:27:28] Quant Extracting 406.4 to 408.4 m/z (7.225832 to 80.90331 min) [10:27:28] Quant Extracting 408.4 to 410.4 m/z (7.1942625 to 88.63035 min) [10:27:28] Quant Extracting 410.4 to 412.4 m/z (4.40889 to 81.649086 min) [10:27:28] Quant Extracting 412.4 to 414.4 m/z (5.8511157 to 78.96431 min) [10:27:28] Quant Extracting 414.4 to 416.4 m/z (5.592664 to 80.42074 min) [10:27:29] Quant Extracting 416.4 to 418.4 m/z (5.982831 to 84.282646 min) [10:27:29] Quant Extracting 418.4 to 420.4 m/z (7.0353904 to 80.13152 min) [10:27:29] Quant Extracting 420.4 to 422.4 m/z (7.133649 to 82.428665 min) [10:27:29] Quant Extracting 422.4 to 424.4 m/z (7.133649 to 79.09706 min) [10:27:29] Quant Extracting 424.4 to 426.4 m/z (3.691619 to 85.622055 min) [10:27:29] Quant Extracting 426.4 to 428.4 m/z (7.134795 to 78.194176 min) [10:27:29] Quant Extracting 428.4 to 430.4 m/z (7.1359415 to 79.81059 min) [10:27:29] Quant Extracting 430.4 to 432.4 m/z (6.6092887 to 81.07119 min) [10:27:29] Quant Extracting 432.4 to 434.4 m/z (9.044129 to 81.8821 min) [10:27:29] Quant Extracting 434.4 to 436.4 m/z (7.137088 to 92.21054 min) [10:27:29] Quant Extracting 436.4 to 438.4 m/z (7.1382346 to 84.907745 min) [10:27:30] Quant Extracting 438.4 to 440.5 m/z (4.9079328 to 85.39727 min) [10:27:30] Quant Extracting 440.5 to 442.5 m/z (6.6815033 to 84.0278 min) [10:27:30] Quant Extracting 442.5 to 444.5 m/z (7.139381 to 81.14206 min) [10:27:30] Quant Extracting 444.5 to 446.5 m/z (7.817685 to 82.826614 min) [10:27:30] Quant Extracting 446.5 to 448.5 m/z (7.1405272 to 85.56234 min) [10:27:30] Quant Extracting 448.5 to 450.5 m/z (7.1731057 to 80.81862 min) [10:27:30] Quant Extracting 450.5 to 452.5 m/z (4.3549495 to 87.49975 min) [10:27:30] Quant Extracting 452.5 to 454.5 m/z (7.3359976 to 90.145195 min) [10:27:30] Quant Extracting 454.5 to 456.5 m/z (7.175398 to 84.29737 min) [10:27:31] Quant Extracting 456.5 to 458.5 m/z (7.1439667 to 92.31937 min) [10:27:31] Quant Extracting 458.5 to 460.5 m/z (5.4743776 to 92.184006 min) [10:27:31] Quant Extracting 460.5 to 462.5 m/z (6.159859 to 88.22042 min) [10:27:31] Quant Extracting 462.5 to 464.5 m/z (6.8182354 to 89.4623 min) [10:27:31] Quant Extracting 464.5 to 466.5 m/z (7.274821 to 87.30714 min) [10:27:31] Quant Extracting 466.5 to 468.5 m/z (8.085691 to 87.700554 min) [10:27:31] Quant Extracting 468.5 to 470.5 m/z (7.147404 to 88.87655 min) [10:27:31] Quant Extracting 470.5 to 472.5 m/z (8.345084 to 100.773346 min) [10:27:31] Quant Extracting 472.5 to 474.5 m/z (7.1485505 to 92.06108 min) [10:27:32] Quant Extracting 474.5 to 476.5 m/z (7.7652254 to 86.71651 min) [10:27:32] Quant Extracting 476.5 to 478.5 m/z (8.120817 to 89.53137 min) [10:27:32] Quant Extracting 478.5 to 480.5 m/z (7.50511 to 88.388596 min) [10:27:32] Quant Extracting 480.5 to 482.5 m/z (7.150842 to 91.53307 min) [10:27:32] Quant Extracting 482.5 to 484.5 m/z (5.806946 to 88.25954 min) [10:27:32] Quant Extracting 484.5 to 486.5 m/z (7.1193533 to 89.501465 min) [10:27:32] Quant Extracting 486.5 to 488.5 m/z (7.1845684 to 90.87858 min) [10:27:32] Quant Extracting 488.5 to 490.5 m/z (7.1531353 to 92.492775 min) [10:27:32] Quant Extracting 490.5 to 492.5 m/z (7.1531353 to 87.7396 min) [10:27:32] Quant Extracting 492.5 to 494.5 m/z (7.1542807 to 89.601776 min) [10:27:32] Quant Extracting 494.5 to 496.5 m/z (6.5989127 to 93.35647 min) [10:27:32] Quant Extracting 496.5 to 498.5 m/z (7.155427 to 90.81734 min) [10:27:33] Quant Extracting 498.5 to 500.5 m/z (7.155427 to 89.047874 min) [10:27:33] Quant Extracting 500.5 to 502.5 m/z (7.1880097 to 87.31751 min) [10:27:33] Attempted extraction for: 10072, found 10072 [10:27:33] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML (10072 entries)... [10:27:33] Writing 10072 peptides to entries table... [10:27:34] Writing 10072 peptides to peptidequants table... [10:27:35] Finished writing to Encyclopedia ELIB at Wed Jul 17 10:27:35 BST 2024 [10:27:36] Writing local target/decoy peptides: 10072/101, pi0: 0.930809 [10:27:36] Writing local target/decoy proteins: 3407/34 [10:27:38] Finished analysis! 10072 peptides identified at 1.0% FDR (17.8 minutes) [10:27:38] Generating chromatogram library (2 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [10:27:42] EncyclopeDIA version 2.12.30 [10:27:43] Getting count of protein accessions... [10:27:43] Using EncyclopeDIA 2.X Scoring System [10:27:43] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML ... [10:27:43] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML ... [10:27:43] Parsed 1% [10:27:43] Parsed 2% [10:27:44] Parsed 3% [10:27:44] Parsed 4% [10:27:44] Parsed 5% [10:27:45] Parsed 6% [10:27:45] Parsed 7% [10:27:45] Parsed 8% [10:27:46] Parsed 9% [10:27:46] Parsed 10% [10:27:48] Parsed 11% [10:27:48] Parsed 12% [10:27:49] Parsed 13% [10:27:50] Parsed 14% [10:27:51] Parsed 15% [10:27:52] Parsed 16% [10:27:54] Parsed 17% [10:27:57] Parsed 18% [10:28:00] Parsed 19% [10:28:01] Parsed 20% [10:28:01] Parsed 21% [10:28:02] Parsed 22% [10:28:03] Parsed 23% [10:28:03] Parsed 24% [10:28:05] Parsed 25% [10:28:06] Parsed 26% [10:28:07] Parsed 27% [10:28:07] Parsed 28% [10:28:08] Parsed 29% [10:28:09] Parsed 30% [10:28:10] Parsed 31% [10:28:11] Parsed 32% [10:28:13] Parsed 33% [10:28:14] Parsed 34% [10:28:17] Parsed 35% [10:28:19] Parsed 36% [10:28:23] Parsed 37% [10:28:27] Parsed 38% [10:28:28] Parsed 39% [10:28:29] Parsed 40% [10:28:30] Parsed 41% [10:28:30] Parsed 42% [10:28:31] Parsed 43% [10:28:32] Parsed 44% [10:28:33] Parsed 45% [10:28:34] Parsed 46% [10:28:35] Parsed 47% [10:28:37] Parsed 48% [10:28:39] Parsed 49% [10:28:42] Parsed 50% [10:28:42] Parsed 51% [10:28:43] Parsed 52% [10:28:44] Parsed 53% [10:28:44] Parsed 54% [10:28:45] Parsed 55% [10:28:46] Parsed 56% [10:28:47] Parsed 57% [10:28:48] Parsed 58% [10:28:49] Parsed 59% [10:28:50] Parsed 60% [10:28:52] Parsed 61% [10:28:54] Parsed 62% [10:28:56] Parsed 63% [10:28:59] Parsed 64% [10:29:02] Parsed 65% [10:29:04] Parsed 66% [10:29:09] Parsed 67% [10:29:12] Parsed 68% [10:29:16] Parsed 69% [10:29:19] Parsed 70% [10:29:25] Parsed 71% [10:29:34] Parsed 72% [10:29:34] Parsed 73% [10:29:35] Parsed 74% [10:29:36] Parsed 75% [10:29:37] Parsed 76% [10:29:38] Parsed 77% [10:29:38] Parsed 78% [10:29:40] Parsed 79% [10:29:40] Parsed 80% [10:29:41] Parsed 81% [10:29:43] Parsed 82% [10:29:45] Parsed 83% [10:29:47] Parsed 84% [10:29:51] Parsed 85% [10:29:53] Parsed 86% [10:29:57] Parsed 87% [10:30:01] Parsed 88% [10:30:05] Parsed 89% [10:30:09] Parsed 90% [10:30:14] Parsed 91% [10:30:18] Parsed 92% [10:30:23] Parsed 93% [10:30:26] Parsed 94% [10:30:31] Parsed 95% [10:30:36] Parsed 96% [10:30:41] Parsed 97% [10:30:51] Parsed 98% [10:30:52] Parsed 99% [10:30:53] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.dia ... [10:30:54] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.dia! [10:30:54] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML [10:30:54] Library File: UP000005640_9606-z3_nce27-prosit.dlib [10:30:54] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.elib [10:30:54] Parameters: [10:30:54] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [10:30:54] Converting files... [10:30:54] Calculating features... [10:30:54] Processing precursors scans... [10:30:54] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:30:54] Processing 498.5 to 500.5 m/z, (3.9180331 second duty cycle) [10:30:56] 6260 peptides remaining for 498.5 to 500.5... [10:30:57] 5751 peptides remaining for 498.5 to 500.5... [10:30:57] 5283 peptides remaining for 498.5 to 500.5... [10:30:58] 4772 peptides remaining for 498.5 to 500.5... [10:30:58] 4262 peptides remaining for 498.5 to 500.5... [10:30:59] 3757 peptides remaining for 498.5 to 500.5... [10:30:59] 3229 peptides remaining for 498.5 to 500.5... [10:31:00] 2713 peptides remaining for 498.5 to 500.5... [10:31:00] 2185 peptides remaining for 498.5 to 500.5... [10:31:01] 1673 peptides remaining for 498.5 to 500.5... [10:31:01] 1136 peptides remaining for 498.5 to 500.5... [10:31:02] 618 peptides remaining for 498.5 to 500.5... [10:31:03] 23 peptides remaining for 498.5 to 500.5... [10:31:03] Processing 500.5 to 502.5 m/z, (1.9590155 second duty cycle) [10:31:05] 7660 peptides remaining for 500.5 to 502.5... [10:31:05] 7214 peptides remaining for 500.5 to 502.5... [10:31:06] 6775 peptides remaining for 500.5 to 502.5... [10:31:06] 6339 peptides remaining for 500.5 to 502.5... [10:31:07] 5918 peptides remaining for 500.5 to 502.5... [10:31:07] 5474 peptides remaining for 500.5 to 502.5... [10:31:08] 5023 peptides remaining for 500.5 to 502.5... [10:31:09] 4559 peptides remaining for 500.5 to 502.5... [10:31:09] 4114 peptides remaining for 500.5 to 502.5... [10:31:10] 3653 peptides remaining for 500.5 to 502.5... [10:31:10] 3224 peptides remaining for 500.5 to 502.5... [10:31:11] 2794 peptides remaining for 500.5 to 502.5... [10:31:11] 2337 peptides remaining for 500.5 to 502.5... [10:31:12] 1896 peptides remaining for 500.5 to 502.5... [10:31:12] 1436 peptides remaining for 500.5 to 502.5... [10:31:13] 969 peptides remaining for 500.5 to 502.5... [10:31:13] 512 peptides remaining for 500.5 to 502.5... [10:31:14] 55 peptides remaining for 500.5 to 502.5... [10:31:14] Processing 502.5 to 504.5 m/z, (1.9590371 second duty cycle) [10:31:16] 7075 peptides remaining for 502.5 to 504.5... [10:31:16] 6634 peptides remaining for 502.5 to 504.5... [10:31:17] 6203 peptides remaining for 502.5 to 504.5... [10:31:17] 5768 peptides remaining for 502.5 to 504.5... [10:31:18] 5332 peptides remaining for 502.5 to 504.5... [10:31:18] 4901 peptides remaining for 502.5 to 504.5... [10:31:19] 4465 peptides remaining for 502.5 to 504.5... [10:31:20] 4028 peptides remaining for 502.5 to 504.5... [10:31:20] 3593 peptides remaining for 502.5 to 504.5... [10:31:21] 3143 peptides remaining for 502.5 to 504.5... [10:31:21] 2708 peptides remaining for 502.5 to 504.5... [10:31:22] 2273 peptides remaining for 502.5 to 504.5... [10:31:22] 1838 peptides remaining for 502.5 to 504.5... [10:31:23] 1380 peptides remaining for 502.5 to 504.5... [10:31:23] 953 peptides remaining for 502.5 to 504.5... [10:31:24] 522 peptides remaining for 502.5 to 504.5... [10:31:24] 101 peptides remaining for 502.5 to 504.5... [10:31:25] Processing 504.5 to 506.5 m/z, (1.9590156 second duty cycle) [10:31:26] 6641 peptides remaining for 504.5 to 506.5... [10:31:27] 6224 peptides remaining for 504.5 to 506.5... [10:31:28] 5786 peptides remaining for 504.5 to 506.5... [10:31:28] 5357 peptides remaining for 504.5 to 506.5... [10:31:29] 4936 peptides remaining for 504.5 to 506.5... [10:31:29] 4495 peptides remaining for 504.5 to 506.5... [10:31:30] 4081 peptides remaining for 504.5 to 506.5... [10:31:30] 3658 peptides remaining for 504.5 to 506.5... [10:31:31] 3246 peptides remaining for 504.5 to 506.5... [10:31:31] 2838 peptides remaining for 504.5 to 506.5... [10:31:32] 2411 peptides remaining for 504.5 to 506.5... [10:31:32] 1980 peptides remaining for 504.5 to 506.5... [10:31:33] 1576 peptides remaining for 504.5 to 506.5... [10:31:33] 1163 peptides remaining for 504.5 to 506.5... [10:31:34] 766 peptides remaining for 504.5 to 506.5... [10:31:34] 364 peptides remaining for 504.5 to 506.5... [10:31:35] Processing 506.5 to 508.5 m/z, (1.9590372 second duty cycle) [10:31:36] 7135 peptides remaining for 506.5 to 508.5... [10:31:37] 6708 peptides remaining for 506.5 to 508.5... [10:31:37] 6287 peptides remaining for 506.5 to 508.5... [10:31:38] 5873 peptides remaining for 506.5 to 508.5... [10:31:38] 5443 peptides remaining for 506.5 to 508.5... [10:31:39] 5011 peptides remaining for 506.5 to 508.5... [10:31:40] 4587 peptides remaining for 506.5 to 508.5... [10:31:40] 4168 peptides remaining for 506.5 to 508.5... [10:31:41] 3741 peptides remaining for 506.5 to 508.5... [10:31:41] 3329 peptides remaining for 506.5 to 508.5... [10:31:42] 2917 peptides remaining for 506.5 to 508.5... [10:31:42] 2512 peptides remaining for 506.5 to 508.5... [10:31:43] 2104 peptides remaining for 506.5 to 508.5... [10:31:43] 1693 peptides remaining for 506.5 to 508.5... [10:31:44] 1292 peptides remaining for 506.5 to 508.5... [10:31:44] 879 peptides remaining for 506.5 to 508.5... [10:31:45] 493 peptides remaining for 506.5 to 508.5... [10:31:45] 73 peptides remaining for 506.5 to 508.5... [10:31:46] Processing 508.5 to 510.5 m/z, (1.9590154 second duty cycle) [10:31:47] 7488 peptides remaining for 508.5 to 510.5... [10:31:48] 7043 peptides remaining for 508.5 to 510.5... [10:31:48] 6614 peptides remaining for 508.5 to 510.5... [10:31:49] 6195 peptides remaining for 508.5 to 510.5... [10:31:49] 5771 peptides remaining for 508.5 to 510.5... [10:31:50] 5346 peptides remaining for 508.5 to 510.5... [10:31:50] 4907 peptides remaining for 508.5 to 510.5... [10:31:51] 4474 peptides remaining for 508.5 to 510.5... [10:31:51] 4038 peptides remaining for 508.5 to 510.5... [10:31:52] 3614 peptides remaining for 508.5 to 510.5... [10:31:52] 3164 peptides remaining for 508.5 to 510.5... [10:31:53] 2748 peptides remaining for 508.5 to 510.5... [10:31:54] 2320 peptides remaining for 508.5 to 510.5... [10:31:54] 1895 peptides remaining for 508.5 to 510.5... [10:31:55] 1466 peptides remaining for 508.5 to 510.5... [10:31:55] 1056 peptides remaining for 508.5 to 510.5... [10:31:56] 631 peptides remaining for 508.5 to 510.5... [10:31:56] 214 peptides remaining for 508.5 to 510.5... [10:31:57] Processing 510.5 to 512.5 m/z, (1.959037 second duty cycle) [10:31:58] 6974 peptides remaining for 510.5 to 512.5... [10:31:59] 6550 peptides remaining for 510.5 to 512.5... [10:31:59] 6120 peptides remaining for 510.5 to 512.5... [10:32:00] 5687 peptides remaining for 510.5 to 512.5... [10:32:00] 5273 peptides remaining for 510.5 to 512.5... [10:32:01] 4844 peptides remaining for 510.5 to 512.5... [10:32:01] 4414 peptides remaining for 510.5 to 512.5... [10:32:02] 3979 peptides remaining for 510.5 to 512.5... [10:32:02] 3554 peptides remaining for 510.5 to 512.5... [10:32:03] 3135 peptides remaining for 510.5 to 512.5... [10:32:03] 2712 peptides remaining for 510.5 to 512.5... [10:32:04] 2303 peptides remaining for 510.5 to 512.5... [10:32:04] 1884 peptides remaining for 510.5 to 512.5... [10:32:05] 1485 peptides remaining for 510.5 to 512.5... [10:32:05] 1072 peptides remaining for 510.5 to 512.5... [10:32:06] 657 peptides remaining for 510.5 to 512.5... [10:32:06] 236 peptides remaining for 510.5 to 512.5... [10:32:07] Processing 512.5 to 514.5 m/z, (1.9590155 second duty cycle) [10:32:09] 6607 peptides remaining for 512.5 to 514.5... [10:32:09] 6184 peptides remaining for 512.5 to 514.5... [10:32:10] 5755 peptides remaining for 512.5 to 514.5... [10:32:10] 5309 peptides remaining for 512.5 to 514.5... [10:32:11] 4897 peptides remaining for 512.5 to 514.5... [10:32:11] 4502 peptides remaining for 512.5 to 514.5... [10:32:12] 4119 peptides remaining for 512.5 to 514.5... [10:32:12] 3699 peptides remaining for 512.5 to 514.5... [10:32:13] 3278 peptides remaining for 512.5 to 514.5... [10:32:13] 2852 peptides remaining for 512.5 to 514.5... [10:32:14] 2421 peptides remaining for 512.5 to 514.5... [10:32:14] 2016 peptides remaining for 512.5 to 514.5... [10:32:15] 1615 peptides remaining for 512.5 to 514.5... [10:32:15] 1194 peptides remaining for 512.5 to 514.5... [10:32:16] 788 peptides remaining for 512.5 to 514.5... [10:32:16] 364 peptides remaining for 512.5 to 514.5... [10:32:17] Processing 514.5 to 516.5 m/z, (1.959037 second duty cycle) [10:32:19] 7342 peptides remaining for 514.5 to 516.5... [10:32:19] 6902 peptides remaining for 514.5 to 516.5... [10:32:20] 6478 peptides remaining for 514.5 to 516.5... [10:32:20] 6045 peptides remaining for 514.5 to 516.5... [10:32:21] 5623 peptides remaining for 514.5 to 516.5... [10:32:21] 5195 peptides remaining for 514.5 to 516.5... [10:32:22] 4796 peptides remaining for 514.5 to 516.5... [10:32:22] 4373 peptides remaining for 514.5 to 516.5... [10:32:23] 3955 peptides remaining for 514.5 to 516.5... [10:32:23] 3537 peptides remaining for 514.5 to 516.5... [10:32:24] 3103 peptides remaining for 514.5 to 516.5... [10:32:24] 2684 peptides remaining for 514.5 to 516.5... [10:32:25] 2270 peptides remaining for 514.5 to 516.5... [10:32:25] 1874 peptides remaining for 514.5 to 516.5... [10:32:26] 1450 peptides remaining for 514.5 to 516.5... [10:32:26] 1035 peptides remaining for 514.5 to 516.5... [10:32:27] 635 peptides remaining for 514.5 to 516.5... [10:32:27] 212 peptides remaining for 514.5 to 516.5... [10:32:28] Processing 516.5 to 518.5 m/z, (1.9590155 second duty cycle) [10:32:29] 7196 peptides remaining for 516.5 to 518.5... [10:32:30] 6787 peptides remaining for 516.5 to 518.5... [10:32:30] 6359 peptides remaining for 516.5 to 518.5... [10:32:31] 5940 peptides remaining for 516.5 to 518.5... [10:32:32] 5500 peptides remaining for 516.5 to 518.5... [10:32:32] 5116 peptides remaining for 516.5 to 518.5... [10:32:33] 4723 peptides remaining for 516.5 to 518.5... [10:32:33] 4298 peptides remaining for 516.5 to 518.5... [10:32:34] 3866 peptides remaining for 516.5 to 518.5... [10:32:34] 3436 peptides remaining for 516.5 to 518.5... [10:32:35] 3013 peptides remaining for 516.5 to 518.5... [10:32:35] 2599 peptides remaining for 516.5 to 518.5... [10:32:36] 2178 peptides remaining for 516.5 to 518.5... [10:32:36] 1766 peptides remaining for 516.5 to 518.5... [10:32:37] 1363 peptides remaining for 516.5 to 518.5... [10:32:37] 950 peptides remaining for 516.5 to 518.5... [10:32:38] 534 peptides remaining for 516.5 to 518.5... [10:32:38] 137 peptides remaining for 516.5 to 518.5... [10:32:39] Processing 518.5 to 520.5 m/z, (1.9590372 second duty cycle) [10:32:40] 6657 peptides remaining for 518.5 to 520.5... [10:32:41] 6243 peptides remaining for 518.5 to 520.5... [10:32:41] 5830 peptides remaining for 518.5 to 520.5... [10:32:42] 5435 peptides remaining for 518.5 to 520.5... [10:32:42] 5017 peptides remaining for 518.5 to 520.5... [10:32:43] 4589 peptides remaining for 518.5 to 520.5... [10:32:43] 4182 peptides remaining for 518.5 to 520.5... [10:32:44] 3781 peptides remaining for 518.5 to 520.5... [10:32:44] 3367 peptides remaining for 518.5 to 520.5... [10:32:45] 2965 peptides remaining for 518.5 to 520.5... [10:32:45] 2569 peptides remaining for 518.5 to 520.5... [10:32:46] 2163 peptides remaining for 518.5 to 520.5... [10:32:46] 1755 peptides remaining for 518.5 to 520.5... [10:32:47] 1356 peptides remaining for 518.5 to 520.5... [10:32:47] 955 peptides remaining for 518.5 to 520.5... [10:32:48] 559 peptides remaining for 518.5 to 520.5... [10:32:48] 139 peptides remaining for 518.5 to 520.5... [10:32:49] Processing 520.5 to 522.5 m/z, (1.9590156 second duty cycle) [10:32:51] 6921 peptides remaining for 520.5 to 522.5... [10:32:51] 6518 peptides remaining for 520.5 to 522.5... [10:32:52] 6108 peptides remaining for 520.5 to 522.5... [10:32:52] 5676 peptides remaining for 520.5 to 522.5... [10:32:53] 5277 peptides remaining for 520.5 to 522.5... [10:32:53] 4861 peptides remaining for 520.5 to 522.5... [10:32:54] 4462 peptides remaining for 520.5 to 522.5... [10:32:54] 4056 peptides remaining for 520.5 to 522.5... [10:32:55] 3653 peptides remaining for 520.5 to 522.5... [10:32:55] 3233 peptides remaining for 520.5 to 522.5... [10:32:56] 2821 peptides remaining for 520.5 to 522.5... [10:32:56] 2404 peptides remaining for 520.5 to 522.5... [10:32:57] 1991 peptides remaining for 520.5 to 522.5... [10:32:57] 1598 peptides remaining for 520.5 to 522.5... [10:32:58] 1210 peptides remaining for 520.5 to 522.5... [10:32:58] 792 peptides remaining for 520.5 to 522.5... [10:32:59] 362 peptides remaining for 520.5 to 522.5... [10:32:59] 0 peptides remaining for 520.5 to 522.5... [10:33:00] Processing 522.5 to 524.5 m/z, (1.9590371 second duty cycle) [10:33:02] 7136 peptides remaining for 522.5 to 524.5... [10:33:02] 6727 peptides remaining for 522.5 to 524.5... [10:33:03] 6299 peptides remaining for 522.5 to 524.5... [10:33:03] 5876 peptides remaining for 522.5 to 524.5... [10:33:04] 5473 peptides remaining for 522.5 to 524.5... [10:33:04] 5067 peptides remaining for 522.5 to 524.5... [10:33:05] 4627 peptides remaining for 522.5 to 524.5... [10:33:05] 4229 peptides remaining for 522.5 to 524.5... [10:33:06] 3824 peptides remaining for 522.5 to 524.5... [10:33:06] 3415 peptides remaining for 522.5 to 524.5... [10:33:07] 2996 peptides remaining for 522.5 to 524.5... [10:33:07] 2582 peptides remaining for 522.5 to 524.5... [10:33:08] 2159 peptides remaining for 522.5 to 524.5... [10:33:08] 1752 peptides remaining for 522.5 to 524.5... [10:33:09] 1333 peptides remaining for 522.5 to 524.5... [10:33:09] 928 peptides remaining for 522.5 to 524.5... [10:33:10] 535 peptides remaining for 522.5 to 524.5... [10:33:11] 138 peptides remaining for 522.5 to 524.5... [10:33:11] Processing 524.5 to 526.5 m/z, (1.9590155 second duty cycle) [10:33:13] 6885 peptides remaining for 524.5 to 526.5... [10:33:13] 6506 peptides remaining for 524.5 to 526.5... [10:33:14] 6080 peptides remaining for 524.5 to 526.5... [10:33:14] 5676 peptides remaining for 524.5 to 526.5... [10:33:15] 5289 peptides remaining for 524.5 to 526.5... [10:33:15] 4875 peptides remaining for 524.5 to 526.5... [10:33:16] 4457 peptides remaining for 524.5 to 526.5... [10:33:16] 4047 peptides remaining for 524.5 to 526.5... [10:33:17] 3622 peptides remaining for 524.5 to 526.5... [10:33:17] 3211 peptides remaining for 524.5 to 526.5... [10:33:18] 2805 peptides remaining for 524.5 to 526.5... [10:33:18] 2403 peptides remaining for 524.5 to 526.5... [10:33:19] 1994 peptides remaining for 524.5 to 526.5... [10:33:19] 1600 peptides remaining for 524.5 to 526.5... [10:33:20] 1201 peptides remaining for 524.5 to 526.5... [10:33:21] 800 peptides remaining for 524.5 to 526.5... [10:33:21] 408 peptides remaining for 524.5 to 526.5... [10:33:22] 9 peptides remaining for 524.5 to 526.5... [10:33:22] Processing 526.5 to 528.5 m/z, (1.9590371 second duty cycle) [10:33:24] 6347 peptides remaining for 526.5 to 528.5... [10:33:24] 5925 peptides remaining for 526.5 to 528.5... [10:33:25] 5511 peptides remaining for 526.5 to 528.5... [10:33:25] 5117 peptides remaining for 526.5 to 528.5... [10:33:26] 4713 peptides remaining for 526.5 to 528.5... [10:33:26] 4297 peptides remaining for 526.5 to 528.5... [10:33:27] 3903 peptides remaining for 526.5 to 528.5... [10:33:27] 3507 peptides remaining for 526.5 to 528.5... [10:33:28] 3100 peptides remaining for 526.5 to 528.5... [10:33:28] 2693 peptides remaining for 526.5 to 528.5... [10:33:29] 2284 peptides remaining for 526.5 to 528.5... [10:33:30] 1870 peptides remaining for 526.5 to 528.5... [10:33:30] 1448 peptides remaining for 526.5 to 528.5... [10:33:31] 1043 peptides remaining for 526.5 to 528.5... [10:33:31] 656 peptides remaining for 526.5 to 528.5... [10:33:32] 234 peptides remaining for 526.5 to 528.5... [10:33:32] Processing 528.5 to 530.5 m/z, (1.9590156 second duty cycle) [10:33:34] 7203 peptides remaining for 528.5 to 530.5... [10:33:34] 6796 peptides remaining for 528.5 to 530.5... [10:33:35] 6395 peptides remaining for 528.5 to 530.5... [10:33:35] 5982 peptides remaining for 528.5 to 530.5... [10:33:36] 5570 peptides remaining for 528.5 to 530.5... [10:33:36] 5173 peptides remaining for 528.5 to 530.5... [10:33:37] 4752 peptides remaining for 528.5 to 530.5... [10:33:37] 4347 peptides remaining for 528.5 to 530.5... [10:33:38] 3941 peptides remaining for 528.5 to 530.5... [10:33:38] 3528 peptides remaining for 528.5 to 530.5... [10:33:39] 3133 peptides remaining for 528.5 to 530.5... [10:33:39] 2717 peptides remaining for 528.5 to 530.5... [10:33:40] 2328 peptides remaining for 528.5 to 530.5... [10:33:40] 1934 peptides remaining for 528.5 to 530.5... [10:33:41] 1534 peptides remaining for 528.5 to 530.5... [10:33:41] 1148 peptides remaining for 528.5 to 530.5... [10:33:42] 749 peptides remaining for 528.5 to 530.5... [10:33:42] 344 peptides remaining for 528.5 to 530.5... [10:33:43] Processing 530.5 to 532.5 m/z, (1.9590371 second duty cycle) [10:33:45] 7040 peptides remaining for 530.5 to 532.5... [10:33:45] 6641 peptides remaining for 530.5 to 532.5... [10:33:46] 6235 peptides remaining for 530.5 to 532.5... [10:33:46] 5825 peptides remaining for 530.5 to 532.5... [10:33:47] 5410 peptides remaining for 530.5 to 532.5... [10:33:47] 4992 peptides remaining for 530.5 to 532.5... [10:33:48] 4582 peptides remaining for 530.5 to 532.5... [10:33:48] 4172 peptides remaining for 530.5 to 532.5... [10:33:49] 3761 peptides remaining for 530.5 to 532.5... [10:33:49] 3339 peptides remaining for 530.5 to 532.5... [10:33:50] 2936 peptides remaining for 530.5 to 532.5... [10:33:50] 2520 peptides remaining for 530.5 to 532.5... [10:33:51] 2124 peptides remaining for 530.5 to 532.5... [10:33:51] 1741 peptides remaining for 530.5 to 532.5... [10:33:52] 1329 peptides remaining for 530.5 to 532.5... [10:33:52] 933 peptides remaining for 530.5 to 532.5... [10:33:53] 493 peptides remaining for 530.5 to 532.5... [10:33:53] 87 peptides remaining for 530.5 to 532.5... [10:33:54] Processing 532.5 to 534.5 m/z, (1.9590156 second duty cycle) [10:33:56] 6563 peptides remaining for 532.5 to 534.5... [10:33:56] 6157 peptides remaining for 532.5 to 534.5... [10:33:57] 5748 peptides remaining for 532.5 to 534.5... [10:33:57] 5356 peptides remaining for 532.5 to 534.5... [10:33:58] 4965 peptides remaining for 532.5 to 534.5... [10:33:58] 4553 peptides remaining for 532.5 to 534.5... [10:33:59] 4148 peptides remaining for 532.5 to 534.5... [10:33:59] 3751 peptides remaining for 532.5 to 534.5... [10:34:00] 3365 peptides remaining for 532.5 to 534.5... [10:34:00] 2934 peptides remaining for 532.5 to 534.5... [10:34:01] 2526 peptides remaining for 532.5 to 534.5... [10:34:01] 2115 peptides remaining for 532.5 to 534.5... [10:34:02] 1726 peptides remaining for 532.5 to 534.5... [10:34:02] 1320 peptides remaining for 532.5 to 534.5... [10:34:03] 926 peptides remaining for 532.5 to 534.5... [10:34:03] 510 peptides remaining for 532.5 to 534.5... [10:34:04] 119 peptides remaining for 532.5 to 534.5... [10:34:04] Processing 534.5 to 536.5 m/z, (1.9590371 second duty cycle) [10:34:06] 6551 peptides remaining for 534.5 to 536.5... [10:34:07] 6168 peptides remaining for 534.5 to 536.5... [10:34:07] 5743 peptides remaining for 534.5 to 536.5... [10:34:08] 5353 peptides remaining for 534.5 to 536.5... [10:34:08] 4945 peptides remaining for 534.5 to 536.5... [10:34:09] 4542 peptides remaining for 534.5 to 536.5... [10:34:09] 4144 peptides remaining for 534.5 to 536.5... [10:34:10] 3757 peptides remaining for 534.5 to 536.5... [10:34:10] 3339 peptides remaining for 534.5 to 536.5... [10:34:11] 2936 peptides remaining for 534.5 to 536.5... [10:34:11] 2528 peptides remaining for 534.5 to 536.5... [10:34:12] 2140 peptides remaining for 534.5 to 536.5... [10:34:12] 1748 peptides remaining for 534.5 to 536.5... [10:34:13] 1384 peptides remaining for 534.5 to 536.5... [10:34:13] 1013 peptides remaining for 534.5 to 536.5... [10:34:14] 619 peptides remaining for 534.5 to 536.5... [10:34:14] 220 peptides remaining for 534.5 to 536.5... [10:34:15] Processing 536.5 to 538.5 m/z, (1.9590155 second duty cycle) [10:34:17] 7168 peptides remaining for 536.5 to 538.5... [10:34:17] 6769 peptides remaining for 536.5 to 538.5... [10:34:18] 6365 peptides remaining for 536.5 to 538.5... [10:34:18] 5964 peptides remaining for 536.5 to 538.5... [10:34:19] 5568 peptides remaining for 536.5 to 538.5... [10:34:19] 5178 peptides remaining for 536.5 to 538.5... [10:34:20] 4783 peptides remaining for 536.5 to 538.5... [10:34:20] 4364 peptides remaining for 536.5 to 538.5... [10:34:21] 3970 peptides remaining for 536.5 to 538.5... [10:34:21] 3584 peptides remaining for 536.5 to 538.5... [10:34:22] 3171 peptides remaining for 536.5 to 538.5... [10:34:22] 2780 peptides remaining for 536.5 to 538.5... [10:34:23] 2379 peptides remaining for 536.5 to 538.5... [10:34:23] 1977 peptides remaining for 536.5 to 538.5... [10:34:24] 1590 peptides remaining for 536.5 to 538.5... [10:34:24] 1212 peptides remaining for 536.5 to 538.5... [10:34:25] 817 peptides remaining for 536.5 to 538.5... [10:34:25] 422 peptides remaining for 536.5 to 538.5... [10:34:26] 21 peptides remaining for 536.5 to 538.5... [10:34:26] Processing 538.5 to 540.5 m/z, (1.9590372 second duty cycle) [10:34:28] 6771 peptides remaining for 538.5 to 540.5... [10:34:29] 6377 peptides remaining for 538.5 to 540.5... [10:34:29] 5982 peptides remaining for 538.5 to 540.5... [10:34:30] 5572 peptides remaining for 538.5 to 540.5... [10:34:30] 5157 peptides remaining for 538.5 to 540.5... [10:34:31] 4768 peptides remaining for 538.5 to 540.5... [10:34:31] 4367 peptides remaining for 538.5 to 540.5... [10:34:32] 3979 peptides remaining for 538.5 to 540.5... [10:34:32] 3578 peptides remaining for 538.5 to 540.5... [10:34:33] 3182 peptides remaining for 538.5 to 540.5... [10:34:33] 2787 peptides remaining for 538.5 to 540.5... [10:34:34] 2377 peptides remaining for 538.5 to 540.5... [10:34:34] 1976 peptides remaining for 538.5 to 540.5... [10:34:35] 1580 peptides remaining for 538.5 to 540.5... [10:34:36] 1175 peptides remaining for 538.5 to 540.5... [10:34:36] 787 peptides remaining for 538.5 to 540.5... [10:34:37] 409 peptides remaining for 538.5 to 540.5... [10:34:37] 14 peptides remaining for 538.5 to 540.5... [10:34:38] Processing 540.5 to 542.5 m/z, (1.9590158 second duty cycle) [10:34:39] 6213 peptides remaining for 540.5 to 542.5... [10:34:40] 5827 peptides remaining for 540.5 to 542.5... [10:34:40] 5417 peptides remaining for 540.5 to 542.5... [10:34:41] 5012 peptides remaining for 540.5 to 542.5... [10:34:41] 4619 peptides remaining for 540.5 to 542.5... [10:34:42] 4232 peptides remaining for 540.5 to 542.5... [10:34:42] 3848 peptides remaining for 540.5 to 542.5... [10:34:43] 3461 peptides remaining for 540.5 to 542.5... [10:34:43] 3048 peptides remaining for 540.5 to 542.5... [10:34:44] 2647 peptides remaining for 540.5 to 542.5... [10:34:44] 2220 peptides remaining for 540.5 to 542.5... [10:34:45] 1826 peptides remaining for 540.5 to 542.5... [10:34:45] 1438 peptides remaining for 540.5 to 542.5... [10:34:46] 1039 peptides remaining for 540.5 to 542.5... [10:34:46] 653 peptides remaining for 540.5 to 542.5... [10:34:47] 269 peptides remaining for 540.5 to 542.5... [10:34:47] Processing 542.5 to 544.5 m/z, (1.9590372 second duty cycle) [10:34:49] 6882 peptides remaining for 542.5 to 544.5... [10:34:50] 6506 peptides remaining for 542.5 to 544.5... [10:34:50] 6110 peptides remaining for 542.5 to 544.5... [10:34:51] 5714 peptides remaining for 542.5 to 544.5... [10:34:51] 5333 peptides remaining for 542.5 to 544.5... [10:34:52] 4946 peptides remaining for 542.5 to 544.5... [10:34:52] 4547 peptides remaining for 542.5 to 544.5... [10:34:53] 4160 peptides remaining for 542.5 to 544.5... [10:34:53] 3775 peptides remaining for 542.5 to 544.5... [10:34:54] 3371 peptides remaining for 542.5 to 544.5... [10:34:54] 2994 peptides remaining for 542.5 to 544.5... [10:34:55] 2604 peptides remaining for 542.5 to 544.5... [10:34:55] 2216 peptides remaining for 542.5 to 544.5... [10:34:56] 1825 peptides remaining for 542.5 to 544.5... [10:34:56] 1453 peptides remaining for 542.5 to 544.5... [10:34:57] 1077 peptides remaining for 542.5 to 544.5... [10:34:57] 702 peptides remaining for 542.5 to 544.5... [10:34:58] 300 peptides remaining for 542.5 to 544.5... [10:34:58] Processing 544.5 to 546.5 m/z, (1.9590156 second duty cycle) [10:35:00] 6966 peptides remaining for 544.5 to 546.5... [10:35:01] 6568 peptides remaining for 544.5 to 546.5... [10:35:01] 6148 peptides remaining for 544.5 to 546.5... [10:35:02] 5764 peptides remaining for 544.5 to 546.5... [10:35:02] 5374 peptides remaining for 544.5 to 546.5... [10:35:03] 4981 peptides remaining for 544.5 to 546.5... [10:35:03] 4597 peptides remaining for 544.5 to 546.5... [10:35:04] 4218 peptides remaining for 544.5 to 546.5... [10:35:04] 3815 peptides remaining for 544.5 to 546.5... [10:35:05] 3438 peptides remaining for 544.5 to 546.5... [10:35:05] 3050 peptides remaining for 544.5 to 546.5... [10:35:06] 2674 peptides remaining for 544.5 to 546.5... [10:35:06] 2298 peptides remaining for 544.5 to 546.5... [10:35:07] 1930 peptides remaining for 544.5 to 546.5... [10:35:07] 1542 peptides remaining for 544.5 to 546.5... [10:35:08] 1166 peptides remaining for 544.5 to 546.5... [10:35:08] 783 peptides remaining for 544.5 to 546.5... [10:35:09] 403 peptides remaining for 544.5 to 546.5... [10:35:09] 17 peptides remaining for 544.5 to 546.5... [10:35:10] Processing 546.5 to 548.5 m/z, (1.959037 second duty cycle) [10:35:12] 6204 peptides remaining for 546.5 to 548.5... [10:35:12] 5808 peptides remaining for 546.5 to 548.5... [10:35:13] 5412 peptides remaining for 546.5 to 548.5... [10:35:13] 5023 peptides remaining for 546.5 to 548.5... [10:35:14] 4637 peptides remaining for 546.5 to 548.5... [10:35:14] 4254 peptides remaining for 546.5 to 548.5... [10:35:15] 3866 peptides remaining for 546.5 to 548.5... [10:35:15] 3460 peptides remaining for 546.5 to 548.5... [10:35:16] 3054 peptides remaining for 546.5 to 548.5... [10:35:17] 2655 peptides remaining for 546.5 to 548.5... [10:35:17] 2261 peptides remaining for 546.5 to 548.5... [10:35:18] 1866 peptides remaining for 546.5 to 548.5... [10:35:18] 1486 peptides remaining for 546.5 to 548.5... [10:35:19] 1089 peptides remaining for 546.5 to 548.5... [10:35:19] 715 peptides remaining for 546.5 to 548.5... [10:35:20] 338 peptides remaining for 546.5 to 548.5... [10:35:20] 0 peptides remaining for 546.5 to 548.5... [10:35:21] Processing 548.5 to 550.5 m/z, (1.9590155 second duty cycle) [10:35:22] 6422 peptides remaining for 548.5 to 550.5... [10:35:23] 6054 peptides remaining for 548.5 to 550.5... [10:35:23] 5645 peptides remaining for 548.5 to 550.5... [10:35:24] 5250 peptides remaining for 548.5 to 550.5... [10:35:24] 4856 peptides remaining for 548.5 to 550.5... [10:35:25] 4463 peptides remaining for 548.5 to 550.5... [10:35:25] 4077 peptides remaining for 548.5 to 550.5... [10:35:26] 3686 peptides remaining for 548.5 to 550.5... [10:35:26] 3295 peptides remaining for 548.5 to 550.5... [10:35:27] 2909 peptides remaining for 548.5 to 550.5... [10:35:27] 2516 peptides remaining for 548.5 to 550.5... [10:35:28] 2114 peptides remaining for 548.5 to 550.5... [10:35:28] 1715 peptides remaining for 548.5 to 550.5... [10:35:29] 1306 peptides remaining for 548.5 to 550.5... [10:35:29] 930 peptides remaining for 548.5 to 550.5... [10:35:30] 547 peptides remaining for 548.5 to 550.5... [10:35:31] 143 peptides remaining for 548.5 to 550.5... [10:35:31] Processing 550.5 to 552.5 m/z, (1.9590371 second duty cycle) [10:35:33] 6863 peptides remaining for 550.5 to 552.5... [10:35:33] 6471 peptides remaining for 550.5 to 552.5... [10:35:34] 6061 peptides remaining for 550.5 to 552.5... [10:35:34] 5657 peptides remaining for 550.5 to 552.5... [10:35:35] 5270 peptides remaining for 550.5 to 552.5... [10:35:35] 4866 peptides remaining for 550.5 to 552.5... [10:35:36] 4481 peptides remaining for 550.5 to 552.5... [10:35:36] 4091 peptides remaining for 550.5 to 552.5... [10:35:37] 3716 peptides remaining for 550.5 to 552.5... [10:35:37] 3337 peptides remaining for 550.5 to 552.5... [10:35:38] 2945 peptides remaining for 550.5 to 552.5... [10:35:38] 2557 peptides remaining for 550.5 to 552.5... [10:35:39] 2185 peptides remaining for 550.5 to 552.5... [10:35:39] 1804 peptides remaining for 550.5 to 552.5... [10:35:40] 1420 peptides remaining for 550.5 to 552.5... [10:35:40] 1038 peptides remaining for 550.5 to 552.5... [10:35:41] 662 peptides remaining for 550.5 to 552.5... [10:35:41] 245 peptides remaining for 550.5 to 552.5... [10:35:42] Processing 552.5 to 554.5 m/z, (1.9590156 second duty cycle) [10:35:44] 6689 peptides remaining for 552.5 to 554.5... [10:35:44] 6301 peptides remaining for 552.5 to 554.5... [10:35:45] 5903 peptides remaining for 552.5 to 554.5... [10:35:45] 5504 peptides remaining for 552.5 to 554.5... [10:35:46] 5106 peptides remaining for 552.5 to 554.5... [10:35:46] 4703 peptides remaining for 552.5 to 554.5... [10:35:47] 4321 peptides remaining for 552.5 to 554.5... [10:35:47] 3935 peptides remaining for 552.5 to 554.5... [10:35:48] 3535 peptides remaining for 552.5 to 554.5... [10:35:48] 3130 peptides remaining for 552.5 to 554.5... [10:35:49] 2739 peptides remaining for 552.5 to 554.5... [10:35:49] 2351 peptides remaining for 552.5 to 554.5... [10:35:50] 1980 peptides remaining for 552.5 to 554.5... [10:35:50] 1590 peptides remaining for 552.5 to 554.5... [10:35:51] 1217 peptides remaining for 552.5 to 554.5... [10:35:51] 840 peptides remaining for 552.5 to 554.5... [10:35:52] 462 peptides remaining for 552.5 to 554.5... [10:35:52] 80 peptides remaining for 552.5 to 554.5... [10:35:53] Processing 554.5 to 556.5 m/z, (1.9590372 second duty cycle) [10:35:54] 6059 peptides remaining for 554.5 to 556.5... [10:35:55] 5687 peptides remaining for 554.5 to 556.5... [10:35:55] 5279 peptides remaining for 554.5 to 556.5... [10:35:56] 4886 peptides remaining for 554.5 to 556.5... [10:35:57] 4476 peptides remaining for 554.5 to 556.5... [10:35:57] 4091 peptides remaining for 554.5 to 556.5... [10:35:58] 3698 peptides remaining for 554.5 to 556.5... [10:35:58] 3313 peptides remaining for 554.5 to 556.5... [10:35:59] 2955 peptides remaining for 554.5 to 556.5... [10:35:59] 2569 peptides remaining for 554.5 to 556.5... [10:36:00] 2177 peptides remaining for 554.5 to 556.5... [10:36:00] 1784 peptides remaining for 554.5 to 556.5... [10:36:01] 1408 peptides remaining for 554.5 to 556.5... [10:36:01] 1017 peptides remaining for 554.5 to 556.5... [10:36:02] 645 peptides remaining for 554.5 to 556.5... [10:36:02] 273 peptides remaining for 554.5 to 556.5... [10:36:03] Processing 556.5 to 558.5 m/z, (1.9590156 second duty cycle) [10:36:04] 6417 peptides remaining for 556.5 to 558.5... [10:36:05] 6024 peptides remaining for 556.5 to 558.5... [10:36:05] 5635 peptides remaining for 556.5 to 558.5... [10:36:06] 5238 peptides remaining for 556.5 to 558.5... [10:36:06] 4858 peptides remaining for 556.5 to 558.5... [10:36:07] 4476 peptides remaining for 556.5 to 558.5... [10:36:07] 4085 peptides remaining for 556.5 to 558.5... [10:36:08] 3712 peptides remaining for 556.5 to 558.5... [10:36:08] 3348 peptides remaining for 556.5 to 558.5... [10:36:09] 2960 peptides remaining for 556.5 to 558.5... [10:36:10] 2566 peptides remaining for 556.5 to 558.5... [10:36:10] 2199 peptides remaining for 556.5 to 558.5... [10:36:11] 1803 peptides remaining for 556.5 to 558.5... [10:36:11] 1416 peptides remaining for 556.5 to 558.5... [10:36:12] 1041 peptides remaining for 556.5 to 558.5... [10:36:12] 684 peptides remaining for 556.5 to 558.5... [10:36:13] 294 peptides remaining for 556.5 to 558.5... [10:36:13] Processing 558.5 to 560.5 m/z, (1.9590372 second duty cycle) [10:36:15] 6742 peptides remaining for 558.5 to 560.5... [10:36:15] 6361 peptides remaining for 558.5 to 560.5... [10:36:16] 5974 peptides remaining for 558.5 to 560.5... [10:36:16] 5570 peptides remaining for 558.5 to 560.5... [10:36:17] 5181 peptides remaining for 558.5 to 560.5... [10:36:17] 4783 peptides remaining for 558.5 to 560.5... [10:36:18] 4388 peptides remaining for 558.5 to 560.5... [10:36:18] 4008 peptides remaining for 558.5 to 560.5... [10:36:19] 3618 peptides remaining for 558.5 to 560.5... [10:36:20] 3250 peptides remaining for 558.5 to 560.5... [10:36:20] 2869 peptides remaining for 558.5 to 560.5... [10:36:21] 2495 peptides remaining for 558.5 to 560.5... [10:36:21] 2125 peptides remaining for 558.5 to 560.5... [10:36:22] 1755 peptides remaining for 558.5 to 560.5... [10:36:22] 1386 peptides remaining for 558.5 to 560.5... [10:36:23] 1007 peptides remaining for 558.5 to 560.5... [10:36:23] 626 peptides remaining for 558.5 to 560.5... [10:36:24] 239 peptides remaining for 558.5 to 560.5... [10:36:24] Processing 560.5 to 562.5 m/z, (1.9590156 second duty cycle) [10:36:26] 6312 peptides remaining for 560.5 to 562.5... [10:36:26] 5932 peptides remaining for 560.5 to 562.5... [10:36:27] 5527 peptides remaining for 560.5 to 562.5... [10:36:27] 5138 peptides remaining for 560.5 to 562.5... [10:36:28] 4758 peptides remaining for 560.5 to 562.5... [10:36:28] 4382 peptides remaining for 560.5 to 562.5... [10:36:29] 4001 peptides remaining for 560.5 to 562.5... [10:36:30] 3618 peptides remaining for 560.5 to 562.5... [10:36:30] 3232 peptides remaining for 560.5 to 562.5... [10:36:31] 2844 peptides remaining for 560.5 to 562.5... [10:36:31] 2451 peptides remaining for 560.5 to 562.5... [10:36:32] 2067 peptides remaining for 560.5 to 562.5... [10:36:32] 1703 peptides remaining for 560.5 to 562.5... [10:36:33] 1326 peptides remaining for 560.5 to 562.5... [10:36:33] 963 peptides remaining for 560.5 to 562.5... [10:36:34] 577 peptides remaining for 560.5 to 562.5... [10:36:34] 197 peptides remaining for 560.5 to 562.5... [10:36:35] Processing 562.5 to 564.5 m/z, (1.9590372 second duty cycle) [10:36:36] 6227 peptides remaining for 562.5 to 564.5... [10:36:37] 5839 peptides remaining for 562.5 to 564.5... [10:36:37] 5452 peptides remaining for 562.5 to 564.5... [10:36:38] 5074 peptides remaining for 562.5 to 564.5... [10:36:38] 4702 peptides remaining for 562.5 to 564.5... [10:36:39] 4323 peptides remaining for 562.5 to 564.5... [10:36:39] 3931 peptides remaining for 562.5 to 564.5... [10:36:40] 3559 peptides remaining for 562.5 to 564.5... [10:36:41] 3188 peptides remaining for 562.5 to 564.5... [10:36:41] 2813 peptides remaining for 562.5 to 564.5... [10:36:42] 2433 peptides remaining for 562.5 to 564.5... [10:36:42] 2050 peptides remaining for 562.5 to 564.5... [10:36:43] 1668 peptides remaining for 562.5 to 564.5... [10:36:43] 1305 peptides remaining for 562.5 to 564.5... [10:36:44] 939 peptides remaining for 562.5 to 564.5... [10:36:44] 570 peptides remaining for 562.5 to 564.5... [10:36:45] 192 peptides remaining for 562.5 to 564.5... [10:36:45] Processing 564.5 to 566.5 m/z, (1.9590158 second duty cycle) [10:36:47] 6608 peptides remaining for 564.5 to 566.5... [10:36:47] 6251 peptides remaining for 564.5 to 566.5... [10:36:48] 5903 peptides remaining for 564.5 to 566.5... [10:36:48] 5511 peptides remaining for 564.5 to 566.5... [10:36:49] 5123 peptides remaining for 564.5 to 566.5... [10:36:49] 4757 peptides remaining for 564.5 to 566.5... [10:36:50] 4353 peptides remaining for 564.5 to 566.5... [10:36:50] 3975 peptides remaining for 564.5 to 566.5... [10:36:51] 3597 peptides remaining for 564.5 to 566.5... [10:36:51] 3226 peptides remaining for 564.5 to 566.5... [10:36:52] 2842 peptides remaining for 564.5 to 566.5... [10:36:52] 2457 peptides remaining for 564.5 to 566.5... [10:36:53] 2078 peptides remaining for 564.5 to 566.5... [10:36:53] 1709 peptides remaining for 564.5 to 566.5... [10:36:54] 1335 peptides remaining for 564.5 to 566.5... [10:36:54] 964 peptides remaining for 564.5 to 566.5... [10:36:55] 567 peptides remaining for 564.5 to 566.5... [10:36:56] 176 peptides remaining for 564.5 to 566.5... [10:36:56] Processing 566.5 to 568.5 m/z, (1.9590371 second duty cycle) [10:36:58] 6475 peptides remaining for 566.5 to 568.5... [10:36:58] 6111 peptides remaining for 566.5 to 568.5... [10:36:59] 5702 peptides remaining for 566.5 to 568.5... [10:36:59] 5321 peptides remaining for 566.5 to 568.5... [10:37:00] 4949 peptides remaining for 566.5 to 568.5... [10:37:00] 4578 peptides remaining for 566.5 to 568.5... [10:37:01] 4185 peptides remaining for 566.5 to 568.5... [10:37:01] 3813 peptides remaining for 566.5 to 568.5... [10:37:02] 3445 peptides remaining for 566.5 to 568.5... [10:37:02] 3056 peptides remaining for 566.5 to 568.5... [10:37:03] 2683 peptides remaining for 566.5 to 568.5... [10:37:04] 2282 peptides remaining for 566.5 to 568.5... [10:37:04] 1905 peptides remaining for 566.5 to 568.5... [10:37:05] 1541 peptides remaining for 566.5 to 568.5... [10:37:05] 1166 peptides remaining for 566.5 to 568.5... [10:37:06] 791 peptides remaining for 566.5 to 568.5... [10:37:06] 419 peptides remaining for 566.5 to 568.5... [10:37:07] 55 peptides remaining for 566.5 to 568.5... [10:37:07] Processing 568.5 to 570.5 m/z, (1.9590156 second duty cycle) [10:37:09] 6019 peptides remaining for 568.5 to 570.5... [10:37:09] 5963 peptides remaining for 568.5 to 570.5... [10:37:10] 5580 peptides remaining for 568.5 to 570.5... [10:37:10] 5189 peptides remaining for 568.5 to 570.5... [10:37:11] 4827 peptides remaining for 568.5 to 570.5... [10:37:11] 4460 peptides remaining for 568.5 to 570.5... [10:37:12] 4077 peptides remaining for 568.5 to 570.5... [10:37:12] 3699 peptides remaining for 568.5 to 570.5... [10:37:13] 3321 peptides remaining for 568.5 to 570.5... [10:37:13] 2956 peptides remaining for 568.5 to 570.5... [10:37:14] 2577 peptides remaining for 568.5 to 570.5... [10:37:14] 2200 peptides remaining for 568.5 to 570.5... [10:37:15] 1830 peptides remaining for 568.5 to 570.5... [10:37:16] 1461 peptides remaining for 568.5 to 570.5... [10:37:16] 1112 peptides remaining for 568.5 to 570.5... [10:37:17] 750 peptides remaining for 568.5 to 570.5... [10:37:17] 380 peptides remaining for 568.5 to 570.5... [10:37:18] 0 peptides remaining for 568.5 to 570.5... [10:37:18] Processing 570.5 to 572.5 m/z, (1.9591262 second duty cycle) [10:37:20] 6382 peptides remaining for 570.5 to 572.5... [10:37:20] 6007 peptides remaining for 570.5 to 572.5... [10:37:21] 5615 peptides remaining for 570.5 to 572.5... [10:37:21] 5227 peptides remaining for 570.5 to 572.5... [10:37:22] 4848 peptides remaining for 570.5 to 572.5... [10:37:22] 4464 peptides remaining for 570.5 to 572.5... [10:37:23] 4073 peptides remaining for 570.5 to 572.5... [10:37:23] 3700 peptides remaining for 570.5 to 572.5... [10:37:24] 3327 peptides remaining for 570.5 to 572.5... [10:37:24] 2957 peptides remaining for 570.5 to 572.5... [10:37:25] 2581 peptides remaining for 570.5 to 572.5... [10:37:25] 2208 peptides remaining for 570.5 to 572.5... [10:37:26] 1835 peptides remaining for 570.5 to 572.5... [10:37:26] 1427 peptides remaining for 570.5 to 572.5... [10:37:27] 1067 peptides remaining for 570.5 to 572.5... [10:37:28] 691 peptides remaining for 570.5 to 572.5... [10:37:28] 311 peptides remaining for 570.5 to 572.5... [10:37:29] Processing 572.5 to 574.5 m/z, (1.9591047 second duty cycle) [10:37:30] 6569 peptides remaining for 572.5 to 574.5... [10:37:31] 6179 peptides remaining for 572.5 to 574.5... [10:37:31] 5791 peptides remaining for 572.5 to 574.5... [10:37:32] 5414 peptides remaining for 572.5 to 574.5... [10:37:32] 5075 peptides remaining for 572.5 to 574.5... [10:37:33] 4687 peptides remaining for 572.5 to 574.5... [10:37:33] 4298 peptides remaining for 572.5 to 574.5... [10:37:34] 3904 peptides remaining for 572.5 to 574.5... [10:37:34] 3527 peptides remaining for 572.5 to 574.5... [10:37:35] 3147 peptides remaining for 572.5 to 574.5... [10:37:35] 2776 peptides remaining for 572.5 to 574.5... [10:37:36] 2409 peptides remaining for 572.5 to 574.5... [10:37:36] 2041 peptides remaining for 572.5 to 574.5... [10:37:37] 1674 peptides remaining for 572.5 to 574.5... [10:37:37] 1315 peptides remaining for 572.5 to 574.5... [10:37:38] 950 peptides remaining for 572.5 to 574.5... [10:37:38] 586 peptides remaining for 572.5 to 574.5... [10:37:39] 199 peptides remaining for 572.5 to 574.5... [10:37:39] Processing 574.5 to 576.5 m/z, (1.9591262 second duty cycle) [10:37:41] 6117 peptides remaining for 574.5 to 576.5... [10:37:42] 5736 peptides remaining for 574.5 to 576.5... [10:37:42] 5339 peptides remaining for 574.5 to 576.5... [10:37:43] 4953 peptides remaining for 574.5 to 576.5... [10:37:43] 4578 peptides remaining for 574.5 to 576.5... [10:37:44] 4198 peptides remaining for 574.5 to 576.5... [10:37:44] 3839 peptides remaining for 574.5 to 576.5... [10:37:45] 3473 peptides remaining for 574.5 to 576.5... [10:37:45] 3095 peptides remaining for 574.5 to 576.5... [10:37:46] 2721 peptides remaining for 574.5 to 576.5... [10:37:46] 2351 peptides remaining for 574.5 to 576.5... [10:37:47] 1976 peptides remaining for 574.5 to 576.5... [10:37:47] 1615 peptides remaining for 574.5 to 576.5... [10:37:48] 1244 peptides remaining for 574.5 to 576.5... [10:37:48] 874 peptides remaining for 574.5 to 576.5... [10:37:49] 517 peptides remaining for 574.5 to 576.5... [10:37:49] 148 peptides remaining for 574.5 to 576.5... [10:37:50] Processing 576.5 to 578.5 m/z, (1.9591047 second duty cycle) [10:37:52] 6026 peptides remaining for 576.5 to 578.5... [10:37:52] 5650 peptides remaining for 576.5 to 578.5... [10:37:53] 5266 peptides remaining for 576.5 to 578.5... [10:37:53] 4893 peptides remaining for 576.5 to 578.5... [10:37:54] 4508 peptides remaining for 576.5 to 578.5... [10:37:54] 4145 peptides remaining for 576.5 to 578.5... [10:37:55] 3766 peptides remaining for 576.5 to 578.5... [10:37:55] 3402 peptides remaining for 576.5 to 578.5... [10:37:56] 3031 peptides remaining for 576.5 to 578.5... [10:37:56] 2682 peptides remaining for 576.5 to 578.5... [10:37:57] 2302 peptides remaining for 576.5 to 578.5... [10:37:57] 1946 peptides remaining for 576.5 to 578.5... [10:37:58] 1580 peptides remaining for 576.5 to 578.5... [10:37:59] 1229 peptides remaining for 576.5 to 578.5... [10:37:59] 876 peptides remaining for 576.5 to 578.5... [10:38:00] 508 peptides remaining for 576.5 to 578.5... [10:38:00] 144 peptides remaining for 576.5 to 578.5... [10:38:01] Processing 578.5 to 580.5 m/z, (1.9590869 second duty cycle) [10:38:02] 6481 peptides remaining for 578.5 to 580.5... [10:38:03] 6105 peptides remaining for 578.5 to 580.5... [10:38:03] 5713 peptides remaining for 578.5 to 580.5... [10:38:04] 5339 peptides remaining for 578.5 to 580.5... [10:38:04] 4974 peptides remaining for 578.5 to 580.5... [10:38:05] 4609 peptides remaining for 578.5 to 580.5... [10:38:05] 4225 peptides remaining for 578.5 to 580.5... [10:38:06] 3857 peptides remaining for 578.5 to 580.5... [10:38:06] 3491 peptides remaining for 578.5 to 580.5... [10:38:07] 3130 peptides remaining for 578.5 to 580.5... [10:38:07] 2768 peptides remaining for 578.5 to 580.5... [10:38:08] 2402 peptides remaining for 578.5 to 580.5... [10:38:08] 2035 peptides remaining for 578.5 to 580.5... [10:38:09] 1671 peptides remaining for 578.5 to 580.5... [10:38:09] 1308 peptides remaining for 578.5 to 580.5... [10:38:10] 946 peptides remaining for 578.5 to 580.5... [10:38:11] 579 peptides remaining for 578.5 to 580.5... [10:38:11] 228 peptides remaining for 578.5 to 580.5... [10:38:12] Processing 580.5 to 582.5 m/z, (1.9590871 second duty cycle) [10:38:13] 6312 peptides remaining for 580.5 to 582.5... [10:38:14] 5934 peptides remaining for 580.5 to 582.5... [10:38:14] 5555 peptides remaining for 580.5 to 582.5... [10:38:15] 5198 peptides remaining for 580.5 to 582.5... [10:38:15] 4820 peptides remaining for 580.5 to 582.5... [10:38:16] 4459 peptides remaining for 580.5 to 582.5... [10:38:16] 4089 peptides remaining for 580.5 to 582.5... [10:38:17] 3740 peptides remaining for 580.5 to 582.5... [10:38:17] 3378 peptides remaining for 580.5 to 582.5... [10:38:18] 2998 peptides remaining for 580.5 to 582.5... [10:38:18] 2629 peptides remaining for 580.5 to 582.5... [10:38:19] 2264 peptides remaining for 580.5 to 582.5... [10:38:19] 1912 peptides remaining for 580.5 to 582.5... [10:38:20] 1553 peptides remaining for 580.5 to 582.5... [10:38:20] 1184 peptides remaining for 580.5 to 582.5... [10:38:21] 815 peptides remaining for 580.5 to 582.5... [10:38:21] 456 peptides remaining for 580.5 to 582.5... [10:38:22] 87 peptides remaining for 580.5 to 582.5... [10:38:22] Processing 582.5 to 584.5 m/z, (1.9590871 second duty cycle) [10:38:24] 6066 peptides remaining for 582.5 to 584.5... [10:38:25] 5706 peptides remaining for 582.5 to 584.5... [10:38:25] 5325 peptides remaining for 582.5 to 584.5... [10:38:26] 4956 peptides remaining for 582.5 to 584.5... [10:38:26] 4592 peptides remaining for 582.5 to 584.5... [10:38:27] 4207 peptides remaining for 582.5 to 584.5... [10:38:27] 3837 peptides remaining for 582.5 to 584.5... [10:38:28] 3476 peptides remaining for 582.5 to 584.5... [10:38:28] 3111 peptides remaining for 582.5 to 584.5... [10:38:29] 2736 peptides remaining for 582.5 to 584.5... [10:38:29] 2369 peptides remaining for 582.5 to 584.5... [10:38:30] 1988 peptides remaining for 582.5 to 584.5... [10:38:30] 1627 peptides remaining for 582.5 to 584.5... [10:38:31] 1279 peptides remaining for 582.5 to 584.5... [10:38:31] 906 peptides remaining for 582.5 to 584.5... [10:38:32] 558 peptides remaining for 582.5 to 584.5... [10:38:32] 185 peptides remaining for 582.5 to 584.5... [10:38:33] Processing 584.5 to 586.5 m/z, (1.9590871 second duty cycle) [10:38:34] 6071 peptides remaining for 584.5 to 586.5... [10:38:35] 5698 peptides remaining for 584.5 to 586.5... [10:38:36] 5317 peptides remaining for 584.5 to 586.5... [10:38:36] 4944 peptides remaining for 584.5 to 586.5... [10:38:37] 4592 peptides remaining for 584.5 to 586.5... [10:38:37] 4219 peptides remaining for 584.5 to 586.5... [10:38:38] 3851 peptides remaining for 584.5 to 586.5... [10:38:38] 3460 peptides remaining for 584.5 to 586.5... [10:38:39] 3093 peptides remaining for 584.5 to 586.5... [10:38:39] 2726 peptides remaining for 584.5 to 586.5... [10:38:40] 2358 peptides remaining for 584.5 to 586.5... [10:38:40] 1991 peptides remaining for 584.5 to 586.5... [10:38:41] 1636 peptides remaining for 584.5 to 586.5... [10:38:41] 1273 peptides remaining for 584.5 to 586.5... [10:38:42] 900 peptides remaining for 584.5 to 586.5... [10:38:42] 546 peptides remaining for 584.5 to 586.5... [10:38:43] 175 peptides remaining for 584.5 to 586.5... [10:38:43] Processing 586.5 to 588.5 m/z, (1.9590871 second duty cycle) [10:38:45] 6446 peptides remaining for 586.5 to 588.5... [10:38:46] 6064 peptides remaining for 586.5 to 588.5... [10:38:46] 5686 peptides remaining for 586.5 to 588.5... [10:38:47] 5313 peptides remaining for 586.5 to 588.5... [10:38:47] 4949 peptides remaining for 586.5 to 588.5... [10:38:48] 4585 peptides remaining for 586.5 to 588.5... [10:38:48] 4229 peptides remaining for 586.5 to 588.5... [10:38:49] 3846 peptides remaining for 586.5 to 588.5... [10:38:49] 3468 peptides remaining for 586.5 to 588.5... [10:38:50] 3094 peptides remaining for 586.5 to 588.5... [10:38:50] 2746 peptides remaining for 586.5 to 588.5... [10:38:51] 2390 peptides remaining for 586.5 to 588.5... [10:38:51] 2024 peptides remaining for 586.5 to 588.5... [10:38:52] 1667 peptides remaining for 586.5 to 588.5... [10:38:52] 1309 peptides remaining for 586.5 to 588.5... [10:38:53] 931 peptides remaining for 586.5 to 588.5... [10:38:53] 588 peptides remaining for 586.5 to 588.5... [10:38:54] 216 peptides remaining for 586.5 to 588.5... [10:38:54] Processing 588.5 to 590.5 m/z, (1.9590873 second duty cycle) [10:38:56] 6338 peptides remaining for 588.5 to 590.5... [10:38:56] 5966 peptides remaining for 588.5 to 590.5... [10:38:57] 5586 peptides remaining for 588.5 to 590.5... [10:38:57] 5211 peptides remaining for 588.5 to 590.5... [10:38:58] 4852 peptides remaining for 588.5 to 590.5... [10:38:58] 4485 peptides remaining for 588.5 to 590.5... [10:38:59] 4125 peptides remaining for 588.5 to 590.5... [10:39:00] 3747 peptides remaining for 588.5 to 590.5... [10:39:00] 3382 peptides remaining for 588.5 to 590.5... [10:39:01] 3008 peptides remaining for 588.5 to 590.5... [10:39:01] 2639 peptides remaining for 588.5 to 590.5... [10:39:02] 2265 peptides remaining for 588.5 to 590.5... [10:39:02] 1895 peptides remaining for 588.5 to 590.5... [10:39:03] 1536 peptides remaining for 588.5 to 590.5... [10:39:03] 1172 peptides remaining for 588.5 to 590.5... [10:39:04] 818 peptides remaining for 588.5 to 590.5... [10:39:04] 467 peptides remaining for 588.5 to 590.5... [10:39:05] 88 peptides remaining for 588.5 to 590.5... [10:39:05] Processing 590.5 to 592.5 m/z, (1.9590873 second duty cycle) [10:39:07] 5997 peptides remaining for 590.5 to 592.5... [10:39:07] 5645 peptides remaining for 590.5 to 592.5... [10:39:08] 5280 peptides remaining for 590.5 to 592.5... [10:39:08] 4926 peptides remaining for 590.5 to 592.5... [10:39:09] 4579 peptides remaining for 590.5 to 592.5... [10:39:09] 4230 peptides remaining for 590.5 to 592.5... [10:39:10] 3869 peptides remaining for 590.5 to 592.5... [10:39:10] 3512 peptides remaining for 590.5 to 592.5... [10:39:11] 3164 peptides remaining for 590.5 to 592.5... [10:39:11] 2810 peptides remaining for 590.5 to 592.5... [10:39:12] 2455 peptides remaining for 590.5 to 592.5... [10:39:12] 2113 peptides remaining for 590.5 to 592.5... [10:39:13] 1748 peptides remaining for 590.5 to 592.5... [10:39:14] 1373 peptides remaining for 590.5 to 592.5... [10:39:14] 1012 peptides remaining for 590.5 to 592.5... [10:39:15] 675 peptides remaining for 590.5 to 592.5... [10:39:15] 327 peptides remaining for 590.5 to 592.5... [10:39:16] 0 peptides remaining for 590.5 to 592.5... [10:39:16] Processing 592.5 to 594.5 m/z, (1.9590871 second duty cycle) [10:39:18] 6293 peptides remaining for 592.5 to 594.5... [10:39:18] 5955 peptides remaining for 592.5 to 594.5... [10:39:19] 5591 peptides remaining for 592.5 to 594.5... [10:39:19] 5233 peptides remaining for 592.5 to 594.5... [10:39:20] 4885 peptides remaining for 592.5 to 594.5... [10:39:20] 4530 peptides remaining for 592.5 to 594.5... [10:39:21] 4187 peptides remaining for 592.5 to 594.5... [10:39:21] 3829 peptides remaining for 592.5 to 594.5... [10:39:22] 3470 peptides remaining for 592.5 to 594.5... [10:39:22] 3112 peptides remaining for 592.5 to 594.5... [10:39:23] 2760 peptides remaining for 592.5 to 594.5... [10:39:23] 2406 peptides remaining for 592.5 to 594.5... [10:39:24] 2075 peptides remaining for 592.5 to 594.5... [10:39:24] 1715 peptides remaining for 592.5 to 594.5... [10:39:25] 1372 peptides remaining for 592.5 to 594.5... [10:39:25] 1032 peptides remaining for 592.5 to 594.5... [10:39:26] 673 peptides remaining for 592.5 to 594.5... [10:39:26] 324 peptides remaining for 592.5 to 594.5... [10:39:27] 0 peptides remaining for 592.5 to 594.5... [10:39:27] Processing 594.5 to 596.5 m/z, (1.9590871 second duty cycle) [10:39:30] 6227 peptides remaining for 594.5 to 596.5... [10:39:30] 5871 peptides remaining for 594.5 to 596.5... [10:39:31] 5498 peptides remaining for 594.5 to 596.5... [10:39:31] 5123 peptides remaining for 594.5 to 596.5... [10:39:32] 4750 peptides remaining for 594.5 to 596.5... [10:39:32] 4396 peptides remaining for 594.5 to 596.5... [10:39:33] 4036 peptides remaining for 594.5 to 596.5... [10:39:34] 3677 peptides remaining for 594.5 to 596.5... [10:39:34] 3312 peptides remaining for 594.5 to 596.5... [10:39:35] 2947 peptides remaining for 594.5 to 596.5... [10:39:35] 2599 peptides remaining for 594.5 to 596.5... [10:39:36] 2244 peptides remaining for 594.5 to 596.5... [10:39:36] 1896 peptides remaining for 594.5 to 596.5... [10:39:37] 1553 peptides remaining for 594.5 to 596.5... [10:39:37] 1217 peptides remaining for 594.5 to 596.5... [10:39:38] 872 peptides remaining for 594.5 to 596.5... [10:39:38] 534 peptides remaining for 594.5 to 596.5... [10:39:39] 187 peptides remaining for 594.5 to 596.5... [10:39:39] Processing 596.5 to 598.5 m/z, (1.9590874 second duty cycle) [10:39:41] 5850 peptides remaining for 596.5 to 598.5... [10:39:41] 5492 peptides remaining for 596.5 to 598.5... [10:39:42] 5103 peptides remaining for 596.5 to 598.5... [10:39:42] 4759 peptides remaining for 596.5 to 598.5... [10:39:43] 4405 peptides remaining for 596.5 to 598.5... [10:39:43] 4053 peptides remaining for 596.5 to 598.5... [10:39:44] 3696 peptides remaining for 596.5 to 598.5... [10:39:44] 3314 peptides remaining for 596.5 to 598.5... [10:39:45] 2949 peptides remaining for 596.5 to 598.5... [10:39:45] 2589 peptides remaining for 596.5 to 598.5... [10:39:46] 2221 peptides remaining for 596.5 to 598.5... [10:39:47] 1862 peptides remaining for 596.5 to 598.5... [10:39:47] 1501 peptides remaining for 596.5 to 598.5... [10:39:48] 1145 peptides remaining for 596.5 to 598.5... [10:39:48] 790 peptides remaining for 596.5 to 598.5... [10:39:49] 445 peptides remaining for 596.5 to 598.5... [10:39:49] 81 peptides remaining for 596.5 to 598.5... [10:39:50] Processing 598.5 to 600.5 m/z, (1.9590874 second duty cycle) [10:39:51] 5977 peptides remaining for 598.5 to 600.5... [10:39:52] 5612 peptides remaining for 598.5 to 600.5... [10:39:52] 5229 peptides remaining for 598.5 to 600.5... [10:39:53] 4863 peptides remaining for 598.5 to 600.5... [10:39:53] 4507 peptides remaining for 598.5 to 600.5... [10:39:54] 4154 peptides remaining for 598.5 to 600.5... [10:39:54] 3780 peptides remaining for 598.5 to 600.5... [10:39:55] 3405 peptides remaining for 598.5 to 600.5... [10:39:55] 3052 peptides remaining for 598.5 to 600.5... [10:39:56] 2690 peptides remaining for 598.5 to 600.5... [10:39:56] 2325 peptides remaining for 598.5 to 600.5... [10:39:57] 1966 peptides remaining for 598.5 to 600.5... [10:39:57] 1592 peptides remaining for 598.5 to 600.5... [10:39:58] 1238 peptides remaining for 598.5 to 600.5... [10:39:58] 874 peptides remaining for 598.5 to 600.5... [10:39:59] 520 peptides remaining for 598.5 to 600.5... [10:40:00] 144 peptides remaining for 598.5 to 600.5... [10:40:00] Processing 600.5 to 602.5 m/z, (3.9179518 second duty cycle) [10:40:02] 6144 peptides remaining for 600.5 to 602.5... [10:40:02] 5601 peptides remaining for 600.5 to 602.5... [10:40:03] 5051 peptides remaining for 600.5 to 602.5... [10:40:03] 4489 peptides remaining for 600.5 to 602.5... [10:40:04] 3929 peptides remaining for 600.5 to 602.5... [10:40:04] 3339 peptides remaining for 600.5 to 602.5... [10:40:05] 2778 peptides remaining for 600.5 to 602.5... [10:40:05] 2211 peptides remaining for 600.5 to 602.5... [10:40:06] 1667 peptides remaining for 600.5 to 602.5... [10:40:06] 1096 peptides remaining for 600.5 to 602.5... [10:40:07] 529 peptides remaining for 600.5 to 602.5... [10:40:07] 0 peptides remaining for 600.5 to 602.5... [10:40:08] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:40:33] Sorted feature file in 25.51 seconds wall clock time [10:40:33] File size check: 488001839 vs 488001839 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:40:33] 1230353 total peptides processed. [10:40:33] Running Percolator... [10:40:33] Executing [cmd /c C:\Windows\Temp\tmp93FD.java\Percolator-v3-01-4064630017248637303.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt] [10:40:34] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [10:40:34] Copyright (c) 2006-9 University of Washington. All rights reserved. [10:40:34] Written by Lukas Käll (lukall@u.washington.edu) in the [10:40:34] Department of Genome Sciences at the University of Washington. [10:40:34] Issued command: [10:40:34] C:\Windows\Temp\tmp93FD.java\Percolator-v3-01-4064630017248637303.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:40:34] Started Wed Jul 17 10:40:34 2024 [10:40:34] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [10:40:34] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:40:34] Features: [10:40:34] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:40:42] Processing line 1000000 [10:40:44] Found 1230353 PSMs [10:40:44] Separate target and decoy search inputs detected, using mix-max method. [10:40:44] Train/test set contains 251148 positives and 248852 negatives, size ratio=1.00923 and pi0=1 [10:40:45] Selecting Cpos by cross-validation. [10:40:45] Selecting Cneg by cross-validation. [10:40:48] Split 1: Selected feature 22 as initial search direction. Could separate 2206 training set positives in that direction. [10:40:52] Split 2: Selected feature 22 as initial search direction. Could separate 2282 training set positives in that direction. [10:40:55] Split 3: Selected feature 22 as initial search direction. Could separate 2260 training set positives in that direction. [10:40:56] Found 3166 test set positives with q<0.01 in initial direction [10:40:56] Reading in data and feature calculation took 21.926 cpu seconds or 22 seconds wall clock time. [10:40:56] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [10:41:16] Iteration 1: Estimated 6547 PSMs with q<0.01 [10:41:42] Iteration 2: Estimated 7092 PSMs with q<0.01 [10:42:09] Iteration 3: Estimated 7262 PSMs with q<0.01 [10:42:09] Learned normalized SVM weights for the 3 cross-validation splits: [10:42:09] Split1 Split2 Split3 FeatureName [10:42:09] -0.0914 -0.3292 -0.3220 primary [10:42:09] -0.1210 -0.1017 -0.1959 xCorrLib [10:42:09] 0.2867 0.2156 0.3500 xCorrModel [10:42:09] 0.3521 0.1369 0.3950 dotProduct [10:42:09] 0.0008 0.0104 -0.0223 contrastAngle [10:42:09] 0.2415 0.3169 0.2577 logit [10:42:09] 0.2851 0.1709 0.3122 sumOfSquaredErrors [10:42:09] 0.2478 0.5357 0.4775 numberOfMatchingPeaks [10:42:09] 0.0454 -0.0380 0.1174 numberOfMatchingPeaksAboveThreshold [10:42:09] 0.0142 -0.0400 0.0838 averageFragmentDeltaMasses [10:42:09] 0.0645 0.1493 0.1619 isotopeDotProduct [10:42:09] 0.0196 0.0668 0.0563 averageParentDeltaMass [10:42:09] -0.0587 -0.0391 -0.1060 percentBlankOverMono [10:42:09] 0.0342 -0.0032 0.0016 numberPrecursorMatch [10:42:09] -0.6302 -0.5069 -0.7122 lnSp [10:42:09] 0.4651 0.3279 0.4381 maxLadderLength [10:42:09] 0.1318 0.0789 0.1854 evalue [10:42:09] -0.0004 -0.0132 -0.0059 correlationToGaussian [10:42:09] 0.0661 0.0375 0.0173 correlationToPrecursor [10:42:09] 0.0337 -0.0147 0.0525 isIntegratedSignal [10:42:09] 0.0680 0.1068 0.1048 isIntegratedPrecursor [10:42:09] 0.5145 0.4886 0.5354 numPeaksWithGoodCorrelation [10:42:09] -0.2756 -0.2426 -0.3411 numMissedCleavage [10:42:09] -0.5093 -0.2890 -0.8370 pepLength [10:42:09] 0.0000 0.0000 0.0000 charge1 [10:42:09] 0.0280 0.1240 -0.0063 charge2 [10:42:09] -0.0280 -0.1240 0.0063 charge3 [10:42:09] 0.0000 0.0000 0.0000 charge4 [10:42:09] -0.0468 -0.0580 0.0494 precursorMz [10:42:09] 0.2712 0.3138 0.3053 precursorMass [10:42:09] -0.1357 -0.0978 -0.1070 RTinMin [10:42:09] -3.2590 -3.2286 -3.7023 m0 [10:42:09] Found 7005 test set PSMs with q<0.01. [10:42:10] Scoring full list of PSMs with trained SVMs. [10:42:10] Features: [10:42:10] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:42:18] Processing line 1000000 [10:42:20] Found 1230353 PSMs [10:42:20] Evaluated set contained 618724 positives and 611629 negatives. [10:42:22] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [10:42:25] Selecting pi_0=0.926498 [10:42:25] Calculating q values. [10:42:25] New pi_0 estimate on final list yields 17002 target peptides with q<0.01. [10:42:25] Calculating posterior error probabilities (PEPs). [10:42:27] Processing took 90.91 cpu seconds or 90 seconds wall clock time. [10:42:37] First pass: 17002 peptides identified at 1.0% FDR [10:42:37] Generating retention time mapping using 17008 points... [10:42:37] Enough data points (17008) to perform KDE alignment. [10:42:39] Enough data points (16324) to perform KDE alignment. [10:42:40] Enough data points (17008) to perform KDE alignment. [10:42:42] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:42:47] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:43:05] Sorted feature file in 18.45 seconds wall clock time [10:43:05] File size check: 352175929 vs 352175929 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:43:05] Executing [cmd /c C:\Windows\Temp\tmp93FD.java\Percolator-v3-01-8933666060418735824.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt] [10:43:06] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [10:43:06] Copyright (c) 2006-9 University of Washington. All rights reserved. [10:43:06] Written by Lukas Käll (lukall@u.washington.edu) in the [10:43:06] Department of Genome Sciences at the University of Washington. [10:43:06] Issued command: [10:43:06] C:\Windows\Temp\tmp93FD.java\Percolator-v3-01-8933666060418735824.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:43:06] Started Wed Jul 17 10:43:06 2024 [10:43:06] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [10:43:06] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [10:43:06] Features: [10:43:06] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:43:14] Found 829910 PSMs [10:43:14] Separate target and decoy search inputs detected, using mix-max method. [10:43:14] Train/test set contains 248152 positives and 251848 negatives, size ratio=0.985324 and pi0=1 [10:43:15] Selecting Cpos by cross-validation. [10:43:15] Selecting Cneg by cross-validation. [10:43:19] Split 1: Selected feature 22 as initial search direction. Could separate 3261 training set positives in that direction. [10:43:22] Split 2: Selected feature 22 as initial search direction. Could separate 3270 training set positives in that direction. [10:43:26] Split 3: Selected feature 22 as initial search direction. Could separate 3267 training set positives in that direction. [10:43:26] Found 4546 test set positives with q<0.01 in initial direction [10:43:26] Reading in data and feature calculation took 20.526 cpu seconds or 20 seconds wall clock time. [10:43:26] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [10:43:49] Iteration 1: Estimated 8895 PSMs with q<0.01 [10:44:20] Iteration 2: Estimated 10068 PSMs with q<0.01 [10:44:51] Iteration 3: Estimated 10190 PSMs with q<0.01 [10:45:21] Iteration 4: Estimated 10258 PSMs with q<0.01 [10:45:52] Iteration 5: Estimated 10316 PSMs with q<0.01 [10:46:23] Iteration 6: Estimated 10335 PSMs with q<0.01 [10:46:54] Iteration 7: Estimated 10358 PSMs with q<0.01 [10:47:25] Iteration 8: Estimated 10371 PSMs with q<0.01 [10:47:56] Iteration 9: Estimated 10350 PSMs with q<0.01 [10:48:27] Iteration 10: Estimated 10346 PSMs with q<0.01 [10:48:27] Learned normalized SVM weights for the 3 cross-validation splits: [10:48:27] Split1 Split2 Split3 FeatureName [10:48:27] -1.4562 -1.2304 -1.1307 primary [10:48:27] -0.2740 -0.0440 -0.2596 xCorrLib [10:48:27] 0.4577 0.2525 0.4329 xCorrModel [10:48:27] 1.1572 0.3134 0.7963 dotProduct [10:48:27] -0.8200 0.3925 0.0406 contrastAngle [10:48:27] 0.5989 0.2796 0.1429 logit [10:48:27] 0.2819 0.4075 0.3148 sumOfSquaredErrors [10:48:27] 1.7993 1.4920 1.5396 numberOfMatchingPeaks [10:48:27] 0.0884 0.0084 0.0432 numberOfMatchingPeaksAboveThreshold [10:48:27] -0.0417 -0.0709 -0.0411 averageFragmentDeltaMasses [10:48:27] -0.0599 0.0416 0.0060 isotopeDotProduct [10:48:27] 0.0322 0.0232 0.0010 averageParentDeltaMass [10:48:27] -0.1094 -0.2141 -0.1626 percentBlankOverMono [10:48:27] 0.0595 -0.0113 0.0348 numberPrecursorMatch [10:48:27] -0.8635 -1.1003 -0.9871 lnSp [10:48:27] 0.5325 0.8029 0.6500 maxLadderLength [10:48:27] 0.2190 0.2450 0.1587 evalue [10:48:27] 0.2016 0.2197 0.2296 correlationToGaussian [10:48:27] 0.1322 0.0668 0.1181 correlationToPrecursor [10:48:27] 0.3974 0.2811 0.1876 isIntegratedSignal [10:48:27] 0.1916 0.1896 0.0839 isIntegratedPrecursor [10:48:27] 0.4781 0.7748 0.5622 numPeaksWithGoodCorrelation [10:48:27] 0.0836 0.0497 0.0839 deltaRT [10:48:27] -0.1564 -0.2159 -0.1611 ms1MassError [10:48:27] -0.1182 -0.1657 -0.1485 ms2MassError [10:48:27] -0.6300 -0.7174 -0.5184 numMissedCleavage [10:48:27] -0.5039 -0.9134 -0.7633 pepLength [10:48:27] 0.0000 0.0000 0.0000 charge1 [10:48:27] 0.9212 0.1087 0.1935 charge2 [10:48:27] -0.9212 -0.1087 -0.1935 charge3 [10:48:27] 0.0000 0.0000 0.0000 charge4 [10:48:27] -0.4637 -0.0447 -0.0996 precursorMz [10:48:27] 2.0254 0.6857 0.7491 precursorMass [10:48:27] -0.1284 -0.1920 -0.1330 RTinMin [10:48:27] -4.6592 -5.3257 -4.5915 m0 [10:48:27] Found 10191 test set PSMs with q<0.01. [10:48:27] Scoring full list of PSMs with trained SVMs. [10:48:28] Features: [10:48:28] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [10:48:35] Found 829910 PSMs [10:48:35] Evaluated set contained 412138 positives and 417772 negatives. [10:48:37] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [10:48:39] Selecting pi_0=0.93436 [10:48:39] Calculating q values. [10:48:39] New pi_0 estimate on final list yields 17396 target peptides with q<0.01. [10:48:39] Calculating posterior error probabilities (PEPs). [10:48:40] Processing took 314.1 cpu seconds or 314 seconds wall clock time. [10:48:51] Generating retention time mapping using 17402 points... [10:48:51] Enough data points (17402) to perform KDE alignment. [10:48:53] Enough data points (16782) to perform KDE alignment. [10:48:53] Enough data points (17402) to perform KDE alignment. [10:48:55] Writing elib result library... [10:48:55] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 17396 vs local peptides: 17396 [10:48:55] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML... [10:48:55] Extracting Spectral Data for 17396 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML... [10:48:55] Number of global peptides: 17396 vs local peptides: 17396 [10:48:58] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [10:48:58] Parsed features and scores for 17396 peptides. [10:48:58] Extracting 17396 peptides... [10:48:58] Quant Extracting 498.5 to 500.5 m/z (7.1619444 to 89.01073 min) [10:48:59] Quant Extracting 500.5 to 502.5 m/z (7.620101 to 87.22735 min) [10:48:59] Quant Extracting 502.5 to 504.5 m/z (7.163096 to 90.015976 min) [10:48:59] Quant Extracting 504.5 to 506.5 m/z (7.6543427 to 92.82457 min) [10:48:59] Quant Extracting 506.5 to 508.5 m/z (7.1642475 to 93.48359 min) [10:48:59] Quant Extracting 508.5 to 510.5 m/z (7.1642475 to 93.58259 min) [10:48:59] Quant Extracting 510.5 to 512.5 m/z (7.165399 to 90.574234 min) [10:49:00] Quant Extracting 512.5 to 514.5 m/z (7.165399 to 90.89893 min) [10:49:00] Quant Extracting 514.5 to 516.5 m/z (7.1665497 to 91.32369 min) [10:49:00] Quant Extracting 516.5 to 518.5 m/z (7.494504 to 91.22619 min) [10:49:00] Quant Extracting 518.5 to 520.5 m/z (7.167702 to 92.04628 min) [10:49:00] Quant Extracting 520.5 to 522.5 m/z (7.167702 to 92.274086 min) [10:49:00] Quant Extracting 522.5 to 524.5 m/z (6.166393 to 96.222626 min) [10:49:00] Quant Extracting 524.5 to 526.5 m/z (7.1688485 to 89.92775 min) [10:49:01] Quant Extracting 526.5 to 528.5 m/z (7.172818 to 91.6248 min) [10:49:01] Quant Extracting 528.5 to 530.5 m/z (7.172818 to 96.46027 min) [10:49:01] Quant Extracting 530.5 to 532.5 m/z (7.1739697 to 95.72987 min) [10:49:01] Quant Extracting 532.5 to 534.5 m/z (6.135904 to 89.63908 min) [10:49:01] Quant Extracting 534.5 to 536.5 m/z (7.175116 to 94.511894 min) [10:49:01] Quant Extracting 536.5 to 538.5 m/z (7.1434765 to 92.08405 min) [10:49:01] Quant Extracting 538.5 to 540.5 m/z (7.1434765 to 92.80497 min) [10:49:01] Quant Extracting 540.5 to 542.5 m/z (7.2408743 to 95.99597 min) [10:49:01] Quant Extracting 542.5 to 544.5 m/z (7.5025744 to 95.86544 min) [10:49:01] Quant Extracting 544.5 to 546.5 m/z (7.145805 to 94.383095 min) [10:49:01] Quant Extracting 546.5 to 548.5 m/z (7.145805 to 91.43503 min) [10:49:01] Quant Extracting 548.5 to 550.5 m/z (7.1469502 to 97.19701 min) [10:49:02] Quant Extracting 550.5 to 552.5 m/z (7.1469502 to 91.46825 min) [10:49:02] Quant Extracting 552.5 to 554.5 m/z (7.148113 to 94.25449 min) [10:49:02] Quant Extracting 554.5 to 556.5 m/z (8.02563 to 93.82591 min) [10:49:02] Quant Extracting 556.5 to 558.5 m/z (7.1492643 to 89.12401 min) [10:49:02] Quant Extracting 558.5 to 560.5 m/z (7.1492643 to 93.20341 min) [10:49:02] Quant Extracting 560.5 to 562.5 m/z (6.74928 to 92.3832 min) [10:49:02] Quant Extracting 562.5 to 564.5 m/z (7.1831594 to 97.7693 min) [10:49:02] Quant Extracting 564.5 to 566.5 m/z (7.1515675 to 99.21385 min) [10:49:02] Quant Extracting 566.5 to 568.5 m/z (7.1515675 to 94.61944 min) [10:49:02] Quant Extracting 568.5 to 570.5 m/z (7.15272 to 94.75257 min) [10:49:02] Quant Extracting 570.5 to 572.5 m/z (7.15272 to 89.7788 min) [10:49:03] Quant Extracting 572.5 to 574.5 m/z (7.1538706 to 92.618004 min) [10:49:03] Quant Extracting 574.5 to 576.5 m/z (7.1538706 to 94.49007 min) [10:49:03] Quant Extracting 576.5 to 578.5 m/z (7.7400613 to 99.08244 min) [10:49:03] Quant Extracting 578.5 to 580.5 m/z (7.155017 to 93.044785 min) [10:49:03] Quant Extracting 580.5 to 582.5 m/z (7.15618 to 94.426796 min) [10:49:03] Quant Extracting 582.5 to 584.5 m/z (7.15618 to 94.72354 min) [10:49:03] Quant Extracting 584.5 to 586.5 m/z (7.18891 to 93.97038 min) [10:49:03] Quant Extracting 586.5 to 588.5 m/z (7.1573243 to 93.57228 min) [10:49:03] Quant Extracting 588.5 to 590.5 m/z (7.158486 to 97.94399 min) [10:49:03] Quant Extracting 590.5 to 592.5 m/z (7.158486 to 93.31065 min) [10:49:04] Quant Extracting 592.5 to 594.5 m/z (7.159632 to 94.99125 min) [10:49:04] Quant Extracting 594.5 to 596.5 m/z (7.159632 to 92.00622 min) [10:49:04] Quant Extracting 596.5 to 598.5 m/z (12.738337 to 93.545746 min) [10:49:04] Quant Extracting 598.5 to 600.5 m/z (7.160793 to 94.49696 min) [10:49:04] Quant Extracting 600.5 to 602.5 m/z (7.6520357 to 100.747856 min) [10:49:05] Attempted extraction for: 17396, found 17396 [10:49:05] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML (17396 entries)... [10:49:05] Writing 17396 peptides to entries table... [10:49:06] Writing 17396 peptides to peptidequants table... [10:49:08] Finished writing to Encyclopedia ELIB at Wed Jul 17 10:49:08 BST 2024 [10:49:08] Writing local target/decoy peptides: 17396/180, pi0: 0.93436 [10:49:09] Writing local target/decoy proteins: 4637/46 [10:49:11] Finished analysis! 17396 peptides identified at 1.0% FDR (18.3 minutes) [10:49:11] Generating chromatogram library (3 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [10:49:15] EncyclopeDIA version 2.12.30 [10:49:16] Getting count of protein accessions... [10:49:16] Using EncyclopeDIA 2.X Scoring System [10:49:16] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML ... [10:49:16] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML ... 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[10:51:48] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.dia! [10:51:48] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML [10:51:48] Library File: UP000005640_9606-z3_nce27-prosit.dlib [10:51:48] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.elib [10:51:48] Parameters: [10:51:48] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [10:51:48] Converting files... [10:51:48] Calculating features... [10:51:48] Processing precursors scans... [10:51:49] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [10:51:49] Processing 598.5 to 600.5 m/z, (3.9266944 second duty cycle) [10:51:51] 6080 peptides remaining for 598.5 to 600.5... [10:51:52] 6030 peptides remaining for 598.5 to 600.5... [10:51:52] 5822 peptides remaining for 598.5 to 600.5... [10:51:53] 5538 peptides remaining for 598.5 to 600.5... [10:51:53] 5227 peptides remaining for 598.5 to 600.5... [10:51:54] 4764 peptides remaining for 598.5 to 600.5... [10:51:54] 4276 peptides remaining for 598.5 to 600.5... [10:51:55] 3771 peptides remaining for 598.5 to 600.5... [10:51:55] 3305 peptides remaining for 598.5 to 600.5... [10:51:56] 2785 peptides remaining for 598.5 to 600.5... [10:51:56] 2228 peptides remaining for 598.5 to 600.5... [10:51:57] 1700 peptides remaining for 598.5 to 600.5... [10:51:57] 1155 peptides remaining for 598.5 to 600.5... [10:51:58] 616 peptides remaining for 598.5 to 600.5... [10:51:58] 57 peptides remaining for 598.5 to 600.5... [10:51:59] Processing 600.5 to 602.5 m/z, (1.9634008 second duty cycle) [10:52:01] 6133 peptides remaining for 600.5 to 602.5... [10:52:01] 5741 peptides remaining for 600.5 to 602.5... [10:52:02] 5333 peptides remaining for 600.5 to 602.5... [10:52:02] 4919 peptides remaining for 600.5 to 602.5... [10:52:03] 4513 peptides remaining for 600.5 to 602.5... [10:52:03] 4075 peptides remaining for 600.5 to 602.5... [10:52:04] 3662 peptides remaining for 600.5 to 602.5... [10:52:04] 3260 peptides remaining for 600.5 to 602.5... [10:52:05] 2852 peptides remaining for 600.5 to 602.5... [10:52:05] 2446 peptides remaining for 600.5 to 602.5... [10:52:06] 2036 peptides remaining for 600.5 to 602.5... [10:52:06] 1640 peptides remaining for 600.5 to 602.5... [10:52:07] 1240 peptides remaining for 600.5 to 602.5... [10:52:07] 813 peptides remaining for 600.5 to 602.5... [10:52:08] 403 peptides remaining for 600.5 to 602.5... [10:52:09] 0 peptides remaining for 600.5 to 602.5... [10:52:09] Processing 602.5 to 604.5 m/z, (1.9634008 second duty cycle) [10:52:11] 6118 peptides remaining for 602.5 to 604.5... [10:52:11] 5727 peptides remaining for 602.5 to 604.5... [10:52:12] 5315 peptides remaining for 602.5 to 604.5... [10:52:12] 4934 peptides remaining for 602.5 to 604.5... [10:52:13] 4548 peptides remaining for 602.5 to 604.5... [10:52:13] 4170 peptides remaining for 602.5 to 604.5... [10:52:14] 3760 peptides remaining for 602.5 to 604.5... [10:52:14] 3367 peptides remaining for 602.5 to 604.5... [10:52:15] 2990 peptides remaining for 602.5 to 604.5... [10:52:15] 2607 peptides remaining for 602.5 to 604.5... [10:52:16] 2207 peptides remaining for 602.5 to 604.5... [10:52:16] 1807 peptides remaining for 602.5 to 604.5... [10:52:17] 1416 peptides remaining for 602.5 to 604.5... [10:52:17] 1022 peptides remaining for 602.5 to 604.5... [10:52:18] 618 peptides remaining for 602.5 to 604.5... [10:52:18] 220 peptides remaining for 602.5 to 604.5... [10:52:19] Processing 604.5 to 606.5 m/z, (1.9634011 second duty cycle) [10:52:21] 5575 peptides remaining for 604.5 to 606.5... [10:52:21] 5151 peptides remaining for 604.5 to 606.5... [10:52:22] 4809 peptides remaining for 604.5 to 606.5... [10:52:22] 4400 peptides remaining for 604.5 to 606.5... [10:52:23] 3999 peptides remaining for 604.5 to 606.5... [10:52:23] 3603 peptides remaining for 604.5 to 606.5... [10:52:24] 3208 peptides remaining for 604.5 to 606.5... [10:52:24] 2833 peptides remaining for 604.5 to 606.5... [10:52:25] 2444 peptides remaining for 604.5 to 606.5... [10:52:25] 2047 peptides remaining for 604.5 to 606.5... [10:52:26] 1677 peptides remaining for 604.5 to 606.5... [10:52:26] 1297 peptides remaining for 604.5 to 606.5... [10:52:27] 904 peptides remaining for 604.5 to 606.5... [10:52:27] 525 peptides remaining for 604.5 to 606.5... [10:52:28] 143 peptides remaining for 604.5 to 606.5... [10:52:29] Processing 606.5 to 608.5 m/z, (1.9634011 second duty cycle) [10:52:30] 6164 peptides remaining for 606.5 to 608.5... [10:52:31] 5782 peptides remaining for 606.5 to 608.5... [10:52:31] 5376 peptides remaining for 606.5 to 608.5... [10:52:32] 4992 peptides remaining for 606.5 to 608.5... [10:52:32] 4633 peptides remaining for 606.5 to 608.5... [10:52:33] 4249 peptides remaining for 606.5 to 608.5... [10:52:33] 3857 peptides remaining for 606.5 to 608.5... [10:52:34] 3466 peptides remaining for 606.5 to 608.5... [10:52:34] 3082 peptides remaining for 606.5 to 608.5... [10:52:35] 2697 peptides remaining for 606.5 to 608.5... [10:52:35] 2312 peptides remaining for 606.5 to 608.5... [10:52:36] 1920 peptides remaining for 606.5 to 608.5... [10:52:36] 1537 peptides remaining for 606.5 to 608.5... [10:52:37] 1156 peptides remaining for 606.5 to 608.5... [10:52:37] 783 peptides remaining for 606.5 to 608.5... [10:52:38] 408 peptides remaining for 606.5 to 608.5... [10:52:39] 10 peptides remaining for 606.5 to 608.5... [10:52:39] Processing 608.5 to 610.5 m/z, (1.963401 second duty cycle) [10:52:41] 6009 peptides remaining for 608.5 to 610.5... [10:52:41] 5623 peptides remaining for 608.5 to 610.5... [10:52:42] 5225 peptides remaining for 608.5 to 610.5... [10:52:42] 4853 peptides remaining for 608.5 to 610.5... [10:52:43] 4459 peptides remaining for 608.5 to 610.5... [10:52:43] 4080 peptides remaining for 608.5 to 610.5... [10:52:44] 3687 peptides remaining for 608.5 to 610.5... [10:52:44] 3292 peptides remaining for 608.5 to 610.5... [10:52:45] 2925 peptides remaining for 608.5 to 610.5... [10:52:45] 2528 peptides remaining for 608.5 to 610.5... [10:52:46] 2146 peptides remaining for 608.5 to 610.5... [10:52:46] 1764 peptides remaining for 608.5 to 610.5... [10:52:47] 1359 peptides remaining for 608.5 to 610.5... [10:52:47] 968 peptides remaining for 608.5 to 610.5... [10:52:48] 576 peptides remaining for 608.5 to 610.5... [10:52:49] 209 peptides remaining for 608.5 to 610.5... [10:52:49] Processing 610.5 to 612.5 m/z, (1.963401 second duty cycle) [10:52:51] 5855 peptides remaining for 610.5 to 612.5... [10:52:51] 5477 peptides remaining for 610.5 to 612.5... [10:52:52] 5079 peptides remaining for 610.5 to 612.5... [10:52:52] 4686 peptides remaining for 610.5 to 612.5... [10:52:53] 4327 peptides remaining for 610.5 to 612.5... [10:52:53] 3931 peptides remaining for 610.5 to 612.5... [10:52:54] 3543 peptides remaining for 610.5 to 612.5... [10:52:54] 3166 peptides remaining for 610.5 to 612.5... [10:52:55] 2795 peptides remaining for 610.5 to 612.5... [10:52:55] 2412 peptides remaining for 610.5 to 612.5... [10:52:56] 2033 peptides remaining for 610.5 to 612.5... [10:52:56] 1637 peptides remaining for 610.5 to 612.5... [10:52:57] 1273 peptides remaining for 610.5 to 612.5... [10:52:57] 906 peptides remaining for 610.5 to 612.5... [10:52:58] 522 peptides remaining for 610.5 to 612.5... [10:52:58] 154 peptides remaining for 610.5 to 612.5... [10:52:59] Processing 612.5 to 614.5 m/z, (1.9634008 second duty cycle) [10:53:01] 5668 peptides remaining for 612.5 to 614.5... [10:53:01] 5286 peptides remaining for 612.5 to 614.5... [10:53:02] 4885 peptides remaining for 612.5 to 614.5... [10:53:02] 4493 peptides remaining for 612.5 to 614.5... [10:53:03] 4123 peptides remaining for 612.5 to 614.5... [10:53:03] 3743 peptides remaining for 612.5 to 614.5... [10:53:04] 3376 peptides remaining for 612.5 to 614.5... [10:53:04] 3007 peptides remaining for 612.5 to 614.5... [10:53:05] 2622 peptides remaining for 612.5 to 614.5... [10:53:05] 2243 peptides remaining for 612.5 to 614.5... [10:53:06] 1849 peptides remaining for 612.5 to 614.5... [10:53:06] 1460 peptides remaining for 612.5 to 614.5... [10:53:07] 1090 peptides remaining for 612.5 to 614.5... [10:53:07] 725 peptides remaining for 612.5 to 614.5... [10:53:08] 354 peptides remaining for 612.5 to 614.5... [10:53:08] 0 peptides remaining for 612.5 to 614.5... [10:53:09] Processing 614.5 to 616.5 m/z, (1.9634008 second duty cycle) [10:53:11] 6190 peptides remaining for 614.5 to 616.5... [10:53:11] 5799 peptides remaining for 614.5 to 616.5... [10:53:12] 5387 peptides remaining for 614.5 to 616.5... [10:53:12] 4994 peptides remaining for 614.5 to 616.5... [10:53:13] 4630 peptides remaining for 614.5 to 616.5... [10:53:13] 4251 peptides remaining for 614.5 to 616.5... [10:53:14] 3872 peptides remaining for 614.5 to 616.5... [10:53:14] 3483 peptides remaining for 614.5 to 616.5... [10:53:15] 3105 peptides remaining for 614.5 to 616.5... [10:53:15] 2733 peptides remaining for 614.5 to 616.5... [10:53:16] 2367 peptides remaining for 614.5 to 616.5... [10:53:16] 1976 peptides remaining for 614.5 to 616.5... [10:53:17] 1578 peptides remaining for 614.5 to 616.5... [10:53:17] 1212 peptides remaining for 614.5 to 616.5... [10:53:18] 836 peptides remaining for 614.5 to 616.5... [10:53:18] 450 peptides remaining for 614.5 to 616.5... [10:53:19] 60 peptides remaining for 614.5 to 616.5... [10:53:19] Processing 616.5 to 618.5 m/z, (1.963401 second duty cycle) [10:53:21] 5858 peptides remaining for 616.5 to 618.5... [10:53:22] 5467 peptides remaining for 616.5 to 618.5... [10:53:22] 5074 peptides remaining for 616.5 to 618.5... [10:53:23] 4690 peptides remaining for 616.5 to 618.5... [10:53:23] 4294 peptides remaining for 616.5 to 618.5... [10:53:24] 3925 peptides remaining for 616.5 to 618.5... [10:53:24] 3540 peptides remaining for 616.5 to 618.5... [10:53:25] 3165 peptides remaining for 616.5 to 618.5... [10:53:25] 2781 peptides remaining for 616.5 to 618.5... [10:53:26] 2378 peptides remaining for 616.5 to 618.5... [10:53:27] 1984 peptides remaining for 616.5 to 618.5... [10:53:27] 1619 peptides remaining for 616.5 to 618.5... [10:53:28] 1238 peptides remaining for 616.5 to 618.5... [10:53:28] 851 peptides remaining for 616.5 to 618.5... [10:53:29] 482 peptides remaining for 616.5 to 618.5... [10:53:29] 94 peptides remaining for 616.5 to 618.5... [10:53:30] Processing 618.5 to 620.5 m/z, (1.963401 second duty cycle) [10:53:31] 5579 peptides remaining for 618.5 to 620.5... [10:53:32] 5211 peptides remaining for 618.5 to 620.5... [10:53:32] 4804 peptides remaining for 618.5 to 620.5... [10:53:33] 4412 peptides remaining for 618.5 to 620.5... [10:53:33] 4034 peptides remaining for 618.5 to 620.5... [10:53:34] 3629 peptides remaining for 618.5 to 620.5... [10:53:34] 3245 peptides remaining for 618.5 to 620.5... [10:53:35] 2875 peptides remaining for 618.5 to 620.5... [10:53:36] 2489 peptides remaining for 618.5 to 620.5... [10:53:36] 2105 peptides remaining for 618.5 to 620.5... [10:53:37] 1726 peptides remaining for 618.5 to 620.5... [10:53:37] 1333 peptides remaining for 618.5 to 620.5... [10:53:38] 941 peptides remaining for 618.5 to 620.5... [10:53:38] 578 peptides remaining for 618.5 to 620.5... [10:53:39] 193 peptides remaining for 618.5 to 620.5... [10:53:39] Processing 620.5 to 622.5 m/z, (1.963401 second duty cycle) [10:53:41] 5620 peptides remaining for 620.5 to 622.5... [10:53:41] 5227 peptides remaining for 620.5 to 622.5... [10:53:42] 4825 peptides remaining for 620.5 to 622.5... [10:53:42] 4429 peptides remaining for 620.5 to 622.5... [10:53:43] 4054 peptides remaining for 620.5 to 622.5... [10:53:43] 3664 peptides remaining for 620.5 to 622.5... [10:53:44] 3293 peptides remaining for 620.5 to 622.5... [10:53:44] 2904 peptides remaining for 620.5 to 622.5... [10:53:45] 2526 peptides remaining for 620.5 to 622.5... [10:53:45] 2127 peptides remaining for 620.5 to 622.5... [10:53:46] 1743 peptides remaining for 620.5 to 622.5... [10:53:46] 1358 peptides remaining for 620.5 to 622.5... [10:53:47] 978 peptides remaining for 620.5 to 622.5... [10:53:47] 601 peptides remaining for 620.5 to 622.5... [10:53:48] 210 peptides remaining for 620.5 to 622.5... [10:53:49] Processing 622.5 to 624.5 m/z, (1.963401 second duty cycle) [10:53:50] 5893 peptides remaining for 622.5 to 624.5... [10:53:51] 5488 peptides remaining for 622.5 to 624.5... [10:53:51] 5088 peptides remaining for 622.5 to 624.5... [10:53:52] 4699 peptides remaining for 622.5 to 624.5... [10:53:52] 4321 peptides remaining for 622.5 to 624.5... [10:53:53] 3962 peptides remaining for 622.5 to 624.5... [10:53:53] 3585 peptides remaining for 622.5 to 624.5... [10:53:54] 3197 peptides remaining for 622.5 to 624.5... [10:53:54] 2801 peptides remaining for 622.5 to 624.5... [10:53:55] 2400 peptides remaining for 622.5 to 624.5... [10:53:55] 2025 peptides remaining for 622.5 to 624.5... [10:53:56] 1629 peptides remaining for 622.5 to 624.5... [10:53:56] 1248 peptides remaining for 622.5 to 624.5... [10:53:57] 870 peptides remaining for 622.5 to 624.5... [10:53:58] 478 peptides remaining for 622.5 to 624.5... [10:53:58] 95 peptides remaining for 622.5 to 624.5... [10:53:59] Processing 624.5 to 626.5 m/z, (1.963401 second duty cycle) [10:54:00] 5699 peptides remaining for 624.5 to 626.5... [10:54:01] 5313 peptides remaining for 624.5 to 626.5... [10:54:01] 4919 peptides remaining for 624.5 to 626.5... [10:54:02] 4539 peptides remaining for 624.5 to 626.5... [10:54:02] 4168 peptides remaining for 624.5 to 626.5... [10:54:03] 3788 peptides remaining for 624.5 to 626.5... [10:54:03] 3403 peptides remaining for 624.5 to 626.5... [10:54:04] 3045 peptides remaining for 624.5 to 626.5... [10:54:04] 2670 peptides remaining for 624.5 to 626.5... [10:54:05] 2293 peptides remaining for 624.5 to 626.5... [10:54:05] 1915 peptides remaining for 624.5 to 626.5... [10:54:06] 1535 peptides remaining for 624.5 to 626.5... [10:54:06] 1150 peptides remaining for 624.5 to 626.5... [10:54:07] 758 peptides remaining for 624.5 to 626.5... [10:54:07] 404 peptides remaining for 624.5 to 626.5... [10:54:08] 18 peptides remaining for 624.5 to 626.5... [10:54:08] Processing 626.5 to 628.5 m/z, (1.963401 second duty cycle) [10:54:10] 5583 peptides remaining for 626.5 to 628.5... [10:54:11] 5212 peptides remaining for 626.5 to 628.5... [10:54:11] 4828 peptides remaining for 626.5 to 628.5... [10:54:12] 4473 peptides remaining for 626.5 to 628.5... [10:54:12] 4111 peptides remaining for 626.5 to 628.5... [10:54:13] 3732 peptides remaining for 626.5 to 628.5... [10:54:13] 3359 peptides remaining for 626.5 to 628.5... [10:54:14] 2978 peptides remaining for 626.5 to 628.5... [10:54:14] 2604 peptides remaining for 626.5 to 628.5... [10:54:15] 2245 peptides remaining for 626.5 to 628.5... [10:54:15] 1885 peptides remaining for 626.5 to 628.5... [10:54:16] 1507 peptides remaining for 626.5 to 628.5... [10:54:16] 1121 peptides remaining for 626.5 to 628.5... [10:54:17] 734 peptides remaining for 626.5 to 628.5... [10:54:17] 365 peptides remaining for 626.5 to 628.5... [10:54:18] 0 peptides remaining for 626.5 to 628.5... [10:54:18] Processing 628.5 to 630.5 m/z, (1.963401 second duty cycle) [10:54:20] 5974 peptides remaining for 628.5 to 630.5... [10:54:21] 5608 peptides remaining for 628.5 to 630.5... [10:54:21] 5232 peptides remaining for 628.5 to 630.5... [10:54:22] 4838 peptides remaining for 628.5 to 630.5... [10:54:22] 4439 peptides remaining for 628.5 to 630.5... [10:54:23] 4053 peptides remaining for 628.5 to 630.5... [10:54:23] 3677 peptides remaining for 628.5 to 630.5... [10:54:24] 3299 peptides remaining for 628.5 to 630.5... [10:54:24] 2932 peptides remaining for 628.5 to 630.5... [10:54:25] 2560 peptides remaining for 628.5 to 630.5... [10:54:25] 2165 peptides remaining for 628.5 to 630.5... [10:54:26] 1773 peptides remaining for 628.5 to 630.5... [10:54:26] 1390 peptides remaining for 628.5 to 630.5... [10:54:27] 1005 peptides remaining for 628.5 to 630.5... [10:54:27] 652 peptides remaining for 628.5 to 630.5... [10:54:28] 293 peptides remaining for 628.5 to 630.5... [10:54:28] Processing 630.5 to 632.5 m/z, (1.9634008 second duty cycle) [10:54:30] 5862 peptides remaining for 630.5 to 632.5... [10:54:31] 5475 peptides remaining for 630.5 to 632.5... [10:54:31] 5102 peptides remaining for 630.5 to 632.5... [10:54:32] 4734 peptides remaining for 630.5 to 632.5... [10:54:32] 4373 peptides remaining for 630.5 to 632.5... [10:54:33] 3982 peptides remaining for 630.5 to 632.5... [10:54:33] 3614 peptides remaining for 630.5 to 632.5... [10:54:34] 3235 peptides remaining for 630.5 to 632.5... [10:54:34] 2860 peptides remaining for 630.5 to 632.5... [10:54:35] 2474 peptides remaining for 630.5 to 632.5... [10:54:35] 2085 peptides remaining for 630.5 to 632.5... [10:54:36] 1705 peptides remaining for 630.5 to 632.5... [10:54:36] 1338 peptides remaining for 630.5 to 632.5... [10:54:37] 975 peptides remaining for 630.5 to 632.5... [10:54:37] 611 peptides remaining for 630.5 to 632.5... [10:54:38] 241 peptides remaining for 630.5 to 632.5... [10:54:38] Processing 632.5 to 634.5 m/z, (1.963401 second duty cycle) [10:54:40] 5415 peptides remaining for 632.5 to 634.5... [10:54:41] 5001 peptides remaining for 632.5 to 634.5... [10:54:41] 4610 peptides remaining for 632.5 to 634.5... [10:54:42] 4238 peptides remaining for 632.5 to 634.5... [10:54:42] 3853 peptides remaining for 632.5 to 634.5... [10:54:43] 3467 peptides remaining for 632.5 to 634.5... [10:54:43] 3096 peptides remaining for 632.5 to 634.5... [10:54:44] 2720 peptides remaining for 632.5 to 634.5... [10:54:44] 2329 peptides remaining for 632.5 to 634.5... [10:54:45] 1948 peptides remaining for 632.5 to 634.5... [10:54:45] 1558 peptides remaining for 632.5 to 634.5... [10:54:46] 1154 peptides remaining for 632.5 to 634.5... [10:54:46] 774 peptides remaining for 632.5 to 634.5... [10:54:47] 397 peptides remaining for 632.5 to 634.5... [10:54:47] 25 peptides remaining for 632.5 to 634.5... [10:54:48] Processing 634.5 to 636.5 m/z, (1.9634008 second duty cycle) [10:54:50] 5590 peptides remaining for 634.5 to 636.5... [10:54:50] 5215 peptides remaining for 634.5 to 636.5... [10:54:51] 4825 peptides remaining for 634.5 to 636.5... [10:54:51] 4437 peptides remaining for 634.5 to 636.5... [10:54:52] 4067 peptides remaining for 634.5 to 636.5... [10:54:52] 3678 peptides remaining for 634.5 to 636.5... [10:54:53] 3298 peptides remaining for 634.5 to 636.5... [10:54:53] 2930 peptides remaining for 634.5 to 636.5... [10:54:54] 2560 peptides remaining for 634.5 to 636.5... [10:54:54] 2186 peptides remaining for 634.5 to 636.5... [10:54:55] 1797 peptides remaining for 634.5 to 636.5... [10:54:55] 1418 peptides remaining for 634.5 to 636.5... [10:54:56] 1037 peptides remaining for 634.5 to 636.5... [10:54:56] 671 peptides remaining for 634.5 to 636.5... [10:54:57] 311 peptides remaining for 634.5 to 636.5... [10:54:57] Processing 636.5 to 638.5 m/z, (1.9634011 second duty cycle) [10:54:59] 5698 peptides remaining for 636.5 to 638.5... [10:54:59] 5325 peptides remaining for 636.5 to 638.5... [10:55:00] 4928 peptides remaining for 636.5 to 638.5... [10:55:00] 4551 peptides remaining for 636.5 to 638.5... [10:55:01] 4185 peptides remaining for 636.5 to 638.5... [10:55:02] 3807 peptides remaining for 636.5 to 638.5... [10:55:02] 3438 peptides remaining for 636.5 to 638.5... [10:55:03] 3068 peptides remaining for 636.5 to 638.5... [10:55:03] 2698 peptides remaining for 636.5 to 638.5... [10:55:04] 2321 peptides remaining for 636.5 to 638.5... [10:55:04] 1943 peptides remaining for 636.5 to 638.5... [10:55:05] 1573 peptides remaining for 636.5 to 638.5... [10:55:05] 1219 peptides remaining for 636.5 to 638.5... [10:55:06] 857 peptides remaining for 636.5 to 638.5... [10:55:06] 500 peptides remaining for 636.5 to 638.5... [10:55:07] 112 peptides remaining for 636.5 to 638.5... [10:55:07] Processing 638.5 to 640.5 m/z, (1.9634013 second duty cycle) [10:55:09] 5615 peptides remaining for 638.5 to 640.5... [10:55:09] 5262 peptides remaining for 638.5 to 640.5... [10:55:10] 4884 peptides remaining for 638.5 to 640.5... [10:55:10] 4509 peptides remaining for 638.5 to 640.5... [10:55:11] 4132 peptides remaining for 638.5 to 640.5... [10:55:11] 3769 peptides remaining for 638.5 to 640.5... [10:55:12] 3391 peptides remaining for 638.5 to 640.5... [10:55:12] 3015 peptides remaining for 638.5 to 640.5... [10:55:13] 2648 peptides remaining for 638.5 to 640.5... [10:55:13] 2280 peptides remaining for 638.5 to 640.5... [10:55:14] 1915 peptides remaining for 638.5 to 640.5... [10:55:15] 1536 peptides remaining for 638.5 to 640.5... [10:55:15] 1173 peptides remaining for 638.5 to 640.5... [10:55:16] 807 peptides remaining for 638.5 to 640.5... [10:55:16] 445 peptides remaining for 638.5 to 640.5... [10:55:17] 97 peptides remaining for 638.5 to 640.5... [10:55:17] Processing 640.5 to 642.5 m/z, (1.9634013 second duty cycle) [10:55:19] 5258 peptides remaining for 640.5 to 642.5... [10:55:19] 4874 peptides remaining for 640.5 to 642.5... [10:55:20] 4505 peptides remaining for 640.5 to 642.5... [10:55:20] 4127 peptides remaining for 640.5 to 642.5... [10:55:21] 3765 peptides remaining for 640.5 to 642.5... [10:55:21] 3395 peptides remaining for 640.5 to 642.5... [10:55:22] 3022 peptides remaining for 640.5 to 642.5... [10:55:22] 2654 peptides remaining for 640.5 to 642.5... [10:55:23] 2296 peptides remaining for 640.5 to 642.5... [10:55:23] 1914 peptides remaining for 640.5 to 642.5... [10:55:24] 1561 peptides remaining for 640.5 to 642.5... [10:55:25] 1182 peptides remaining for 640.5 to 642.5... [10:55:25] 830 peptides remaining for 640.5 to 642.5... [10:55:26] 476 peptides remaining for 640.5 to 642.5... [10:55:26] 124 peptides remaining for 640.5 to 642.5... [10:55:27] Processing 642.5 to 644.5 m/z, (1.9634013 second duty cycle) [10:55:28] 5571 peptides remaining for 642.5 to 644.5... [10:55:29] 5226 peptides remaining for 642.5 to 644.5... [10:55:29] 4856 peptides remaining for 642.5 to 644.5... [10:55:30] 4476 peptides remaining for 642.5 to 644.5... [10:55:30] 4110 peptides remaining for 642.5 to 644.5... [10:55:31] 3738 peptides remaining for 642.5 to 644.5... [10:55:31] 3369 peptides remaining for 642.5 to 644.5... [10:55:32] 2996 peptides remaining for 642.5 to 644.5... [10:55:32] 2633 peptides remaining for 642.5 to 644.5... [10:55:33] 2266 peptides remaining for 642.5 to 644.5... [10:55:33] 1889 peptides remaining for 642.5 to 644.5... [10:55:34] 1507 peptides remaining for 642.5 to 644.5... [10:55:34] 1146 peptides remaining for 642.5 to 644.5... [10:55:35] 765 peptides remaining for 642.5 to 644.5... [10:55:36] 412 peptides remaining for 642.5 to 644.5... [10:55:36] 42 peptides remaining for 642.5 to 644.5... [10:55:37] Processing 644.5 to 646.5 m/z, (1.9634013 second duty cycle) [10:55:38] 5757 peptides remaining for 644.5 to 646.5... [10:55:39] 5395 peptides remaining for 644.5 to 646.5... [10:55:39] 5013 peptides remaining for 644.5 to 646.5... [10:55:40] 4645 peptides remaining for 644.5 to 646.5... [10:55:40] 4288 peptides remaining for 644.5 to 646.5... [10:55:41] 3925 peptides remaining for 644.5 to 646.5... [10:55:41] 3579 peptides remaining for 644.5 to 646.5... [10:55:42] 3262 peptides remaining for 644.5 to 646.5... [10:55:42] 2980 peptides remaining for 644.5 to 646.5... [10:55:43] 2709 peptides remaining for 644.5 to 646.5... [10:55:43] 2408 peptides remaining for 644.5 to 646.5... [10:55:44] 2116 peptides remaining for 644.5 to 646.5... [10:55:44] 1837 peptides remaining for 644.5 to 646.5... [10:55:45] 1549 peptides remaining for 644.5 to 646.5... [10:55:45] 1271 peptides remaining for 644.5 to 646.5... [10:55:46] 923 peptides remaining for 644.5 to 646.5... [10:55:47] 567 peptides remaining for 644.5 to 646.5... [10:55:47] 200 peptides remaining for 644.5 to 646.5... [10:55:48] Processing 646.5 to 648.5 m/z, (1.9634013 second duty cycle) [10:55:49] 5539 peptides remaining for 646.5 to 648.5... [10:55:50] 5181 peptides remaining for 646.5 to 648.5... [10:55:50] 4803 peptides remaining for 646.5 to 648.5... [10:55:51] 4449 peptides remaining for 646.5 to 648.5... [10:55:51] 4077 peptides remaining for 646.5 to 648.5... [10:55:52] 3708 peptides remaining for 646.5 to 648.5... [10:55:52] 3341 peptides remaining for 646.5 to 648.5... [10:55:53] 2963 peptides remaining for 646.5 to 648.5... [10:55:53] 2593 peptides remaining for 646.5 to 648.5... [10:55:54] 2228 peptides remaining for 646.5 to 648.5... [10:55:54] 1876 peptides remaining for 646.5 to 648.5... [10:55:55] 1537 peptides remaining for 646.5 to 648.5... [10:55:55] 1179 peptides remaining for 646.5 to 648.5... [10:55:56] 831 peptides remaining for 646.5 to 648.5... [10:55:57] 449 peptides remaining for 646.5 to 648.5... [10:55:57] 82 peptides remaining for 646.5 to 648.5... [10:55:58] Processing 648.5 to 650.5 m/z, (1.9634013 second duty cycle) [10:55:59] 5359 peptides remaining for 648.5 to 650.5... [10:56:00] 4992 peptides remaining for 648.5 to 650.5... [10:56:00] 4620 peptides remaining for 648.5 to 650.5... [10:56:01] 4247 peptides remaining for 648.5 to 650.5... [10:56:01] 3901 peptides remaining for 648.5 to 650.5... [10:56:02] 3537 peptides remaining for 648.5 to 650.5... [10:56:02] 3188 peptides remaining for 648.5 to 650.5... [10:56:03] 2831 peptides remaining for 648.5 to 650.5... [10:56:03] 2473 peptides remaining for 648.5 to 650.5... [10:56:04] 2118 peptides remaining for 648.5 to 650.5... [10:56:04] 1760 peptides remaining for 648.5 to 650.5... [10:56:05] 1401 peptides remaining for 648.5 to 650.5... [10:56:05] 1045 peptides remaining for 648.5 to 650.5... [10:56:06] 659 peptides remaining for 648.5 to 650.5... [10:56:06] 308 peptides remaining for 648.5 to 650.5... [10:56:07] Processing 650.5 to 652.5 m/z, (1.9634013 second duty cycle) [10:56:09] 5524 peptides remaining for 650.5 to 652.5... [10:56:09] 5158 peptides remaining for 650.5 to 652.5... [10:56:10] 4802 peptides remaining for 650.5 to 652.5... [10:56:10] 4436 peptides remaining for 650.5 to 652.5... [10:56:11] 4075 peptides remaining for 650.5 to 652.5... [10:56:11] 3710 peptides remaining for 650.5 to 652.5... [10:56:12] 3352 peptides remaining for 650.5 to 652.5... [10:56:12] 3008 peptides remaining for 650.5 to 652.5... [10:56:13] 2665 peptides remaining for 650.5 to 652.5... [10:56:13] 2307 peptides remaining for 650.5 to 652.5... [10:56:14] 1951 peptides remaining for 650.5 to 652.5... [10:56:14] 1624 peptides remaining for 650.5 to 652.5... [10:56:15] 1277 peptides remaining for 650.5 to 652.5... [10:56:15] 925 peptides remaining for 650.5 to 652.5... [10:56:16] 556 peptides remaining for 650.5 to 652.5... [10:56:16] 209 peptides remaining for 650.5 to 652.5... [10:56:17] Processing 652.5 to 654.5 m/z, (1.9634011 second duty cycle) [10:56:19] 5274 peptides remaining for 652.5 to 654.5... [10:56:19] 4916 peptides remaining for 652.5 to 654.5... [10:56:20] 4560 peptides remaining for 652.5 to 654.5... [10:56:21] 4202 peptides remaining for 652.5 to 654.5... [10:56:21] 3855 peptides remaining for 652.5 to 654.5... [10:56:22] 3514 peptides remaining for 652.5 to 654.5... [10:56:22] 3154 peptides remaining for 652.5 to 654.5... [10:56:23] 2789 peptides remaining for 652.5 to 654.5... [10:56:23] 2433 peptides remaining for 652.5 to 654.5... [10:56:24] 2078 peptides remaining for 652.5 to 654.5... [10:56:24] 1736 peptides remaining for 652.5 to 654.5... [10:56:25] 1377 peptides remaining for 652.5 to 654.5... [10:56:25] 1035 peptides remaining for 652.5 to 654.5... [10:56:26] 688 peptides remaining for 652.5 to 654.5... [10:56:26] 351 peptides remaining for 652.5 to 654.5... [10:56:27] 0 peptides remaining for 652.5 to 654.5... [10:56:27] Processing 654.5 to 656.5 m/z, (1.9634011 second duty cycle) [10:56:29] 5354 peptides remaining for 654.5 to 656.5... [10:56:29] 4981 peptides remaining for 654.5 to 656.5... [10:56:30] 4634 peptides remaining for 654.5 to 656.5... [10:56:31] 4297 peptides remaining for 654.5 to 656.5... [10:56:31] 3942 peptides remaining for 654.5 to 656.5... [10:56:32] 3595 peptides remaining for 654.5 to 656.5... [10:56:32] 3235 peptides remaining for 654.5 to 656.5... [10:56:33] 2854 peptides remaining for 654.5 to 656.5... [10:56:33] 2513 peptides remaining for 654.5 to 656.5... [10:56:34] 2162 peptides remaining for 654.5 to 656.5... [10:56:34] 1813 peptides remaining for 654.5 to 656.5... [10:56:35] 1465 peptides remaining for 654.5 to 656.5... [10:56:35] 1116 peptides remaining for 654.5 to 656.5... [10:56:36] 768 peptides remaining for 654.5 to 656.5... [10:56:36] 420 peptides remaining for 654.5 to 656.5... [10:56:37] 79 peptides remaining for 654.5 to 656.5... [10:56:37] Processing 656.5 to 658.5 m/z, (1.9634013 second duty cycle) [10:56:39] 5386 peptides remaining for 656.5 to 658.5... [10:56:39] 5046 peptides remaining for 656.5 to 658.5... [10:56:40] 4676 peptides remaining for 656.5 to 658.5... [10:56:40] 4330 peptides remaining for 656.5 to 658.5... [10:56:41] 3957 peptides remaining for 656.5 to 658.5... [10:56:41] 3594 peptides remaining for 656.5 to 658.5... [10:56:42] 3222 peptides remaining for 656.5 to 658.5... [10:56:43] 2847 peptides remaining for 656.5 to 658.5... [10:56:43] 2481 peptides remaining for 656.5 to 658.5... [10:56:44] 2125 peptides remaining for 656.5 to 658.5... [10:56:44] 1774 peptides remaining for 656.5 to 658.5... [10:56:45] 1417 peptides remaining for 656.5 to 658.5... [10:56:45] 1059 peptides remaining for 656.5 to 658.5... [10:56:46] 713 peptides remaining for 656.5 to 658.5... [10:56:46] 362 peptides remaining for 656.5 to 658.5... [10:56:47] 9 peptides remaining for 656.5 to 658.5... [10:56:47] Processing 658.5 to 660.6 m/z, (1.9634013 second duty cycle) [10:56:49] 5500 peptides remaining for 658.5 to 660.6... [10:56:50] 5153 peptides remaining for 658.5 to 660.6... [10:56:50] 4749 peptides remaining for 658.5 to 660.6... [10:56:51] 4390 peptides remaining for 658.5 to 660.6... [10:56:51] 4025 peptides remaining for 658.5 to 660.6... [10:56:52] 3671 peptides remaining for 658.5 to 660.6... [10:56:52] 3312 peptides remaining for 658.5 to 660.6... [10:56:53] 2931 peptides remaining for 658.5 to 660.6... [10:56:53] 2586 peptides remaining for 658.5 to 660.6... [10:56:54] 2229 peptides remaining for 658.5 to 660.6... [10:56:54] 1876 peptides remaining for 658.5 to 660.6... [10:56:55] 1526 peptides remaining for 658.5 to 660.6... [10:56:55] 1163 peptides remaining for 658.5 to 660.6... [10:56:56] 799 peptides remaining for 658.5 to 660.6... [10:56:56] 444 peptides remaining for 658.5 to 660.6... [10:56:57] 80 peptides remaining for 658.5 to 660.6... [10:56:57] Processing 660.6 to 662.6 m/z, (1.9634013 second duty cycle) [10:56:59] 5298 peptides remaining for 660.6 to 662.6... [10:56:59] 4928 peptides remaining for 660.6 to 662.6... [10:57:00] 4561 peptides remaining for 660.6 to 662.6... [10:57:00] 4205 peptides remaining for 660.6 to 662.6... [10:57:01] 3850 peptides remaining for 660.6 to 662.6... [10:57:02] 3481 peptides remaining for 660.6 to 662.6... [10:57:02] 3140 peptides remaining for 660.6 to 662.6... [10:57:03] 2780 peptides remaining for 660.6 to 662.6... [10:57:03] 2434 peptides remaining for 660.6 to 662.6... [10:57:04] 2078 peptides remaining for 660.6 to 662.6... [10:57:04] 1722 peptides remaining for 660.6 to 662.6... [10:57:05] 1386 peptides remaining for 660.6 to 662.6... [10:57:05] 1029 peptides remaining for 660.6 to 662.6... [10:57:06] 683 peptides remaining for 660.6 to 662.6... [10:57:06] 344 peptides remaining for 660.6 to 662.6... [10:57:07] 0 peptides remaining for 660.6 to 662.6... [10:57:07] Processing 662.6 to 664.6 m/z, (1.9634013 second duty cycle) [10:57:09] 5157 peptides remaining for 662.6 to 664.6... [10:57:09] 4781 peptides remaining for 662.6 to 664.6... [10:57:10] 4414 peptides remaining for 662.6 to 664.6... [10:57:10] 4051 peptides remaining for 662.6 to 664.6... [10:57:11] 3693 peptides remaining for 662.6 to 664.6... [10:57:11] 3325 peptides remaining for 662.6 to 664.6... [10:57:12] 2974 peptides remaining for 662.6 to 664.6... [10:57:13] 2595 peptides remaining for 662.6 to 664.6... [10:57:13] 2243 peptides remaining for 662.6 to 664.6... [10:57:14] 1875 peptides remaining for 662.6 to 664.6... [10:57:14] 1509 peptides remaining for 662.6 to 664.6... [10:57:15] 1149 peptides remaining for 662.6 to 664.6... [10:57:15] 778 peptides remaining for 662.6 to 664.6... [10:57:16] 411 peptides remaining for 662.6 to 664.6... [10:57:16] 44 peptides remaining for 662.6 to 664.6... [10:57:17] Processing 664.6 to 666.6 m/z, (1.9634014 second duty cycle) [10:57:18] 5637 peptides remaining for 664.6 to 666.6... [10:57:19] 5269 peptides remaining for 664.6 to 666.6... [10:57:19] 4885 peptides remaining for 664.6 to 666.6... [10:57:20] 4522 peptides remaining for 664.6 to 666.6... [10:57:20] 4166 peptides remaining for 664.6 to 666.6... [10:57:21] 3801 peptides remaining for 664.6 to 666.6... [10:57:21] 3428 peptides remaining for 664.6 to 666.6... [10:57:22] 3056 peptides remaining for 664.6 to 666.6... [10:57:22] 2691 peptides remaining for 664.6 to 666.6... [10:57:23] 2337 peptides remaining for 664.6 to 666.6... [10:57:23] 1986 peptides remaining for 664.6 to 666.6... [10:57:24] 1617 peptides remaining for 664.6 to 666.6... [10:57:24] 1250 peptides remaining for 664.6 to 666.6... [10:57:25] 905 peptides remaining for 664.6 to 666.6... [10:57:26] 550 peptides remaining for 664.6 to 666.6... [10:57:26] 189 peptides remaining for 664.6 to 666.6... [10:57:27] Processing 666.6 to 668.6 m/z, (1.9634014 second duty cycle) [10:57:28] 5442 peptides remaining for 666.6 to 668.6... [10:57:29] 5093 peptides remaining for 666.6 to 668.6... [10:57:29] 4720 peptides remaining for 666.6 to 668.6... [10:57:30] 4378 peptides remaining for 666.6 to 668.6... [10:57:30] 3999 peptides remaining for 666.6 to 668.6... [10:57:31] 3654 peptides remaining for 666.6 to 668.6... [10:57:31] 3314 peptides remaining for 666.6 to 668.6... [10:57:32] 2966 peptides remaining for 666.6 to 668.6... [10:57:32] 2661 peptides remaining for 666.6 to 668.6... [10:57:33] 2298 peptides remaining for 666.6 to 668.6... [10:57:33] 1947 peptides remaining for 666.6 to 668.6... [10:57:34] 1581 peptides remaining for 666.6 to 668.6... [10:57:34] 1231 peptides remaining for 666.6 to 668.6... [10:57:35] 882 peptides remaining for 666.6 to 668.6... [10:57:35] 499 peptides remaining for 666.6 to 668.6... [10:57:36] 136 peptides remaining for 666.6 to 668.6... [10:57:36] Processing 668.6 to 670.6 m/z, (1.9634011 second duty cycle) [10:57:38] 5178 peptides remaining for 668.6 to 670.6... [10:57:39] 4814 peptides remaining for 668.6 to 670.6... [10:57:39] 4450 peptides remaining for 668.6 to 670.6... [10:57:40] 4101 peptides remaining for 668.6 to 670.6... [10:57:40] 3743 peptides remaining for 668.6 to 670.6... [10:57:41] 3403 peptides remaining for 668.6 to 670.6... [10:57:41] 3035 peptides remaining for 668.6 to 670.6... [10:57:42] 2683 peptides remaining for 668.6 to 670.6... [10:57:42] 2319 peptides remaining for 668.6 to 670.6... [10:57:43] 1967 peptides remaining for 668.6 to 670.6... [10:57:43] 1618 peptides remaining for 668.6 to 670.6... [10:57:44] 1261 peptides remaining for 668.6 to 670.6... [10:57:44] 923 peptides remaining for 668.6 to 670.6... [10:57:45] 581 peptides remaining for 668.6 to 670.6... [10:57:45] 221 peptides remaining for 668.6 to 670.6... [10:57:46] Processing 670.6 to 672.6 m/z, (1.9634011 second duty cycle) [10:57:47] 5313 peptides remaining for 670.6 to 672.6... [10:57:48] 4955 peptides remaining for 670.6 to 672.6... [10:57:49] 4592 peptides remaining for 670.6 to 672.6... [10:57:49] 4242 peptides remaining for 670.6 to 672.6... [10:57:50] 3895 peptides remaining for 670.6 to 672.6... [10:57:50] 3560 peptides remaining for 670.6 to 672.6... [10:57:51] 3203 peptides remaining for 670.6 to 672.6... [10:57:51] 2864 peptides remaining for 670.6 to 672.6... [10:57:52] 2525 peptides remaining for 670.6 to 672.6... [10:57:52] 2193 peptides remaining for 670.6 to 672.6... [10:57:53] 1839 peptides remaining for 670.6 to 672.6... [10:57:53] 1496 peptides remaining for 670.6 to 672.6... [10:57:54] 1150 peptides remaining for 670.6 to 672.6... [10:57:54] 792 peptides remaining for 670.6 to 672.6... [10:57:55] 458 peptides remaining for 670.6 to 672.6... [10:57:55] 100 peptides remaining for 670.6 to 672.6... [10:57:56] Processing 672.6 to 674.6 m/z, (1.9633632 second duty cycle) [10:57:57] 5343 peptides remaining for 672.6 to 674.6... [10:57:58] 4993 peptides remaining for 672.6 to 674.6... [10:57:58] 4655 peptides remaining for 672.6 to 674.6... [10:57:59] 4320 peptides remaining for 672.6 to 674.6... [10:57:59] 3969 peptides remaining for 672.6 to 674.6... [10:58:00] 3623 peptides remaining for 672.6 to 674.6... [10:58:01] 3271 peptides remaining for 672.6 to 674.6... [10:58:01] 2914 peptides remaining for 672.6 to 674.6... [10:58:02] 2566 peptides remaining for 672.6 to 674.6... [10:58:02] 2213 peptides remaining for 672.6 to 674.6... [10:58:03] 1866 peptides remaining for 672.6 to 674.6... [10:58:03] 1519 peptides remaining for 672.6 to 674.6... [10:58:04] 1154 peptides remaining for 672.6 to 674.6... [10:58:04] 814 peptides remaining for 672.6 to 674.6... [10:58:05] 457 peptides remaining for 672.6 to 674.6... [10:58:05] 114 peptides remaining for 672.6 to 674.6... [10:58:06] Processing 674.6 to 676.6 m/z, (1.963385 second duty cycle) [10:58:07] 5347 peptides remaining for 674.6 to 676.6... [10:58:08] 4993 peptides remaining for 674.6 to 676.6... [10:58:08] 4634 peptides remaining for 674.6 to 676.6... [10:58:09] 4263 peptides remaining for 674.6 to 676.6... [10:58:09] 3911 peptides remaining for 674.6 to 676.6... [10:58:10] 3559 peptides remaining for 674.6 to 676.6... [10:58:11] 3210 peptides remaining for 674.6 to 676.6... [10:58:11] 2849 peptides remaining for 674.6 to 676.6... [10:58:12] 2494 peptides remaining for 674.6 to 676.6... [10:58:12] 2141 peptides remaining for 674.6 to 676.6... [10:58:13] 1784 peptides remaining for 674.6 to 676.6... [10:58:13] 1428 peptides remaining for 674.6 to 676.6... [10:58:14] 1081 peptides remaining for 674.6 to 676.6... [10:58:14] 739 peptides remaining for 674.6 to 676.6... [10:58:15] 395 peptides remaining for 674.6 to 676.6... [10:58:15] 38 peptides remaining for 674.6 to 676.6... [10:58:16] Processing 676.6 to 678.6 m/z, (1.9633634 second duty cycle) [10:58:17] 5147 peptides remaining for 676.6 to 678.6... [10:58:18] 4788 peptides remaining for 676.6 to 678.6... [10:58:18] 4420 peptides remaining for 676.6 to 678.6... [10:58:19] 4072 peptides remaining for 676.6 to 678.6... [10:58:19] 3727 peptides remaining for 676.6 to 678.6... [10:58:20] 3368 peptides remaining for 676.6 to 678.6... [10:58:21] 3029 peptides remaining for 676.6 to 678.6... [10:58:21] 2680 peptides remaining for 676.6 to 678.6... [10:58:22] 2314 peptides remaining for 676.6 to 678.6... [10:58:22] 1962 peptides remaining for 676.6 to 678.6... [10:58:23] 1611 peptides remaining for 676.6 to 678.6... [10:58:23] 1269 peptides remaining for 676.6 to 678.6... [10:58:24] 914 peptides remaining for 676.6 to 678.6... [10:58:24] 563 peptides remaining for 676.6 to 678.6... [10:58:25] 231 peptides remaining for 676.6 to 678.6... [10:58:25] Processing 678.6 to 680.6 m/z, (1.9633849 second duty cycle) [10:58:27] 5437 peptides remaining for 678.6 to 680.6... [10:58:27] 5071 peptides remaining for 678.6 to 680.6... [10:58:28] 4706 peptides remaining for 678.6 to 680.6... [10:58:28] 4366 peptides remaining for 678.6 to 680.6... [10:58:29] 3996 peptides remaining for 678.6 to 680.6... [10:58:29] 3643 peptides remaining for 678.6 to 680.6... [10:58:30] 3294 peptides remaining for 678.6 to 680.6... [10:58:30] 2934 peptides remaining for 678.6 to 680.6... [10:58:31] 2588 peptides remaining for 678.6 to 680.6... [10:58:31] 2227 peptides remaining for 678.6 to 680.6... [10:58:32] 1878 peptides remaining for 678.6 to 680.6... [10:58:33] 1532 peptides remaining for 678.6 to 680.6... [10:58:33] 1184 peptides remaining for 678.6 to 680.6... [10:58:34] 824 peptides remaining for 678.6 to 680.6... [10:58:34] 469 peptides remaining for 678.6 to 680.6... [10:58:35] 97 peptides remaining for 678.6 to 680.6... [10:58:35] Processing 680.6 to 682.6 m/z, (1.9633632 second duty cycle) [10:58:37] 5200 peptides remaining for 680.6 to 682.6... [10:58:38] 4841 peptides remaining for 680.6 to 682.6... [10:58:38] 4478 peptides remaining for 680.6 to 682.6... [10:58:39] 4136 peptides remaining for 680.6 to 682.6... [10:58:39] 3786 peptides remaining for 680.6 to 682.6... [10:58:40] 3435 peptides remaining for 680.6 to 682.6... [10:58:40] 3077 peptides remaining for 680.6 to 682.6... [10:58:41] 2739 peptides remaining for 680.6 to 682.6... [10:58:41] 2385 peptides remaining for 680.6 to 682.6... [10:58:42] 2043 peptides remaining for 680.6 to 682.6... [10:58:42] 1687 peptides remaining for 680.6 to 682.6... [10:58:43] 1326 peptides remaining for 680.6 to 682.6... [10:58:43] 971 peptides remaining for 680.6 to 682.6... [10:58:44] 627 peptides remaining for 680.6 to 682.6... [10:58:45] 267 peptides remaining for 680.6 to 682.6... [10:58:45] Processing 682.6 to 684.6 m/z, (1.9633851 second duty cycle) [10:58:47] 5073 peptides remaining for 682.6 to 684.6... [10:58:47] 4734 peptides remaining for 682.6 to 684.6... [10:58:48] 4371 peptides remaining for 682.6 to 684.6... [10:58:48] 4021 peptides remaining for 682.6 to 684.6... [10:58:49] 3692 peptides remaining for 682.6 to 684.6... [10:58:49] 3351 peptides remaining for 682.6 to 684.6... [10:58:50] 3010 peptides remaining for 682.6 to 684.6... [10:58:50] 2670 peptides remaining for 682.6 to 684.6... [10:58:51] 2333 peptides remaining for 682.6 to 684.6... [10:58:51] 2011 peptides remaining for 682.6 to 684.6... [10:58:52] 1669 peptides remaining for 682.6 to 684.6... [10:58:52] 1338 peptides remaining for 682.6 to 684.6... [10:58:53] 1014 peptides remaining for 682.6 to 684.6... [10:58:53] 670 peptides remaining for 682.6 to 684.6... [10:58:54] 324 peptides remaining for 682.6 to 684.6... [10:58:54] 0 peptides remaining for 682.6 to 684.6... [10:58:55] Processing 684.6 to 686.6 m/z, (1.9633635 second duty cycle) [10:58:57] 5052 peptides remaining for 684.6 to 686.6... [10:58:57] 4715 peptides remaining for 684.6 to 686.6... [10:58:58] 4351 peptides remaining for 684.6 to 686.6... [10:58:58] 4017 peptides remaining for 684.6 to 686.6... [10:58:59] 3683 peptides remaining for 684.6 to 686.6... [10:58:59] 3362 peptides remaining for 684.6 to 686.6... [10:59:00] 3030 peptides remaining for 684.6 to 686.6... [10:59:00] 2691 peptides remaining for 684.6 to 686.6... [10:59:01] 2360 peptides remaining for 684.6 to 686.6... [10:59:01] 2017 peptides remaining for 684.6 to 686.6... [10:59:02] 1686 peptides remaining for 684.6 to 686.6... [10:59:02] 1350 peptides remaining for 684.6 to 686.6... [10:59:03] 1020 peptides remaining for 684.6 to 686.6... [10:59:03] 690 peptides remaining for 684.6 to 686.6... [10:59:04] 350 peptides remaining for 684.6 to 686.6... [10:59:04] 25 peptides remaining for 684.6 to 686.6... [10:59:05] Processing 686.6 to 688.6 m/z, (1.9634743 second duty cycle) [10:59:07] 5307 peptides remaining for 686.6 to 688.6... [10:59:07] 4957 peptides remaining for 686.6 to 688.6... [10:59:08] 4612 peptides remaining for 686.6 to 688.6... [10:59:08] 4270 peptides remaining for 686.6 to 688.6... [10:59:09] 3925 peptides remaining for 686.6 to 688.6... [10:59:09] 3584 peptides remaining for 686.6 to 688.6... [10:59:10] 3241 peptides remaining for 686.6 to 688.6... [10:59:10] 2889 peptides remaining for 686.6 to 688.6... [10:59:11] 2556 peptides remaining for 686.6 to 688.6... [10:59:11] 2216 peptides remaining for 686.6 to 688.6... [10:59:12] 1854 peptides remaining for 686.6 to 688.6... [10:59:12] 1511 peptides remaining for 686.6 to 688.6... [10:59:13] 1170 peptides remaining for 686.6 to 688.6... [10:59:13] 829 peptides remaining for 686.6 to 688.6... [10:59:14] 493 peptides remaining for 686.6 to 688.6... [10:59:14] 150 peptides remaining for 686.6 to 688.6... [10:59:15] Processing 688.6 to 690.6 m/z, (1.9634527 second duty cycle) [10:59:17] 5119 peptides remaining for 688.6 to 690.6... [10:59:17] 4775 peptides remaining for 688.6 to 690.6... [10:59:18] 4426 peptides remaining for 688.6 to 690.6... [10:59:18] 4080 peptides remaining for 688.6 to 690.6... [10:59:19] 3750 peptides remaining for 688.6 to 690.6... [10:59:19] 3410 peptides remaining for 688.6 to 690.6... [10:59:20] 3059 peptides remaining for 688.6 to 690.6... [10:59:20] 2718 peptides remaining for 688.6 to 690.6... [10:59:21] 2363 peptides remaining for 688.6 to 690.6... [10:59:21] 2021 peptides remaining for 688.6 to 690.6... [10:59:22] 1667 peptides remaining for 688.6 to 690.6... [10:59:22] 1314 peptides remaining for 688.6 to 690.6... [10:59:23] 971 peptides remaining for 688.6 to 690.6... [10:59:23] 642 peptides remaining for 688.6 to 690.6... [10:59:24] 290 peptides remaining for 688.6 to 690.6... [10:59:24] Processing 690.6 to 692.6 m/z, (1.9634744 second duty cycle) [10:59:26] 5109 peptides remaining for 690.6 to 692.6... [10:59:27] 4767 peptides remaining for 690.6 to 692.6... [10:59:27] 4404 peptides remaining for 690.6 to 692.6... [10:59:28] 4067 peptides remaining for 690.6 to 692.6... [10:59:28] 3723 peptides remaining for 690.6 to 692.6... [10:59:29] 3392 peptides remaining for 690.6 to 692.6... [10:59:29] 3057 peptides remaining for 690.6 to 692.6... [10:59:30] 2720 peptides remaining for 690.6 to 692.6... [10:59:30] 2369 peptides remaining for 690.6 to 692.6... [10:59:31] 2018 peptides remaining for 690.6 to 692.6... [10:59:31] 1683 peptides remaining for 690.6 to 692.6... [10:59:32] 1346 peptides remaining for 690.6 to 692.6... [10:59:32] 996 peptides remaining for 690.6 to 692.6... [10:59:33] 666 peptides remaining for 690.6 to 692.6... [10:59:33] 343 peptides remaining for 690.6 to 692.6... [10:59:34] 22 peptides remaining for 690.6 to 692.6... [10:59:34] Processing 692.6 to 694.6 m/z, (1.9634527 second duty cycle) [10:59:36] 5163 peptides remaining for 692.6 to 694.6... [10:59:37] 4784 peptides remaining for 692.6 to 694.6... [10:59:37] 4434 peptides remaining for 692.6 to 694.6... [10:59:38] 4079 peptides remaining for 692.6 to 694.6... [10:59:38] 3722 peptides remaining for 692.6 to 694.6... [10:59:39] 3368 peptides remaining for 692.6 to 694.6... [10:59:39] 3000 peptides remaining for 692.6 to 694.6... [10:59:40] 2661 peptides remaining for 692.6 to 694.6... [10:59:40] 2330 peptides remaining for 692.6 to 694.6... [10:59:41] 1990 peptides remaining for 692.6 to 694.6... [10:59:41] 1632 peptides remaining for 692.6 to 694.6... [10:59:42] 1291 peptides remaining for 692.6 to 694.6... [10:59:42] 940 peptides remaining for 692.6 to 694.6... [10:59:43] 582 peptides remaining for 692.6 to 694.6... [10:59:43] 235 peptides remaining for 692.6 to 694.6... [10:59:44] Processing 694.6 to 696.6 m/z, (1.9634744 second duty cycle) [10:59:46] 5308 peptides remaining for 694.6 to 696.6... [10:59:46] 4958 peptides remaining for 694.6 to 696.6... [10:59:47] 4584 peptides remaining for 694.6 to 696.6... [10:59:47] 4232 peptides remaining for 694.6 to 696.6... [10:59:48] 3886 peptides remaining for 694.6 to 696.6... [10:59:48] 3545 peptides remaining for 694.6 to 696.6... [10:59:49] 3185 peptides remaining for 694.6 to 696.6... [10:59:49] 2845 peptides remaining for 694.6 to 696.6... [10:59:50] 2506 peptides remaining for 694.6 to 696.6... [10:59:50] 2148 peptides remaining for 694.6 to 696.6... [10:59:51] 1808 peptides remaining for 694.6 to 696.6... [10:59:51] 1464 peptides remaining for 694.6 to 696.6... [10:59:52] 1131 peptides remaining for 694.6 to 696.6... [10:59:52] 791 peptides remaining for 694.6 to 696.6... [10:59:53] 447 peptides remaining for 694.6 to 696.6... [10:59:53] 96 peptides remaining for 694.6 to 696.6... [10:59:54] Processing 696.6 to 698.6 m/z, (1.9634527 second duty cycle) [10:59:56] 4933 peptides remaining for 696.6 to 698.6... [10:59:56] 4582 peptides remaining for 696.6 to 698.6... [10:59:57] 4204 peptides remaining for 696.6 to 698.6... [10:59:57] 3841 peptides remaining for 696.6 to 698.6... [10:59:58] 3510 peptides remaining for 696.6 to 698.6... [10:59:58] 3170 peptides remaining for 696.6 to 698.6... [10:59:59] 2828 peptides remaining for 696.6 to 698.6... [10:59:59] 2486 peptides remaining for 696.6 to 698.6... [11:00:00] 2161 peptides remaining for 696.6 to 698.6... [11:00:00] 1813 peptides remaining for 696.6 to 698.6... [11:00:01] 1457 peptides remaining for 696.6 to 698.6... [11:00:01] 1110 peptides remaining for 696.6 to 698.6... [11:00:02] 746 peptides remaining for 696.6 to 698.6... [11:00:02] 409 peptides remaining for 696.6 to 698.6... [11:00:03] 65 peptides remaining for 696.6 to 698.6... [11:00:03] Processing 698.6 to 700.6 m/z, (1.9634744 second duty cycle) [11:00:05] 4973 peptides remaining for 698.6 to 700.6... [11:00:06] 4624 peptides remaining for 698.6 to 700.6... [11:00:06] 4275 peptides remaining for 698.6 to 700.6... [11:00:07] 3934 peptides remaining for 698.6 to 700.6... [11:00:07] 3599 peptides remaining for 698.6 to 700.6... [11:00:08] 3270 peptides remaining for 698.6 to 700.6... [11:00:08] 2920 peptides remaining for 698.6 to 700.6... [11:00:09] 2581 peptides remaining for 698.6 to 700.6... [11:00:09] 2227 peptides remaining for 698.6 to 700.6... [11:00:10] 1891 peptides remaining for 698.6 to 700.6... [11:00:10] 1536 peptides remaining for 698.6 to 700.6... [11:00:11] 1188 peptides remaining for 698.6 to 700.6... [11:00:11] 845 peptides remaining for 698.6 to 700.6... [11:00:12] 517 peptides remaining for 698.6 to 700.6... [11:00:12] 175 peptides remaining for 698.6 to 700.6... [11:00:13] Processing 700.6 to 702.6 m/z, (3.926695 second duty cycle) [11:00:14] 5002 peptides remaining for 700.6 to 702.6... [11:00:15] 4461 peptides remaining for 700.6 to 702.6... [11:00:15] 3929 peptides remaining for 700.6 to 702.6... [11:00:16] 3396 peptides remaining for 700.6 to 702.6... [11:00:16] 2865 peptides remaining for 700.6 to 702.6... [11:00:17] 2337 peptides remaining for 700.6 to 702.6... [11:00:18] 1819 peptides remaining for 700.6 to 702.6... [11:00:18] 1304 peptides remaining for 700.6 to 702.6... [11:00:19] 785 peptides remaining for 700.6 to 702.6... [11:00:19] 253 peptides remaining for 700.6 to 702.6... [11:00:20] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:00:42] Sorted feature file in 22.63 seconds wall clock time [11:00:42] File size check: 396257489 vs 396257489 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:00:42] 984687 total peptides processed. [11:00:42] Running Percolator... [11:00:42] Executing [cmd /c C:\Windows\Temp\tmp4FA1.java\Percolator-v3-01-7400196674017275906.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt] [11:00:43] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:00:43] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:00:43] Written by Lukas Käll (lukall@u.washington.edu) in the [11:00:43] Department of Genome Sciences at the University of Washington. [11:00:43] Issued command: [11:00:43] C:\Windows\Temp\tmp4FA1.java\Percolator-v3-01-7400196674017275906.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:00:43] Started Wed Jul 17 11:00:43 2024 [11:00:43] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [11:00:43] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:00:43] Features: [11:00:43] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:00:51] Found 984687 PSMs [11:00:51] Separate target and decoy search inputs detected, using mix-max method. [11:00:51] Train/test set contains 251139 positives and 248861 negatives, size ratio=1.00915 and pi0=1 [11:00:52] Selecting Cpos by cross-validation. [11:00:52] Selecting Cneg by cross-validation. [11:00:56] Split 1: Selected feature 2 as initial search direction. Could separate 2885 training set positives in that direction. [11:00:59] Split 2: Selected feature 2 as initial search direction. Could separate 2811 training set positives in that direction. [11:01:02] Split 3: Selected feature 22 as initial search direction. Could separate 2769 training set positives in that direction. [11:01:02] Found 4031 test set positives with q<0.01 in initial direction [11:01:02] Reading in data and feature calculation took 19.542 cpu seconds or 19 seconds wall clock time. [11:01:02] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:01:25] Iteration 1: Estimated 6962 PSMs with q<0.01 [11:01:50] Iteration 2: Estimated 7885 PSMs with q<0.01 [11:02:16] Iteration 3: Estimated 8119 PSMs with q<0.01 [11:02:16] Learned normalized SVM weights for the 3 cross-validation splits: [11:02:16] Split1 Split2 Split3 FeatureName [11:02:16] -0.6576 -0.3946 -0.4992 primary [11:02:16] 0.2074 0.1216 -0.1055 xCorrLib [11:02:16] 0.4615 0.3641 0.2976 xCorrModel [11:02:16] -0.1200 0.1111 0.3106 dotProduct [11:02:16] 1.6977 0.6311 0.7983 contrastAngle [11:02:16] -0.8704 0.0408 -0.3824 logit [11:02:16] 0.3607 0.3917 0.3527 sumOfSquaredErrors [11:02:16] 1.0721 0.6364 0.6145 numberOfMatchingPeaks [11:02:16] 0.1573 0.1381 0.1659 numberOfMatchingPeaksAboveThreshold [11:02:16] 0.0579 0.0242 0.0437 averageFragmentDeltaMasses [11:02:16] 0.1057 0.0636 0.0431 isotopeDotProduct [11:02:16] -0.0170 0.0087 0.0350 averageParentDeltaMass [11:02:16] -0.1311 -0.0581 -0.1377 percentBlankOverMono [11:02:16] 0.0030 0.0127 0.0044 numberPrecursorMatch [11:02:16] -1.3965 -0.8765 -0.7402 lnSp [11:02:16] 0.6358 0.4323 0.4727 maxLadderLength [11:02:16] 0.2160 0.0429 0.0896 evalue [11:02:16] -0.0066 0.0714 -0.0109 correlationToGaussian [11:02:16] 0.1489 0.0847 0.0658 correlationToPrecursor [11:02:16] -0.0802 -0.0191 -0.0677 isIntegratedSignal [11:02:16] -0.0447 -0.0029 0.0013 isIntegratedPrecursor [11:02:16] 0.6991 0.5029 0.6271 numPeaksWithGoodCorrelation [11:02:16] -0.5211 -0.3081 -0.4359 numMissedCleavage [11:02:16] -0.9824 -0.5439 -0.3634 pepLength [11:02:16] 0.0000 0.0000 0.0000 charge1 [11:02:16] -0.1007 -0.0816 -0.0899 charge2 [11:02:16] 0.1007 0.0816 0.0899 charge3 [11:02:16] 0.0000 0.0000 0.0000 charge4 [11:02:16] 0.1626 0.0298 0.0738 precursorMz [11:02:16] 0.0802 -0.0272 -0.1764 precursorMass [11:02:16] -0.1555 -0.0362 -0.0841 RTinMin [11:02:16] -4.7203 -3.7647 -3.6646 m0 [11:02:16] Found 6737 test set PSMs with q<0.01. [11:02:16] Scoring full list of PSMs with trained SVMs. [11:02:17] Features: [11:02:17] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:02:25] Found 984687 PSMs [11:02:25] Evaluated set contained 494275 positives and 490412 negatives. [11:02:27] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:02:29] Selecting pi_0=0.933267 [11:02:29] Calculating q values. [11:02:29] New pi_0 estimate on final list yields 15534 target peptides with q<0.01. [11:02:29] Calculating posterior error probabilities (PEPs). [11:02:31] Processing took 88.41 cpu seconds or 89 seconds wall clock time. [11:02:39] First pass: 15534 peptides identified at 1.0% FDR [11:02:40] Generating retention time mapping using 15534 points... [11:02:40] Enough data points (15534) to perform KDE alignment. [11:02:42] Enough data points (14748) to perform KDE alignment. [11:02:42] Enough data points (15534) to perform KDE alignment. [11:02:45] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:02:49] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:03:05] Sorted feature file in 16.21 seconds wall clock time [11:03:05] File size check: 304303355 vs 304303355 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:03:05] Executing [cmd /c C:\Windows\Temp\tmp4FA1.java\Percolator-v3-01-7990761881800238556.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt] [11:03:06] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:03:06] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:03:06] Written by Lukas Käll (lukall@u.washington.edu) in the [11:03:06] Department of Genome Sciences at the University of Washington. [11:03:06] Issued command: [11:03:06] C:\Windows\Temp\tmp4FA1.java\Percolator-v3-01-7990761881800238556.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:03:06] Started Wed Jul 17 11:03:06 2024 [11:03:06] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [11:03:06] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:03:06] Features: [11:03:06] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:03:12] Found 707513 PSMs [11:03:13] Separate target and decoy search inputs detected, using mix-max method. [11:03:13] Train/test set contains 247657 positives and 252343 negatives, size ratio=0.98143 and pi0=1 [11:03:14] Selecting Cpos by cross-validation. [11:03:14] Selecting Cneg by cross-validation. [11:03:17] Split 1: Selected feature 2 as initial search direction. Could separate 3924 training set positives in that direction. [11:03:21] Split 2: Selected feature 2 as initial search direction. Could separate 4080 training set positives in that direction. [11:03:24] Split 3: Selected feature 2 as initial search direction. Could separate 4143 training set positives in that direction. [11:03:25] Found 6037 test set positives with q<0.01 in initial direction [11:03:25] Reading in data and feature calculation took 18.939 cpu seconds or 19 seconds wall clock time. [11:03:25] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:03:53] Iteration 1: Estimated 9615 PSMs with q<0.01 [11:04:22] Iteration 2: Estimated 10603 PSMs with q<0.01 [11:04:52] Iteration 3: Estimated 10945 PSMs with q<0.01 [11:05:23] Iteration 4: Estimated 11065 PSMs with q<0.01 [11:05:53] Iteration 5: Estimated 11110 PSMs with q<0.01 [11:06:24] Iteration 6: Estimated 11100 PSMs with q<0.01 [11:06:54] Iteration 7: Estimated 11123 PSMs with q<0.01 [11:07:24] Iteration 8: Estimated 11136 PSMs with q<0.01 [11:07:55] Iteration 9: Estimated 11129 PSMs with q<0.01 [11:08:25] Iteration 10: Estimated 11143 PSMs with q<0.01 [11:08:25] Learned normalized SVM weights for the 3 cross-validation splits: [11:08:25] Split1 Split2 Split3 FeatureName [11:08:25] -0.7133 -0.8633 -0.5809 primary [11:08:25] -0.0962 0.0279 -0.1417 xCorrLib [11:08:25] 0.3985 0.3604 0.4627 xCorrModel [11:08:25] 0.8598 0.0843 0.4386 dotProduct [11:08:25] 1.2341 0.9612 1.2243 contrastAngle [11:08:25] -0.9759 -0.0055 -0.7125 logit [11:08:25] 0.4951 0.4436 0.3364 sumOfSquaredErrors [11:08:25] 1.0583 1.2913 0.9984 numberOfMatchingPeaks [11:08:25] 0.2811 0.1109 0.0627 numberOfMatchingPeaksAboveThreshold [11:08:25] -0.1608 -0.1013 -0.2304 averageFragmentDeltaMasses [11:08:25] -0.0270 -0.1467 0.1019 isotopeDotProduct [11:08:25] -0.1275 -0.1501 -0.0806 averageParentDeltaMass [11:08:25] -0.2146 -0.2530 -0.1519 percentBlankOverMono [11:08:25] 0.0221 0.1047 -0.0218 numberPrecursorMatch [11:08:25] -1.2216 -1.0505 -1.1449 lnSp [11:08:25] 0.7829 0.6680 0.6816 maxLadderLength [11:08:25] 0.3402 0.2435 0.3161 evalue [11:08:25] 0.2001 0.3383 0.4384 correlationToGaussian [11:08:25] 0.0211 -0.0612 0.0904 correlationToPrecursor [11:08:25] 0.1074 0.0161 0.0889 isIntegratedSignal [11:08:25] -0.0257 0.0145 -0.0432 isIntegratedPrecursor [11:08:25] 0.7961 0.7352 0.8167 numPeaksWithGoodCorrelation [11:08:25] 0.0232 0.0455 -0.0220 deltaRT [11:08:25] -0.2102 -0.2322 -0.1423 ms1MassError [11:08:25] -0.3360 -0.3113 -0.3489 ms2MassError [11:08:25] -0.8291 -0.7681 -0.8510 numMissedCleavage [11:08:25] -1.0118 -1.0430 -0.8980 pepLength [11:08:25] 0.0000 0.0000 0.0000 charge1 [11:08:25] -0.0029 0.0099 -0.0917 charge2 [11:08:25] 0.0029 -0.0099 0.0917 charge3 [11:08:25] 0.0000 0.0000 0.0000 charge4 [11:08:25] 0.1195 0.0633 0.0891 precursorMz [11:08:25] 0.4255 0.5497 0.2129 precursorMass [11:08:25] -0.1509 -0.1039 -0.1802 RTinMin [11:08:25] -5.6117 -5.4868 -5.4637 m0 [11:08:26] Found 10850 test set PSMs with q<0.01. [11:08:26] Scoring full list of PSMs with trained SVMs. [11:08:26] Features: [11:08:26] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:08:33] Found 707513 PSMs [11:08:33] Evaluated set contained 350471 positives and 357042 negatives. [11:08:35] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:08:37] Selecting pi_0=0.938075 [11:08:37] Calculating q values. [11:08:37] New pi_0 estimate on final list yields 15830 target peptides with q<0.01. [11:08:37] Calculating posterior error probabilities (PEPs). [11:08:38] Processing took 313.8 cpu seconds or 313 seconds wall clock time. [11:08:49] Generating retention time mapping using 15830 points... [11:08:49] Enough data points (15830) to perform KDE alignment. [11:08:51] Enough data points (15058) to perform KDE alignment. [11:08:51] Enough data points (15830) to perform KDE alignment. [11:08:53] Writing elib result library... [11:08:53] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 15830 vs local peptides: 15830 [11:08:53] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML... [11:08:53] Extracting Spectral Data for 15830 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML... [11:08:53] Number of global peptides: 15830 vs local peptides: 15830 [11:08:56] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [11:08:56] Parsed features and scores for 15830 peptides. [11:08:56] Extracting 15830 peptides... [11:08:56] Quant Extracting 598.5 to 600.5 m/z (7.303168 to 94.448555 min) [11:08:56] Quant Extracting 600.5 to 602.5 m/z (7.1413045 to 94.90519 min) [11:08:56] Quant Extracting 602.5 to 604.5 m/z (8.882516 to 97.766945 min) [11:08:56] Quant Extracting 604.5 to 606.5 m/z (7.7750425 to 97.0411 min) [11:08:56] Quant Extracting 606.5 to 608.5 m/z (7.14245 to 98.758255 min) [11:08:57] Quant Extracting 608.5 to 610.5 m/z (7.143613 to 96.348946 min) [11:08:57] Quant Extracting 610.5 to 612.5 m/z (7.143613 to 93.79904 min) [11:08:57] Quant Extracting 612.5 to 614.5 m/z (7.644376 to 95.69468 min) [11:08:57] Quant Extracting 614.5 to 616.5 m/z (7.144763 to 99.73087 min) [11:08:57] Quant Extracting 616.5 to 618.5 m/z (7.1459146 to 97.93661 min) [11:08:57] Quant Extracting 618.5 to 620.5 m/z (7.1459146 to 96.68429 min) [11:08:57] Quant Extracting 620.5 to 622.5 m/z (12.372965 to 96.156265 min) [11:08:58] Quant Extracting 622.5 to 624.5 m/z (9.088123 to 93.50985 min) [11:08:58] Quant Extracting 624.5 to 626.5 m/z (7.1482177 to 93.64097 min) [11:08:58] Quant Extracting 626.5 to 628.5 m/z (7.1482177 to 92.082184 min) [11:08:58] Quant Extracting 628.5 to 630.5 m/z (7.1493692 to 99.84212 min) [11:08:58] Quant Extracting 630.5 to 632.5 m/z (7.1493692 to 94.13105 min) [11:08:58] Quant Extracting 632.5 to 634.5 m/z (7.150521 to 97.37867 min) [11:08:58] Quant Extracting 634.5 to 636.5 m/z (10.45854 to 96.061485 min) [11:08:58] Quant Extracting 636.5 to 638.5 m/z (7.151667 to 92.83033 min) [11:08:58] Quant Extracting 638.5 to 640.5 m/z (7.151667 to 95.407845 min) [11:08:59] Quant Extracting 640.5 to 642.5 m/z (7.187245 to 96.85461 min) [11:08:59] Quant Extracting 642.5 to 644.5 m/z (15.372149 to 92.50853 min) [11:08:59] Quant Extracting 644.5 to 646.5 m/z (7.886121 to 95.442276 min) [11:08:59] Quant Extracting 646.5 to 648.5 m/z (9.323615 to 97.1837 min) [11:08:59] Quant Extracting 648.5 to 650.5 m/z (11.049104 to 97.983 min) [11:08:59] Quant Extracting 650.5 to 652.5 m/z (7.157914 to 96.20105 min) [11:08:59] Quant Extracting 652.5 to 654.5 m/z (7.1590605 to 95.706215 min) [11:08:59] Quant Extracting 654.5 to 656.5 m/z (7.1590605 to 98.24793 min) [11:08:59] Quant Extracting 656.5 to 658.5 m/z (12.609829 to 95.1534 min) [11:08:59] Quant Extracting 658.5 to 660.6 m/z (7.1930075 to 97.31936 min) [11:08:59] Quant Extracting 660.6 to 662.6 m/z (7.1930075 to 96.69581 min) [11:08:59] Quant Extracting 662.6 to 664.6 m/z (15.766329 to 96.56555 min) [11:09:00] Quant Extracting 664.6 to 666.6 m/z (7.1625032 to 95.05735 min) [11:09:00] Quant Extracting 666.6 to 668.6 m/z (10.69729 to 96.140144 min) [11:09:00] Quant Extracting 668.6 to 670.6 m/z (7.1636534 to 96.50121 min) [11:09:00] Quant Extracting 670.6 to 672.6 m/z (10.66656 to 95.84699 min) [11:09:00] Quant Extracting 672.6 to 674.6 m/z (11.348186 to 96.04302 min) [11:09:00] Quant Extracting 674.6 to 676.6 m/z (7.1648 to 96.86382 min) [11:09:00] Quant Extracting 676.6 to 678.6 m/z (11.48184 to 100.74897 min) [11:09:00] Quant Extracting 678.6 to 680.6 m/z (9.956067 to 100.74897 min) [11:09:00] Quant Extracting 680.6 to 682.6 m/z (9.4645605 to 97.36254 min) [11:09:00] Quant Extracting 682.6 to 684.6 m/z (16.455542 to 99.583855 min) [11:09:00] Quant Extracting 684.6 to 686.6 m/z (8.61642 to 100.75127 min) [11:09:01] Quant Extracting 686.6 to 688.6 m/z (7.1682534 to 99.89301 min) [11:09:01] Quant Extracting 688.6 to 690.6 m/z (11.028763 to 98.19213 min) [11:09:01] Quant Extracting 690.6 to 692.6 m/z (7.1694 to 95.81942 min) [11:09:01] Quant Extracting 692.6 to 694.6 m/z (7.1705446 to 100.753586 min) [11:09:01] Quant Extracting 694.6 to 696.6 m/z (7.1705446 to 96.57478 min) [11:09:01] Quant Extracting 696.6 to 698.6 m/z (7.3020163 to 99.96364 min) [11:09:01] Quant Extracting 698.6 to 700.6 m/z (11.811245 to 98.689735 min) [11:09:01] Quant Extracting 700.6 to 702.6 m/z (7.140152 to 99.287445 min) [11:09:01] Attempted extraction for: 15830, found 15830 [11:09:01] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML (15830 entries)... [11:09:01] Writing 15830 peptides to entries table... [11:09:03] Writing 15830 peptides to peptidequants table... [11:09:05] Finished writing to Encyclopedia ELIB at Wed Jul 17 11:09:05 BST 2024 [11:09:06] Writing local target/decoy peptides: 15830/165, pi0: 0.938075 [11:09:06] Writing local target/decoy proteins: 4966/49 [11:09:08] Finished analysis! 15830 peptides identified at 1.0% FDR (17.3 minutes) [11:09:08] Generating chromatogram library (4 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [11:09:12] EncyclopeDIA version 2.12.30 [11:09:13] Getting count of protein accessions... [11:09:13] Using EncyclopeDIA 2.X Scoring System [11:09:13] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML ... [11:09:13] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML ... 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[11:11:52] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.dia! [11:11:52] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML [11:11:52] Library File: UP000005640_9606-z3_nce27-prosit.dlib [11:11:52] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.elib [11:11:52] Parameters: [11:11:52] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [11:11:52] Converting files... [11:11:52] Calculating features... [11:11:52] Processing precursors scans... [11:11:52] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:11:52] Processing 698.6 to 700.6 m/z, (3.933251 second duty cycle) [11:11:55] 4763 peptides remaining for 698.6 to 700.6... [11:11:55] 4359 peptides remaining for 698.6 to 700.6... [11:11:56] 3902 peptides remaining for 698.6 to 700.6... [11:11:56] 3452 peptides remaining for 698.6 to 700.6... [11:11:57] 3006 peptides remaining for 698.6 to 700.6... [11:11:57] 2558 peptides remaining for 698.6 to 700.6... [11:11:58] 2100 peptides remaining for 698.6 to 700.6... [11:11:58] 1642 peptides remaining for 698.6 to 700.6... [11:11:59] 1154 peptides remaining for 698.6 to 700.6... [11:11:59] 696 peptides remaining for 698.6 to 700.6... [11:12:00] 230 peptides remaining for 698.6 to 700.6... [11:12:00] Processing 700.6 to 702.6 m/z, (1.9666405 second duty cycle) [11:12:02] 4937 peptides remaining for 700.6 to 702.6... [11:12:03] 4608 peptides remaining for 700.6 to 702.6... [11:12:03] 4274 peptides remaining for 700.6 to 702.6... [11:12:04] 3945 peptides remaining for 700.6 to 702.6... [11:12:04] 3619 peptides remaining for 700.6 to 702.6... [11:12:05] 3304 peptides remaining for 700.6 to 702.6... [11:12:05] 2968 peptides remaining for 700.6 to 702.6... [11:12:06] 2658 peptides remaining for 700.6 to 702.6... [11:12:06] 2341 peptides remaining for 700.6 to 702.6... [11:12:07] 2024 peptides remaining for 700.6 to 702.6... [11:12:07] 1714 peptides remaining for 700.6 to 702.6... [11:12:08] 1390 peptides remaining for 700.6 to 702.6... [11:12:09] 1075 peptides remaining for 700.6 to 702.6... [11:12:09] 740 peptides remaining for 700.6 to 702.6... [11:12:10] 409 peptides remaining for 700.6 to 702.6... [11:12:10] 67 peptides remaining for 700.6 to 702.6... [11:12:11] Processing 702.6 to 704.6 m/z, (1.9666623 second duty cycle) [11:12:12] 4963 peptides remaining for 702.6 to 704.6... [11:12:13] 4647 peptides remaining for 702.6 to 704.6... [11:12:13] 4321 peptides remaining for 702.6 to 704.6... [11:12:14] 4016 peptides remaining for 702.6 to 704.6... [11:12:14] 3706 peptides remaining for 702.6 to 704.6... [11:12:15] 3416 peptides remaining for 702.6 to 704.6... [11:12:15] 3099 peptides remaining for 702.6 to 704.6... [11:12:16] 2780 peptides remaining for 702.6 to 704.6... [11:12:16] 2468 peptides remaining for 702.6 to 704.6... [11:12:17] 2152 peptides remaining for 702.6 to 704.6... [11:12:17] 1829 peptides remaining for 702.6 to 704.6... [11:12:18] 1511 peptides remaining for 702.6 to 704.6... [11:12:18] 1200 peptides remaining for 702.6 to 704.6... [11:12:19] 895 peptides remaining for 702.6 to 704.6... [11:12:20] 564 peptides remaining for 702.6 to 704.6... [11:12:20] 242 peptides remaining for 702.6 to 704.6... [11:12:21] Processing 704.6 to 706.6 m/z, (1.9666408 second duty cycle) [11:12:22] 4884 peptides remaining for 704.6 to 706.6... [11:12:23] 4555 peptides remaining for 704.6 to 706.6... [11:12:23] 4243 peptides remaining for 704.6 to 706.6... [11:12:24] 3931 peptides remaining for 704.6 to 706.6... [11:12:24] 3618 peptides remaining for 704.6 to 706.6... [11:12:25] 3304 peptides remaining for 704.6 to 706.6... [11:12:25] 2993 peptides remaining for 704.6 to 706.6... [11:12:26] 2683 peptides remaining for 704.6 to 706.6... [11:12:26] 2373 peptides remaining for 704.6 to 706.6... [11:12:27] 2048 peptides remaining for 704.6 to 706.6... [11:12:27] 1707 peptides remaining for 704.6 to 706.6... [11:12:28] 1399 peptides remaining for 704.6 to 706.6... [11:12:28] 1087 peptides remaining for 704.6 to 706.6... [11:12:29] 776 peptides remaining for 704.6 to 706.6... [11:12:29] 482 peptides remaining for 704.6 to 706.6... [11:12:30] 154 peptides remaining for 704.6 to 706.6... [11:12:30] Processing 706.6 to 708.6 m/z, (1.9666624 second duty cycle) [11:12:32] 4937 peptides remaining for 706.6 to 708.6... [11:12:33] 4625 peptides remaining for 706.6 to 708.6... [11:12:33] 4290 peptides remaining for 706.6 to 708.6... [11:12:34] 3971 peptides remaining for 706.6 to 708.6... [11:12:34] 3658 peptides remaining for 706.6 to 708.6... [11:12:35] 3348 peptides remaining for 706.6 to 708.6... [11:12:35] 3045 peptides remaining for 706.6 to 708.6... [11:12:36] 2777 peptides remaining for 706.6 to 708.6... [11:12:36] 2475 peptides remaining for 706.6 to 708.6... [11:12:37] 2150 peptides remaining for 706.6 to 708.6... [11:12:37] 1848 peptides remaining for 706.6 to 708.6... [11:12:38] 1543 peptides remaining for 706.6 to 708.6... [11:12:38] 1249 peptides remaining for 706.6 to 708.6... [11:12:39] 936 peptides remaining for 706.6 to 708.6... [11:12:39] 630 peptides remaining for 706.6 to 708.6... [11:12:40] 311 peptides remaining for 706.6 to 708.6... [11:12:40] 0 peptides remaining for 706.6 to 708.6... [11:12:41] Processing 708.6 to 710.6 m/z, (1.9666406 second duty cycle) [11:12:43] 5003 peptides remaining for 708.6 to 710.6... [11:12:43] 4676 peptides remaining for 708.6 to 710.6... [11:12:44] 4352 peptides remaining for 708.6 to 710.6... [11:12:44] 4027 peptides remaining for 708.6 to 710.6... [11:12:45] 3700 peptides remaining for 708.6 to 710.6... [11:12:45] 3391 peptides remaining for 708.6 to 710.6... [11:12:46] 3097 peptides remaining for 708.6 to 710.6... [11:12:46] 2778 peptides remaining for 708.6 to 710.6... [11:12:47] 2470 peptides remaining for 708.6 to 710.6... [11:12:47] 2140 peptides remaining for 708.6 to 710.6... [11:12:48] 1821 peptides remaining for 708.6 to 710.6... [11:12:48] 1493 peptides remaining for 708.6 to 710.6... [11:12:49] 1176 peptides remaining for 708.6 to 710.6... [11:12:49] 853 peptides remaining for 708.6 to 710.6... [11:12:50] 530 peptides remaining for 708.6 to 710.6... [11:12:50] 202 peptides remaining for 708.6 to 710.6... [11:12:51] Processing 710.6 to 712.6 m/z, (1.9666623 second duty cycle) [11:12:53] 4877 peptides remaining for 710.6 to 712.6... [11:12:53] 4554 peptides remaining for 710.6 to 712.6... [11:12:54] 4228 peptides remaining for 710.6 to 712.6... [11:12:54] 3904 peptides remaining for 710.6 to 712.6... [11:12:55] 3596 peptides remaining for 710.6 to 712.6... [11:12:55] 3283 peptides remaining for 710.6 to 712.6... [11:12:56] 2974 peptides remaining for 710.6 to 712.6... [11:12:56] 2665 peptides remaining for 710.6 to 712.6... [11:12:57] 2362 peptides remaining for 710.6 to 712.6... [11:12:57] 2057 peptides remaining for 710.6 to 712.6... [11:12:58] 1742 peptides remaining for 710.6 to 712.6... [11:12:58] 1422 peptides remaining for 710.6 to 712.6... [11:12:59] 1113 peptides remaining for 710.6 to 712.6... [11:12:59] 808 peptides remaining for 710.6 to 712.6... [11:13:00] 499 peptides remaining for 710.6 to 712.6... [11:13:00] 169 peptides remaining for 710.6 to 712.6... [11:13:01] Processing 712.6 to 714.6 m/z, (1.9666408 second duty cycle) [11:13:03] 4906 peptides remaining for 712.6 to 714.6... [11:13:03] 4575 peptides remaining for 712.6 to 714.6... [11:13:04] 4252 peptides remaining for 712.6 to 714.6... [11:13:04] 3934 peptides remaining for 712.6 to 714.6... [11:13:05] 3620 peptides remaining for 712.6 to 714.6... [11:13:05] 3323 peptides remaining for 712.6 to 714.6... [11:13:06] 3003 peptides remaining for 712.6 to 714.6... [11:13:06] 2686 peptides remaining for 712.6 to 714.6... [11:13:07] 2384 peptides remaining for 712.6 to 714.6... [11:13:07] 2074 peptides remaining for 712.6 to 714.6... [11:13:08] 1759 peptides remaining for 712.6 to 714.6... [11:13:08] 1469 peptides remaining for 712.6 to 714.6... [11:13:09] 1159 peptides remaining for 712.6 to 714.6... [11:13:09] 841 peptides remaining for 712.6 to 714.6... [11:13:10] 523 peptides remaining for 712.6 to 714.6... [11:13:10] 203 peptides remaining for 712.6 to 714.6... [11:13:11] Processing 714.6 to 716.6 m/z, (1.9666622 second duty cycle) [11:13:13] 5096 peptides remaining for 714.6 to 716.6... [11:13:13] 4782 peptides remaining for 714.6 to 716.6... [11:13:14] 4452 peptides remaining for 714.6 to 716.6... [11:13:14] 4146 peptides remaining for 714.6 to 716.6... [11:13:15] 3830 peptides remaining for 714.6 to 716.6... [11:13:15] 3531 peptides remaining for 714.6 to 716.6... [11:13:16] 3223 peptides remaining for 714.6 to 716.6... [11:13:16] 2922 peptides remaining for 714.6 to 716.6... [11:13:17] 2633 peptides remaining for 714.6 to 716.6... [11:13:17] 2359 peptides remaining for 714.6 to 716.6... [11:13:18] 2031 peptides remaining for 714.6 to 716.6... [11:13:18] 1735 peptides remaining for 714.6 to 716.6... [11:13:19] 1431 peptides remaining for 714.6 to 716.6... [11:13:19] 1146 peptides remaining for 714.6 to 716.6... [11:13:20] 826 peptides remaining for 714.6 to 716.6... [11:13:20] 526 peptides remaining for 714.6 to 716.6... [11:13:21] 216 peptides remaining for 714.6 to 716.6... [11:13:21] Processing 716.6 to 718.6 m/z, (1.9666408 second duty cycle) [11:13:23] 4825 peptides remaining for 716.6 to 718.6... [11:13:23] 4503 peptides remaining for 716.6 to 718.6... [11:13:24] 4181 peptides remaining for 716.6 to 718.6... [11:13:25] 3880 peptides remaining for 716.6 to 718.6... [11:13:25] 3580 peptides remaining for 716.6 to 718.6... [11:13:26] 3289 peptides remaining for 716.6 to 718.6... [11:13:26] 2979 peptides remaining for 716.6 to 718.6... [11:13:27] 2670 peptides remaining for 716.6 to 718.6... [11:13:27] 2380 peptides remaining for 716.6 to 718.6... [11:13:28] 2084 peptides remaining for 716.6 to 718.6... [11:13:28] 1780 peptides remaining for 716.6 to 718.6... [11:13:29] 1473 peptides remaining for 716.6 to 718.6... [11:13:29] 1153 peptides remaining for 716.6 to 718.6... [11:13:30] 853 peptides remaining for 716.6 to 718.6... [11:13:30] 543 peptides remaining for 716.6 to 718.6... [11:13:31] 231 peptides remaining for 716.6 to 718.6... [11:13:31] Processing 718.6 to 720.6 m/z, (1.9666624 second duty cycle) [11:13:33] 4786 peptides remaining for 718.6 to 720.6... [11:13:33] 4464 peptides remaining for 718.6 to 720.6... [11:13:34] 4144 peptides remaining for 718.6 to 720.6... [11:13:34] 3835 peptides remaining for 718.6 to 720.6... [11:13:35] 3530 peptides remaining for 718.6 to 720.6... [11:13:35] 3239 peptides remaining for 718.6 to 720.6... [11:13:36] 2929 peptides remaining for 718.6 to 720.6... [11:13:37] 2614 peptides remaining for 718.6 to 720.6... [11:13:37] 2313 peptides remaining for 718.6 to 720.6... [11:13:38] 1989 peptides remaining for 718.6 to 720.6... [11:13:38] 1677 peptides remaining for 718.6 to 720.6... [11:13:39] 1383 peptides remaining for 718.6 to 720.6... [11:13:39] 1061 peptides remaining for 718.6 to 720.6... [11:13:40] 763 peptides remaining for 718.6 to 720.6... [11:13:40] 451 peptides remaining for 718.6 to 720.6... [11:13:41] 151 peptides remaining for 718.6 to 720.6... [11:13:41] Processing 720.6 to 722.6 m/z, (1.966641 second duty cycle) [11:13:43] 4867 peptides remaining for 720.6 to 722.6... [11:13:43] 4559 peptides remaining for 720.6 to 722.6... [11:13:44] 4235 peptides remaining for 720.6 to 722.6... [11:13:44] 3937 peptides remaining for 720.6 to 722.6... [11:13:45] 3634 peptides remaining for 720.6 to 722.6... [11:13:45] 3326 peptides remaining for 720.6 to 722.6... [11:13:46] 3026 peptides remaining for 720.6 to 722.6... [11:13:46] 2715 peptides remaining for 720.6 to 722.6... [11:13:47] 2425 peptides remaining for 720.6 to 722.6... [11:13:47] 2133 peptides remaining for 720.6 to 722.6... [11:13:48] 1850 peptides remaining for 720.6 to 722.6... [11:13:48] 1555 peptides remaining for 720.6 to 722.6... [11:13:49] 1255 peptides remaining for 720.6 to 722.6... [11:13:50] 954 peptides remaining for 720.6 to 722.6... [11:13:50] 655 peptides remaining for 720.6 to 722.6... [11:13:51] 356 peptides remaining for 720.6 to 722.6... [11:13:51] 43 peptides remaining for 720.6 to 722.6... [11:13:52] Processing 722.6 to 724.6 m/z, (1.9666624 second duty cycle) [11:13:53] 4952 peptides remaining for 722.6 to 724.6... [11:13:54] 4643 peptides remaining for 722.6 to 724.6... [11:13:54] 4328 peptides remaining for 722.6 to 724.6... [11:13:55] 4019 peptides remaining for 722.6 to 724.6... [11:13:55] 3718 peptides remaining for 722.6 to 724.6... [11:13:56] 3430 peptides remaining for 722.6 to 724.6... [11:13:56] 3118 peptides remaining for 722.6 to 724.6... [11:13:57] 2805 peptides remaining for 722.6 to 724.6... [11:13:57] 2503 peptides remaining for 722.6 to 724.6... [11:13:58] 2213 peptides remaining for 722.6 to 724.6... [11:13:58] 1921 peptides remaining for 722.6 to 724.6... [11:13:59] 1614 peptides remaining for 722.6 to 724.6... [11:13:59] 1308 peptides remaining for 722.6 to 724.6... [11:14:00] 1015 peptides remaining for 722.6 to 724.6... [11:14:00] 720 peptides remaining for 722.6 to 724.6... [11:14:01] 418 peptides remaining for 722.6 to 724.6... [11:14:01] 100 peptides remaining for 722.6 to 724.6... [11:14:02] Processing 724.6 to 726.6 m/z, (1.9666408 second duty cycle) [11:14:04] 4934 peptides remaining for 724.6 to 726.6... [11:14:04] 4619 peptides remaining for 724.6 to 726.6... [11:14:05] 4304 peptides remaining for 724.6 to 726.6... [11:14:05] 3996 peptides remaining for 724.6 to 726.6... [11:14:06] 3693 peptides remaining for 724.6 to 726.6... [11:14:06] 3398 peptides remaining for 724.6 to 726.6... [11:14:07] 3103 peptides remaining for 724.6 to 726.6... [11:14:07] 2798 peptides remaining for 724.6 to 726.6... [11:14:08] 2506 peptides remaining for 724.6 to 726.6... [11:14:08] 2209 peptides remaining for 724.6 to 726.6... [11:14:09] 1920 peptides remaining for 724.6 to 726.6... [11:14:09] 1611 peptides remaining for 724.6 to 726.6... [11:14:10] 1316 peptides remaining for 724.6 to 726.6... [11:14:10] 1005 peptides remaining for 724.6 to 726.6... [11:14:11] 707 peptides remaining for 724.6 to 726.6... [11:14:12] 386 peptides remaining for 724.6 to 726.6... [11:14:12] 87 peptides remaining for 724.6 to 726.6... [11:14:13] Processing 726.6 to 728.6 m/z, (1.9666623 second duty cycle) [11:14:14] 4724 peptides remaining for 726.6 to 728.6... [11:14:15] 4411 peptides remaining for 726.6 to 728.6... [11:14:15] 4109 peptides remaining for 726.6 to 728.6... [11:14:16] 3799 peptides remaining for 726.6 to 728.6... [11:14:16] 3495 peptides remaining for 726.6 to 728.6... [11:14:17] 3192 peptides remaining for 726.6 to 728.6... [11:14:17] 2895 peptides remaining for 726.6 to 728.6... [11:14:18] 2592 peptides remaining for 726.6 to 728.6... [11:14:18] 2305 peptides remaining for 726.6 to 728.6... [11:14:19] 2027 peptides remaining for 726.6 to 728.6... [11:14:19] 1723 peptides remaining for 726.6 to 728.6... [11:14:20] 1426 peptides remaining for 726.6 to 728.6... [11:14:20] 1118 peptides remaining for 726.6 to 728.6... [11:14:21] 827 peptides remaining for 726.6 to 728.6... [11:14:21] 523 peptides remaining for 726.6 to 728.6... [11:14:22] 214 peptides remaining for 726.6 to 728.6... [11:14:23] Processing 728.6 to 730.6 m/z, (1.9666408 second duty cycle) [11:14:24] 4936 peptides remaining for 728.6 to 730.6... [11:14:25] 4633 peptides remaining for 728.6 to 730.6... [11:14:25] 4320 peptides remaining for 728.6 to 730.6... [11:14:26] 4021 peptides remaining for 728.6 to 730.6... [11:14:26] 3724 peptides remaining for 728.6 to 730.6... [11:14:27] 3430 peptides remaining for 728.6 to 730.6... [11:14:27] 3135 peptides remaining for 728.6 to 730.6... [11:14:28] 2831 peptides remaining for 728.6 to 730.6... [11:14:28] 2538 peptides remaining for 728.6 to 730.6... [11:14:29] 2240 peptides remaining for 728.6 to 730.6... [11:14:29] 1947 peptides remaining for 728.6 to 730.6... [11:14:30] 1658 peptides remaining for 728.6 to 730.6... [11:14:30] 1340 peptides remaining for 728.6 to 730.6... [11:14:31] 1035 peptides remaining for 728.6 to 730.6... [11:14:31] 721 peptides remaining for 728.6 to 730.6... [11:14:32] 410 peptides remaining for 728.6 to 730.6... [11:14:32] 76 peptides remaining for 728.6 to 730.6... [11:14:33] Processing 730.6 to 732.6 m/z, (1.9666625 second duty cycle) [11:14:34] 4823 peptides remaining for 730.6 to 732.6... [11:14:35] 4521 peptides remaining for 730.6 to 732.6... [11:14:36] 4201 peptides remaining for 730.6 to 732.6... [11:14:36] 3899 peptides remaining for 730.6 to 732.6... [11:14:37] 3602 peptides remaining for 730.6 to 732.6... [11:14:37] 3305 peptides remaining for 730.6 to 732.6... [11:14:38] 3010 peptides remaining for 730.6 to 732.6... [11:14:38] 2695 peptides remaining for 730.6 to 732.6... [11:14:39] 2393 peptides remaining for 730.6 to 732.6... [11:14:39] 2089 peptides remaining for 730.6 to 732.6... [11:14:40] 1772 peptides remaining for 730.6 to 732.6... [11:14:40] 1490 peptides remaining for 730.6 to 732.6... [11:14:41] 1176 peptides remaining for 730.6 to 732.6... [11:14:41] 883 peptides remaining for 730.6 to 732.6... [11:14:42] 581 peptides remaining for 730.6 to 732.6... [11:14:42] 256 peptides remaining for 730.6 to 732.6... [11:14:43] Processing 732.6 to 734.6 m/z, (1.9666408 second duty cycle) [11:14:44] 4591 peptides remaining for 732.6 to 734.6... [11:14:45] 4273 peptides remaining for 732.6 to 734.6... [11:14:45] 3952 peptides remaining for 732.6 to 734.6... [11:14:46] 3653 peptides remaining for 732.6 to 734.6... [11:14:46] 3371 peptides remaining for 732.6 to 734.6... [11:14:47] 3078 peptides remaining for 732.6 to 734.6... [11:14:47] 2776 peptides remaining for 732.6 to 734.6... [11:14:48] 2459 peptides remaining for 732.6 to 734.6... [11:14:48] 2158 peptides remaining for 732.6 to 734.6... [11:14:49] 1854 peptides remaining for 732.6 to 734.6... [11:14:49] 1535 peptides remaining for 732.6 to 734.6... [11:14:50] 1227 peptides remaining for 732.6 to 734.6... [11:14:51] 936 peptides remaining for 732.6 to 734.6... [11:14:51] 635 peptides remaining for 732.6 to 734.6... [11:14:52] 331 peptides remaining for 732.6 to 734.6... [11:14:52] 25 peptides remaining for 732.6 to 734.6... [11:14:53] Processing 734.6 to 736.6 m/z, (1.9666623 second duty cycle) [11:14:54] 4730 peptides remaining for 734.6 to 736.6... [11:14:55] 4407 peptides remaining for 734.6 to 736.6... [11:14:55] 4089 peptides remaining for 734.6 to 736.6... [11:14:56] 3786 peptides remaining for 734.6 to 736.6... [11:14:56] 3493 peptides remaining for 734.6 to 736.6... [11:14:57] 3176 peptides remaining for 734.6 to 736.6... [11:14:57] 2875 peptides remaining for 734.6 to 736.6... [11:14:58] 2576 peptides remaining for 734.6 to 736.6... [11:14:58] 2269 peptides remaining for 734.6 to 736.6... [11:14:59] 1965 peptides remaining for 734.6 to 736.6... [11:14:59] 1653 peptides remaining for 734.6 to 736.6... [11:15:00] 1352 peptides remaining for 734.6 to 736.6... [11:15:00] 1041 peptides remaining for 734.6 to 736.6... [11:15:01] 732 peptides remaining for 734.6 to 736.6... [11:15:01] 428 peptides remaining for 734.6 to 736.6... [11:15:02] 111 peptides remaining for 734.6 to 736.6... [11:15:02] Processing 736.6 to 738.6 m/z, (1.9666406 second duty cycle) [11:15:04] 4765 peptides remaining for 736.6 to 738.6... [11:15:05] 4460 peptides remaining for 736.6 to 738.6... [11:15:05] 4148 peptides remaining for 736.6 to 738.6... [11:15:06] 3850 peptides remaining for 736.6 to 738.6... [11:15:06] 3562 peptides remaining for 736.6 to 738.6... [11:15:07] 3271 peptides remaining for 736.6 to 738.6... [11:15:07] 2975 peptides remaining for 736.6 to 738.6... [11:15:08] 2659 peptides remaining for 736.6 to 738.6... [11:15:08] 2365 peptides remaining for 736.6 to 738.6... [11:15:09] 2053 peptides remaining for 736.6 to 738.6... [11:15:09] 1758 peptides remaining for 736.6 to 738.6... [11:15:10] 1458 peptides remaining for 736.6 to 738.6... [11:15:10] 1152 peptides remaining for 736.6 to 738.6... [11:15:11] 852 peptides remaining for 736.6 to 738.6... [11:15:11] 538 peptides remaining for 736.6 to 738.6... [11:15:12] 229 peptides remaining for 736.6 to 738.6... [11:15:12] Processing 738.6 to 740.6 m/z, (1.9666253 second duty cycle) [11:15:14] 4780 peptides remaining for 738.6 to 740.6... [11:15:15] 4479 peptides remaining for 738.6 to 740.6... [11:15:15] 4165 peptides remaining for 738.6 to 740.6... [11:15:16] 3878 peptides remaining for 738.6 to 740.6... [11:15:16] 3593 peptides remaining for 738.6 to 740.6... [11:15:17] 3328 peptides remaining for 738.6 to 740.6... [11:15:17] 3025 peptides remaining for 738.6 to 740.6... [11:15:18] 2725 peptides remaining for 738.6 to 740.6... [11:15:18] 2422 peptides remaining for 738.6 to 740.6... [11:15:19] 2131 peptides remaining for 738.6 to 740.6... [11:15:19] 1856 peptides remaining for 738.6 to 740.6... [11:15:20] 1540 peptides remaining for 738.6 to 740.6... [11:15:20] 1231 peptides remaining for 738.6 to 740.6... [11:15:21] 947 peptides remaining for 738.6 to 740.6... [11:15:21] 646 peptides remaining for 738.6 to 740.6... [11:15:22] 347 peptides remaining for 738.6 to 740.6... [11:15:22] 41 peptides remaining for 738.6 to 740.6... [11:15:23] Processing 740.6 to 742.6 m/z, (1.9666253 second duty cycle) [11:15:24] 4632 peptides remaining for 740.6 to 742.6... [11:15:25] 4334 peptides remaining for 740.6 to 742.6... [11:15:25] 4013 peptides remaining for 740.6 to 742.6... [11:15:26] 3707 peptides remaining for 740.6 to 742.6... [11:15:26] 3414 peptides remaining for 740.6 to 742.6... [11:15:27] 3132 peptides remaining for 740.6 to 742.6... [11:15:28] 2826 peptides remaining for 740.6 to 742.6... [11:15:28] 2529 peptides remaining for 740.6 to 742.6... [11:15:29] 2235 peptides remaining for 740.6 to 742.6... [11:15:29] 1942 peptides remaining for 740.6 to 742.6... [11:15:30] 1651 peptides remaining for 740.6 to 742.6... [11:15:30] 1359 peptides remaining for 740.6 to 742.6... [11:15:31] 1057 peptides remaining for 740.6 to 742.6... [11:15:31] 777 peptides remaining for 740.6 to 742.6... [11:15:32] 476 peptides remaining for 740.6 to 742.6... [11:15:32] 171 peptides remaining for 740.6 to 742.6... [11:15:33] Processing 742.6 to 744.6 m/z, (1.9666253 second duty cycle) [11:15:34] 4814 peptides remaining for 742.6 to 744.6... [11:15:35] 4515 peptides remaining for 742.6 to 744.6... [11:15:35] 4197 peptides remaining for 742.6 to 744.6... [11:15:36] 3896 peptides remaining for 742.6 to 744.6... [11:15:36] 3598 peptides remaining for 742.6 to 744.6... [11:15:37] 3314 peptides remaining for 742.6 to 744.6... [11:15:37] 3021 peptides remaining for 742.6 to 744.6... [11:15:38] 2721 peptides remaining for 742.6 to 744.6... [11:15:38] 2439 peptides remaining for 742.6 to 744.6... [11:15:39] 2142 peptides remaining for 742.6 to 744.6... [11:15:39] 1847 peptides remaining for 742.6 to 744.6... [11:15:40] 1552 peptides remaining for 742.6 to 744.6... [11:15:40] 1252 peptides remaining for 742.6 to 744.6... [11:15:41] 952 peptides remaining for 742.6 to 744.6... [11:15:41] 653 peptides remaining for 742.6 to 744.6... [11:15:42] 363 peptides remaining for 742.6 to 744.6... [11:15:43] 53 peptides remaining for 742.6 to 744.6... [11:15:43] Processing 744.6 to 746.6 m/z, (1.9666255 second duty cycle) [11:15:45] 4631 peptides remaining for 744.6 to 746.6... [11:15:45] 4326 peptides remaining for 744.6 to 746.6... [11:15:46] 4022 peptides remaining for 744.6 to 746.6... [11:15:46] 3718 peptides remaining for 744.6 to 746.6... [11:15:47] 3430 peptides remaining for 744.6 to 746.6... [11:15:47] 3125 peptides remaining for 744.6 to 746.6... [11:15:48] 2823 peptides remaining for 744.6 to 746.6... [11:15:48] 2524 peptides remaining for 744.6 to 746.6... [11:15:49] 2228 peptides remaining for 744.6 to 746.6... [11:15:49] 1930 peptides remaining for 744.6 to 746.6... [11:15:50] 1627 peptides remaining for 744.6 to 746.6... [11:15:50] 1318 peptides remaining for 744.6 to 746.6... [11:15:51] 1034 peptides remaining for 744.6 to 746.6... [11:15:51] 746 peptides remaining for 744.6 to 746.6... [11:15:52] 460 peptides remaining for 744.6 to 746.6... [11:15:52] 153 peptides remaining for 744.6 to 746.6... [11:15:53] Processing 746.6 to 748.6 m/z, (1.9666255 second duty cycle) [11:15:55] 4578 peptides remaining for 746.6 to 748.6... [11:15:55] 4245 peptides remaining for 746.6 to 748.6... [11:15:56] 3952 peptides remaining for 746.6 to 748.6... [11:15:56] 3669 peptides remaining for 746.6 to 748.6... [11:15:57] 3379 peptides remaining for 746.6 to 748.6... [11:15:57] 3086 peptides remaining for 746.6 to 748.6... [11:15:58] 2783 peptides remaining for 746.6 to 748.6... [11:15:58] 2488 peptides remaining for 746.6 to 748.6... [11:15:59] 2194 peptides remaining for 746.6 to 748.6... [11:15:59] 1904 peptides remaining for 746.6 to 748.6... [11:16:00] 1618 peptides remaining for 746.6 to 748.6... [11:16:00] 1320 peptides remaining for 746.6 to 748.6... [11:16:01] 1013 peptides remaining for 746.6 to 748.6... [11:16:01] 712 peptides remaining for 746.6 to 748.6... [11:16:02] 427 peptides remaining for 746.6 to 748.6... [11:16:02] 106 peptides remaining for 746.6 to 748.6... [11:16:03] Processing 748.6 to 750.6 m/z, (1.9666253 second duty cycle) [11:16:04] 4547 peptides remaining for 748.6 to 750.6... [11:16:05] 4236 peptides remaining for 748.6 to 750.6... [11:16:06] 3924 peptides remaining for 748.6 to 750.6... [11:16:06] 3630 peptides remaining for 748.6 to 750.6... [11:16:07] 3344 peptides remaining for 748.6 to 750.6... [11:16:07] 3062 peptides remaining for 748.6 to 750.6... [11:16:08] 2759 peptides remaining for 748.6 to 750.6... [11:16:08] 2459 peptides remaining for 748.6 to 750.6... [11:16:09] 2166 peptides remaining for 748.6 to 750.6... [11:16:09] 1879 peptides remaining for 748.6 to 750.6... [11:16:10] 1592 peptides remaining for 748.6 to 750.6... [11:16:10] 1290 peptides remaining for 748.6 to 750.6... [11:16:11] 988 peptides remaining for 748.6 to 750.6... [11:16:11] 685 peptides remaining for 748.6 to 750.6... [11:16:12] 397 peptides remaining for 748.6 to 750.6... [11:16:12] 80 peptides remaining for 748.6 to 750.6... [11:16:13] Processing 750.6 to 752.6 m/z, (1.9666253 second duty cycle) [11:16:14] 4740 peptides remaining for 750.6 to 752.6... [11:16:15] 4448 peptides remaining for 750.6 to 752.6... [11:16:15] 4122 peptides remaining for 750.6 to 752.6... [11:16:16] 3826 peptides remaining for 750.6 to 752.6... [11:16:16] 3538 peptides remaining for 750.6 to 752.6... [11:16:17] 3239 peptides remaining for 750.6 to 752.6... [11:16:17] 2943 peptides remaining for 750.6 to 752.6... [11:16:18] 2656 peptides remaining for 750.6 to 752.6... [11:16:18] 2354 peptides remaining for 750.6 to 752.6... [11:16:19] 2066 peptides remaining for 750.6 to 752.6... [11:16:20] 1785 peptides remaining for 750.6 to 752.6... [11:16:20] 1488 peptides remaining for 750.6 to 752.6... [11:16:21] 1197 peptides remaining for 750.6 to 752.6... [11:16:21] 893 peptides remaining for 750.6 to 752.6... [11:16:22] 606 peptides remaining for 750.6 to 752.6... [11:16:22] 320 peptides remaining for 750.6 to 752.6... [11:16:23] 1 peptides remaining for 750.6 to 752.6... [11:16:23] Processing 752.6 to 754.6 m/z, (1.9666256 second duty cycle) [11:16:25] 4534 peptides remaining for 752.6 to 754.6... [11:16:25] 4242 peptides remaining for 752.6 to 754.6... [11:16:26] 3936 peptides remaining for 752.6 to 754.6... [11:16:26] 3634 peptides remaining for 752.6 to 754.6... [11:16:27] 3343 peptides remaining for 752.6 to 754.6... [11:16:27] 3047 peptides remaining for 752.6 to 754.6... [11:16:28] 2758 peptides remaining for 752.6 to 754.6... [11:16:28] 2464 peptides remaining for 752.6 to 754.6... [11:16:29] 2181 peptides remaining for 752.6 to 754.6... [11:16:29] 1904 peptides remaining for 752.6 to 754.6... [11:16:30] 1621 peptides remaining for 752.6 to 754.6... [11:16:31] 1335 peptides remaining for 752.6 to 754.6... [11:16:31] 1041 peptides remaining for 752.6 to 754.6... [11:16:32] 758 peptides remaining for 752.6 to 754.6... [11:16:32] 450 peptides remaining for 752.6 to 754.6... [11:16:33] 145 peptides remaining for 752.6 to 754.6... [11:16:33] Processing 754.6 to 756.6 m/z, (1.9666256 second duty cycle) [11:16:35] 4531 peptides remaining for 754.6 to 756.6... [11:16:35] 4240 peptides remaining for 754.6 to 756.6... [11:16:36] 3926 peptides remaining for 754.6 to 756.6... [11:16:36] 3622 peptides remaining for 754.6 to 756.6... [11:16:37] 3320 peptides remaining for 754.6 to 756.6... [11:16:37] 3036 peptides remaining for 754.6 to 756.6... [11:16:38] 2737 peptides remaining for 754.6 to 756.6... [11:16:38] 2449 peptides remaining for 754.6 to 756.6... [11:16:39] 2174 peptides remaining for 754.6 to 756.6... [11:16:39] 1886 peptides remaining for 754.6 to 756.6... [11:16:40] 1598 peptides remaining for 754.6 to 756.6... [11:16:40] 1299 peptides remaining for 754.6 to 756.6... [11:16:41] 1015 peptides remaining for 754.6 to 756.6... [11:16:41] 718 peptides remaining for 754.6 to 756.6... [11:16:42] 428 peptides remaining for 754.6 to 756.6... [11:16:43] 125 peptides remaining for 754.6 to 756.6... [11:16:43] Processing 756.6 to 758.6 m/z, (1.9666253 second duty cycle) [11:16:45] 4606 peptides remaining for 756.6 to 758.6... [11:16:45] 4314 peptides remaining for 756.6 to 758.6... [11:16:46] 3998 peptides remaining for 756.6 to 758.6... [11:16:46] 3695 peptides remaining for 756.6 to 758.6... [11:16:47] 3403 peptides remaining for 756.6 to 758.6... [11:16:47] 3102 peptides remaining for 756.6 to 758.6... [11:16:48] 2796 peptides remaining for 756.6 to 758.6... [11:16:48] 2505 peptides remaining for 756.6 to 758.6... [11:16:49] 2218 peptides remaining for 756.6 to 758.6... [11:16:49] 1942 peptides remaining for 756.6 to 758.6... [11:16:50] 1649 peptides remaining for 756.6 to 758.6... [11:16:50] 1352 peptides remaining for 756.6 to 758.6... [11:16:51] 1059 peptides remaining for 756.6 to 758.6... [11:16:51] 768 peptides remaining for 756.6 to 758.6... [11:16:52] 485 peptides remaining for 756.6 to 758.6... [11:16:53] 183 peptides remaining for 756.6 to 758.6... [11:16:53] Processing 758.6 to 760.6 m/z, (1.9666253 second duty cycle) [11:16:55] 4629 peptides remaining for 758.6 to 760.6... [11:16:55] 4328 peptides remaining for 758.6 to 760.6... [11:16:56] 4018 peptides remaining for 758.6 to 760.6... [11:16:56] 3725 peptides remaining for 758.6 to 760.6... [11:16:57] 3446 peptides remaining for 758.6 to 760.6... [11:16:57] 3162 peptides remaining for 758.6 to 760.6... [11:16:58] 2874 peptides remaining for 758.6 to 760.6... [11:16:58] 2584 peptides remaining for 758.6 to 760.6... [11:16:59] 2288 peptides remaining for 758.6 to 760.6... [11:16:59] 1988 peptides remaining for 758.6 to 760.6... [11:17:00] 1711 peptides remaining for 758.6 to 760.6... [11:17:00] 1427 peptides remaining for 758.6 to 760.6... [11:17:01] 1130 peptides remaining for 758.6 to 760.6... [11:17:01] 841 peptides remaining for 758.6 to 760.6... [11:17:02] 553 peptides remaining for 758.6 to 760.6... [11:17:02] 261 peptides remaining for 758.6 to 760.6... [11:17:03] Processing 760.6 to 762.6 m/z, (1.9666255 second duty cycle) [11:17:04] 4586 peptides remaining for 760.6 to 762.6... [11:17:05] 4294 peptides remaining for 760.6 to 762.6... [11:17:05] 3980 peptides remaining for 760.6 to 762.6... [11:17:06] 3693 peptides remaining for 760.6 to 762.6... [11:17:07] 3408 peptides remaining for 760.6 to 762.6... [11:17:07] 3123 peptides remaining for 760.6 to 762.6... [11:17:08] 2839 peptides remaining for 760.6 to 762.6... [11:17:08] 2531 peptides remaining for 760.6 to 762.6... [11:17:09] 2240 peptides remaining for 760.6 to 762.6... [11:17:09] 1954 peptides remaining for 760.6 to 762.6... [11:17:10] 1648 peptides remaining for 760.6 to 762.6... [11:17:10] 1361 peptides remaining for 760.6 to 762.6... [11:17:11] 1065 peptides remaining for 760.6 to 762.6... [11:17:11] 772 peptides remaining for 760.6 to 762.6... [11:17:12] 479 peptides remaining for 760.6 to 762.6... [11:17:12] 175 peptides remaining for 760.6 to 762.6... [11:17:13] Processing 762.6 to 764.6 m/z, (1.9666255 second duty cycle) [11:17:14] 4525 peptides remaining for 762.6 to 764.6... [11:17:15] 4228 peptides remaining for 762.6 to 764.6... [11:17:15] 3923 peptides remaining for 762.6 to 764.6... [11:17:16] 3636 peptides remaining for 762.6 to 764.6... [11:17:16] 3352 peptides remaining for 762.6 to 764.6... [11:17:17] 3082 peptides remaining for 762.6 to 764.6... [11:17:17] 2811 peptides remaining for 762.6 to 764.6... [11:17:18] 2514 peptides remaining for 762.6 to 764.6... [11:17:18] 2234 peptides remaining for 762.6 to 764.6... [11:17:19] 1942 peptides remaining for 762.6 to 764.6... [11:17:19] 1644 peptides remaining for 762.6 to 764.6... [11:17:20] 1357 peptides remaining for 762.6 to 764.6... [11:17:21] 1065 peptides remaining for 762.6 to 764.6... [11:17:21] 767 peptides remaining for 762.6 to 764.6... [11:17:22] 477 peptides remaining for 762.6 to 764.6... [11:17:22] 178 peptides remaining for 762.6 to 764.6... [11:17:23] Processing 764.6 to 766.6 m/z, (1.9666253 second duty cycle) [11:17:24] 4464 peptides remaining for 764.6 to 766.6... [11:17:25] 4161 peptides remaining for 764.6 to 766.6... [11:17:25] 3844 peptides remaining for 764.6 to 766.6... [11:17:26] 3545 peptides remaining for 764.6 to 766.6... [11:17:26] 3250 peptides remaining for 764.6 to 766.6... [11:17:27] 2943 peptides remaining for 764.6 to 766.6... [11:17:27] 2648 peptides remaining for 764.6 to 766.6... [11:17:28] 2344 peptides remaining for 764.6 to 766.6... [11:17:28] 2060 peptides remaining for 764.6 to 766.6... [11:17:29] 1765 peptides remaining for 764.6 to 766.6... [11:17:29] 1479 peptides remaining for 764.6 to 766.6... [11:17:30] 1187 peptides remaining for 764.6 to 766.6... [11:17:30] 909 peptides remaining for 764.6 to 766.6... [11:17:31] 615 peptides remaining for 764.6 to 766.6... [11:17:31] 322 peptides remaining for 764.6 to 766.6... [11:17:32] 2 peptides remaining for 764.6 to 766.6... [11:17:32] Processing 766.6 to 768.6 m/z, (1.9666253 second duty cycle) [11:17:34] 4544 peptides remaining for 766.6 to 768.6... [11:17:35] 4259 peptides remaining for 766.6 to 768.6... [11:17:35] 3949 peptides remaining for 766.6 to 768.6... [11:17:36] 3659 peptides remaining for 766.6 to 768.6... [11:17:36] 3368 peptides remaining for 766.6 to 768.6... [11:17:37] 3078 peptides remaining for 766.6 to 768.6... [11:17:37] 2779 peptides remaining for 766.6 to 768.6... [11:17:38] 2495 peptides remaining for 766.6 to 768.6... [11:17:39] 2212 peptides remaining for 766.6 to 768.6... [11:17:39] 1919 peptides remaining for 766.6 to 768.6... [11:17:40] 1623 peptides remaining for 766.6 to 768.6... [11:17:40] 1324 peptides remaining for 766.6 to 768.6... [11:17:41] 1036 peptides remaining for 766.6 to 768.6... [11:17:41] 718 peptides remaining for 766.6 to 768.6... [11:17:42] 434 peptides remaining for 766.6 to 768.6... [11:17:42] 131 peptides remaining for 766.6 to 768.6... [11:17:43] Processing 768.6 to 770.6 m/z, (1.9666258 second duty cycle) [11:17:44] 4364 peptides remaining for 768.6 to 770.6... [11:17:45] 4077 peptides remaining for 768.6 to 770.6... [11:17:45] 3787 peptides remaining for 768.6 to 770.6... [11:17:46] 3492 peptides remaining for 768.6 to 770.6... [11:17:46] 3208 peptides remaining for 768.6 to 770.6... [11:17:47] 2924 peptides remaining for 768.6 to 770.6... [11:17:47] 2629 peptides remaining for 768.6 to 770.6... [11:17:48] 2336 peptides remaining for 768.6 to 770.6... [11:17:48] 2039 peptides remaining for 768.6 to 770.6... [11:17:49] 1758 peptides remaining for 768.6 to 770.6... [11:17:49] 1462 peptides remaining for 768.6 to 770.6... [11:17:50] 1178 peptides remaining for 768.6 to 770.6... [11:17:51] 887 peptides remaining for 768.6 to 770.6... [11:17:51] 596 peptides remaining for 768.6 to 770.6... [11:17:52] 295 peptides remaining for 768.6 to 770.6... [11:17:52] 0 peptides remaining for 768.6 to 770.6... [11:17:53] Processing 770.6 to 772.6 m/z, (1.9666259 second duty cycle) [11:17:54] 4507 peptides remaining for 770.6 to 772.6... [11:17:55] 4208 peptides remaining for 770.6 to 772.6... [11:17:55] 3907 peptides remaining for 770.6 to 772.6... [11:17:56] 3613 peptides remaining for 770.6 to 772.6... [11:17:56] 3327 peptides remaining for 770.6 to 772.6... [11:17:57] 3051 peptides remaining for 770.6 to 772.6... [11:17:57] 2766 peptides remaining for 770.6 to 772.6... [11:17:58] 2478 peptides remaining for 770.6 to 772.6... [11:17:58] 2192 peptides remaining for 770.6 to 772.6... [11:17:59] 1910 peptides remaining for 770.6 to 772.6... [11:17:59] 1621 peptides remaining for 770.6 to 772.6... [11:18:00] 1334 peptides remaining for 770.6 to 772.6... [11:18:00] 1022 peptides remaining for 770.6 to 772.6... [11:18:01] 726 peptides remaining for 770.6 to 772.6... [11:18:01] 425 peptides remaining for 770.6 to 772.6... [11:18:02] 123 peptides remaining for 770.6 to 772.6... [11:18:02] Processing 772.6 to 774.6 m/z, (1.9666256 second duty cycle) [11:18:04] 4352 peptides remaining for 772.6 to 774.6... [11:18:05] 4043 peptides remaining for 772.6 to 774.6... [11:18:05] 3731 peptides remaining for 772.6 to 774.6... [11:18:06] 3436 peptides remaining for 772.6 to 774.6... [11:18:06] 3149 peptides remaining for 772.6 to 774.6... [11:18:07] 2864 peptides remaining for 772.6 to 774.6... [11:18:07] 2565 peptides remaining for 772.6 to 774.6... [11:18:08] 2274 peptides remaining for 772.6 to 774.6... [11:18:08] 1980 peptides remaining for 772.6 to 774.6... [11:18:09] 1705 peptides remaining for 772.6 to 774.6... [11:18:09] 1408 peptides remaining for 772.6 to 774.6... [11:18:10] 1108 peptides remaining for 772.6 to 774.6... [11:18:10] 820 peptides remaining for 772.6 to 774.6... [11:18:11] 531 peptides remaining for 772.6 to 774.6... [11:18:11] 234 peptides remaining for 772.6 to 774.6... [11:18:12] Processing 774.6 to 776.6 m/z, (1.9666256 second duty cycle) [11:18:13] 4466 peptides remaining for 774.6 to 776.6... [11:18:14] 4167 peptides remaining for 774.6 to 776.6... [11:18:14] 3864 peptides remaining for 774.6 to 776.6... [11:18:15] 3570 peptides remaining for 774.6 to 776.6... [11:18:15] 3287 peptides remaining for 774.6 to 776.6... [11:18:16] 3010 peptides remaining for 774.6 to 776.6... [11:18:16] 2732 peptides remaining for 774.6 to 776.6... [11:18:17] 2457 peptides remaining for 774.6 to 776.6... [11:18:17] 2197 peptides remaining for 774.6 to 776.6... [11:18:18] 1900 peptides remaining for 774.6 to 776.6... [11:18:18] 1603 peptides remaining for 774.6 to 776.6... [11:18:19] 1321 peptides remaining for 774.6 to 776.6... [11:18:20] 1031 peptides remaining for 774.6 to 776.6... [11:18:20] 744 peptides remaining for 774.6 to 776.6... [11:18:21] 442 peptides remaining for 774.6 to 776.6... [11:18:21] 147 peptides remaining for 774.6 to 776.6... [11:18:22] Processing 776.6 to 778.6 m/z, (1.9666255 second duty cycle) [11:18:23] 4380 peptides remaining for 776.6 to 778.6... [11:18:24] 4093 peptides remaining for 776.6 to 778.6... [11:18:24] 3786 peptides remaining for 776.6 to 778.6... [11:18:25] 3501 peptides remaining for 776.6 to 778.6... [11:18:25] 3217 peptides remaining for 776.6 to 778.6... [11:18:26] 2935 peptides remaining for 776.6 to 778.6... [11:18:26] 2657 peptides remaining for 776.6 to 778.6... [11:18:27] 2376 peptides remaining for 776.6 to 778.6... [11:18:27] 2088 peptides remaining for 776.6 to 778.6... [11:18:28] 1802 peptides remaining for 776.6 to 778.6... [11:18:28] 1500 peptides remaining for 776.6 to 778.6... [11:18:29] 1216 peptides remaining for 776.6 to 778.6... [11:18:29] 931 peptides remaining for 776.6 to 778.6... [11:18:30] 637 peptides remaining for 776.6 to 778.6... [11:18:30] 348 peptides remaining for 776.6 to 778.6... [11:18:31] 31 peptides remaining for 776.6 to 778.6... [11:18:31] Processing 778.6 to 780.6 m/z, (1.9666255 second duty cycle) [11:18:33] 4488 peptides remaining for 778.6 to 780.6... [11:18:34] 4163 peptides remaining for 778.6 to 780.6... [11:18:34] 3859 peptides remaining for 778.6 to 780.6... [11:18:35] 3572 peptides remaining for 778.6 to 780.6... [11:18:35] 3282 peptides remaining for 778.6 to 780.6... [11:18:36] 3007 peptides remaining for 778.6 to 780.6... [11:18:36] 2734 peptides remaining for 778.6 to 780.6... [11:18:37] 2438 peptides remaining for 778.6 to 780.6... [11:18:37] 2155 peptides remaining for 778.6 to 780.6... [11:18:38] 1861 peptides remaining for 778.6 to 780.6... [11:18:38] 1552 peptides remaining for 778.6 to 780.6... [11:18:39] 1276 peptides remaining for 778.6 to 780.6... [11:18:39] 995 peptides remaining for 778.6 to 780.6... [11:18:40] 708 peptides remaining for 778.6 to 780.6... [11:18:40] 419 peptides remaining for 778.6 to 780.6... [11:18:41] 105 peptides remaining for 778.6 to 780.6... [11:18:41] Processing 780.6 to 782.6 m/z, (1.9666256 second duty cycle) [11:18:43] 4417 peptides remaining for 780.6 to 782.6... [11:18:43] 4124 peptides remaining for 780.6 to 782.6... [11:18:44] 3812 peptides remaining for 780.6 to 782.6... [11:18:45] 3498 peptides remaining for 780.6 to 782.6... [11:18:45] 3198 peptides remaining for 780.6 to 782.6... [11:18:46] 2906 peptides remaining for 780.6 to 782.6... [11:18:46] 2623 peptides remaining for 780.6 to 782.6... [11:18:47] 2346 peptides remaining for 780.6 to 782.6... [11:18:47] 2057 peptides remaining for 780.6 to 782.6... [11:18:48] 1772 peptides remaining for 780.6 to 782.6... [11:18:48] 1477 peptides remaining for 780.6 to 782.6... [11:18:49] 1191 peptides remaining for 780.6 to 782.6... [11:18:49] 887 peptides remaining for 780.6 to 782.6... [11:18:50] 591 peptides remaining for 780.6 to 782.6... [11:18:50] 299 peptides remaining for 780.6 to 782.6... [11:18:51] 0 peptides remaining for 780.6 to 782.6... [11:18:51] Processing 782.6 to 784.6 m/z, (1.9666256 second duty cycle) [11:18:53] 4238 peptides remaining for 782.6 to 784.6... [11:18:53] 3942 peptides remaining for 782.6 to 784.6... [11:18:54] 3641 peptides remaining for 782.6 to 784.6... [11:18:54] 3356 peptides remaining for 782.6 to 784.6... [11:18:55] 3076 peptides remaining for 782.6 to 784.6... [11:18:55] 2801 peptides remaining for 782.6 to 784.6... [11:18:56] 2498 peptides remaining for 782.6 to 784.6... [11:18:56] 2209 peptides remaining for 782.6 to 784.6... [11:18:57] 1928 peptides remaining for 782.6 to 784.6... [11:18:57] 1650 peptides remaining for 782.6 to 784.6... [11:18:58] 1358 peptides remaining for 782.6 to 784.6... [11:18:58] 1068 peptides remaining for 782.6 to 784.6... [11:18:59] 791 peptides remaining for 782.6 to 784.6... [11:19:00] 508 peptides remaining for 782.6 to 784.6... [11:19:00] 217 peptides remaining for 782.6 to 784.6... [11:19:01] Processing 784.6 to 786.6 m/z, (1.9666256 second duty cycle) [11:19:02] 4300 peptides remaining for 784.6 to 786.6... [11:19:03] 3999 peptides remaining for 784.6 to 786.6... [11:19:03] 3700 peptides remaining for 784.6 to 786.6... [11:19:04] 3404 peptides remaining for 784.6 to 786.6... [11:19:04] 3117 peptides remaining for 784.6 to 786.6... [11:19:05] 2823 peptides remaining for 784.6 to 786.6... [11:19:05] 2538 peptides remaining for 784.6 to 786.6... [11:19:06] 2253 peptides remaining for 784.6 to 786.6... [11:19:06] 1973 peptides remaining for 784.6 to 786.6... [11:19:07] 1681 peptides remaining for 784.6 to 786.6... [11:19:07] 1396 peptides remaining for 784.6 to 786.6... [11:19:08] 1111 peptides remaining for 784.6 to 786.6... [11:19:08] 829 peptides remaining for 784.6 to 786.6... [11:19:09] 536 peptides remaining for 784.6 to 786.6... [11:19:09] 244 peptides remaining for 784.6 to 786.6... [11:19:10] Processing 786.6 to 788.6 m/z, (1.9666256 second duty cycle) [11:19:12] 4426 peptides remaining for 786.6 to 788.6... [11:19:12] 4115 peptides remaining for 786.6 to 788.6... [11:19:13] 3818 peptides remaining for 786.6 to 788.6... [11:19:13] 3523 peptides remaining for 786.6 to 788.6... [11:19:14] 3210 peptides remaining for 786.6 to 788.6... [11:19:14] 2939 peptides remaining for 786.6 to 788.6... [11:19:15] 2646 peptides remaining for 786.6 to 788.6... [11:19:15] 2365 peptides remaining for 786.6 to 788.6... [11:19:16] 2073 peptides remaining for 786.6 to 788.6... [11:19:16] 1789 peptides remaining for 786.6 to 788.6... [11:19:17] 1504 peptides remaining for 786.6 to 788.6... [11:19:17] 1202 peptides remaining for 786.6 to 788.6... [11:19:18] 909 peptides remaining for 786.6 to 788.6... [11:19:18] 617 peptides remaining for 786.6 to 788.6... [11:19:19] 335 peptides remaining for 786.6 to 788.6... [11:19:19] 19 peptides remaining for 786.6 to 788.6... [11:19:20] Processing 788.6 to 790.6 m/z, (1.9666258 second duty cycle) [11:19:22] 4243 peptides remaining for 788.6 to 790.6... [11:19:22] 3950 peptides remaining for 788.6 to 790.6... [11:19:23] 3653 peptides remaining for 788.6 to 790.6... [11:19:23] 3390 peptides remaining for 788.6 to 790.6... [11:19:24] 3113 peptides remaining for 788.6 to 790.6... [11:19:24] 2832 peptides remaining for 788.6 to 790.6... [11:19:25] 2541 peptides remaining for 788.6 to 790.6... [11:19:25] 2258 peptides remaining for 788.6 to 790.6... [11:19:26] 1976 peptides remaining for 788.6 to 790.6... [11:19:26] 1698 peptides remaining for 788.6 to 790.6... [11:19:27] 1406 peptides remaining for 788.6 to 790.6... [11:19:27] 1121 peptides remaining for 788.6 to 790.6... [11:19:28] 833 peptides remaining for 788.6 to 790.6... [11:19:28] 550 peptides remaining for 788.6 to 790.6... [11:19:29] 264 peptides remaining for 788.6 to 790.6... [11:19:29] 0 peptides remaining for 788.6 to 790.6... [11:19:30] Processing 790.6 to 792.6 m/z, (1.9666256 second duty cycle) [11:19:31] 4172 peptides remaining for 790.6 to 792.6... [11:19:32] 3879 peptides remaining for 790.6 to 792.6... [11:19:32] 3572 peptides remaining for 790.6 to 792.6... [11:19:33] 3279 peptides remaining for 790.6 to 792.6... [11:19:33] 3007 peptides remaining for 790.6 to 792.6... [11:19:34] 2725 peptides remaining for 790.6 to 792.6... [11:19:34] 2443 peptides remaining for 790.6 to 792.6... [11:19:35] 2146 peptides remaining for 790.6 to 792.6... [11:19:35] 1867 peptides remaining for 790.6 to 792.6... [11:19:36] 1585 peptides remaining for 790.6 to 792.6... [11:19:36] 1304 peptides remaining for 790.6 to 792.6... [11:19:37] 1017 peptides remaining for 790.6 to 792.6... [11:19:37] 738 peptides remaining for 790.6 to 792.6... [11:19:38] 436 peptides remaining for 790.6 to 792.6... [11:19:39] 124 peptides remaining for 790.6 to 792.6... [11:19:39] Processing 792.6 to 794.6 m/z, (1.9666256 second duty cycle) [11:19:41] 4329 peptides remaining for 792.6 to 794.6... [11:19:41] 4035 peptides remaining for 792.6 to 794.6... [11:19:42] 3736 peptides remaining for 792.6 to 794.6... [11:19:42] 3445 peptides remaining for 792.6 to 794.6... [11:19:43] 3174 peptides remaining for 792.6 to 794.6... [11:19:43] 2890 peptides remaining for 792.6 to 794.6... [11:19:44] 2605 peptides remaining for 792.6 to 794.6... [11:19:44] 2323 peptides remaining for 792.6 to 794.6... [11:19:45] 2049 peptides remaining for 792.6 to 794.6... [11:19:45] 1759 peptides remaining for 792.6 to 794.6... [11:19:46] 1464 peptides remaining for 792.6 to 794.6... [11:19:46] 1178 peptides remaining for 792.6 to 794.6... [11:19:47] 890 peptides remaining for 792.6 to 794.6... [11:19:47] 605 peptides remaining for 792.6 to 794.6... [11:19:48] 321 peptides remaining for 792.6 to 794.6... [11:19:48] 20 peptides remaining for 792.6 to 794.6... [11:19:49] Processing 794.6 to 796.6 m/z, (1.9666255 second duty cycle) [11:19:51] 4341 peptides remaining for 794.6 to 796.6... [11:19:51] 4045 peptides remaining for 794.6 to 796.6... [11:19:52] 3732 peptides remaining for 794.6 to 796.6... [11:19:52] 3436 peptides remaining for 794.6 to 796.6... [11:19:53] 3154 peptides remaining for 794.6 to 796.6... [11:19:53] 2865 peptides remaining for 794.6 to 796.6... [11:19:54] 2577 peptides remaining for 794.6 to 796.6... [11:19:54] 2290 peptides remaining for 794.6 to 796.6... [11:19:55] 2007 peptides remaining for 794.6 to 796.6... [11:19:55] 1710 peptides remaining for 794.6 to 796.6... [11:19:56] 1427 peptides remaining for 794.6 to 796.6... [11:19:56] 1142 peptides remaining for 794.6 to 796.6... [11:19:57] 854 peptides remaining for 794.6 to 796.6... [11:19:57] 574 peptides remaining for 794.6 to 796.6... [11:19:58] 301 peptides remaining for 794.6 to 796.6... [11:19:58] 11 peptides remaining for 794.6 to 796.6... [11:19:59] Processing 796.6 to 798.6 m/z, (1.9667151 second duty cycle) [11:20:00] 4165 peptides remaining for 796.6 to 798.6... [11:20:01] 3866 peptides remaining for 796.6 to 798.6... [11:20:01] 3563 peptides remaining for 796.6 to 798.6... [11:20:02] 3275 peptides remaining for 796.6 to 798.6... [11:20:02] 2992 peptides remaining for 796.6 to 798.6... [11:20:03] 2707 peptides remaining for 796.6 to 798.6... [11:20:03] 2416 peptides remaining for 796.6 to 798.6... [11:20:04] 2123 peptides remaining for 796.6 to 798.6... [11:20:04] 1834 peptides remaining for 796.6 to 798.6... [11:20:05] 1561 peptides remaining for 796.6 to 798.6... [11:20:06] 1268 peptides remaining for 796.6 to 798.6... [11:20:06] 983 peptides remaining for 796.6 to 798.6... [11:20:07] 701 peptides remaining for 796.6 to 798.6... [11:20:07] 431 peptides remaining for 796.6 to 798.6... [11:20:08] 135 peptides remaining for 796.6 to 798.6... [11:20:08] Processing 798.6 to 800.6 m/z, (1.9667151 second duty cycle) [11:20:10] 4228 peptides remaining for 798.6 to 800.6... [11:20:11] 3927 peptides remaining for 798.6 to 800.6... [11:20:11] 3608 peptides remaining for 798.6 to 800.6... [11:20:12] 3331 peptides remaining for 798.6 to 800.6... [11:20:12] 3051 peptides remaining for 798.6 to 800.6... [11:20:13] 2781 peptides remaining for 798.6 to 800.6... [11:20:13] 2503 peptides remaining for 798.6 to 800.6... [11:20:14] 2227 peptides remaining for 798.6 to 800.6... [11:20:14] 1928 peptides remaining for 798.6 to 800.6... [11:20:15] 1641 peptides remaining for 798.6 to 800.6... [11:20:15] 1352 peptides remaining for 798.6 to 800.6... [11:20:16] 1065 peptides remaining for 798.6 to 800.6... [11:20:16] 785 peptides remaining for 798.6 to 800.6... [11:20:17] 497 peptides remaining for 798.6 to 800.6... [11:20:17] 199 peptides remaining for 798.6 to 800.6... [11:20:18] Processing 800.6 to 802.6 m/z, (3.9331467 second duty cycle) [11:20:19] 4174 peptides remaining for 800.6 to 802.6... [11:20:20] 3690 peptides remaining for 800.6 to 802.6... [11:20:20] 3214 peptides remaining for 800.6 to 802.6... [11:20:21] 2745 peptides remaining for 800.6 to 802.6... [11:20:21] 2252 peptides remaining for 800.6 to 802.6... [11:20:22] 1774 peptides remaining for 800.6 to 802.6... [11:20:22] 1293 peptides remaining for 800.6 to 802.6... [11:20:23] 813 peptides remaining for 800.6 to 802.6... [11:20:23] 349 peptides remaining for 800.6 to 802.6... [11:20:24] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:20:41] Sorted feature file in 16.56 seconds wall clock time [11:20:41] File size check: 319305821 vs 319305821 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:20:41] 784761 total peptides processed. [11:20:41] Running Percolator... [11:20:41] Executing [cmd /c C:\Windows\Temp\tmp932B.java\Percolator-v3-01-5265969489128631572.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt] [11:20:41] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:20:41] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:20:41] Written by Lukas Käll (lukall@u.washington.edu) in the [11:20:41] Department of Genome Sciences at the University of Washington. [11:20:41] Issued command: [11:20:41] C:\Windows\Temp\tmp932B.java\Percolator-v3-01-5265969489128631572.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:20:41] Started Wed Jul 17 11:20:41 2024 [11:20:41] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [11:20:41] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:20:41] Features: [11:20:41] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:20:48] Found 784761 PSMs [11:20:48] Separate target and decoy search inputs detected, using mix-max method. [11:20:48] Train/test set contains 249995 positives and 250005 negatives, size ratio=0.99996 and pi0=1 [11:20:49] Selecting Cpos by cross-validation. [11:20:49] Selecting Cneg by cross-validation. [11:20:52] Split 1: Selected feature 3 as initial search direction. Could separate 2973 training set positives in that direction. [11:20:56] Split 2: Selected feature 2 as initial search direction. Could separate 3043 training set positives in that direction. [11:20:59] Split 3: Selected feature 3 as initial search direction. Could separate 2956 training set positives in that direction. [11:20:59] Found 4245 test set positives with q<0.01 in initial direction [11:20:59] Reading in data and feature calculation took 17.859 cpu seconds or 18 seconds wall clock time. [11:20:59] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:21:24] Iteration 1: Estimated 6580 PSMs with q<0.01 [11:21:49] Iteration 2: Estimated 7352 PSMs with q<0.01 [11:22:16] Iteration 3: Estimated 7641 PSMs with q<0.01 [11:22:16] Learned normalized SVM weights for the 3 cross-validation splits: [11:22:16] Split1 Split2 Split3 FeatureName [11:22:16] -0.5643 -0.6567 -0.3564 primary [11:22:16] -0.0997 0.1742 -0.1492 xCorrLib [11:22:16] 0.5123 0.3503 0.6008 xCorrModel [11:22:16] -0.1271 -0.3177 -0.2404 dotProduct [11:22:16] 0.9021 1.1715 0.7196 contrastAngle [11:22:16] -0.3150 -0.3160 0.0579 logit [11:22:16] 0.1969 0.2650 0.2451 sumOfSquaredErrors [11:22:16] 0.6349 0.8057 0.5668 numberOfMatchingPeaks [11:22:16] 0.1671 0.2369 0.1434 numberOfMatchingPeaksAboveThreshold [11:22:16] 0.0128 0.0104 0.0443 averageFragmentDeltaMasses [11:22:16] 0.3122 0.3140 0.3482 isotopeDotProduct [11:22:16] 0.1238 0.0969 0.0689 averageParentDeltaMass [11:22:16] 0.0722 -0.0210 0.0374 percentBlankOverMono [11:22:16] -0.0802 -0.1992 -0.1981 numberPrecursorMatch [11:22:16] -0.7648 -0.8612 -0.9188 lnSp [11:22:16] 0.4027 0.4565 0.4548 maxLadderLength [11:22:16] 0.1692 0.2306 0.2186 evalue [11:22:16] 0.1343 0.1226 0.0818 correlationToGaussian [11:22:16] 0.0436 0.0549 0.0846 correlationToPrecursor [11:22:16] -0.0222 -0.0606 -0.0757 isIntegratedSignal [11:22:16] 0.0723 0.0749 0.0056 isIntegratedPrecursor [11:22:16] 0.4993 0.3644 0.4737 numPeaksWithGoodCorrelation [11:22:16] -0.3673 -0.4570 -0.3387 numMissedCleavage [11:22:16] -0.1863 -0.4073 -0.4973 pepLength [11:22:16] 0.0000 0.0000 0.0000 charge1 [11:22:16] 0.0329 -0.1520 -0.0487 charge2 [11:22:16] -0.0329 0.1520 0.0487 charge3 [11:22:16] 0.0000 0.0000 0.0000 charge4 [11:22:16] 0.0676 0.0656 0.0770 precursorMz [11:22:16] -0.1311 -0.2395 -0.0578 precursorMass [11:22:16] -0.0476 -0.0662 0.0359 RTinMin [11:22:16] -3.6908 -3.9311 -3.7940 m0 [11:22:16] Found 7542 test set PSMs with q<0.01. [11:22:16] Scoring full list of PSMs with trained SVMs. [11:22:16] Features: [11:22:16] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:22:23] Found 784761 PSMs [11:22:23] Evaluated set contained 392256 positives and 392505 negatives. [11:22:25] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:22:27] Selecting pi_0=0.9461 [11:22:27] Calculating q values. [11:22:27] New pi_0 estimate on final list yields 11583 target peptides with q<0.01. [11:22:27] Calculating posterior error probabilities (PEPs). [11:22:28] Processing took 89.19 cpu seconds or 89 seconds wall clock time. [11:22:35] First pass: 11583 peptides identified at 1.0% FDR [11:22:36] Generating retention time mapping using 11584 points... [11:22:36] Enough data points (11584) to perform KDE alignment. [11:22:37] Enough data points (10817) to perform KDE alignment. [11:22:38] Enough data points (11584) to perform KDE alignment. [11:22:40] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:22:43] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:22:56] Sorted feature file in 12.75 seconds wall clock time [11:22:56] File size check: 249823910 vs 249823910 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:22:56] Executing [cmd /c C:\Windows\Temp\tmp932B.java\Percolator-v3-01-1872875036182979212.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt] [11:22:56] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:22:56] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:22:56] Written by Lukas Käll (lukall@u.washington.edu) in the [11:22:56] Department of Genome Sciences at the University of Washington. [11:22:56] Issued command: [11:22:56] C:\Windows\Temp\tmp932B.java\Percolator-v3-01-1872875036182979212.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:22:56] Started Wed Jul 17 11:22:56 2024 [11:22:56] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [11:22:56] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:22:56] Features: [11:22:56] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:23:01] Found 575050 PSMs [11:23:02] Separate target and decoy search inputs detected, using mix-max method. [11:23:02] Train/test set contains 247218 positives and 252782 negatives, size ratio=0.977989 and pi0=1 [11:23:03] Selecting Cpos by cross-validation. [11:23:03] Selecting Cneg by cross-validation. [11:23:06] Split 1: Selected feature 3 as initial search direction. Could separate 4016 training set positives in that direction. [11:23:10] Split 2: Selected feature 2 as initial search direction. Could separate 4189 training set positives in that direction. [11:23:13] Split 3: Selected feature 3 as initial search direction. Could separate 3957 training set positives in that direction. [11:23:13] Found 5852 test set positives with q<0.01 in initial direction [11:23:13] Reading in data and feature calculation took 17.375 cpu seconds or 17 seconds wall clock time. [11:23:13] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:23:41] Iteration 1: Estimated 8866 PSMs with q<0.01 [11:24:10] Iteration 2: Estimated 9793 PSMs with q<0.01 [11:24:39] Iteration 3: Estimated 10080 PSMs with q<0.01 [11:25:09] Iteration 4: Estimated 10119 PSMs with q<0.01 [11:25:39] Iteration 5: Estimated 10146 PSMs with q<0.01 [11:26:09] Iteration 6: Estimated 10130 PSMs with q<0.01 [11:26:39] Iteration 7: Estimated 10147 PSMs with q<0.01 [11:27:09] Iteration 8: Estimated 10137 PSMs with q<0.01 [11:27:39] Iteration 9: Estimated 10122 PSMs with q<0.01 [11:28:09] Iteration 10: Estimated 10164 PSMs with q<0.01 [11:28:09] Learned normalized SVM weights for the 3 cross-validation splits: [11:28:09] Split1 Split2 Split3 FeatureName [11:28:09] -2.0961 -1.5585 -0.2401 primary [11:28:09] -0.1416 -0.0099 -0.0658 xCorrLib [11:28:09] 0.4996 0.4840 0.4496 xCorrModel [11:28:09] 0.2671 -0.0107 0.2200 dotProduct [11:28:09] 0.3301 1.1727 0.8011 contrastAngle [11:28:09] 0.5279 -0.2048 -0.4090 logit [11:28:09] 0.2956 0.3022 0.1755 sumOfSquaredErrors [11:28:09] 2.3784 1.9546 0.4357 numberOfMatchingPeaks [11:28:09] 0.3329 0.2584 0.2479 numberOfMatchingPeaksAboveThreshold [11:28:09] 0.0890 -0.0363 -0.0114 averageFragmentDeltaMasses [11:28:09] 0.3515 0.3464 0.2101 isotopeDotProduct [11:28:09] 0.0658 0.0034 0.0332 averageParentDeltaMass [11:28:09] 0.0083 -0.0603 -0.0643 percentBlankOverMono [11:28:09] -0.0859 -0.2071 -0.0625 numberPrecursorMatch [11:28:09] -1.1817 -1.2219 -0.8135 lnSp [11:28:09] 0.6332 0.6715 0.4723 maxLadderLength [11:28:09] 0.3213 0.3326 0.2680 evalue [11:28:09] 0.4202 0.4739 0.2195 correlationToGaussian [11:28:09] -0.0055 0.0702 -0.0090 correlationToPrecursor [11:28:09] -0.1508 -0.0543 -0.0421 isIntegratedSignal [11:28:09] 0.1346 -0.0110 -0.0097 isIntegratedPrecursor [11:28:09] 0.7964 0.6338 0.5395 numPeaksWithGoodCorrelation [11:28:09] 0.0511 -0.0303 -0.0467 deltaRT [11:28:09] 0.0180 -0.0235 -0.0507 ms1MassError [11:28:09] -0.0980 -0.1413 -0.0793 ms2MassError [11:28:09] -0.7135 -0.5259 -0.4556 numMissedCleavage [11:28:09] -0.9208 -0.5252 -0.5558 pepLength [11:28:09] 0.0000 0.0000 0.0000 charge1 [11:28:09] -0.1813 -0.0736 -0.0612 charge2 [11:28:09] 0.1813 0.0736 0.0612 charge3 [11:28:09] 0.0000 0.0000 0.0000 charge4 [11:28:09] 0.1513 -0.0112 0.0017 precursorMz [11:28:09] -0.1192 -0.2667 -0.0264 precursorMass [11:28:09] -0.0804 -0.0491 -0.1121 RTinMin [11:28:09] -5.2831 -4.7645 -3.5925 m0 [11:28:09] Found 10017 test set PSMs with q<0.01. [11:28:09] Scoring full list of PSMs with trained SVMs. [11:28:10] Features: [11:28:10] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:28:15] Found 575050 PSMs [11:28:15] Evaluated set contained 284529 positives and 290521 negatives. [11:28:17] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:28:18] Selecting pi_0=0.948827 [11:28:18] Calculating q values. [11:28:18] New pi_0 estimate on final list yields 11610 target peptides with q<0.01. [11:28:18] Calculating posterior error probabilities (PEPs). [11:28:20] Processing took 306.4 cpu seconds or 307 seconds wall clock time. [11:28:27] Generating retention time mapping using 11611 points... [11:28:27] Enough data points (11611) to perform KDE alignment. [11:28:28] Enough data points (10872) to perform KDE alignment. [11:28:29] Enough data points (11611) to perform KDE alignment. [11:28:30] Writing elib result library... [11:28:30] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 11610 vs local peptides: 11610 [11:28:30] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML... [11:28:30] Extracting Spectral Data for 11610 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML... [11:28:30] Number of global peptides: 11610 vs local peptides: 11610 [11:28:32] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [11:28:32] Parsed features and scores for 11610 peptides. [11:28:32] Extracting 11610 peptides... [11:28:32] Quant Extracting 698.6 to 700.6 m/z (11.861911 to 97.63197 min) [11:28:33] Quant Extracting 700.6 to 702.6 m/z (7.144798 to 100.76034 min) [11:28:33] Quant Extracting 702.6 to 704.6 m/z (7.144798 to 94.56869 min) [11:28:33] Quant Extracting 704.6 to 706.6 m/z (7.1459594 to 99.566315 min) [11:28:33] Quant Extracting 706.6 to 708.6 m/z (7.1459594 to 99.93076 min) [11:28:33] Quant Extracting 708.6 to 710.6 m/z (7.1471057 to 100.729866 min) [11:28:33] Quant Extracting 710.6 to 712.6 m/z (7.657666 to 97.929405 min) [11:28:33] Quant Extracting 712.6 to 714.6 m/z (7.148267 to 97.86492 min) [11:28:34] Quant Extracting 714.6 to 716.6 m/z (11.76819 to 96.06772 min) [11:28:34] Quant Extracting 716.6 to 718.6 m/z (9.23903 to 100.06606 min) [11:28:34] Quant Extracting 718.6 to 720.6 m/z (7.5243206 to 95.80925 min) [11:28:34] Quant Extracting 720.6 to 722.6 m/z (7.1505737 to 99.308205 min) [11:28:34] Quant Extracting 722.6 to 724.6 m/z (7.1505737 to 96.88819 min) [11:28:34] Quant Extracting 724.6 to 726.6 m/z (7.15172 to 96.200096 min) [11:28:34] Quant Extracting 726.6 to 728.6 m/z (12.724364 to 95.25939 min) [11:28:35] Quant Extracting 728.6 to 730.6 m/z (7.152891 to 94.54368 min) [11:28:35] Quant Extracting 730.6 to 732.6 m/z (13.019784 to 96.29959 min) [11:28:35] Quant Extracting 732.6 to 734.6 m/z (14.797693 to 99.50818 min) [11:28:35] Quant Extracting 734.6 to 736.6 m/z (14.106993 to 97.70786 min) [11:28:35] Quant Extracting 736.6 to 738.6 m/z (15.8758745 to 100.7707 min) [11:28:35] Quant Extracting 738.6 to 740.6 m/z (18.330626 to 95.717445 min) [11:28:35] Quant Extracting 740.6 to 742.6 m/z (7.1909595 to 93.63803 min) [11:28:35] Quant Extracting 742.6 to 744.6 m/z (11.971879 to 99.11924 min) [11:28:35] Quant Extracting 744.6 to 746.6 m/z (7.1602945 to 98.466385 min) [11:28:36] Quant Extracting 746.6 to 748.6 m/z (13.814836 to 99.18574 min) [11:28:36] Quant Extracting 748.6 to 750.6 m/z (21.106731 to 96.96144 min) [11:28:36] Quant Extracting 750.6 to 752.6 m/z (7.161441 to 97.81002 min) [11:28:36] Quant Extracting 752.6 to 754.6 m/z (14.803454 to 97.450966 min) [11:28:36] Quant Extracting 754.6 to 756.6 m/z (9.11885 to 95.75494 min) [11:28:36] Quant Extracting 756.6 to 758.6 m/z (18.437054 to 95.65848 min) [11:28:36] Quant Extracting 758.6 to 760.6 m/z (7.163749 to 100.34538 min) [11:28:36] Quant Extracting 760.6 to 762.6 m/z (14.641605 to 100.77761 min) [11:28:36] Quant Extracting 762.6 to 764.6 m/z (15.037811 to 100.0173 min) [11:28:36] Quant Extracting 764.6 to 766.6 m/z (23.881416 to 96.60606 min) [11:28:36] Quant Extracting 766.6 to 768.6 m/z (7.1660533 to 98.24386 min) [11:28:36] Quant Extracting 768.6 to 770.6 m/z (11.459097 to 99.42251 min) [11:28:37] Quant Extracting 770.6 to 772.6 m/z (7.167204 to 96.0869 min) [11:28:37] Quant Extracting 772.6 to 774.6 m/z (13.263523 to 94.4295 min) [11:28:37] Quant Extracting 774.6 to 776.6 m/z (12.11527 to 97.48992 min) [11:28:37] Quant Extracting 776.6 to 778.6 m/z (14.944239 to 100.749466 min) [11:28:37] Quant Extracting 778.6 to 780.6 m/z (7.169507 to 98.01784 min) [11:28:37] Quant Extracting 780.6 to 782.6 m/z (19.978573 to 98.47676 min) [11:28:37] Quant Extracting 782.6 to 784.6 m/z (12.444914 to 97.39475 min) [11:28:37] Quant Extracting 784.6 to 786.6 m/z (19.198862 to 97.72502 min) [11:28:37] Quant Extracting 786.6 to 788.6 m/z (8.475271 to 93.943 min) [11:28:37] Quant Extracting 788.6 to 790.6 m/z (24.244534 to 100.75572 min) [11:28:37] Quant Extracting 790.6 to 792.6 m/z (13.33504 to 100.18979 min) [11:28:37] Quant Extracting 792.6 to 794.6 m/z (13.860883 to 94.8893 min) [11:28:38] Quant Extracting 794.6 to 796.6 m/z (20.566673 to 95.66888 min) [11:28:38] Quant Extracting 796.6 to 798.6 m/z (13.86203 to 95.67299 min) [11:28:38] Quant Extracting 798.6 to 800.6 m/z (14.819307 to 99.138626 min) [11:28:38] Quant Extracting 800.6 to 802.6 m/z (21.77673 to 96.48568 min) [11:28:38] Attempted extraction for: 11610, found 11610 [11:28:38] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML (11610 entries)... [11:28:38] Writing 11610 peptides to entries table... [11:28:39] Writing 11610 peptides to peptidequants table... [11:28:40] Finished writing to Encyclopedia ELIB at Wed Jul 17 11:28:40 BST 2024 [11:28:41] Writing local target/decoy peptides: 11610/120, pi0: 0.948827 [11:28:41] Writing local target/decoy proteins: 4517/45 [11:28:43] Finished analysis! 11610 peptides identified at 1.0% FDR (16.8 minutes) [11:28:43] Generating chromatogram library (5 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [11:28:46] EncyclopeDIA version 2.12.30 [11:28:47] Getting count of protein accessions... [11:28:47] Using EncyclopeDIA 2.X Scoring System [11:28:47] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML ... [11:28:47] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML ... [11:28:48] Parsed 1% [11:28:48] Parsed 2% [11:28:48] Parsed 3% [11:28:48] Parsed 4% [11:28:48] Parsed 5% [11:28:49] Parsed 6% [11:28:49] Parsed 7% [11:28:49] Parsed 8% [11:28:49] Parsed 9% [11:28:50] Parsed 10% [11:28:50] Parsed 11% [11:28:50] Parsed 12% [11:28:51] Parsed 13% [11:28:51] Parsed 14% [11:28:52] Parsed 15% [11:28:52] Parsed 16% [11:28:52] Parsed 17% [11:28:53] Parsed 18% [11:28:53] Parsed 19% [11:28:54] Parsed 20% [11:28:54] Parsed 21% [11:28:54] Parsed 22% [11:28:55] Parsed 23% [11:28:55] Parsed 24% [11:28:55] Parsed 25% [11:28:56] Parsed 26% [11:28:56] Parsed 27% [11:28:57] Parsed 28% [11:28:57] Parsed 29% [11:28:58] Parsed 30% [11:28:58] Parsed 31% [11:28:59] Parsed 32% [11:29:00] Parsed 33% [11:29:00] Parsed 34% [11:29:01] Parsed 35% [11:29:01] Parsed 36% [11:29:01] Parsed 37% [11:29:02] Parsed 38% [11:29:02] Parsed 39% [11:29:03] Parsed 40% [11:29:03] Parsed 41% [11:29:04] Parsed 42% [11:29:05] Parsed 43% [11:29:05] Parsed 44% [11:29:06] Parsed 45% [11:29:07] Parsed 46% [11:29:08] Parsed 47% [11:29:08] Parsed 48% [11:29:09] Parsed 49% [11:29:09] Parsed 50% [11:29:10] Parsed 51% [11:29:11] Parsed 52% [11:29:11] Parsed 53% [11:29:13] Parsed 54% [11:29:14] Parsed 55% [11:29:15] Parsed 56% [11:29:17] Parsed 57% [11:29:19] Parsed 58% [11:29:20] Parsed 59% [11:29:23] Parsed 60% [11:29:25] Parsed 61% [11:29:28] Parsed 62% [11:29:31] Parsed 63% [11:29:38] Parsed 64% [11:29:39] Parsed 65% [11:29:39] Parsed 66% [11:29:40] Parsed 67% [11:29:40] Parsed 68% [11:29:41] Parsed 69% [11:29:42] Parsed 70% [11:29:42] Parsed 71% [11:29:43] Parsed 72% [11:29:44] Parsed 73% [11:29:44] Parsed 74% [11:29:45] Parsed 75% [11:29:46] Parsed 76% [11:29:47] Parsed 77% [11:29:48] Parsed 78% [11:29:49] Parsed 79% [11:29:49] Parsed 80% [11:29:50] Parsed 81% [11:29:51] Parsed 82% [11:29:51] Parsed 83% [11:29:52] Parsed 84% [11:29:53] Parsed 85% [11:29:54] Parsed 86% [11:29:55] Parsed 87% [11:29:56] Parsed 88% [11:29:58] Parsed 89% [11:30:00] Parsed 90% [11:30:02] Parsed 91% [11:30:04] Parsed 92% [11:30:06] Parsed 93% [11:30:09] Parsed 94% [11:30:12] Parsed 95% [11:30:14] Parsed 96% [11:30:17] Parsed 97% [11:30:20] Parsed 98% [11:30:21] Parsed 99% [11:30:27] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.dia ... [11:30:28] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.dia! [11:30:28] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML [11:30:28] Library File: UP000005640_9606-z3_nce27-prosit.dlib [11:30:28] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.elib [11:30:28] Parameters: [11:30:28] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [11:30:28] Converting files... [11:30:28] Calculating features... [11:30:28] Processing precursors scans... [11:30:28] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:30:28] Processing 798.6 to 800.6 m/z, (3.9508963 second duty cycle) [11:30:30] 4333 peptides remaining for 798.6 to 800.6... [11:30:31] 4255 peptides remaining for 798.6 to 800.6... [11:30:31] 4116 peptides remaining for 798.6 to 800.6... [11:30:32] 3780 peptides remaining for 798.6 to 800.6... [11:30:32] 3387 peptides remaining for 798.6 to 800.6... [11:30:33] 3008 peptides remaining for 798.6 to 800.6... [11:30:33] 2577 peptides remaining for 798.6 to 800.6... [11:30:34] 2133 peptides remaining for 798.6 to 800.6... [11:30:34] 1654 peptides remaining for 798.6 to 800.6... [11:30:35] 1164 peptides remaining for 798.6 to 800.6... [11:30:35] 658 peptides remaining for 798.6 to 800.6... [11:30:36] 182 peptides remaining for 798.6 to 800.6... [11:30:36] Processing 800.6 to 802.6 m/z, (1.9754604 second duty cycle) [11:30:38] 4179 peptides remaining for 800.6 to 802.6... [11:30:39] 3846 peptides remaining for 800.6 to 802.6... [11:30:39] 3532 peptides remaining for 800.6 to 802.6... [11:30:40] 3207 peptides remaining for 800.6 to 802.6... [11:30:40] 2890 peptides remaining for 800.6 to 802.6... [11:30:41] 2566 peptides remaining for 800.6 to 802.6... [11:30:41] 2220 peptides remaining for 800.6 to 802.6... [11:30:42] 1906 peptides remaining for 800.6 to 802.6... [11:30:42] 1593 peptides remaining for 800.6 to 802.6... [11:30:43] 1276 peptides remaining for 800.6 to 802.6... [11:30:43] 949 peptides remaining for 800.6 to 802.6... [11:30:44] 632 peptides remaining for 800.6 to 802.6... [11:30:44] 301 peptides remaining for 800.6 to 802.6... [11:30:45] Processing 802.6 to 804.6 m/z, (1.9754473 second duty cycle) [11:30:46] 4082 peptides remaining for 802.6 to 804.6... [11:30:47] 3755 peptides remaining for 802.6 to 804.6... [11:30:48] 3437 peptides remaining for 802.6 to 804.6... [11:30:48] 3124 peptides remaining for 802.6 to 804.6... [11:30:49] 2812 peptides remaining for 802.6 to 804.6... [11:30:49] 2487 peptides remaining for 802.6 to 804.6... [11:30:50] 2170 peptides remaining for 802.6 to 804.6... [11:30:50] 1853 peptides remaining for 802.6 to 804.6... [11:30:51] 1556 peptides remaining for 802.6 to 804.6... [11:30:51] 1243 peptides remaining for 802.6 to 804.6... [11:30:52] 930 peptides remaining for 802.6 to 804.6... [11:30:52] 608 peptides remaining for 802.6 to 804.6... [11:30:53] 269 peptides remaining for 802.6 to 804.6... [11:30:53] Processing 804.6 to 806.6 m/z, (1.9754472 second duty cycle) [11:30:55] 4141 peptides remaining for 804.6 to 806.6... [11:30:55] 3804 peptides remaining for 804.6 to 806.6... [11:30:56] 3465 peptides remaining for 804.6 to 806.6... [11:30:56] 3135 peptides remaining for 804.6 to 806.6... [11:30:57] 2826 peptides remaining for 804.6 to 806.6... [11:30:57] 2511 peptides remaining for 804.6 to 806.6... [11:30:58] 2200 peptides remaining for 804.6 to 806.6... [11:30:58] 1882 peptides remaining for 804.6 to 806.6... [11:30:59] 1568 peptides remaining for 804.6 to 806.6... [11:31:00] 1248 peptides remaining for 804.6 to 806.6... [11:31:00] 941 peptides remaining for 804.6 to 806.6... [11:31:01] 622 peptides remaining for 804.6 to 806.6... [11:31:01] 291 peptides remaining for 804.6 to 806.6... [11:31:02] Processing 806.6 to 808.6 m/z, (1.9754472 second duty cycle) [11:31:03] 4128 peptides remaining for 806.6 to 808.6... [11:31:04] 3795 peptides remaining for 806.6 to 808.6... [11:31:04] 3457 peptides remaining for 806.6 to 808.6... [11:31:05] 3136 peptides remaining for 806.6 to 808.6... [11:31:05] 2819 peptides remaining for 806.6 to 808.6... [11:31:06] 2516 peptides remaining for 806.6 to 808.6... [11:31:06] 2194 peptides remaining for 806.6 to 808.6... [11:31:07] 1886 peptides remaining for 806.6 to 808.6... [11:31:07] 1572 peptides remaining for 806.6 to 808.6... [11:31:08] 1256 peptides remaining for 806.6 to 808.6... [11:31:08] 937 peptides remaining for 806.6 to 808.6... [11:31:09] 627 peptides remaining for 806.6 to 808.6... [11:31:09] 312 peptides remaining for 806.6 to 808.6... [11:31:10] 0 peptides remaining for 806.6 to 808.6... [11:31:10] Processing 808.6 to 810.6 m/z, (1.9754472 second duty cycle) [11:31:12] 4233 peptides remaining for 808.6 to 810.6... [11:31:12] 3906 peptides remaining for 808.6 to 810.6... [11:31:13] 3581 peptides remaining for 808.6 to 810.6... [11:31:13] 3270 peptides remaining for 808.6 to 810.6... [11:31:14] 3011 peptides remaining for 808.6 to 810.6... [11:31:15] 2709 peptides remaining for 808.6 to 810.6... [11:31:15] 2383 peptides remaining for 808.6 to 810.6... [11:31:16] 2073 peptides remaining for 808.6 to 810.6... [11:31:16] 1762 peptides remaining for 808.6 to 810.6... [11:31:17] 1456 peptides remaining for 808.6 to 810.6... [11:31:17] 1153 peptides remaining for 808.6 to 810.6... [11:31:18] 838 peptides remaining for 808.6 to 810.6... [11:31:18] 508 peptides remaining for 808.6 to 810.6... [11:31:19] 178 peptides remaining for 808.6 to 810.6... [11:31:19] Processing 810.6 to 812.6 m/z, (1.9754472 second duty cycle) [11:31:21] 3955 peptides remaining for 810.6 to 812.6... [11:31:21] 3640 peptides remaining for 810.6 to 812.6... [11:31:22] 3324 peptides remaining for 810.6 to 812.6... [11:31:22] 3025 peptides remaining for 810.6 to 812.6... [11:31:23] 2731 peptides remaining for 810.6 to 812.6... [11:31:23] 2414 peptides remaining for 810.6 to 812.6... [11:31:24] 2101 peptides remaining for 810.6 to 812.6... [11:31:24] 1795 peptides remaining for 810.6 to 812.6... [11:31:25] 1469 peptides remaining for 810.6 to 812.6... [11:31:25] 1154 peptides remaining for 810.6 to 812.6... [11:31:26] 845 peptides remaining for 810.6 to 812.6... [11:31:26] 533 peptides remaining for 810.6 to 812.6... [11:31:27] 216 peptides remaining for 810.6 to 812.6... [11:31:27] Processing 812.6 to 814.6 m/z, (1.975447 second duty cycle) [11:31:29] 4032 peptides remaining for 812.6 to 814.6... [11:31:30] 3721 peptides remaining for 812.6 to 814.6... [11:31:30] 3391 peptides remaining for 812.6 to 814.6... [11:31:31] 3073 peptides remaining for 812.6 to 814.6... [11:31:31] 2772 peptides remaining for 812.6 to 814.6... [11:31:32] 2457 peptides remaining for 812.6 to 814.6... [11:31:32] 2138 peptides remaining for 812.6 to 814.6... [11:31:33] 1826 peptides remaining for 812.6 to 814.6... [11:31:33] 1517 peptides remaining for 812.6 to 814.6... [11:31:34] 1203 peptides remaining for 812.6 to 814.6... [11:31:34] 885 peptides remaining for 812.6 to 814.6... [11:31:35] 565 peptides remaining for 812.6 to 814.6... [11:31:35] 254 peptides remaining for 812.6 to 814.6... [11:31:36] Processing 814.6 to 816.6 m/z, (1.975447 second duty cycle) [11:31:37] 4219 peptides remaining for 814.6 to 816.6... [11:31:38] 3896 peptides remaining for 814.6 to 816.6... [11:31:38] 3595 peptides remaining for 814.6 to 816.6... [11:31:39] 3294 peptides remaining for 814.6 to 816.6... [11:31:40] 3004 peptides remaining for 814.6 to 816.6... [11:31:40] 2699 peptides remaining for 814.6 to 816.6... [11:31:41] 2398 peptides remaining for 814.6 to 816.6... [11:31:41] 2099 peptides remaining for 814.6 to 816.6... [11:31:42] 1808 peptides remaining for 814.6 to 816.6... [11:31:42] 1491 peptides remaining for 814.6 to 816.6... [11:31:43] 1196 peptides remaining for 814.6 to 816.6... [11:31:43] 907 peptides remaining for 814.6 to 816.6... [11:31:44] 614 peptides remaining for 814.6 to 816.6... [11:31:44] 293 peptides remaining for 814.6 to 816.6... [11:31:45] 0 peptides remaining for 814.6 to 816.6... [11:31:45] Processing 816.6 to 818.6 m/z, (1.975447 second duty cycle) [11:31:47] 4112 peptides remaining for 816.6 to 818.6... [11:31:47] 3793 peptides remaining for 816.6 to 818.6... [11:31:48] 3483 peptides remaining for 816.6 to 818.6... [11:31:48] 3176 peptides remaining for 816.6 to 818.6... [11:31:49] 2886 peptides remaining for 816.6 to 818.6... [11:31:49] 2582 peptides remaining for 816.6 to 818.6... [11:31:50] 2268 peptides remaining for 816.6 to 818.6... [11:31:50] 1963 peptides remaining for 816.6 to 818.6... [11:31:51] 1675 peptides remaining for 816.6 to 818.6... [11:31:52] 1364 peptides remaining for 816.6 to 818.6... [11:31:52] 1061 peptides remaining for 816.6 to 818.6... [11:31:53] 763 peptides remaining for 816.6 to 818.6... [11:31:53] 448 peptides remaining for 816.6 to 818.6... [11:31:54] 131 peptides remaining for 816.6 to 818.6... [11:31:54] Processing 818.6 to 820.6 m/z, (1.975447 second duty cycle) [11:31:56] 3976 peptides remaining for 818.6 to 820.6... [11:31:56] 3650 peptides remaining for 818.6 to 820.6... [11:31:57] 3336 peptides remaining for 818.6 to 820.6... [11:31:57] 3031 peptides remaining for 818.6 to 820.6... [11:31:58] 2731 peptides remaining for 818.6 to 820.6... [11:31:58] 2420 peptides remaining for 818.6 to 820.6... [11:31:59] 2121 peptides remaining for 818.6 to 820.6... [11:31:59] 1823 peptides remaining for 818.6 to 820.6... [11:32:00] 1508 peptides remaining for 818.6 to 820.6... [11:32:00] 1190 peptides remaining for 818.6 to 820.6... [11:32:01] 882 peptides remaining for 818.6 to 820.6... [11:32:01] 570 peptides remaining for 818.6 to 820.6... [11:32:02] 272 peptides remaining for 818.6 to 820.6... [11:32:02] Processing 820.6 to 822.6 m/z, (1.975447 second duty cycle) [11:32:04] 4003 peptides remaining for 820.6 to 822.6... [11:32:05] 3686 peptides remaining for 820.6 to 822.6... [11:32:05] 3361 peptides remaining for 820.6 to 822.6... [11:32:06] 3067 peptides remaining for 820.6 to 822.6... [11:32:06] 2765 peptides remaining for 820.6 to 822.6... [11:32:07] 2465 peptides remaining for 820.6 to 822.6... [11:32:07] 2152 peptides remaining for 820.6 to 822.6... [11:32:08] 1850 peptides remaining for 820.6 to 822.6... [11:32:08] 1531 peptides remaining for 820.6 to 822.6... [11:32:09] 1226 peptides remaining for 820.6 to 822.6... [11:32:09] 914 peptides remaining for 820.6 to 822.6... [11:32:10] 617 peptides remaining for 820.6 to 822.6... [11:32:10] 333 peptides remaining for 820.6 to 822.6... [11:32:11] 20 peptides remaining for 820.6 to 822.6... [11:32:11] Processing 822.6 to 824.6 m/z, (1.975447 second duty cycle) [11:32:13] 4139 peptides remaining for 822.6 to 824.6... [11:32:14] 3827 peptides remaining for 822.6 to 824.6... [11:32:14] 3524 peptides remaining for 822.6 to 824.6... [11:32:15] 3239 peptides remaining for 822.6 to 824.6... [11:32:15] 2948 peptides remaining for 822.6 to 824.6... [11:32:16] 2649 peptides remaining for 822.6 to 824.6... [11:32:16] 2342 peptides remaining for 822.6 to 824.6... [11:32:17] 2062 peptides remaining for 822.6 to 824.6... [11:32:17] 1767 peptides remaining for 822.6 to 824.6... [11:32:18] 1497 peptides remaining for 822.6 to 824.6... [11:32:18] 1237 peptides remaining for 822.6 to 824.6... [11:32:19] 980 peptides remaining for 822.6 to 824.6... [11:32:19] 714 peptides remaining for 822.6 to 824.6... [11:32:20] 461 peptides remaining for 822.6 to 824.6... [11:32:20] 205 peptides remaining for 822.6 to 824.6... [11:32:21] Processing 824.6 to 826.6 m/z, (1.9755372 second duty cycle) [11:32:22] 3951 peptides remaining for 824.6 to 826.6... [11:32:23] 3639 peptides remaining for 824.6 to 826.6... [11:32:23] 3326 peptides remaining for 824.6 to 826.6... [11:32:24] 3030 peptides remaining for 824.6 to 826.6... [11:32:24] 2722 peptides remaining for 824.6 to 826.6... [11:32:25] 2428 peptides remaining for 824.6 to 826.6... [11:32:25] 2127 peptides remaining for 824.6 to 826.6... [11:32:26] 1837 peptides remaining for 824.6 to 826.6... [11:32:26] 1524 peptides remaining for 824.6 to 826.6... [11:32:27] 1222 peptides remaining for 824.6 to 826.6... [11:32:27] 927 peptides remaining for 824.6 to 826.6... [11:32:28] 634 peptides remaining for 824.6 to 826.6... [11:32:29] 326 peptides remaining for 824.6 to 826.6... [11:32:29] 20 peptides remaining for 824.6 to 826.6... [11:32:30] Processing 826.6 to 828.6 m/z, (1.9755372 second duty cycle) [11:32:31] 4045 peptides remaining for 826.6 to 828.6... [11:32:32] 3718 peptides remaining for 826.6 to 828.6... [11:32:32] 3420 peptides remaining for 826.6 to 828.6... [11:32:33] 3145 peptides remaining for 826.6 to 828.6... [11:32:33] 2833 peptides remaining for 826.6 to 828.6... [11:32:34] 2532 peptides remaining for 826.6 to 828.6... [11:32:34] 2227 peptides remaining for 826.6 to 828.6... [11:32:35] 1927 peptides remaining for 826.6 to 828.6... [11:32:35] 1625 peptides remaining for 826.6 to 828.6... [11:32:36] 1318 peptides remaining for 826.6 to 828.6... [11:32:36] 1009 peptides remaining for 826.6 to 828.6... [11:32:37] 706 peptides remaining for 826.6 to 828.6... [11:32:37] 409 peptides remaining for 826.6 to 828.6... [11:32:38] 90 peptides remaining for 826.6 to 828.6... [11:32:38] Processing 828.6 to 830.6 m/z, (1.9755371 second duty cycle) [11:32:40] 3933 peptides remaining for 828.6 to 830.6... [11:32:41] 3601 peptides remaining for 828.6 to 830.6... [11:32:41] 3272 peptides remaining for 828.6 to 830.6... [11:32:42] 2969 peptides remaining for 828.6 to 830.6... [11:32:42] 2658 peptides remaining for 828.6 to 830.6... [11:32:43] 2362 peptides remaining for 828.6 to 830.6... [11:32:43] 2068 peptides remaining for 828.6 to 830.6... [11:32:44] 1774 peptides remaining for 828.6 to 830.6... [11:32:44] 1474 peptides remaining for 828.6 to 830.6... [11:32:45] 1172 peptides remaining for 828.6 to 830.6... [11:32:45] 860 peptides remaining for 828.6 to 830.6... [11:32:46] 546 peptides remaining for 828.6 to 830.6... [11:32:46] 253 peptides remaining for 828.6 to 830.6... [11:32:47] Processing 830.6 to 832.6 m/z, (1.9755371 second duty cycle) [11:32:48] 3907 peptides remaining for 830.6 to 832.6... [11:32:49] 3597 peptides remaining for 830.6 to 832.6... [11:32:49] 3292 peptides remaining for 830.6 to 832.6... [11:32:50] 2996 peptides remaining for 830.6 to 832.6... [11:32:51] 2689 peptides remaining for 830.6 to 832.6... [11:32:51] 2390 peptides remaining for 830.6 to 832.6... [11:32:52] 2078 peptides remaining for 830.6 to 832.6... [11:32:52] 1765 peptides remaining for 830.6 to 832.6... [11:32:53] 1465 peptides remaining for 830.6 to 832.6... [11:32:53] 1172 peptides remaining for 830.6 to 832.6... [11:32:54] 867 peptides remaining for 830.6 to 832.6... [11:32:54] 571 peptides remaining for 830.6 to 832.6... [11:32:55] 267 peptides remaining for 830.6 to 832.6... [11:32:55] 0 peptides remaining for 830.6 to 832.6... [11:32:56] Processing 832.6 to 834.6 m/z, (1.9755374 second duty cycle) [11:32:57] 3845 peptides remaining for 832.6 to 834.6... [11:32:58] 3535 peptides remaining for 832.6 to 834.6... [11:32:58] 3232 peptides remaining for 832.6 to 834.6... [11:32:59] 2924 peptides remaining for 832.6 to 834.6... [11:32:59] 2628 peptides remaining for 832.6 to 834.6... [11:33:00] 2325 peptides remaining for 832.6 to 834.6... [11:33:00] 2024 peptides remaining for 832.6 to 834.6... [11:33:01] 1729 peptides remaining for 832.6 to 834.6... [11:33:01] 1439 peptides remaining for 832.6 to 834.6... [11:33:02] 1127 peptides remaining for 832.6 to 834.6... [11:33:02] 823 peptides remaining for 832.6 to 834.6... [11:33:03] 517 peptides remaining for 832.6 to 834.6... [11:33:04] 211 peptides remaining for 832.6 to 834.6... [11:33:04] Processing 834.6 to 836.6 m/z, (1.9755374 second duty cycle) [11:33:06] 3914 peptides remaining for 834.6 to 836.6... [11:33:06] 3604 peptides remaining for 834.6 to 836.6... [11:33:07] 3274 peptides remaining for 834.6 to 836.6... [11:33:07] 2977 peptides remaining for 834.6 to 836.6... [11:33:08] 2683 peptides remaining for 834.6 to 836.6... [11:33:08] 2374 peptides remaining for 834.6 to 836.6... [11:33:09] 2066 peptides remaining for 834.6 to 836.6... [11:33:09] 1760 peptides remaining for 834.6 to 836.6... [11:33:10] 1455 peptides remaining for 834.6 to 836.6... [11:33:10] 1153 peptides remaining for 834.6 to 836.6... [11:33:11] 844 peptides remaining for 834.6 to 836.6... [11:33:11] 537 peptides remaining for 834.6 to 836.6... [11:33:12] 235 peptides remaining for 834.6 to 836.6... [11:33:12] Processing 836.6 to 838.6 m/z, (1.9755372 second duty cycle) [11:33:14] 3888 peptides remaining for 836.6 to 838.6... [11:33:14] 3572 peptides remaining for 836.6 to 838.6... [11:33:15] 3263 peptides remaining for 836.6 to 838.6... [11:33:15] 2962 peptides remaining for 836.6 to 838.6... [11:33:16] 2663 peptides remaining for 836.6 to 838.6... [11:33:17] 2348 peptides remaining for 836.6 to 838.6... [11:33:17] 2040 peptides remaining for 836.6 to 838.6... [11:33:18] 1735 peptides remaining for 836.6 to 838.6... [11:33:18] 1437 peptides remaining for 836.6 to 838.6... [11:33:19] 1136 peptides remaining for 836.6 to 838.6... [11:33:19] 837 peptides remaining for 836.6 to 838.6... [11:33:20] 545 peptides remaining for 836.6 to 838.6... [11:33:20] 258 peptides remaining for 836.6 to 838.6... [11:33:21] Processing 838.6 to 840.6 m/z, (1.9755372 second duty cycle) [11:33:22] 3917 peptides remaining for 838.6 to 840.6... [11:33:23] 3594 peptides remaining for 838.6 to 840.6... [11:33:23] 3297 peptides remaining for 838.6 to 840.6... [11:33:24] 3005 peptides remaining for 838.6 to 840.6... [11:33:24] 2710 peptides remaining for 838.6 to 840.6... [11:33:25] 2411 peptides remaining for 838.6 to 840.6... [11:33:25] 2121 peptides remaining for 838.6 to 840.6... [11:33:26] 1814 peptides remaining for 838.6 to 840.6... [11:33:26] 1523 peptides remaining for 838.6 to 840.6... [11:33:27] 1217 peptides remaining for 838.6 to 840.6... [11:33:27] 924 peptides remaining for 838.6 to 840.6... [11:33:28] 629 peptides remaining for 838.6 to 840.6... [11:33:28] 336 peptides remaining for 838.6 to 840.6... [11:33:29] 8 peptides remaining for 838.6 to 840.6... [11:33:30] Processing 840.6 to 842.6 m/z, (1.9755372 second duty cycle) [11:33:31] 3791 peptides remaining for 840.6 to 842.6... [11:33:32] 3450 peptides remaining for 840.6 to 842.6... [11:33:32] 3133 peptides remaining for 840.6 to 842.6... [11:33:33] 2843 peptides remaining for 840.6 to 842.6... [11:33:33] 2543 peptides remaining for 840.6 to 842.6... [11:33:34] 2239 peptides remaining for 840.6 to 842.6... [11:33:34] 1934 peptides remaining for 840.6 to 842.6... [11:33:35] 1641 peptides remaining for 840.6 to 842.6... [11:33:35] 1355 peptides remaining for 840.6 to 842.6... [11:33:36] 1043 peptides remaining for 840.6 to 842.6... [11:33:36] 755 peptides remaining for 840.6 to 842.6... [11:33:37] 448 peptides remaining for 840.6 to 842.6... [11:33:37] 127 peptides remaining for 840.6 to 842.6... [11:33:38] Processing 842.6 to 844.6 m/z, (1.9755372 second duty cycle) [11:33:39] 3935 peptides remaining for 842.6 to 844.6... [11:33:40] 3623 peptides remaining for 842.6 to 844.6... [11:33:41] 3296 peptides remaining for 842.6 to 844.6... [11:33:41] 2996 peptides remaining for 842.6 to 844.6... [11:33:42] 2699 peptides remaining for 842.6 to 844.6... [11:33:42] 2400 peptides remaining for 842.6 to 844.6... [11:33:43] 2083 peptides remaining for 842.6 to 844.6... [11:33:43] 1784 peptides remaining for 842.6 to 844.6... [11:33:44] 1491 peptides remaining for 842.6 to 844.6... [11:33:44] 1195 peptides remaining for 842.6 to 844.6... [11:33:45] 898 peptides remaining for 842.6 to 844.6... [11:33:45] 603 peptides remaining for 842.6 to 844.6... [11:33:46] 285 peptides remaining for 842.6 to 844.6... [11:33:46] 0 peptides remaining for 842.6 to 844.6... [11:33:47] Processing 844.6 to 846.6 m/z, (1.9755372 second duty cycle) [11:33:48] 3763 peptides remaining for 844.6 to 846.6... [11:33:49] 3454 peptides remaining for 844.6 to 846.6... [11:33:49] 3132 peptides remaining for 844.6 to 846.6... [11:33:50] 2841 peptides remaining for 844.6 to 846.6... [11:33:50] 2555 peptides remaining for 844.6 to 846.6... [11:33:51] 2257 peptides remaining for 844.6 to 846.6... [11:33:51] 1950 peptides remaining for 844.6 to 846.6... [11:33:52] 1650 peptides remaining for 844.6 to 846.6... [11:33:52] 1357 peptides remaining for 844.6 to 846.6... [11:33:53] 1048 peptides remaining for 844.6 to 846.6... [11:33:53] 738 peptides remaining for 844.6 to 846.6... [11:33:54] 436 peptides remaining for 844.6 to 846.6... [11:33:54] 110 peptides remaining for 844.6 to 846.6... [11:33:55] Processing 846.6 to 848.6 m/z, (1.9755372 second duty cycle) [11:33:57] 3785 peptides remaining for 846.6 to 848.6... [11:33:57] 3467 peptides remaining for 846.6 to 848.6... [11:33:58] 3156 peptides remaining for 846.6 to 848.6... [11:33:58] 2867 peptides remaining for 846.6 to 848.6... [11:33:59] 2571 peptides remaining for 846.6 to 848.6... [11:33:59] 2257 peptides remaining for 846.6 to 848.6... [11:34:00] 1957 peptides remaining for 846.6 to 848.6... [11:34:00] 1657 peptides remaining for 846.6 to 848.6... [11:34:01] 1372 peptides remaining for 846.6 to 848.6... [11:34:01] 1073 peptides remaining for 846.6 to 848.6... [11:34:02] 769 peptides remaining for 846.6 to 848.6... [11:34:02] 469 peptides remaining for 846.6 to 848.6... [11:34:03] 150 peptides remaining for 846.6 to 848.6... [11:34:03] Processing 848.6 to 850.6 m/z, (1.9755374 second duty cycle) [11:34:05] 3857 peptides remaining for 848.6 to 850.6... [11:34:06] 3547 peptides remaining for 848.6 to 850.6... [11:34:06] 3235 peptides remaining for 848.6 to 850.6... [11:34:07] 2955 peptides remaining for 848.6 to 850.6... [11:34:07] 2653 peptides remaining for 848.6 to 850.6... [11:34:08] 2371 peptides remaining for 848.6 to 850.6... [11:34:08] 2080 peptides remaining for 848.6 to 850.6... [11:34:09] 1799 peptides remaining for 848.6 to 850.6... [11:34:09] 1515 peptides remaining for 848.6 to 850.6... [11:34:10] 1232 peptides remaining for 848.6 to 850.6... [11:34:10] 939 peptides remaining for 848.6 to 850.6... [11:34:11] 648 peptides remaining for 848.6 to 850.6... [11:34:11] 333 peptides remaining for 848.6 to 850.6... [11:34:12] 33 peptides remaining for 848.6 to 850.6... [11:34:12] Processing 850.6 to 852.6 m/z, (1.9755372 second duty cycle) [11:34:14] 3826 peptides remaining for 850.6 to 852.6... [11:34:14] 3509 peptides remaining for 850.6 to 852.6... [11:34:15] 3196 peptides remaining for 850.6 to 852.6... [11:34:15] 2886 peptides remaining for 850.6 to 852.6... [11:34:16] 2609 peptides remaining for 850.6 to 852.6... [11:34:16] 2310 peptides remaining for 850.6 to 852.6... [11:34:17] 2011 peptides remaining for 850.6 to 852.6... [11:34:17] 1714 peptides remaining for 850.6 to 852.6... [11:34:18] 1416 peptides remaining for 850.6 to 852.6... [11:34:19] 1109 peptides remaining for 850.6 to 852.6... [11:34:19] 811 peptides remaining for 850.6 to 852.6... [11:34:20] 510 peptides remaining for 850.6 to 852.6... [11:34:20] 196 peptides remaining for 850.6 to 852.6... [11:34:21] Processing 852.6 to 854.6 m/z, (1.9755374 second duty cycle) [11:34:22] 3763 peptides remaining for 852.6 to 854.6... [11:34:23] 3457 peptides remaining for 852.6 to 854.6... [11:34:23] 3140 peptides remaining for 852.6 to 854.6... [11:34:24] 2854 peptides remaining for 852.6 to 854.6... [11:34:24] 2552 peptides remaining for 852.6 to 854.6... [11:34:25] 2244 peptides remaining for 852.6 to 854.6... [11:34:25] 1949 peptides remaining for 852.6 to 854.6... [11:34:26] 1651 peptides remaining for 852.6 to 854.6... [11:34:26] 1357 peptides remaining for 852.6 to 854.6... [11:34:27] 1053 peptides remaining for 852.6 to 854.6... [11:34:27] 748 peptides remaining for 852.6 to 854.6... [11:34:28] 441 peptides remaining for 852.6 to 854.6... [11:34:28] 142 peptides remaining for 852.6 to 854.6... [11:34:29] Processing 854.6 to 856.6 m/z, (1.9755374 second duty cycle) [11:34:31] 3728 peptides remaining for 854.6 to 856.6... [11:34:31] 3397 peptides remaining for 854.6 to 856.6... [11:34:32] 3091 peptides remaining for 854.6 to 856.6... [11:34:32] 2790 peptides remaining for 854.6 to 856.6... [11:34:33] 2503 peptides remaining for 854.6 to 856.6... [11:34:33] 2201 peptides remaining for 854.6 to 856.6... [11:34:34] 1907 peptides remaining for 854.6 to 856.6... [11:34:34] 1600 peptides remaining for 854.6 to 856.6... [11:34:35] 1311 peptides remaining for 854.6 to 856.6... [11:34:35] 1015 peptides remaining for 854.6 to 856.6... [11:34:36] 705 peptides remaining for 854.6 to 856.6... [11:34:36] 402 peptides remaining for 854.6 to 856.6... [11:34:37] 95 peptides remaining for 854.6 to 856.6... [11:34:37] Processing 856.6 to 858.6 m/z, (1.9755374 second duty cycle) [11:34:39] 3777 peptides remaining for 856.6 to 858.6... [11:34:39] 3457 peptides remaining for 856.6 to 858.6... [11:34:40] 3150 peptides remaining for 856.6 to 858.6... [11:34:40] 2851 peptides remaining for 856.6 to 858.6... [11:34:41] 2556 peptides remaining for 856.6 to 858.6... [11:34:41] 2260 peptides remaining for 856.6 to 858.6... [11:34:42] 1978 peptides remaining for 856.6 to 858.6... [11:34:42] 1684 peptides remaining for 856.6 to 858.6... [11:34:43] 1396 peptides remaining for 856.6 to 858.6... [11:34:43] 1100 peptides remaining for 856.6 to 858.6... [11:34:44] 803 peptides remaining for 856.6 to 858.6... [11:34:44] 500 peptides remaining for 856.6 to 858.6... [11:34:45] 196 peptides remaining for 856.6 to 858.6... [11:34:46] Processing 858.6 to 860.6 m/z, (1.9755374 second duty cycle) [11:34:47] 3790 peptides remaining for 858.6 to 860.6... [11:34:48] 3482 peptides remaining for 858.6 to 860.6... [11:34:48] 3168 peptides remaining for 858.6 to 860.6... [11:34:49] 2876 peptides remaining for 858.6 to 860.6... [11:34:49] 2592 peptides remaining for 858.6 to 860.6... [11:34:50] 2296 peptides remaining for 858.6 to 860.6... [11:34:50] 1996 peptides remaining for 858.6 to 860.6... [11:34:51] 1707 peptides remaining for 858.6 to 860.6... [11:34:51] 1412 peptides remaining for 858.6 to 860.6... [11:34:52] 1122 peptides remaining for 858.6 to 860.6... [11:34:52] 806 peptides remaining for 858.6 to 860.6... [11:34:53] 508 peptides remaining for 858.6 to 860.6... [11:34:53] 211 peptides remaining for 858.6 to 860.6... [11:34:54] Processing 860.6 to 862.6 m/z, (1.9755375 second duty cycle) [11:34:56] 3763 peptides remaining for 860.6 to 862.6... [11:34:56] 3421 peptides remaining for 860.6 to 862.6... [11:34:57] 3128 peptides remaining for 860.6 to 862.6... [11:34:57] 2846 peptides remaining for 860.6 to 862.6... [11:34:58] 2544 peptides remaining for 860.6 to 862.6... [11:34:58] 2233 peptides remaining for 860.6 to 862.6... [11:34:59] 1948 peptides remaining for 860.6 to 862.6... [11:34:59] 1658 peptides remaining for 860.6 to 862.6... [11:35:00] 1352 peptides remaining for 860.6 to 862.6... [11:35:00] 1042 peptides remaining for 860.6 to 862.6... [11:35:01] 732 peptides remaining for 860.6 to 862.6... [11:35:01] 423 peptides remaining for 860.6 to 862.6... [11:35:02] 108 peptides remaining for 860.6 to 862.6... [11:35:02] Processing 862.6 to 864.6 m/z, (1.9755375 second duty cycle) [11:35:04] 3710 peptides remaining for 862.6 to 864.6... [11:35:04] 3406 peptides remaining for 862.6 to 864.6... [11:35:05] 3098 peptides remaining for 862.6 to 864.6... [11:35:05] 2800 peptides remaining for 862.6 to 864.6... [11:35:06] 2501 peptides remaining for 862.6 to 864.6... [11:35:06] 2217 peptides remaining for 862.6 to 864.6... [11:35:07] 1917 peptides remaining for 862.6 to 864.6... [11:35:07] 1628 peptides remaining for 862.6 to 864.6... [11:35:08] 1336 peptides remaining for 862.6 to 864.6... [11:35:08] 1052 peptides remaining for 862.6 to 864.6... [11:35:09] 758 peptides remaining for 862.6 to 864.6... [11:35:09] 454 peptides remaining for 862.6 to 864.6... [11:35:10] 143 peptides remaining for 862.6 to 864.6... [11:35:10] Processing 864.6 to 866.6 m/z, (1.9755379 second duty cycle) [11:35:12] 3802 peptides remaining for 864.6 to 866.6... [11:35:13] 3489 peptides remaining for 864.6 to 866.6... [11:35:13] 3172 peptides remaining for 864.6 to 866.6... [11:35:14] 2884 peptides remaining for 864.6 to 866.6... [11:35:14] 2584 peptides remaining for 864.6 to 866.6... [11:35:15] 2297 peptides remaining for 864.6 to 866.6... [11:35:15] 2005 peptides remaining for 864.6 to 866.6... [11:35:16] 1717 peptides remaining for 864.6 to 866.6... [11:35:16] 1419 peptides remaining for 864.6 to 866.6... [11:35:17] 1130 peptides remaining for 864.6 to 866.6... [11:35:17] 826 peptides remaining for 864.6 to 866.6... [11:35:18] 524 peptides remaining for 864.6 to 866.6... [11:35:18] 224 peptides remaining for 864.6 to 866.6... [11:35:19] Processing 866.6 to 868.6 m/z, (1.9755379 second duty cycle) [11:35:20] 3729 peptides remaining for 866.6 to 868.6... [11:35:21] 3423 peptides remaining for 866.6 to 868.6... [11:35:21] 3101 peptides remaining for 866.6 to 868.6... [11:35:22] 2839 peptides remaining for 866.6 to 868.6... [11:35:22] 2532 peptides remaining for 866.6 to 868.6... [11:35:23] 2243 peptides remaining for 866.6 to 868.6... [11:35:24] 1946 peptides remaining for 866.6 to 868.6... [11:35:24] 1658 peptides remaining for 866.6 to 868.6... [11:35:25] 1363 peptides remaining for 866.6 to 868.6... [11:35:25] 1059 peptides remaining for 866.6 to 868.6... [11:35:26] 772 peptides remaining for 866.6 to 868.6... [11:35:26] 472 peptides remaining for 866.6 to 868.6... [11:35:27] 183 peptides remaining for 866.6 to 868.6... [11:35:27] Processing 868.6 to 870.6 m/z, (1.9755379 second duty cycle) [11:35:29] 3674 peptides remaining for 868.6 to 870.6... [11:35:29] 3372 peptides remaining for 868.6 to 870.6... [11:35:30] 3060 peptides remaining for 868.6 to 870.6... [11:35:30] 2764 peptides remaining for 868.6 to 870.6... [11:35:31] 2464 peptides remaining for 868.6 to 870.6... [11:35:31] 2177 peptides remaining for 868.6 to 870.6... [11:35:32] 1884 peptides remaining for 868.6 to 870.6... [11:35:32] 1587 peptides remaining for 868.6 to 870.6... [11:35:33] 1294 peptides remaining for 868.6 to 870.6... [11:35:33] 997 peptides remaining for 868.6 to 870.6... [11:35:34] 698 peptides remaining for 868.6 to 870.6... [11:35:34] 403 peptides remaining for 868.6 to 870.6... [11:35:35] 97 peptides remaining for 868.6 to 870.6... [11:35:35] Processing 870.6 to 872.6 m/z, (1.9755379 second duty cycle) [11:35:37] 3567 peptides remaining for 870.6 to 872.6... [11:35:37] 3258 peptides remaining for 870.6 to 872.6... [11:35:38] 2947 peptides remaining for 870.6 to 872.6... [11:35:39] 2666 peptides remaining for 870.6 to 872.6... [11:35:39] 2369 peptides remaining for 870.6 to 872.6... [11:35:40] 2074 peptides remaining for 870.6 to 872.6... [11:35:40] 1790 peptides remaining for 870.6 to 872.6... [11:35:41] 1504 peptides remaining for 870.6 to 872.6... [11:35:41] 1215 peptides remaining for 870.6 to 872.6... [11:35:42] 908 peptides remaining for 870.6 to 872.6... [11:35:42] 606 peptides remaining for 870.6 to 872.6... [11:35:43] 310 peptides remaining for 870.6 to 872.6... [11:35:43] 2 peptides remaining for 870.6 to 872.6... [11:35:44] Processing 872.6 to 874.6 m/z, (1.9755379 second duty cycle) [11:35:45] 3791 peptides remaining for 872.6 to 874.6... [11:35:46] 3478 peptides remaining for 872.6 to 874.6... [11:35:46] 3183 peptides remaining for 872.6 to 874.6... [11:35:47] 2893 peptides remaining for 872.6 to 874.6... [11:35:47] 2607 peptides remaining for 872.6 to 874.6... [11:35:48] 2312 peptides remaining for 872.6 to 874.6... [11:35:48] 2035 peptides remaining for 872.6 to 874.6... [11:35:49] 1741 peptides remaining for 872.6 to 874.6... [11:35:49] 1445 peptides remaining for 872.6 to 874.6... [11:35:50] 1149 peptides remaining for 872.6 to 874.6... [11:35:50] 861 peptides remaining for 872.6 to 874.6... [11:35:51] 565 peptides remaining for 872.6 to 874.6... [11:35:51] 268 peptides remaining for 872.6 to 874.6... [11:35:52] Processing 874.6 to 876.6 m/z, (1.9755379 second duty cycle) [11:35:53] 3709 peptides remaining for 874.6 to 876.6... [11:35:54] 3406 peptides remaining for 874.6 to 876.6... [11:35:54] 3096 peptides remaining for 874.6 to 876.6... [11:35:55] 2818 peptides remaining for 874.6 to 876.6... [11:35:55] 2514 peptides remaining for 874.6 to 876.6... [11:35:56] 2211 peptides remaining for 874.6 to 876.6... [11:35:56] 1926 peptides remaining for 874.6 to 876.6... [11:35:57] 1631 peptides remaining for 874.6 to 876.6... [11:35:57] 1348 peptides remaining for 874.6 to 876.6... [11:35:58] 1056 peptides remaining for 874.6 to 876.6... [11:35:59] 767 peptides remaining for 874.6 to 876.6... [11:35:59] 471 peptides remaining for 874.6 to 876.6... [11:36:00] 148 peptides remaining for 874.6 to 876.6... [11:36:00] Processing 876.6 to 878.6 m/z, (1.9755379 second duty cycle) [11:36:02] 3598 peptides remaining for 876.6 to 878.6... [11:36:02] 3296 peptides remaining for 876.6 to 878.6... [11:36:03] 2985 peptides remaining for 876.6 to 878.6... [11:36:03] 2687 peptides remaining for 876.6 to 878.6... [11:36:04] 2388 peptides remaining for 876.6 to 878.6... [11:36:04] 2098 peptides remaining for 876.6 to 878.6... [11:36:05] 1815 peptides remaining for 876.6 to 878.6... [11:36:05] 1525 peptides remaining for 876.6 to 878.6... [11:36:06] 1236 peptides remaining for 876.6 to 878.6... [11:36:06] 929 peptides remaining for 876.6 to 878.6... [11:36:07] 637 peptides remaining for 876.6 to 878.6... [11:36:07] 338 peptides remaining for 876.6 to 878.6... [11:36:08] 22 peptides remaining for 876.6 to 878.6... [11:36:08] Processing 878.6 to 880.7 m/z, (1.9755379 second duty cycle) [11:36:10] 3689 peptides remaining for 878.6 to 880.7... [11:36:10] 3390 peptides remaining for 878.6 to 880.7... [11:36:11] 3079 peptides remaining for 878.6 to 880.7... [11:36:11] 2778 peptides remaining for 878.6 to 880.7... [11:36:12] 2493 peptides remaining for 878.6 to 880.7... [11:36:12] 2184 peptides remaining for 878.6 to 880.7... [11:36:13] 1901 peptides remaining for 878.6 to 880.7... [11:36:13] 1611 peptides remaining for 878.6 to 880.7... [11:36:14] 1310 peptides remaining for 878.6 to 880.7... [11:36:14] 1021 peptides remaining for 878.6 to 880.7... [11:36:15] 720 peptides remaining for 878.6 to 880.7... [11:36:16] 423 peptides remaining for 878.6 to 880.7... [11:36:16] 118 peptides remaining for 878.6 to 880.7... [11:36:17] Processing 880.7 to 882.7 m/z, (1.9755379 second duty cycle) [11:36:18] 3650 peptides remaining for 880.7 to 882.7... [11:36:19] 3575 peptides remaining for 880.7 to 882.7... [11:36:19] 3262 peptides remaining for 880.7 to 882.7... [11:36:20] 2943 peptides remaining for 880.7 to 882.7... [11:36:20] 2651 peptides remaining for 880.7 to 882.7... [11:36:21] 2373 peptides remaining for 880.7 to 882.7... [11:36:21] 2084 peptides remaining for 880.7 to 882.7... [11:36:22] 1801 peptides remaining for 880.7 to 882.7... [11:36:22] 1507 peptides remaining for 880.7 to 882.7... [11:36:23] 1206 peptides remaining for 880.7 to 882.7... [11:36:23] 918 peptides remaining for 880.7 to 882.7... [11:36:24] 615 peptides remaining for 880.7 to 882.7... [11:36:24] 308 peptides remaining for 880.7 to 882.7... [11:36:25] 6 peptides remaining for 880.7 to 882.7... [11:36:25] Processing 882.7 to 884.7 m/z, (1.9755379 second duty cycle) [11:36:27] 3680 peptides remaining for 882.7 to 884.7... [11:36:27] 3365 peptides remaining for 882.7 to 884.7... [11:36:28] 3053 peptides remaining for 882.7 to 884.7... [11:36:28] 2765 peptides remaining for 882.7 to 884.7... [11:36:29] 2476 peptides remaining for 882.7 to 884.7... [11:36:29] 2176 peptides remaining for 882.7 to 884.7... [11:36:30] 1885 peptides remaining for 882.7 to 884.7... [11:36:31] 1593 peptides remaining for 882.7 to 884.7... [11:36:31] 1302 peptides remaining for 882.7 to 884.7... [11:36:32] 1012 peptides remaining for 882.7 to 884.7... [11:36:32] 701 peptides remaining for 882.7 to 884.7... [11:36:33] 402 peptides remaining for 882.7 to 884.7... [11:36:33] 92 peptides remaining for 882.7 to 884.7... [11:36:34] Processing 884.7 to 886.7 m/z, (1.975538 second duty cycle) [11:36:35] 3747 peptides remaining for 884.7 to 886.7... [11:36:36] 3438 peptides remaining for 884.7 to 886.7... [11:36:36] 3125 peptides remaining for 884.7 to 886.7... [11:36:37] 2831 peptides remaining for 884.7 to 886.7... [11:36:37] 2533 peptides remaining for 884.7 to 886.7... [11:36:38] 2251 peptides remaining for 884.7 to 886.7... [11:36:38] 1955 peptides remaining for 884.7 to 886.7... [11:36:39] 1665 peptides remaining for 884.7 to 886.7... [11:36:39] 1365 peptides remaining for 884.7 to 886.7... [11:36:40] 1086 peptides remaining for 884.7 to 886.7... [11:36:40] 790 peptides remaining for 884.7 to 886.7... [11:36:41] 487 peptides remaining for 884.7 to 886.7... [11:36:41] 178 peptides remaining for 884.7 to 886.7... [11:36:42] Processing 886.7 to 888.7 m/z, (1.975538 second duty cycle) [11:36:44] 3586 peptides remaining for 886.7 to 888.7... [11:36:44] 3280 peptides remaining for 886.7 to 888.7... [11:36:45] 2971 peptides remaining for 886.7 to 888.7... [11:36:45] 2684 peptides remaining for 886.7 to 888.7... [11:36:46] 2405 peptides remaining for 886.7 to 888.7... [11:36:46] 2092 peptides remaining for 886.7 to 888.7... [11:36:47] 1813 peptides remaining for 886.7 to 888.7... [11:36:47] 1525 peptides remaining for 886.7 to 888.7... [11:36:48] 1232 peptides remaining for 886.7 to 888.7... [11:36:48] 926 peptides remaining for 886.7 to 888.7... [11:36:49] 629 peptides remaining for 886.7 to 888.7... [11:36:49] 337 peptides remaining for 886.7 to 888.7... [11:36:50] 23 peptides remaining for 886.7 to 888.7... [11:36:50] Processing 888.7 to 890.7 m/z, (1.9755379 second duty cycle) [11:36:52] 3728 peptides remaining for 888.7 to 890.7... [11:36:52] 3433 peptides remaining for 888.7 to 890.7... [11:36:53] 3124 peptides remaining for 888.7 to 890.7... [11:36:53] 2845 peptides remaining for 888.7 to 890.7... [11:36:54] 2564 peptides remaining for 888.7 to 890.7... [11:36:54] 2265 peptides remaining for 888.7 to 890.7... [11:36:55] 1978 peptides remaining for 888.7 to 890.7... [11:36:55] 1696 peptides remaining for 888.7 to 890.7... [11:36:56] 1415 peptides remaining for 888.7 to 890.7... [11:36:56] 1114 peptides remaining for 888.7 to 890.7... [11:36:57] 816 peptides remaining for 888.7 to 890.7... [11:36:58] 525 peptides remaining for 888.7 to 890.7... [11:36:58] 237 peptides remaining for 888.7 to 890.7... [11:36:59] Processing 890.7 to 892.7 m/z, (1.9755379 second duty cycle) [11:37:00] 3558 peptides remaining for 890.7 to 892.7... [11:37:01] 3240 peptides remaining for 890.7 to 892.7... [11:37:01] 2935 peptides remaining for 890.7 to 892.7... [11:37:02] 2660 peptides remaining for 890.7 to 892.7... [11:37:02] 2360 peptides remaining for 890.7 to 892.7... [11:37:03] 2073 peptides remaining for 890.7 to 892.7... [11:37:03] 1785 peptides remaining for 890.7 to 892.7... [11:37:04] 1501 peptides remaining for 890.7 to 892.7... [11:37:04] 1213 peptides remaining for 890.7 to 892.7... [11:37:05] 914 peptides remaining for 890.7 to 892.7... [11:37:05] 621 peptides remaining for 890.7 to 892.7... [11:37:06] 328 peptides remaining for 890.7 to 892.7... [11:37:06] 25 peptides remaining for 890.7 to 892.7... [11:37:07] Processing 892.7 to 894.7 m/z, (1.9755379 second duty cycle) [11:37:08] 3522 peptides remaining for 892.7 to 894.7... [11:37:09] 3196 peptides remaining for 892.7 to 894.7... [11:37:09] 2883 peptides remaining for 892.7 to 894.7... [11:37:10] 2587 peptides remaining for 892.7 to 894.7... [11:37:11] 2305 peptides remaining for 892.7 to 894.7... [11:37:11] 2000 peptides remaining for 892.7 to 894.7... [11:37:12] 1711 peptides remaining for 892.7 to 894.7... [11:37:12] 1421 peptides remaining for 892.7 to 894.7... [11:37:13] 1133 peptides remaining for 892.7 to 894.7... [11:37:13] 831 peptides remaining for 892.7 to 894.7... [11:37:14] 531 peptides remaining for 892.7 to 894.7... [11:37:14] 224 peptides remaining for 892.7 to 894.7... [11:37:15] Processing 894.7 to 896.7 m/z, (1.9755379 second duty cycle) [11:37:16] 3632 peptides remaining for 894.7 to 896.7... [11:37:17] 3331 peptides remaining for 894.7 to 896.7... [11:37:17] 3006 peptides remaining for 894.7 to 896.7... [11:37:18] 2726 peptides remaining for 894.7 to 896.7... [11:37:18] 2456 peptides remaining for 894.7 to 896.7... [11:37:19] 2167 peptides remaining for 894.7 to 896.7... [11:37:19] 1889 peptides remaining for 894.7 to 896.7... [11:37:20] 1609 peptides remaining for 894.7 to 896.7... [11:37:21] 1318 peptides remaining for 894.7 to 896.7... [11:37:21] 1017 peptides remaining for 894.7 to 896.7... [11:37:22] 721 peptides remaining for 894.7 to 896.7... [11:37:22] 433 peptides remaining for 894.7 to 896.7... [11:37:23] 119 peptides remaining for 894.7 to 896.7... [11:37:23] Processing 896.7 to 898.7 m/z, (1.9755381 second duty cycle) [11:37:25] 3666 peptides remaining for 896.7 to 898.7... [11:37:25] 3347 peptides remaining for 896.7 to 898.7... [11:37:26] 3038 peptides remaining for 896.7 to 898.7... [11:37:26] 2741 peptides remaining for 896.7 to 898.7... [11:37:27] 2446 peptides remaining for 896.7 to 898.7... [11:37:27] 2151 peptides remaining for 896.7 to 898.7... [11:37:28] 1863 peptides remaining for 896.7 to 898.7... [11:37:28] 1577 peptides remaining for 896.7 to 898.7... [11:37:29] 1281 peptides remaining for 896.7 to 898.7... [11:37:29] 993 peptides remaining for 896.7 to 898.7... [11:37:30] 700 peptides remaining for 896.7 to 898.7... [11:37:30] 398 peptides remaining for 896.7 to 898.7... [11:37:31] 98 peptides remaining for 896.7 to 898.7... [11:37:32] Processing 898.7 to 900.7 m/z, (1.9755381 second duty cycle) [11:37:33] 3424 peptides remaining for 898.7 to 900.7... [11:37:34] 3138 peptides remaining for 898.7 to 900.7... [11:37:34] 2841 peptides remaining for 898.7 to 900.7... [11:37:35] 2550 peptides remaining for 898.7 to 900.7... [11:37:35] 2270 peptides remaining for 898.7 to 900.7... [11:37:36] 1974 peptides remaining for 898.7 to 900.7... [11:37:36] 1682 peptides remaining for 898.7 to 900.7... [11:37:37] 1400 peptides remaining for 898.7 to 900.7... [11:37:37] 1137 peptides remaining for 898.7 to 900.7... [11:37:38] 868 peptides remaining for 898.7 to 900.7... [11:37:38] 614 peptides remaining for 898.7 to 900.7... [11:37:39] 352 peptides remaining for 898.7 to 900.7... [11:37:39] 76 peptides remaining for 898.7 to 900.7... [11:37:40] Processing 900.7 to 902.7 m/z, (3.950803 second duty cycle) [11:37:41] 3452 peptides remaining for 900.7 to 902.7... [11:37:42] 2925 peptides remaining for 900.7 to 902.7... [11:37:43] 2436 peptides remaining for 900.7 to 902.7... [11:37:43] 1969 peptides remaining for 900.7 to 902.7... [11:37:44] 1462 peptides remaining for 900.7 to 902.7... [11:37:44] 970 peptides remaining for 900.7 to 902.7... [11:37:45] 484 peptides remaining for 900.7 to 902.7... [11:37:45] 0 peptides remaining for 900.7 to 902.7... [11:37:46] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:38:00] Sorted feature file in 13.95 seconds wall clock time [11:38:00] File size check: 250692491 vs 250692491 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:38:00] 609363 total peptides processed. [11:38:00] Running Percolator... [11:38:00] Executing [cmd /c C:\Windows\Temp\tmp7E74.java\Percolator-v3-01-6338944973478761187.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt] [11:38:00] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:38:00] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:38:00] Written by Lukas Käll (lukall@u.washington.edu) in the [11:38:00] Department of Genome Sciences at the University of Washington. [11:38:00] Issued command: [11:38:00] C:\Windows\Temp\tmp7E74.java\Percolator-v3-01-6338944973478761187.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:38:00] Started Wed Jul 17 11:38:00 2024 [11:38:00] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [11:38:00] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:38:00] Features: [11:38:00] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:38:05] Found 609363 PSMs [11:38:06] Separate target and decoy search inputs detected, using mix-max method. [11:38:06] Train/test set contains 248822 positives and 251178 negatives, size ratio=0.99062 and pi0=1 [11:38:07] Selecting Cpos by cross-validation. [11:38:07] Selecting Cneg by cross-validation. [11:38:10] Split 1: Selected feature 3 as initial search direction. Could separate 2946 training set positives in that direction. [11:38:13] Split 2: Selected feature 3 as initial search direction. Could separate 3009 training set positives in that direction. [11:38:16] Split 3: Selected feature 2 as initial search direction. Could separate 2991 training set positives in that direction. [11:38:16] Found 4323 test set positives with q<0.01 in initial direction [11:38:16] Reading in data and feature calculation took 16.22 cpu seconds or 16 seconds wall clock time. [11:38:16] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:38:40] Iteration 1: Estimated 6170 PSMs with q<0.01 [11:39:06] Iteration 2: Estimated 6607 PSMs with q<0.01 [11:39:31] Iteration 3: Estimated 6703 PSMs with q<0.01 [11:39:31] Learned normalized SVM weights for the 3 cross-validation splits: [11:39:31] Split1 Split2 Split3 FeatureName [11:39:31] -0.1141 -1.2392 -0.6609 primary [11:39:31] 0.0420 0.0171 0.5519 xCorrLib [11:39:31] 0.5667 0.6227 0.1153 xCorrModel [11:39:31] 0.0631 -0.0238 0.2392 dotProduct [11:39:31] 0.4995 1.1232 0.7722 contrastAngle [11:39:31] -0.0775 -0.5331 -0.4066 logit [11:39:31] 0.1471 0.2574 0.2510 sumOfSquaredErrors [11:39:31] 0.0924 1.2675 0.6905 numberOfMatchingPeaks [11:39:31] 0.3520 0.5133 0.3398 numberOfMatchingPeaksAboveThreshold [11:39:31] 0.0387 -0.0198 0.0010 averageFragmentDeltaMasses [11:39:31] 0.2899 0.6382 0.4517 isotopeDotProduct [11:39:31] 0.1435 0.2053 0.1230 averageParentDeltaMass [11:39:31] 0.0098 0.0155 -0.0513 percentBlankOverMono [11:39:31] -0.0252 -0.1900 -0.0610 numberPrecursorMatch [11:39:31] -0.7133 -1.0358 -0.9635 lnSp [11:39:31] 0.4327 0.5028 0.5414 maxLadderLength [11:39:31] 0.1917 0.2256 0.2772 evalue [11:39:31] 0.0120 0.0078 0.0572 correlationToGaussian [11:39:31] -0.0238 0.0681 -0.0751 correlationToPrecursor [11:39:31] -0.0785 -0.0323 -0.1390 isIntegratedSignal [11:39:31] 0.0753 0.2253 0.2427 isIntegratedPrecursor [11:39:31] 0.3149 0.3915 0.3600 numPeaksWithGoodCorrelation [11:39:31] -0.3338 -0.9445 -0.8313 numMissedCleavage [11:39:31] -0.5681 -0.6897 -0.4012 pepLength [11:39:31] 0.0000 0.0000 0.0000 charge1 [11:39:31] -0.0743 0.2581 0.0761 charge2 [11:39:31] 0.0743 -0.2581 -0.0761 charge3 [11:39:31] 0.0000 0.0000 0.0000 charge4 [11:39:31] 0.2333 0.1717 0.1581 precursorMz [11:39:31] 0.1305 0.8401 0.2508 precursorMass [11:39:31] -0.0727 -0.1214 0.0074 RTinMin [11:39:31] -3.3318 -4.9264 -4.6603 m0 [11:39:31] Found 6599 test set PSMs with q<0.01. [11:39:31] Scoring full list of PSMs with trained SVMs. [11:39:32] Features: [11:39:32] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:39:37] Found 609363 PSMs [11:39:37] Evaluated set contained 303308 positives and 306055 negatives. [11:39:39] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:39:40] Selecting pi_0=0.957042 [11:39:40] Calculating q values. [11:39:40] New pi_0 estimate on final list yields 7887 target peptides with q<0.01. [11:39:40] Calculating posterior error probabilities (PEPs). [11:39:41] Processing took 85.22 cpu seconds or 85 seconds wall clock time. [11:39:47] First pass: 7887 peptides identified at 1.0% FDR [11:39:47] Generating retention time mapping using 7887 points... [11:39:47] Enough data points (7887) to perform KDE alignment. [11:39:49] Enough data points (7411) to perform KDE alignment. [11:39:49] Enough data points (7887) to perform KDE alignment. [11:39:50] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:39:53] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:40:04] Sorted feature file in 10.18 seconds wall clock time [11:40:04] File size check: 200836704 vs 200836704 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:40:04] Executing [cmd /c C:\Windows\Temp\tmp7E74.java\Percolator-v3-01-6117816341461281846.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt] [11:40:04] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:40:04] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:40:04] Written by Lukas Käll (lukall@u.washington.edu) in the [11:40:04] Department of Genome Sciences at the University of Washington. [11:40:04] Issued command: [11:40:04] C:\Windows\Temp\tmp7E74.java\Percolator-v3-01-6117816341461281846.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:40:04] Started Wed Jul 17 11:40:04 2024 [11:40:04] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [11:40:04] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:40:04] Features: [11:40:04] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:40:09] Found 457590 PSMs [11:40:09] Separate target and decoy search inputs detected, using mix-max method. [11:40:09] Train/test set contains 226889 positives and 230701 negatives, size ratio=0.983476 and pi0=1 [11:40:09] Selecting Cpos by cross-validation. [11:40:09] Selecting Cneg by cross-validation. [11:40:12] Split 1: Selected feature 3 as initial search direction. Could separate 3500 training set positives in that direction. [11:40:15] Split 2: Selected feature 3 as initial search direction. Could separate 3527 training set positives in that direction. [11:40:18] Split 3: Selected feature 3 as initial search direction. Could separate 3584 training set positives in that direction. [11:40:18] Found 5279 test set positives with q<0.01 in initial direction [11:40:18] Reading in data and feature calculation took 14.328 cpu seconds or 14 seconds wall clock time. [11:40:18] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:40:42] Iteration 1: Estimated 7083 PSMs with q<0.01 [11:41:07] Iteration 2: Estimated 7663 PSMs with q<0.01 [11:41:33] Iteration 3: Estimated 7886 PSMs with q<0.01 [11:41:58] Iteration 4: Estimated 7975 PSMs with q<0.01 [11:42:24] Iteration 5: Estimated 8001 PSMs with q<0.01 [11:42:49] Iteration 6: Estimated 8012 PSMs with q<0.01 [11:43:15] Iteration 7: Estimated 8008 PSMs with q<0.01 [11:43:40] Iteration 8: Estimated 8026 PSMs with q<0.01 [11:44:06] Iteration 9: Estimated 8026 PSMs with q<0.01 [11:44:32] Iteration 10: Estimated 8024 PSMs with q<0.01 [11:44:32] Learned normalized SVM weights for the 3 cross-validation splits: [11:44:32] Split1 Split2 Split3 FeatureName [11:44:32] -1.9292 -1.3943 -1.6890 primary [11:44:32] 0.1018 0.0064 0.1112 xCorrLib [11:44:32] 0.6131 0.4976 0.3557 xCorrModel [11:44:32] 0.4741 0.0955 0.6071 dotProduct [11:44:32] 1.1628 1.2863 0.9898 contrastAngle [11:44:32] -0.7929 -0.7419 -0.8775 logit [11:44:32] 0.1894 0.1192 0.3013 sumOfSquaredErrors [11:44:32] 2.4492 1.8322 1.9257 numberOfMatchingPeaks [11:44:32] 0.4606 0.3589 0.4454 numberOfMatchingPeaksAboveThreshold [11:44:32] 0.0154 -0.0214 -0.0625 averageFragmentDeltaMasses [11:44:32] 0.4314 0.6382 0.2481 isotopeDotProduct [11:44:32] 0.0874 0.1981 0.1201 averageParentDeltaMass [11:44:32] -0.0881 -0.0048 -0.1284 percentBlankOverMono [11:44:32] -0.1385 -0.2349 -0.0106 numberPrecursorMatch [11:44:32] -1.3825 -1.1656 -1.0263 lnSp [11:44:32] 0.5616 0.5091 0.5063 maxLadderLength [11:44:32] 0.2969 0.2509 0.3151 evalue [11:44:32] 0.2856 0.5549 -0.0399 correlationToGaussian [11:44:32] -0.1371 -0.0042 -0.1011 correlationToPrecursor [11:44:32] -0.0816 -0.0499 -0.0007 isIntegratedSignal [11:44:32] 0.1360 0.3839 0.1832 isIntegratedPrecursor [11:44:32] 0.5601 0.4990 0.4974 numPeaksWithGoodCorrelation [11:44:32] 0.0786 0.1306 0.0778 deltaRT [11:44:32] -0.1059 -0.0506 -0.0972 ms1MassError [11:44:32] -0.1646 -0.0828 -0.2403 ms2MassError [11:44:32] -0.8245 -0.6362 -0.9264 numMissedCleavage [11:44:32] -0.9591 -0.5403 -0.8196 pepLength [11:44:32] 0.0000 0.0000 0.0000 charge1 [11:44:32] -0.0663 0.1090 -0.1704 charge2 [11:44:32] 0.0663 -0.1090 0.1704 charge3 [11:44:32] 0.0000 0.0000 0.0000 charge4 [11:44:32] 0.2952 0.1456 0.1666 precursorMz [11:44:32] 0.1511 0.3744 0.1079 precursorMass [11:44:32] -0.2754 -0.1226 -0.1354 RTinMin [11:44:32] -5.6516 -5.1226 -4.8308 m0 [11:44:32] Found 7512 test set PSMs with q<0.01. [11:44:32] Scoring full list of PSMs with trained SVMs. [11:44:33] Features: [11:44:33] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:44:37] Found 457590 PSMs [11:44:37] Evaluated set contained 226889 positives and 230701 negatives. [11:44:39] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:44:40] Selecting pi_0=0.95831 [11:44:40] Calculating q values. [11:44:40] New pi_0 estimate on final list yields 7983 target peptides with q<0.01. [11:44:40] Calculating posterior error probabilities (PEPs). [11:44:41] Processing took 262.9 cpu seconds or 263 seconds wall clock time. [11:44:47] Generating retention time mapping using 7983 points... [11:44:47] Enough data points (7983) to perform KDE alignment. [11:44:48] Enough data points (7451) to perform KDE alignment. [11:44:49] Enough data points (7983) to perform KDE alignment. [11:44:49] Writing elib result library... [11:44:50] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 7983 vs local peptides: 7983 [11:44:50] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML... [11:44:50] Extracting Spectral Data for 7983 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML... [11:44:50] Number of global peptides: 7983 vs local peptides: 7983 [11:44:51] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [11:44:51] Parsed features and scores for 7983 peptides. [11:44:51] Extracting 7983 peptides... [11:44:51] Quant Extracting 798.6 to 800.6 m/z (14.779507 to 99.13028 min) [11:44:51] Quant Extracting 800.6 to 802.6 m/z (32.00032 to 96.490074 min) [11:44:51] Quant Extracting 802.6 to 804.6 m/z (7.17771 to 96.42487 min) [11:44:51] Quant Extracting 804.6 to 806.6 m/z (16.567493 to 95.38258 min) [11:44:52] Quant Extracting 806.6 to 808.6 m/z (21.80359 to 96.75114 min) [11:44:52] Quant Extracting 808.6 to 810.6 m/z (16.933178 to 95.93853 min) [11:44:52] Quant Extracting 810.6 to 812.6 m/z (18.277426 to 99.26905 min) [11:44:52] Quant Extracting 812.6 to 814.6 m/z (13.120923 to 96.52555 min) [11:44:52] Quant Extracting 814.6 to 816.6 m/z (25.685167 to 100.74693 min) [11:44:52] Quant Extracting 816.6 to 818.6 m/z (23.522383 to 100.74693 min) [11:44:52] Quant Extracting 818.6 to 820.6 m/z (24.014902 to 94.9647 min) [11:44:52] Quant Extracting 820.6 to 822.6 m/z (7.1506753 to 96.00695 min) [11:44:52] Quant Extracting 822.6 to 824.6 m/z (26.085835 to 98.28536 min) [11:44:53] Quant Extracting 824.6 to 826.6 m/z (15.118076 to 97.799416 min) [11:44:53] Quant Extracting 826.6 to 828.6 m/z (15.3192425 to 100.75039 min) [11:44:53] Quant Extracting 828.6 to 830.6 m/z (30.579884 to 100.75039 min) [11:44:53] Quant Extracting 830.6 to 832.6 m/z (25.627459 to 100.65079 min) [11:44:53] Quant Extracting 832.6 to 834.6 m/z (26.711168 to 97.8335 min) [11:44:53] Quant Extracting 834.6 to 836.6 m/z (22.570507 to 95.523766 min) [11:44:53] Quant Extracting 836.6 to 838.6 m/z (17.316748 to 100.18094 min) [11:44:53] Quant Extracting 838.6 to 840.6 m/z (7.1915965 to 100.75384 min) [11:44:53] Quant Extracting 840.6 to 842.6 m/z (10.959421 to 94.87385 min) [11:44:54] Quant Extracting 842.6 to 844.6 m/z (7.159274 to 100.48604 min) [11:44:54] Quant Extracting 844.6 to 846.6 m/z (20.771584 to 100.75499 min) [11:44:54] Quant Extracting 846.6 to 848.6 m/z (20.70827 to 99.18009 min) [11:44:54] Quant Extracting 848.6 to 850.6 m/z (14.4211 to 95.070656 min) [11:44:54] Quant Extracting 850.6 to 852.6 m/z (27.87219 to 100.75729 min) [11:44:54] Quant Extracting 852.6 to 854.6 m/z (28.20104 to 93.00035 min) [11:44:54] Quant Extracting 854.6 to 856.6 m/z (16.582487 to 109.15364 min) [11:44:54] Quant Extracting 856.6 to 858.6 m/z (28.430265 to 100.19076 min) [11:44:54] Quant Extracting 858.6 to 860.6 m/z (23.205387 to 98.9537 min) [11:44:55] Quant Extracting 860.6 to 862.6 m/z (20.615461 to 97.8098 min) [11:44:55] Quant Extracting 862.6 to 864.6 m/z (24.619785 to 98.72438 min) [11:44:55] Quant Extracting 864.6 to 866.6 m/z (14.45911 to 98.92256 min) [11:44:55] Quant Extracting 866.6 to 868.6 m/z (18.4956 to 96.96626 min) [11:44:55] Quant Extracting 868.6 to 870.6 m/z (26.262568 to 109.15829 min) [11:44:55] Quant Extracting 870.6 to 872.6 m/z (13.919558 to 96.24953 min) [11:44:55] Quant Extracting 872.6 to 874.6 m/z (11.490806 to 96.25068 min) [11:44:55] Quant Extracting 874.6 to 876.6 m/z (25.771837 to 98.13993 min) [11:44:55] Quant Extracting 876.6 to 878.6 m/z (19.653936 to 96.18672 min) [11:44:55] Quant Extracting 878.6 to 880.7 m/z (25.575623 to 100.59647 min) [11:44:55] Quant Extracting 880.7 to 882.7 m/z (24.625547 to 96.05737 min) [11:44:55] Quant Extracting 882.7 to 884.7 m/z (28.829348 to 96.711205 min) [11:44:56] Quant Extracting 884.7 to 886.7 m/z (30.952982 to 109.16289 min) [11:44:56] Quant Extracting 886.7 to 888.7 m/z (16.495777 to 98.04661 min) [11:44:56] Quant Extracting 888.7 to 890.7 m/z (9.807313 to 96.9085 min) [11:44:56] Quant Extracting 890.7 to 892.7 m/z (17.969063 to 95.73444 min) [11:44:56] Quant Extracting 892.7 to 894.7 m/z (26.007545 to 109.16519 min) [11:44:56] Quant Extracting 894.7 to 896.7 m/z (19.796904 to 100.635864 min) [11:44:56] Quant Extracting 896.7 to 898.7 m/z (19.394854 to 96.87773 min) [11:44:56] Quant Extracting 898.7 to 900.7 m/z (37.63573 to 98.80039 min) [11:44:56] Quant Extracting 900.7 to 902.7 m/z (24.466963 to 109.13272 min) [11:44:56] Attempted extraction for: 7983, found 7983 [11:44:56] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML (7983 entries)... [11:44:56] Writing 7983 peptides to entries table... [11:44:57] Writing 7983 peptides to peptidequants table... [11:44:58] Finished writing to Encyclopedia ELIB at Wed Jul 17 11:44:58 BST 2024 [11:44:59] Writing local target/decoy peptides: 7983/81, pi0: 0.95831 [11:44:59] Writing local target/decoy proteins: 3856/38 [11:45:00] Finished analysis! 7983 peptides identified at 1.0% FDR (14.5 minutes) [11:45:00] Generating chromatogram library (6 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [11:45:04] EncyclopeDIA version 2.12.30 [11:45:05] Getting count of protein accessions... [11:45:05] Using EncyclopeDIA 2.X Scoring System [11:45:05] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML ... [11:45:05] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML ... 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[11:46:35] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.dia! [11:46:35] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML [11:46:35] Library File: UP000005640_9606-z3_nce27-prosit.dlib [11:46:35] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.elib [11:46:35] Parameters: [11:46:35] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [11:46:35] Converting files... [11:46:35] Calculating features... [11:46:35] Processing precursors scans... [11:46:35] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:46:35] Processing 898.7 to 900.7 m/z, (3.9816327 second duty cycle) [11:46:37] 3413 peptides remaining for 898.7 to 900.7... [11:46:38] 3067 peptides remaining for 898.7 to 900.7... [11:46:38] 2655 peptides remaining for 898.7 to 900.7... [11:46:39] 2230 peptides remaining for 898.7 to 900.7... [11:46:39] 1804 peptides remaining for 898.7 to 900.7... [11:46:40] 1364 peptides remaining for 898.7 to 900.7... [11:46:40] 933 peptides remaining for 898.7 to 900.7... [11:46:41] 495 peptides remaining for 898.7 to 900.7... [11:46:41] 51 peptides remaining for 898.7 to 900.7... [11:46:42] Processing 900.7 to 902.7 m/z, (1.9908545 second duty cycle) [11:46:44] 3503 peptides remaining for 900.7 to 902.7... [11:46:44] 3195 peptides remaining for 900.7 to 902.7... [11:46:45] 2894 peptides remaining for 900.7 to 902.7... [11:46:45] 2611 peptides remaining for 900.7 to 902.7... [11:46:46] 2332 peptides remaining for 900.7 to 902.7... [11:46:46] 2044 peptides remaining for 900.7 to 902.7... [11:46:47] 1764 peptides remaining for 900.7 to 902.7... [11:46:47] 1479 peptides remaining for 900.7 to 902.7... [11:46:48] 1186 peptides remaining for 900.7 to 902.7... [11:46:48] 884 peptides remaining for 900.7 to 902.7... [11:46:49] 582 peptides remaining for 900.7 to 902.7... [11:46:49] 292 peptides remaining for 900.7 to 902.7... [11:46:50] 0 peptides remaining for 900.7 to 902.7... [11:46:50] Processing 902.7 to 904.7 m/z, (1.9908545 second duty cycle) [11:46:52] 3608 peptides remaining for 902.7 to 904.7... [11:46:53] 3316 peptides remaining for 902.7 to 904.7... [11:46:53] 3018 peptides remaining for 902.7 to 904.7... [11:46:54] 2736 peptides remaining for 902.7 to 904.7... [11:46:54] 2445 peptides remaining for 902.7 to 904.7... [11:46:55] 2161 peptides remaining for 902.7 to 904.7... [11:46:55] 1858 peptides remaining for 902.7 to 904.7... [11:46:56] 1570 peptides remaining for 902.7 to 904.7... [11:46:56] 1285 peptides remaining for 902.7 to 904.7... [11:46:57] 986 peptides remaining for 902.7 to 904.7... [11:46:57] 707 peptides remaining for 902.7 to 904.7... [11:46:58] 411 peptides remaining for 902.7 to 904.7... [11:46:58] 98 peptides remaining for 902.7 to 904.7... [11:46:59] Processing 904.7 to 906.7 m/z, (1.9908547 second duty cycle) [11:47:00] 3548 peptides remaining for 904.7 to 906.7... [11:47:01] 3239 peptides remaining for 904.7 to 906.7... [11:47:01] 2931 peptides remaining for 904.7 to 906.7... [11:47:02] 2635 peptides remaining for 904.7 to 906.7... [11:47:02] 2322 peptides remaining for 904.7 to 906.7... [11:47:03] 2036 peptides remaining for 904.7 to 906.7... [11:47:03] 1741 peptides remaining for 904.7 to 906.7... [11:47:04] 1461 peptides remaining for 904.7 to 906.7... [11:47:05] 1178 peptides remaining for 904.7 to 906.7... [11:47:05] 898 peptides remaining for 904.7 to 906.7... [11:47:06] 612 peptides remaining for 904.7 to 906.7... [11:47:06] 326 peptides remaining for 904.7 to 906.7... [11:47:07] 23 peptides remaining for 904.7 to 906.7... [11:47:07] Processing 906.7 to 908.7 m/z, (1.9908549 second duty cycle) [11:47:09] 3384 peptides remaining for 906.7 to 908.7... [11:47:09] 3060 peptides remaining for 906.7 to 908.7... [11:47:10] 2756 peptides remaining for 906.7 to 908.7... [11:47:10] 2487 peptides remaining for 906.7 to 908.7... [11:47:11] 2192 peptides remaining for 906.7 to 908.7... [11:47:11] 1898 peptides remaining for 906.7 to 908.7... [11:47:12] 1604 peptides remaining for 906.7 to 908.7... [11:47:12] 1320 peptides remaining for 906.7 to 908.7... [11:47:13] 1025 peptides remaining for 906.7 to 908.7... [11:47:13] 736 peptides remaining for 906.7 to 908.7... [11:47:14] 459 peptides remaining for 906.7 to 908.7... [11:47:14] 149 peptides remaining for 906.7 to 908.7... [11:47:15] Processing 908.7 to 910.7 m/z, (1.9908546 second duty cycle) [11:47:16] 3459 peptides remaining for 908.7 to 910.7... [11:47:17] 3139 peptides remaining for 908.7 to 910.7... [11:47:18] 2826 peptides remaining for 908.7 to 910.7... [11:47:18] 2541 peptides remaining for 908.7 to 910.7... [11:47:19] 2247 peptides remaining for 908.7 to 910.7... [11:47:19] 1966 peptides remaining for 908.7 to 910.7... [11:47:20] 1683 peptides remaining for 908.7 to 910.7... [11:47:20] 1395 peptides remaining for 908.7 to 910.7... [11:47:21] 1116 peptides remaining for 908.7 to 910.7... [11:47:21] 817 peptides remaining for 908.7 to 910.7... [11:47:22] 521 peptides remaining for 908.7 to 910.7... [11:47:22] 224 peptides remaining for 908.7 to 910.7... [11:47:23] Processing 910.7 to 912.7 m/z, (1.9908546 second duty cycle) [11:47:24] 3564 peptides remaining for 910.7 to 912.7... [11:47:25] 3249 peptides remaining for 910.7 to 912.7... [11:47:25] 2945 peptides remaining for 910.7 to 912.7... [11:47:26] 2654 peptides remaining for 910.7 to 912.7... [11:47:26] 2365 peptides remaining for 910.7 to 912.7... [11:47:27] 2084 peptides remaining for 910.7 to 912.7... [11:47:27] 1790 peptides remaining for 910.7 to 912.7... [11:47:28] 1501 peptides remaining for 910.7 to 912.7... [11:47:28] 1216 peptides remaining for 910.7 to 912.7... [11:47:29] 920 peptides remaining for 910.7 to 912.7... [11:47:29] 628 peptides remaining for 910.7 to 912.7... [11:47:30] 347 peptides remaining for 910.7 to 912.7... [11:47:30] 32 peptides remaining for 910.7 to 912.7... [11:47:31] Processing 912.7 to 914.7 m/z, (1.9908546 second duty cycle) [11:47:33] 3485 peptides remaining for 912.7 to 914.7... [11:47:33] 3182 peptides remaining for 912.7 to 914.7... [11:47:34] 2867 peptides remaining for 912.7 to 914.7... [11:47:34] 2589 peptides remaining for 912.7 to 914.7... [11:47:35] 2310 peptides remaining for 912.7 to 914.7... [11:47:35] 2017 peptides remaining for 912.7 to 914.7... [11:47:36] 1733 peptides remaining for 912.7 to 914.7... [11:47:36] 1455 peptides remaining for 912.7 to 914.7... [11:47:37] 1172 peptides remaining for 912.7 to 914.7... [11:47:37] 890 peptides remaining for 912.7 to 914.7... [11:47:38] 603 peptides remaining for 912.7 to 914.7... [11:47:38] 313 peptides remaining for 912.7 to 914.7... [11:47:39] 3 peptides remaining for 912.7 to 914.7... [11:47:39] Processing 914.7 to 916.7 m/z, (1.9908546 second duty cycle) [11:47:41] 3400 peptides remaining for 914.7 to 916.7... [11:47:41] 3088 peptides remaining for 914.7 to 916.7... [11:47:42] 2789 peptides remaining for 914.7 to 916.7... [11:47:42] 2498 peptides remaining for 914.7 to 916.7... [11:47:43] 2213 peptides remaining for 914.7 to 916.7... [11:47:43] 1935 peptides remaining for 914.7 to 916.7... [11:47:44] 1660 peptides remaining for 914.7 to 916.7... [11:47:44] 1394 peptides remaining for 914.7 to 916.7... [11:47:45] 1096 peptides remaining for 914.7 to 916.7... [11:47:45] 811 peptides remaining for 914.7 to 916.7... [11:47:46] 520 peptides remaining for 914.7 to 916.7... [11:47:46] 234 peptides remaining for 914.7 to 916.7... [11:47:47] Processing 916.7 to 918.7 m/z, (1.9908546 second duty cycle) [11:47:49] 3474 peptides remaining for 916.7 to 918.7... [11:47:49] 3180 peptides remaining for 916.7 to 918.7... [11:47:50] 2886 peptides remaining for 916.7 to 918.7... [11:47:50] 2609 peptides remaining for 916.7 to 918.7... [11:47:51] 2323 peptides remaining for 916.7 to 918.7... [11:47:51] 2038 peptides remaining for 916.7 to 918.7... [11:47:52] 1759 peptides remaining for 916.7 to 918.7... [11:47:52] 1486 peptides remaining for 916.7 to 918.7... [11:47:53] 1214 peptides remaining for 916.7 to 918.7... [11:47:53] 930 peptides remaining for 916.7 to 918.7... [11:47:54] 649 peptides remaining for 916.7 to 918.7... [11:47:54] 358 peptides remaining for 916.7 to 918.7... [11:47:55] 47 peptides remaining for 916.7 to 918.7... [11:47:55] Processing 918.7 to 920.7 m/z, (1.9908546 second duty cycle) [11:47:57] 3505 peptides remaining for 918.7 to 920.7... [11:47:57] 3196 peptides remaining for 918.7 to 920.7... [11:47:58] 2901 peptides remaining for 918.7 to 920.7... [11:47:58] 2619 peptides remaining for 918.7 to 920.7... [11:47:59] 2338 peptides remaining for 918.7 to 920.7... [11:48:00] 2055 peptides remaining for 918.7 to 920.7... [11:48:00] 1779 peptides remaining for 918.7 to 920.7... [11:48:01] 1497 peptides remaining for 918.7 to 920.7... [11:48:01] 1214 peptides remaining for 918.7 to 920.7... [11:48:02] 925 peptides remaining for 918.7 to 920.7... [11:48:02] 649 peptides remaining for 918.7 to 920.7... [11:48:03] 358 peptides remaining for 918.7 to 920.7... [11:48:03] 55 peptides remaining for 918.7 to 920.7... [11:48:04] Processing 920.7 to 922.7 m/z, (1.9908546 second duty cycle) [11:48:05] 3449 peptides remaining for 920.7 to 922.7... [11:48:06] 3167 peptides remaining for 920.7 to 922.7... [11:48:06] 2861 peptides remaining for 920.7 to 922.7... [11:48:07] 2575 peptides remaining for 920.7 to 922.7... [11:48:07] 2294 peptides remaining for 920.7 to 922.7... [11:48:08] 2000 peptides remaining for 920.7 to 922.7... [11:48:08] 1712 peptides remaining for 920.7 to 922.7... [11:48:09] 1425 peptides remaining for 920.7 to 922.7... [11:48:09] 1145 peptides remaining for 920.7 to 922.7... [11:48:10] 860 peptides remaining for 920.7 to 922.7... [11:48:10] 571 peptides remaining for 920.7 to 922.7... [11:48:11] 294 peptides remaining for 920.7 to 922.7... [11:48:11] 0 peptides remaining for 920.7 to 922.7... [11:48:12] Processing 922.7 to 924.7 m/z, (1.9908545 second duty cycle) [11:48:13] 3404 peptides remaining for 922.7 to 924.7... [11:48:14] 3074 peptides remaining for 922.7 to 924.7... [11:48:14] 2791 peptides remaining for 922.7 to 924.7... [11:48:15] 2513 peptides remaining for 922.7 to 924.7... [11:48:15] 2234 peptides remaining for 922.7 to 924.7... [11:48:16] 1942 peptides remaining for 922.7 to 924.7... [11:48:16] 1656 peptides remaining for 922.7 to 924.7... [11:48:17] 1381 peptides remaining for 922.7 to 924.7... [11:48:18] 1101 peptides remaining for 922.7 to 924.7... [11:48:18] 827 peptides remaining for 922.7 to 924.7... [11:48:19] 534 peptides remaining for 922.7 to 924.7... [11:48:19] 248 peptides remaining for 922.7 to 924.7... [11:48:20] Processing 924.7 to 926.7 m/z, (1.9908549 second duty cycle) [11:48:21] 3402 peptides remaining for 924.7 to 926.7... [11:48:22] 3081 peptides remaining for 924.7 to 926.7... [11:48:22] 2791 peptides remaining for 924.7 to 926.7... [11:48:23] 2512 peptides remaining for 924.7 to 926.7... [11:48:23] 2235 peptides remaining for 924.7 to 926.7... [11:48:24] 1942 peptides remaining for 924.7 to 926.7... [11:48:24] 1665 peptides remaining for 924.7 to 926.7... [11:48:25] 1370 peptides remaining for 924.7 to 926.7... [11:48:25] 1081 peptides remaining for 924.7 to 926.7... [11:48:26] 801 peptides remaining for 924.7 to 926.7... [11:48:26] 512 peptides remaining for 924.7 to 926.7... [11:48:27] 232 peptides remaining for 924.7 to 926.7... [11:48:27] Processing 926.7 to 928.7 m/z, (1.9908549 second duty cycle) [11:48:29] 3426 peptides remaining for 926.7 to 928.7... [11:48:29] 3121 peptides remaining for 926.7 to 928.7... [11:48:30] 2812 peptides remaining for 926.7 to 928.7... [11:48:31] 2533 peptides remaining for 926.7 to 928.7... [11:48:31] 2245 peptides remaining for 926.7 to 928.7... [11:48:32] 1946 peptides remaining for 926.7 to 928.7... [11:48:32] 1673 peptides remaining for 926.7 to 928.7... [11:48:33] 1390 peptides remaining for 926.7 to 928.7... [11:48:33] 1114 peptides remaining for 926.7 to 928.7... [11:48:34] 844 peptides remaining for 926.7 to 928.7... [11:48:34] 540 peptides remaining for 926.7 to 928.7... [11:48:35] 246 peptides remaining for 926.7 to 928.7... [11:48:35] Processing 928.7 to 930.7 m/z, (1.9908547 second duty cycle) [11:48:37] 3314 peptides remaining for 928.7 to 930.7... [11:48:37] 3007 peptides remaining for 928.7 to 930.7... [11:48:38] 2706 peptides remaining for 928.7 to 930.7... [11:48:38] 2416 peptides remaining for 928.7 to 930.7... [11:48:39] 2130 peptides remaining for 928.7 to 930.7... [11:48:39] 1839 peptides remaining for 928.7 to 930.7... [11:48:40] 1569 peptides remaining for 928.7 to 930.7... [11:48:40] 1293 peptides remaining for 928.7 to 930.7... [11:48:41] 996 peptides remaining for 928.7 to 930.7... [11:48:41] 701 peptides remaining for 928.7 to 930.7... [11:48:42] 415 peptides remaining for 928.7 to 930.7... [11:48:42] 104 peptides remaining for 928.7 to 930.7... [11:48:43] Processing 930.7 to 932.7 m/z, (1.9908547 second duty cycle) [11:48:44] 3460 peptides remaining for 930.7 to 932.7... [11:48:45] 3147 peptides remaining for 930.7 to 932.7... [11:48:45] 2845 peptides remaining for 930.7 to 932.7... [11:48:46] 2579 peptides remaining for 930.7 to 932.7... [11:48:47] 2312 peptides remaining for 930.7 to 932.7... [11:48:47] 2026 peptides remaining for 930.7 to 932.7... [11:48:48] 1749 peptides remaining for 930.7 to 932.7... [11:48:48] 1479 peptides remaining for 930.7 to 932.7... [11:48:49] 1218 peptides remaining for 930.7 to 932.7... [11:48:49] 939 peptides remaining for 930.7 to 932.7... [11:48:50] 657 peptides remaining for 930.7 to 932.7... [11:48:50] 365 peptides remaining for 930.7 to 932.7... [11:48:51] 64 peptides remaining for 930.7 to 932.7... [11:48:51] Processing 932.7 to 934.7 m/z, (1.9908547 second duty cycle) [11:48:53] 3401 peptides remaining for 932.7 to 934.7... [11:48:53] 3090 peptides remaining for 932.7 to 934.7... [11:48:54] 2795 peptides remaining for 932.7 to 934.7... [11:48:54] 2512 peptides remaining for 932.7 to 934.7... [11:48:55] 2229 peptides remaining for 932.7 to 934.7... [11:48:55] 1951 peptides remaining for 932.7 to 934.7... [11:48:56] 1674 peptides remaining for 932.7 to 934.7... [11:48:56] 1399 peptides remaining for 932.7 to 934.7... [11:48:57] 1111 peptides remaining for 932.7 to 934.7... [11:48:57] 829 peptides remaining for 932.7 to 934.7... [11:48:58] 540 peptides remaining for 932.7 to 934.7... [11:48:58] 268 peptides remaining for 932.7 to 934.7... [11:48:59] 0 peptides remaining for 932.7 to 934.7... [11:48:59] Processing 934.7 to 936.7 m/z, (1.9908547 second duty cycle) [11:49:01] 3315 peptides remaining for 934.7 to 936.7... [11:49:01] 3010 peptides remaining for 934.7 to 936.7... [11:49:02] 2707 peptides remaining for 934.7 to 936.7... [11:49:03] 2429 peptides remaining for 934.7 to 936.7... [11:49:03] 2153 peptides remaining for 934.7 to 936.7... [11:49:04] 1856 peptides remaining for 934.7 to 936.7... [11:49:04] 1588 peptides remaining for 934.7 to 936.7... [11:49:05] 1305 peptides remaining for 934.7 to 936.7... [11:49:05] 1018 peptides remaining for 934.7 to 936.7... [11:49:06] 741 peptides remaining for 934.7 to 936.7... [11:49:06] 450 peptides remaining for 934.7 to 936.7... [11:49:07] 160 peptides remaining for 934.7 to 936.7... [11:49:07] Processing 936.7 to 938.7 m/z, (1.9908547 second duty cycle) [11:49:09] 3300 peptides remaining for 936.7 to 938.7... [11:49:09] 3007 peptides remaining for 936.7 to 938.7... [11:49:10] 2712 peptides remaining for 936.7 to 938.7... [11:49:10] 2433 peptides remaining for 936.7 to 938.7... [11:49:11] 2158 peptides remaining for 936.7 to 938.7... [11:49:11] 1864 peptides remaining for 936.7 to 938.7... [11:49:12] 1588 peptides remaining for 936.7 to 938.7... [11:49:12] 1327 peptides remaining for 936.7 to 938.7... [11:49:13] 1054 peptides remaining for 936.7 to 938.7... [11:49:13] 766 peptides remaining for 936.7 to 938.7... [11:49:14] 478 peptides remaining for 936.7 to 938.7... [11:49:14] 186 peptides remaining for 936.7 to 938.7... [11:49:15] Processing 938.7 to 940.7 m/z, (1.9908547 second duty cycle) [11:49:16] 3311 peptides remaining for 938.7 to 940.7... [11:49:17] 3020 peptides remaining for 938.7 to 940.7... [11:49:17] 2729 peptides remaining for 938.7 to 940.7... [11:49:18] 2453 peptides remaining for 938.7 to 940.7... [11:49:18] 2175 peptides remaining for 938.7 to 940.7... [11:49:19] 1891 peptides remaining for 938.7 to 940.7... [11:49:20] 1616 peptides remaining for 938.7 to 940.7... [11:49:20] 1339 peptides remaining for 938.7 to 940.7... [11:49:21] 1045 peptides remaining for 938.7 to 940.7... [11:49:21] 756 peptides remaining for 938.7 to 940.7... [11:49:22] 461 peptides remaining for 938.7 to 940.7... [11:49:22] 149 peptides remaining for 938.7 to 940.7... [11:49:23] Processing 940.7 to 942.7 m/z, (1.9908243 second duty cycle) [11:49:24] 3308 peptides remaining for 940.7 to 942.7... [11:49:25] 2998 peptides remaining for 940.7 to 942.7... [11:49:25] 2698 peptides remaining for 940.7 to 942.7... [11:49:26] 2411 peptides remaining for 940.7 to 942.7... [11:49:26] 2124 peptides remaining for 940.7 to 942.7... [11:49:27] 1850 peptides remaining for 940.7 to 942.7... [11:49:27] 1568 peptides remaining for 940.7 to 942.7... [11:49:28] 1305 peptides remaining for 940.7 to 942.7... [11:49:28] 1021 peptides remaining for 940.7 to 942.7... [11:49:29] 738 peptides remaining for 940.7 to 942.7... [11:49:29] 446 peptides remaining for 940.7 to 942.7... [11:49:30] 145 peptides remaining for 940.7 to 942.7... [11:49:30] Processing 942.7 to 944.7 m/z, (1.9908466 second duty cycle) [11:49:32] 3358 peptides remaining for 942.7 to 944.7... [11:49:33] 3042 peptides remaining for 942.7 to 944.7... [11:49:33] 2753 peptides remaining for 942.7 to 944.7... [11:49:34] 2464 peptides remaining for 942.7 to 944.7... [11:49:34] 2189 peptides remaining for 942.7 to 944.7... [11:49:35] 1899 peptides remaining for 942.7 to 944.7... [11:49:35] 1632 peptides remaining for 942.7 to 944.7... [11:49:36] 1358 peptides remaining for 942.7 to 944.7... [11:49:36] 1072 peptides remaining for 942.7 to 944.7... [11:49:37] 785 peptides remaining for 942.7 to 944.7... [11:49:37] 494 peptides remaining for 942.7 to 944.7... [11:49:38] 212 peptides remaining for 942.7 to 944.7... [11:49:38] Processing 944.7 to 946.7 m/z, (1.9908248 second duty cycle) [11:49:40] 3272 peptides remaining for 944.7 to 946.7... [11:49:40] 2951 peptides remaining for 944.7 to 946.7... [11:49:41] 2662 peptides remaining for 944.7 to 946.7... [11:49:41] 2386 peptides remaining for 944.7 to 946.7... [11:49:42] 2104 peptides remaining for 944.7 to 946.7... [11:49:42] 1824 peptides remaining for 944.7 to 946.7... [11:49:43] 1550 peptides remaining for 944.7 to 946.7... [11:49:43] 1276 peptides remaining for 944.7 to 946.7... [11:49:44] 996 peptides remaining for 944.7 to 946.7... [11:49:44] 707 peptides remaining for 944.7 to 946.7... [11:49:45] 413 peptides remaining for 944.7 to 946.7... [11:49:46] 113 peptides remaining for 944.7 to 946.7... [11:49:46] Processing 946.7 to 948.7 m/z, (1.9908468 second duty cycle) [11:49:48] 3287 peptides remaining for 946.7 to 948.7... [11:49:48] 2987 peptides remaining for 946.7 to 948.7... [11:49:49] 2699 peptides remaining for 946.7 to 948.7... [11:49:49] 2421 peptides remaining for 946.7 to 948.7... [11:49:50] 2141 peptides remaining for 946.7 to 948.7... [11:49:50] 1859 peptides remaining for 946.7 to 948.7... [11:49:51] 1578 peptides remaining for 946.7 to 948.7... [11:49:51] 1295 peptides remaining for 946.7 to 948.7... [11:49:52] 1011 peptides remaining for 946.7 to 948.7... [11:49:52] 737 peptides remaining for 946.7 to 948.7... [11:49:53] 457 peptides remaining for 946.7 to 948.7... [11:49:53] 157 peptides remaining for 946.7 to 948.7... [11:49:54] Processing 948.7 to 950.7 m/z, (1.9908246 second duty cycle) [11:49:55] 3193 peptides remaining for 948.7 to 950.7... [11:49:56] 2883 peptides remaining for 948.7 to 950.7... [11:49:56] 2587 peptides remaining for 948.7 to 950.7... [11:49:57] 2310 peptides remaining for 948.7 to 950.7... [11:49:57] 2023 peptides remaining for 948.7 to 950.7... [11:49:58] 1742 peptides remaining for 948.7 to 950.7... [11:49:58] 1467 peptides remaining for 948.7 to 950.7... [11:49:59] 1197 peptides remaining for 948.7 to 950.7... [11:49:59] 913 peptides remaining for 948.7 to 950.7... [11:50:00] 635 peptides remaining for 948.7 to 950.7... [11:50:01] 351 peptides remaining for 948.7 to 950.7... [11:50:01] 44 peptides remaining for 948.7 to 950.7... [11:50:02] Processing 950.7 to 952.7 m/z, (1.9908463 second duty cycle) [11:50:03] 3258 peptides remaining for 950.7 to 952.7... [11:50:04] 2956 peptides remaining for 950.7 to 952.7... [11:50:04] 2668 peptides remaining for 950.7 to 952.7... [11:50:05] 2391 peptides remaining for 950.7 to 952.7... [11:50:05] 2094 peptides remaining for 950.7 to 952.7... [11:50:06] 1809 peptides remaining for 950.7 to 952.7... [11:50:06] 1547 peptides remaining for 950.7 to 952.7... [11:50:07] 1265 peptides remaining for 950.7 to 952.7... [11:50:07] 992 peptides remaining for 950.7 to 952.7... [11:50:08] 726 peptides remaining for 950.7 to 952.7... [11:50:08] 421 peptides remaining for 950.7 to 952.7... [11:50:09] 126 peptides remaining for 950.7 to 952.7... [11:50:09] Processing 952.7 to 954.7 m/z, (1.9908243 second duty cycle) [11:50:11] 3114 peptides remaining for 952.7 to 954.7... [11:50:12] 2801 peptides remaining for 952.7 to 954.7... [11:50:12] 2515 peptides remaining for 952.7 to 954.7... [11:50:13] 2241 peptides remaining for 952.7 to 954.7... [11:50:13] 1951 peptides remaining for 952.7 to 954.7... [11:50:14] 1662 peptides remaining for 952.7 to 954.7... [11:50:14] 1372 peptides remaining for 952.7 to 954.7... [11:50:15] 1094 peptides remaining for 952.7 to 954.7... [11:50:15] 811 peptides remaining for 952.7 to 954.7... [11:50:16] 528 peptides remaining for 952.7 to 954.7... [11:50:16] 234 peptides remaining for 952.7 to 954.7... [11:50:17] Processing 954.7 to 956.7 m/z, (1.9908466 second duty cycle) [11:50:18] 3184 peptides remaining for 954.7 to 956.7... [11:50:19] 2885 peptides remaining for 954.7 to 956.7... [11:50:19] 2596 peptides remaining for 954.7 to 956.7... [11:50:20] 2330 peptides remaining for 954.7 to 956.7... [11:50:20] 2052 peptides remaining for 954.7 to 956.7... [11:50:21] 1779 peptides remaining for 954.7 to 956.7... [11:50:21] 1510 peptides remaining for 954.7 to 956.7... [11:50:22] 1253 peptides remaining for 954.7 to 956.7... [11:50:22] 978 peptides remaining for 954.7 to 956.7... [11:50:23] 697 peptides remaining for 954.7 to 956.7... [11:50:24] 410 peptides remaining for 954.7 to 956.7... [11:50:24] 107 peptides remaining for 954.7 to 956.7... [11:50:25] Processing 956.7 to 958.7 m/z, (1.9908247 second duty cycle) [11:50:26] 3248 peptides remaining for 956.7 to 958.7... [11:50:27] 2966 peptides remaining for 956.7 to 958.7... [11:50:27] 2666 peptides remaining for 956.7 to 958.7... [11:50:28] 2391 peptides remaining for 956.7 to 958.7... [11:50:28] 2107 peptides remaining for 956.7 to 958.7... [11:50:29] 1820 peptides remaining for 956.7 to 958.7... [11:50:29] 1552 peptides remaining for 956.7 to 958.7... [11:50:30] 1273 peptides remaining for 956.7 to 958.7... [11:50:30] 1003 peptides remaining for 956.7 to 958.7... [11:50:31] 724 peptides remaining for 956.7 to 958.7... [11:50:31] 437 peptides remaining for 956.7 to 958.7... [11:50:32] 155 peptides remaining for 956.7 to 958.7... [11:50:32] Processing 958.7 to 960.7 m/z, (1.9908465 second duty cycle) [11:50:34] 3232 peptides remaining for 958.7 to 960.7... [11:50:34] 2936 peptides remaining for 958.7 to 960.7... [11:50:35] 2656 peptides remaining for 958.7 to 960.7... [11:50:35] 2387 peptides remaining for 958.7 to 960.7... [11:50:36] 2112 peptides remaining for 958.7 to 960.7... [11:50:36] 1821 peptides remaining for 958.7 to 960.7... [11:50:37] 1525 peptides remaining for 958.7 to 960.7... [11:50:38] 1265 peptides remaining for 958.7 to 960.7... [11:50:38] 996 peptides remaining for 958.7 to 960.7... [11:50:39] 715 peptides remaining for 958.7 to 960.7... [11:50:39] 433 peptides remaining for 958.7 to 960.7... [11:50:40] 149 peptides remaining for 958.7 to 960.7... [11:50:40] Processing 960.7 to 962.7 m/z, (1.9908247 second duty cycle) [11:50:42] 3124 peptides remaining for 960.7 to 962.7... [11:50:42] 2826 peptides remaining for 960.7 to 962.7... [11:50:43] 2549 peptides remaining for 960.7 to 962.7... [11:50:43] 2266 peptides remaining for 960.7 to 962.7... [11:50:44] 1999 peptides remaining for 960.7 to 962.7... [11:50:44] 1707 peptides remaining for 960.7 to 962.7... [11:50:45] 1441 peptides remaining for 960.7 to 962.7... [11:50:45] 1169 peptides remaining for 960.7 to 962.7... [11:50:46] 893 peptides remaining for 960.7 to 962.7... [11:50:46] 600 peptides remaining for 960.7 to 962.7... [11:50:47] 345 peptides remaining for 960.7 to 962.7... [11:50:47] 38 peptides remaining for 960.7 to 962.7... [11:50:48] Processing 962.7 to 964.7 m/z, (1.9908468 second duty cycle) [11:50:49] 3161 peptides remaining for 962.7 to 964.7... [11:50:50] 2870 peptides remaining for 962.7 to 964.7... [11:50:51] 2569 peptides remaining for 962.7 to 964.7... [11:50:51] 2301 peptides remaining for 962.7 to 964.7... [11:50:52] 2025 peptides remaining for 962.7 to 964.7... [11:50:52] 1754 peptides remaining for 962.7 to 964.7... [11:50:53] 1484 peptides remaining for 962.7 to 964.7... [11:50:53] 1215 peptides remaining for 962.7 to 964.7... [11:50:54] 937 peptides remaining for 962.7 to 964.7... [11:50:54] 651 peptides remaining for 962.7 to 964.7... [11:50:55] 364 peptides remaining for 962.7 to 964.7... [11:50:55] 62 peptides remaining for 962.7 to 964.7... [11:50:56] Processing 964.7 to 966.7 m/z, (1.9908248 second duty cycle) [11:50:57] 3138 peptides remaining for 964.7 to 966.7... [11:50:58] 2817 peptides remaining for 964.7 to 966.7... [11:50:58] 2537 peptides remaining for 964.7 to 966.7... [11:50:59] 2263 peptides remaining for 964.7 to 966.7... [11:50:59] 1992 peptides remaining for 964.7 to 966.7... [11:51:00] 1723 peptides remaining for 964.7 to 966.7... [11:51:00] 1444 peptides remaining for 964.7 to 966.7... [11:51:01] 1171 peptides remaining for 964.7 to 966.7... [11:51:01] 893 peptides remaining for 964.7 to 966.7... [11:51:02] 620 peptides remaining for 964.7 to 966.7... [11:51:02] 339 peptides remaining for 964.7 to 966.7... [11:51:03] 34 peptides remaining for 964.7 to 966.7... [11:51:03] Processing 966.7 to 968.7 m/z, (1.9908466 second duty cycle) [11:51:05] 3174 peptides remaining for 966.7 to 968.7... [11:51:06] 2871 peptides remaining for 966.7 to 968.7... [11:51:06] 2587 peptides remaining for 966.7 to 968.7... [11:51:07] 2320 peptides remaining for 966.7 to 968.7... [11:51:07] 2039 peptides remaining for 966.7 to 968.7... [11:51:08] 1765 peptides remaining for 966.7 to 968.7... [11:51:08] 1488 peptides remaining for 966.7 to 968.7... [11:51:09] 1222 peptides remaining for 966.7 to 968.7... [11:51:09] 942 peptides remaining for 966.7 to 968.7... [11:51:10] 677 peptides remaining for 966.7 to 968.7... [11:51:10] 397 peptides remaining for 966.7 to 968.7... [11:51:11] 98 peptides remaining for 966.7 to 968.7... [11:51:11] Processing 968.7 to 970.7 m/z, (1.9908248 second duty cycle) [11:51:13] 3095 peptides remaining for 968.7 to 970.7... [11:51:13] 2793 peptides remaining for 968.7 to 970.7... [11:51:14] 2504 peptides remaining for 968.7 to 970.7... [11:51:14] 2222 peptides remaining for 968.7 to 970.7... [11:51:15] 1940 peptides remaining for 968.7 to 970.7... [11:51:15] 1652 peptides remaining for 968.7 to 970.7... [11:51:16] 1385 peptides remaining for 968.7 to 970.7... [11:51:16] 1123 peptides remaining for 968.7 to 970.7... [11:51:17] 848 peptides remaining for 968.7 to 970.7... [11:51:17] 565 peptides remaining for 968.7 to 970.7... [11:51:18] 275 peptides remaining for 968.7 to 970.7... [11:51:18] 0 peptides remaining for 968.7 to 970.7... [11:51:19] Processing 970.7 to 972.7 m/z, (1.9908468 second duty cycle) [11:51:21] 3146 peptides remaining for 970.7 to 972.7... [11:51:21] 2830 peptides remaining for 970.7 to 972.7... [11:51:22] 2564 peptides remaining for 970.7 to 972.7... [11:51:22] 2289 peptides remaining for 970.7 to 972.7... [11:51:23] 2018 peptides remaining for 970.7 to 972.7... [11:51:23] 1750 peptides remaining for 970.7 to 972.7... [11:51:24] 1479 peptides remaining for 970.7 to 972.7... [11:51:24] 1217 peptides remaining for 970.7 to 972.7... [11:51:25] 923 peptides remaining for 970.7 to 972.7... [11:51:25] 629 peptides remaining for 970.7 to 972.7... [11:51:26] 353 peptides remaining for 970.7 to 972.7... [11:51:26] 55 peptides remaining for 970.7 to 972.7... [11:51:27] Processing 972.7 to 974.7 m/z, (1.9908247 second duty cycle) [11:51:28] 3133 peptides remaining for 972.7 to 974.7... [11:51:29] 2836 peptides remaining for 972.7 to 974.7... [11:51:29] 2575 peptides remaining for 972.7 to 974.7... [11:51:30] 2312 peptides remaining for 972.7 to 974.7... [11:51:30] 2036 peptides remaining for 972.7 to 974.7... [11:51:31] 1755 peptides remaining for 972.7 to 974.7... [11:51:31] 1483 peptides remaining for 972.7 to 974.7... [11:51:32] 1212 peptides remaining for 972.7 to 974.7... [11:51:32] 943 peptides remaining for 972.7 to 974.7... [11:51:33] 644 peptides remaining for 972.7 to 974.7... [11:51:33] 360 peptides remaining for 972.7 to 974.7... [11:51:34] 47 peptides remaining for 972.7 to 974.7... [11:51:34] Processing 974.7 to 976.7 m/z, (1.9909371 second duty cycle) [11:51:36] 3115 peptides remaining for 974.7 to 976.7... [11:51:37] 2798 peptides remaining for 974.7 to 976.7... [11:51:37] 2519 peptides remaining for 974.7 to 976.7... [11:51:38] 2247 peptides remaining for 974.7 to 976.7... [11:51:38] 1979 peptides remaining for 974.7 to 976.7... [11:51:39] 1704 peptides remaining for 974.7 to 976.7... [11:51:39] 1441 peptides remaining for 974.7 to 976.7... [11:51:40] 1156 peptides remaining for 974.7 to 976.7... [11:51:40] 882 peptides remaining for 974.7 to 976.7... [11:51:41] 609 peptides remaining for 974.7 to 976.7... [11:51:41] 329 peptides remaining for 974.7 to 976.7... [11:51:42] 38 peptides remaining for 974.7 to 976.7... [11:51:42] Processing 976.7 to 978.7 m/z, (1.9909152 second duty cycle) [11:51:44] 3041 peptides remaining for 976.7 to 978.7... [11:51:44] 2744 peptides remaining for 976.7 to 978.7... [11:51:45] 2461 peptides remaining for 976.7 to 978.7... [11:51:45] 2203 peptides remaining for 976.7 to 978.7... [11:51:46] 1928 peptides remaining for 976.7 to 978.7... [11:51:46] 1658 peptides remaining for 976.7 to 978.7... [11:51:47] 1396 peptides remaining for 976.7 to 978.7... [11:51:47] 1124 peptides remaining for 976.7 to 978.7... [11:51:48] 842 peptides remaining for 976.7 to 978.7... [11:51:48] 558 peptides remaining for 976.7 to 978.7... [11:51:49] 275 peptides remaining for 976.7 to 978.7... [11:51:49] 0 peptides remaining for 976.7 to 978.7... [11:51:50] Processing 978.7 to 980.7 m/z, (1.9909371 second duty cycle) [11:51:51] 2925 peptides remaining for 978.7 to 980.7... [11:51:52] 2615 peptides remaining for 978.7 to 980.7... [11:51:52] 2329 peptides remaining for 978.7 to 980.7... [11:51:53] 2054 peptides remaining for 978.7 to 980.7... [11:51:53] 1784 peptides remaining for 978.7 to 980.7... [11:51:54] 1518 peptides remaining for 978.7 to 980.7... [11:51:54] 1259 peptides remaining for 978.7 to 980.7... [11:51:55] 997 peptides remaining for 978.7 to 980.7... [11:51:56] 717 peptides remaining for 978.7 to 980.7... [11:51:56] 444 peptides remaining for 978.7 to 980.7... [11:51:57] 136 peptides remaining for 978.7 to 980.7... [11:51:57] Processing 980.7 to 982.7 m/z, (1.9909153 second duty cycle) [11:51:59] 3042 peptides remaining for 980.7 to 982.7... [11:51:59] 2722 peptides remaining for 980.7 to 982.7... [11:52:00] 2439 peptides remaining for 980.7 to 982.7... [11:52:00] 2175 peptides remaining for 980.7 to 982.7... [11:52:01] 1912 peptides remaining for 980.7 to 982.7... [11:52:01] 1636 peptides remaining for 980.7 to 982.7... [11:52:02] 1357 peptides remaining for 980.7 to 982.7... [11:52:02] 1076 peptides remaining for 980.7 to 982.7... [11:52:03] 811 peptides remaining for 980.7 to 982.7... [11:52:03] 526 peptides remaining for 980.7 to 982.7... [11:52:04] 235 peptides remaining for 980.7 to 982.7... [11:52:04] Processing 982.7 to 984.7 m/z, (1.9909371 second duty cycle) [11:52:06] 2998 peptides remaining for 982.7 to 984.7... [11:52:06] 2695 peptides remaining for 982.7 to 984.7... [11:52:07] 2410 peptides remaining for 982.7 to 984.7... [11:52:07] 2137 peptides remaining for 982.7 to 984.7... [11:52:08] 1870 peptides remaining for 982.7 to 984.7... [11:52:09] 1594 peptides remaining for 982.7 to 984.7... [11:52:09] 1315 peptides remaining for 982.7 to 984.7... [11:52:10] 1039 peptides remaining for 982.7 to 984.7... [11:52:10] 757 peptides remaining for 982.7 to 984.7... [11:52:11] 496 peptides remaining for 982.7 to 984.7... [11:52:11] 220 peptides remaining for 982.7 to 984.7... [11:52:12] Processing 984.7 to 986.7 m/z, (1.9909153 second duty cycle) [11:52:13] 2998 peptides remaining for 984.7 to 986.7... [11:52:14] 2694 peptides remaining for 984.7 to 986.7... [11:52:14] 2398 peptides remaining for 984.7 to 986.7... [11:52:15] 2138 peptides remaining for 984.7 to 986.7... [11:52:15] 1868 peptides remaining for 984.7 to 986.7... [11:52:16] 1611 peptides remaining for 984.7 to 986.7... [11:52:16] 1334 peptides remaining for 984.7 to 986.7... [11:52:17] 1061 peptides remaining for 984.7 to 986.7... [11:52:17] 786 peptides remaining for 984.7 to 986.7... [11:52:18] 509 peptides remaining for 984.7 to 986.7... [11:52:18] 241 peptides remaining for 984.7 to 986.7... [11:52:19] Processing 986.7 to 988.7 m/z, (1.9909371 second duty cycle) [11:52:20] 3004 peptides remaining for 986.7 to 988.7... [11:52:21] 2696 peptides remaining for 986.7 to 988.7... [11:52:21] 2410 peptides remaining for 986.7 to 988.7... [11:52:22] 2131 peptides remaining for 986.7 to 988.7... [11:52:22] 1861 peptides remaining for 986.7 to 988.7... [11:52:23] 1593 peptides remaining for 986.7 to 988.7... [11:52:23] 1319 peptides remaining for 986.7 to 988.7... [11:52:24] 1055 peptides remaining for 986.7 to 988.7... [11:52:24] 789 peptides remaining for 986.7 to 988.7... [11:52:25] 517 peptides remaining for 986.7 to 988.7... [11:52:26] 260 peptides remaining for 986.7 to 988.7... [11:52:26] 0 peptides remaining for 986.7 to 988.7... [11:52:27] Processing 988.7 to 990.7 m/z, (1.9909152 second duty cycle) [11:52:28] 2980 peptides remaining for 988.7 to 990.7... [11:52:29] 2679 peptides remaining for 988.7 to 990.7... [11:52:29] 2399 peptides remaining for 988.7 to 990.7... [11:52:30] 2120 peptides remaining for 988.7 to 990.7... [11:52:30] 1849 peptides remaining for 988.7 to 990.7... [11:52:31] 1589 peptides remaining for 988.7 to 990.7... [11:52:31] 1309 peptides remaining for 988.7 to 990.7... [11:52:32] 1044 peptides remaining for 988.7 to 990.7... [11:52:32] 783 peptides remaining for 988.7 to 990.7... [11:52:33] 518 peptides remaining for 988.7 to 990.7... [11:52:33] 230 peptides remaining for 988.7 to 990.7... [11:52:34] Processing 990.7 to 992.7 m/z, (1.9909372 second duty cycle) [11:52:35] 3026 peptides remaining for 990.7 to 992.7... [11:52:36] 2732 peptides remaining for 990.7 to 992.7... [11:52:36] 2451 peptides remaining for 990.7 to 992.7... [11:52:37] 2177 peptides remaining for 990.7 to 992.7... [11:52:37] 1897 peptides remaining for 990.7 to 992.7... [11:52:38] 1623 peptides remaining for 990.7 to 992.7... [11:52:38] 1353 peptides remaining for 990.7 to 992.7... [11:52:39] 1097 peptides remaining for 990.7 to 992.7... [11:52:39] 818 peptides remaining for 990.7 to 992.7... [11:52:40] 533 peptides remaining for 990.7 to 992.7... [11:52:40] 250 peptides remaining for 990.7 to 992.7... [11:52:41] Processing 992.7 to 994.7 m/z, (1.9909153 second duty cycle) [11:52:43] 2934 peptides remaining for 992.7 to 994.7... [11:52:43] 2626 peptides remaining for 992.7 to 994.7... [11:52:44] 2341 peptides remaining for 992.7 to 994.7... [11:52:44] 2077 peptides remaining for 992.7 to 994.7... [11:52:45] 1789 peptides remaining for 992.7 to 994.7... [11:52:45] 1520 peptides remaining for 992.7 to 994.7... [11:52:46] 1259 peptides remaining for 992.7 to 994.7... [11:52:46] 992 peptides remaining for 992.7 to 994.7... [11:52:47] 731 peptides remaining for 992.7 to 994.7... [11:52:47] 453 peptides remaining for 992.7 to 994.7... [11:52:48] 163 peptides remaining for 992.7 to 994.7... [11:52:48] Processing 994.7 to 996.7 m/z, (1.9909371 second duty cycle) [11:52:50] 2923 peptides remaining for 994.7 to 996.7... [11:52:50] 2625 peptides remaining for 994.7 to 996.7... [11:52:51] 2336 peptides remaining for 994.7 to 996.7... [11:52:51] 2060 peptides remaining for 994.7 to 996.7... [11:52:52] 1782 peptides remaining for 994.7 to 996.7... [11:52:52] 1521 peptides remaining for 994.7 to 996.7... [11:52:53] 1250 peptides remaining for 994.7 to 996.7... [11:52:53] 994 peptides remaining for 994.7 to 996.7... [11:52:54] 729 peptides remaining for 994.7 to 996.7... [11:52:54] 451 peptides remaining for 994.7 to 996.7... [11:52:55] 172 peptides remaining for 994.7 to 996.7... [11:52:55] Processing 996.7 to 998.7 m/z, (1.9909153 second duty cycle) [11:52:57] 3033 peptides remaining for 996.7 to 998.7... [11:52:57] 2967 peptides remaining for 996.7 to 998.7... [11:52:58] 2662 peptides remaining for 996.7 to 998.7... [11:52:58] 2371 peptides remaining for 996.7 to 998.7... [11:52:59] 2102 peptides remaining for 996.7 to 998.7... [11:52:59] 1844 peptides remaining for 996.7 to 998.7... [11:53:00] 1569 peptides remaining for 996.7 to 998.7... [11:53:00] 1306 peptides remaining for 996.7 to 998.7... [11:53:01] 1030 peptides remaining for 996.7 to 998.7... [11:53:01] 759 peptides remaining for 996.7 to 998.7... [11:53:02] 469 peptides remaining for 996.7 to 998.7... [11:53:03] 185 peptides remaining for 996.7 to 998.7... [11:53:03] Processing 998.7 to 1000.7 m/z, (1.9909372 second duty cycle) [11:53:05] 2978 peptides remaining for 998.7 to 1000.7... [11:53:05] 2696 peptides remaining for 998.7 to 1000.7... [11:53:06] 2412 peptides remaining for 998.7 to 1000.7... [11:53:06] 2151 peptides remaining for 998.7 to 1000.7... [11:53:07] 1885 peptides remaining for 998.7 to 1000.7... [11:53:07] 1604 peptides remaining for 998.7 to 1000.7... [11:53:08] 1336 peptides remaining for 998.7 to 1000.7... [11:53:08] 1066 peptides remaining for 998.7 to 1000.7... [11:53:09] 793 peptides remaining for 998.7 to 1000.7... [11:53:09] 511 peptides remaining for 998.7 to 1000.7... [11:53:10] 229 peptides remaining for 998.7 to 1000.7... [11:53:10] Processing 1000.7 to 1002.7 m/z, (3.9816349 second duty cycle) [11:53:12] 2922 peptides remaining for 1000.7 to 1002.7... [11:53:12] 2416 peptides remaining for 1000.7 to 1002.7... [11:53:13] 1923 peptides remaining for 1000.7 to 1002.7... [11:53:13] 1463 peptides remaining for 1000.7 to 1002.7... [11:53:14] 978 peptides remaining for 1000.7 to 1002.7... [11:53:14] 492 peptides remaining for 1000.7 to 1002.7... [11:53:15] 0 peptides remaining for 1000.7 to 1002.7... [11:53:15] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:53:25] Sorted feature file in 9.97 seconds wall clock time [11:53:25] File size check: 202242654 vs 202242654 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:53:25] 485474 total peptides processed. [11:53:25] Running Percolator... [11:53:25] Executing [cmd /c C:\Windows\Temp\tmp698C.java\Percolator-v3-01-4178273244859010828.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt] [11:53:26] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:53:26] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:53:26] Written by Lukas Käll (lukall@u.washington.edu) in the [11:53:26] Department of Genome Sciences at the University of Washington. [11:53:26] Issued command: [11:53:26] C:\Windows\Temp\tmp698C.java\Percolator-v3-01-4178273244859010828.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:53:26] Started Wed Jul 17 11:53:26 2024 [11:53:26] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [11:53:26] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:53:26] Features: [11:53:26] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:53:30] Found 485474 PSMs [11:53:30] Separate target and decoy search inputs detected, using mix-max method. [11:53:30] Train/test set contains 242334 positives and 243140 negatives, size ratio=0.996685 and pi0=1 [11:53:31] Selecting Cpos by cross-validation. [11:53:31] Selecting Cneg by cross-validation. [11:53:34] Split 1: Selected feature 3 as initial search direction. Could separate 2307 training set positives in that direction. [11:53:37] Split 2: Selected feature 3 as initial search direction. Could separate 2329 training set positives in that direction. [11:53:40] Split 3: Selected feature 3 as initial search direction. Could separate 2491 training set positives in that direction. [11:53:40] Found 3556 test set positives with q<0.01 in initial direction [11:53:40] Reading in data and feature calculation took 14.724 cpu seconds or 14 seconds wall clock time. [11:53:40] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:54:04] Iteration 1: Estimated 4693 PSMs with q<0.01 [11:54:28] Iteration 2: Estimated 5106 PSMs with q<0.01 [11:54:53] Iteration 3: Estimated 5364 PSMs with q<0.01 [11:54:53] Learned normalized SVM weights for the 3 cross-validation splits: [11:54:53] Split1 Split2 Split3 FeatureName [11:54:53] -1.3720 -1.4260 -1.1477 primary [11:54:53] 0.0273 -0.1408 -0.0591 xCorrLib [11:54:53] 0.5173 0.4630 0.4020 xCorrModel [11:54:53] 0.0387 -0.2368 -0.1930 dotProduct [11:54:53] 0.5872 0.7503 0.7675 contrastAngle [11:54:53] -0.1360 -0.3659 -0.4711 logit [11:54:53] 0.1378 -0.1894 -0.0738 sumOfSquaredErrors [11:54:53] 1.0700 1.3723 1.1893 numberOfMatchingPeaks [11:54:53] 0.7133 0.7001 0.4222 numberOfMatchingPeaksAboveThreshold [11:54:53] 0.0765 0.0309 0.0385 averageFragmentDeltaMasses [11:54:53] 0.1115 0.2347 0.1851 isotopeDotProduct [11:54:53] 0.1523 0.1267 0.1353 averageParentDeltaMass [11:54:53] -0.0371 0.0387 -0.0249 percentBlankOverMono [11:54:53] 0.2112 0.0736 0.0807 numberPrecursorMatch [11:54:53] -0.9309 -0.8609 -0.7176 lnSp [11:54:53] 0.4125 0.3516 0.2696 maxLadderLength [11:54:53] 0.0832 0.1000 0.0784 evalue [11:54:53] -0.0131 0.0394 0.0382 correlationToGaussian [11:54:53] 0.0485 -0.0459 0.0112 correlationToPrecursor [11:54:53] -0.0387 0.0109 0.0248 isIntegratedSignal [11:54:53] -0.0896 0.0823 -0.0170 isIntegratedPrecursor [11:54:53] 0.2730 0.2466 0.1866 numPeaksWithGoodCorrelation [11:54:53] -0.2997 -0.3322 -0.2989 numMissedCleavage [11:54:53] -0.2785 -0.4887 -0.2309 pepLength [11:54:53] 0.0000 0.0000 0.0000 charge1 [11:54:53] -0.0091 -0.2866 0.0363 charge2 [11:54:53] 0.0091 0.2866 -0.0363 charge3 [11:54:53] 0.0000 0.0000 0.0000 charge4 [11:54:53] 0.0343 0.1524 -0.0129 precursorMz [11:54:53] -0.0259 -0.5352 -0.0554 precursorMass [11:54:53] -0.1799 -0.1170 -0.0389 RTinMin [11:54:53] -3.7978 -3.6855 -3.1038 m0 [11:54:53] Found 5129 test set PSMs with q<0.01. [11:54:53] Scoring full list of PSMs with trained SVMs. [11:54:53] Features: [11:54:53] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:54:58] Found 485474 PSMs [11:54:58] Evaluated set contained 242334 positives and 243140 negatives. [11:54:59] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:55:00] Selecting pi_0=0.968323 [11:55:00] Calculating q values. [11:55:01] New pi_0 estimate on final list yields 4977 target peptides with q<0.01. [11:55:01] Calculating posterior error probabilities (PEPs). [11:55:02] Processing took 81.67 cpu seconds or 82 seconds wall clock time. [11:55:07] First pass: 4977 peptides identified at 1.0% FDR [11:55:07] Generating retention time mapping using 4977 points... [11:55:07] Enough data points (4977) to perform KDE alignment. [11:55:08] Enough data points (4650) to perform KDE alignment. [11:55:08] Enough data points (4977) to perform KDE alignment. [11:55:09] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:55:12] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:55:20] Sorted feature file in 8.17 seconds wall clock time [11:55:20] File size check: 164676367 vs 164676367 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [11:55:20] Executing [cmd /c C:\Windows\Temp\tmp698C.java\Percolator-v3-01-2131251171531413050.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt] [11:55:21] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [11:55:21] Copyright (c) 2006-9 University of Washington. All rights reserved. [11:55:21] Written by Lukas Käll (lukall@u.washington.edu) in the [11:55:21] Department of Genome Sciences at the University of Washington. [11:55:21] Issued command: [11:55:21] C:\Windows\Temp\tmp698C.java\Percolator-v3-01-2131251171531413050.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:55:21] Started Wed Jul 17 11:55:21 2024 [11:55:21] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [11:55:21] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:55:21] Features: [11:55:21] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:55:24] Found 371045 PSMs [11:55:24] Separate target and decoy search inputs detected, using mix-max method. [11:55:24] Train/test set contains 184908 positives and 186137 negatives, size ratio=0.993397 and pi0=1 [11:55:25] Selecting Cpos by cross-validation. [11:55:25] Selecting Cneg by cross-validation. [11:55:27] Split 1: Selected feature 3 as initial search direction. Could separate 2294 training set positives in that direction. [11:55:30] Split 2: Selected feature 3 as initial search direction. Could separate 2344 training set positives in that direction. [11:55:32] Split 3: Selected feature 3 as initial search direction. Could separate 2405 training set positives in that direction. [11:55:32] Found 3506 test set positives with q<0.01 in initial direction [11:55:32] Reading in data and feature calculation took 11.523 cpu seconds or 11 seconds wall clock time. [11:55:32] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [11:55:50] Iteration 1: Estimated 4556 PSMs with q<0.01 [11:56:09] Iteration 2: Estimated 4836 PSMs with q<0.01 [11:56:28] Iteration 3: Estimated 4993 PSMs with q<0.01 [11:56:47] Iteration 4: Estimated 5115 PSMs with q<0.01 [11:57:06] Iteration 5: Estimated 5195 PSMs with q<0.01 [11:57:26] Iteration 6: Estimated 5245 PSMs with q<0.01 [11:57:45] Iteration 7: Estimated 5252 PSMs with q<0.01 [11:58:05] Iteration 8: Estimated 5254 PSMs with q<0.01 [11:58:25] Iteration 9: Estimated 5277 PSMs with q<0.01 [11:58:45] Iteration 10: Estimated 5272 PSMs with q<0.01 [11:58:45] Learned normalized SVM weights for the 3 cross-validation splits: [11:58:45] Split1 Split2 Split3 FeatureName [11:58:45] -4.1363 -1.0355 -1.2294 primary [11:58:45] -0.0592 0.0375 0.0227 xCorrLib [11:58:45] 1.1180 0.3834 0.3898 xCorrModel [11:58:45] 0.1838 0.0975 0.0258 dotProduct [11:58:45] 2.1239 0.6008 0.5396 contrastAngle [11:58:45] -1.7773 -0.5757 -0.2367 logit [11:58:45] 0.3009 -0.0991 -0.0367 sumOfSquaredErrors [11:58:45] 3.7194 0.8531 1.1331 numberOfMatchingPeaks [11:58:45] 1.8174 0.3997 0.4458 numberOfMatchingPeaksAboveThreshold [11:58:45] -0.0672 0.0229 0.0295 averageFragmentDeltaMasses [11:58:45] 0.3128 0.1889 0.1938 isotopeDotProduct [11:58:45] 0.0371 0.0938 0.1597 averageParentDeltaMass [11:58:45] 0.0641 0.0149 -0.0266 percentBlankOverMono [11:58:45] 0.2396 0.1183 0.0752 numberPrecursorMatch [11:58:45] -2.4669 -0.6563 -0.7220 lnSp [11:58:45] 0.8097 0.2992 0.3022 maxLadderLength [11:58:45] 0.2834 0.1552 0.1595 evalue [11:58:45] 0.5873 0.3438 -0.0235 correlationToGaussian [11:58:45] 0.1007 -0.0465 0.0025 correlationToPrecursor [11:58:45] -0.1801 -0.0159 0.0053 isIntegratedSignal [11:58:45] -0.0361 0.0835 -0.0259 isIntegratedPrecursor [11:58:45] 0.8199 0.3756 0.2849 numPeaksWithGoodCorrelation [11:58:45] -0.1146 -0.0815 -0.0353 deltaRT [11:58:45] -0.0357 -0.0059 -0.0138 ms1MassError [11:58:45] -0.0291 -0.0161 -0.0395 ms2MassError [11:58:45] -0.5002 -0.2222 -0.3456 numMissedCleavage [11:58:45] -0.4435 -0.1325 -0.0956 pepLength [11:58:45] 0.0000 0.0000 0.0000 charge1 [11:58:45] -0.5259 0.0391 0.0514 charge2 [11:58:45] 0.5259 -0.0391 -0.0514 charge3 [11:58:45] 0.0000 0.0000 0.0000 charge4 [11:58:45] 0.2144 -0.0183 -0.0210 precursorMz [11:58:45] -1.6881 0.0016 -0.0713 precursorMass [11:58:45] -0.6058 -0.1843 -0.1350 RTinMin [11:58:45] -7.3903 -3.2556 -3.1218 m0 [11:58:45] Found 5109 test set PSMs with q<0.01. [11:58:45] Scoring full list of PSMs with trained SVMs. [11:58:45] Features: [11:58:45] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [11:58:49] Found 371045 PSMs [11:58:49] Evaluated set contained 184908 positives and 186137 negatives. [11:58:50] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [11:58:51] Selecting pi_0=0.966304 [11:58:51] Calculating q values. [11:58:51] New pi_0 estimate on final list yields 5243 target peptides with q<0.01. [11:58:51] Calculating posterior error probabilities (PEPs). [11:58:53] Processing took 200.5 cpu seconds or 201 seconds wall clock time. [11:58:58] Generating retention time mapping using 5243 points... [11:58:58] Enough data points (5243) to perform KDE alignment. [11:58:59] Enough data points (4810) to perform KDE alignment. [11:58:59] Enough data points (5243) to perform KDE alignment. [11:58:59] Writing elib result library... [11:59:00] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 5243 vs local peptides: 5243 [11:59:00] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML... [11:59:00] Extracting Spectral Data for 5243 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML... [11:59:00] Number of global peptides: 5243 vs local peptides: 5243 [11:59:01] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [11:59:01] Parsed features and scores for 5243 peptides. [11:59:01] Extracting 5243 peptides... [11:59:01] Quant Extracting 898.7 to 900.7 m/z (37.748646 to 100.01625 min) [11:59:01] Quant Extracting 900.7 to 902.7 m/z (24.358051 to 94.0974 min) [11:59:01] Quant Extracting 902.7 to 904.7 m/z (31.268599 to 99.35391 min) [11:59:01] Quant Extracting 904.7 to 906.7 m/z (24.991976 to 99.6522 min) [11:59:02] Quant Extracting 906.7 to 908.7 m/z (20.567942 to 97.6191 min) [11:59:02] Quant Extracting 908.7 to 910.7 m/z (19.66163 to 100.76185 min) [11:59:02] Quant Extracting 910.7 to 912.7 m/z (25.127546 to 100.45754 min) [11:59:02] Quant Extracting 912.7 to 914.7 m/z (27.700434 to 95.46634 min) [11:59:02] Quant Extracting 914.7 to 916.7 m/z (30.774055 to 97.3263 min) [11:59:02] Quant Extracting 916.7 to 918.7 m/z (30.973091 to 99.35737 min) [11:59:02] Quant Extracting 918.7 to 920.7 m/z (18.850525 to 95.532295 min) [11:59:02] Quant Extracting 920.7 to 922.7 m/z (26.169252 to 100.6309 min) [11:59:02] Quant Extracting 922.7 to 924.7 m/z (37.2603 to 98.540764 min) [11:59:02] Quant Extracting 924.7 to 926.7 m/z (20.070272 to 98.99862 min) [11:59:02] Quant Extracting 926.7 to 928.7 m/z (27.774403 to 96.448746 min) [11:59:03] Quant Extracting 928.7 to 930.7 m/z (10.034467 to 100.7676 min) [11:59:03] Quant Extracting 930.7 to 932.7 m/z (32.503784 to 93.749054 min) [11:59:03] Quant Extracting 932.7 to 934.7 m/z (33.997623 to 99.630295 min) [11:59:03] Quant Extracting 934.7 to 936.7 m/z (42.16493 to 96.84146 min) [11:59:03] Quant Extracting 936.7 to 938.7 m/z (24.272333 to 97.59483 min) [11:59:03] Quant Extracting 938.7 to 940.7 m/z (23.213993 to 94.82427 min) [11:59:03] Quant Extracting 940.7 to 942.7 m/z (34.433105 to 97.99227 min) [11:59:03] Quant Extracting 942.7 to 944.7 m/z (26.240929 to 97.72853 min) [11:59:03] Quant Extracting 944.7 to 946.7 m/z (37.764713 to 99.7667 min) [11:59:03] Quant Extracting 946.7 to 948.7 m/z (18.175486 to 95.70312 min) [11:59:03] Quant Extracting 948.7 to 950.7 m/z (26.636045 to 100.40182 min) [11:59:03] Quant Extracting 950.7 to 952.7 m/z (35.662067 to 100.301956 min) [11:59:04] Quant Extracting 952.7 to 954.7 m/z (32.08076 to 95.93276 min) [11:59:04] Quant Extracting 954.7 to 956.7 m/z (32.615005 to 96.229706 min) [11:59:04] Quant Extracting 956.7 to 958.7 m/z (40.8306 to 95.38133 min) [11:59:04] Quant Extracting 958.7 to 960.7 m/z (31.386238 to 96.36077 min) [11:59:04] Quant Extracting 960.7 to 962.7 m/z (7.1688914 to 100.74516 min) [11:59:04] Quant Extracting 962.7 to 964.7 m/z (37.80262 to 96.7194 min) [11:59:04] Quant Extracting 964.7 to 966.7 m/z (27.347464 to 100.74914 min) [11:59:04] Quant Extracting 966.7 to 968.7 m/z (16.303738 to 100.74914 min) [11:59:04] Quant Extracting 968.7 to 970.7 m/z (16.957401 to 100.75028 min) [11:59:04] Quant Extracting 970.7 to 972.7 m/z (29.321745 to 97.345856 min) [11:59:04] Quant Extracting 972.7 to 974.7 m/z (32.02395 to 97.903786 min) [11:59:04] Quant Extracting 974.7 to 976.7 m/z (30.426657 to 96.04028 min) [11:59:05] Quant Extracting 976.7 to 978.7 m/z (28.986387 to 96.13853 min) [11:59:05] Quant Extracting 978.7 to 980.7 m/z (29.391577 to 99.57754 min) [11:59:05] Quant Extracting 980.7 to 982.7 m/z (19.311155 to 100.75378 min) [11:59:05] Quant Extracting 982.7 to 984.7 m/z (36.32842 to 98.55808 min) [11:59:05] Quant Extracting 984.7 to 986.7 m/z (15.802401 to 99.97736 min) [11:59:05] Quant Extracting 986.7 to 988.7 m/z (31.096163 to 100.75493 min) [11:59:05] Quant Extracting 988.7 to 990.7 m/z (27.792868 to 100.75608 min) [11:59:05] Quant Extracting 990.7 to 992.7 m/z (34.151905 to 95.75076 min) [11:59:05] Quant Extracting 992.7 to 994.7 m/z (38.73744 to 95.39467 min) [11:59:05] Quant Extracting 994.7 to 996.7 m/z (29.70062 to 100.757225 min) [11:59:05] Quant Extracting 996.7 to 998.7 m/z (42.120056 to 100.758385 min) [11:59:05] Quant Extracting 998.7 to 1000.7 m/z (42.350365 to 97.12379 min) [11:59:05] Quant Extracting 1000.7 to 1002.7 m/z (16.042398 to 94.874504 min) [11:59:05] Attempted extraction for: 5243, found 5243 [11:59:05] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML (5243 entries)... [11:59:05] Writing 5243 peptides to entries table... [11:59:06] Writing 5243 peptides to peptidequants table... [11:59:06] Finished writing to Encyclopedia ELIB at Wed Jul 17 11:59:06 BST 2024 [11:59:07] Writing local target/decoy peptides: 5243/52, pi0: 0.966304 [11:59:07] Writing local target/decoy proteins: 3145/31 [11:59:08] Finished analysis! 5243 peptides identified at 1.0% FDR (12.6 minutes) [11:59:08] Generating chromatogram library (7 of 7): UP000005640_9606-z3_nce27.elib Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom" -libexport -o "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" SearchToLIB EncyclopeDIA version 2.12.30 Parameters: -i E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom -f E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta -l E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib -o E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib -a true -blib false -alignOnly false -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [11:59:14] Attempting to process 12 searches... [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.dia.features.txt [11:59:23] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [11:59:23] Using Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML to extract representative search parameters [11:59:23] Running global Percolator analysis. [11:59:23] Found indicies for sequence: 37, primary: 3, and deltaRT: 25 [11:59:23] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:25] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:28] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:30] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:31] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:34] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:37] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:39] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:43] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:45] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:47] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:48] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.features.txt [11:59:53] Found 2262718 total peptides, writing to new Percolator input file... [12:00:07] Executing [cmd /c C:\Windows\Temp\tmp59BF.java\Percolator-v3-01-1707241033233044616.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_results.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_results.txt.2147483647.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_features.txt] [12:00:07] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:00:07] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:00:07] Written by Lukas Käll (lukall@u.washington.edu) in the [12:00:07] Department of Genome Sciences at the University of Washington. [12:00:07] Issued command: [12:00:07] C:\Windows\Temp\tmp59BF.java\Percolator-v3-01-1707241033233044616.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_results.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_results.txt.2147483647.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_features.txt [12:00:07] Started Wed Jul 17 12:00:07 2024 [12:00:07] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [12:00:07] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_chrom\UP000005640_9606-z3_nce27_concatenated_features.txt [12:00:07] Features: [12:00:07] consistencyScore absDeltaDeltaRT irqDeltaRT primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:00:18] Processing line 1000000 [12:00:25] Processing line 2000000 [12:00:27] Found 2262718 PSMs [12:00:27] Separate target and decoy search inputs detected, using mix-max method. [12:00:27] Train/test set contains 250342 positives and 249658 negatives, size ratio=1.00274 and pi0=1 [12:00:28] Selecting Cpos by cross-validation. [12:00:28] Selecting Cneg by cross-validation. [12:00:32] Split 1: Selected feature 6 as initial search direction. Could separate 4650 training set positives in that direction. [12:00:36] Split 2: Selected feature 5 as initial search direction. Could separate 4523 training set positives in that direction. [12:00:40] Split 3: Selected feature 5 as initial search direction. Could separate 4643 training set positives in that direction. [12:00:40] Found 6583 test set positives with q<0.01 in initial direction [12:00:40] Reading in data and feature calculation took 33.082 cpu seconds or 33 seconds wall clock time. [12:00:40] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:01:10] Iteration 1: Estimated 10580 PSMs with q<0.01 [12:01:44] Iteration 2: Estimated 12452 PSMs with q<0.01 [12:02:31] Iteration 3: Estimated 12953 PSMs with q<0.01 [12:03:15] Iteration 4: Estimated 13071 PSMs with q<0.01 [12:03:47] Iteration 5: Estimated 13204 PSMs with q<0.01 [12:04:20] Iteration 6: Estimated 13195 PSMs with q<0.01 [12:04:53] Iteration 7: Estimated 13208 PSMs with q<0.01 [12:05:26] Iteration 8: Estimated 13254 PSMs with q<0.01 [12:05:59] Iteration 9: Estimated 13267 PSMs with q<0.01 [12:06:32] Iteration 10: Estimated 13254 PSMs with q<0.01 [12:06:32] Learned normalized SVM weights for the 3 cross-validation splits: [12:06:32] Split1 Split2 Split3 FeatureName [12:06:32] -0.1559 -0.2738 -0.0664 consistencyScore [12:06:32] 0.0442 -0.0465 -0.0428 absDeltaDeltaRT [12:06:32] -0.0058 0.0517 -0.0202 irqDeltaRT [12:06:32] -2.4665 -0.7762 -3.8064 primary [12:06:32] -0.1641 -0.0599 -0.0895 xCorrLib [12:06:32] 0.6275 0.3013 0.6522 xCorrModel [12:06:32] 1.2802 0.5816 2.3505 dotProduct [12:06:32] -0.2488 0.5025 -1.1965 contrastAngle [12:06:32] 0.2597 -0.0943 0.6145 logit [12:06:32] 0.4222 0.3779 0.4938 sumOfSquaredErrors [12:06:32] 3.0449 1.2277 4.5356 numberOfMatchingPeaks [12:06:32] 0.0476 0.1406 0.0908 numberOfMatchingPeaksAboveThreshold [12:06:32] -0.0558 -0.0376 -0.0250 averageFragmentDeltaMasses [12:06:32] 0.1316 0.1488 0.3125 isotopeDotProduct [12:06:32] 0.0481 0.0070 -0.0595 averageParentDeltaMass [12:06:32] -0.0380 0.0105 -0.0766 percentBlankOverMono [12:06:32] 0.0452 0.0331 -0.0830 numberPrecursorMatch [12:06:32] -1.7400 -1.0973 -2.0795 lnSp [12:06:32] 0.9528 0.7204 1.0948 maxLadderLength [12:06:32] 0.1733 0.1722 0.2549 evalue [12:06:32] 0.4469 0.3233 0.6115 correlationToGaussian [12:06:32] 0.1542 0.1102 0.1407 correlationToPrecursor [12:06:32] 0.0317 0.0435 0.0555 isIntegratedSignal [12:06:32] 0.1002 0.0262 0.2084 isIntegratedPrecursor [12:06:32] 1.0645 0.7621 1.1325 numPeaksWithGoodCorrelation [12:06:32] 0.0488 0.0362 0.0133 deltaRT [12:06:32] 0.0017 -0.0574 -0.1509 ms1MassError [12:06:32] -0.2299 -0.1730 -0.1104 ms2MassError [12:06:32] -0.6029 -0.4639 -0.7488 numMissedCleavage [12:06:32] -2.0583 -1.3496 -2.5011 pepLength [12:06:32] 0.0000 0.0000 0.0000 charge1 [12:06:32] 0.0773 -0.0664 0.1564 charge2 [12:06:32] -0.0773 0.0664 -0.1564 charge3 [12:06:32] 0.0000 0.0000 0.0000 charge4 [12:06:32] -0.0655 0.3583 -0.3152 precursorMz [12:06:32] 1.0151 0.1159 1.6781 precursorMass [12:06:32] -0.2972 -0.2355 -0.4600 RTinMin [12:06:32] -5.9943 -4.6279 -7.3535 m0 [12:06:32] Found 12905 test set PSMs with q<0.01. [12:06:32] Scoring full list of PSMs with trained SVMs. [12:06:33] Features: [12:06:33] consistencyScore absDeltaDeltaRT irqDeltaRT primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:06:43] Processing line 1000000 [12:06:53] Processing line 2000000 [12:06:56] Found 2262718 PSMs [12:06:56] Evaluated set contained 1131583 positives and 1131135 negatives. [12:06:58] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:07:02] Selecting pi_0=0.932379 [12:07:02] Calculating q values. [12:07:02] New pi_0 estimate on final list yields 58652 target peptides with q<0.01. [12:07:02] Calculating posterior error probabilities (PEPs). [12:07:04] Processing took 383.7 cpu seconds or 384 seconds wall clock time. [12:07:35] Identified 58652 peptides across all files at a 1.0% FDR threshold. [12:07:35] Inferring peak boundaries across files... [12:07:35] Adding library [UP000005640_9606-z3_nce27-prosit.dlib] to ion tracker... [12:08:00] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:00] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:01] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:01] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:01] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:01] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [12:08:02] Found quantitative ions for 58652 total peptides (58652 with 3 or more high quality peaks) across all runs. [12:08:03] Setting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML as the seed experiment. [12:08:04] Enough data points (502) to perform KDE alignment. [12:08:05] Enough data points (505) to perform KDE alignment. [12:08:08] Enough data points (774) to perform KDE alignment. [12:08:09] Enough data points (1577) to perform KDE alignment. [12:08:10] Enough data points (52) to perform KDE alignment. [12:08:11] ...Finished peak inference. [12:08:11] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 10072 [12:08:11] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML... [12:08:11] Extracting Spectral Data for 10072 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML... [12:08:11] Wrote 502 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML [12:08:12] Number of global peptides: 58652 vs local peptides: 10072 [12:08:14] Found additional 46711 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:08:14] Parsed features and scores for 58652 peptides. [12:08:14] Extracting 58652 peptides... [12:08:14] Quant Extracting 398.4 to 400.4 m/z (7.179955 to 78.312225 min) [12:08:15] Quant Extracting 400.4 to 402.4 m/z (5.2905254 to 79.832504 min) [12:08:15] Quant Extracting 402.4 to 404.4 m/z (7.179955 to 80.35251 min) [12:08:15] Quant Extracting 404.4 to 406.4 m/z (7.15772 to 81.93882 min) [12:08:15] Quant Extracting 406.4 to 408.4 m/z (7.225832 to 80.90331 min) [12:08:15] Quant Extracting 408.4 to 410.4 m/z (7.179955 to 80.35482 min) [12:08:15] Quant Extracting 410.4 to 412.4 m/z (4.40889 to 81.649086 min) [12:08:15] Quant Extracting 412.4 to 414.4 m/z (5.8511157 to 78.96431 min) [12:08:15] Quant Extracting 414.4 to 416.4 m/z (5.592664 to 86.99362 min) [12:08:15] Quant Extracting 416.4 to 418.4 m/z (5.982831 to 84.282646 min) [12:08:16] Quant Extracting 418.4 to 420.4 m/z (7.0353904 to 80.13152 min) [12:08:16] Quant Extracting 420.4 to 422.4 m/z (7.179955 to 85.49 min) [12:08:16] Quant Extracting 422.4 to 424.4 m/z (7.133649 to 82.493164 min) [12:08:16] Quant Extracting 424.4 to 426.4 m/z (3.691619 to 85.06626 min) [12:08:16] Quant Extracting 426.4 to 428.4 m/z (7.179955 to 80.88869 min) [12:08:16] Quant Extracting 428.4 to 430.4 m/z (7.1359415 to 79.81059 min) [12:08:16] Quant Extracting 430.4 to 432.4 m/z (6.6092887 to 83.24473 min) [12:08:16] Quant Extracting 432.4 to 434.4 m/z (7.2656045 to 83.21292 min) [12:08:16] Quant Extracting 434.4 to 436.4 m/z (7.137088 to 89.02334 min) [12:08:16] Quant Extracting 436.4 to 438.4 m/z (7.1382346 to 81.688995 min) [12:08:16] Quant Extracting 438.4 to 440.5 m/z (4.9079328 to 85.39727 min) [12:08:17] Quant Extracting 440.5 to 442.5 m/z (6.6815033 to 87.52633 min) [12:08:17] Quant Extracting 442.5 to 444.5 m/z (7.139381 to 83.99585 min) [12:08:17] Quant Extracting 444.5 to 446.5 m/z (7.817685 to 87.16665 min) [12:08:17] Quant Extracting 446.5 to 448.5 m/z (7.1405272 to 81.07864 min) [12:08:17] Quant Extracting 448.5 to 450.5 m/z (7.179955 to 80.81862 min) [12:08:17] Quant Extracting 450.5 to 452.5 m/z (4.3549495 to 83.574936 min) [12:08:17] Quant Extracting 452.5 to 454.5 m/z (7.3359976 to 85.69533 min) [12:08:17] Quant Extracting 454.5 to 456.5 m/z (7.175398 to 84.198616 min) [12:08:17] Quant Extracting 456.5 to 458.5 m/z (7.1439667 to 84.65463 min) [12:08:17] Quant Extracting 458.5 to 460.5 m/z (5.4743776 to 85.733116 min) [12:08:17] Quant Extracting 460.5 to 462.5 m/z (6.159859 to 85.733116 min) [12:08:18] Quant Extracting 462.5 to 464.5 m/z (6.8182354 to 87.30714 min) [12:08:18] Quant Extracting 464.5 to 466.5 m/z (7.274821 to 87.30714 min) [12:08:18] Quant Extracting 466.5 to 468.5 m/z (7.791749 to 84.94883 min) [12:08:18] Quant Extracting 468.5 to 470.5 m/z (7.1788373 to 88.87655 min) [12:08:18] Quant Extracting 470.5 to 472.5 m/z (8.345084 to 100.773346 min) [12:08:18] Quant Extracting 472.5 to 474.5 m/z (7.1485505 to 83.19143 min) [12:08:18] Quant Extracting 474.5 to 476.5 m/z (7.181129 to 88.42078 min) [12:08:18] Quant Extracting 476.5 to 478.5 m/z (7.179955 to 89.047874 min) [12:08:18] Quant Extracting 478.5 to 480.5 m/z (7.50511 to 88.02986 min) [12:08:18] Quant Extracting 480.5 to 482.5 m/z (7.150842 to 87.6386 min) [12:08:19] Quant Extracting 482.5 to 484.5 m/z (5.806946 to 88.25954 min) [12:08:19] Quant Extracting 484.5 to 486.5 m/z (7.1193533 to 89.076225 min) [12:08:19] Quant Extracting 486.5 to 488.5 m/z (7.1845684 to 90.87858 min) [12:08:19] Quant Extracting 488.5 to 490.5 m/z (7.1531353 to 86.45799 min) [12:08:19] Quant Extracting 490.5 to 492.5 m/z (7.1531353 to 85.41551 min) [12:08:19] Quant Extracting 492.5 to 494.5 m/z (7.1542807 to 85.18738 min) [12:08:19] Quant Extracting 494.5 to 496.5 m/z (6.5989127 to 86.557976 min) [12:08:19] Quant Extracting 496.5 to 498.5 m/z (7.155427 to 89.047874 min) [12:08:19] Quant Extracting 498.5 to 500.5 m/z (7.155427 to 88.06765 min) [12:08:19] Quant Extracting 500.5 to 502.5 m/z (7.1880097 to 87.31751 min) [12:08:20] Attempted extraction for: 58652, found 11941 [12:08:20] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML (11941 entries)... [12:08:20] Writing 11941 peptides to entries table... [12:08:20] Writing 11941 peptides to peptidequants table... [12:08:21] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:08:21 BST 2024 [12:08:23] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 17396 [12:08:23] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML... [12:08:23] Extracting Spectral Data for 17396 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML... [12:08:23] Wrote 0 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML [12:08:23] Number of global peptides: 58652 vs local peptides: 17396 [12:08:26] Found additional 42816 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:08:26] Parsed features and scores for 58652 peptides. [12:08:26] Extracting 58652 peptides... [12:08:26] Quant Extracting 498.5 to 500.5 m/z (7.1619444 to 88.03474 min) [12:08:26] Quant Extracting 500.5 to 502.5 m/z (7.194508 to 87.22735 min) [12:08:26] Quant Extracting 502.5 to 504.5 m/z (7.163096 to 88.55836 min) [12:08:26] Quant Extracting 504.5 to 506.5 m/z (7.6543427 to 92.82457 min) [12:08:27] Quant Extracting 506.5 to 508.5 m/z (7.1642475 to 92.172676 min) [12:08:27] Quant Extracting 508.5 to 510.5 m/z (7.1642475 to 93.58259 min) [12:08:27] Quant Extracting 510.5 to 512.5 m/z (7.165399 to 86.25647 min) [12:08:27] Quant Extracting 512.5 to 514.5 m/z (7.165399 to 86.67744 min) [12:08:27] Quant Extracting 514.5 to 516.5 m/z (7.1665497 to 91.32369 min) [12:08:27] Quant Extracting 516.5 to 518.5 m/z (7.1665497 to 89.893585 min) [12:08:27] Quant Extracting 518.5 to 520.5 m/z (7.167702 to 92.04628 min) [12:08:27] Quant Extracting 520.5 to 522.5 m/z (7.167702 to 92.01429 min) [12:08:28] Quant Extracting 522.5 to 524.5 m/z (6.166393 to 88.95316 min) [12:08:28] Quant Extracting 524.5 to 526.5 m/z (7.1688485 to 89.92775 min) [12:08:28] Quant Extracting 526.5 to 528.5 m/z (7.172818 to 91.6248 min) [12:08:28] Quant Extracting 528.5 to 530.5 m/z (7.172818 to 88.533455 min) [12:08:28] Quant Extracting 530.5 to 532.5 m/z (7.1739697 to 88.955475 min) [12:08:28] Quant Extracting 532.5 to 534.5 m/z (6.135904 to 88.63133 min) [12:08:28] Quant Extracting 534.5 to 536.5 m/z (7.175116 to 93.55728 min) [12:08:28] Quant Extracting 536.5 to 538.5 m/z (7.1434765 to 91.39943 min) [12:08:28] Quant Extracting 538.5 to 540.5 m/z (7.1434765 to 92.80497 min) [12:08:28] Quant Extracting 540.5 to 542.5 m/z (7.2408743 to 95.99597 min) [12:08:29] Quant Extracting 542.5 to 544.5 m/z (7.5025744 to 91.564316 min) [12:08:29] Quant Extracting 544.5 to 546.5 m/z (7.145805 to 91.564316 min) [12:08:29] Quant Extracting 546.5 to 548.5 m/z (7.145805 to 91.43503 min) [12:08:29] Quant Extracting 548.5 to 550.5 m/z (7.1469502 to 97.19701 min) [12:08:29] Quant Extracting 550.5 to 552.5 m/z (7.1469502 to 90.19652 min) [12:08:29] Quant Extracting 552.5 to 554.5 m/z (7.148113 to 94.25449 min) [12:08:29] Quant Extracting 554.5 to 556.5 m/z (8.02563 to 89.31998 min) [12:08:29] Quant Extracting 556.5 to 558.5 m/z (7.1492643 to 87.8597 min) [12:08:29] Quant Extracting 558.5 to 560.5 m/z (7.1492643 to 92.48341 min) [12:08:30] Quant Extracting 560.5 to 562.5 m/z (6.74928 to 90.52324 min) [12:08:30] Quant Extracting 562.5 to 564.5 m/z (7.1831594 to 97.7693 min) [12:08:30] Quant Extracting 564.5 to 566.5 m/z (7.1515675 to 92.94241 min) [12:08:30] Quant Extracting 566.5 to 568.5 m/z (7.1515675 to 94.61944 min) [12:08:30] Quant Extracting 568.5 to 570.5 m/z (7.15272 to 92.19112 min) [12:08:30] Quant Extracting 570.5 to 572.5 m/z (7.15272 to 89.16321 min) [12:08:30] Quant Extracting 572.5 to 574.5 m/z (7.1538706 to 88.026665 min) [12:08:30] Quant Extracting 574.5 to 576.5 m/z (7.1538706 to 94.49007 min) [12:08:31] Quant Extracting 576.5 to 578.5 m/z (7.7400613 to 97.541824 min) [12:08:31] Quant Extracting 578.5 to 580.5 m/z (7.155017 to 92.09672 min) [12:08:31] Quant Extracting 580.5 to 582.5 m/z (7.15618 to 94.426796 min) [12:08:31] Quant Extracting 582.5 to 584.5 m/z (7.15618 to 92.55586 min) [12:08:31] Quant Extracting 584.5 to 586.5 m/z (7.18891 to 91.379974 min) [12:08:31] Quant Extracting 586.5 to 588.5 m/z (7.1573243 to 93.57228 min) [12:08:31] Quant Extracting 588.5 to 590.5 m/z (7.158486 to 97.94399 min) [12:08:31] Quant Extracting 590.5 to 592.5 m/z (7.158486 to 92.623764 min) [12:08:31] Quant Extracting 592.5 to 594.5 m/z (7.159632 to 92.689384 min) [12:08:32] Quant Extracting 594.5 to 596.5 m/z (7.159632 to 91.08899 min) [12:08:32] Quant Extracting 596.5 to 598.5 m/z (12.738337 to 93.545746 min) [12:08:32] Quant Extracting 598.5 to 600.5 m/z (7.160793 to 94.49696 min) [12:08:32] Quant Extracting 600.5 to 602.5 m/z (7.225191 to 100.747856 min) [12:08:32] Attempted extraction for: 58652, found 15836 [12:08:32] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-500_600mz_DIA_Cond-50cm_01.mzML (15836 entries)... [12:08:32] Writing 15836 peptides to entries table... [12:08:33] Writing 15836 peptides to peptidequants table... [12:08:34] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:08:34 BST 2024 [12:08:35] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 15830 [12:08:35] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML... [12:08:35] Extracting Spectral Data for 15830 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML... [12:08:35] Wrote 505 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML [12:08:36] Number of global peptides: 58652 vs local peptides: 15830 [12:08:38] Found additional 45836 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:08:38] Parsed features and scores for 58652 peptides. [12:08:38] Extracting 58652 peptides... [12:08:38] Quant Extracting 598.5 to 600.5 m/z (7.3294473 to 94.448555 min) [12:08:38] Quant Extracting 600.5 to 602.5 m/z (7.1413045 to 94.448555 min) [12:08:38] Quant Extracting 602.5 to 604.5 m/z (8.882516 to 94.48174 min) [12:08:38] Quant Extracting 604.5 to 606.5 m/z (7.7750425 to 97.0411 min) [12:08:39] Quant Extracting 606.5 to 608.5 m/z (7.14245 to 94.18944 min) [12:08:39] Quant Extracting 608.5 to 610.5 m/z (7.143613 to 93.96119 min) [12:08:39] Quant Extracting 610.5 to 612.5 m/z (7.143613 to 93.79904 min) [12:08:39] Quant Extracting 612.5 to 614.5 m/z (7.644376 to 95.69468 min) [12:08:39] Quant Extracting 614.5 to 616.5 m/z (7.144763 to 99.73087 min) [12:08:39] Quant Extracting 616.5 to 618.5 m/z (7.1459146 to 97.93661 min) [12:08:39] Quant Extracting 618.5 to 620.5 m/z (7.1459146 to 94.910965 min) [12:08:39] Quant Extracting 620.5 to 622.5 m/z (12.372965 to 96.156265 min) [12:08:39] Quant Extracting 622.5 to 624.5 m/z (12.273181 to 93.50985 min) [12:08:39] Quant Extracting 624.5 to 626.5 m/z (7.1482177 to 93.64097 min) [12:08:40] Quant Extracting 626.5 to 628.5 m/z (7.1482177 to 91.271935 min) [12:08:40] Quant Extracting 628.5 to 630.5 m/z (7.1493692 to 96.12625 min) [12:08:40] Quant Extracting 630.5 to 632.5 m/z (7.1493692 to 92.63462 min) [12:08:40] Quant Extracting 632.5 to 634.5 m/z (7.150521 to 97.37867 min) [12:08:40] Quant Extracting 634.5 to 636.5 m/z (10.45854 to 96.061485 min) [12:08:40] Quant Extracting 636.5 to 638.5 m/z (7.151667 to 91.60012 min) [12:08:40] Quant Extracting 638.5 to 640.5 m/z (7.151667 to 95.407845 min) [12:08:40] Quant Extracting 640.5 to 642.5 m/z (7.187245 to 96.85461 min) [12:08:40] Quant Extracting 642.5 to 644.5 m/z (15.372149 to 92.410904 min) [12:08:40] Quant Extracting 644.5 to 646.5 m/z (7.886121 to 95.442276 min) [12:08:41] Quant Extracting 646.5 to 648.5 m/z (9.323615 to 97.1837 min) [12:08:41] Quant Extracting 648.5 to 650.5 m/z (16.801847 to 97.41578 min) [12:08:41] Quant Extracting 650.5 to 652.5 m/z (8.05184 to 96.20105 min) [12:08:41] Quant Extracting 652.5 to 654.5 m/z (7.1590605 to 95.706215 min) [12:08:41] Quant Extracting 654.5 to 656.5 m/z (12.934369 to 95.25029 min) [12:08:41] Quant Extracting 656.5 to 658.5 m/z (12.609829 to 95.1534 min) [12:08:41] Quant Extracting 658.5 to 660.6 m/z (14.951982 to 97.31936 min) [12:08:41] Quant Extracting 660.6 to 662.6 m/z (7.1930075 to 95.38155 min) [12:08:41] Quant Extracting 662.6 to 664.6 m/z (16.058409 to 93.19671 min) [12:08:41] Quant Extracting 664.6 to 666.6 m/z (7.1625032 to 95.05735 min) [12:08:42] Quant Extracting 666.6 to 668.6 m/z (14.402146 to 96.140144 min) [12:08:42] Quant Extracting 668.6 to 670.6 m/z (7.1636534 to 96.50121 min) [12:08:42] Quant Extracting 670.6 to 672.6 m/z (10.796378 to 93.653656 min) [12:08:42] Quant Extracting 672.6 to 674.6 m/z (16.190437 to 96.04302 min) [12:08:42] Quant Extracting 674.6 to 676.6 m/z (7.1648 to 96.86382 min) [12:08:42] Quant Extracting 676.6 to 678.6 m/z (18.140947 to 96.66818 min) [12:08:42] Quant Extracting 678.6 to 680.6 m/z (16.127855 to 98.222374 min) [12:08:42] Quant Extracting 680.6 to 682.6 m/z (9.4645605 to 97.36254 min) [12:08:42] Quant Extracting 682.6 to 684.6 m/z (16.455542 to 99.583855 min) [12:08:43] Quant Extracting 684.6 to 686.6 m/z (8.61642 to 95.128296 min) [12:08:43] Quant Extracting 686.6 to 688.6 m/z (7.1682534 to 99.89301 min) [12:08:43] Quant Extracting 688.6 to 690.6 m/z (11.028763 to 98.19213 min) [12:08:43] Quant Extracting 690.6 to 692.6 m/z (7.1694 to 95.81942 min) [12:08:43] Quant Extracting 692.6 to 694.6 m/z (7.1705446 to 100.753586 min) [12:08:43] Quant Extracting 694.6 to 696.6 m/z (13.955089 to 96.57478 min) [12:08:43] Quant Extracting 696.6 to 698.6 m/z (7.3020163 to 99.96364 min) [12:08:43] Quant Extracting 698.6 to 700.6 m/z (11.811245 to 98.689735 min) [12:08:43] Quant Extracting 700.6 to 702.6 m/z (7.140152 to 96.378784 min) [12:08:44] Attempted extraction for: 58652, found 12816 [12:08:44] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-600_700mz_DIA_Cond-50cm_01.mzML (12816 entries)... [12:08:44] Writing 12816 peptides to entries table... [12:08:44] Writing 12816 peptides to peptidequants table... [12:08:45] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:08:45 BST 2024 [12:08:46] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 11610 [12:08:46] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML... [12:08:46] Extracting Spectral Data for 11610 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML... [12:08:46] Wrote 774 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML [12:08:46] Number of global peptides: 58652 vs local peptides: 11610 [12:08:48] Found additional 48860 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:08:49] Parsed features and scores for 58652 peptides. [12:08:49] Extracting 58652 peptides... [12:08:49] Quant Extracting 698.6 to 700.6 m/z (11.861911 to 97.63197 min) [12:08:49] Quant Extracting 700.6 to 702.6 m/z (7.144798 to 100.76034 min) [12:08:49] Quant Extracting 702.6 to 704.6 m/z (7.144798 to 93.01012 min) [12:08:49] Quant Extracting 704.6 to 706.6 m/z (7.1459594 to 99.566315 min) [12:08:49] Quant Extracting 706.6 to 708.6 m/z (7.1459594 to 99.93076 min) [12:08:49] Quant Extracting 708.6 to 710.6 m/z (7.1471057 to 100.729866 min) [12:08:49] Quant Extracting 710.6 to 712.6 m/z (7.657666 to 97.929405 min) [12:08:49] Quant Extracting 712.6 to 714.6 m/z (7.148267 to 97.86492 min) [12:08:49] Quant Extracting 714.6 to 716.6 m/z (11.76819 to 92.23833 min) [12:08:50] Quant Extracting 716.6 to 718.6 m/z (9.23903 to 100.06606 min) [12:08:50] Quant Extracting 718.6 to 720.6 m/z (7.5243206 to 95.80925 min) [12:08:50] Quant Extracting 720.6 to 722.6 m/z (7.1505737 to 99.308205 min) [12:08:50] Quant Extracting 722.6 to 724.6 m/z (7.1505737 to 95.68106 min) [12:08:50] Quant Extracting 724.6 to 726.6 m/z (11.055265 to 94.931526 min) [12:08:50] Quant Extracting 726.6 to 728.6 m/z (15.645957 to 95.25939 min) [12:08:50] Quant Extracting 728.6 to 730.6 m/z (7.152891 to 94.54368 min) [12:08:50] Quant Extracting 730.6 to 732.6 m/z (13.019784 to 96.29959 min) [12:08:50] Quant Extracting 732.6 to 734.6 m/z (14.797693 to 99.50818 min) [12:08:50] Quant Extracting 734.6 to 736.6 m/z (20.972883 to 97.70786 min) [12:08:51] Quant Extracting 736.6 to 738.6 m/z (15.8758745 to 100.7707 min) [12:08:51] Quant Extracting 738.6 to 740.6 m/z (18.330626 to 95.717445 min) [12:08:51] Quant Extracting 740.6 to 742.6 m/z (7.1909595 to 93.63803 min) [12:08:51] Quant Extracting 742.6 to 744.6 m/z (13.715831 to 99.11924 min) [12:08:51] Quant Extracting 744.6 to 746.6 m/z (7.1602945 to 98.466385 min) [12:08:51] Quant Extracting 746.6 to 748.6 m/z (13.814836 to 99.18574 min) [12:08:51] Quant Extracting 748.6 to 750.6 m/z (21.106731 to 96.96144 min) [12:08:51] Quant Extracting 750.6 to 752.6 m/z (7.161441 to 97.81002 min) [12:08:51] Quant Extracting 752.6 to 754.6 m/z (14.803454 to 93.2854 min) [12:08:51] Quant Extracting 754.6 to 756.6 m/z (9.11885 to 95.75494 min) [12:08:52] Quant Extracting 756.6 to 758.6 m/z (18.437054 to 95.65848 min) [12:08:52] Quant Extracting 758.6 to 760.6 m/z (25.048988 to 100.34538 min) [12:08:52] Quant Extracting 760.6 to 762.6 m/z (15.232698 to 100.77761 min) [12:08:52] Quant Extracting 762.6 to 764.6 m/z (15.037811 to 100.0173 min) [12:08:52] Quant Extracting 764.6 to 766.6 m/z (23.881416 to 96.60606 min) [12:08:52] Quant Extracting 766.6 to 768.6 m/z (12.080798 to 95.36894 min) [12:08:52] Quant Extracting 768.6 to 770.6 m/z (19.194248 to 99.42251 min) [12:08:52] Quant Extracting 770.6 to 772.6 m/z (7.167204 to 96.0869 min) [12:08:52] Quant Extracting 772.6 to 774.6 m/z (13.263523 to 94.4295 min) [12:08:52] Quant Extracting 774.6 to 776.6 m/z (12.11527 to 97.48992 min) [12:08:53] Quant Extracting 776.6 to 778.6 m/z (23.561504 to 100.749466 min) [12:08:53] Quant Extracting 778.6 to 780.6 m/z (18.969147 to 98.01784 min) [12:08:53] Quant Extracting 780.6 to 782.6 m/z (19.978573 to 98.47676 min) [12:08:53] Quant Extracting 782.6 to 784.6 m/z (21.051922 to 97.39475 min) [12:08:53] Quant Extracting 784.6 to 786.6 m/z (19.198862 to 97.72502 min) [12:08:53] Quant Extracting 786.6 to 788.6 m/z (8.475271 to 93.39214 min) [12:08:53] Quant Extracting 788.6 to 790.6 m/z (24.244534 to 97.759445 min) [12:08:53] Quant Extracting 790.6 to 792.6 m/z (13.33504 to 100.18979 min) [12:08:53] Quant Extracting 792.6 to 794.6 m/z (13.860883 to 94.8893 min) [12:08:53] Quant Extracting 794.6 to 796.6 m/z (20.566673 to 95.66888 min) [12:08:54] Quant Extracting 796.6 to 798.6 m/z (16.547237 to 95.67299 min) [12:08:54] Quant Extracting 798.6 to 800.6 m/z (14.819307 to 99.138626 min) [12:08:54] Quant Extracting 800.6 to 802.6 m/z (29.121706 to 96.48568 min) [12:08:54] Attempted extraction for: 58652, found 9792 [12:08:54] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-700_800mz_DIA_Cond-50cm_01.mzML (9792 entries)... [12:08:54] Writing 9792 peptides to entries table... [12:08:55] Writing 9792 peptides to peptidequants table... [12:08:55] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:08:55 BST 2024 [12:08:56] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 7983 [12:08:56] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML... [12:08:56] Extracting Spectral Data for 7983 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML... [12:08:56] Wrote 1577 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML [12:08:56] Number of global peptides: 58652 vs local peptides: 7983 [12:08:58] Found additional 52229 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:08:58] Parsed features and scores for 58652 peptides. [12:08:58] Extracting 58652 peptides... [12:08:58] Quant Extracting 798.6 to 800.6 m/z (14.779507 to 99.13028 min) [12:08:58] Quant Extracting 800.6 to 802.6 m/z (29.062075 to 96.490074 min) [12:08:58] Quant Extracting 802.6 to 804.6 m/z (18.209223 to 94.732994 min) [12:08:58] Quant Extracting 804.6 to 806.6 m/z (16.567493 to 95.38258 min) [12:08:58] Quant Extracting 806.6 to 808.6 m/z (21.80359 to 96.75114 min) [12:08:58] Quant Extracting 808.6 to 810.6 m/z (16.933178 to 95.93853 min) [12:08:58] Quant Extracting 810.6 to 812.6 m/z (18.277426 to 99.26905 min) [12:08:58] Quant Extracting 812.6 to 814.6 m/z (13.120923 to 96.52555 min) [12:08:59] Quant Extracting 814.6 to 816.6 m/z (26.738726 to 100.141 min) [12:08:59] Quant Extracting 816.6 to 818.6 m/z (23.522383 to 100.74693 min) [12:08:59] Quant Extracting 818.6 to 820.6 m/z (24.014902 to 94.9647 min) [12:08:59] Quant Extracting 820.6 to 822.6 m/z (7.1506753 to 96.00695 min) [12:08:59] Quant Extracting 822.6 to 824.6 m/z (26.085835 to 98.28536 min) [12:08:59] Quant Extracting 824.6 to 826.6 m/z (15.118076 to 94.44833 min) [12:08:59] Quant Extracting 826.6 to 828.6 m/z (15.3192425 to 100.75039 min) [12:08:59] Quant Extracting 828.6 to 830.6 m/z (30.579884 to 100.75039 min) [12:08:59] Quant Extracting 830.6 to 832.6 m/z (25.627459 to 100.65079 min) [12:08:59] Quant Extracting 832.6 to 834.6 m/z (26.711168 to 97.8335 min) [12:08:59] Quant Extracting 834.6 to 836.6 m/z (22.570507 to 95.523766 min) [12:09:00] Quant Extracting 836.6 to 838.6 m/z (17.316748 to 100.18094 min) [12:09:00] Quant Extracting 838.6 to 840.6 m/z (7.1915965 to 100.75384 min) [12:09:00] Quant Extracting 840.6 to 842.6 m/z (10.959421 to 94.87385 min) [12:09:00] Quant Extracting 842.6 to 844.6 m/z (22.737402 to 99.096405 min) [12:09:00] Quant Extracting 844.6 to 846.6 m/z (20.771584 to 100.75499 min) [12:09:00] Quant Extracting 846.6 to 848.6 m/z (20.70827 to 99.18009 min) [12:09:00] Quant Extracting 848.6 to 850.6 m/z (14.4211 to 95.070656 min) [12:09:00] Quant Extracting 850.6 to 852.6 m/z (30.26021 to 100.75729 min) [12:09:00] Quant Extracting 852.6 to 854.6 m/z (29.278677 to 93.00035 min) [12:09:00] Quant Extracting 854.6 to 856.6 m/z (16.582487 to 95.98424 min) [12:09:01] Quant Extracting 856.6 to 858.6 m/z (33.061142 to 100.19076 min) [12:09:01] Quant Extracting 858.6 to 860.6 m/z (23.205387 to 98.9537 min) [12:09:01] Quant Extracting 860.6 to 862.6 m/z (28.072058 to 97.8098 min) [12:09:01] Quant Extracting 862.6 to 864.6 m/z (33.814537 to 98.72438 min) [12:09:01] Quant Extracting 864.6 to 866.6 m/z (14.45911 to 98.92256 min) [12:09:01] Quant Extracting 866.6 to 868.6 m/z (18.4956 to 96.96626 min) [12:09:01] Quant Extracting 868.6 to 870.6 m/z (26.262568 to 100.76189 min) [12:09:01] Quant Extracting 870.6 to 872.6 m/z (17.292625 to 94.39756 min) [12:09:02] Quant Extracting 872.6 to 874.6 m/z (33.426872 to 94.139496 min) [12:09:02] Quant Extracting 874.6 to 876.6 m/z (25.771837 to 98.13993 min) [12:09:02] Quant Extracting 876.6 to 878.6 m/z (19.653936 to 96.18672 min) [12:09:02] Quant Extracting 878.6 to 880.7 m/z (25.575623 to 100.59647 min) [12:09:02] Quant Extracting 880.7 to 882.7 m/z (41.789803 to 96.05737 min) [12:09:02] Quant Extracting 882.7 to 884.7 m/z (31.700932 to 96.22104 min) [12:09:02] Quant Extracting 884.7 to 886.7 m/z (35.968952 to 97.94895 min) [12:09:02] Quant Extracting 886.7 to 888.7 m/z (25.249872 to 96.68044 min) [12:09:02] Quant Extracting 888.7 to 890.7 m/z (31.605465 to 96.9085 min) [12:09:02] Quant Extracting 890.7 to 892.7 m/z (17.969063 to 95.73444 min) [12:09:02] Quant Extracting 892.7 to 894.7 m/z (26.007545 to 95.76761 min) [12:09:03] Quant Extracting 894.7 to 896.7 m/z (21.472832 to 100.635864 min) [12:09:03] Quant Extracting 896.7 to 898.7 m/z (19.394854 to 96.87773 min) [12:09:03] Quant Extracting 898.7 to 900.7 m/z (44.133198 to 98.80039 min) [12:09:03] Quant Extracting 900.7 to 902.7 m/z (27.159548 to 94.147575 min) [12:09:03] Attempted extraction for: 58652, found 6423 [12:09:03] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-800_900mz_DIA_Cond-50cm_01.mzML (6423 entries)... [12:09:03] Writing 6423 peptides to entries table... [12:09:03] Writing 6423 peptides to peptidequants table... [12:09:04] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:09:04 BST 2024 [12:09:04] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML: Number of global peptides: 58652 vs local peptides: 5243 [12:09:04] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML... [12:09:04] Extracting Spectral Data for 5243 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML... [12:09:04] Wrote 52 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML [12:09:04] Number of global peptides: 58652 vs local peptides: 5243 [12:09:06] Found additional 54771 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:09:06] Parsed features and scores for 58652 peptides. [12:09:06] Extracting 58652 peptides... [12:09:06] Quant Extracting 898.7 to 900.7 m/z (44.25709 to 98.76146 min) [12:09:06] Quant Extracting 900.7 to 902.7 m/z (27.15606 to 94.0974 min) [12:09:06] Quant Extracting 902.7 to 904.7 m/z (31.268599 to 99.35391 min) [12:09:06] Quant Extracting 904.7 to 906.7 m/z (24.991976 to 99.6522 min) [12:09:06] Quant Extracting 906.7 to 908.7 m/z (28.829649 to 95.1076 min) [12:09:06] Quant Extracting 908.7 to 910.7 m/z (21.841345 to 98.698586 min) [12:09:06] Quant Extracting 910.7 to 912.7 m/z (25.127546 to 100.45754 min) [12:09:06] Quant Extracting 912.7 to 914.7 m/z (27.700434 to 95.46634 min) [12:09:07] Quant Extracting 914.7 to 916.7 m/z (30.774055 to 97.3263 min) [12:09:07] Quant Extracting 916.7 to 918.7 m/z (33.89401 to 95.46749 min) [12:09:07] Quant Extracting 918.7 to 920.7 m/z (37.855297 to 95.532295 min) [12:09:07] Quant Extracting 920.7 to 922.7 m/z (26.169252 to 100.6309 min) [12:09:07] Quant Extracting 922.7 to 924.7 m/z (37.2603 to 95.76113 min) [12:09:07] Quant Extracting 924.7 to 926.7 m/z (27.806787 to 98.99862 min) [12:09:07] Quant Extracting 926.7 to 928.7 m/z (27.774403 to 94.39664 min) [12:09:07] Quant Extracting 928.7 to 930.7 m/z (10.034467 to 100.7676 min) [12:09:07] Quant Extracting 930.7 to 932.7 m/z (34.46307 to 93.49015 min) [12:09:08] Quant Extracting 932.7 to 934.7 m/z (37.892044 to 99.630295 min) [12:09:08] Quant Extracting 934.7 to 936.7 m/z (42.16493 to 96.84146 min) [12:09:08] Quant Extracting 936.7 to 938.7 m/z (44.107807 to 97.59483 min) [12:09:08] Quant Extracting 938.7 to 940.7 m/z (31.513073 to 94.82427 min) [12:09:08] Quant Extracting 940.7 to 942.7 m/z (40.368393 to 97.99227 min) [12:09:08] Quant Extracting 942.7 to 944.7 m/z (26.240929 to 97.72853 min) [12:09:08] Quant Extracting 944.7 to 946.7 m/z (40.175068 to 99.7667 min) [12:09:08] Quant Extracting 946.7 to 948.7 m/z (18.175486 to 95.70312 min) [12:09:08] Quant Extracting 948.7 to 950.7 m/z (36.09074 to 100.40182 min) [12:09:08] Quant Extracting 950.7 to 952.7 m/z (35.662067 to 97.46795 min) [12:09:08] Quant Extracting 952.7 to 954.7 m/z (32.08076 to 95.93276 min) [12:09:09] Quant Extracting 954.7 to 956.7 m/z (36.255455 to 96.229706 min) [12:09:09] Quant Extracting 956.7 to 958.7 m/z (40.8306 to 95.15456 min) [12:09:09] Quant Extracting 958.7 to 960.7 m/z (31.386238 to 95.28465 min) [12:09:09] Quant Extracting 960.7 to 962.7 m/z (39.78705 to 100.74516 min) [12:09:09] Quant Extracting 962.7 to 964.7 m/z (41.06114 to 94.24719 min) [12:09:09] Quant Extracting 964.7 to 966.7 m/z (27.347464 to 100.74914 min) [12:09:09] Quant Extracting 966.7 to 968.7 m/z (39.558174 to 94.15174 min) [12:09:09] Quant Extracting 968.7 to 970.7 m/z (16.957401 to 100.75028 min) [12:09:09] Quant Extracting 970.7 to 972.7 m/z (29.321745 to 97.345856 min) [12:09:09] Quant Extracting 972.7 to 974.7 m/z (40.183132 to 97.903786 min) [12:09:09] Quant Extracting 974.7 to 976.7 m/z (30.426657 to 95.54842 min) [12:09:10] Quant Extracting 976.7 to 978.7 m/z (28.986387 to 95.322296 min) [12:09:10] Quant Extracting 978.7 to 980.7 m/z (29.391577 to 99.57754 min) [12:09:10] Quant Extracting 980.7 to 982.7 m/z (19.311155 to 100.75378 min) [12:09:10] Quant Extracting 982.7 to 984.7 m/z (41.62233 to 98.168434 min) [12:09:10] Quant Extracting 984.7 to 986.7 m/z (15.802401 to 99.97736 min) [12:09:10] Quant Extracting 986.7 to 988.7 m/z (43.337296 to 91.824 min) [12:09:10] Quant Extracting 988.7 to 990.7 m/z (29.29336 to 96.59749 min) [12:09:10] Quant Extracting 990.7 to 992.7 m/z (34.151905 to 95.75076 min) [12:09:10] Quant Extracting 992.7 to 994.7 m/z (38.73744 to 95.362885 min) [12:09:10] Quant Extracting 994.7 to 996.7 m/z (40.54884 to 96.56668 min) [12:09:10] Quant Extracting 996.7 to 998.7 m/z (48.377 to 100.758385 min) [12:09:11] Quant Extracting 998.7 to 1000.7 m/z (42.350365 to 97.12379 min) [12:09:11] Quant Extracting 1000.7 to 1002.7 m/z (16.042398 to 94.874504 min) [12:09:11] Attempted extraction for: 58652, found 3881 [12:09:11] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-900_1000mz_DIA_Cond-50cm_01.mzML (3881 entries)... [12:09:11] Writing 3881 peptides to entries table... [12:09:11] Writing 3881 peptides to peptidequants table... [12:09:11] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:09:11 BST 2024 [12:09:14] Writing global target/decoy peptides: 58652/613, pi0: 0.932379 [12:09:15] Writing global target/decoy proteins: 6434/64 [12:09:23] Getting source files... [12:09:23] Found 6 data files [12:09:23] 10000 records processed... [12:09:23] 20000 records processed... [12:09:24] 30000 records processed... [12:09:24] 40000 records processed... [12:09:24] 50000 records processed... [12:09:24] 60000 records processed... [12:09:24] Finished processing 60689 records, found 58652 quantitative unique peptides. Writing reports... [12:09:25] Inconsistent number of fragments in 58647 of 58652 peptides [12:09:25] Finished writing peptide report for 344694 unique peptides! [12:09:25] Finished writing protein report for 6434 protein groups! Generating quantification library (1 of 5): Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" [12:09:30] EncyclopeDIA version 2.12.30 [12:09:30] Getting count of protein accessions... [12:09:30] Using EncyclopeDIA 2.X Scoring System [12:09:30] Indexing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML ... [12:09:30] Converting Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML ... [12:09:30] Parsed 1% [12:09:31] Parsed 2% [12:09:31] Parsed 3% [12:09:32] Parsed 4% [12:09:32] Parsed 5% [12:09:33] Parsed 6% [12:09:33] Parsed 7% [12:09:34] Parsed 8% [12:09:34] Parsed 9% [12:09:35] Parsed 10% [12:09:36] Parsed 11% [12:09:37] Parsed 12% [12:09:38] Parsed 13% [12:09:39] Parsed 14% [12:09:41] Parsed 15% [12:09:43] Parsed 16% [12:09:45] Parsed 17% [12:09:46] Parsed 18% [12:09:47] Parsed 19% [12:09:48] Parsed 20% [12:09:49] Parsed 21% [12:09:51] Parsed 22% [12:09:52] Parsed 23% [12:09:54] Parsed 24% [12:09:55] Parsed 25% [12:09:56] Parsed 26% [12:09:57] Parsed 27% [12:09:59] Parsed 28% [12:10:01] Parsed 29% [12:10:05] Parsed 30% [12:10:10] Parsed 31% [12:10:15] Parsed 32% [12:10:20] Parsed 33% [12:10:26] Parsed 34% [12:10:35] Parsed 35% [12:10:36] Parsed 36% [12:10:37] Parsed 37% [12:10:38] Parsed 38% [12:10:40] Parsed 39% [12:10:43] Parsed 40% [12:10:46] Parsed 41% [12:10:51] Parsed 42% [12:10:56] Parsed 43% [12:11:01] Parsed 44% [12:11:06] Parsed 45% [12:11:12] Parsed 46% [12:11:13] Parsed 47% [12:11:14] Parsed 48% [12:11:16] Parsed 49% [12:11:18] Parsed 50% [12:11:21] Parsed 51% [12:11:24] Parsed 52% [12:11:29] Parsed 53% [12:11:34] Parsed 54% [12:11:39] Parsed 55% [12:11:45] Parsed 56% [12:11:51] Parsed 57% [12:11:58] Parsed 58% [12:12:05] Parsed 59% [12:12:13] Parsed 60% [12:12:20] Parsed 61% [12:12:29] Parsed 62% [12:12:40] Parsed 63% [12:12:51] Parsed 64% [12:13:10] Parsed 65% [12:13:11] Parsed 66% [12:13:13] Parsed 67% [12:13:16] Parsed 68% [12:13:21] Parsed 69% [12:13:26] Parsed 70% [12:13:31] Parsed 71% [12:13:37] Parsed 72% [12:13:43] Parsed 73% [12:13:49] Parsed 74% [12:13:56] Parsed 75% [12:14:04] Parsed 76% [12:14:12] Parsed 77% [12:14:20] Parsed 78% [12:14:30] Parsed 79% [12:14:44] Parsed 80% [12:14:45] Parsed 81% [12:14:47] Parsed 82% [12:14:51] Parsed 83% [12:14:55] Parsed 84% [12:15:00] Parsed 85% [12:15:05] Parsed 86% [12:15:10] Parsed 87% [12:15:15] Parsed 88% [12:15:21] Parsed 89% [12:15:27] Parsed 90% [12:15:34] Parsed 91% [12:15:40] Parsed 92% [12:15:47] Parsed 93% [12:15:55] Parsed 94% [12:16:01] Parsed 95% [12:16:10] Parsed 96% [12:16:20] Parsed 97% [12:16:27] Parsed 98% [12:16:31] Parsed 99% [12:16:39] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.dia ... [12:16:40] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.dia! [12:16:40] Input File: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML [12:16:40] Library File: UP000005640_9606-z3_nce27.elib [12:16:40] Result File: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.elib [12:16:40] Parameters: [12:16:40] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [12:16:40] Converting files... [12:16:40] Calculating features... [12:16:40] Processing precursors scans... [12:16:40] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt.unsorted [12:16:40] Processing 396.4 to 400.4 m/z, (5.851922 second duty cycle) [12:16:41] 67 peptides remaining for 396.4 to 400.4... [12:16:42] 35 peptides remaining for 396.4 to 400.4... [12:16:42] Processing 400.4 to 404.4 m/z, (2.9259038 second duty cycle) [12:16:43] 201 peptides remaining for 400.4 to 404.4... [12:16:43] Processing 404.4 to 408.4 m/z, (2.9259207 second duty cycle) [12:16:43] 237 peptides remaining for 404.4 to 408.4... [12:16:44] 0 peptides remaining for 404.4 to 408.4... [12:16:44] Processing 408.4 to 412.4 m/z, (2.9259038 second duty cycle) [12:16:44] 277 peptides remaining for 408.4 to 412.4... [12:16:45] Processing 412.4 to 416.4 m/z, (2.925921 second duty cycle) [12:16:45] 315 peptides remaining for 412.4 to 416.4... [12:16:46] Processing 416.4 to 420.4 m/z, (2.9259036 second duty cycle) [12:16:46] 302 peptides remaining for 416.4 to 420.4... [12:16:46] Processing 420.4 to 424.4 m/z, (2.9259207 second duty cycle) [12:16:47] 287 peptides remaining for 420.4 to 424.4... [12:16:47] Processing 424.4 to 428.4 m/z, (2.9259038 second duty cycle) [12:16:47] 304 peptides remaining for 424.4 to 428.4... [12:16:48] Processing 428.4 to 432.4 m/z, (2.9259207 second duty cycle) [12:16:48] 339 peptides remaining for 428.4 to 432.4... [12:16:48] Processing 432.4 to 436.4 m/z, (2.9259036 second duty cycle) [12:16:49] 377 peptides remaining for 432.4 to 436.4... [12:16:49] Processing 436.4 to 440.5 m/z, (2.925927 second duty cycle) [12:16:49] 519 peptides remaining for 436.4 to 440.5... [12:16:50] Processing 440.5 to 444.5 m/z, (2.9259098 second duty cycle) [12:16:50] 473 peptides remaining for 440.5 to 444.5... [12:16:50] Processing 444.5 to 448.5 m/z, (2.9259613 second duty cycle) [12:16:51] 368 peptides remaining for 444.5 to 448.5... [12:16:51] Processing 448.5 to 452.5 m/z, (2.925961 second duty cycle) [12:16:51] 452 peptides remaining for 448.5 to 452.5... [12:16:52] Processing 452.5 to 456.5 m/z, (2.925961 second duty cycle) [12:16:52] 416 peptides remaining for 452.5 to 456.5... [12:16:52] Processing 456.5 to 460.5 m/z, (2.925961 second duty cycle) [12:16:53] 509 peptides remaining for 456.5 to 460.5... [12:16:53] Processing 460.5 to 464.5 m/z, (2.9259613 second duty cycle) [12:16:53] 489 peptides remaining for 460.5 to 464.5... [12:16:54] Processing 464.5 to 468.5 m/z, (2.925961 second duty cycle) [12:16:54] 604 peptides remaining for 464.5 to 468.5... [12:16:54] Processing 468.5 to 472.5 m/z, (2.9259608 second duty cycle) [12:16:55] 492 peptides remaining for 468.5 to 472.5... [12:16:55] Processing 472.5 to 476.5 m/z, (2.925961 second duty cycle) [12:16:55] 498 peptides remaining for 472.5 to 476.5... [12:16:56] Processing 476.5 to 480.5 m/z, (2.925961 second duty cycle) [12:16:56] 497 peptides remaining for 476.5 to 480.5... [12:16:57] Processing 480.5 to 484.5 m/z, (2.9259613 second duty cycle) [12:16:57] 578 peptides remaining for 480.5 to 484.5... [12:16:57] 156 peptides remaining for 480.5 to 484.5... [12:16:58] Processing 484.5 to 488.5 m/z, (2.9259613 second duty cycle) [12:16:58] 511 peptides remaining for 484.5 to 488.5... [12:16:58] 90 peptides remaining for 484.5 to 488.5... [12:16:59] Processing 488.5 to 492.5 m/z, (2.925961 second duty cycle) [12:16:59] 473 peptides remaining for 488.5 to 492.5... [12:17:00] Processing 492.5 to 496.5 m/z, (2.9259608 second duty cycle) [12:17:00] 543 peptides remaining for 492.5 to 496.5... [12:17:00] Processing 496.5 to 500.5 m/z, (2.9259613 second duty cycle) [12:17:00] 710 peptides remaining for 496.5 to 500.5... [12:17:01] Processing 500.5 to 504.5 m/z, (2.925961 second duty cycle) [12:17:01] 859 peptides remaining for 500.5 to 504.5... [12:17:02] Processing 504.5 to 508.5 m/z, (2.925961 second duty cycle) [12:17:02] 493 peptides remaining for 504.5 to 508.5... [12:17:02] Processing 508.5 to 512.5 m/z, (2.925961 second duty cycle) [12:17:02] 634 peptides remaining for 508.5 to 512.5... [12:17:03] Processing 512.5 to 516.5 m/z, (2.925961 second duty cycle) [12:17:03] 589 peptides remaining for 512.5 to 516.5... [12:17:03] Processing 516.5 to 520.5 m/z, (2.925961 second duty cycle) [12:17:04] 536 peptides remaining for 516.5 to 520.5... [12:17:04] Processing 520.5 to 524.5 m/z, (2.925961 second duty cycle) [12:17:04] 594 peptides remaining for 520.5 to 524.5... [12:17:05] Processing 524.5 to 528.5 m/z, (2.925961 second duty cycle) [12:17:05] 552 peptides remaining for 524.5 to 528.5... [12:17:05] Processing 528.5 to 532.5 m/z, (2.925961 second duty cycle) [12:17:06] 627 peptides remaining for 528.5 to 532.5... [12:17:06] Processing 532.5 to 536.5 m/z, (2.925961 second duty cycle) [12:17:06] 513 peptides remaining for 532.5 to 536.5... [12:17:07] Processing 536.5 to 540.5 m/z, (2.9259613 second duty cycle) [12:17:07] 591 peptides remaining for 536.5 to 540.5... [12:17:08] Processing 540.5 to 544.5 m/z, (2.925961 second duty cycle) [12:17:08] 593 peptides remaining for 540.5 to 544.5... [12:17:08] Processing 544.5 to 548.5 m/z, (2.925961 second duty cycle) [12:17:08] 584 peptides remaining for 544.5 to 548.5... [12:17:09] Processing 548.5 to 552.5 m/z, (2.925961 second duty cycle) [12:17:09] 582 peptides remaining for 548.5 to 552.5... [12:17:10] Processing 552.5 to 556.5 m/z, (2.9259613 second duty cycle) [12:17:10] 601 peptides remaining for 552.5 to 556.5... [12:17:10] Processing 556.5 to 560.5 m/z, (2.9259613 second duty cycle) [12:17:10] 604 peptides remaining for 556.5 to 560.5... [12:17:11] Processing 560.5 to 564.5 m/z, (2.925961 second duty cycle) [12:17:11] 533 peptides remaining for 560.5 to 564.5... [12:17:12] Processing 564.5 to 568.5 m/z, (2.9259608 second duty cycle) [12:17:12] 676 peptides remaining for 564.5 to 568.5... [12:17:12] Processing 568.5 to 572.5 m/z, (2.925961 second duty cycle) [12:17:12] 535 peptides remaining for 568.5 to 572.5... [12:17:13] Processing 572.5 to 576.5 m/z, (2.925961 second duty cycle) [12:17:13] 627 peptides remaining for 572.5 to 576.5... [12:17:14] Processing 576.5 to 580.5 m/z, (2.9259613 second duty cycle) [12:17:14] 583 peptides remaining for 576.5 to 580.5... [12:17:14] Processing 580.5 to 584.5 m/z, (2.925961 second duty cycle) [12:17:14] 569 peptides remaining for 580.5 to 584.5... [12:17:15] Processing 584.5 to 588.5 m/z, (2.925961 second duty cycle) [12:17:15] 601 peptides remaining for 584.5 to 588.5... [12:17:16] Processing 588.5 to 592.5 m/z, (2.925961 second duty cycle) [12:17:16] 514 peptides remaining for 588.5 to 592.5... [12:17:16] Processing 592.5 to 596.5 m/z, (2.9259613 second duty cycle) [12:17:16] 591 peptides remaining for 592.5 to 596.5... [12:17:17] Processing 596.5 to 600.5 m/z, (2.925961 second duty cycle) [12:17:17] 738 peptides remaining for 596.5 to 600.5... [12:17:18] Processing 600.5 to 604.5 m/z, (2.925961 second duty cycle) [12:17:18] 842 peptides remaining for 600.5 to 604.5... [12:17:18] Processing 604.5 to 608.5 m/z, (2.925961 second duty cycle) [12:17:18] 475 peptides remaining for 604.5 to 608.5... [12:17:19] Processing 608.5 to 612.5 m/z, (2.925961 second duty cycle) [12:17:19] 515 peptides remaining for 608.5 to 612.5... [12:17:20] Processing 612.5 to 616.5 m/z, (2.925961 second duty cycle) [12:17:20] 523 peptides remaining for 612.5 to 616.5... [12:17:20] Processing 616.5 to 620.5 m/z, (2.925961 second duty cycle) [12:17:20] 493 peptides remaining for 616.5 to 620.5... [12:17:21] Processing 620.5 to 624.5 m/z, (2.9259613 second duty cycle) [12:17:21] 499 peptides remaining for 620.5 to 624.5... [12:17:22] Processing 624.5 to 628.5 m/z, (2.9259608 second duty cycle) [12:17:22] 449 peptides remaining for 624.5 to 628.5... [12:17:22] Processing 628.5 to 632.5 m/z, (2.9259608 second duty cycle) [12:17:23] 475 peptides remaining for 628.5 to 632.5... [12:17:23] Processing 632.5 to 636.5 m/z, (2.9259608 second duty cycle) [12:17:23] 420 peptides remaining for 632.5 to 636.5... [12:17:24] Processing 636.5 to 640.5 m/z, (2.925961 second duty cycle) [12:17:24] 483 peptides remaining for 636.5 to 640.5... [12:17:24] Processing 640.5 to 644.5 m/z, (2.9259608 second duty cycle) [12:17:25] 415 peptides remaining for 640.5 to 644.5... [12:17:25] Processing 644.5 to 648.5 m/z, (2.9259608 second duty cycle) [12:17:25] 509 peptides remaining for 644.5 to 648.5... [12:17:26] Processing 648.5 to 652.5 m/z, (2.9259608 second duty cycle) [12:17:26] 419 peptides remaining for 648.5 to 652.5... [12:17:26] Processing 652.5 to 656.5 m/z, (2.9259608 second duty cycle) [12:17:27] 419 peptides remaining for 652.5 to 656.5... [12:17:27] Processing 656.5 to 660.6 m/z, (2.9259608 second duty cycle) [12:17:27] 432 peptides remaining for 656.5 to 660.6... [12:17:28] Processing 660.6 to 664.6 m/z, (2.9259608 second duty cycle) [12:17:28] 419 peptides remaining for 660.6 to 664.6... [12:17:28] Processing 664.6 to 668.6 m/z, (2.9259608 second duty cycle) [12:17:29] 440 peptides remaining for 664.6 to 668.6... [12:17:29] Processing 668.6 to 672.6 m/z, (2.9259608 second duty cycle) [12:17:29] 434 peptides remaining for 668.6 to 672.6... [12:17:30] Processing 672.6 to 676.6 m/z, (2.925961 second duty cycle) [12:17:30] 455 peptides remaining for 672.6 to 676.6... [12:17:30] Processing 676.6 to 680.6 m/z, (2.925961 second duty cycle) [12:17:30] 451 peptides remaining for 676.6 to 680.6... [12:17:31] Processing 680.6 to 684.6 m/z, (2.9259608 second duty cycle) [12:17:31] 427 peptides remaining for 680.6 to 684.6... [12:17:32] Processing 684.6 to 688.6 m/z, (2.9259608 second duty cycle) [12:17:32] 426 peptides remaining for 684.6 to 688.6... [12:17:32] Processing 688.6 to 692.6 m/z, (2.925961 second duty cycle) [12:17:32] 423 peptides remaining for 688.6 to 692.6... [12:17:33] Processing 692.6 to 696.6 m/z, (2.925961 second duty cycle) [12:17:33] 448 peptides remaining for 692.6 to 696.6... [12:17:34] Processing 696.6 to 700.6 m/z, (2.925961 second duty cycle) [12:17:34] 558 peptides remaining for 696.6 to 700.6... [12:17:34] Processing 700.6 to 704.6 m/z, (2.925961 second duty cycle) [12:17:34] 671 peptides remaining for 700.6 to 704.6... [12:17:35] Processing 704.6 to 708.6 m/z, (2.925961 second duty cycle) [12:17:35] 393 peptides remaining for 704.6 to 708.6... [12:17:36] Processing 708.6 to 712.6 m/z, (2.925961 second duty cycle) [12:17:36] 410 peptides remaining for 708.6 to 712.6... [12:17:36] Processing 712.6 to 716.6 m/z, (2.925961 second duty cycle) [12:17:36] 417 peptides remaining for 712.6 to 716.6... [12:17:37] Processing 716.6 to 720.6 m/z, (2.925961 second duty cycle) [12:17:37] 368 peptides remaining for 716.6 to 720.6... [12:17:38] Processing 720.6 to 724.6 m/z, (2.925961 second duty cycle) [12:17:38] 371 peptides remaining for 720.6 to 724.6... [12:17:38] Processing 724.6 to 728.6 m/z, (2.925961 second duty cycle) [12:17:38] 372 peptides remaining for 724.6 to 728.6... [12:17:39] Processing 728.6 to 732.6 m/z, (2.925961 second duty cycle) [12:17:39] 363 peptides remaining for 728.6 to 732.6... [12:17:40] Processing 732.6 to 736.6 m/z, (2.925961 second duty cycle) [12:17:40] 371 peptides remaining for 732.6 to 736.6... [12:17:40] Processing 736.6 to 740.6 m/z, (2.9259608 second duty cycle) [12:17:40] 346 peptides remaining for 736.6 to 740.6... [12:17:41] Processing 740.6 to 744.6 m/z, (2.9259608 second duty cycle) [12:17:41] 332 peptides remaining for 740.6 to 744.6... [12:17:42] Processing 744.6 to 748.6 m/z, (2.925961 second duty cycle) [12:17:42] 365 peptides remaining for 744.6 to 748.6... [12:17:42] Processing 748.6 to 752.6 m/z, (2.925961 second duty cycle) [12:17:42] 313 peptides remaining for 748.6 to 752.6... [12:17:43] Processing 752.6 to 756.6 m/z, (2.925961 second duty cycle) [12:17:43] 311 peptides remaining for 752.6 to 756.6... [12:17:44] Processing 756.6 to 760.6 m/z, (2.925961 second duty cycle) [12:17:44] 343 peptides remaining for 756.6 to 760.6... [12:17:44] Processing 760.6 to 764.6 m/z, (2.925961 second duty cycle) [12:17:44] 339 peptides remaining for 760.6 to 764.6... [12:17:45] Processing 764.6 to 768.6 m/z, (2.925961 second duty cycle) [12:17:45] 342 peptides remaining for 764.6 to 768.6... [12:17:46] Processing 768.6 to 772.6 m/z, (2.925961 second duty cycle) [12:17:46] 318 peptides remaining for 768.6 to 772.6... [12:17:46] Processing 772.6 to 776.6 m/z, (2.925961 second duty cycle) [12:17:46] 315 peptides remaining for 772.6 to 776.6... [12:17:47] Processing 776.6 to 780.6 m/z, (2.9259608 second duty cycle) [12:17:47] 294 peptides remaining for 776.6 to 780.6... [12:17:48] Processing 780.6 to 784.6 m/z, (2.925961 second duty cycle) [12:17:48] 290 peptides remaining for 780.6 to 784.6... [12:17:48] Processing 784.6 to 788.6 m/z, (2.925961 second duty cycle) [12:17:48] 304 peptides remaining for 784.6 to 788.6... [12:17:49] Processing 788.6 to 792.6 m/z, (2.925961 second duty cycle) [12:17:49] 299 peptides remaining for 788.6 to 792.6... [12:17:50] Processing 792.6 to 796.6 m/z, (2.925961 second duty cycle) [12:17:50] 276 peptides remaining for 792.6 to 796.6... [12:17:50] Processing 796.6 to 800.6 m/z, (2.925961 second duty cycle) [12:17:50] 419 peptides remaining for 796.6 to 800.6... [12:17:51] Processing 800.6 to 804.6 m/z, (2.925961 second duty cycle) [12:17:51] 380 peptides remaining for 800.6 to 804.6... [12:17:52] Processing 804.6 to 808.6 m/z, (2.925961 second duty cycle) [12:17:52] 236 peptides remaining for 804.6 to 808.6... [12:17:52] Processing 808.6 to 812.6 m/z, (2.925961 second duty cycle) [12:17:52] 286 peptides remaining for 808.6 to 812.6... [12:17:53] Processing 812.6 to 816.6 m/z, (2.9259608 second duty cycle) [12:17:53] 242 peptides remaining for 812.6 to 816.6... [12:17:54] Processing 816.6 to 820.6 m/z, (2.925961 second duty cycle) [12:17:54] 248 peptides remaining for 816.6 to 820.6... [12:17:54] Processing 820.6 to 824.6 m/z, (2.925961 second duty cycle) [12:17:54] 226 peptides remaining for 820.6 to 824.6... [12:17:55] Processing 824.6 to 828.6 m/z, (2.925961 second duty cycle) [12:17:55] 268 peptides remaining for 824.6 to 828.6... [12:17:56] Processing 828.6 to 832.6 m/z, (2.9259608 second duty cycle) [12:17:56] 254 peptides remaining for 828.6 to 832.6... [12:17:56] Processing 832.6 to 836.6 m/z, (2.925961 second duty cycle) [12:17:56] 225 peptides remaining for 832.6 to 836.6... [12:17:57] Processing 836.6 to 840.6 m/z, (2.925961 second duty cycle) [12:17:57] 223 peptides remaining for 836.6 to 840.6... [12:17:57] Processing 840.6 to 844.6 m/z, (2.925961 second duty cycle) [12:17:58] 236 peptides remaining for 840.6 to 844.6... [12:17:58] Processing 844.6 to 848.6 m/z, (2.925961 second duty cycle) [12:17:58] 234 peptides remaining for 844.6 to 848.6... [12:17:59] Processing 848.6 to 852.6 m/z, (2.9259608 second duty cycle) [12:17:59] 234 peptides remaining for 848.6 to 852.6... [12:17:59] Processing 852.6 to 856.6 m/z, (2.925961 second duty cycle) [12:18:00] 194 peptides remaining for 852.6 to 856.6... [12:18:00] Processing 856.6 to 860.6 m/z, (2.925961 second duty cycle) [12:18:00] 216 peptides remaining for 856.6 to 860.6... [12:18:01] Processing 860.6 to 864.6 m/z, (2.925961 second duty cycle) [12:18:01] 185 peptides remaining for 860.6 to 864.6... [12:18:01] Processing 864.6 to 868.6 m/z, (2.925961 second duty cycle) [12:18:02] 179 peptides remaining for 864.6 to 868.6... [12:18:02] Processing 868.6 to 872.6 m/z, (2.925961 second duty cycle) [12:18:02] 180 peptides remaining for 868.6 to 872.6... [12:18:03] Processing 872.6 to 876.6 m/z, (2.9259608 second duty cycle) [12:18:03] 207 peptides remaining for 872.6 to 876.6... [12:18:03] Processing 876.6 to 880.7 m/z, (2.9259608 second duty cycle) [12:18:04] 159 peptides remaining for 876.6 to 880.7... [12:18:04] Processing 880.7 to 884.7 m/z, (2.925961 second duty cycle) [12:18:04] 184 peptides remaining for 880.7 to 884.7... [12:18:05] Processing 884.7 to 888.7 m/z, (2.925961 second duty cycle) [12:18:05] 154 peptides remaining for 884.7 to 888.7... [12:18:05] Processing 888.7 to 892.7 m/z, (2.925961 second duty cycle) [12:18:05] 154 peptides remaining for 888.7 to 892.7... [12:18:06] Processing 892.7 to 896.7 m/z, (2.925961 second duty cycle) [12:18:06] 147 peptides remaining for 892.7 to 896.7... [12:18:07] Processing 896.7 to 900.7 m/z, (2.9259608 second duty cycle) [12:18:07] 219 peptides remaining for 896.7 to 900.7... [12:18:07] Processing 900.7 to 904.7 m/z, (2.9259608 second duty cycle) [12:18:07] 221 peptides remaining for 900.7 to 904.7... [12:18:08] Processing 904.7 to 908.7 m/z, (2.9259608 second duty cycle) [12:18:08] 137 peptides remaining for 904.7 to 908.7... [12:18:09] Processing 908.7 to 912.7 m/z, (2.9259608 second duty cycle) [12:18:09] 159 peptides remaining for 908.7 to 912.7... [12:18:09] Processing 912.7 to 916.7 m/z, (2.9259605 second duty cycle) [12:18:09] 139 peptides remaining for 912.7 to 916.7... [12:18:10] Processing 916.7 to 920.7 m/z, (2.9259608 second duty cycle) [12:18:10] 137 peptides remaining for 916.7 to 920.7... [12:18:11] Processing 920.7 to 924.7 m/z, (2.9259608 second duty cycle) [12:18:11] 133 peptides remaining for 920.7 to 924.7... [12:18:11] Processing 924.7 to 928.7 m/z, (2.9259608 second duty cycle) [12:18:11] 129 peptides remaining for 924.7 to 928.7... [12:18:12] Processing 928.7 to 932.7 m/z, (2.9259608 second duty cycle) [12:18:12] 114 peptides remaining for 928.7 to 932.7... [12:18:13] Processing 932.7 to 936.7 m/z, (2.9259608 second duty cycle) [12:18:13] 108 peptides remaining for 932.7 to 936.7... [12:18:13] Processing 936.7 to 940.7 m/z, (2.9259608 second duty cycle) [12:18:13] 140 peptides remaining for 936.7 to 940.7... [12:18:14] Processing 940.7 to 944.7 m/z, (2.9259608 second duty cycle) [12:18:14] 106 peptides remaining for 940.7 to 944.7... [12:18:14] Processing 944.7 to 948.7 m/z, (2.9259608 second duty cycle) [12:18:15] 120 peptides remaining for 944.7 to 948.7... [12:18:15] Processing 948.7 to 952.7 m/z, (2.9259608 second duty cycle) [12:18:15] 149 peptides remaining for 948.7 to 952.7... [12:18:16] Processing 952.7 to 956.7 m/z, (2.925961 second duty cycle) [12:18:16] 121 peptides remaining for 952.7 to 956.7... [12:18:16] Processing 956.7 to 960.7 m/z, (2.925961 second duty cycle) [12:18:17] 138 peptides remaining for 956.7 to 960.7... [12:18:17] Processing 960.7 to 964.7 m/z, (2.9259608 second duty cycle) [12:18:17] 107 peptides remaining for 960.7 to 964.7... [12:18:18] Processing 964.7 to 968.7 m/z, (2.9259608 second duty cycle) [12:18:18] 120 peptides remaining for 964.7 to 968.7... [12:18:18] Processing 968.7 to 972.7 m/z, (2.9259608 second duty cycle) [12:18:19] 91 peptides remaining for 968.7 to 972.7... [12:18:19] Processing 972.7 to 976.7 m/z, (2.9259608 second duty cycle) [12:18:19] 83 peptides remaining for 972.7 to 976.7... [12:18:20] Processing 976.7 to 980.7 m/z, (2.9259608 second duty cycle) [12:18:20] 94 peptides remaining for 976.7 to 980.7... [12:18:20] Processing 980.7 to 984.7 m/z, (2.9259608 second duty cycle) [12:18:20] 64 peptides remaining for 980.7 to 984.7... [12:18:21] Processing 984.7 to 988.7 m/z, (2.925961 second duty cycle) [12:18:21] 73 peptides remaining for 984.7 to 988.7... [12:18:22] Processing 988.7 to 992.7 m/z, (2.9259608 second duty cycle) [12:18:22] 96 peptides remaining for 988.7 to 992.7... [12:18:22] Processing 992.7 to 996.7 m/z, (2.925961 second duty cycle) [12:18:22] 82 peptides remaining for 992.7 to 996.7... [12:18:23] Processing 996.7 to 1000.7 m/z, (2.925961 second duty cycle) [12:18:23] 55 peptides remaining for 996.7 to 1000.7... [12:18:24] Processing 1000.7 to 1004.7 m/z, (5.851814 second duty cycle) [12:18:24] 20 peptides remaining for 1000.7 to 1004.7... [12:18:24] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:18:27] Sorted feature file in 3.27 seconds wall clock time [12:18:27] File size check: 55717433 vs 55717433 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt.unsorted [12:18:28] 148020 total peptides processed. [12:18:28] Running Percolator... [12:18:28] Executing [cmd /c C:\Windows\Temp\tmpC82E.java\Percolator-v3-01-7674349436417118432.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt] [12:18:28] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:18:28] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:18:28] Written by Lukas Käll (lukall@u.washington.edu) in the [12:18:28] Department of Genome Sciences at the University of Washington. [12:18:28] Issued command: [12:18:28] C:\Windows\Temp\tmpC82E.java\Percolator-v3-01-7674349436417118432.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:18:28] Started Wed Jul 17 12:18:28 2024 [12:18:28] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [12:18:28] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:18:28] Features: [12:18:28] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:18:29] Found 148020 PSMs [12:18:29] Separate target and decoy search inputs detected, using mix-max method. [12:18:29] Train/test set contains 79909 positives and 68111 negatives, size ratio=1.17322 and pi0=1 [12:18:29] Warning: The mix-max procedure is not well behaved when # targets (79909) != # decoys (68111). Consider using target-decoy competition (-Y flag). [12:18:29] Selecting Cpos by cross-validation. [12:18:29] Selecting Cneg by cross-validation. [12:18:30] Split 1: Selected feature 3 as initial search direction. Could separate 15135 training set positives in that direction. [12:18:31] Split 2: Selected feature 3 as initial search direction. Could separate 15130 training set positives in that direction. [12:18:31] Split 3: Selected feature 3 as initial search direction. Could separate 15514 training set positives in that direction. [12:18:31] Found 22914 test set positives with q<0.01 in initial direction [12:18:31] Reading in data and feature calculation took 3.495 cpu seconds or 3 seconds wall clock time. [12:18:31] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:18:37] Iteration 1: Estimated 35396 PSMs with q<0.01 [12:18:46] Iteration 2: Estimated 38643 PSMs with q<0.01 [12:18:56] Iteration 3: Estimated 39231 PSMs with q<0.01 [12:18:56] Learned normalized SVM weights for the 3 cross-validation splits: [12:18:56] Split1 Split2 Split3 FeatureName [12:18:56] -0.3633 -0.3581 -0.7620 primary [12:18:56] -0.0954 -0.0570 -0.0564 xCorrLib [12:18:56] 1.1776 1.1932 1.1984 xCorrModel [12:18:56] -1.4282 -1.6114 -1.7593 dotProduct [12:18:56] 1.8670 2.1105 2.3896 contrastAngle [12:18:56] -0.3680 -0.4295 -0.6865 logit [12:18:56] -1.2525 -1.1967 -1.2206 sumOfSquaredErrors [12:18:56] 1.0523 1.1508 1.5554 numberOfMatchingPeaks [12:18:56] -0.0547 -0.0430 -0.0030 numberOfMatchingPeaksAboveThreshold [12:18:56] -0.0059 0.0354 -0.0148 averageFragmentDeltaMasses [12:18:56] 0.0647 0.2219 0.3171 isotopeDotProduct [12:18:56] -0.0347 -0.0285 0.0015 averageParentDeltaMass [12:18:56] -0.0440 0.0108 0.0387 percentBlankOverMono [12:18:56] -0.0575 -0.1589 -0.1624 numberPrecursorMatch [12:18:56] -1.0364 -1.1077 -1.1738 lnSp [12:18:56] 0.1533 0.1419 0.1945 maxLadderLength [12:18:56] -0.0521 -0.0385 -0.0168 evalue [12:18:56] 0.3567 0.3624 0.2914 correlationToGaussian [12:18:56] 0.1663 0.1717 0.1372 correlationToPrecursor [12:18:56] 0.0650 0.0694 0.1052 isIntegratedSignal [12:18:56] 0.0870 0.0964 0.0860 isIntegratedPrecursor [12:18:56] 0.7401 0.6958 0.7031 numPeaksWithGoodCorrelation [12:18:56] -0.0471 -0.1049 -0.1016 numMissedCleavage [12:18:56] -0.4890 -0.2554 -0.4465 pepLength [12:18:56] 0.0000 0.0000 0.0000 charge1 [12:18:56] -0.1014 -0.1975 -0.1891 charge2 [12:18:56] 0.1014 0.1975 0.1891 charge3 [12:18:56] 0.0000 0.0000 0.0000 charge4 [12:18:56] 0.5095 0.7723 0.7328 precursorMz [12:18:56] 0.0805 -0.4007 -0.2089 precursorMass [12:18:56] -0.1135 -0.0961 -0.1277 RTinMin [12:18:56] -1.8431 -1.8722 -1.8230 m0 [12:18:56] Found 38897 test set PSMs with q<0.01. [12:18:56] Scoring full list of PSMs with trained SVMs. [12:18:56] Features: [12:18:56] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:18:57] Found 148020 PSMs [12:18:57] Evaluated set contained 79909 positives and 68111 negatives. [12:18:59] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:18:59] Selecting pi_0=0.210812 [12:18:59] Calculating q values. [12:18:59] New pi_0 estimate on final list yields 40128 target peptides with q<0.01. [12:18:59] Calculating posterior error probabilities (PEPs). [12:19:00] Processing took 28.81 cpu seconds or 29 seconds wall clock time. [12:19:02] First pass: 40128 peptides identified at 1.0% FDR [12:19:02] Generating retention time mapping using 41576 points... [12:19:02] Enough data points (41576) to perform KDE alignment. [12:19:05] Enough data points (35025) to perform KDE alignment. [12:19:06] Enough data points (41576) to perform KDE alignment. [12:19:10] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt.unsorted [12:19:11] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:19:14] Sorted feature file in 2.73 seconds wall clock time [12:19:14] File size check: 49265854 vs 49265854 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt.unsorted [12:19:14] Executing [cmd /c C:\Windows\Temp\tmpC82E.java\Percolator-v3-01-2587424302613454957.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt] [12:19:14] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:19:14] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:19:14] Written by Lukas Käll (lukall@u.washington.edu) in the [12:19:14] Department of Genome Sciences at the University of Washington. [12:19:14] Issued command: [12:19:14] C:\Windows\Temp\tmpC82E.java\Percolator-v3-01-2587424302613454957.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:19:14] Started Wed Jul 17 12:19:14 2024 [12:19:14] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [12:19:14] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [12:19:14] Features: [12:19:14] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:19:16] Found 121360 PSMs [12:19:16] Separate target and decoy search inputs detected, using mix-max method. [12:19:16] Train/test set contains 60681 positives and 60679 negatives, size ratio=1.00003 and pi0=1 [12:19:16] Selecting Cpos by cross-validation. [12:19:16] Selecting Cneg by cross-validation. [12:19:16] Split 1: Selected feature 3 as initial search direction. Could separate 15419 training set positives in that direction. [12:19:17] Split 2: Selected feature 3 as initial search direction. Could separate 15232 training set positives in that direction. [12:19:17] Split 3: Selected feature 3 as initial search direction. Could separate 15213 training set positives in that direction. [12:19:17] Found 22903 test set positives with q<0.01 in initial direction [12:19:17] Reading in data and feature calculation took 2.882 cpu seconds or 3 seconds wall clock time. [12:19:17] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:19:23] Iteration 1: Estimated 38174 PSMs with q<0.01 [12:19:32] Iteration 2: Estimated 43155 PSMs with q<0.01 [12:19:45] Iteration 3: Estimated 44535 PSMs with q<0.01 [12:19:59] Iteration 4: Estimated 44915 PSMs with q<0.01 [12:20:13] Iteration 5: Estimated 44930 PSMs with q<0.01 [12:20:27] Iteration 6: Estimated 44939 PSMs with q<0.01 [12:20:42] Iteration 7: Estimated 44939 PSMs with q<0.01 [12:20:56] Iteration 8: Estimated 44946 PSMs with q<0.01 [12:21:10] Iteration 9: Estimated 44947 PSMs with q<0.01 [12:21:25] Iteration 10: Estimated 44945 PSMs with q<0.01 [12:21:25] Learned normalized SVM weights for the 3 cross-validation splits: [12:21:25] Split1 Split2 Split3 FeatureName [12:21:25] -0.3080 -0.5712 -0.2525 primary [12:21:25] -0.2771 -0.1912 -0.2515 xCorrLib [12:21:25] 0.7625 0.7244 0.7978 xCorrModel [12:21:25] -0.7628 0.6088 -0.5686 dotProduct [12:21:25] 1.3953 0.2314 1.1065 contrastAngle [12:21:25] -0.1628 0.2220 -0.0189 logit [12:21:25] -0.6524 -0.6136 -0.7221 sumOfSquaredErrors [12:21:25] 0.9859 1.1612 0.8854 numberOfMatchingPeaks [12:21:25] -0.0537 0.0144 -0.0500 numberOfMatchingPeaksAboveThreshold [12:21:25] 0.0106 0.0046 0.0253 averageFragmentDeltaMasses [12:21:25] -0.0749 -0.0788 -0.2266 isotopeDotProduct [12:21:25] -0.1183 -0.0930 -0.1524 averageParentDeltaMass [12:21:25] -0.0303 -0.0509 -0.0849 percentBlankOverMono [12:21:25] -0.2029 -0.1289 -0.1577 numberPrecursorMatch [12:21:25] -1.2149 -1.0242 -1.1608 lnSp [12:21:25] 0.2382 0.1702 0.2251 maxLadderLength [12:21:25] 0.0195 0.0284 0.0104 evalue [12:21:25] 0.3386 0.2352 0.3527 correlationToGaussian [12:21:25] 0.0531 0.0500 0.0051 correlationToPrecursor [12:21:25] 0.0656 0.0057 0.0622 isIntegratedSignal [12:21:25] -0.1320 -0.1028 -0.0754 isIntegratedPrecursor [12:21:25] 0.5540 0.4962 0.5619 numPeaksWithGoodCorrelation [12:21:25] -39.0909 -41.5082 -41.4920 deltaRT [12:21:25] -0.0791 0.0264 -0.0917 ms1MassError [12:21:25] 0.0263 0.0336 0.0433 ms2MassError [12:21:25] -0.1293 -0.1056 -0.0922 numMissedCleavage [12:21:25] -0.3486 -0.3855 -0.1284 pepLength [12:21:25] 0.0000 0.0000 0.0000 charge1 [12:21:25] -0.1836 -0.1825 -0.2270 charge2 [12:21:25] 0.1836 0.1825 0.2270 charge3 [12:21:25] 0.0000 0.0000 0.0000 charge4 [12:21:25] 0.4678 0.5152 0.6369 precursorMz [12:21:25] -0.2875 -0.2373 -0.6635 precursorMass [12:21:25] -0.0494 -0.0641 -0.0776 RTinMin [12:21:25] -29.0779 -31.0861 -30.8879 m0 [12:21:25] Found 44849 test set PSMs with q<0.01. [12:21:25] Scoring full list of PSMs with trained SVMs. [12:21:25] Features: [12:21:25] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:21:26] Found 121360 PSMs [12:21:26] Evaluated set contained 60681 positives and 60679 negatives. [12:21:27] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:21:28] Selecting pi_0=0.231985 [12:21:28] Calculating q values. [12:21:28] New pi_0 estimate on final list yields 45387 target peptides with q<0.01. [12:21:28] Calculating posterior error probabilities (PEPs). [12:21:29] Processing took 132.1 cpu seconds or 132 seconds wall clock time. [12:21:31] Generating retention time mapping using 47028 points... [12:21:31] Enough data points (47028) to perform KDE alignment. [12:21:34] Enough data points (37625) to perform KDE alignment. [12:21:35] Enough data points (47028) to perform KDE alignment. [12:21:39] Writing elib result library... [12:21:39] Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML: Number of global peptides: 45387 vs local peptides: 45387 [12:21:39] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML... [12:21:39] Extracting Spectral Data for 45387 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML... [12:21:39] Number of global peptides: 45387 vs local peptides: 45387 [12:21:39] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:21:39] Parsed features and scores for 45387 peptides. [12:21:39] Extracting 45387 peptides... [12:21:39] Quant Extracting 396.4 to 400.4 m/z (7.3304963 to 77.461266 min) [12:21:40] Quant Extracting 400.4 to 404.4 m/z (5.2314596 to 80.34574 min) [12:21:40] Quant Extracting 404.4 to 408.4 m/z (7.13663 to 81.912025 min) [12:21:40] Quant Extracting 408.4 to 412.4 m/z (4.4502664 to 81.618744 min) [12:21:40] Quant Extracting 412.4 to 416.4 m/z (5.917088 to 87.047676 min) [12:21:40] Quant Extracting 416.4 to 420.4 m/z (6.0630393 to 82.15529 min) [12:21:40] Quant Extracting 420.4 to 424.4 m/z (7.1378603 to 82.449905 min) [12:21:40] Quant Extracting 424.4 to 428.4 m/z (7.2856293 to 85.142235 min) [12:21:40] Quant Extracting 428.4 to 432.4 m/z (7.1384754 to 83.283356 min) [12:21:40] Quant Extracting 432.4 to 436.4 m/z (7.1384754 to 81.91448 min) [12:21:41] Quant Extracting 436.4 to 440.5 m/z (7.139091 to 85.43689 min) [12:21:41] Quant Extracting 440.5 to 444.5 m/z (6.748151 to 87.539024 min) [12:21:41] Quant Extracting 444.5 to 448.5 m/z (7.1397066 to 87.245575 min) [12:21:41] Quant Extracting 448.5 to 452.5 m/z (4.3045506 to 83.527214 min) [12:21:41] Quant Extracting 452.5 to 456.5 m/z (7.14032 to 84.26206 min) [12:21:41] Quant Extracting 456.5 to 460.5 m/z (7.14032 to 85.77762 min) [12:21:41] Quant Extracting 460.5 to 464.5 m/z (6.21487 to 87.34547 min) [12:21:41] Quant Extracting 464.5 to 468.5 m/z (7.3354177 to 87.298744 min) [12:21:42] Quant Extracting 468.5 to 472.5 m/z (7.1910176 to 87.786446 min) [12:21:42] Quant Extracting 472.5 to 476.5 m/z (7.2383394 to 88.47207 min) [12:21:42] Quant Extracting 476.5 to 480.5 m/z (7.3877096 to 88.029816 min) [12:21:42] Quant Extracting 480.5 to 484.5 m/z (5.8239565 to 88.22527 min) [12:21:42] Quant Extracting 484.5 to 488.5 m/z (7.1427794 to 90.92208 min) [12:21:42] Quant Extracting 488.5 to 492.5 m/z (7.1427794 to 86.51692 min) [12:21:42] Quant Extracting 492.5 to 496.5 m/z (7.143394 to 86.56425 min) [12:21:43] Quant Extracting 496.5 to 500.5 m/z (7.143394 to 89.10861 min) [12:21:43] Quant Extracting 500.5 to 504.5 m/z (7.1440043 to 88.61985 min) [12:21:43] Quant Extracting 504.5 to 508.5 m/z (7.1440043 to 92.83199 min) [12:21:43] Quant Extracting 508.5 to 512.5 m/z (7.1451945 to 93.667496 min) [12:21:43] Quant Extracting 512.5 to 516.5 m/z (7.1451945 to 86.956985 min) [12:21:43] Quant Extracting 516.5 to 520.5 m/z (7.14581 to 92.10092 min) [12:21:43] Quant Extracting 520.5 to 524.5 m/z (6.1684356 to 90.28565 min) [12:21:43] Quant Extracting 524.5 to 528.5 m/z (7.1464243 to 91.71061 min) [12:21:43] Quant Extracting 528.5 to 532.5 m/z (7.1464243 to 89.014885 min) [12:21:43] Quant Extracting 532.5 to 536.5 m/z (7.14704 to 93.717255 min) [12:21:43] Quant Extracting 536.5 to 540.5 m/z (7.14704 to 92.787766 min) [12:21:44] Quant Extracting 540.5 to 544.5 m/z (7.1476564 to 96.02295 min) [12:21:44] Quant Extracting 544.5 to 548.5 m/z (7.1476564 to 91.66111 min) [12:21:44] Quant Extracting 548.5 to 552.5 m/z (7.1482706 to 97.20183 min) [12:21:44] Quant Extracting 552.5 to 556.5 m/z (7.1482706 to 94.26131 min) [12:21:44] Quant Extracting 556.5 to 560.5 m/z (7.148887 to 90.24085 min) [12:21:44] Quant Extracting 560.5 to 564.5 m/z (6.71067 to 97.79309 min) [12:21:44] Quant Extracting 564.5 to 568.5 m/z (8.274328 to 92.8375 min) [12:21:44] Quant Extracting 568.5 to 572.5 m/z (7.1495028 to 92.24929 min) [12:21:44] Quant Extracting 572.5 to 576.5 m/z (7.150118 to 92.496124 min) [12:21:44] Quant Extracting 576.5 to 580.5 m/z (7.150118 to 97.597046 min) [12:21:45] Quant Extracting 580.5 to 584.5 m/z (7.1507325 to 94.409706 min) [12:21:45] Quant Extracting 584.5 to 588.5 m/z (7.1507325 to 93.478195 min) [12:21:45] Quant Extracting 588.5 to 592.5 m/z (7.151349 to 97.99038 min) [12:21:45] Quant Extracting 592.5 to 596.5 m/z (7.151349 to 91.02932 min) [12:21:45] Quant Extracting 596.5 to 600.5 m/z (7.151963 to 93.575645 min) [12:21:45] Quant Extracting 600.5 to 604.5 m/z (7.151963 to 94.55913 min) [12:21:45] Quant Extracting 604.5 to 608.5 m/z (7.15258 to 97.05855 min) [12:21:45] Quant Extracting 608.5 to 612.5 m/z (10.5093355 to 93.774185 min) [12:21:45] Quant Extracting 612.5 to 616.5 m/z (7.1531954 to 99.85737 min) [12:21:45] Quant Extracting 616.5 to 620.5 m/z (7.7399993 to 94.901726 min) [12:21:45] Quant Extracting 620.5 to 624.5 m/z (12.254529 to 95.73495 min) [12:21:46] Quant Extracting 624.5 to 628.5 m/z (7.1538105 to 93.62537 min) [12:21:46] Quant Extracting 628.5 to 632.5 m/z (7.154426 to 96.32565 min) [12:21:46] Quant Extracting 632.5 to 636.5 m/z (7.154426 to 97.50452 min) [12:21:46] Quant Extracting 636.5 to 640.5 m/z (7.1550417 to 95.442085 min) [12:21:46] Quant Extracting 640.5 to 644.5 m/z (10.511795 to 96.915085 min) [12:21:46] Quant Extracting 644.5 to 648.5 m/z (9.543322 to 95.49058 min) [12:21:46] Quant Extracting 648.5 to 652.5 m/z (11.094175 to 96.27612 min) [12:21:46] Quant Extracting 652.5 to 656.5 m/z (9.059458 to 95.29573 min) [12:21:46] Quant Extracting 656.5 to 660.6 m/z (14.58421 to 97.40772 min) [12:21:46] Quant Extracting 660.6 to 664.6 m/z (17.58839 to 95.39499 min) [12:21:47] Quant Extracting 664.6 to 668.6 m/z (19.3323 to 96.17872 min) [12:21:47] Quant Extracting 668.6 to 672.6 m/z (12.015721 to 95.152214 min) [12:21:47] Quant Extracting 672.6 to 676.6 m/z (7.157502 to 96.96483 min) [12:21:47] Quant Extracting 676.6 to 680.6 m/z (16.136282 to 98.339165 min) [12:21:47] Quant Extracting 680.6 to 684.6 m/z (9.5936575 to 99.66563 min) [12:21:47] Quant Extracting 684.6 to 688.6 m/z (8.6736555 to 95.20136 min) [12:21:47] Quant Extracting 688.6 to 692.6 m/z (7.158733 to 98.1443 min) [12:21:47] Quant Extracting 692.6 to 696.6 m/z (10.612377 to 100.75145 min) [12:21:47] Quant Extracting 696.6 to 700.6 m/z (7.3538237 to 96.279816 min) [12:21:47] Quant Extracting 700.6 to 704.6 m/z (10.225707 to 100.75206 min) [12:21:47] Quant Extracting 704.6 to 708.6 m/z (13.277055 to 99.9634 min) [12:21:48] Quant Extracting 708.6 to 712.6 m/z (7.1605783 to 100.80056 min) [12:21:48] Quant Extracting 712.6 to 716.6 m/z (12.405939 to 97.85205 min) [12:21:48] Quant Extracting 716.6 to 720.6 m/z (9.693532 to 100.1613 min) [12:21:48] Quant Extracting 720.6 to 724.6 m/z (13.569297 to 99.37458 min) [12:21:48] Quant Extracting 724.6 to 728.6 m/z (11.099713 to 95.05788 min) [12:21:48] Quant Extracting 728.6 to 732.6 m/z (7.1618094 to 96.33364 min) [12:21:48] Quant Extracting 732.6 to 736.6 m/z (14.783606 to 99.521706 min) [12:21:48] Quant Extracting 736.6 to 740.6 m/z (15.85046 to 100.755135 min) [12:21:48] Quant Extracting 740.6 to 744.6 m/z (8.969425 to 99.129616 min) [12:21:48] Quant Extracting 744.6 to 748.6 m/z (7.16304 to 99.129616 min) [12:21:49] Quant Extracting 748.6 to 752.6 m/z (21.083715 to 97.85513 min) [12:21:49] Quant Extracting 752.6 to 756.6 m/z (9.211842 to 95.84406 min) [12:21:49] Quant Extracting 756.6 to 760.6 m/z (22.875158 to 95.64677 min) [12:21:49] Quant Extracting 760.6 to 764.6 m/z (15.174144 to 100.75755 min) [12:21:49] Quant Extracting 764.6 to 768.6 m/z (12.023118 to 96.77674 min) [12:21:49] Quant Extracting 768.6 to 772.6 m/z (16.48154 to 99.42554 min) [12:21:49] Quant Extracting 772.6 to 776.6 m/z (12.072626 to 94.42448 min) [12:21:49] Quant Extracting 776.6 to 780.6 m/z (18.953957 to 100.75878 min) [12:21:49] Quant Extracting 780.6 to 784.6 m/z (19.923346 to 97.41751 min) [12:21:49] Quant Extracting 784.6 to 788.6 m/z (8.389688 to 97.75896 min) [12:21:49] Quant Extracting 788.6 to 792.6 m/z (13.236509 to 100.36474 min) [12:21:50] Quant Extracting 792.6 to 796.6 m/z (13.865961 to 95.69713 min) [12:21:50] Quant Extracting 796.6 to 800.6 m/z (14.789097 to 99.23255 min) [12:21:50] Quant Extracting 800.6 to 804.6 m/z (18.181087 to 96.5819 min) [12:21:50] Quant Extracting 804.6 to 808.6 m/z (22.10416 to 96.83111 min) [12:21:50] Quant Extracting 808.6 to 812.6 m/z (16.872433 to 95.65165 min) [12:21:50] Quant Extracting 812.6 to 816.6 m/z (13.0917845 to 100.16926 min) [12:21:50] Quant Extracting 816.6 to 820.6 m/z (23.512218 to 98.055504 min) [12:21:50] Quant Extracting 820.6 to 824.6 m/z (14.159556 to 96.04504 min) [12:21:50] Quant Extracting 824.6 to 828.6 m/z (15.323156 to 100.76247 min) [12:21:50] Quant Extracting 828.6 to 832.6 m/z (25.59633 to 100.71114 min) [12:21:50] Quant Extracting 832.6 to 836.6 m/z (24.289371 to 95.40791 min) [12:21:50] Quant Extracting 836.6 to 840.6 m/z (7.1704235 to 100.763084 min) [12:21:51] Quant Extracting 840.6 to 844.6 m/z (11.012663 to 96.09361 min) [12:21:51] Quant Extracting 844.6 to 848.6 m/z (20.607233 to 98.79611 min) [12:21:51] Quant Extracting 848.6 to 852.6 m/z (14.502664 to 100.76431 min) [12:21:51] Quant Extracting 852.6 to 856.6 m/z (16.538044 to 96.0475 min) [12:21:51] Quant Extracting 856.6 to 860.6 m/z (23.173662 to 100.21964 min) [12:21:51] Quant Extracting 860.6 to 864.6 m/z (28.020739 to 98.79735 min) [12:21:51] Quant Extracting 864.6 to 868.6 m/z (23.659967 to 99.09214 min) [12:21:51] Quant Extracting 868.6 to 872.6 m/z (26.277555 to 100.76554 min) [12:21:51] Quant Extracting 872.6 to 876.6 m/z (25.746452 to 97.667656 min) [12:21:51] Quant Extracting 876.6 to 880.7 m/z (32.480762 to 98.20857 min) [12:21:51] Quant Extracting 880.7 to 884.7 m/z (31.705639 to 96.1959 min) [12:21:52] Quant Extracting 884.7 to 888.7 m/z (25.213518 to 96.73864 min) [12:21:52] Quant Extracting 888.7 to 892.7 m/z (28.7502 to 96.98201 min) [12:21:52] Quant Extracting 892.7 to 896.7 m/z (21.336761 to 100.71664 min) [12:21:52] Quant Extracting 896.7 to 900.7 m/z (19.447733 to 98.847694 min) [12:21:52] Quant Extracting 900.7 to 904.7 m/z (27.15255 to 99.48729 min) [12:21:52] Quant Extracting 904.7 to 908.7 m/z (28.848196 to 99.82933 min) [12:21:52] Quant Extracting 908.7 to 912.7 m/z (21.871338 to 100.520515 min) [12:21:52] Quant Extracting 912.7 to 916.7 m/z (28.315462 to 95.17187 min) [12:21:52] Quant Extracting 916.7 to 920.7 m/z (33.887592 to 95.56284 min) [12:21:52] Quant Extracting 920.7 to 924.7 m/z (37.474926 to 96.54442 min) [12:21:52] Quant Extracting 924.7 to 928.7 m/z (27.687593 to 98.3588 min) [12:21:52] Quant Extracting 928.7 to 932.7 m/z (10.050297 to 98.947 min) [12:21:52] Quant Extracting 932.7 to 936.7 m/z (37.765915 to 99.73317 min) [12:21:53] Quant Extracting 936.7 to 940.7 m/z (37.52339 to 97.672585 min) [12:21:53] Quant Extracting 940.7 to 944.7 m/z (34.4225 to 97.82258 min) [12:21:53] Quant Extracting 944.7 to 948.7 m/z (37.186497 to 99.88377 min) [12:21:53] Quant Extracting 948.7 to 952.7 m/z (35.732155 to 100.37705 min) [12:21:53] Quant Extracting 952.7 to 956.7 m/z (32.051903 to 96.10279 min) [12:21:53] Quant Extracting 956.7 to 960.7 m/z (31.518042 to 95.41831 min) [12:21:53] Quant Extracting 960.7 to 964.7 m/z (39.70583 to 96.15478 min) [12:21:53] Quant Extracting 964.7 to 968.7 m/z (27.303288 to 98.85324 min) [12:21:53] Quant Extracting 968.7 to 972.7 m/z (29.385872 to 97.67503 min) [12:21:53] Quant Extracting 972.7 to 976.7 m/z (30.45371 to 98.119125 min) [12:21:53] Quant Extracting 976.7 to 980.7 m/z (29.047426 to 99.736244 min) [12:21:53] Quant Extracting 980.7 to 984.7 m/z (19.356865 to 98.3152 min) [12:21:53] Quant Extracting 984.7 to 988.7 m/z (15.820453 to 100.08412 min) [12:21:54] Quant Extracting 988.7 to 992.7 m/z (34.038013 to 96.74663 min) [12:21:54] Quant Extracting 992.7 to 996.7 m/z (38.78642 to 96.597244 min) [12:21:54] Quant Extracting 996.7 to 1000.7 m/z (42.279045 to 97.23685 min) [12:21:54] Quant Extracting 1000.7 to 1004.7 m/z (16.112293 to 95.02863 min) [12:21:54] Attempted extraction for: 45387, found 45387 [12:21:54] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML (45387 entries)... [12:21:54] Writing 45387 peptides to entries table... [12:21:58] Writing 45387 peptides to peptidequants table... [12:22:01] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:22:01 BST 2024 [12:22:02] Writing local target/decoy peptides: 45387/1724, pi0: 0.231985 [12:22:03] Writing local target/decoy proteins: 5686/56 [12:22:06] Finished analysis! 45387 peptides identified at 1.0% FDR (5.4 minutes) [12:22:06] Generating quantification library (2 of 5): Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" [12:22:10] EncyclopeDIA version 2.12.30 [12:22:10] Getting count of protein accessions... [12:22:10] Using EncyclopeDIA 2.X Scoring System [12:22:10] Indexing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML ... [12:22:10] Converting Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML ... [12:22:11] Parsed 1% [12:22:11] Parsed 2% [12:22:12] Parsed 3% [12:22:12] Parsed 4% [12:22:12] Parsed 5% [12:22:13] Parsed 6% [12:22:14] Parsed 7% [12:22:14] Parsed 8% [12:22:15] Parsed 9% [12:22:16] Parsed 10% [12:22:16] Parsed 11% [12:22:17] Parsed 12% [12:22:18] Parsed 13% [12:22:20] Parsed 14% [12:22:21] Parsed 15% [12:22:23] Parsed 16% [12:22:26] Parsed 17% [12:22:27] Parsed 18% [12:22:28] Parsed 19% [12:22:29] Parsed 20% [12:22:30] Parsed 21% [12:22:32] Parsed 22% [12:22:34] Parsed 23% [12:22:35] Parsed 24% [12:22:36] Parsed 25% [12:22:38] Parsed 26% [12:22:39] Parsed 27% [12:22:40] Parsed 28% [12:22:42] Parsed 29% [12:22:44] Parsed 30% [12:22:48] Parsed 31% [12:22:52] Parsed 32% [12:22:58] Parsed 33% [12:23:03] Parsed 34% [12:23:12] Parsed 35% [12:23:13] Parsed 36% [12:23:14] Parsed 37% [12:23:16] Parsed 38% [12:23:17] Parsed 39% [12:23:20] Parsed 40% [12:23:23] Parsed 41% [12:23:27] Parsed 42% [12:23:32] Parsed 43% [12:23:37] Parsed 44% [12:23:42] Parsed 45% [12:23:49] Parsed 46% [12:23:50] Parsed 47% [12:23:52] Parsed 48% [12:23:54] Parsed 49% [12:23:57] Parsed 50% [12:24:00] Parsed 51% [12:24:05] Parsed 52% [12:24:10] Parsed 53% [12:24:15] Parsed 54% [12:24:20] Parsed 55% [12:24:25] Parsed 56% [12:24:32] Parsed 57% [12:24:37] Parsed 58% [12:24:44] Parsed 59% [12:24:52] Parsed 60% [12:25:01] Parsed 61% [12:25:10] Parsed 62% [12:25:20] Parsed 63% [12:25:30] Parsed 64% [12:25:52] Parsed 65% [12:25:53] Parsed 66% [12:25:54] Parsed 67% [12:25:57] Parsed 68% [12:26:01] Parsed 69% [12:26:06] Parsed 70% [12:26:10] Parsed 71% [12:26:15] Parsed 72% [12:26:21] Parsed 73% [12:26:27] Parsed 74% [12:26:33] Parsed 75% [12:26:41] Parsed 76% [12:26:48] Parsed 77% [12:26:55] Parsed 78% [12:27:04] Parsed 79% [12:27:20] Parsed 80% [12:27:22] Parsed 81% [12:27:23] Parsed 82% [12:27:26] Parsed 83% [12:27:30] Parsed 84% [12:27:34] Parsed 85% [12:27:39] Parsed 86% [12:27:44] Parsed 87% [12:27:49] Parsed 88% [12:27:54] Parsed 89% [12:28:00] Parsed 90% [12:28:05] Parsed 91% [12:28:11] Parsed 92% [12:28:17] Parsed 93% [12:28:23] Parsed 94% [12:28:30] Parsed 95% [12:28:40] Parsed 96% [12:28:48] Parsed 97% [12:28:55] Parsed 98% [12:28:58] Parsed 99% [12:29:05] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.dia ... [12:29:06] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.dia! [12:29:06] Input File: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML [12:29:06] Library File: UP000005640_9606-z3_nce27.elib [12:29:06] Result File: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.elib [12:29:06] Parameters: [12:29:06] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [12:29:06] Converting files... [12:29:06] Calculating features... [12:29:06] Processing precursors scans... [12:29:06] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt.unsorted [12:29:06] Processing 396.4 to 400.4 m/z, (5.853102 second duty cycle) [12:29:06] 67 peptides remaining for 396.4 to 400.4... [12:29:07] 67 peptides remaining for 396.4 to 400.4... [12:29:07] Processing 400.4 to 404.4 m/z, (2.9265912 second duty cycle) [12:29:08] 201 peptides remaining for 400.4 to 404.4... [12:29:08] Processing 404.4 to 408.4 m/z, (2.9265912 second duty cycle) [12:29:08] 237 peptides remaining for 404.4 to 408.4... [12:29:09] Processing 408.4 to 412.4 m/z, (2.9265916 second duty cycle) [12:29:09] 283 peptides remaining for 408.4 to 412.4... [12:29:09] Processing 412.4 to 416.4 m/z, (2.9265914 second duty cycle) [12:29:10] 303 peptides remaining for 412.4 to 416.4... [12:29:10] Processing 416.4 to 420.4 m/z, (2.9265912 second duty cycle) [12:29:10] 299 peptides remaining for 416.4 to 420.4... [12:29:11] Processing 420.4 to 424.4 m/z, (2.9265912 second duty cycle) [12:29:11] 321 peptides remaining for 420.4 to 424.4... [12:29:12] Processing 424.4 to 428.4 m/z, (2.9265912 second duty cycle) [12:29:12] 304 peptides remaining for 424.4 to 428.4... [12:29:12] Processing 428.4 to 432.4 m/z, (2.9265912 second duty cycle) [12:29:12] 366 peptides remaining for 428.4 to 432.4... [12:29:13] Processing 432.4 to 436.4 m/z, (2.9265914 second duty cycle) [12:29:13] 377 peptides remaining for 432.4 to 436.4... [12:29:14] Processing 436.4 to 440.5 m/z, (2.9265914 second duty cycle) [12:29:14] 519 peptides remaining for 436.4 to 440.5... [12:29:14] 0 peptides remaining for 436.4 to 440.5... [12:29:15] Processing 440.5 to 444.5 m/z, (2.9265912 second duty cycle) [12:29:15] 467 peptides remaining for 440.5 to 444.5... [12:29:15] Processing 444.5 to 448.5 m/z, (2.9265912 second duty cycle) [12:29:16] 368 peptides remaining for 444.5 to 448.5... [12:29:16] Processing 448.5 to 452.5 m/z, (2.9265912 second duty cycle) [12:29:16] 454 peptides remaining for 448.5 to 452.5... [12:29:17] Processing 452.5 to 456.5 m/z, (2.9265912 second duty cycle) [12:29:17] 385 peptides remaining for 452.5 to 456.5... [12:29:17] Processing 456.5 to 460.5 m/z, (2.9265914 second duty cycle) [12:29:18] 508 peptides remaining for 456.5 to 460.5... [12:29:18] Processing 460.5 to 464.5 m/z, (2.9265914 second duty cycle) [12:29:18] 490 peptides remaining for 460.5 to 464.5... [12:29:19] Processing 464.5 to 468.5 m/z, (2.9265912 second duty cycle) [12:29:19] 604 peptides remaining for 464.5 to 468.5... [12:29:19] Processing 468.5 to 472.5 m/z, (2.9265912 second duty cycle) [12:29:20] 496 peptides remaining for 468.5 to 472.5... [12:29:20] Processing 472.5 to 476.5 m/z, (2.9265916 second duty cycle) [12:29:20] 496 peptides remaining for 472.5 to 476.5... [12:29:21] Processing 476.5 to 480.5 m/z, (2.9265914 second duty cycle) [12:29:21] 494 peptides remaining for 476.5 to 480.5... [12:29:21] Processing 480.5 to 484.5 m/z, (2.9265914 second duty cycle) [12:29:22] 578 peptides remaining for 480.5 to 484.5... [12:29:22] 0 peptides remaining for 480.5 to 484.5... [12:29:23] Processing 484.5 to 488.5 m/z, (2.9265914 second duty cycle) [12:29:23] 511 peptides remaining for 484.5 to 488.5... [12:29:23] Processing 488.5 to 492.5 m/z, (2.9265916 second duty cycle) [12:29:23] 475 peptides remaining for 488.5 to 492.5... [12:29:24] Processing 492.5 to 496.5 m/z, (2.9265914 second duty cycle) [12:29:24] 544 peptides remaining for 492.5 to 496.5... [12:29:24] Processing 496.5 to 500.5 m/z, (2.9265916 second duty cycle) [12:29:25] 661 peptides remaining for 496.5 to 500.5... [12:29:25] Processing 500.5 to 504.5 m/z, (2.9265914 second duty cycle) [12:29:25] 861 peptides remaining for 500.5 to 504.5... [12:29:26] Processing 504.5 to 508.5 m/z, (2.9265914 second duty cycle) [12:29:26] 491 peptides remaining for 504.5 to 508.5... [12:29:27] Processing 508.5 to 512.5 m/z, (2.9265914 second duty cycle) [12:29:27] 632 peptides remaining for 508.5 to 512.5... [12:29:27] Processing 512.5 to 516.5 m/z, (2.9265914 second duty cycle) [12:29:27] 581 peptides remaining for 512.5 to 516.5... [12:29:28] Processing 516.5 to 520.5 m/z, (2.9265914 second duty cycle) [12:29:28] 527 peptides remaining for 516.5 to 520.5... [12:29:29] Processing 520.5 to 524.5 m/z, (2.9265916 second duty cycle) [12:29:29] 594 peptides remaining for 520.5 to 524.5... [12:29:29] Processing 524.5 to 528.5 m/z, (2.9265916 second duty cycle) [12:29:29] 550 peptides remaining for 524.5 to 528.5... [12:29:30] Processing 528.5 to 532.5 m/z, (2.9265914 second duty cycle) [12:29:30] 627 peptides remaining for 528.5 to 532.5... [12:29:31] Processing 532.5 to 536.5 m/z, (2.9265914 second duty cycle) [12:29:31] 515 peptides remaining for 532.5 to 536.5... [12:29:31] Processing 536.5 to 540.5 m/z, (2.9265912 second duty cycle) [12:29:31] 591 peptides remaining for 536.5 to 540.5... [12:29:32] 0 peptides remaining for 536.5 to 540.5... [12:29:32] Processing 540.5 to 544.5 m/z, (2.9265912 second duty cycle) [12:29:32] 593 peptides remaining for 540.5 to 544.5... [12:29:33] Processing 544.5 to 548.5 m/z, (2.9265914 second duty cycle) [12:29:33] 587 peptides remaining for 544.5 to 548.5... [12:29:34] Processing 548.5 to 552.5 m/z, (2.9265914 second duty cycle) [12:29:34] 578 peptides remaining for 548.5 to 552.5... [12:29:34] Processing 552.5 to 556.5 m/z, (2.9265912 second duty cycle) [12:29:34] 601 peptides remaining for 552.5 to 556.5... [12:29:35] Processing 556.5 to 560.5 m/z, (2.9265912 second duty cycle) [12:29:35] 606 peptides remaining for 556.5 to 560.5... [12:29:36] Processing 560.5 to 564.5 m/z, (2.9265912 second duty cycle) [12:29:36] 533 peptides remaining for 560.5 to 564.5... [12:29:36] Processing 564.5 to 568.5 m/z, (2.9265912 second duty cycle) [12:29:36] 668 peptides remaining for 564.5 to 568.5... [12:29:37] Processing 568.5 to 572.5 m/z, (2.9265912 second duty cycle) [12:29:37] 556 peptides remaining for 568.5 to 572.5... [12:29:38] Processing 572.5 to 576.5 m/z, (2.9265912 second duty cycle) [12:29:38] 611 peptides remaining for 572.5 to 576.5... [12:29:38] Processing 576.5 to 580.5 m/z, (2.9265912 second duty cycle) [12:29:38] 586 peptides remaining for 576.5 to 580.5... [12:29:39] Processing 580.5 to 584.5 m/z, (2.9265912 second duty cycle) [12:29:39] 570 peptides remaining for 580.5 to 584.5... [12:29:40] Processing 584.5 to 588.5 m/z, (2.9265912 second duty cycle) [12:29:40] 601 peptides remaining for 584.5 to 588.5... [12:29:40] Processing 588.5 to 592.5 m/z, (2.9265912 second duty cycle) [12:29:40] 515 peptides remaining for 588.5 to 592.5... [12:29:41] Processing 592.5 to 596.5 m/z, (2.9265912 second duty cycle) [12:29:41] 592 peptides remaining for 592.5 to 596.5... [12:29:41] Processing 596.5 to 600.5 m/z, (2.9265912 second duty cycle) [12:29:42] 735 peptides remaining for 596.5 to 600.5... [12:29:42] Processing 600.5 to 604.5 m/z, (2.9265912 second duty cycle) [12:29:42] 780 peptides remaining for 600.5 to 604.5... [12:29:43] Processing 604.5 to 608.5 m/z, (2.9265912 second duty cycle) [12:29:43] 475 peptides remaining for 604.5 to 608.5... [12:29:44] Processing 608.5 to 612.5 m/z, (2.9265912 second duty cycle) [12:29:44] 513 peptides remaining for 608.5 to 612.5... [12:29:44] Processing 612.5 to 616.5 m/z, (2.9265912 second duty cycle) [12:29:44] 517 peptides remaining for 612.5 to 616.5... [12:29:45] Processing 616.5 to 620.5 m/z, (2.9265912 second duty cycle) [12:29:45] 488 peptides remaining for 616.5 to 620.5... [12:29:46] Processing 620.5 to 624.5 m/z, (2.9265912 second duty cycle) [12:29:46] 499 peptides remaining for 620.5 to 624.5... [12:29:46] Processing 624.5 to 628.5 m/z, (2.9265912 second duty cycle) [12:29:46] 450 peptides remaining for 624.5 to 628.5... [12:29:47] Processing 628.5 to 632.5 m/z, (2.9265912 second duty cycle) [12:29:47] 479 peptides remaining for 628.5 to 632.5... [12:29:48] Processing 632.5 to 636.5 m/z, (2.9265912 second duty cycle) [12:29:48] 388 peptides remaining for 632.5 to 636.5... [12:29:48] Processing 636.5 to 640.5 m/z, (2.9265912 second duty cycle) [12:29:48] 479 peptides remaining for 636.5 to 640.5... [12:29:49] Processing 640.5 to 644.5 m/z, (2.9265912 second duty cycle) [12:29:49] 415 peptides remaining for 640.5 to 644.5... [12:29:50] Processing 644.5 to 648.5 m/z, (2.9265912 second duty cycle) [12:29:50] 529 peptides remaining for 644.5 to 648.5... [12:29:50] Processing 648.5 to 652.5 m/z, (2.9265912 second duty cycle) [12:29:50] 408 peptides remaining for 648.5 to 652.5... [12:29:51] Processing 652.5 to 656.5 m/z, (2.9265912 second duty cycle) [12:29:51] 419 peptides remaining for 652.5 to 656.5... [12:29:51] Processing 656.5 to 660.6 m/z, (2.9265912 second duty cycle) [12:29:52] 432 peptides remaining for 656.5 to 660.6... [12:29:52] Processing 660.6 to 664.6 m/z, (2.9265912 second duty cycle) [12:29:52] 419 peptides remaining for 660.6 to 664.6... [12:29:53] Processing 664.6 to 668.6 m/z, (2.9265912 second duty cycle) [12:29:53] 440 peptides remaining for 664.6 to 668.6... [12:29:53] Processing 668.6 to 672.6 m/z, (2.9265912 second duty cycle) [12:29:54] 434 peptides remaining for 668.6 to 672.6... [12:29:54] Processing 672.6 to 676.6 m/z, (2.9265912 second duty cycle) [12:29:54] 455 peptides remaining for 672.6 to 676.6... [12:29:55] Processing 676.6 to 680.6 m/z, (2.9265912 second duty cycle) [12:29:55] 451 peptides remaining for 676.6 to 680.6... [12:29:56] Processing 680.6 to 684.6 m/z, (2.9265912 second duty cycle) [12:29:56] 427 peptides remaining for 680.6 to 684.6... [12:29:56] Processing 684.6 to 688.6 m/z, (2.9265912 second duty cycle) [12:29:56] 435 peptides remaining for 684.6 to 688.6... [12:29:57] Processing 688.6 to 692.6 m/z, (2.9265912 second duty cycle) [12:29:57] 423 peptides remaining for 688.6 to 692.6... [12:29:58] Processing 692.6 to 696.6 m/z, (2.9265912 second duty cycle) [12:29:58] 448 peptides remaining for 692.6 to 696.6... [12:29:58] Processing 696.6 to 700.6 m/z, (2.9265912 second duty cycle) [12:29:58] 558 peptides remaining for 696.6 to 700.6... [12:29:59] Processing 700.6 to 704.6 m/z, (2.9265912 second duty cycle) [12:29:59] 672 peptides remaining for 700.6 to 704.6... [12:30:00] Processing 704.6 to 708.6 m/z, (2.9265912 second duty cycle) [12:30:00] 393 peptides remaining for 704.6 to 708.6... [12:30:00] Processing 708.6 to 712.6 m/z, (2.9265912 second duty cycle) [12:30:00] 410 peptides remaining for 708.6 to 712.6... [12:30:01] Processing 712.6 to 716.6 m/z, (2.9265912 second duty cycle) [12:30:01] 413 peptides remaining for 712.6 to 716.6... [12:30:02] Processing 716.6 to 720.6 m/z, (2.9265912 second duty cycle) [12:30:02] 368 peptides remaining for 716.6 to 720.6... [12:30:02] Processing 720.6 to 724.6 m/z, (2.9265912 second duty cycle) [12:30:02] 371 peptides remaining for 720.6 to 724.6... [12:30:03] Processing 724.6 to 728.6 m/z, (2.9265912 second duty cycle) [12:30:03] 372 peptides remaining for 724.6 to 728.6... [12:30:04] Processing 728.6 to 732.6 m/z, (2.9265912 second duty cycle) [12:30:04] 363 peptides remaining for 728.6 to 732.6... [12:30:04] Processing 732.6 to 736.6 m/z, (2.9265912 second duty cycle) [12:30:04] 371 peptides remaining for 732.6 to 736.6... [12:30:05] Processing 736.6 to 740.6 m/z, (2.9265912 second duty cycle) [12:30:05] 357 peptides remaining for 736.6 to 740.6... [12:30:06] Processing 740.6 to 744.6 m/z, (2.9265914 second duty cycle) [12:30:06] 332 peptides remaining for 740.6 to 744.6... [12:30:06] Processing 744.6 to 748.6 m/z, (2.9265912 second duty cycle) [12:30:06] 365 peptides remaining for 744.6 to 748.6... [12:30:07] Processing 748.6 to 752.6 m/z, (2.9265912 second duty cycle) [12:30:07] 313 peptides remaining for 748.6 to 752.6... [12:30:07] Processing 752.6 to 756.6 m/z, (2.9265974 second duty cycle) [12:30:08] 311 peptides remaining for 752.6 to 756.6... [12:30:08] Processing 756.6 to 760.6 m/z, (2.9265974 second duty cycle) [12:30:08] 319 peptides remaining for 756.6 to 760.6... [12:30:09] Processing 760.6 to 764.6 m/z, (2.926494 second duty cycle) [12:30:09] 339 peptides remaining for 760.6 to 764.6... [12:30:09] Processing 764.6 to 768.6 m/z, (2.9265108 second duty cycle) [12:30:10] 342 peptides remaining for 764.6 to 768.6... [12:30:10] Processing 768.6 to 772.6 m/z, (2.9264936 second duty cycle) [12:30:10] 318 peptides remaining for 768.6 to 772.6... [12:30:11] Processing 772.6 to 776.6 m/z, (2.9265108 second duty cycle) [12:30:11] 315 peptides remaining for 772.6 to 776.6... [12:30:11] Processing 776.6 to 780.6 m/z, (2.926494 second duty cycle) [12:30:12] 294 peptides remaining for 776.6 to 780.6... [12:30:12] Processing 780.6 to 784.6 m/z, (2.926511 second duty cycle) [12:30:12] 290 peptides remaining for 780.6 to 784.6... [12:30:13] Processing 784.6 to 788.6 m/z, (2.9264936 second duty cycle) [12:30:13] 304 peptides remaining for 784.6 to 788.6... [12:30:13] Processing 788.6 to 792.6 m/z, (2.9265108 second duty cycle) [12:30:14] 298 peptides remaining for 788.6 to 792.6... [12:30:14] Processing 792.6 to 796.6 m/z, (2.9264936 second duty cycle) [12:30:14] 281 peptides remaining for 792.6 to 796.6... [12:30:15] Processing 796.6 to 800.6 m/z, (2.9265108 second duty cycle) [12:30:15] 395 peptides remaining for 796.6 to 800.6... [12:30:15] Processing 800.6 to 804.6 m/z, (2.9264936 second duty cycle) [12:30:16] 406 peptides remaining for 800.6 to 804.6... [12:30:16] Processing 804.6 to 808.6 m/z, (2.9265108 second duty cycle) [12:30:16] 236 peptides remaining for 804.6 to 808.6... [12:30:17] Processing 808.6 to 812.6 m/z, (2.926494 second duty cycle) [12:30:17] 286 peptides remaining for 808.6 to 812.6... [12:30:17] Processing 812.6 to 816.6 m/z, (2.9265108 second duty cycle) [12:30:17] 242 peptides remaining for 812.6 to 816.6... [12:30:18] Processing 816.6 to 820.6 m/z, (2.9264936 second duty cycle) [12:30:18] 248 peptides remaining for 816.6 to 820.6... [12:30:19] Processing 820.6 to 824.6 m/z, (2.9265108 second duty cycle) [12:30:19] 236 peptides remaining for 820.6 to 824.6... [12:30:19] Processing 824.6 to 828.6 m/z, (2.9264936 second duty cycle) [12:30:19] 268 peptides remaining for 824.6 to 828.6... [12:30:20] Processing 828.6 to 832.6 m/z, (2.9265108 second duty cycle) [12:30:20] 254 peptides remaining for 828.6 to 832.6... [12:30:21] Processing 832.6 to 836.6 m/z, (2.926494 second duty cycle) [12:30:21] 210 peptides remaining for 832.6 to 836.6... [12:30:21] Processing 836.6 to 840.6 m/z, (2.9265108 second duty cycle) [12:30:21] 223 peptides remaining for 836.6 to 840.6... [12:30:22] Processing 840.6 to 844.6 m/z, (2.9264936 second duty cycle) [12:30:22] 236 peptides remaining for 840.6 to 844.6... [12:30:23] Processing 844.6 to 848.6 m/z, (2.9265108 second duty cycle) [12:30:23] 234 peptides remaining for 844.6 to 848.6... [12:30:23] Processing 848.6 to 852.6 m/z, (2.926494 second duty cycle) [12:30:23] 234 peptides remaining for 848.6 to 852.6... [12:30:24] Processing 852.6 to 856.6 m/z, (2.9265108 second duty cycle) [12:30:24] 197 peptides remaining for 852.6 to 856.6... [12:30:24] Processing 856.6 to 860.6 m/z, (2.9264936 second duty cycle) [12:30:25] 216 peptides remaining for 856.6 to 860.6... [12:30:25] Processing 860.6 to 864.6 m/z, (2.9265268 second duty cycle) [12:30:25] 185 peptides remaining for 860.6 to 864.6... [12:30:26] Processing 864.6 to 868.6 m/z, (2.9265094 second duty cycle) [12:30:26] 176 peptides remaining for 864.6 to 868.6... [12:30:26] Processing 868.6 to 872.6 m/z, (2.9265268 second duty cycle) [12:30:27] 180 peptides remaining for 868.6 to 872.6... [12:30:27] Processing 872.6 to 876.6 m/z, (2.9265094 second duty cycle) [12:30:27] 207 peptides remaining for 872.6 to 876.6... [12:30:28] Processing 876.6 to 880.7 m/z, (2.9265268 second duty cycle) [12:30:28] 159 peptides remaining for 876.6 to 880.7... [12:30:28] Processing 880.7 to 884.7 m/z, (2.9265094 second duty cycle) [12:30:29] 184 peptides remaining for 880.7 to 884.7... [12:30:29] Processing 884.7 to 888.7 m/z, (2.9265268 second duty cycle) [12:30:29] 154 peptides remaining for 884.7 to 888.7... [12:30:30] Processing 888.7 to 892.7 m/z, (2.9265094 second duty cycle) [12:30:30] 149 peptides remaining for 888.7 to 892.7... [12:30:30] Processing 892.7 to 896.7 m/z, (2.9265268 second duty cycle) [12:30:31] 149 peptides remaining for 892.7 to 896.7... [12:30:31] Processing 896.7 to 900.7 m/z, (2.9265094 second duty cycle) [12:30:31] 210 peptides remaining for 896.7 to 900.7... [12:30:32] Processing 900.7 to 904.7 m/z, (2.926527 second duty cycle) [12:30:32] 222 peptides remaining for 900.7 to 904.7... [12:30:32] Processing 904.7 to 908.7 m/z, (2.9265096 second duty cycle) [12:30:33] 137 peptides remaining for 904.7 to 908.7... [12:30:33] Processing 908.7 to 912.7 m/z, (2.9265268 second duty cycle) [12:30:33] 159 peptides remaining for 908.7 to 912.7... [12:30:34] Processing 912.7 to 916.7 m/z, (2.9265094 second duty cycle) [12:30:34] 137 peptides remaining for 912.7 to 916.7... [12:30:34] Processing 916.7 to 920.7 m/z, (2.9265268 second duty cycle) [12:30:35] 133 peptides remaining for 916.7 to 920.7... [12:30:35] Processing 920.7 to 924.7 m/z, (2.9265096 second duty cycle) [12:30:35] 135 peptides remaining for 920.7 to 924.7... [12:30:36] Processing 924.7 to 928.7 m/z, (2.9265268 second duty cycle) [12:30:36] 132 peptides remaining for 924.7 to 928.7... [12:30:36] Processing 928.7 to 932.7 m/z, (2.9265094 second duty cycle) [12:30:36] 114 peptides remaining for 928.7 to 932.7... [12:30:37] Processing 932.7 to 936.7 m/z, (2.9265268 second duty cycle) [12:30:37] 108 peptides remaining for 932.7 to 936.7... [12:30:38] Processing 936.7 to 940.7 m/z, (2.9265094 second duty cycle) [12:30:38] 140 peptides remaining for 936.7 to 940.7... [12:30:38] Processing 940.7 to 944.7 m/z, (2.9265265 second duty cycle) [12:30:38] 106 peptides remaining for 940.7 to 944.7... [12:30:39] Processing 944.7 to 948.7 m/z, (2.9265091 second duty cycle) [12:30:39] 120 peptides remaining for 944.7 to 948.7... [12:30:40] Processing 948.7 to 952.7 m/z, (2.9265265 second duty cycle) [12:30:40] 149 peptides remaining for 948.7 to 952.7... [12:30:40] Processing 952.7 to 956.7 m/z, (2.9265091 second duty cycle) [12:30:40] 121 peptides remaining for 952.7 to 956.7... [12:30:41] Processing 956.7 to 960.7 m/z, (2.9265268 second duty cycle) [12:30:41] 139 peptides remaining for 956.7 to 960.7... [12:30:41] Processing 960.7 to 964.7 m/z, (2.9265094 second duty cycle) [12:30:42] 107 peptides remaining for 960.7 to 964.7... [12:30:42] Processing 964.7 to 968.7 m/z, (2.9265265 second duty cycle) [12:30:42] 120 peptides remaining for 964.7 to 968.7... [12:30:43] Processing 968.7 to 972.7 m/z, (2.9265091 second duty cycle) [12:30:43] 92 peptides remaining for 968.7 to 972.7... [12:30:43] Processing 972.7 to 976.7 m/z, (2.9265265 second duty cycle) [12:30:44] 83 peptides remaining for 972.7 to 976.7... [12:30:44] Processing 976.7 to 980.7 m/z, (2.9265094 second duty cycle) [12:30:44] 94 peptides remaining for 976.7 to 980.7... [12:30:45] Processing 980.7 to 984.7 m/z, (2.9265265 second duty cycle) [12:30:45] 64 peptides remaining for 980.7 to 984.7... [12:30:45] Processing 984.7 to 988.7 m/z, (2.9265091 second duty cycle) [12:30:46] 73 peptides remaining for 984.7 to 988.7... [12:30:46] Processing 988.7 to 992.7 m/z, (2.9265265 second duty cycle) [12:30:46] 96 peptides remaining for 988.7 to 992.7... [12:30:47] Processing 992.7 to 996.7 m/z, (2.9265094 second duty cycle) [12:30:47] 82 peptides remaining for 992.7 to 996.7... [12:30:47] Processing 996.7 to 1000.7 m/z, (2.9265265 second duty cycle) [12:30:48] 55 peptides remaining for 996.7 to 1000.7... [12:30:48] Processing 1000.7 to 1004.7 m/z, (5.8531017 second duty cycle) [12:30:48] 20 peptides remaining for 1000.7 to 1004.7... [12:30:49] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:30:52] Sorted feature file in 3.23 seconds wall clock time [12:30:52] File size check: 55725743 vs 55725743 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt.unsorted [12:30:52] 148087 total peptides processed. [12:30:52] Running Percolator... [12:30:52] Executing [cmd /c C:\Windows\Temp\tmp610E.java\Percolator-v3-01-4897791407403187019.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt] [12:30:53] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:30:53] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:30:53] Written by Lukas Käll (lukall@u.washington.edu) in the [12:30:53] Department of Genome Sciences at the University of Washington. [12:30:53] Issued command: [12:30:53] C:\Windows\Temp\tmp610E.java\Percolator-v3-01-4897791407403187019.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:30:53] Started Wed Jul 17 12:30:52 2024 [12:30:53] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [12:30:53] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:30:53] Features: [12:30:53] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:30:54] Found 148087 PSMs [12:30:54] Separate target and decoy search inputs detected, using mix-max method. [12:30:54] Train/test set contains 79820 positives and 68267 negatives, size ratio=1.16923 and pi0=1 [12:30:54] Warning: The mix-max procedure is not well behaved when # targets (79820) != # decoys (68267). Consider using target-decoy competition (-Y flag). [12:30:54] Selecting Cpos by cross-validation. [12:30:54] Selecting Cneg by cross-validation. [12:30:55] Split 1: Selected feature 3 as initial search direction. Could separate 15327 training set positives in that direction. [12:30:55] Split 2: Selected feature 3 as initial search direction. Could separate 14951 training set positives in that direction. [12:30:56] Split 3: Selected feature 3 as initial search direction. Could separate 15272 training set positives in that direction. [12:30:56] Found 22890 test set positives with q<0.01 in initial direction [12:30:56] Reading in data and feature calculation took 3.686 cpu seconds or 4 seconds wall clock time. [12:30:56] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:31:02] Iteration 1: Estimated 35284 PSMs with q<0.01 [12:31:11] Iteration 2: Estimated 38465 PSMs with q<0.01 [12:31:20] Iteration 3: Estimated 39059 PSMs with q<0.01 [12:31:20] Learned normalized SVM weights for the 3 cross-validation splits: [12:31:20] Split1 Split2 Split3 FeatureName [12:31:20] -0.3861 -0.6370 -0.5216 primary [12:31:20] -0.1043 -0.0884 -0.1454 xCorrLib [12:31:20] 1.3316 1.2159 1.2567 xCorrModel [12:31:20] -1.5728 -1.4670 -1.4308 dotProduct [12:31:20] 2.1162 1.9513 1.8800 contrastAngle [12:31:20] -0.3969 -0.3738 -0.4236 logit [12:31:20] -1.0572 -1.3126 -1.4463 sumOfSquaredErrors [12:31:20] 1.0691 1.4118 1.2905 numberOfMatchingPeaks [12:31:20] -0.0573 -0.0370 -0.0093 numberOfMatchingPeaksAboveThreshold [12:31:20] 0.0060 -0.0131 -0.0326 averageFragmentDeltaMasses [12:31:20] 0.3095 0.2697 0.2613 isotopeDotProduct [12:31:20] 0.0459 0.0212 0.0455 averageParentDeltaMass [12:31:20] 0.0336 0.0549 0.0546 percentBlankOverMono [12:31:20] -0.1129 -0.1051 -0.0356 numberPrecursorMatch [12:31:20] -1.0957 -1.2296 -1.1646 lnSp [12:31:20] 0.1543 0.1312 0.0971 maxLadderLength [12:31:20] -0.0397 -0.0388 -0.0425 evalue [12:31:20] 0.2929 0.2502 0.1530 correlationToGaussian [12:31:20] 0.0892 0.1751 0.1084 correlationToPrecursor [12:31:20] 0.1239 0.1267 0.1184 isIntegratedSignal [12:31:20] 0.0861 0.0661 0.0823 isIntegratedPrecursor [12:31:20] 0.8343 0.8113 0.9075 numPeaksWithGoodCorrelation [12:31:20] -0.0604 -0.0996 -0.1151 numMissedCleavage [12:31:20] -0.4201 -0.3990 -0.3528 pepLength [12:31:20] 0.0000 0.0000 0.0000 charge1 [12:31:20] -0.2575 -0.1366 -0.1343 charge2 [12:31:20] 0.2575 0.1366 0.1343 charge3 [12:31:20] 0.0000 0.0000 0.0000 charge4 [12:31:20] 0.9064 0.6298 0.5272 precursorMz [12:31:20] -0.4259 -0.1600 -0.1696 precursorMass [12:31:20] -0.1243 -0.1321 -0.0531 RTinMin [12:31:20] -1.8692 -1.9172 -1.9439 m0 [12:31:20] Found 38945 test set PSMs with q<0.01. [12:31:21] Scoring full list of PSMs with trained SVMs. [12:31:21] Features: [12:31:21] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:31:22] Found 148087 PSMs [12:31:22] Evaluated set contained 79820 positives and 68267 negatives. [12:31:23] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:31:23] Selecting pi_0=0.210555 [12:31:23] Calculating q values. [12:31:23] New pi_0 estimate on final list yields 40046 target peptides with q<0.01. [12:31:23] Calculating posterior error probabilities (PEPs). [12:31:25] Processing took 28.54 cpu seconds or 29 seconds wall clock time. [12:31:26] First pass: 40046 peptides identified at 1.0% FDR [12:31:27] Generating retention time mapping using 41498 points... [12:31:27] Enough data points (41498) to perform KDE alignment. [12:31:30] Enough data points (34925) to perform KDE alignment. [12:31:31] Enough data points (41498) to perform KDE alignment. [12:31:35] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt.unsorted [12:31:36] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:31:39] Sorted feature file in 2.71 seconds wall clock time [12:31:39] File size check: 49226785 vs 49226785 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt.unsorted [12:31:39] Executing [cmd /c C:\Windows\Temp\tmp610E.java\Percolator-v3-01-7860801589641226697.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt] [12:31:39] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:31:39] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:31:39] Written by Lukas Käll (lukall@u.washington.edu) in the [12:31:39] Department of Genome Sciences at the University of Washington. [12:31:39] Issued command: [12:31:39] C:\Windows\Temp\tmp610E.java\Percolator-v3-01-7860801589641226697.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:31:39] Started Wed Jul 17 12:31:39 2024 [12:31:39] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [12:31:39] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [12:31:39] Features: [12:31:39] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:31:40] Found 121360 PSMs [12:31:40] Separate target and decoy search inputs detected, using mix-max method. [12:31:40] Train/test set contains 60681 positives and 60679 negatives, size ratio=1.00003 and pi0=1 [12:31:40] Selecting Cpos by cross-validation. [12:31:40] Selecting Cneg by cross-validation. [12:31:41] Split 1: Selected feature 3 as initial search direction. Could separate 14927 training set positives in that direction. [12:31:41] Split 2: Selected feature 3 as initial search direction. Could separate 14762 training set positives in that direction. [12:31:42] Split 3: Selected feature 3 as initial search direction. Could separate 15386 training set positives in that direction. [12:31:42] Found 22649 test set positives with q<0.01 in initial direction [12:31:42] Reading in data and feature calculation took 2.887 cpu seconds or 3 seconds wall clock time. [12:31:42] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:31:47] Iteration 1: Estimated 37971 PSMs with q<0.01 [12:31:57] Iteration 2: Estimated 42935 PSMs with q<0.01 [12:32:10] Iteration 3: Estimated 44269 PSMs with q<0.01 [12:32:24] Iteration 4: Estimated 44786 PSMs with q<0.01 [12:32:39] Iteration 5: Estimated 44895 PSMs with q<0.01 [12:32:53] Iteration 6: Estimated 44893 PSMs with q<0.01 [12:33:08] Iteration 7: Estimated 44909 PSMs with q<0.01 [12:33:22] Iteration 8: Estimated 44919 PSMs with q<0.01 [12:33:36] Iteration 9: Estimated 44921 PSMs with q<0.01 [12:33:51] Iteration 10: Estimated 44923 PSMs with q<0.01 [12:33:51] Learned normalized SVM weights for the 3 cross-validation splits: [12:33:51] Split1 Split2 Split3 FeatureName [12:33:51] -0.4702 -0.4956 -0.6973 primary [12:33:51] -0.2234 -0.2852 -0.2552 xCorrLib [12:33:51] 0.7739 0.8414 0.8373 xCorrModel [12:33:51] -0.6099 -0.6580 -0.0502 dotProduct [12:33:51] 1.0790 1.1035 0.6900 contrastAngle [12:33:51] 0.0098 0.0267 0.2238 logit [12:33:51] -0.8195 -0.8189 -0.6645 sumOfSquaredErrors [12:33:51] 1.1709 1.1302 1.4007 numberOfMatchingPeaks [12:33:51] -0.0086 0.0044 -0.0415 numberOfMatchingPeaksAboveThreshold [12:33:51] 0.0094 0.0357 0.0169 averageFragmentDeltaMasses [12:33:51] -0.1582 -0.2281 -0.1004 isotopeDotProduct [12:33:51] -0.1312 -0.1231 -0.1159 averageParentDeltaMass [12:33:51] -0.0109 -0.0541 -0.0054 percentBlankOverMono [12:33:51] -0.1165 -0.0160 -0.1185 numberPrecursorMatch [12:33:51] -1.1923 -1.1968 -1.2348 lnSp [12:33:51] 0.1680 0.2108 0.1981 maxLadderLength [12:33:51] 0.0037 0.0126 0.0289 evalue [12:33:51] 0.3470 0.2810 0.3008 correlationToGaussian [12:33:51] -0.0584 -0.0039 -0.0402 correlationToPrecursor [12:33:51] 0.1234 0.0217 0.1113 isIntegratedSignal [12:33:51] -0.0333 -0.0455 -0.0698 isIntegratedPrecursor [12:33:51] 0.5717 0.5751 0.5105 numPeaksWithGoodCorrelation [12:33:51] -41.2223 -40.8406 -41.6749 deltaRT [12:33:51] -0.1160 -0.0970 -0.0766 ms1MassError [12:33:51] 0.0252 0.0211 -0.0057 ms2MassError [12:33:51] -0.1013 -0.1224 -0.0962 numMissedCleavage [12:33:51] -0.2514 -0.2947 -0.3351 pepLength [12:33:51] 0.0000 0.0000 0.0000 charge1 [12:33:51] -0.1644 -0.1615 -0.1948 charge2 [12:33:51] 0.1644 0.1615 0.1948 charge3 [12:33:51] 0.0000 0.0000 0.0000 charge4 [12:33:51] 0.5016 0.4611 0.5805 precursorMz [12:33:51] -0.3981 -0.2542 -0.3967 precursorMass [12:33:51] -0.0816 -0.0678 -0.1043 RTinMin [12:33:51] -30.7993 -30.4231 -31.1778 m0 [12:33:51] Found 44871 test set PSMs with q<0.01. [12:33:51] Scoring full list of PSMs with trained SVMs. [12:33:51] Features: [12:33:51] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:33:52] Found 121360 PSMs [12:33:52] Evaluated set contained 60681 positives and 60679 negatives. [12:33:54] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:33:54] Selecting pi_0=0.232699 [12:33:54] Calculating q values. [12:33:54] New pi_0 estimate on final list yields 45338 target peptides with q<0.01. [12:33:54] Calculating posterior error probabilities (PEPs). [12:33:55] Processing took 133.5 cpu seconds or 133 seconds wall clock time. [12:33:57] Generating retention time mapping using 46980 points... [12:33:57] Enough data points (46980) to perform KDE alignment. [12:34:01] Enough data points (37588) to perform KDE alignment. [12:34:02] Enough data points (46980) to perform KDE alignment. [12:34:05] Writing elib result library... [12:34:05] Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML: Number of global peptides: 45338 vs local peptides: 45338 [12:34:05] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML... [12:34:05] Extracting Spectral Data for 45338 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML... [12:34:05] Number of global peptides: 45338 vs local peptides: 45338 [12:34:06] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:34:06] Parsed features and scores for 45338 peptides. [12:34:06] Extracting 45338 peptides... [12:34:06] Quant Extracting 396.4 to 400.4 m/z (7.328947 to 78.24973 min) [12:34:06] Quant Extracting 400.4 to 404.4 m/z (5.2280536 to 80.450294 min) [12:34:06] Quant Extracting 404.4 to 408.4 m/z (7.1349926 to 81.91802 min) [12:34:06] Quant Extracting 408.4 to 412.4 m/z (4.347999 to 81.57463 min) [12:34:06] Quant Extracting 412.4 to 416.4 m/z (5.8169026 to 87.00602 min) [12:34:06] Quant Extracting 416.4 to 420.4 m/z (5.962843 to 82.06273 min) [12:34:07] Quant Extracting 420.4 to 424.4 m/z (7.1362233 to 82.455894 min) [12:34:07] Quant Extracting 424.4 to 428.4 m/z (8.309397 to 85.09614 min) [12:34:07] Quant Extracting 428.4 to 432.4 m/z (7.1863046 to 83.33652 min) [12:34:07] Quant Extracting 432.4 to 436.4 m/z (7.136839 to 81.82189 min) [12:34:07] Quant Extracting 436.4 to 440.5 m/z (4.7881336 to 85.44085 min) [12:34:07] Quant Extracting 440.5 to 444.5 m/z (7.137454 to 85.24608 min) [12:34:07] Quant Extracting 444.5 to 448.5 m/z (7.1380696 to 87.251274 min) [12:34:07] Quant Extracting 448.5 to 452.5 m/z (4.252419 to 82.7516 min) [12:34:08] Quant Extracting 452.5 to 456.5 m/z (7.1386843 to 84.21843 min) [12:34:08] Quant Extracting 456.5 to 460.5 m/z (7.1386843 to 85.73672 min) [12:34:08] Quant Extracting 460.5 to 464.5 m/z (6.2133303 to 87.34935 min) [12:34:08] Quant Extracting 464.5 to 468.5 m/z (7.582532 to 87.25251 min) [12:34:08] Quant Extracting 468.5 to 472.5 m/z (7.139916 to 87.695335 min) [12:34:08] Quant Extracting 472.5 to 476.5 m/z (7.236676 to 88.42759 min) [12:34:08] Quant Extracting 476.5 to 480.5 m/z (7.3351045 to 88.08681 min) [12:34:08] Quant Extracting 480.5 to 484.5 m/z (5.7237997 to 88.18605 min) [12:34:09] Quant Extracting 484.5 to 488.5 m/z (7.1411467 to 90.82909 min) [12:34:09] Quant Extracting 488.5 to 492.5 m/z (7.1411467 to 86.470795 min) [12:34:09] Quant Extracting 492.5 to 496.5 m/z (6.6540403 to 86.57003 min) [12:34:09] Quant Extracting 496.5 to 500.5 m/z (7.1417623 to 89.11606 min) [12:34:09] Quant Extracting 500.5 to 504.5 m/z (7.1423717 to 88.52871 min) [12:34:09] Quant Extracting 504.5 to 508.5 m/z (7.1423717 to 92.2028 min) [12:34:09] Quant Extracting 508.5 to 512.5 m/z (7.143561 to 93.622604 min) [12:34:10] Quant Extracting 512.5 to 516.5 m/z (7.143561 to 86.915375 min) [12:34:10] Quant Extracting 516.5 to 520.5 m/z (7.144176 to 92.007965 min) [12:34:10] Quant Extracting 520.5 to 524.5 m/z (6.1668954 to 92.05587 min) [12:34:10] Quant Extracting 524.5 to 528.5 m/z (7.1447897 to 88.87586 min) [12:34:10] Quant Extracting 528.5 to 532.5 m/z (7.1447897 to 89.02234 min) [12:34:10] Quant Extracting 532.5 to 536.5 m/z (7.145404 to 93.576546 min) [12:34:10] Quant Extracting 536.5 to 540.5 m/z (7.145404 to 92.84078 min) [12:34:10] Quant Extracting 540.5 to 544.5 m/z (7.1460204 to 96.03242 min) [12:34:10] Quant Extracting 544.5 to 548.5 m/z (7.1460204 to 91.568146 min) [12:34:11] Quant Extracting 548.5 to 552.5 m/z (7.146635 to 96.62303 min) [12:34:11] Quant Extracting 552.5 to 556.5 m/z (7.146635 to 94.21754 min) [12:34:11] Quant Extracting 556.5 to 560.5 m/z (7.1472483 to 92.44984 min) [12:34:11] Quant Extracting 560.5 to 564.5 m/z (7.1472483 to 97.70389 min) [12:34:11] Quant Extracting 564.5 to 568.5 m/z (8.078052 to 92.89218 min) [12:34:11] Quant Extracting 568.5 to 572.5 m/z (7.147864 to 92.15818 min) [12:34:11] Quant Extracting 572.5 to 576.5 m/z (7.148479 to 92.451065 min) [12:34:11] Quant Extracting 576.5 to 580.5 m/z (7.148479 to 97.50968 min) [12:34:11] Quant Extracting 580.5 to 584.5 m/z (7.1490927 to 94.41734 min) [12:34:11] Quant Extracting 584.5 to 588.5 m/z (7.1490927 to 93.52951 min) [12:34:12] Quant Extracting 588.5 to 592.5 m/z (7.1497083 to 94.80885 min) [12:34:12] Quant Extracting 592.5 to 596.5 m/z (7.1497083 to 90.93631 min) [12:34:12] Quant Extracting 596.5 to 600.5 m/z (7.1503224 to 92.16064 min) [12:34:12] Quant Extracting 600.5 to 604.5 m/z (7.1503224 to 94.66538 min) [12:34:12] Quant Extracting 604.5 to 608.5 m/z (7.150938 to 97.018265 min) [12:34:12] Quant Extracting 608.5 to 612.5 m/z (10.070998 to 93.68135 min) [12:34:12] Quant Extracting 612.5 to 616.5 m/z (7.1515512 to 99.71741 min) [12:34:12] Quant Extracting 616.5 to 620.5 m/z (7.1515512 to 94.95889 min) [12:34:12] Quant Extracting 620.5 to 624.5 m/z (12.252651 to 96.23586 min) [12:34:12] Quant Extracting 624.5 to 628.5 m/z (7.152166 to 93.63121 min) [12:34:12] Quant Extracting 628.5 to 632.5 m/z (7.152781 to 96.13785 min) [12:34:13] Quant Extracting 632.5 to 636.5 m/z (8.91013 to 97.462616 min) [12:34:13] Quant Extracting 636.5 to 640.5 m/z (7.2022815 to 95.35468 min) [12:34:13] Quant Extracting 640.5 to 644.5 m/z (10.51048 to 96.873146 min) [12:34:13] Quant Extracting 644.5 to 648.5 m/z (9.299252 to 95.50002 min) [12:34:13] Quant Extracting 648.5 to 652.5 m/z (11.043232 to 96.285614 min) [12:34:13] Quant Extracting 652.5 to 656.5 m/z (7.1546264 to 95.69612 min) [12:34:13] Quant Extracting 656.5 to 660.6 m/z (14.485251 to 93.535034 min) [12:34:13] Quant Extracting 660.6 to 664.6 m/z (17.586748 to 93.14475 min) [12:34:13] Quant Extracting 664.6 to 668.6 m/z (15.599667 to 96.1882 min) [12:34:13] Quant Extracting 668.6 to 672.6 m/z (11.626722 to 95.061226 min) [12:34:13] Quant Extracting 672.6 to 676.6 m/z (7.155856 to 96.7297 min) [12:34:14] Quant Extracting 676.6 to 680.6 m/z (16.085264 to 98.34859 min) [12:34:14] Quant Extracting 680.6 to 684.6 m/z (9.49537 to 99.57643 min) [12:34:14] Quant Extracting 684.6 to 688.6 m/z (7.1570864 to 95.16108 min) [12:34:14] Quant Extracting 688.6 to 692.6 m/z (7.1570864 to 96.53548 min) [12:34:14] Quant Extracting 692.6 to 696.6 m/z (10.514171 to 100.758896 min) [12:34:14] Quant Extracting 696.6 to 700.6 m/z (7.450778 to 93.244 min) [12:34:14] Quant Extracting 700.6 to 704.6 m/z (10.175399 to 100.759514 min) [12:34:14] Quant Extracting 704.6 to 708.6 m/z (7.158316 to 100.02012 min) [12:34:14] Quant Extracting 708.6 to 712.6 m/z (7.1589303 to 96.144005 min) [12:34:14] Quant Extracting 712.6 to 716.6 m/z (12.356836 to 97.8142 min) [12:34:14] Quant Extracting 716.6 to 720.6 m/z (9.207964 to 100.11999 min) [12:34:15] Quant Extracting 720.6 to 724.6 m/z (13.470511 to 99.48268 min) [12:34:15] Quant Extracting 724.6 to 728.6 m/z (15.944275 to 94.966896 min) [12:34:15] Quant Extracting 728.6 to 732.6 m/z (7.1601605 to 94.576614 min) [12:34:15] Quant Extracting 732.6 to 736.6 m/z (14.878583 to 97.76469 min) [12:34:15] Quant Extracting 736.6 to 740.6 m/z (15.8486 to 100.76259 min) [12:34:15] Quant Extracting 740.6 to 744.6 m/z (8.968077 to 99.139015 min) [12:34:15] Quant Extracting 744.6 to 748.6 m/z (13.716105 to 99.190384 min) [12:34:15] Quant Extracting 748.6 to 752.6 m/z (21.034039 to 97.816666 min) [12:34:15] Quant Extracting 752.6 to 756.6 m/z (9.066119 to 95.75487 min) [12:34:15] Quant Extracting 756.6 to 760.6 m/z (18.368933 to 95.75487 min) [12:34:16] Quant Extracting 760.6 to 764.6 m/z (14.9282875 to 100.765 min) [12:34:16] Quant Extracting 764.6 to 768.6 m/z (12.021241 to 96.73703 min) [12:34:16] Quant Extracting 768.6 to 772.6 m/z (16.479643 to 99.48695 min) [12:34:16] Quant Extracting 772.6 to 776.6 m/z (12.021857 to 97.52502 min) [12:34:16] Quant Extracting 776.6 to 780.6 m/z (18.952425 to 98.015175 min) [12:34:16] Quant Extracting 780.6 to 784.6 m/z (19.922606 to 98.50474 min) [12:34:16] Quant Extracting 784.6 to 788.6 m/z (8.435163 to 97.572945 min) [12:34:16] Quant Extracting 788.6 to 792.6 m/z (13.331801 to 100.275475 min) [12:34:16] Quant Extracting 792.6 to 796.6 m/z (13.817175 to 95.75852 min) [12:34:16] Quant Extracting 796.6 to 800.6 m/z (14.787262 to 99.24199 min) [12:34:16] Quant Extracting 800.6 to 804.6 m/z (18.276405 to 96.591354 min) [12:34:16] Quant Extracting 804.6 to 808.6 m/z (16.579826 to 96.787445 min) [12:34:17] Quant Extracting 808.6 to 812.6 m/z (16.921045 to 95.66111 min) [12:34:17] Quant Extracting 812.6 to 816.6 m/z (13.139807 to 100.22599 min) [12:34:17] Quant Extracting 816.6 to 820.6 m/z (23.55852 to 98.1169 min) [12:34:17] Quant Extracting 820.6 to 824.6 m/z (14.110154 to 98.35965 min) [12:34:17] Quant Extracting 824.6 to 828.6 m/z (19.82908 to 100.76993 min) [12:34:17] Quant Extracting 828.6 to 832.6 m/z (25.548676 to 100.71862 min) [12:34:17] Quant Extracting 832.6 to 836.6 m/z (24.289629 to 97.824 min) [12:34:17] Quant Extracting 836.6 to 840.6 m/z (18.229223 to 100.77054 min) [12:34:17] Quant Extracting 840.6 to 844.6 m/z (10.863888 to 96.05637 min) [12:34:17] Quant Extracting 844.6 to 848.6 m/z (20.653831 to 98.65562 min) [12:34:18] Quant Extracting 848.6 to 852.6 m/z (14.450238 to 100.77177 min) [12:34:18] Quant Extracting 852.6 to 856.6 m/z (16.680305 to 96.056984 min) [12:34:18] Quant Extracting 856.6 to 860.6 m/z (23.173372 to 100.281006 min) [12:34:18] Quant Extracting 860.6 to 864.6 m/z (27.923979 to 98.75605 min) [12:34:18] Quant Extracting 864.6 to 868.6 m/z (21.867638 to 99.101524 min) [12:34:18] Quant Extracting 868.6 to 872.6 m/z (26.229845 to 96.30339 min) [12:34:18] Quant Extracting 872.6 to 876.6 m/z (25.696026 to 97.62981 min) [12:34:18] Quant Extracting 876.6 to 880.7 m/z (32.48147 to 100.62425 min) [12:34:18] Quant Extracting 880.7 to 884.7 m/z (31.75642 to 96.30401 min) [12:34:18] Quant Extracting 884.7 to 888.7 m/z (25.213312 to 96.69734 min) [12:34:18] Quant Extracting 888.7 to 892.7 m/z (28.653307 to 97.04099 min) [12:34:18] Quant Extracting 892.7 to 896.7 m/z (21.336178 to 100.724106 min) [12:34:18] Quant Extracting 896.7 to 900.7 m/z (19.44642 to 98.906685 min) [12:34:19] Quant Extracting 900.7 to 904.7 m/z (27.104462 to 99.544685 min) [12:34:19] Quant Extracting 904.7 to 908.7 m/z (26.426888 to 99.79149 min) [12:34:19] Quant Extracting 908.7 to 912.7 m/z (21.967468 to 98.85837 min) [12:34:19] Quant Extracting 912.7 to 916.7 m/z (28.315416 to 95.12813 min) [12:34:19] Quant Extracting 916.7 to 920.7 m/z (33.839294 to 95.62016 min) [12:34:19] Quant Extracting 920.7 to 924.7 m/z (37.328915 to 96.55387 min) [12:34:19] Quant Extracting 924.7 to 928.7 m/z (27.638708 to 99.10582 min) [12:34:19] Quant Extracting 928.7 to 932.7 m/z (9.952045 to 98.95641 min) [12:34:19] Quant Extracting 932.7 to 936.7 m/z (37.66937 to 96.9933 min) [12:34:19] Quant Extracting 936.7 to 940.7 m/z (37.37968 to 96.16241 min) [12:34:19] Quant Extracting 940.7 to 944.7 m/z (34.422894 to 97.78126 min) [12:34:19] Quant Extracting 944.7 to 948.7 m/z (18.190504 to 99.89323 min) [12:34:20] Quant Extracting 948.7 to 952.7 m/z (35.58675 to 100.485054 min) [12:34:20] Quant Extracting 952.7 to 956.7 m/z (36.120323 to 96.360916 min) [12:34:20] Quant Extracting 956.7 to 960.7 m/z (31.325203 to 95.23045 min) [12:34:20] Quant Extracting 960.7 to 964.7 m/z (39.559566 to 96.06559 min) [12:34:20] Quant Extracting 964.7 to 968.7 m/z (27.254078 to 98.911606 min) [12:34:20] Quant Extracting 968.7 to 972.7 m/z (29.385962 to 97.73583 min) [12:34:20] Quant Extracting 972.7 to 976.7 m/z (30.406843 to 98.029945 min) [12:34:20] Quant Extracting 976.7 to 980.7 m/z (28.997967 to 99.69839 min) [12:34:20] Quant Extracting 980.7 to 984.7 m/z (19.306505 to 98.27389 min) [12:34:20] Quant Extracting 984.7 to 988.7 m/z (41.066288 to 100.04221 min) [12:34:20] Quant Extracting 988.7 to 992.7 m/z (33.941765 to 96.75427 min) [12:34:20] Quant Extracting 992.7 to 996.7 m/z (38.690105 to 96.658066 min) [12:34:20] Quant Extracting 996.7 to 1000.7 m/z (42.084534 to 97.29419 min) [12:34:21] Quant Extracting 1000.7 to 1004.7 m/z (16.013647 to 95.03624 min) [12:34:21] Attempted extraction for: 45338, found 45338 [12:34:21] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML (45338 entries)... [12:34:21] Writing 45338 peptides to entries table... [12:34:25] Writing 45338 peptides to peptidequants table... [12:34:29] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:34:29 BST 2024 [12:34:29] Writing local target/decoy peptides: 45338/1717, pi0: 0.232699 [12:34:30] Writing local target/decoy proteins: 5637/56 [12:34:34] Finished analysis! 45338 peptides identified at 1.0% FDR (5.5 minutes) [12:34:34] Generating quantification library (3 of 5): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" [12:34:37] EncyclopeDIA version 2.12.30 [12:34:37] Getting count of protein accessions... [12:34:37] Using EncyclopeDIA 2.X Scoring System [12:34:37] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML ... [12:34:37] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML ... [12:34:38] Parsed 1% [12:34:38] Parsed 2% [12:34:38] Parsed 3% [12:34:39] Parsed 4% [12:34:39] Parsed 5% [12:34:40] Parsed 6% [12:34:40] Parsed 7% [12:34:41] Parsed 8% [12:34:42] Parsed 9% [12:34:42] Parsed 10% [12:34:43] Parsed 11% [12:34:44] Parsed 12% [12:34:45] Parsed 13% [12:34:47] Parsed 14% [12:34:48] Parsed 15% [12:34:50] Parsed 16% [12:34:53] Parsed 17% [12:34:54] Parsed 18% [12:34:55] Parsed 19% [12:34:56] Parsed 20% [12:34:57] Parsed 21% [12:34:58] Parsed 22% [12:35:00] Parsed 23% [12:35:01] Parsed 24% [12:35:02] Parsed 25% [12:35:03] Parsed 26% [12:35:04] Parsed 27% [12:35:06] Parsed 28% [12:35:07] Parsed 29% [12:35:09] Parsed 30% [12:35:11] Parsed 31% [12:35:16] Parsed 32% [12:35:20] Parsed 33% [12:35:26] Parsed 34% [12:35:34] Parsed 35% [12:35:35] Parsed 36% [12:35:36] Parsed 37% [12:35:37] Parsed 38% [12:35:40] Parsed 39% [12:35:43] Parsed 40% [12:35:47] Parsed 41% [12:35:51] Parsed 42% [12:35:56] Parsed 43% [12:36:02] Parsed 44% [12:36:08] Parsed 45% [12:36:14] Parsed 46% [12:36:15] Parsed 47% [12:36:17] Parsed 48% [12:36:20] Parsed 49% [12:36:23] Parsed 50% [12:36:28] Parsed 51% [12:36:33] Parsed 52% [12:36:37] Parsed 53% [12:36:42] Parsed 54% [12:36:48] Parsed 55% [12:36:54] Parsed 56% [12:37:00] Parsed 57% [12:37:07] Parsed 58% [12:37:15] Parsed 59% [12:37:23] Parsed 60% [12:37:30] Parsed 61% [12:37:39] Parsed 62% [12:37:50] Parsed 63% [12:38:09] Parsed 64% [12:38:19] Parsed 65% [12:38:20] Parsed 66% [12:38:22] Parsed 67% [12:38:25] Parsed 68% [12:38:29] Parsed 69% [12:38:34] Parsed 70% [12:38:38] Parsed 71% [12:38:44] Parsed 72% [12:38:50] Parsed 73% [12:38:57] Parsed 74% [12:39:03] Parsed 75% [12:39:11] Parsed 76% [12:39:18] Parsed 77% [12:39:27] Parsed 78% [12:39:36] Parsed 79% [12:39:56] Parsed 80% [12:39:57] Parsed 81% [12:39:59] Parsed 82% [12:40:01] Parsed 83% [12:40:06] Parsed 84% [12:40:11] Parsed 85% [12:40:16] Parsed 86% [12:40:21] Parsed 87% [12:40:26] Parsed 88% [12:40:32] Parsed 89% [12:40:38] Parsed 90% [12:40:44] Parsed 91% [12:40:50] Parsed 92% [12:40:56] Parsed 93% [12:41:03] Parsed 94% [12:41:11] Parsed 95% [12:41:19] Parsed 96% [12:41:26] Parsed 97% [12:41:35] Parsed 98% [12:41:39] Parsed 99% [12:41:46] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.dia ... [12:41:47] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.dia! [12:41:47] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML [12:41:47] Library File: UP000005640_9606-z3_nce27.elib [12:41:47] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.elib [12:41:47] Parameters: [12:41:47] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [12:41:47] Converting files... [12:41:47] Calculating features... [12:41:47] Processing precursors scans... [12:41:47] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt.unsorted [12:41:47] Processing 396.4 to 400.4 m/z, (5.854342 second duty cycle) [12:41:47] 67 peptides remaining for 396.4 to 400.4... [12:41:48] 67 peptides remaining for 396.4 to 400.4... [12:41:48] Processing 400.4 to 404.4 m/z, (2.927168 second duty cycle) [12:41:49] 201 peptides remaining for 400.4 to 404.4... [12:41:49] 0 peptides remaining for 400.4 to 404.4... [12:41:50] Processing 404.4 to 408.4 m/z, (2.927168 second duty cycle) [12:41:50] 231 peptides remaining for 404.4 to 408.4... [12:41:50] Processing 408.4 to 412.4 m/z, (2.9271681 second duty cycle) [12:41:50] 286 peptides remaining for 408.4 to 412.4... [12:41:51] Processing 412.4 to 416.4 m/z, (2.9271681 second duty cycle) [12:41:51] 294 peptides remaining for 412.4 to 416.4... [12:41:52] Processing 416.4 to 420.4 m/z, (2.9271677 second duty cycle) [12:41:52] 302 peptides remaining for 416.4 to 420.4... [12:41:52] Processing 420.4 to 424.4 m/z, (2.9271677 second duty cycle) [12:41:53] 321 peptides remaining for 420.4 to 424.4... [12:41:53] Processing 424.4 to 428.4 m/z, (2.927168 second duty cycle) [12:41:53] 304 peptides remaining for 424.4 to 428.4... [12:41:54] Processing 428.4 to 432.4 m/z, (2.9271677 second duty cycle) [12:41:54] 366 peptides remaining for 428.4 to 432.4... [12:41:54] Processing 432.4 to 436.4 m/z, (2.9271677 second duty cycle) [12:41:54] 377 peptides remaining for 432.4 to 436.4... [12:41:55] Processing 436.4 to 440.5 m/z, (2.927168 second duty cycle) [12:41:55] 519 peptides remaining for 436.4 to 440.5... [12:41:56] Processing 440.5 to 444.5 m/z, (2.9271677 second duty cycle) [12:41:56] 473 peptides remaining for 440.5 to 444.5... [12:41:56] Processing 444.5 to 448.5 m/z, (2.9271677 second duty cycle) [12:41:56] 368 peptides remaining for 444.5 to 448.5... [12:41:57] Processing 448.5 to 452.5 m/z, (2.9271677 second duty cycle) [12:41:57] 454 peptides remaining for 448.5 to 452.5... [12:41:57] Processing 452.5 to 456.5 m/z, (2.927168 second duty cycle) [12:41:58] 417 peptides remaining for 452.5 to 456.5... [12:41:58] Processing 456.5 to 460.5 m/z, (2.927168 second duty cycle) [12:41:58] 509 peptides remaining for 456.5 to 460.5... [12:41:59] Processing 460.5 to 464.5 m/z, (2.927168 second duty cycle) [12:41:59] 491 peptides remaining for 460.5 to 464.5... [12:41:59] Processing 464.5 to 468.5 m/z, (2.9271677 second duty cycle) [12:42:00] 604 peptides remaining for 464.5 to 468.5... [12:42:00] Processing 468.5 to 472.5 m/z, (2.927168 second duty cycle) [12:42:00] 496 peptides remaining for 468.5 to 472.5... [12:42:01] Processing 472.5 to 476.5 m/z, (2.927168 second duty cycle) [12:42:01] 498 peptides remaining for 472.5 to 476.5... [12:42:01] Processing 476.5 to 480.5 m/z, (2.9271677 second duty cycle) [12:42:02] 500 peptides remaining for 476.5 to 480.5... [12:42:02] Processing 480.5 to 484.5 m/z, (2.9271736 second duty cycle) [12:42:02] 578 peptides remaining for 480.5 to 484.5... [12:42:03] Processing 484.5 to 488.5 m/z, (2.9271736 second duty cycle) [12:42:03] 511 peptides remaining for 484.5 to 488.5... [12:42:03] Processing 488.5 to 492.5 m/z, (2.9271133 second duty cycle) [12:42:04] 475 peptides remaining for 488.5 to 492.5... [12:42:04] Processing 492.5 to 496.5 m/z, (2.9271302 second duty cycle) [12:42:04] 544 peptides remaining for 492.5 to 496.5... [12:42:05] 26 peptides remaining for 492.5 to 496.5... [12:42:05] Processing 496.5 to 500.5 m/z, (2.927113 second duty cycle) [12:42:05] 698 peptides remaining for 496.5 to 500.5... [12:42:06] Processing 500.5 to 504.5 m/z, (2.9271302 second duty cycle) [12:42:06] 847 peptides remaining for 500.5 to 504.5... [12:42:07] Processing 504.5 to 508.5 m/z, (2.927113 second duty cycle) [12:42:07] 486 peptides remaining for 504.5 to 508.5... [12:42:07] Processing 508.5 to 512.5 m/z, (2.9271462 second duty cycle) [12:42:07] 634 peptides remaining for 508.5 to 512.5... [12:42:08] Processing 512.5 to 516.5 m/z, (2.9271293 second duty cycle) [12:42:08] 586 peptides remaining for 512.5 to 516.5... [12:42:09] Processing 516.5 to 520.5 m/z, (2.9271462 second duty cycle) [12:42:09] 533 peptides remaining for 516.5 to 520.5... [12:42:09] Processing 520.5 to 524.5 m/z, (2.9271293 second duty cycle) [12:42:09] 594 peptides remaining for 520.5 to 524.5... [12:42:10] Processing 524.5 to 528.5 m/z, (2.9271462 second duty cycle) [12:42:10] 554 peptides remaining for 524.5 to 528.5... [12:42:11] Processing 528.5 to 532.5 m/z, (2.927129 second duty cycle) [12:42:11] 623 peptides remaining for 528.5 to 532.5... [12:42:11] Processing 532.5 to 536.5 m/z, (2.9271464 second duty cycle) [12:42:11] 514 peptides remaining for 532.5 to 536.5... [12:42:12] Processing 536.5 to 540.5 m/z, (2.9271295 second duty cycle) [12:42:12] 591 peptides remaining for 536.5 to 540.5... [12:42:13] Processing 540.5 to 544.5 m/z, (2.9271462 second duty cycle) [12:42:13] 592 peptides remaining for 540.5 to 544.5... [12:42:13] Processing 544.5 to 548.5 m/z, (2.9271293 second duty cycle) [12:42:13] 587 peptides remaining for 544.5 to 548.5... [12:42:14] Processing 548.5 to 552.5 m/z, (2.9271464 second duty cycle) [12:42:14] 582 peptides remaining for 548.5 to 552.5... [12:42:15] Processing 552.5 to 556.5 m/z, (2.9271295 second duty cycle) [12:42:15] 600 peptides remaining for 552.5 to 556.5... [12:42:15] Processing 556.5 to 560.5 m/z, (2.9271462 second duty cycle) [12:42:15] 603 peptides remaining for 556.5 to 560.5... [12:42:16] Processing 560.5 to 564.5 m/z, (2.9271293 second duty cycle) [12:42:16] 533 peptides remaining for 560.5 to 564.5... [12:42:17] Processing 564.5 to 568.5 m/z, (2.9271462 second duty cycle) [12:42:17] 675 peptides remaining for 564.5 to 568.5... [12:42:17] Processing 568.5 to 572.5 m/z, (2.9271293 second duty cycle) [12:42:17] 556 peptides remaining for 568.5 to 572.5... [12:42:18] Processing 572.5 to 576.5 m/z, (2.9271464 second duty cycle) [12:42:18] 618 peptides remaining for 572.5 to 576.5... [12:42:19] Processing 576.5 to 580.5 m/z, (2.9271295 second duty cycle) [12:42:19] 578 peptides remaining for 576.5 to 580.5... [12:42:19] Processing 580.5 to 584.5 m/z, (2.9271462 second duty cycle) [12:42:19] 570 peptides remaining for 580.5 to 584.5... [12:42:20] Processing 584.5 to 588.5 m/z, (2.9271293 second duty cycle) [12:42:20] 601 peptides remaining for 584.5 to 588.5... [12:42:21] Processing 588.5 to 592.5 m/z, (2.9271462 second duty cycle) [12:42:21] 517 peptides remaining for 588.5 to 592.5... [12:42:21] Processing 592.5 to 596.5 m/z, (2.9271293 second duty cycle) [12:42:21] 589 peptides remaining for 592.5 to 596.5... [12:42:22] Processing 596.5 to 600.5 m/z, (2.9271462 second duty cycle) [12:42:22] 749 peptides remaining for 596.5 to 600.5... [12:42:23] Processing 600.5 to 604.5 m/z, (2.927129 second duty cycle) [12:42:23] 823 peptides remaining for 600.5 to 604.5... [12:42:23] Processing 604.5 to 608.5 m/z, (2.9271462 second duty cycle) [12:42:23] 469 peptides remaining for 604.5 to 608.5... [12:42:24] Processing 608.5 to 612.5 m/z, (2.9271293 second duty cycle) [12:42:24] 506 peptides remaining for 608.5 to 612.5... [12:42:25] Processing 612.5 to 616.5 m/z, (2.9271464 second duty cycle) [12:42:25] 520 peptides remaining for 612.5 to 616.5... [12:42:25] Processing 616.5 to 620.5 m/z, (2.9271295 second duty cycle) [12:42:25] 455 peptides remaining for 616.5 to 620.5... [12:42:26] Processing 620.5 to 624.5 m/z, (2.9271462 second duty cycle) [12:42:26] 491 peptides remaining for 620.5 to 624.5... [12:42:27] Processing 624.5 to 628.5 m/z, (2.927129 second duty cycle) [12:42:27] 450 peptides remaining for 624.5 to 628.5... [12:42:27] Processing 628.5 to 632.5 m/z, (2.9271462 second duty cycle) [12:42:27] 475 peptides remaining for 628.5 to 632.5... [12:42:28] Processing 632.5 to 636.5 m/z, (2.9271293 second duty cycle) [12:42:28] 420 peptides remaining for 632.5 to 636.5... [12:42:29] Processing 636.5 to 640.5 m/z, (2.9271462 second duty cycle) [12:42:29] 483 peptides remaining for 636.5 to 640.5... [12:42:29] Processing 640.5 to 644.5 m/z, (2.927129 second duty cycle) [12:42:29] 415 peptides remaining for 640.5 to 644.5... [12:42:30] Processing 644.5 to 648.5 m/z, (2.9271462 second duty cycle) [12:42:30] 529 peptides remaining for 644.5 to 648.5... [12:42:31] Processing 648.5 to 652.5 m/z, (2.9271293 second duty cycle) [12:42:31] 419 peptides remaining for 648.5 to 652.5... [12:42:31] Processing 652.5 to 656.5 m/z, (2.9271462 second duty cycle) [12:42:31] 419 peptides remaining for 652.5 to 656.5... [12:42:32] Processing 656.5 to 660.6 m/z, (2.9271293 second duty cycle) [12:42:32] 431 peptides remaining for 656.5 to 660.6... [12:42:33] Processing 660.6 to 664.6 m/z, (2.9271462 second duty cycle) [12:42:33] 418 peptides remaining for 660.6 to 664.6... [12:42:33] Processing 664.6 to 668.6 m/z, (2.927129 second duty cycle) [12:42:34] 440 peptides remaining for 664.6 to 668.6... [12:42:34] Processing 668.6 to 672.6 m/z, (2.9271462 second duty cycle) [12:42:34] 434 peptides remaining for 668.6 to 672.6... [12:42:35] Processing 672.6 to 676.6 m/z, (2.927129 second duty cycle) [12:42:35] 455 peptides remaining for 672.6 to 676.6... [12:42:35] Processing 676.6 to 680.6 m/z, (2.9271462 second duty cycle) [12:42:36] 451 peptides remaining for 676.6 to 680.6... [12:42:36] Processing 680.6 to 684.6 m/z, (2.927129 second duty cycle) [12:42:36] 427 peptides remaining for 680.6 to 684.6... [12:42:37] Processing 684.6 to 688.6 m/z, (2.927146 second duty cycle) [12:42:37] 439 peptides remaining for 684.6 to 688.6... [12:42:37] Processing 688.6 to 692.6 m/z, (2.927129 second duty cycle) [12:42:38] 420 peptides remaining for 688.6 to 692.6... [12:42:38] Processing 692.6 to 696.6 m/z, (2.9271462 second duty cycle) [12:42:38] 448 peptides remaining for 692.6 to 696.6... [12:42:39] Processing 696.6 to 700.6 m/z, (2.927129 second duty cycle) [12:42:39] 558 peptides remaining for 696.6 to 700.6... [12:42:39] Processing 700.6 to 704.6 m/z, (2.927146 second duty cycle) [12:42:40] 670 peptides remaining for 700.6 to 704.6... [12:42:40] Processing 704.6 to 708.6 m/z, (2.927129 second duty cycle) [12:42:40] 393 peptides remaining for 704.6 to 708.6... [12:42:41] Processing 708.6 to 712.6 m/z, (2.927146 second duty cycle) [12:42:41] 410 peptides remaining for 708.6 to 712.6... [12:42:41] Processing 712.6 to 716.6 m/z, (2.927129 second duty cycle) [12:42:42] 417 peptides remaining for 712.6 to 716.6... [12:42:42] Processing 716.6 to 720.6 m/z, (2.927146 second duty cycle) [12:42:42] 368 peptides remaining for 716.6 to 720.6... [12:42:43] Processing 720.6 to 724.6 m/z, (2.927129 second duty cycle) [12:42:43] 371 peptides remaining for 720.6 to 724.6... [12:42:43] Processing 724.6 to 728.6 m/z, (2.927146 second duty cycle) [12:42:43] 372 peptides remaining for 724.6 to 728.6... [12:42:44] Processing 728.6 to 732.6 m/z, (2.9271288 second duty cycle) [12:42:44] 363 peptides remaining for 728.6 to 732.6... [12:42:45] Processing 732.6 to 736.6 m/z, (2.927146 second duty cycle) [12:42:45] 371 peptides remaining for 732.6 to 736.6... [12:42:45] Processing 736.6 to 740.6 m/z, (2.927129 second duty cycle) [12:42:45] 357 peptides remaining for 736.6 to 740.6... [12:42:46] Processing 740.6 to 744.6 m/z, (2.9271457 second duty cycle) [12:42:46] 332 peptides remaining for 740.6 to 744.6... [12:42:47] Processing 744.6 to 748.6 m/z, (2.9271288 second duty cycle) [12:42:47] 365 peptides remaining for 744.6 to 748.6... [12:42:47] Processing 748.6 to 752.6 m/z, (2.927146 second duty cycle) [12:42:47] 313 peptides remaining for 748.6 to 752.6... [12:42:48] Processing 752.6 to 756.6 m/z, (2.927129 second duty cycle) [12:42:48] 311 peptides remaining for 752.6 to 756.6... [12:42:49] Processing 756.6 to 760.6 m/z, (2.927146 second duty cycle) [12:42:49] 343 peptides remaining for 756.6 to 760.6... [12:42:49] Processing 760.6 to 764.6 m/z, (2.927113 second duty cycle) [12:42:49] 339 peptides remaining for 760.6 to 764.6... [12:42:50] Processing 764.6 to 768.6 m/z, (2.92713 second duty cycle) [12:42:50] 326 peptides remaining for 764.6 to 768.6... [12:42:50] Processing 768.6 to 772.6 m/z, (2.9271128 second duty cycle) [12:42:51] 313 peptides remaining for 768.6 to 772.6... [12:42:51] Processing 772.6 to 776.6 m/z, (2.92713 second duty cycle) [12:42:51] 315 peptides remaining for 772.6 to 776.6... [12:42:52] Processing 776.6 to 780.6 m/z, (2.927113 second duty cycle) [12:42:52] 294 peptides remaining for 776.6 to 780.6... [12:42:53] Processing 780.6 to 784.6 m/z, (2.92713 second duty cycle) [12:42:53] 290 peptides remaining for 780.6 to 784.6... [12:42:53] Processing 784.6 to 788.6 m/z, (2.9271128 second duty cycle) [12:42:53] 299 peptides remaining for 784.6 to 788.6... [12:42:54] Processing 788.6 to 792.6 m/z, (2.92713 second duty cycle) [12:42:54] 299 peptides remaining for 788.6 to 792.6... [12:42:55] Processing 792.6 to 796.6 m/z, (2.9271126 second duty cycle) [12:42:55] 281 peptides remaining for 792.6 to 796.6... [12:42:55] Processing 796.6 to 800.6 m/z, (2.9271297 second duty cycle) [12:42:55] 419 peptides remaining for 796.6 to 800.6... [12:42:56] Processing 800.6 to 804.6 m/z, (2.9271123 second duty cycle) [12:42:56] 411 peptides remaining for 800.6 to 804.6... [12:42:57] Processing 804.6 to 808.6 m/z, (2.92713 second duty cycle) [12:42:57] 236 peptides remaining for 804.6 to 808.6... [12:42:57] Processing 808.6 to 812.6 m/z, (2.9271126 second duty cycle) [12:42:57] 284 peptides remaining for 808.6 to 812.6... [12:42:58] Processing 812.6 to 816.6 m/z, (2.9271297 second duty cycle) [12:42:58] 242 peptides remaining for 812.6 to 816.6... [12:42:58] Processing 816.6 to 820.6 m/z, (2.9271123 second duty cycle) [12:42:59] 245 peptides remaining for 816.6 to 820.6... [12:42:59] Processing 820.6 to 824.6 m/z, (2.9271297 second duty cycle) [12:42:59] 236 peptides remaining for 820.6 to 824.6... [12:43:00] Processing 824.6 to 828.6 m/z, (2.9271123 second duty cycle) [12:43:00] 268 peptides remaining for 824.6 to 828.6... [12:43:00] Processing 828.6 to 832.6 m/z, (2.92713 second duty cycle) [12:43:01] 254 peptides remaining for 828.6 to 832.6... [12:43:01] Processing 832.6 to 836.6 m/z, (2.9271126 second duty cycle) [12:43:01] 225 peptides remaining for 832.6 to 836.6... [12:43:02] Processing 836.6 to 840.6 m/z, (2.9271297 second duty cycle) [12:43:02] 223 peptides remaining for 836.6 to 840.6... [12:43:02] Processing 840.6 to 844.6 m/z, (2.9271123 second duty cycle) [12:43:03] 236 peptides remaining for 840.6 to 844.6... [12:43:03] Processing 844.6 to 848.6 m/z, (2.92713 second duty cycle) [12:43:03] 234 peptides remaining for 844.6 to 848.6... [12:43:04] Processing 848.6 to 852.6 m/z, (2.9271126 second duty cycle) [12:43:04] 234 peptides remaining for 848.6 to 852.6... [12:43:04] Processing 852.6 to 856.6 m/z, (2.9271297 second duty cycle) [12:43:04] 193 peptides remaining for 852.6 to 856.6... [12:43:05] Processing 856.6 to 860.6 m/z, (2.9271123 second duty cycle) [12:43:05] 216 peptides remaining for 856.6 to 860.6... [12:43:06] Processing 860.6 to 864.6 m/z, (2.9271455 second duty cycle) [12:43:06] 185 peptides remaining for 860.6 to 864.6... [12:43:06] Processing 864.6 to 868.6 m/z, (2.9271286 second duty cycle) [12:43:06] 179 peptides remaining for 864.6 to 868.6... [12:43:07] Processing 868.6 to 872.6 m/z, (2.9271455 second duty cycle) [12:43:07] 180 peptides remaining for 868.6 to 872.6... [12:43:08] Processing 872.6 to 876.6 m/z, (2.9271283 second duty cycle) [12:43:08] 207 peptides remaining for 872.6 to 876.6... [12:43:08] Processing 876.6 to 880.7 m/z, (2.9271455 second duty cycle) [12:43:08] 159 peptides remaining for 876.6 to 880.7... [12:43:09] Processing 880.7 to 884.7 m/z, (2.9271283 second duty cycle) [12:43:09] 184 peptides remaining for 880.7 to 884.7... [12:43:10] Processing 884.7 to 888.7 m/z, (2.9271457 second duty cycle) [12:43:10] 152 peptides remaining for 884.7 to 888.7... [12:43:10] Processing 888.7 to 892.7 m/z, (2.9271286 second duty cycle) [12:43:10] 153 peptides remaining for 888.7 to 892.7... [12:43:11] Processing 892.7 to 896.7 m/z, (2.9271455 second duty cycle) [12:43:11] 149 peptides remaining for 892.7 to 896.7... [12:43:11] Processing 896.7 to 900.7 m/z, (2.9271286 second duty cycle) [12:43:12] 215 peptides remaining for 896.7 to 900.7... [12:43:12] Processing 900.7 to 904.7 m/z, (2.9271457 second duty cycle) [12:43:12] 222 peptides remaining for 900.7 to 904.7... [12:43:13] Processing 904.7 to 908.7 m/z, (2.9271286 second duty cycle) [12:43:13] 136 peptides remaining for 904.7 to 908.7... [12:43:13] Processing 908.7 to 912.7 m/z, (2.9271455 second duty cycle) [12:43:14] 160 peptides remaining for 908.7 to 912.7... [12:43:14] Processing 912.7 to 916.7 m/z, (2.9271283 second duty cycle) [12:43:14] 139 peptides remaining for 912.7 to 916.7... [12:43:15] Processing 916.7 to 920.7 m/z, (2.9271455 second duty cycle) [12:43:15] 137 peptides remaining for 916.7 to 920.7... [12:43:15] Processing 920.7 to 924.7 m/z, (2.9271288 second duty cycle) [12:43:16] 135 peptides remaining for 920.7 to 924.7... [12:43:16] Processing 924.7 to 928.7 m/z, (2.9271457 second duty cycle) [12:43:16] 132 peptides remaining for 924.7 to 928.7... [12:43:17] Processing 928.7 to 932.7 m/z, (2.9271286 second duty cycle) [12:43:17] 112 peptides remaining for 928.7 to 932.7... [12:43:17] Processing 932.7 to 936.7 m/z, (2.9271455 second duty cycle) [12:43:18] 104 peptides remaining for 932.7 to 936.7... [12:43:18] Processing 936.7 to 940.7 m/z, (2.9271286 second duty cycle) [12:43:18] 140 peptides remaining for 936.7 to 940.7... [12:43:19] Processing 940.7 to 944.7 m/z, (2.9271457 second duty cycle) [12:43:19] 106 peptides remaining for 940.7 to 944.7... [12:43:19] Processing 944.7 to 948.7 m/z, (2.9271288 second duty cycle) [12:43:20] 120 peptides remaining for 944.7 to 948.7... [12:43:20] Processing 948.7 to 952.7 m/z, (2.9271457 second duty cycle) [12:43:20] 149 peptides remaining for 948.7 to 952.7... [12:43:21] Processing 952.7 to 956.7 m/z, (2.9271286 second duty cycle) [12:43:21] 121 peptides remaining for 952.7 to 956.7... [12:43:21] Processing 956.7 to 960.7 m/z, (2.9271457 second duty cycle) [12:43:21] 137 peptides remaining for 956.7 to 960.7... [12:43:22] Processing 960.7 to 964.7 m/z, (2.9271286 second duty cycle) [12:43:22] 107 peptides remaining for 960.7 to 964.7... [12:43:23] Processing 964.7 to 968.7 m/z, (2.9271457 second duty cycle) [12:43:23] 120 peptides remaining for 964.7 to 968.7... [12:43:23] Processing 968.7 to 972.7 m/z, (2.9271286 second duty cycle) [12:43:23] 91 peptides remaining for 968.7 to 972.7... [12:43:24] Processing 972.7 to 976.7 m/z, (2.9271455 second duty cycle) [12:43:24] 83 peptides remaining for 972.7 to 976.7... [12:43:25] Processing 976.7 to 980.7 m/z, (2.9271288 second duty cycle) [12:43:25] 94 peptides remaining for 976.7 to 980.7... [12:43:25] Processing 980.7 to 984.7 m/z, (2.9271457 second duty cycle) [12:43:25] 65 peptides remaining for 980.7 to 984.7... [12:43:26] Processing 984.7 to 988.7 m/z, (2.9271288 second duty cycle) [12:43:26] 73 peptides remaining for 984.7 to 988.7... [12:43:27] Processing 988.7 to 992.7 m/z, (2.9271455 second duty cycle) [12:43:27] 95 peptides remaining for 988.7 to 992.7... [12:43:27] Processing 992.7 to 996.7 m/z, (2.9271288 second duty cycle) [12:43:27] 82 peptides remaining for 992.7 to 996.7... [12:43:28] Processing 996.7 to 1000.7 m/z, (2.9271457 second duty cycle) [12:43:28] 55 peptides remaining for 996.7 to 1000.7... [12:43:28] Processing 1000.7 to 1004.7 m/z, (5.8543415 second duty cycle) [12:43:29] 20 peptides remaining for 1000.7 to 1004.7... [12:43:29] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:43:32] Sorted feature file in 3.32 seconds wall clock time [12:43:32] File size check: 56358282 vs 56358282 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt.unsorted [12:43:32] 148933 total peptides processed. [12:43:32] Running Percolator... [12:43:32] Executing [cmd /c C:\Windows\Temp\tmpC830.java\Percolator-v3-01-1822678182455841233.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt] [12:43:33] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:43:33] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:43:33] Written by Lukas Käll (lukall@u.washington.edu) in the [12:43:33] Department of Genome Sciences at the University of Washington. [12:43:33] Issued command: [12:43:33] C:\Windows\Temp\tmpC830.java\Percolator-v3-01-1822678182455841233.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:43:33] Started Wed Jul 17 12:43:33 2024 [12:43:33] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [12:43:33] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:43:33] Features: [12:43:33] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:43:34] Found 148933 PSMs [12:43:34] Separate target and decoy search inputs detected, using mix-max method. [12:43:34] Train/test set contains 80306 positives and 68627 negatives, size ratio=1.17018 and pi0=1 [12:43:34] Warning: The mix-max procedure is not well behaved when # targets (80306) != # decoys (68627). Consider using target-decoy competition (-Y flag). [12:43:34] Selecting Cpos by cross-validation. [12:43:34] Selecting Cneg by cross-validation. [12:43:35] Split 1: Selected feature 3 as initial search direction. Could separate 15923 training set positives in that direction. [12:43:36] Split 2: Selected feature 3 as initial search direction. Could separate 15691 training set positives in that direction. [12:43:36] Split 3: Selected feature 3 as initial search direction. Could separate 15401 training set positives in that direction. [12:43:36] Found 23347 test set positives with q<0.01 in initial direction [12:43:36] Reading in data and feature calculation took 3.544 cpu seconds or 3 seconds wall clock time. [12:43:36] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:43:43] Iteration 1: Estimated 34820 PSMs with q<0.01 [12:43:51] Iteration 2: Estimated 38366 PSMs with q<0.01 [12:44:01] Iteration 3: Estimated 39292 PSMs with q<0.01 [12:44:01] Learned normalized SVM weights for the 3 cross-validation splits: [12:44:01] Split1 Split2 Split3 FeatureName [12:44:01] -0.7557 -0.9469 -0.7826 primary [12:44:01] -0.0709 -0.0480 -0.0813 xCorrLib [12:44:01] 1.2849 1.2726 1.3436 xCorrModel [12:44:01] -1.3214 -1.4426 -1.5226 dotProduct [12:44:01] 1.9429 1.9828 2.2339 contrastAngle [12:44:01] -0.4324 -0.4054 -0.6765 logit [12:44:01] -1.1378 -1.2323 -1.1298 sumOfSquaredErrors [12:44:01] 1.4409 1.6739 1.5221 numberOfMatchingPeaks [12:44:01] 0.0174 -0.0236 -0.0213 numberOfMatchingPeaksAboveThreshold [12:44:01] -0.0047 -0.0069 -0.0238 averageFragmentDeltaMasses [12:44:01] 0.2794 0.1590 0.3905 isotopeDotProduct [12:44:01] 0.0562 0.0356 0.0017 averageParentDeltaMass [12:44:01] 0.0582 0.0296 0.1056 percentBlankOverMono [12:44:01] -0.0394 0.0544 -0.1793 numberPrecursorMatch [12:44:01] -1.1579 -1.1298 -1.1231 lnSp [12:44:01] 0.1373 0.1254 0.0666 maxLadderLength [12:44:01] -0.0584 -0.0197 -0.0241 evalue [12:44:01] 0.2032 0.3168 0.2182 correlationToGaussian [12:44:01] 0.2377 0.1364 0.2328 correlationToPrecursor [12:44:01] 0.1131 0.0900 0.0943 isIntegratedSignal [12:44:01] -0.0066 0.0229 -0.0058 isIntegratedPrecursor [12:44:01] 0.7874 0.7343 0.7469 numPeaksWithGoodCorrelation [12:44:01] -0.1039 -0.1055 -0.1061 numMissedCleavage [12:44:01] -0.4394 -0.4911 -0.5516 pepLength [12:44:01] 0.0000 0.0000 0.0000 charge1 [12:44:01] -0.1592 -0.1813 -0.1071 charge2 [12:44:01] 0.1592 0.1813 0.1071 charge3 [12:44:01] 0.0000 0.0000 0.0000 charge4 [12:44:01] 0.6696 0.7008 0.5235 precursorMz [12:44:01] -0.1654 -0.1835 0.1125 precursorMass [12:44:01] -0.1651 -0.1421 -0.1102 RTinMin [12:44:01] -1.8947 -1.9177 -1.9031 m0 [12:44:01] Found 39282 test set PSMs with q<0.01. [12:44:01] Scoring full list of PSMs with trained SVMs. [12:44:01] Features: [12:44:01] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:44:02] Found 148933 PSMs [12:44:02] Evaluated set contained 80306 positives and 68627 negatives. [12:44:04] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:44:04] Selecting pi_0=0.202997 [12:44:04] Calculating q values. [12:44:04] New pi_0 estimate on final list yields 40392 target peptides with q<0.01. [12:44:04] Calculating posterior error probabilities (PEPs). [12:44:05] Processing took 28.73 cpu seconds or 29 seconds wall clock time. [12:44:07] First pass: 40392 peptides identified at 1.0% FDR [12:44:07] Generating retention time mapping using 41853 points... [12:44:07] Enough data points (41853) to perform KDE alignment. [12:44:10] Enough data points (35283) to perform KDE alignment. [12:44:11] Enough data points (41853) to perform KDE alignment. [12:44:15] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt.unsorted [12:44:16] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:44:19] Sorted feature file in 2.82 seconds wall clock time [12:44:19] File size check: 49495836 vs 49495836 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt.unsorted [12:44:19] Executing [cmd /c C:\Windows\Temp\tmpC830.java\Percolator-v3-01-298456220879584324.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt] [12:44:19] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:44:19] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:44:19] Written by Lukas Käll (lukall@u.washington.edu) in the [12:44:19] Department of Genome Sciences at the University of Washington. [12:44:19] Issued command: [12:44:19] C:\Windows\Temp\tmpC830.java\Percolator-v3-01-298456220879584324.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:44:19] Started Wed Jul 17 12:44:19 2024 [12:44:19] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [12:44:19] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [12:44:19] Features: [12:44:19] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:44:20] Found 121360 PSMs [12:44:20] Separate target and decoy search inputs detected, using mix-max method. [12:44:20] Train/test set contains 60681 positives and 60679 negatives, size ratio=1.00003 and pi0=1 [12:44:21] Selecting Cpos by cross-validation. [12:44:21] Selecting Cneg by cross-validation. [12:44:21] Split 1: Selected feature 3 as initial search direction. Could separate 15591 training set positives in that direction. [12:44:22] Split 2: Selected feature 3 as initial search direction. Could separate 15517 training set positives in that direction. [12:44:22] Split 3: Selected feature 3 as initial search direction. Could separate 15355 training set positives in that direction. [12:44:22] Found 23170 test set positives with q<0.01 in initial direction [12:44:22] Reading in data and feature calculation took 2.843 cpu seconds or 3 seconds wall clock time. [12:44:22] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:44:27] Iteration 1: Estimated 37204 PSMs with q<0.01 [12:44:37] Iteration 2: Estimated 43309 PSMs with q<0.01 [12:44:51] Iteration 3: Estimated 44920 PSMs with q<0.01 [12:45:05] Iteration 4: Estimated 45362 PSMs with q<0.01 [12:45:19] Iteration 5: Estimated 45418 PSMs with q<0.01 [12:45:33] Iteration 6: Estimated 45421 PSMs with q<0.01 [12:45:48] Iteration 7: Estimated 45403 PSMs with q<0.01 [12:46:02] Iteration 8: Estimated 45410 PSMs with q<0.01 [12:46:17] Iteration 9: Estimated 45417 PSMs with q<0.01 [12:46:31] Iteration 10: Estimated 45414 PSMs with q<0.01 [12:46:31] Learned normalized SVM weights for the 3 cross-validation splits: [12:46:31] Split1 Split2 Split3 FeatureName [12:46:31] -0.6759 -0.6454 -0.7666 primary [12:46:31] -0.2701 -0.2289 -0.2128 xCorrLib [12:46:31] 0.9264 0.8305 0.7738 xCorrModel [12:46:31] -0.5439 -0.4722 -0.1302 dotProduct [12:46:31] 1.2240 1.0602 0.9089 contrastAngle [12:46:31] -0.1290 -0.1167 0.0217 logit [12:46:31] -0.6663 -0.8354 -0.5373 sumOfSquaredErrors [12:46:31] 1.4097 1.3041 1.4207 numberOfMatchingPeaks [12:46:31] -0.0017 -0.0093 0.0054 numberOfMatchingPeaksAboveThreshold [12:46:31] -0.0032 -0.0147 -0.0190 averageFragmentDeltaMasses [12:46:31] -0.1399 -0.1004 -0.0618 isotopeDotProduct [12:46:31] -0.0715 -0.1113 -0.0753 averageParentDeltaMass [12:46:31] -0.0047 -0.0123 0.0181 percentBlankOverMono [12:46:31] -0.1031 -0.0667 -0.1574 numberPrecursorMatch [12:46:31] -1.2914 -1.1967 -1.2084 lnSp [12:46:31] 0.1794 0.2116 0.1950 maxLadderLength [12:46:31] 0.0232 0.0544 0.0205 evalue [12:46:31] 0.4367 0.4074 0.3811 correlationToGaussian [12:46:31] 0.0452 0.0194 0.0688 correlationToPrecursor [12:46:31] 0.1745 0.1645 0.0955 isIntegratedSignal [12:46:31] -0.1155 -0.1043 -0.1672 isIntegratedPrecursor [12:46:31] 0.4885 0.5589 0.5173 numPeaksWithGoodCorrelation [12:46:31] -35.9618 -37.5567 -38.4373 deltaRT [12:46:31] -0.1263 -0.0197 -0.0934 ms1MassError [12:46:31] -0.0075 0.0196 0.0057 ms2MassError [12:46:31] -0.1346 -0.1498 -0.1317 numMissedCleavage [12:46:31] -0.4586 -0.2489 -0.4349 pepLength [12:46:31] 0.0000 0.0000 0.0000 charge1 [12:46:31] -0.1858 -0.2600 -0.1822 charge2 [12:46:31] 0.1858 0.2600 0.1822 charge3 [12:46:31] 0.0000 0.0000 0.0000 charge4 [12:46:31] 0.5205 0.6979 0.5228 precursorMz [12:46:31] -0.2912 -0.6908 -0.2503 precursorMass [12:46:31] -0.1207 -0.0636 -0.1296 RTinMin [12:46:31] -26.4266 -27.9721 -28.5819 m0 [12:46:31] Found 45282 test set PSMs with q<0.01. [12:46:31] Scoring full list of PSMs with trained SVMs. [12:46:31] Features: [12:46:31] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:46:33] Found 121360 PSMs [12:46:33] Evaluated set contained 60681 positives and 60679 negatives. [12:46:34] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:46:34] Selecting pi_0=0.223611 [12:46:34] Calculating q values. [12:46:34] New pi_0 estimate on final list yields 45813 target peptides with q<0.01. [12:46:34] Calculating posterior error probabilities (PEPs). [12:46:36] Processing took 133.6 cpu seconds or 134 seconds wall clock time. [12:46:38] Generating retention time mapping using 47449 points... [12:46:38] Enough data points (47449) to perform KDE alignment. [12:46:41] Enough data points (37851) to perform KDE alignment. [12:46:42] Enough data points (47449) to perform KDE alignment. [12:46:45] Writing elib result library... [12:46:46] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML: Number of global peptides: 45813 vs local peptides: 45813 [12:46:46] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML... [12:46:46] Extracting Spectral Data for 45813 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML... [12:46:46] Number of global peptides: 45813 vs local peptides: 45813 [12:46:46] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:46:46] Parsed features and scores for 45813 peptides. [12:46:46] Extracting 45813 peptides... [12:46:46] Quant Extracting 396.4 to 400.4 m/z (7.2311535 to 77.24618 min) [12:46:46] Quant Extracting 400.4 to 404.4 m/z (5.2279234 to 80.32585 min) [12:46:46] Quant Extracting 404.4 to 408.4 m/z (7.1844788 to 81.84077 min) [12:46:47] Quant Extracting 408.4 to 412.4 m/z (4.349891 to 81.54688 min) [12:46:47] Quant Extracting 412.4 to 416.4 m/z (5.816812 to 86.884995 min) [12:46:47] Quant Extracting 416.4 to 420.4 m/z (6.0128803 to 82.03674 min) [12:46:47] Quant Extracting 420.4 to 424.4 m/z (7.1857038 to 85.41554 min) [12:46:47] Quant Extracting 424.4 to 428.4 m/z (7.232999 to 84.97349 min) [12:46:47] Quant Extracting 428.4 to 432.4 m/z (7.186314 to 83.21375 min) [12:46:47] Quant Extracting 432.4 to 436.4 m/z (7.3312936 to 81.74403 min) [12:46:47] Quant Extracting 436.4 to 440.5 m/z (7.137438 to 85.31819 min) [12:46:48] Quant Extracting 440.5 to 444.5 m/z (7.137438 to 85.22202 min) [12:46:48] Quant Extracting 444.5 to 448.5 m/z (7.823253 to 87.08284 min) [12:46:48] Quant Extracting 448.5 to 452.5 m/z (4.3010325 to 83.46231 min) [12:46:48] Quant Extracting 452.5 to 456.5 m/z (7.138669 to 84.14525 min) [12:46:48] Quant Extracting 456.5 to 460.5 m/z (7.1887603 to 85.61388 min) [12:46:48] Quant Extracting 460.5 to 464.5 m/z (6.2114167 to 87.230034 min) [12:46:48] Quant Extracting 464.5 to 468.5 m/z (7.2870383 to 87.183334 min) [12:46:48] Quant Extracting 468.5 to 472.5 m/z (8.020196 to 100.76267 min) [12:46:48] Quant Extracting 472.5 to 476.5 m/z (7.1899843 to 88.30833 min) [12:46:48] Quant Extracting 476.5 to 480.5 m/z (7.386142 to 87.91617 min) [12:46:49] Quant Extracting 480.5 to 484.5 m/z (5.7237163 to 88.11166 min) [12:46:49] Quant Extracting 484.5 to 488.5 m/z (7.1411266 to 90.80837 min) [12:46:49] Quant Extracting 488.5 to 492.5 m/z (7.191216 to 86.34973 min) [12:46:49] Quant Extracting 492.5 to 496.5 m/z (6.7507873 to 86.40166 min) [12:46:49] Quant Extracting 496.5 to 500.5 m/z (7.1417418 to 89.04692 min) [12:46:49] Quant Extracting 500.5 to 504.5 m/z (7.142352 to 88.4076 min) [12:46:49] Quant Extracting 504.5 to 508.5 m/z (7.142352 to 92.08347 min) [12:46:49] Quant Extracting 508.5 to 512.5 m/z (7.1435413 to 93.50322 min) [12:46:49] Quant Extracting 512.5 to 516.5 m/z (7.1435413 to 92.524124 min) [12:46:49] Quant Extracting 516.5 to 520.5 m/z (7.1930623 to 91.93653 min) [12:46:49] Quant Extracting 520.5 to 524.5 m/z (6.166783 to 90.17379 min) [12:46:50] Quant Extracting 524.5 to 528.5 m/z (7.1447735 to 91.54438 min) [12:46:50] Quant Extracting 528.5 to 532.5 m/z (7.1447735 to 88.90127 min) [12:46:50] Quant Extracting 532.5 to 536.5 m/z (7.1453867 to 93.50506 min) [12:46:50] Quant Extracting 536.5 to 540.5 m/z (7.1453867 to 92.67417 min) [12:46:50] Quant Extracting 540.5 to 544.5 m/z (7.1460032 to 95.9111 min) [12:46:50] Quant Extracting 544.5 to 548.5 m/z (7.1460032 to 91.49833 min) [12:46:50] Quant Extracting 548.5 to 552.5 m/z (7.146619 to 96.59864 min) [12:46:50] Quant Extracting 552.5 to 556.5 m/z (7.146619 to 94.14768 min) [12:46:50] Quant Extracting 556.5 to 560.5 m/z (7.147234 to 87.7764 min) [12:46:50] Quant Extracting 560.5 to 564.5 m/z (7.147234 to 97.67766 min) [12:46:50] Quant Extracting 564.5 to 568.5 m/z (7.1478496 to 92.82255 min) [12:46:51] Quant Extracting 568.5 to 572.5 m/z (7.1478496 to 92.13567 min) [12:46:51] Quant Extracting 572.5 to 576.5 m/z (7.148465 to 92.48116 min) [12:46:51] Quant Extracting 576.5 to 580.5 m/z (7.148465 to 97.4816 min) [12:46:51] Quant Extracting 580.5 to 584.5 m/z (7.1490803 to 94.29606 min) [12:46:51] Quant Extracting 584.5 to 588.5 m/z (7.1490803 to 93.313324 min) [12:46:51] Quant Extracting 588.5 to 592.5 m/z (7.149696 to 94.73837 min) [12:46:51] Quant Extracting 592.5 to 596.5 m/z (7.149696 to 92.62711 min) [12:46:51] Quant Extracting 596.5 to 600.5 m/z (7.1503186 to 92.09023 min) [12:46:51] Quant Extracting 600.5 to 604.5 m/z (7.1503186 to 94.34681 min) [12:46:51] Quant Extracting 604.5 to 608.5 m/z (7.1509337 to 96.9431 min) [12:46:52] Quant Extracting 608.5 to 612.5 m/z (7.1509337 to 93.66064 min) [12:46:52] Quant Extracting 612.5 to 616.5 m/z (7.1515493 to 99.59604 min) [12:46:52] Quant Extracting 616.5 to 620.5 m/z (7.1515493 to 94.936295 min) [12:46:52] Quant Extracting 620.5 to 624.5 m/z (12.2998295 to 95.57237 min) [12:46:52] Quant Extracting 624.5 to 628.5 m/z (7.1521635 to 93.511826 min) [12:46:52] Quant Extracting 628.5 to 632.5 m/z (7.152779 to 96.01468 min) [12:46:52] Quant Extracting 632.5 to 636.5 m/z (9.103128 to 97.29044 min) [12:46:52] Quant Extracting 636.5 to 640.5 m/z (7.39845 to 95.37816 min) [12:46:52] Quant Extracting 640.5 to 644.5 m/z (10.509336 to 96.75011 min) [12:46:52] Quant Extracting 644.5 to 648.5 m/z (9.250189 to 92.828705 min) [12:46:52] Quant Extracting 648.5 to 652.5 m/z (11.139043 to 96.1152 min) [12:46:53] Quant Extracting 652.5 to 656.5 m/z (7.1546264 to 95.62559 min) [12:46:53] Quant Extracting 656.5 to 660.6 m/z (14.629488 to 95.0853 min) [12:46:53] Quant Extracting 660.6 to 664.6 m/z (17.53725 to 93.124016 min) [12:46:53] Quant Extracting 664.6 to 668.6 m/z (7.155241 to 96.01775 min) [12:46:53] Quant Extracting 668.6 to 672.6 m/z (11.722691 to 94.93999 min) [12:46:53] Quant Extracting 672.6 to 676.6 m/z (10.074658 to 96.7053 min) [12:46:53] Quant Extracting 676.6 to 680.6 m/z (16.1821 to 98.12686 min) [12:46:53] Quant Extracting 680.6 to 684.6 m/z (9.494177 to 99.50231 min) [12:46:53] Quant Extracting 684.6 to 688.6 m/z (7.1570983 to 95.13851 min) [12:46:53] Quant Extracting 688.6 to 692.6 m/z (7.1570983 to 96.45969 min) [12:46:54] Quant Extracting 692.6 to 696.6 m/z (7.157713 to 100.78045 min) [12:46:54] Quant Extracting 696.6 to 700.6 m/z (7.5489044 to 93.12647 min) [12:46:54] Quant Extracting 700.6 to 704.6 m/z (10.126268 to 93.02846 min) [12:46:54] Quant Extracting 704.6 to 708.6 m/z (7.158328 to 99.896935 min) [12:46:54] Quant Extracting 708.6 to 712.6 m/z (7.1589437 to 100.68489 min) [12:46:54] Quant Extracting 712.6 to 716.6 m/z (12.500228 to 97.73661 min) [12:46:54] Quant Extracting 716.6 to 720.6 m/z (9.2068 to 100.04573 min) [12:46:54] Quant Extracting 720.6 to 724.6 m/z (13.519786 to 95.18886 min) [12:46:54] Quant Extracting 724.6 to 728.6 m/z (15.991935 to 95.18947 min) [12:46:54] Quant Extracting 728.6 to 732.6 m/z (7.1601744 to 96.22 min) [12:46:55] Quant Extracting 732.6 to 736.6 m/z (14.781733 to 97.63984 min) [12:46:55] Quant Extracting 736.6 to 740.6 m/z (15.848374 to 95.679634 min) [12:46:55] Quant Extracting 740.6 to 744.6 m/z (8.917751 to 99.01588 min) [12:46:55] Quant Extracting 744.6 to 748.6 m/z (7.1614056 to 99.06724 min) [12:46:55] Quant Extracting 748.6 to 752.6 m/z (21.129406 to 97.73969 min) [12:46:55] Quant Extracting 752.6 to 756.6 m/z (9.161996 to 95.730415 min) [12:46:55] Quant Extracting 756.6 to 760.6 m/z (22.970272 to 95.63357 min) [12:46:55] Quant Extracting 760.6 to 764.6 m/z (14.978266 to 99.99986 min) [12:46:55] Quant Extracting 764.6 to 768.6 m/z (12.069442 to 96.663155 min) [12:46:55] Quant Extracting 768.6 to 772.6 m/z (7.163252 to 99.31361 min) [12:46:55] Quant Extracting 772.6 to 776.6 m/z (12.070052 to 94.263466 min) [12:46:56] Quant Extracting 776.6 to 780.6 m/z (18.951696 to 97.93882 min) [12:46:56] Quant Extracting 780.6 to 784.6 m/z (19.921247 to 97.30209 min) [12:46:56] Quant Extracting 784.6 to 788.6 m/z (8.387927 to 97.00859 min) [12:46:56] Quant Extracting 788.6 to 792.6 m/z (13.281647 to 100.19782 min) [12:46:56] Quant Extracting 792.6 to 796.6 m/z (13.817151 to 95.68394 min) [12:46:56] Quant Extracting 796.6 to 800.6 m/z (14.834556 to 96.37147 min) [12:46:56] Quant Extracting 800.6 to 804.6 m/z (18.275805 to 96.52025 min) [12:46:56] Quant Extracting 804.6 to 808.6 m/z (16.579472 to 96.66623 min) [12:46:56] Quant Extracting 808.6 to 812.6 m/z (16.870398 to 95.539825 min) [12:46:56] Quant Extracting 812.6 to 816.6 m/z (13.139223 to 100.19966 min) [12:46:56] Quant Extracting 816.6 to 820.6 m/z (23.50998 to 94.85544 min) [12:46:57] Quant Extracting 820.6 to 824.6 m/z (14.110148 to 95.05088 min) [12:46:57] Quant Extracting 824.6 to 828.6 m/z (19.92494 to 98.28673 min) [12:46:57] Quant Extracting 828.6 to 832.6 m/z (25.545433 to 100.6468 min) [12:46:57] Quant Extracting 832.6 to 836.6 m/z (22.587864 to 95.39293 min) [12:46:57] Quant Extracting 836.6 to 840.6 m/z (18.228495 to 100.15419 min) [12:46:57] Quant Extracting 840.6 to 844.6 m/z (10.959826 to 96.03186 min) [12:46:57] Quant Extracting 844.6 to 848.6 m/z (20.74932 to 95.05273 min) [12:46:57] Quant Extracting 848.6 to 852.6 m/z (14.500466 to 100.74544 min) [12:46:57] Quant Extracting 852.6 to 856.6 m/z (16.632967 to 95.98296 min) [12:46:58] Quant Extracting 856.6 to 860.6 m/z (23.171528 to 100.10409 min) [12:46:58] Quant Extracting 860.6 to 864.6 m/z (27.919523 to 98.68189 min) [12:46:58] Quant Extracting 864.6 to 868.6 m/z (21.866096 to 98.87976 min) [12:46:58] Quant Extracting 868.6 to 872.6 m/z (28.98483 to 100.746666 min) [12:46:58] Quant Extracting 872.6 to 876.6 m/z (25.645939 to 97.50495 min) [12:46:58] Quant Extracting 876.6 to 880.7 m/z (32.377876 to 98.09493 min) [12:46:58] Quant Extracting 880.7 to 884.7 m/z (31.653055 to 96.23227 min) [12:46:58] Quant Extracting 884.7 to 888.7 m/z (25.210133 to 96.625046 min) [12:46:58] Quant Extracting 888.7 to 892.7 m/z (28.696022 to 96.86839 min) [12:46:58] Quant Extracting 892.7 to 896.7 m/z (25.84077 to 100.60094 min) [12:46:58] Quant Extracting 896.7 to 900.7 m/z (19.445583 to 98.78361 min) [12:46:59] Quant Extracting 900.7 to 904.7 m/z (27.14828 to 97.70407 min) [12:46:59] Quant Extracting 904.7 to 908.7 m/z (28.746943 to 99.668304 min) [12:46:59] Quant Extracting 908.7 to 912.7 m/z (21.869173 to 98.73349 min) [12:46:59] Quant Extracting 912.7 to 916.7 m/z (27.633183 to 95.15693 min) [12:46:59] Quant Extracting 916.7 to 920.7 m/z (33.784912 to 95.45101 min) [12:46:59] Quant Extracting 920.7 to 924.7 m/z (37.321297 to 96.38127 min) [12:46:59] Quant Extracting 924.7 to 928.7 m/z (27.73118 to 98.34201 min) [12:46:59] Quant Extracting 928.7 to 932.7 m/z (9.998114 to 95.59632 min) [12:46:59] Quant Extracting 932.7 to 936.7 m/z (37.75853 to 96.77343 min) [12:46:59] Quant Extracting 936.7 to 940.7 m/z (37.37205 to 97.6085 min) [12:46:59] Quant Extracting 940.7 to 944.7 m/z (34.319054 to 97.70714 min) [12:46:59] Quant Extracting 944.7 to 948.7 m/z (37.27589 to 99.71866 min) [12:46:59] Quant Extracting 948.7 to 952.7 m/z (36.11226 to 100.360085 min) [12:47:00] Quant Extracting 952.7 to 956.7 m/z (31.996452 to 96.2378 min) [12:47:00] Quant Extracting 956.7 to 960.7 m/z (31.318836 to 93.538246 min) [12:47:00] Quant Extracting 960.7 to 964.7 m/z (39.745052 to 100.75404 min) [12:47:00] Quant Extracting 964.7 to 968.7 m/z (27.299133 to 98.689896 min) [12:47:00] Quant Extracting 968.7 to 972.7 m/z (29.236916 to 100.75466 min) [12:47:00] Quant Extracting 972.7 to 976.7 m/z (30.400667 to 95.600006 min) [12:47:00] Quant Extracting 976.7 to 980.7 m/z (28.896448 to 99.57701 min) [12:47:00] Quant Extracting 980.7 to 984.7 m/z (19.35474 to 96.533775 min) [12:47:00] Quant Extracting 984.7 to 988.7 m/z (33.30637 to 100.01766 min) [12:47:00] Quant Extracting 988.7 to 992.7 m/z (34.081226 to 96.58229 min) [12:47:00] Quant Extracting 992.7 to 996.7 m/z (38.68166 to 96.535 min) [12:47:00] Quant Extracting 996.7 to 1000.7 m/z (49.261024 to 100.75651 min) [12:47:00] Quant Extracting 1000.7 to 1004.7 m/z (16.110205 to 90.99304 min) [12:47:01] Attempted extraction for: 45813, found 45813 [12:47:01] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML (45813 entries)... [12:47:01] Writing 45813 peptides to entries table... [12:47:05] Writing 45813 peptides to peptidequants table... [12:47:08] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:47:08 BST 2024 [12:47:09] Writing local target/decoy peptides: 45813/1796, pi0: 0.223611 [12:47:10] Writing local target/decoy proteins: 5671/56 [12:47:13] Finished analysis! 45813 peptides identified at 1.0% FDR (5.4 minutes) [12:47:13] Generating quantification library (4 of 5): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" [12:47:17] EncyclopeDIA version 2.12.30 [12:47:17] Getting count of protein accessions... [12:47:17] Using EncyclopeDIA 2.X Scoring System [12:47:17] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML ... [12:47:17] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML ... [12:47:18] Parsed 1% [12:47:18] Parsed 2% [12:47:18] Parsed 3% [12:47:19] Parsed 4% [12:47:19] Parsed 5% [12:47:20] Parsed 6% [12:47:20] Parsed 7% [12:47:21] Parsed 8% [12:47:21] Parsed 9% [12:47:22] Parsed 10% [12:47:23] Parsed 11% [12:47:24] Parsed 12% [12:47:25] Parsed 13% [12:47:26] Parsed 14% [12:47:28] Parsed 15% [12:47:29] Parsed 16% [12:47:32] Parsed 17% [12:47:32] Parsed 18% [12:47:34] Parsed 19% [12:47:35] Parsed 20% [12:47:36] Parsed 21% [12:47:37] Parsed 22% [12:47:40] Parsed 23% [12:47:41] Parsed 24% [12:47:42] Parsed 25% [12:47:43] Parsed 26% [12:47:44] Parsed 27% [12:47:46] Parsed 28% [12:47:47] Parsed 29% [12:47:49] Parsed 30% [12:47:52] Parsed 31% [12:47:55] Parsed 32% [12:48:01] Parsed 33% [12:48:06] Parsed 34% [12:48:14] Parsed 35% [12:48:15] Parsed 36% [12:48:16] Parsed 37% [12:48:17] Parsed 38% [12:48:19] Parsed 39% [12:48:22] Parsed 40% [12:48:26] Parsed 41% [12:48:30] Parsed 42% [12:48:34] Parsed 43% [12:48:39] Parsed 44% [12:48:45] Parsed 45% [12:48:52] Parsed 46% [12:48:53] Parsed 47% [12:48:54] Parsed 48% [12:48:56] Parsed 49% [12:48:58] Parsed 50% [12:49:02] Parsed 51% [12:49:06] Parsed 52% [12:49:11] Parsed 53% [12:49:16] Parsed 54% [12:49:21] Parsed 55% [12:49:27] Parsed 56% [12:49:34] Parsed 57% [12:49:40] Parsed 58% [12:49:48] Parsed 59% [12:49:55] Parsed 60% [12:50:04] Parsed 61% [12:50:14] Parsed 62% [12:50:25] Parsed 63% [12:50:36] Parsed 64% [12:50:55] Parsed 65% [12:50:56] Parsed 66% [12:50:57] Parsed 67% [12:51:00] Parsed 68% [12:51:03] Parsed 69% [12:51:08] Parsed 70% [12:51:12] Parsed 71% [12:51:17] Parsed 72% [12:51:23] Parsed 73% [12:51:30] Parsed 74% [12:51:36] Parsed 75% [12:51:44] Parsed 76% [12:51:52] Parsed 77% [12:52:01] Parsed 78% [12:52:09] Parsed 79% [12:52:20] Parsed 80% [12:52:33] Parsed 81% [12:52:34] Parsed 82% [12:52:36] Parsed 83% [12:52:40] Parsed 84% [12:52:45] Parsed 85% [12:52:51] Parsed 86% [12:52:56] Parsed 87% [12:53:02] Parsed 88% [12:53:09] Parsed 89% [12:53:15] Parsed 90% [12:53:20] Parsed 91% [12:53:26] Parsed 92% [12:53:34] Parsed 93% [12:53:44] Parsed 94% [12:53:52] Parsed 95% [12:54:02] Parsed 96% [12:54:10] Parsed 97% [12:54:19] Parsed 98% [12:54:23] Parsed 99% [12:54:30] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.dia ... [12:54:31] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.dia! [12:54:31] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML [12:54:31] Library File: UP000005640_9606-z3_nce27.elib [12:54:31] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.elib [12:54:31] Parameters: [12:54:31] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [12:54:31] Converting files... [12:54:31] Calculating features... [12:54:31] Processing precursors scans... [12:54:31] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt.unsorted [12:54:31] Processing 396.4 to 400.4 m/z, (5.8548756 second duty cycle) [12:54:32] 67 peptides remaining for 396.4 to 400.4... [12:54:33] 4 peptides remaining for 396.4 to 400.4... [12:54:33] Processing 400.4 to 404.4 m/z, (2.9273798 second duty cycle) [12:54:34] 201 peptides remaining for 400.4 to 404.4... [12:54:34] Processing 404.4 to 408.4 m/z, (2.927397 second duty cycle) [12:54:34] 232 peptides remaining for 404.4 to 408.4... [12:54:35] Processing 408.4 to 412.4 m/z, (2.92738 second duty cycle) [12:54:35] 273 peptides remaining for 408.4 to 412.4... [12:54:36] Processing 412.4 to 416.4 m/z, (2.9273973 second duty cycle) [12:54:36] 299 peptides remaining for 412.4 to 416.4... [12:54:36] Processing 416.4 to 420.4 m/z, (2.9273798 second duty cycle) [12:54:37] 301 peptides remaining for 416.4 to 420.4... [12:54:37] Processing 420.4 to 424.4 m/z, (2.9273965 second duty cycle) [12:54:37] 321 peptides remaining for 420.4 to 424.4... [12:54:38] Processing 424.4 to 428.4 m/z, (2.9273794 second duty cycle) [12:54:38] 304 peptides remaining for 424.4 to 428.4... [12:54:38] Processing 428.4 to 432.4 m/z, (2.9273968 second duty cycle) [12:54:39] 367 peptides remaining for 428.4 to 432.4... [12:54:39] Processing 432.4 to 436.4 m/z, (2.9273796 second duty cycle) [12:54:39] 377 peptides remaining for 432.4 to 436.4... [12:54:40] Processing 436.4 to 440.5 m/z, (2.9273968 second duty cycle) [12:54:40] 480 peptides remaining for 436.4 to 440.5... [12:54:40] Processing 440.5 to 444.5 m/z, (2.9273796 second duty cycle) [12:54:40] 473 peptides remaining for 440.5 to 444.5... [12:54:41] Processing 444.5 to 448.5 m/z, (2.9273968 second duty cycle) [12:54:41] 368 peptides remaining for 444.5 to 448.5... [12:54:42] Processing 448.5 to 452.5 m/z, (2.9273796 second duty cycle) [12:54:42] 454 peptides remaining for 448.5 to 452.5... [12:54:42] Processing 452.5 to 456.5 m/z, (2.9273968 second duty cycle) [12:54:42] 400 peptides remaining for 452.5 to 456.5... [12:54:43] Processing 456.5 to 460.5 m/z, (2.9273796 second duty cycle) [12:54:43] 469 peptides remaining for 456.5 to 460.5... [12:54:44] Processing 460.5 to 464.5 m/z, (2.9273968 second duty cycle) [12:54:44] 491 peptides remaining for 460.5 to 464.5... [12:54:44] Processing 464.5 to 468.5 m/z, (2.9273798 second duty cycle) [12:54:44] 604 peptides remaining for 464.5 to 468.5... [12:54:45] Processing 468.5 to 472.5 m/z, (2.9273968 second duty cycle) [12:54:45] 491 peptides remaining for 468.5 to 472.5... [12:54:46] Processing 472.5 to 476.5 m/z, (2.9273796 second duty cycle) [12:54:46] 496 peptides remaining for 472.5 to 476.5... [12:54:46] Processing 476.5 to 480.5 m/z, (2.9273968 second duty cycle) [12:54:46] 500 peptides remaining for 476.5 to 480.5... [12:54:47] Processing 480.5 to 484.5 m/z, (2.9273798 second duty cycle) [12:54:47] 578 peptides remaining for 480.5 to 484.5... [12:54:47] 108 peptides remaining for 480.5 to 484.5... [12:54:48] Processing 484.5 to 488.5 m/z, (2.9273965 second duty cycle) [12:54:48] 511 peptides remaining for 484.5 to 488.5... [12:54:49] 0 peptides remaining for 484.5 to 488.5... [12:54:49] Processing 488.5 to 492.5 m/z, (2.9273796 second duty cycle) [12:54:49] 475 peptides remaining for 488.5 to 492.5... [12:54:50] Processing 492.5 to 496.5 m/z, (2.9273968 second duty cycle) [12:54:50] 543 peptides remaining for 492.5 to 496.5... [12:54:51] Processing 496.5 to 500.5 m/z, (2.9273796 second duty cycle) [12:54:51] 710 peptides remaining for 496.5 to 500.5... [12:54:51] Processing 500.5 to 504.5 m/z, (2.9273968 second duty cycle) [12:54:51] 736 peptides remaining for 500.5 to 504.5... [12:54:52] Processing 504.5 to 508.5 m/z, (2.9273796 second duty cycle) [12:54:52] 489 peptides remaining for 504.5 to 508.5... [12:54:53] Processing 508.5 to 512.5 m/z, (2.9274127 second duty cycle) [12:54:53] 634 peptides remaining for 508.5 to 512.5... [12:54:53] Processing 512.5 to 516.5 m/z, (2.9273953 second duty cycle) [12:54:53] 589 peptides remaining for 512.5 to 516.5... [12:54:54] Processing 516.5 to 520.5 m/z, (2.9274125 second duty cycle) [12:54:54] 533 peptides remaining for 516.5 to 520.5... [12:54:55] Processing 520.5 to 524.5 m/z, (2.9273953 second duty cycle) [12:54:55] 591 peptides remaining for 520.5 to 524.5... [12:54:55] Processing 524.5 to 528.5 m/z, (2.9274127 second duty cycle) [12:54:55] 554 peptides remaining for 524.5 to 528.5... [12:54:56] Processing 528.5 to 532.5 m/z, (2.9273953 second duty cycle) [12:54:56] 619 peptides remaining for 528.5 to 532.5... [12:54:57] Processing 532.5 to 536.5 m/z, (2.9274127 second duty cycle) [12:54:57] 515 peptides remaining for 532.5 to 536.5... [12:54:57] 47 peptides remaining for 532.5 to 536.5... [12:54:58] Processing 536.5 to 540.5 m/z, (2.9273956 second duty cycle) [12:54:58] 591 peptides remaining for 536.5 to 540.5... [12:54:58] 115 peptides remaining for 536.5 to 540.5... [12:54:59] Processing 540.5 to 544.5 m/z, (2.9274125 second duty cycle) [12:54:59] 585 peptides remaining for 540.5 to 544.5... [12:55:00] Processing 544.5 to 548.5 m/z, (2.9273956 second duty cycle) [12:55:00] 588 peptides remaining for 544.5 to 548.5... [12:55:00] Processing 548.5 to 552.5 m/z, (2.9274127 second duty cycle) [12:55:00] 582 peptides remaining for 548.5 to 552.5... [12:55:01] Processing 552.5 to 556.5 m/z, (2.9273953 second duty cycle) [12:55:01] 601 peptides remaining for 552.5 to 556.5... [12:55:02] Processing 556.5 to 560.5 m/z, (2.9274127 second duty cycle) [12:55:02] 606 peptides remaining for 556.5 to 560.5... [12:55:02] Processing 560.5 to 564.5 m/z, (2.9273953 second duty cycle) [12:55:02] 533 peptides remaining for 560.5 to 564.5... [12:55:03] Processing 564.5 to 568.5 m/z, (2.9274127 second duty cycle) [12:55:03] 659 peptides remaining for 564.5 to 568.5... [12:55:04] Processing 568.5 to 572.5 m/z, (2.9273956 second duty cycle) [12:55:04] 556 peptides remaining for 568.5 to 572.5... [12:55:04] Processing 572.5 to 576.5 m/z, (2.9274127 second duty cycle) [12:55:04] 628 peptides remaining for 572.5 to 576.5... [12:55:05] Processing 576.5 to 580.5 m/z, (2.9273956 second duty cycle) [12:55:05] 584 peptides remaining for 576.5 to 580.5... [12:55:06] Processing 580.5 to 584.5 m/z, (2.9274127 second duty cycle) [12:55:06] 570 peptides remaining for 580.5 to 584.5... [12:55:06] Processing 584.5 to 588.5 m/z, (2.9273953 second duty cycle) [12:55:06] 601 peptides remaining for 584.5 to 588.5... [12:55:07] Processing 588.5 to 592.5 m/z, (2.9274127 second duty cycle) [12:55:07] 517 peptides remaining for 588.5 to 592.5... [12:55:08] Processing 592.5 to 596.5 m/z, (2.9273956 second duty cycle) [12:55:08] 593 peptides remaining for 592.5 to 596.5... [12:55:08] Processing 596.5 to 600.5 m/z, (2.9274127 second duty cycle) [12:55:08] 749 peptides remaining for 596.5 to 600.5... [12:55:09] Processing 600.5 to 604.5 m/z, (2.9273953 second duty cycle) [12:55:09] 841 peptides remaining for 600.5 to 604.5... [12:55:10] Processing 604.5 to 608.5 m/z, (2.9274127 second duty cycle) [12:55:10] 475 peptides remaining for 604.5 to 608.5... [12:55:10] Processing 608.5 to 612.5 m/z, (2.9273956 second duty cycle) [12:55:10] 514 peptides remaining for 608.5 to 612.5... [12:55:11] Processing 612.5 to 616.5 m/z, (2.9274127 second duty cycle) [12:55:11] 523 peptides remaining for 612.5 to 616.5... [12:55:12] Processing 616.5 to 620.5 m/z, (2.9273958 second duty cycle) [12:55:12] 485 peptides remaining for 616.5 to 620.5... [12:55:12] Processing 620.5 to 624.5 m/z, (2.9274127 second duty cycle) [12:55:12] 499 peptides remaining for 620.5 to 624.5... [12:55:13] Processing 624.5 to 628.5 m/z, (2.9273953 second duty cycle) [12:55:13] 450 peptides remaining for 624.5 to 628.5... [12:55:14] Processing 628.5 to 632.5 m/z, (2.9274127 second duty cycle) [12:55:14] 474 peptides remaining for 628.5 to 632.5... [12:55:14] Processing 632.5 to 636.5 m/z, (2.9273956 second duty cycle) [12:55:14] 420 peptides remaining for 632.5 to 636.5... [12:55:15] Processing 636.5 to 640.5 m/z, (2.9274127 second duty cycle) [12:55:15] 483 peptides remaining for 636.5 to 640.5... [12:55:16] Processing 640.5 to 644.5 m/z, (2.9273953 second duty cycle) [12:55:16] 415 peptides remaining for 640.5 to 644.5... [12:55:16] Processing 644.5 to 648.5 m/z, (2.9274127 second duty cycle) [12:55:16] 529 peptides remaining for 644.5 to 648.5... [12:55:17] Processing 648.5 to 652.5 m/z, (2.9273956 second duty cycle) [12:55:17] 419 peptides remaining for 648.5 to 652.5... [12:55:18] Processing 652.5 to 656.5 m/z, (2.9274127 second duty cycle) [12:55:18] 419 peptides remaining for 652.5 to 656.5... [12:55:18] Processing 656.5 to 660.6 m/z, (2.9273953 second duty cycle) [12:55:18] 432 peptides remaining for 656.5 to 660.6... [12:55:19] Processing 660.6 to 664.6 m/z, (2.9274125 second duty cycle) [12:55:19] 419 peptides remaining for 660.6 to 664.6... [12:55:20] Processing 664.6 to 668.6 m/z, (2.9273953 second duty cycle) [12:55:20] 440 peptides remaining for 664.6 to 668.6... [12:55:20] Processing 668.6 to 672.6 m/z, (2.9274125 second duty cycle) [12:55:20] 433 peptides remaining for 668.6 to 672.6... [12:55:21] Processing 672.6 to 676.6 m/z, (2.9273956 second duty cycle) [12:55:21] 455 peptides remaining for 672.6 to 676.6... [12:55:22] Processing 676.6 to 680.6 m/z, (2.9274127 second duty cycle) [12:55:22] 451 peptides remaining for 676.6 to 680.6... [12:55:22] Processing 680.6 to 684.6 m/z, (2.9273953 second duty cycle) [12:55:22] 427 peptides remaining for 680.6 to 684.6... [12:55:23] Processing 684.6 to 688.6 m/z, (2.9274127 second duty cycle) [12:55:23] 434 peptides remaining for 684.6 to 688.6... [12:55:24] Processing 688.6 to 692.6 m/z, (2.9273953 second duty cycle) [12:55:24] 423 peptides remaining for 688.6 to 692.6... [12:55:24] Processing 692.6 to 696.6 m/z, (2.9274127 second duty cycle) [12:55:24] 448 peptides remaining for 692.6 to 696.6... [12:55:25] Processing 696.6 to 700.6 m/z, (2.9273953 second duty cycle) [12:55:25] 558 peptides remaining for 696.6 to 700.6... [12:55:26] Processing 700.6 to 704.6 m/z, (2.9274127 second duty cycle) [12:55:26] 669 peptides remaining for 700.6 to 704.6... [12:55:26] Processing 704.6 to 708.6 m/z, (2.9273953 second duty cycle) [12:55:26] 393 peptides remaining for 704.6 to 708.6... [12:55:27] Processing 708.6 to 712.6 m/z, (2.9274127 second duty cycle) [12:55:27] 409 peptides remaining for 708.6 to 712.6... [12:55:28] Processing 712.6 to 716.6 m/z, (2.9273953 second duty cycle) [12:55:28] 417 peptides remaining for 712.6 to 716.6... [12:55:28] Processing 716.6 to 720.6 m/z, (2.9274127 second duty cycle) [12:55:28] 368 peptides remaining for 716.6 to 720.6... [12:55:29] Processing 720.6 to 724.6 m/z, (2.9273953 second duty cycle) [12:55:29] 371 peptides remaining for 720.6 to 724.6... [12:55:30] Processing 724.6 to 728.6 m/z, (2.9274127 second duty cycle) [12:55:30] 372 peptides remaining for 724.6 to 728.6... [12:55:30] Processing 728.6 to 732.6 m/z, (2.9273956 second duty cycle) [12:55:30] 363 peptides remaining for 728.6 to 732.6... [12:55:31] Processing 732.6 to 736.6 m/z, (2.9274127 second duty cycle) [12:55:31] 371 peptides remaining for 732.6 to 736.6... [12:55:32] Processing 736.6 to 740.6 m/z, (2.9273953 second duty cycle) [12:55:32] 357 peptides remaining for 736.6 to 740.6... [12:55:32] Processing 740.6 to 744.6 m/z, (2.9274127 second duty cycle) [12:55:32] 332 peptides remaining for 740.6 to 744.6... [12:55:33] Processing 744.6 to 748.6 m/z, (2.9273953 second duty cycle) [12:55:33] 365 peptides remaining for 744.6 to 748.6... [12:55:33] Processing 748.6 to 752.6 m/z, (2.927413 second duty cycle) [12:55:34] 313 peptides remaining for 748.6 to 752.6... [12:55:34] Processing 752.6 to 756.6 m/z, (2.9273956 second duty cycle) [12:55:34] 311 peptides remaining for 752.6 to 756.6... [12:55:35] Processing 756.6 to 760.6 m/z, (2.9274127 second duty cycle) [12:55:35] 343 peptides remaining for 756.6 to 760.6... [12:55:35] Processing 760.6 to 764.6 m/z, (2.9273796 second duty cycle) [12:55:36] 339 peptides remaining for 760.6 to 764.6... [12:55:36] Processing 764.6 to 768.6 m/z, (2.9273968 second duty cycle) [12:55:36] 342 peptides remaining for 764.6 to 768.6... [12:55:37] Processing 768.6 to 772.6 m/z, (2.9273798 second duty cycle) [12:55:37] 318 peptides remaining for 768.6 to 772.6... [12:55:37] Processing 772.6 to 776.6 m/z, (2.9273968 second duty cycle) [12:55:38] 315 peptides remaining for 772.6 to 776.6... [12:55:38] Processing 776.6 to 780.6 m/z, (2.9273796 second duty cycle) [12:55:38] 294 peptides remaining for 776.6 to 780.6... [12:55:39] Processing 780.6 to 784.6 m/z, (2.9273968 second duty cycle) [12:55:39] 290 peptides remaining for 780.6 to 784.6... [12:55:39] Processing 784.6 to 788.6 m/z, (2.9273796 second duty cycle) [12:55:40] 304 peptides remaining for 784.6 to 788.6... [12:55:40] Processing 788.6 to 792.6 m/z, (2.9273968 second duty cycle) [12:55:40] 281 peptides remaining for 788.6 to 792.6... [12:55:41] Processing 792.6 to 796.6 m/z, (2.9273798 second duty cycle) [12:55:41] 281 peptides remaining for 792.6 to 796.6... [12:55:41] Processing 796.6 to 800.6 m/z, (2.9273968 second duty cycle) [12:55:42] 417 peptides remaining for 796.6 to 800.6... [12:55:42] Processing 800.6 to 804.6 m/z, (2.9273796 second duty cycle) [12:55:42] 411 peptides remaining for 800.6 to 804.6... [12:55:43] Processing 804.6 to 808.6 m/z, (2.9273968 second duty cycle) [12:55:43] 236 peptides remaining for 804.6 to 808.6... [12:55:43] Processing 808.6 to 812.6 m/z, (2.9273796 second duty cycle) [12:55:43] 286 peptides remaining for 808.6 to 812.6... [12:55:44] Processing 812.6 to 816.6 m/z, (2.9273965 second duty cycle) [12:55:44] 242 peptides remaining for 812.6 to 816.6... [12:55:45] Processing 816.6 to 820.6 m/z, (2.9273796 second duty cycle) [12:55:45] 245 peptides remaining for 816.6 to 820.6... [12:55:45] Processing 820.6 to 824.6 m/z, (2.9273968 second duty cycle) [12:55:45] 236 peptides remaining for 820.6 to 824.6... [12:55:46] Processing 824.6 to 828.6 m/z, (2.9273796 second duty cycle) [12:55:46] 268 peptides remaining for 824.6 to 828.6... [12:55:47] Processing 828.6 to 832.6 m/z, (2.9273968 second duty cycle) [12:55:47] 254 peptides remaining for 828.6 to 832.6... [12:55:47] Processing 832.6 to 836.6 m/z, (2.9273796 second duty cycle) [12:55:47] 214 peptides remaining for 832.6 to 836.6... [12:55:48] Processing 836.6 to 840.6 m/z, (2.9273968 second duty cycle) [12:55:48] 223 peptides remaining for 836.6 to 840.6... [12:55:49] Processing 840.6 to 844.6 m/z, (2.9273796 second duty cycle) [12:55:49] 236 peptides remaining for 840.6 to 844.6... [12:55:49] Processing 844.6 to 848.6 m/z, (2.9273968 second duty cycle) [12:55:49] 234 peptides remaining for 844.6 to 848.6... [12:55:50] Processing 848.6 to 852.6 m/z, (2.9273796 second duty cycle) [12:55:50] 234 peptides remaining for 848.6 to 852.6... [12:55:50] Processing 852.6 to 856.6 m/z, (2.9273965 second duty cycle) [12:55:51] 197 peptides remaining for 852.6 to 856.6... [12:55:51] Processing 856.6 to 860.6 m/z, (2.9273796 second duty cycle) [12:55:51] 216 peptides remaining for 856.6 to 860.6... [12:55:52] Processing 860.6 to 864.6 m/z, (2.9274127 second duty cycle) [12:55:52] 183 peptides remaining for 860.6 to 864.6... [12:55:52] Processing 864.6 to 868.6 m/z, (2.9273953 second duty cycle) [12:55:53] 179 peptides remaining for 864.6 to 868.6... [12:55:53] Processing 868.6 to 872.6 m/z, (2.9274127 second duty cycle) [12:55:53] 180 peptides remaining for 868.6 to 872.6... [12:55:54] Processing 872.6 to 876.6 m/z, (2.9273956 second duty cycle) [12:55:54] 205 peptides remaining for 872.6 to 876.6... [12:55:54] Processing 876.6 to 880.7 m/z, (2.9274127 second duty cycle) [12:55:54] 159 peptides remaining for 876.6 to 880.7... [12:55:55] Processing 880.7 to 884.7 m/z, (2.9273953 second duty cycle) [12:55:55] 184 peptides remaining for 880.7 to 884.7... [12:55:56] Processing 884.7 to 888.7 m/z, (2.9274127 second duty cycle) [12:55:56] 154 peptides remaining for 884.7 to 888.7... [12:55:56] Processing 888.7 to 892.7 m/z, (2.9273953 second duty cycle) [12:55:56] 154 peptides remaining for 888.7 to 892.7... [12:55:57] Processing 892.7 to 896.7 m/z, (2.9274127 second duty cycle) [12:55:57] 149 peptides remaining for 892.7 to 896.7... [12:55:58] Processing 896.7 to 900.7 m/z, (2.9273956 second duty cycle) [12:55:58] 219 peptides remaining for 896.7 to 900.7... [12:55:58] Processing 900.7 to 904.7 m/z, (2.927413 second duty cycle) [12:55:58] 222 peptides remaining for 900.7 to 904.7... [12:55:59] Processing 904.7 to 908.7 m/z, (2.9273956 second duty cycle) [12:55:59] 137 peptides remaining for 904.7 to 908.7... [12:56:00] Processing 908.7 to 912.7 m/z, (2.9274125 second duty cycle) [12:56:00] 160 peptides remaining for 908.7 to 912.7... [12:56:00] Processing 912.7 to 916.7 m/z, (2.9273956 second duty cycle) [12:56:00] 136 peptides remaining for 912.7 to 916.7... [12:56:01] Processing 916.7 to 920.7 m/z, (2.9274127 second duty cycle) [12:56:01] 103 peptides remaining for 916.7 to 920.7... [12:56:01] Processing 920.7 to 924.7 m/z, (2.9273956 second duty cycle) [12:56:02] 135 peptides remaining for 920.7 to 924.7... [12:56:02] Processing 924.7 to 928.7 m/z, (2.9274123 second duty cycle) [12:56:02] 132 peptides remaining for 924.7 to 928.7... [12:56:03] Processing 928.7 to 932.7 m/z, (2.9273953 second duty cycle) [12:56:03] 113 peptides remaining for 928.7 to 932.7... [12:56:03] Processing 932.7 to 936.7 m/z, (2.9274125 second duty cycle) [12:56:04] 108 peptides remaining for 932.7 to 936.7... [12:56:04] Processing 936.7 to 940.7 m/z, (2.9273953 second duty cycle) [12:56:04] 140 peptides remaining for 936.7 to 940.7... [12:56:05] Processing 940.7 to 944.7 m/z, (2.9274127 second duty cycle) [12:56:05] 106 peptides remaining for 940.7 to 944.7... [12:56:05] Processing 944.7 to 948.7 m/z, (2.9273956 second duty cycle) [12:56:05] 120 peptides remaining for 944.7 to 948.7... [12:56:06] Processing 948.7 to 952.7 m/z, (2.9274125 second duty cycle) [12:56:06] 145 peptides remaining for 948.7 to 952.7... [12:56:07] Processing 952.7 to 956.7 m/z, (2.9273953 second duty cycle) [12:56:07] 121 peptides remaining for 952.7 to 956.7... [12:56:07] Processing 956.7 to 960.7 m/z, (2.9274127 second duty cycle) [12:56:07] 138 peptides remaining for 956.7 to 960.7... [12:56:08] Processing 960.7 to 964.7 m/z, (2.9273956 second duty cycle) [12:56:08] 107 peptides remaining for 960.7 to 964.7... [12:56:09] Processing 964.7 to 968.7 m/z, (2.9274127 second duty cycle) [12:56:09] 120 peptides remaining for 964.7 to 968.7... [12:56:09] Processing 968.7 to 972.7 m/z, (2.9273953 second duty cycle) [12:56:09] 91 peptides remaining for 968.7 to 972.7... [12:56:10] Processing 972.7 to 976.7 m/z, (2.9274127 second duty cycle) [12:56:10] 82 peptides remaining for 972.7 to 976.7... [12:56:11] Processing 976.7 to 980.7 m/z, (2.9273953 second duty cycle) [12:56:11] 94 peptides remaining for 976.7 to 980.7... [12:56:11] Processing 980.7 to 984.7 m/z, (2.9274127 second duty cycle) [12:56:11] 65 peptides remaining for 980.7 to 984.7... [12:56:12] Processing 984.7 to 988.7 m/z, (2.9273953 second duty cycle) [12:56:12] 73 peptides remaining for 984.7 to 988.7... [12:56:12] Processing 988.7 to 992.7 m/z, (2.9274127 second duty cycle) [12:56:13] 96 peptides remaining for 988.7 to 992.7... [12:56:13] Processing 992.7 to 996.7 m/z, (2.9273953 second duty cycle) [12:56:13] 82 peptides remaining for 992.7 to 996.7... [12:56:14] Processing 996.7 to 1000.7 m/z, (2.9274185 second duty cycle) [12:56:14] 55 peptides remaining for 996.7 to 1000.7... [12:56:14] Processing 1000.7 to 1004.7 m/z, (5.854888 second duty cycle) [12:56:15] 20 peptides remaining for 1000.7 to 1004.7... [12:56:15] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:56:18] Sorted feature file in 3.10 seconds wall clock time [12:56:18] File size check: 56212425 vs 56212425 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt.unsorted [12:56:18] 148500 total peptides processed. [12:56:18] Running Percolator... [12:56:18] Executing [cmd /c C:\Windows\Temp\tmp5FD8.java\Percolator-v3-01-3646376396665764816.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt] [12:56:19] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:56:19] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:56:19] Written by Lukas Käll (lukall@u.washington.edu) in the [12:56:19] Department of Genome Sciences at the University of Washington. [12:56:19] Issued command: [12:56:19] C:\Windows\Temp\tmp5FD8.java\Percolator-v3-01-3646376396665764816.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt.1.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:56:19] Started Wed Jul 17 12:56:19 2024 [12:56:19] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [12:56:19] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:56:19] Features: [12:56:19] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:56:20] Found 148500 PSMs [12:56:20] Separate target and decoy search inputs detected, using mix-max method. [12:56:20] Train/test set contains 80164 positives and 68336 negatives, size ratio=1.17309 and pi0=1 [12:56:20] Warning: The mix-max procedure is not well behaved when # targets (80164) != # decoys (68336). Consider using target-decoy competition (-Y flag). [12:56:20] Selecting Cpos by cross-validation. [12:56:20] Selecting Cneg by cross-validation. [12:56:21] Split 1: Selected feature 3 as initial search direction. Could separate 15082 training set positives in that direction. [12:56:21] Split 2: Selected feature 3 as initial search direction. Could separate 14843 training set positives in that direction. [12:56:22] Split 3: Selected feature 3 as initial search direction. Could separate 15238 training set positives in that direction. [12:56:22] Found 22540 test set positives with q<0.01 in initial direction [12:56:22] Reading in data and feature calculation took 3.614 cpu seconds or 3 seconds wall clock time. [12:56:22] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:56:28] Iteration 1: Estimated 35209 PSMs with q<0.01 [12:56:37] Iteration 2: Estimated 38402 PSMs with q<0.01 [12:56:46] Iteration 3: Estimated 39061 PSMs with q<0.01 [12:56:46] Learned normalized SVM weights for the 3 cross-validation splits: [12:56:46] Split1 Split2 Split3 FeatureName [12:56:46] -0.7607 -0.2642 -0.2500 primary [12:56:46] -0.0843 -0.0711 -0.0034 xCorrLib [12:56:46] 1.1716 1.3359 1.3074 xCorrModel [12:56:46] -1.7109 -1.9270 -1.2830 dotProduct [12:56:46] 2.2345 2.3178 1.9084 contrastAngle [12:56:46] -0.5324 -0.4911 -0.4494 logit [12:56:46] -1.3032 -1.3754 -1.2465 sumOfSquaredErrors [12:56:46] 1.4106 0.9737 0.9890 numberOfMatchingPeaks [12:56:46] -0.0477 -0.0321 -0.0232 numberOfMatchingPeaksAboveThreshold [12:56:46] -0.0406 -0.0184 -0.0337 averageFragmentDeltaMasses [12:56:46] 0.2998 0.4459 0.2685 isotopeDotProduct [12:56:46] -0.0052 0.0861 0.0134 averageParentDeltaMass [12:56:46] 0.0681 0.1003 0.0076 percentBlankOverMono [12:56:46] -0.1270 -0.1207 -0.0940 numberPrecursorMatch [12:56:46] -1.0758 -1.1837 -1.1584 lnSp [12:56:46] 0.1352 0.1569 0.1333 maxLadderLength [12:56:46] -0.0465 -0.0959 -0.0964 evalue [12:56:46] 0.2533 0.2579 0.3673 correlationToGaussian [12:56:46] 0.1890 0.1436 0.1793 correlationToPrecursor [12:56:46] 0.0888 0.1229 0.0907 isIntegratedSignal [12:56:46] 0.0557 0.0476 0.0490 isIntegratedPrecursor [12:56:46] 0.7970 0.8833 0.7986 numPeaksWithGoodCorrelation [12:56:46] -0.1206 -0.0853 -0.1112 numMissedCleavage [12:56:46] -0.3643 -0.5401 -0.4015 pepLength [12:56:46] 0.0000 0.0000 0.0000 charge1 [12:56:46] -0.2124 -0.2085 -0.1510 charge2 [12:56:46] 0.2124 0.2085 0.1510 charge3 [12:56:46] 0.0000 0.0000 0.0000 charge4 [12:56:46] 0.7557 0.8248 0.7016 precursorMz [12:56:46] -0.3417 -0.1519 -0.1692 precursorMass [12:56:46] -0.1124 -0.1803 -0.1447 RTinMin [12:56:46] -1.9084 -2.0052 -1.7071 m0 [12:56:46] Found 38990 test set PSMs with q<0.01. [12:56:47] Scoring full list of PSMs with trained SVMs. [12:56:47] Features: [12:56:47] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:56:48] Found 148500 PSMs [12:56:48] Evaluated set contained 80164 positives and 68336 negatives. [12:56:49] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:56:50] Selecting pi_0=0.204888 [12:56:50] Calculating q values. [12:56:50] New pi_0 estimate on final list yields 40468 target peptides with q<0.01. [12:56:50] Calculating posterior error probabilities (PEPs). [12:56:51] Processing took 28.72 cpu seconds or 29 seconds wall clock time. [12:56:53] First pass: 40468 peptides identified at 1.0% FDR [12:56:53] Generating retention time mapping using 41933 points... [12:56:53] Enough data points (41933) to perform KDE alignment. [12:56:56] Enough data points (35515) to perform KDE alignment. [12:56:57] Enough data points (41933) to perform KDE alignment. [12:57:01] Constructing writer for E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt.unsorted [12:57:02] Sorting results into E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:57:04] Sorted feature file in 2.70 seconds wall clock time [12:57:04] File size check: 49508010 vs 49508010 (diff: 0) Removing temp file E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt.unsorted [12:57:04] Executing [cmd /c C:\Windows\Temp\tmp5FD8.java\Percolator-v3-01-1839392764596539008.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt] [12:57:05] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [12:57:05] Copyright (c) 2006-9 University of Washington. All rights reserved. [12:57:05] Written by Lukas Käll (lukall@u.washington.edu) in the [12:57:05] Department of Genome Sciences at the University of Washington. [12:57:05] Issued command: [12:57:05] C:\Windows\Temp\tmp5FD8.java\Percolator-v3-01-1839392764596539008.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.txt.2.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.encyclopedia.decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:57:05] Started Wed Jul 17 12:57:05 2024 [12:57:05] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [12:57:05] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [12:57:05] Features: [12:57:05] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:57:06] Found 121360 PSMs [12:57:06] Separate target and decoy search inputs detected, using mix-max method. [12:57:06] Train/test set contains 60681 positives and 60679 negatives, size ratio=1.00003 and pi0=1 [12:57:06] Selecting Cpos by cross-validation. [12:57:06] Selecting Cneg by cross-validation. [12:57:07] Split 1: Selected feature 3 as initial search direction. Could separate 15250 training set positives in that direction. [12:57:07] Split 2: Selected feature 3 as initial search direction. Could separate 14484 training set positives in that direction. [12:57:08] Split 3: Selected feature 3 as initial search direction. Could separate 14861 training set positives in that direction. [12:57:08] Found 22202 test set positives with q<0.01 in initial direction [12:57:08] Reading in data and feature calculation took 3.037 cpu seconds or 3 seconds wall clock time. [12:57:08] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [12:57:13] Iteration 1: Estimated 38909 PSMs with q<0.01 [12:57:24] Iteration 2: Estimated 43820 PSMs with q<0.01 [12:57:37] Iteration 3: Estimated 45017 PSMs with q<0.01 [12:57:51] Iteration 4: Estimated 45335 PSMs with q<0.01 [12:58:06] Iteration 5: Estimated 45370 PSMs with q<0.01 [12:58:20] Iteration 6: Estimated 45368 PSMs with q<0.01 [12:58:35] Iteration 7: Estimated 45351 PSMs with q<0.01 [12:58:50] Iteration 8: Estimated 45344 PSMs with q<0.01 [12:59:04] Iteration 9: Estimated 45341 PSMs with q<0.01 [12:59:19] Iteration 10: Estimated 45328 PSMs with q<0.01 [12:59:19] Learned normalized SVM weights for the 3 cross-validation splits: [12:59:19] Split1 Split2 Split3 FeatureName [12:59:19] -0.5152 -0.5775 -0.3448 primary [12:59:19] -0.1955 -0.2330 -0.2484 xCorrLib [12:59:19] 0.8117 0.7760 0.8150 xCorrModel [12:59:19] -0.8800 -0.7917 -0.6983 dotProduct [12:59:19] 1.3709 1.3220 1.1313 contrastAngle [12:59:19] -0.2245 -0.1876 -0.0111 logit [12:59:19] -0.9360 -0.8089 -0.9812 sumOfSquaredErrors [12:59:19] 1.1762 1.2665 1.0330 numberOfMatchingPeaks [12:59:19] -0.0040 -0.0127 -0.0237 numberOfMatchingPeaksAboveThreshold [12:59:19] 0.0040 0.0285 0.0170 averageFragmentDeltaMasses [12:59:19] -0.1117 -0.0461 -0.0978 isotopeDotProduct [12:59:19] -0.1061 -0.1074 -0.1470 averageParentDeltaMass [12:59:19] -0.0007 0.0480 0.0298 percentBlankOverMono [12:59:19] -0.1753 -0.1605 -0.1495 numberPrecursorMatch [12:59:19] -1.2573 -1.2927 -1.3421 lnSp [12:59:19] 0.1930 0.2277 0.1731 maxLadderLength [12:59:19] -0.0209 0.0016 -0.0119 evalue [12:59:19] 0.2798 0.2858 0.2489 correlationToGaussian [12:59:19] 0.0662 0.0415 0.0391 correlationToPrecursor [12:59:19] 0.0745 0.1607 0.1480 isIntegratedSignal [12:59:19] -0.1338 -0.0917 -0.1050 isIntegratedPrecursor [12:59:19] 0.6158 0.5964 0.6005 numPeaksWithGoodCorrelation [12:59:19] -30.8951 -35.7879 -37.1293 deltaRT [12:59:19] -0.1050 -0.0725 -0.0873 ms1MassError [12:59:19] -0.0033 0.0140 0.0092 ms2MassError [12:59:19] -0.0875 -0.0974 -0.1003 numMissedCleavage [12:59:19] -0.2859 -0.2224 -0.3263 pepLength [12:59:19] 0.0000 0.0000 0.0000 charge1 [12:59:19] -0.1289 -0.2392 -0.1292 charge2 [12:59:19] 0.1289 0.2392 0.1292 charge3 [12:59:19] 0.0000 0.0000 0.0000 charge4 [12:59:19] 0.4268 0.6310 0.3968 precursorMz [12:59:19] -0.3010 -0.6792 -0.2576 precursorMass [12:59:19] -0.0834 -0.0776 -0.0702 RTinMin [12:59:19] -22.3569 -26.2353 -27.2477 m0 [12:59:19] Found 45227 test set PSMs with q<0.01. [12:59:19] Scoring full list of PSMs with trained SVMs. [12:59:19] Features: [12:59:19] primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [12:59:20] Found 121360 PSMs [12:59:20] Evaluated set contained 60681 positives and 60679 negatives. [12:59:22] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [12:59:22] Selecting pi_0=0.225039 [12:59:22] Calculating q values. [12:59:22] New pi_0 estimate on final list yields 45709 target peptides with q<0.01. [12:59:22] Calculating posterior error probabilities (PEPs). [12:59:23] Processing took 135.5 cpu seconds or 135 seconds wall clock time. [12:59:25] Generating retention time mapping using 47375 points... [12:59:25] Enough data points (47375) to perform KDE alignment. [12:59:29] Enough data points (38002) to perform KDE alignment. [12:59:29] Enough data points (47375) to perform KDE alignment. [12:59:33] Writing elib result library... [12:59:33] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML: Number of global peptides: 45709 vs local peptides: 45709 [12:59:33] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML... [12:59:33] Extracting Spectral Data for 45709 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML... [12:59:33] Number of global peptides: 45709 vs local peptides: 45709 [12:59:34] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [12:59:34] Parsed features and scores for 45709 peptides. [12:59:34] Extracting 45709 peptides... [12:59:34] Quant Extracting 396.4 to 400.4 m/z (7.425594 to 77.340126 min) [12:59:34] Quant Extracting 400.4 to 404.4 m/z (5.129427 to 80.126076 min) [12:59:34] Quant Extracting 404.4 to 408.4 m/z (7.182784 to 81.83628 min) [12:59:34] Quant Extracting 408.4 to 412.4 m/z (4.3481355 to 81.59427 min) [12:59:34] Quant Extracting 412.4 to 416.4 m/z (5.7638144 to 86.875244 min) [12:59:34] Quant Extracting 416.4 to 420.4 m/z (5.961074 to 84.380325 min) [12:59:34] Quant Extracting 420.4 to 424.4 m/z (7.184003 to 85.409256 min) [12:59:34] Quant Extracting 424.4 to 428.4 m/z (7.2312846 to 84.9205 min) [12:59:34] Quant Extracting 428.4 to 432.4 m/z (7.184613 to 83.16014 min) [12:59:35] Quant Extracting 432.4 to 436.4 m/z (7.185222 to 83.01203 min) [12:59:35] Quant Extracting 436.4 to 440.5 m/z (7.185222 to 85.31188 min) [12:59:35] Quant Extracting 440.5 to 444.5 m/z (7.1858325 to 85.16378 min) [12:59:35] Quant Extracting 444.5 to 448.5 m/z (7.233123 to 87.120415 min) [12:59:35] Quant Extracting 448.5 to 452.5 m/z (4.3512278 to 83.45409 min) [12:59:35] Quant Extracting 452.5 to 456.5 m/z (7.186447 to 84.138824 min) [12:59:35] Quant Extracting 456.5 to 460.5 m/z (7.1870565 to 85.555786 min) [12:59:35] Quant Extracting 460.5 to 464.5 m/z (6.2097383 to 87.27159 min) [12:59:36] Quant Extracting 464.5 to 468.5 m/z (7.2343464 to 87.12165 min) [12:59:36] Quant Extracting 468.5 to 472.5 m/z (7.8738413 to 100.760056 min) [12:59:36] Quant Extracting 472.5 to 476.5 m/z (7.580832 to 88.30036 min) [12:59:36] Quant Extracting 476.5 to 480.5 m/z (7.628183 to 87.90824 min) [12:59:36] Quant Extracting 480.5 to 484.5 m/z (5.722035 to 88.10368 min) [12:59:36] Quant Extracting 484.5 to 488.5 m/z (7.139447 to 90.703476 min) [12:59:36] Quant Extracting 488.5 to 492.5 m/z (7.189505 to 86.39185 min) [12:59:37] Quant Extracting 492.5 to 496.5 m/z (7.189505 to 86.39185 min) [12:59:37] Quant Extracting 496.5 to 500.5 m/z (7.19012 to 89.04074 min) [12:59:37] Quant Extracting 500.5 to 504.5 m/z (7.19012 to 88.39963 min) [12:59:37] Quant Extracting 504.5 to 508.5 m/z (7.1406727 to 92.02895 min) [12:59:37] Quant Extracting 508.5 to 512.5 m/z (7.141861 to 93.59736 min) [12:59:37] Quant Extracting 512.5 to 516.5 m/z (7.1913495 to 86.83187 min) [12:59:37] Quant Extracting 516.5 to 520.5 m/z (7.1913495 to 91.9321 min) [12:59:38] Quant Extracting 520.5 to 524.5 m/z (6.117816 to 91.9321 min) [12:59:38] Quant Extracting 524.5 to 528.5 m/z (7.1919637 to 87.86462 min) [12:59:38] Quant Extracting 528.5 to 532.5 m/z (7.143086 to 88.893265 min) [12:59:38] Quant Extracting 532.5 to 536.5 m/z (7.1437235 to 93.45265 min) [12:59:38] Quant Extracting 536.5 to 540.5 m/z (7.1437235 to 92.716995 min) [12:59:38] Quant Extracting 540.5 to 544.5 m/z (7.2908425 to 95.90465 min) [12:59:38] Quant Extracting 544.5 to 548.5 m/z (7.144339 to 91.4425 min) [12:59:38] Quant Extracting 548.5 to 552.5 m/z (7.1449533 to 96.5939 min) [12:59:38] Quant Extracting 552.5 to 556.5 m/z (7.978184 to 94.14316 min) [12:59:38] Quant Extracting 556.5 to 560.5 m/z (7.145568 to 92.32793 min) [12:59:39] Quant Extracting 560.5 to 564.5 m/z (6.85141 to 97.5266 min) [12:59:39] Quant Extracting 564.5 to 568.5 m/z (8.076311 to 92.8181 min) [12:59:39] Quant Extracting 568.5 to 572.5 m/z (7.1461835 to 92.08399 min) [12:59:39] Quant Extracting 572.5 to 576.5 m/z (7.1467986 to 92.42596 min) [12:59:39] Quant Extracting 576.5 to 580.5 m/z (7.734147 to 97.48056 min) [12:59:39] Quant Extracting 580.5 to 584.5 m/z (7.1474123 to 94.291534 min) [12:59:39] Quant Extracting 584.5 to 588.5 m/z (7.1968813 to 93.407425 min) [12:59:39] Quant Extracting 588.5 to 592.5 m/z (7.1480274 to 94.732025 min) [12:59:39] Quant Extracting 592.5 to 596.5 m/z (7.1480274 to 92.67403 min) [12:59:39] Quant Extracting 596.5 to 600.5 m/z (7.148643 to 93.50547 min) [12:59:40] Quant Extracting 600.5 to 604.5 m/z (7.148643 to 94.44097 min) [12:59:40] Quant Extracting 604.5 to 608.5 m/z (7.1492586 to 96.94019 min) [12:59:40] Quant Extracting 608.5 to 612.5 m/z (10.0227995 to 93.70336 min) [12:59:40] Quant Extracting 612.5 to 616.5 m/z (7.591315 to 99.78884 min) [12:59:40] Quant Extracting 616.5 to 620.5 m/z (7.149873 to 94.92992 min) [12:59:40] Quant Extracting 620.5 to 624.5 m/z (12.203002 to 96.15599 min) [12:59:40] Quant Extracting 624.5 to 628.5 m/z (7.1504874 to 93.50731 min) [12:59:40] Quant Extracting 628.5 to 632.5 m/z (7.1511025 to 96.010086 min) [12:59:40] Quant Extracting 632.5 to 636.5 m/z (8.90932 to 97.289345 min) [12:59:40] Quant Extracting 636.5 to 640.5 m/z (7.248449 to 95.27494 min) [12:59:41] Quant Extracting 640.5 to 644.5 m/z (10.412484 to 96.74718 min) [12:59:41] Quant Extracting 644.5 to 648.5 m/z (9.298157 to 93.313705 min) [12:59:41] Quant Extracting 648.5 to 652.5 m/z (11.1394205 to 96.05921 min) [12:59:41] Quant Extracting 652.5 to 656.5 m/z (7.152947 to 95.27618 min) [12:59:41] Quant Extracting 656.5 to 660.6 m/z (14.532202 to 93.509766 min) [12:59:41] Quant Extracting 660.6 to 664.6 m/z (7.202414 to 95.27679 min) [12:59:41] Quant Extracting 664.6 to 668.6 m/z (19.183228 to 96.01316 min) [12:59:41] Quant Extracting 668.6 to 672.6 m/z (11.91632 to 94.981514 min) [12:59:41] Quant Extracting 672.6 to 676.6 m/z (10.221314 to 96.603745 min) [12:59:41] Quant Extracting 676.6 to 680.6 m/z (16.134176 to 98.17659 min) [12:59:41] Quant Extracting 680.6 to 684.6 m/z (9.350152 to 99.49963 min) [12:59:42] Quant Extracting 684.6 to 688.6 m/z (7.1554065 to 95.08139 min) [12:59:42] Quant Extracting 688.6 to 692.6 m/z (7.1554065 to 96.4077 min) [12:59:42] Quant Extracting 692.6 to 696.6 m/z (7.156021 to 100.777855 min) [12:59:42] Quant Extracting 696.6 to 700.6 m/z (7.401632 to 93.12196 min) [12:59:42] Quant Extracting 700.6 to 704.6 m/z (7.1566367 to 92.92535 min) [12:59:42] Quant Extracting 704.6 to 708.6 m/z (7.1566367 to 99.847 min) [12:59:42] Quant Extracting 708.6 to 712.6 m/z (7.157251 to 100.63437 min) [12:59:42] Quant Extracting 712.6 to 716.6 m/z (12.40333 to 97.73555 min) [12:59:42] Quant Extracting 716.6 to 720.6 m/z (9.255812 to 100.04306 min) [12:59:42] Quant Extracting 720.6 to 724.6 m/z (13.519942 to 99.11179 min) [12:59:43] Quant Extracting 724.6 to 728.6 m/z (11.0977 to 94.254715 min) [12:59:43] Quant Extracting 728.6 to 732.6 m/z (7.1584806 to 96.21534 min) [12:59:43] Quant Extracting 732.6 to 736.6 m/z (14.732206 to 97.63876 min) [12:59:43] Quant Extracting 736.6 to 740.6 m/z (15.751332 to 96.60866 min) [12:59:43] Quant Extracting 740.6 to 744.6 m/z (8.870027 to 99.01501 min) [12:59:43] Quant Extracting 744.6 to 748.6 m/z (13.715867 to 99.06635 min) [12:59:43] Quant Extracting 748.6 to 752.6 m/z (21.031748 to 97.789406 min) [12:59:43] Quant Extracting 752.6 to 756.6 m/z (9.161983 to 95.67444 min) [12:59:43] Quant Extracting 756.6 to 760.6 m/z (23.0187 to 95.57642 min) [12:59:43] Quant Extracting 760.6 to 764.6 m/z (14.978129 to 99.95052 min) [12:59:43] Quant Extracting 764.6 to 768.6 m/z (12.020489 to 96.6584 min) [12:59:44] Quant Extracting 768.6 to 772.6 m/z (16.432095 to 99.31091 min) [12:59:44] Quant Extracting 772.6 to 776.6 m/z (21.663633 to 94.258995 min) [12:59:44] Quant Extracting 776.6 to 780.6 m/z (18.854603 to 97.89108 min) [12:59:44] Quant Extracting 780.6 to 784.6 m/z (19.871347 to 97.64245 min) [12:59:44] Quant Extracting 784.6 to 788.6 m/z (8.484628 to 96.90703 min) [12:59:44] Quant Extracting 788.6 to 792.6 m/z (13.281492 to 100.147804 min) [12:59:44] Quant Extracting 792.6 to 796.6 m/z (13.766846 to 95.63081 min) [12:59:44] Quant Extracting 796.6 to 800.6 m/z (16.481802 to 99.117935 min) [12:59:44] Quant Extracting 800.6 to 804.6 m/z (18.178589 to 96.46359 min) [12:59:44] Quant Extracting 804.6 to 808.6 m/z (22.053766 to 96.71278 min) [12:59:44] Quant Extracting 808.6 to 812.6 m/z (16.823412 to 95.48331 min) [12:59:45] Quant Extracting 812.6 to 816.6 m/z (13.139217 to 100.05101 min) [12:59:45] Quant Extracting 816.6 to 820.6 m/z (28.302946 to 94.75041 min) [12:59:45] Quant Extracting 820.6 to 824.6 m/z (14.060516 to 98.23554 min) [12:59:45] Quant Extracting 824.6 to 828.6 m/z (15.274351 to 98.28568 min) [12:59:45] Quant Extracting 828.6 to 832.6 m/z (25.495825 to 100.64416 min) [12:59:45] Quant Extracting 832.6 to 836.6 m/z (22.490108 to 95.24301 min) [12:59:45] Quant Extracting 836.6 to 840.6 m/z (25.255466 to 100.10018 min) [12:59:45] Quant Extracting 840.6 to 844.6 m/z (10.960115 to 95.97531 min) [12:59:45] Quant Extracting 844.6 to 848.6 m/z (20.701359 to 94.850914 min) [12:59:45] Quant Extracting 848.6 to 852.6 m/z (14.403418 to 100.742836 min) [12:59:45] Quant Extracting 852.6 to 856.6 m/z (16.67995 to 95.8779 min) [12:59:46] Quant Extracting 856.6 to 860.6 m/z (23.124472 to 100.10141 min) [12:59:46] Quant Extracting 860.6 to 864.6 m/z (27.969091 to 98.682816 min) [12:59:46] Quant Extracting 864.6 to 868.6 m/z (21.815058 to 98.92616 min) [12:59:46] Quant Extracting 868.6 to 872.6 m/z (26.176918 to 96.226364 min) [12:59:46] Quant Extracting 872.6 to 876.6 m/z (25.59576 to 94.60655 min) [12:59:46] Quant Extracting 876.6 to 880.7 m/z (32.330406 to 98.14179 min) [12:59:46] Quant Extracting 880.7 to 884.7 m/z (31.653414 to 96.27487 min) [12:59:46] Quant Extracting 884.7 to 888.7 m/z (25.162407 to 96.62031 min) [12:59:46] Quant Extracting 888.7 to 892.7 m/z (28.648998 to 96.86364 min) [12:59:46] Quant Extracting 892.7 to 896.7 m/z (21.382732 to 100.598305 min) [12:59:46] Quant Extracting 896.7 to 900.7 m/z (19.348316 to 98.78269 min) [12:59:46] Quant Extracting 900.7 to 904.7 m/z (27.100529 to 97.65224 min) [12:59:47] Quant Extracting 904.7 to 908.7 m/z (28.7472 to 99.6161 min) [12:59:47] Quant Extracting 908.7 to 912.7 m/z (21.771465 to 98.73438 min) [12:59:47] Quant Extracting 912.7 to 916.7 m/z (27.586031 to 95.4446 min) [12:59:47] Quant Extracting 916.7 to 920.7 m/z (33.785072 to 95.4446 min) [12:59:47] Quant Extracting 920.7 to 924.7 m/z (37.17707 to 96.37474 min) [12:59:47] Quant Extracting 924.7 to 928.7 m/z (27.586645 to 98.24411 min) [12:59:47] Quant Extracting 928.7 to 932.7 m/z (9.901373 to 100.74899 min) [12:59:47] Quant Extracting 932.7 to 936.7 m/z (37.709454 to 96.86733 min) [12:59:47] Quant Extracting 936.7 to 940.7 m/z (37.1783 to 97.60744 min) [12:59:47] Quant Extracting 940.7 to 944.7 m/z (34.27144 to 97.65532 min) [12:59:48] Quant Extracting 944.7 to 948.7 m/z (37.082146 to 99.71601 min) [12:59:48] Quant Extracting 948.7 to 952.7 m/z (35.531815 to 100.35741 min) [12:59:48] Quant Extracting 952.7 to 956.7 m/z (31.899881 to 95.93723 min) [12:59:48] Quant Extracting 956.7 to 960.7 m/z (31.368074 to 95.10288 min) [12:59:48] Quant Extracting 960.7 to 964.7 m/z (39.551174 to 100.75145 min) [12:59:48] Quant Extracting 964.7 to 968.7 m/z (27.202555 to 100.75145 min) [12:59:48] Quant Extracting 968.7 to 972.7 m/z (29.237322 to 100.75206 min) [12:59:48] Quant Extracting 972.7 to 976.7 m/z (30.400875 to 97.85509 min) [12:59:48] Quant Extracting 976.7 to 980.7 m/z (28.946463 to 99.57433 min) [12:59:48] Quant Extracting 980.7 to 984.7 m/z (19.257502 to 100.75268 min) [12:59:48] Quant Extracting 984.7 to 988.7 m/z (40.911392 to 99.96774 min) [12:59:49] Quant Extracting 988.7 to 992.7 m/z (33.935684 to 96.57755 min) [12:59:49] Quant Extracting 992.7 to 996.7 m/z (38.634804 to 96.53028 min) [12:59:49] Quant Extracting 996.7 to 1000.7 m/z (42.223698 to 97.120316 min) [12:59:49] Quant Extracting 1000.7 to 1004.7 m/z (16.013388 to 90.98678 min) [12:59:49] Attempted extraction for: 45709, found 45709 [12:59:49] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML (45709 entries)... [12:59:49] Writing 45709 peptides to entries table... [12:59:53] Writing 45709 peptides to peptidequants table... [12:59:57] Finished writing to Encyclopedia ELIB at Wed Jul 17 12:59:57 BST 2024 [12:59:58] Writing local target/decoy peptides: 45709/1769, pi0: 0.225039 [12:59:59] Writing local target/decoy proteins: 5686/56 [13:00:02] Finished analysis! 45709 peptides identified at 1.0% FDR (5.5 minutes) [13:00:02] Generating quantification library (5 of 5): UP000005640_9606-z3_nce27-quant.elib Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx12288M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\9E07V4L8.KNN\2AXJEH7G.2KX\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\Windows\Temp -v2scoring "True" -i "E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant" -libexport -a -o "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-quant.elib" -f "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta" -l "E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib" SearchToLIB EncyclopeDIA version 2.12.30 Parameters: -i E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant -f E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606.fasta -l E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27.elib -o E:\Proteomics data (E drive)\HeLa_QC\DIA\Fasta files\UP000005640_9606-z3_nce27-quant.elib -a true -blib false -alignOnly false -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 36 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [13:00:06] Attempting to process 8 searches... [13:00:15] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.dia.features.txt [13:00:15] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML, skipping extraction on that file. [13:00:15] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.dia.features.txt [13:00:15] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML, skipping extraction on that file. [13:00:15] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.dia.features.txt [13:00:15] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML, skipping extraction on that file. [13:00:15] Missing feature file: Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.dia.features.txt [13:00:15] Can't find a EncyclopeDIA analysis of Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML, skipping extraction on that file. [13:00:15] Using Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML to extract representative search parameters [13:00:15] Running global Percolator analysis. [13:00:15] Found indicies for sequence: 37, primary: 3, and deltaRT: 25 [13:00:15] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [13:00:15] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [13:00:16] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [13:00:16] Getting delta retention times for input file Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [13:00:17] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.features.txt [13:00:17] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.features.txt [13:00:18] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.features.txt [13:00:18] Parsing Percolator input file Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.features.txt [13:00:19] Found 117274 total peptides, writing to new Percolator input file... [13:00:19] Executing [cmd /c C:\Windows\Temp\tmp1BC1.java\Percolator-v3-01-8370928484454646346.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_results.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_results.txt.2147483647.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_features.txt] [13:00:20] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [13:00:20] Copyright (c) 2006-9 University of Washington. All rights reserved. [13:00:20] Written by Lukas Käll (lukall@u.washington.edu) in the [13:00:20] Department of Genome Sciences at the University of Washington. [13:00:20] Issued command: [13:00:20] C:\Windows\Temp\tmp1BC1.java\Percolator-v3-01-8370928484454646346.exe --results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_results.txt --weights E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_results.txt.2147483647.weights --decoy-results-peptides E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_decoy.txt -y --maxiter 10 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_features.txt [13:00:20] Started Wed Jul 17 13:00:20 2024 [13:00:20] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=10 [13:00:20] Reading tab-delimited input from datafile E:\Proteomics data (E drive)\HeLa_QC\DIA\elib_quant\UP000005640_9606-z3_nce27-quant_concatenated_features.txt [13:00:20] Features: [13:00:20] consistencyScore absDeltaDeltaRT irqDeltaRT primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [13:00:21] Found 117274 PSMs [13:00:21] Separate target and decoy search inputs detected, using mix-max method. [13:00:21] Train/test set contains 58647 positives and 58627 negatives, size ratio=1.00034 and pi0=1 [13:00:21] Selecting Cpos by cross-validation. [13:00:21] Selecting Cneg by cross-validation. [13:00:22] Split 1: Selected feature 25 as initial search direction. Could separate 16010 training set positives in that direction. [13:00:22] Split 2: Selected feature 25 as initial search direction. Could separate 15746 training set positives in that direction. [13:00:23] Split 3: Selected feature 25 as initial search direction. Could separate 15750 training set positives in that direction. [13:00:23] Found 23753 test set positives with q<0.01 in initial direction [13:00:23] Reading in data and feature calculation took 3.125 cpu seconds or 3 seconds wall clock time. [13:00:23] ---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 [13:00:29] Iteration 1: Estimated 36624 PSMs with q<0.01 [13:00:38] Iteration 2: Estimated 43478 PSMs with q<0.01 [13:00:50] Iteration 3: Estimated 45862 PSMs with q<0.01 [13:01:04] Iteration 4: Estimated 46681 PSMs with q<0.01 [13:01:19] Iteration 5: Estimated 46950 PSMs with q<0.01 [13:01:35] Iteration 6: Estimated 47050 PSMs with q<0.01 [13:01:51] Iteration 7: Estimated 47093 PSMs with q<0.01 [13:02:06] Iteration 8: Estimated 47112 PSMs with q<0.01 [13:02:22] Iteration 9: Estimated 47123 PSMs with q<0.01 [13:02:38] Iteration 10: Estimated 47137 PSMs with q<0.01 [13:02:38] Learned normalized SVM weights for the 3 cross-validation splits: [13:02:38] Split1 Split2 Split3 FeatureName [13:02:38] 0.3627 0.3657 0.3740 consistencyScore [13:02:38] -0.0287 -0.0345 -0.0022 absDeltaDeltaRT [13:02:38] -0.0447 -0.0107 -0.0333 irqDeltaRT [13:02:38] -1.1384 -0.6990 -0.9067 primary [13:02:38] -0.2453 -0.2280 -0.2058 xCorrLib [13:02:38] 0.8323 0.7090 0.7052 xCorrModel [13:02:38] -0.2840 -0.3107 -0.0399 dotProduct [13:02:38] 1.0077 1.0598 0.7782 contrastAngle [13:02:38] 0.1744 0.0368 0.1603 logit [13:02:38] -0.3749 -0.3932 -0.3684 sumOfSquaredErrors [13:02:38] 1.4967 0.8864 1.1914 numberOfMatchingPeaks [13:02:38] 0.0078 -0.0130 -0.0299 numberOfMatchingPeaksAboveThreshold [13:02:38] -0.0019 0.0102 0.0130 averageFragmentDeltaMasses [13:02:38] -0.1328 -0.1307 -0.2954 isotopeDotProduct [13:02:38] -0.1177 -0.1015 -0.1501 averageParentDeltaMass [13:02:38] -0.0524 -0.0487 -0.1197 percentBlankOverMono [13:02:38] -0.1351 -0.1350 -0.1462 numberPrecursorMatch [13:02:38] -1.2465 -1.0370 -1.1374 lnSp [13:02:38] 0.1681 0.1891 0.1535 maxLadderLength [13:02:38] 0.0237 -0.0149 -0.0054 evalue [13:02:38] 0.4271 0.3232 0.3179 correlationToGaussian [13:02:38] -0.0789 -0.0224 -0.0456 correlationToPrecursor [13:02:38] 0.2245 0.0459 0.1829 isIntegratedSignal [13:02:38] -0.0635 -0.0758 -0.0961 isIntegratedPrecursor [13:02:38] 0.4138 0.4993 0.4017 numPeaksWithGoodCorrelation [13:02:38] -36.1543 -37.1117 -35.8325 deltaRT [13:02:38] -0.0874 -0.0613 -0.2081 ms1MassError [13:02:38] 0.0162 0.0264 0.0146 ms2MassError [13:02:38] -0.0936 -0.1133 -0.0990 numMissedCleavage [13:02:38] -0.3468 -0.3294 -0.3581 pepLength [13:02:38] 0.0000 0.0000 0.0000 charge1 [13:02:38] -0.0707 -0.2077 -0.1528 charge2 [13:02:38] 0.0707 0.2077 0.1528 charge3 [13:02:38] 0.0000 0.0000 0.0000 charge4 [13:02:38] 0.2864 0.5539 0.4666 precursorMz [13:02:38] -0.0889 -0.4103 -0.3275 precursorMass [13:02:38] -0.0844 -0.0868 -0.0727 RTinMin [13:02:38] -25.3744 -26.0110 -25.1401 m0 [13:02:38] Found 46992 test set PSMs with q<0.01. [13:02:38] Scoring full list of PSMs with trained SVMs. [13:02:38] Features: [13:02:38] consistencyScore absDeltaDeltaRT irqDeltaRT primary xCorrLib xCorrModel dotProduct contrastAngle logit sumOfSquaredErrors numberOfMatchingPeaks numberOfMatchingPeaksAboveThreshold averageFragmentDeltaMasses isotopeDotProduct averageParentDeltaMass percentBlankOverMono numberPrecursorMatch lnSp maxLadderLength evalue correlationToGaussian correlationToPrecursor isIntegratedSignal isIntegratedPrecursor numPeaksWithGoodCorrelation deltaRT ms1MassError ms2MassError numMissedCleavage pepLength charge1 charge2 charge3 charge4 precursorMz precursorMass RTinMin [13:02:39] Found 117274 PSMs [13:02:39] Evaluated set contained 58647 positives and 58627 negatives. [13:02:40] Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. [13:02:41] Selecting pi_0=0.177637 [13:02:41] Calculating q values. [13:02:41] New pi_0 estimate on final list yields 48640 target peptides with q<0.01. [13:02:41] Calculating posterior error probabilities (PEPs). [13:02:42] Processing took 139.1 cpu seconds or 139 seconds wall clock time. [13:02:44] Identified 48640 peptides across all files at a 1.0% FDR threshold. [13:02:44] Inferring peak boundaries across files... [13:02:44] Adding library [UP000005640_9606-z3_nce27.elib] to ion tracker... [13:02:45] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML.elib] to ion tracker... [13:02:46] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML.elib] to ion tracker... [13:02:47] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML.elib] to ion tracker... [13:02:48] Adding results [Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML.elib] to ion tracker... [13:02:49] Found quantitative ions for 48640 total peptides (48616 with 3 or more high quality peaks) across all runs. [13:02:50] Setting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML as the seed experiment. [13:02:51] Enough data points (41751) to perform KDE alignment. [13:03:00] Enough data points (41488) to perform KDE alignment. [13:03:04] Enough data points (41494) to perform KDE alignment. [13:03:09] ...Finished peak inference. [13:03:09] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML: Number of global peptides: 48640 vs local peptides: 45813 [13:03:09] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML... [13:03:09] Extracting Spectral Data for 45813 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML... [13:03:09] Wrote 0 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML [13:03:09] Number of global peptides: 48640 vs local peptides: 45813 [13:03:10] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [13:03:10] Parsed features and scores for 48640 peptides. [13:03:10] Extracting 48640 peptides... [13:03:10] Quant Extracting 396.4 to 400.4 m/z (7.2311535 to 78.20982 min) [13:03:10] Quant Extracting 400.4 to 404.4 m/z (5.2279234 to 80.32585 min) [13:03:10] Quant Extracting 404.4 to 408.4 m/z (7.1844788 to 81.84077 min) [13:03:10] Quant Extracting 408.4 to 412.4 m/z (4.349891 to 81.54688 min) [13:03:10] Quant Extracting 412.4 to 416.4 m/z (5.816812 to 86.884995 min) [13:03:10] Quant Extracting 416.4 to 420.4 m/z (6.0128803 to 82.03674 min) [13:03:10] Quant Extracting 420.4 to 424.4 m/z (7.1857038 to 85.41554 min) [13:03:11] Quant Extracting 424.4 to 428.4 m/z (7.232999 to 84.97349 min) [13:03:11] Quant Extracting 428.4 to 432.4 m/z (7.0756397 to 83.21375 min) [13:03:11] Quant Extracting 432.4 to 436.4 m/z (7.0756397 to 81.74403 min) [13:03:11] Quant Extracting 436.4 to 440.5 m/z (7.137438 to 85.31819 min) [13:03:11] Quant Extracting 440.5 to 444.5 m/z (7.0762553 to 85.22202 min) [13:03:11] Quant Extracting 444.5 to 448.5 m/z (7.146634 to 87.08284 min) [13:03:11] Quant Extracting 448.5 to 452.5 m/z (4.3010325 to 83.46231 min) [13:03:11] Quant Extracting 452.5 to 456.5 m/z (7.138669 to 84.14525 min) [13:03:11] Quant Extracting 456.5 to 460.5 m/z (7.077484 to 85.61388 min) [13:03:11] Quant Extracting 460.5 to 464.5 m/z (6.2114167 to 87.230034 min) [13:03:11] Quant Extracting 464.5 to 468.5 m/z (7.2870383 to 87.183334 min) [13:03:12] Quant Extracting 468.5 to 472.5 m/z (7.09878 to 100.76267 min) [13:03:12] Quant Extracting 472.5 to 476.5 m/z (7.236682 to 88.30833 min) [13:03:12] Quant Extracting 476.5 to 480.5 m/z (7.386142 to 87.91617 min) [13:03:12] Quant Extracting 480.5 to 484.5 m/z (5.7237163 to 88.11166 min) [13:03:12] Quant Extracting 484.5 to 488.5 m/z (7.1411266 to 90.80837 min) [13:03:12] Quant Extracting 488.5 to 492.5 m/z (7.191216 to 86.34973 min) [13:03:12] Quant Extracting 492.5 to 496.5 m/z (7.1417418 to 86.40166 min) [13:03:12] Quant Extracting 496.5 to 500.5 m/z (7.1417418 to 89.04692 min) [13:03:12] Quant Extracting 500.5 to 504.5 m/z (7.142352 to 88.4076 min) [13:03:13] Quant Extracting 504.5 to 508.5 m/z (7.142352 to 92.08347 min) [13:03:13] Quant Extracting 508.5 to 512.5 m/z (7.1435413 to 93.50322 min) [13:03:13] Quant Extracting 512.5 to 516.5 m/z (7.082358 to 92.524124 min) [13:03:13] Quant Extracting 516.5 to 520.5 m/z (7.1930623 to 91.93653 min) [13:03:13] Quant Extracting 520.5 to 524.5 m/z (6.166783 to 91.95909 min) [13:03:13] Quant Extracting 524.5 to 528.5 m/z (7.0835867 to 91.54438 min) [13:03:13] Quant Extracting 528.5 to 532.5 m/z (7.1447735 to 88.90127 min) [13:03:13] Quant Extracting 532.5 to 536.5 m/z (7.1453867 to 93.50506 min) [13:03:13] Quant Extracting 536.5 to 540.5 m/z (7.1453867 to 92.67417 min) [13:03:13] Quant Extracting 540.5 to 544.5 m/z (7.1460032 to 95.9111 min) [13:03:14] Quant Extracting 544.5 to 548.5 m/z (7.1460032 to 91.49833 min) [13:03:14] Quant Extracting 548.5 to 552.5 m/z (7.146619 to 96.59864 min) [13:03:14] Quant Extracting 552.5 to 556.5 m/z (7.146619 to 94.14768 min) [13:03:14] Quant Extracting 556.5 to 560.5 m/z (7.147234 to 92.35515 min) [13:03:14] Quant Extracting 560.5 to 564.5 m/z (6.864503 to 97.67766 min) [13:03:14] Quant Extracting 564.5 to 568.5 m/z (8.077704 to 92.82255 min) [13:03:14] Quant Extracting 568.5 to 572.5 m/z (7.0866647 to 92.13567 min) [13:03:14] Quant Extracting 572.5 to 576.5 m/z (7.0872793 to 92.48116 min) [13:03:14] Quant Extracting 576.5 to 580.5 m/z (7.148465 to 97.4816 min) [13:03:14] Quant Extracting 580.5 to 584.5 m/z (7.1490803 to 94.29606 min) [13:03:15] Quant Extracting 584.5 to 588.5 m/z (7.0878935 to 93.313324 min) [13:03:15] Quant Extracting 588.5 to 592.5 m/z (7.149696 to 94.73837 min) [13:03:15] Quant Extracting 592.5 to 596.5 m/z (7.08851 to 92.62711 min) [13:03:15] Quant Extracting 596.5 to 600.5 m/z (7.1503186 to 92.097176 min) [13:03:15] Quant Extracting 600.5 to 604.5 m/z (7.1503186 to 94.34681 min) [13:03:15] Quant Extracting 604.5 to 608.5 m/z (7.1509337 to 96.9431 min) [13:03:15] Quant Extracting 608.5 to 612.5 m/z (7.1509337 to 93.66064 min) [13:03:15] Quant Extracting 612.5 to 616.5 m/z (7.1515493 to 99.59604 min) [13:03:15] Quant Extracting 616.5 to 620.5 m/z (7.1106772 to 94.936295 min) [13:03:16] Quant Extracting 620.5 to 624.5 m/z (12.2998295 to 96.15598 min) [13:03:16] Quant Extracting 624.5 to 628.5 m/z (7.1521635 to 93.511826 min) [13:03:16] Quant Extracting 628.5 to 632.5 m/z (7.152779 to 96.01468 min) [13:03:16] Quant Extracting 632.5 to 636.5 m/z (7.091586 to 97.29044 min) [13:03:16] Quant Extracting 636.5 to 640.5 m/z (7.39845 to 95.37816 min) [13:03:16] Quant Extracting 640.5 to 644.5 m/z (10.509336 to 96.75011 min) [13:03:16] Quant Extracting 644.5 to 648.5 m/z (9.250189 to 95.3539 min) [13:03:16] Quant Extracting 648.5 to 652.5 m/z (11.139043 to 96.1152 min) [13:03:16] Quant Extracting 652.5 to 656.5 m/z (7.1546264 to 95.62559 min) [13:03:16] Quant Extracting 656.5 to 660.6 m/z (14.629488 to 97.27068 min) [13:03:16] Quant Extracting 660.6 to 664.6 m/z (7.2157054 to 95.276276 min) [13:03:17] Quant Extracting 664.6 to 668.6 m/z (19.183514 to 96.01775 min) [13:03:17] Quant Extracting 668.6 to 672.6 m/z (11.722691 to 94.93999 min) [13:03:17] Quant Extracting 672.6 to 676.6 m/z (7.0932555 to 96.7053 min) [13:03:17] Quant Extracting 676.6 to 680.6 m/z (16.1821 to 98.12686 min) [13:03:17] Quant Extracting 680.6 to 684.6 m/z (9.494177 to 99.50231 min) [13:03:17] Quant Extracting 684.6 to 688.6 m/z (7.1570983 to 95.13851 min) [13:03:17] Quant Extracting 688.6 to 692.6 m/z (7.1570983 to 96.45969 min) [13:03:17] Quant Extracting 692.6 to 696.6 m/z (7.157713 to 100.78045 min) [13:03:17] Quant Extracting 696.6 to 700.6 m/z (7.5489044 to 96.14299 min) [13:03:18] Quant Extracting 700.6 to 704.6 m/z (7.1699014 to 100.64378 min) [13:03:18] Quant Extracting 704.6 to 708.6 m/z (7.158328 to 99.896935 min) [13:03:18] Quant Extracting 708.6 to 712.6 m/z (7.1589437 to 100.68489 min) [13:03:18] Quant Extracting 712.6 to 716.6 m/z (12.500228 to 97.73661 min) [13:03:18] Quant Extracting 716.6 to 720.6 m/z (9.2068 to 100.04573 min) [13:03:18] Quant Extracting 720.6 to 724.6 m/z (13.519786 to 99.11344 min) [13:03:18] Quant Extracting 724.6 to 728.6 m/z (11.14258 to 95.18947 min) [13:03:18] Quant Extracting 728.6 to 732.6 m/z (7.1601744 to 96.22 min) [13:03:18] Quant Extracting 732.6 to 736.6 m/z (14.781733 to 99.38427 min) [13:03:18] Quant Extracting 736.6 to 740.6 m/z (15.848374 to 100.64686 min) [13:03:18] Quant Extracting 740.6 to 744.6 m/z (8.917751 to 99.01588 min) [13:03:19] Quant Extracting 744.6 to 748.6 m/z (7.1614056 to 99.06724 min) [13:03:19] Quant Extracting 748.6 to 752.6 m/z (21.129406 to 97.73969 min) [13:03:19] Quant Extracting 752.6 to 756.6 m/z (9.161996 to 95.730415 min) [13:03:19] Quant Extracting 756.6 to 760.6 m/z (22.970272 to 95.63357 min) [13:03:19] Quant Extracting 760.6 to 764.6 m/z (14.978266 to 100.64928 min) [13:03:19] Quant Extracting 764.6 to 768.6 m/z (12.069442 to 96.663155 min) [13:03:19] Quant Extracting 768.6 to 772.6 m/z (7.163252 to 99.31361 min) [13:03:19] Quant Extracting 772.6 to 776.6 m/z (12.070052 to 94.263466 min) [13:03:19] Quant Extracting 776.6 to 780.6 m/z (18.951696 to 97.93882 min) [13:03:19] Quant Extracting 780.6 to 784.6 m/z (19.921247 to 97.64329 min) [13:03:20] Quant Extracting 784.6 to 788.6 m/z (8.387927 to 97.62186 min) [13:03:20] Quant Extracting 788.6 to 792.6 m/z (13.281647 to 100.19782 min) [13:03:20] Quant Extracting 792.6 to 796.6 m/z (13.817151 to 95.68394 min) [13:03:20] Quant Extracting 796.6 to 800.6 m/z (14.834556 to 99.1196 min) [13:03:20] Quant Extracting 800.6 to 804.6 m/z (18.275805 to 96.52025 min) [13:03:20] Quant Extracting 804.6 to 808.6 m/z (16.579472 to 96.66623 min) [13:03:20] Quant Extracting 808.6 to 812.6 m/z (16.870398 to 95.539825 min) [13:03:20] Quant Extracting 812.6 to 816.6 m/z (13.139223 to 100.19966 min) [13:03:20] Quant Extracting 816.6 to 820.6 m/z (23.50998 to 97.918335 min) [13:03:20] Quant Extracting 820.6 to 824.6 m/z (14.110148 to 96.025314 min) [13:03:21] Quant Extracting 824.6 to 828.6 m/z (15.350979 to 100.65419 min) [13:03:21] Quant Extracting 828.6 to 832.6 m/z (25.545433 to 100.6468 min) [13:03:21] Quant Extracting 832.6 to 836.6 m/z (24.236431 to 95.39293 min) [13:03:21] Quant Extracting 836.6 to 840.6 m/z (18.228495 to 100.65481 min) [13:03:21] Quant Extracting 840.6 to 844.6 m/z (10.959826 to 96.03186 min) [13:03:21] Quant Extracting 844.6 to 848.6 m/z (20.74932 to 98.658806 min) [13:03:21] Quant Extracting 848.6 to 852.6 m/z (14.500466 to 100.74544 min) [13:03:21] Quant Extracting 852.6 to 856.6 m/z (16.632967 to 95.98296 min) [13:03:21] Quant Extracting 856.6 to 860.6 m/z (23.171528 to 100.10409 min) [13:03:21] Quant Extracting 860.6 to 864.6 m/z (27.919523 to 98.68189 min) [13:03:21] Quant Extracting 864.6 to 868.6 m/z (21.866096 to 98.87976 min) [13:03:21] Quant Extracting 868.6 to 872.6 m/z (26.230307 to 100.746666 min) [13:03:22] Quant Extracting 872.6 to 876.6 m/z (25.645939 to 97.50495 min) [13:03:22] Quant Extracting 876.6 to 880.7 m/z (32.377876 to 100.515434 min) [13:03:22] Quant Extracting 880.7 to 884.7 m/z (31.653055 to 96.23227 min) [13:03:22] Quant Extracting 884.7 to 888.7 m/z (25.210133 to 96.625046 min) [13:03:22] Quant Extracting 888.7 to 892.7 m/z (28.696022 to 96.86839 min) [13:03:22] Quant Extracting 892.7 to 896.7 m/z (21.433416 to 100.60094 min) [13:03:22] Quant Extracting 896.7 to 900.7 m/z (19.445583 to 98.78361 min) [13:03:22] Quant Extracting 900.7 to 904.7 m/z (27.14828 to 99.34986 min) [13:03:22] Quant Extracting 904.7 to 908.7 m/z (28.746943 to 99.668304 min) [13:03:22] Quant Extracting 908.7 to 912.7 m/z (21.869173 to 98.73349 min) [13:03:23] Quant Extracting 912.7 to 916.7 m/z (27.633183 to 95.15693 min) [13:03:23] Quant Extracting 916.7 to 920.7 m/z (33.784912 to 95.45101 min) [13:03:23] Quant Extracting 920.7 to 924.7 m/z (37.321297 to 96.38127 min) [13:03:23] Quant Extracting 924.7 to 928.7 m/z (27.73118 to 98.34201 min) [13:03:23] Quant Extracting 928.7 to 932.7 m/z (9.998114 to 100.78045 min) [13:03:23] Quant Extracting 932.7 to 936.7 m/z (37.75853 to 99.595695 min) [13:03:23] Quant Extracting 936.7 to 940.7 m/z (37.37205 to 97.6085 min) [13:03:23] Quant Extracting 940.7 to 944.7 m/z (34.319054 to 97.70714 min) [13:03:23] Quant Extracting 944.7 to 948.7 m/z (37.27589 to 99.71866 min) [13:03:23] Quant Extracting 948.7 to 952.7 m/z (35.619873 to 100.360085 min) [13:03:23] Quant Extracting 952.7 to 956.7 m/z (31.996452 to 96.2378 min) [13:03:23] Quant Extracting 956.7 to 960.7 m/z (31.318836 to 95.10228 min) [13:03:24] Quant Extracting 960.7 to 964.7 m/z (39.745052 to 100.75404 min) [13:03:24] Quant Extracting 964.7 to 968.7 m/z (27.299133 to 98.689896 min) [13:03:24] Quant Extracting 968.7 to 972.7 m/z (29.236916 to 100.75466 min) [13:03:24] Quant Extracting 972.7 to 976.7 m/z (30.400667 to 97.85604 min) [13:03:24] Quant Extracting 976.7 to 980.7 m/z (28.896448 to 99.57701 min) [13:03:24] Quant Extracting 980.7 to 984.7 m/z (19.35474 to 100.78045 min) [13:03:24] Quant Extracting 984.7 to 988.7 m/z (15.755985 to 100.01766 min) [13:03:24] Quant Extracting 988.7 to 992.7 m/z (34.081226 to 96.58229 min) [13:03:24] Quant Extracting 992.7 to 996.7 m/z (38.68166 to 96.535 min) [13:03:24] Quant Extracting 996.7 to 1000.7 m/z (42.315533 to 100.75651 min) [13:03:24] Quant Extracting 1000.7 to 1004.7 m/z (16.110205 to 90.99304 min) [13:03:24] Attempted extraction for: 48640, found 48640 [13:03:24] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_03.mzML (48640 entries)... [13:03:24] Writing 48640 peptides to entries table... [13:03:27] Writing 48640 peptides to peptidequants table... [13:03:30] Finished writing to Encyclopedia ELIB at Wed Jul 17 13:03:30 BST 2024 [13:03:31] Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML: Number of global peptides: 48640 vs local peptides: 45709 [13:03:31] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML... [13:03:31] Extracting Spectral Data for 45709 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML... [13:03:32] Wrote 41751 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML [13:03:32] Number of global peptides: 48640 vs local peptides: 45709 [13:03:32] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [13:03:32] Parsed features and scores for 48640 peptides. [13:03:32] Extracting 48640 peptides... [13:03:32] Quant Extracting 396.4 to 400.4 m/z (7.425594 to 78.19058 min) [13:03:32] Quant Extracting 400.4 to 404.4 m/z (5.129427 to 80.126076 min) [13:03:32] Quant Extracting 404.4 to 408.4 m/z (7.182784 to 81.83628 min) [13:03:33] Quant Extracting 408.4 to 412.4 m/z (4.3481355 to 81.59427 min) [13:03:33] Quant Extracting 412.4 to 416.4 m/z (5.7638144 to 86.875244 min) [13:03:33] Quant Extracting 416.4 to 420.4 m/z (5.961074 to 82.03226 min) [13:03:33] Quant Extracting 420.4 to 424.4 m/z (7.184003 to 85.409256 min) [13:03:33] Quant Extracting 424.4 to 428.4 m/z (7.2312846 to 84.9205 min) [13:03:33] Quant Extracting 428.4 to 432.4 m/z (7.062428 to 83.16014 min) [13:03:33] Quant Extracting 432.4 to 436.4 m/z (7.062428 to 81.73954 min) [13:03:33] Quant Extracting 436.4 to 440.5 m/z (7.1241903 to 85.31188 min) [13:03:33] Quant Extracting 440.5 to 444.5 m/z (7.063043 to 85.16378 min) [13:03:33] Quant Extracting 444.5 to 448.5 m/z (7.1333814 to 87.120415 min) [13:03:34] Quant Extracting 448.5 to 452.5 m/z (4.3512278 to 83.45409 min) [13:03:34] Quant Extracting 452.5 to 456.5 m/z (7.186447 to 84.138824 min) [13:03:34] Quant Extracting 456.5 to 460.5 m/z (7.064271 to 85.555786 min) [13:03:34] Quant Extracting 460.5 to 464.5 m/z (6.2097383 to 87.27159 min) [13:03:34] Quant Extracting 464.5 to 468.5 m/z (7.2343464 to 87.12165 min) [13:03:34] Quant Extracting 468.5 to 472.5 m/z (7.085555 to 100.760056 min) [13:03:34] Quant Extracting 472.5 to 476.5 m/z (7.2233806 to 88.30036 min) [13:03:34] Quant Extracting 476.5 to 480.5 m/z (7.372755 to 87.90824 min) [13:03:34] Quant Extracting 480.5 to 484.5 m/z (5.722035 to 88.10368 min) [13:03:34] Quant Extracting 484.5 to 488.5 m/z (7.1888905 to 90.703476 min) [13:03:35] Quant Extracting 488.5 to 492.5 m/z (7.189505 to 86.39185 min) [13:03:35] Quant Extracting 492.5 to 496.5 m/z (7.189505 to 86.39185 min) [13:03:35] Quant Extracting 496.5 to 500.5 m/z (7.19012 to 89.04074 min) [13:03:35] Quant Extracting 500.5 to 504.5 m/z (7.1291027 to 88.39963 min) [13:03:35] Quant Extracting 504.5 to 508.5 m/z (7.1406727 to 92.02895 min) [13:03:35] Quant Extracting 508.5 to 512.5 m/z (7.130292 to 93.59736 min) [13:03:35] Quant Extracting 512.5 to 516.5 m/z (7.069142 to 92.49681 min) [13:03:35] Quant Extracting 516.5 to 520.5 m/z (7.1797843 to 91.9321 min) [13:03:35] Quant Extracting 520.5 to 524.5 m/z (6.117816 to 91.9321 min) [13:03:35] Quant Extracting 524.5 to 528.5 m/z (7.0703716 to 91.51761 min) [13:03:36] Quant Extracting 528.5 to 532.5 m/z (7.143086 to 88.893265 min) [13:03:36] Quant Extracting 532.5 to 536.5 m/z (7.1437235 to 93.45265 min) [13:03:36] Quant Extracting 536.5 to 540.5 m/z (7.132136 to 92.716995 min) [13:03:36] Quant Extracting 540.5 to 544.5 m/z (7.2908425 to 95.90465 min) [13:03:36] Quant Extracting 544.5 to 548.5 m/z (7.144339 to 91.4425 min) [13:03:36] Quant Extracting 548.5 to 552.5 m/z (7.1449533 to 96.5939 min) [13:03:36] Quant Extracting 552.5 to 556.5 m/z (7.133366 to 94.14316 min) [13:03:36] Quant Extracting 556.5 to 560.5 m/z (7.145568 to 92.32793 min) [13:03:36] Quant Extracting 560.5 to 564.5 m/z (6.85141 to 97.5266 min) [13:03:36] Quant Extracting 564.5 to 568.5 m/z (8.076311 to 92.8181 min) [13:03:36] Quant Extracting 568.5 to 572.5 m/z (7.0734468 to 92.08399 min) [13:03:37] Quant Extracting 572.5 to 576.5 m/z (7.074061 to 92.42596 min) [13:03:37] Quant Extracting 576.5 to 580.5 m/z (7.135211 to 97.48056 min) [13:03:37] Quant Extracting 580.5 to 584.5 m/z (7.1474123 to 94.291534 min) [13:03:37] Quant Extracting 584.5 to 588.5 m/z (7.0746746 to 93.407425 min) [13:03:37] Quant Extracting 588.5 to 592.5 m/z (7.136442 to 94.732025 min) [13:03:37] Quant Extracting 592.5 to 596.5 m/z (7.075291 to 92.67403 min) [13:03:37] Quant Extracting 596.5 to 600.5 m/z (7.1370645 to 92.0701 min) [13:03:37] Quant Extracting 600.5 to 604.5 m/z (7.148643 to 94.44097 min) [13:03:37] Quant Extracting 604.5 to 608.5 m/z (7.1492586 to 96.94019 min) [13:03:37] Quant Extracting 608.5 to 612.5 m/z (7.137679 to 93.70336 min) [13:03:38] Quant Extracting 612.5 to 616.5 m/z (7.1382947 to 99.78884 min) [13:03:38] Quant Extracting 616.5 to 620.5 m/z (7.0974445 to 94.92992 min) [13:03:38] Quant Extracting 620.5 to 624.5 m/z (12.203002 to 96.15599 min) [13:03:38] Quant Extracting 624.5 to 628.5 m/z (7.1504874 to 93.50731 min) [13:03:38] Quant Extracting 628.5 to 632.5 m/z (7.1511025 to 96.010086 min) [13:03:38] Quant Extracting 632.5 to 636.5 m/z (7.0783663 to 97.289345 min) [13:03:38] Quant Extracting 636.5 to 640.5 m/z (7.248449 to 95.27494 min) [13:03:38] Quant Extracting 640.5 to 644.5 m/z (10.412484 to 96.74718 min) [13:03:38] Quant Extracting 644.5 to 648.5 m/z (9.298157 to 95.35436 min) [13:03:38] Quant Extracting 648.5 to 652.5 m/z (11.1394205 to 96.05921 min) [13:03:39] Quant Extracting 652.5 to 656.5 m/z (7.152947 to 95.62589 min) [13:03:39] Quant Extracting 656.5 to 660.6 m/z (14.532202 to 97.270065 min) [13:03:39] Quant Extracting 660.6 to 664.6 m/z (7.202414 to 95.27679 min) [13:03:39] Quant Extracting 664.6 to 668.6 m/z (19.183228 to 96.01316 min) [13:03:39] Quant Extracting 668.6 to 672.6 m/z (11.6774845 to 94.981514 min) [13:03:39] Quant Extracting 672.6 to 676.6 m/z (7.0800333 to 96.603745 min) [13:03:39] Quant Extracting 676.6 to 680.6 m/z (16.134176 to 98.17659 min) [13:03:39] Quant Extracting 680.6 to 684.6 m/z (9.350152 to 99.49963 min) [13:03:39] Quant Extracting 684.6 to 688.6 m/z (7.1554065 to 95.08139 min) [13:03:39] Quant Extracting 688.6 to 692.6 m/z (7.1554065 to 96.4077 min) [13:03:39] Quant Extracting 692.6 to 696.6 m/z (7.156021 to 100.777855 min) [13:03:39] Quant Extracting 696.6 to 700.6 m/z (7.401632 to 96.14302 min) [13:03:40] Quant Extracting 700.6 to 704.6 m/z (7.1566367 to 100.641266 min) [13:03:40] Quant Extracting 704.6 to 708.6 m/z (7.1566367 to 99.847 min) [13:03:40] Quant Extracting 708.6 to 712.6 m/z (7.157251 to 100.63437 min) [13:03:40] Quant Extracting 712.6 to 716.6 m/z (12.40333 to 97.73555 min) [13:03:40] Quant Extracting 716.6 to 720.6 m/z (9.255812 to 100.04306 min) [13:03:40] Quant Extracting 720.6 to 724.6 m/z (13.519942 to 99.11179 min) [13:03:40] Quant Extracting 724.6 to 728.6 m/z (11.0977 to 95.19003 min) [13:03:40] Quant Extracting 728.6 to 732.6 m/z (7.1584806 to 96.21534 min) [13:03:40] Quant Extracting 732.6 to 736.6 m/z (14.732206 to 99.38246 min) [13:03:40] Quant Extracting 736.6 to 740.6 m/z (15.751332 to 100.64434 min) [13:03:41] Quant Extracting 740.6 to 744.6 m/z (8.870027 to 99.01501 min) [13:03:41] Quant Extracting 744.6 to 748.6 m/z (7.1481457 to 99.06635 min) [13:03:41] Quant Extracting 748.6 to 752.6 m/z (21.031748 to 97.789406 min) [13:03:41] Quant Extracting 752.6 to 756.6 m/z (9.161983 to 95.67444 min) [13:03:41] Quant Extracting 756.6 to 760.6 m/z (23.0187 to 95.57642 min) [13:03:41] Quant Extracting 760.6 to 764.6 m/z (14.978129 to 100.64676 min) [13:03:41] Quant Extracting 764.6 to 768.6 m/z (12.020489 to 96.6584 min) [13:03:41] Quant Extracting 768.6 to 772.6 m/z (7.149992 to 99.31091 min) [13:03:41] Quant Extracting 772.6 to 776.6 m/z (12.024648 to 94.258995 min) [13:03:41] Quant Extracting 776.6 to 780.6 m/z (18.854603 to 97.89108 min) [13:03:42] Quant Extracting 780.6 to 784.6 m/z (19.871347 to 97.64245 min) [13:03:42] Quant Extracting 784.6 to 788.6 m/z (8.484628 to 97.62105 min) [13:03:42] Quant Extracting 788.6 to 792.6 m/z (13.281492 to 100.147804 min) [13:03:42] Quant Extracting 792.6 to 796.6 m/z (13.766846 to 95.63081 min) [13:03:42] Quant Extracting 796.6 to 800.6 m/z (14.75822 to 99.117935 min) [13:03:42] Quant Extracting 800.6 to 804.6 m/z (18.178589 to 96.46359 min) [13:03:42] Quant Extracting 804.6 to 808.6 m/z (16.50215 to 96.71278 min) [13:03:42] Quant Extracting 808.6 to 812.6 m/z (16.823412 to 95.48331 min) [13:03:42] Quant Extracting 812.6 to 816.6 m/z (13.139217 to 100.05101 min) [13:03:42] Quant Extracting 816.6 to 820.6 m/z (23.458126 to 97.91735 min) [13:03:42] Quant Extracting 820.6 to 824.6 m/z (14.060516 to 96.025406 min) [13:03:43] Quant Extracting 824.6 to 828.6 m/z (15.274351 to 100.65168 min) [13:03:43] Quant Extracting 828.6 to 832.6 m/z (25.495825 to 100.64416 min) [13:03:43] Quant Extracting 832.6 to 836.6 m/z (24.236532 to 95.39338 min) [13:03:43] Quant Extracting 836.6 to 840.6 m/z (18.150244 to 100.6523 min) [13:03:43] Quant Extracting 840.6 to 844.6 m/z (10.960115 to 95.97531 min) [13:03:43] Quant Extracting 844.6 to 848.6 m/z (20.701359 to 98.6574 min) [13:03:43] Quant Extracting 848.6 to 852.6 m/z (14.403418 to 100.742836 min) [13:03:43] Quant Extracting 852.6 to 856.6 m/z (16.67995 to 95.8779 min) [13:03:43] Quant Extracting 856.6 to 860.6 m/z (23.124472 to 100.10141 min) [13:03:43] Quant Extracting 860.6 to 864.6 m/z (27.969091 to 98.682816 min) [13:03:43] Quant Extracting 864.6 to 868.6 m/z (21.815058 to 98.92616 min) [13:03:44] Quant Extracting 868.6 to 872.6 m/z (26.176918 to 100.74409 min) [13:03:44] Quant Extracting 872.6 to 876.6 m/z (25.59576 to 97.504196 min) [13:03:44] Quant Extracting 876.6 to 880.7 m/z (32.330406 to 100.51299 min) [13:03:44] Quant Extracting 880.7 to 884.7 m/z (31.653414 to 96.27487 min) [13:03:44] Quant Extracting 884.7 to 888.7 m/z (25.162407 to 96.62031 min) [13:03:44] Quant Extracting 888.7 to 892.7 m/z (28.648998 to 96.86364 min) [13:03:44] Quant Extracting 892.7 to 896.7 m/z (21.382732 to 100.598305 min) [13:03:44] Quant Extracting 896.7 to 900.7 m/z (19.348316 to 98.78269 min) [13:03:44] Quant Extracting 900.7 to 904.7 m/z (27.100529 to 99.348076 min) [13:03:44] Quant Extracting 904.7 to 908.7 m/z (28.7472 to 99.6161 min) [13:03:44] Quant Extracting 908.7 to 912.7 m/z (21.771465 to 98.73438 min) [13:03:44] Quant Extracting 912.7 to 916.7 m/z (27.586031 to 95.09917 min) [13:03:45] Quant Extracting 916.7 to 920.7 m/z (33.785072 to 95.4446 min) [13:03:45] Quant Extracting 920.7 to 924.7 m/z (37.17707 to 96.37474 min) [13:03:45] Quant Extracting 924.7 to 928.7 m/z (27.586645 to 98.24411 min) [13:03:45] Quant Extracting 928.7 to 932.7 m/z (9.901373 to 100.74899 min) [13:03:45] Quant Extracting 932.7 to 936.7 m/z (37.709454 to 99.59377 min) [13:03:45] Quant Extracting 936.7 to 940.7 m/z (37.1783 to 97.60744 min) [13:03:45] Quant Extracting 940.7 to 944.7 m/z (34.27144 to 97.65532 min) [13:03:45] Quant Extracting 944.7 to 948.7 m/z (37.082146 to 99.71601 min) [13:03:45] Quant Extracting 948.7 to 952.7 m/z (35.531815 to 100.35741 min) [13:03:45] Quant Extracting 952.7 to 956.7 m/z (31.899881 to 96.23778 min) [13:03:45] Quant Extracting 956.7 to 960.7 m/z (31.368074 to 95.10288 min) [13:03:45] Quant Extracting 960.7 to 964.7 m/z (39.551174 to 100.75145 min) [13:03:45] Quant Extracting 964.7 to 968.7 m/z (27.202555 to 98.64005 min) [13:03:46] Quant Extracting 968.7 to 972.7 m/z (29.237322 to 100.75206 min) [13:03:46] Quant Extracting 972.7 to 976.7 m/z (30.400875 to 97.85509 min) [13:03:46] Quant Extracting 976.7 to 980.7 m/z (28.946463 to 99.57433 min) [13:03:46] Quant Extracting 980.7 to 984.7 m/z (19.257502 to 100.75268 min) [13:03:46] Quant Extracting 984.7 to 988.7 m/z (15.679128 to 99.96774 min) [13:03:46] Quant Extracting 988.7 to 992.7 m/z (33.935684 to 96.57755 min) [13:03:46] Quant Extracting 992.7 to 996.7 m/z (38.634804 to 96.53028 min) [13:03:46] Quant Extracting 996.7 to 1000.7 m/z (42.223698 to 100.74849 min) [13:03:46] Quant Extracting 1000.7 to 1004.7 m/z (16.013388 to 90.98678 min) [13:03:46] Attempted extraction for: 48640, found 48640 [13:03:46] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min_DIA_Cond-50cm_04.mzML (48640 entries)... [13:03:46] Writing 48640 peptides to entries table... [13:03:49] Writing 48640 peptides to peptidequants table... [13:03:52] Finished writing to Encyclopedia ELIB at Wed Jul 17 13:03:52 BST 2024 [13:03:53] Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML: Number of global peptides: 48640 vs local peptides: 45387 [13:03:53] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML... [13:03:53] Extracting Spectral Data for 45387 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML... [13:03:54] Wrote 41488 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML [13:03:54] Number of global peptides: 48640 vs local peptides: 45387 [13:03:54] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [13:03:54] Parsed features and scores for 48640 peptides. [13:03:54] Extracting 48640 peptides... [13:03:54] Quant Extracting 396.4 to 400.4 m/z (7.3304963 to 78.31387 min) [13:03:54] Quant Extracting 400.4 to 404.4 m/z (5.2314596 to 80.34574 min) [13:03:54] Quant Extracting 404.4 to 408.4 m/z (7.13663 to 81.912025 min) [13:03:55] Quant Extracting 408.4 to 412.4 m/z (4.4502664 to 81.618744 min) [13:03:55] Quant Extracting 412.4 to 416.4 m/z (5.917088 to 87.047676 min) [13:03:55] Quant Extracting 416.4 to 420.4 m/z (6.0630393 to 82.15529 min) [13:03:55] Quant Extracting 420.4 to 424.4 m/z (7.1378603 to 85.52096 min) [13:03:55] Quant Extracting 424.4 to 428.4 m/z (7.2856293 to 85.142235 min) [13:03:55] Quant Extracting 428.4 to 432.4 m/z (7.1384754 to 83.283356 min) [13:03:55] Quant Extracting 432.4 to 436.4 m/z (7.1384754 to 81.91448 min) [13:03:55] Quant Extracting 436.4 to 440.5 m/z (7.139091 to 85.43689 min) [13:03:55] Quant Extracting 440.5 to 444.5 m/z (7.139091 to 85.327385 min) [13:03:55] Quant Extracting 444.5 to 448.5 m/z (7.1397066 to 87.245575 min) [13:03:55] Quant Extracting 448.5 to 452.5 m/z (4.3045506 to 83.527214 min) [13:03:56] Quant Extracting 452.5 to 456.5 m/z (7.14032 to 84.26206 min) [13:03:56] Quant Extracting 456.5 to 460.5 m/z (7.14032 to 85.77762 min) [13:03:56] Quant Extracting 460.5 to 464.5 m/z (6.21487 to 87.34547 min) [13:03:56] Quant Extracting 464.5 to 468.5 m/z (7.3354177 to 87.298744 min) [13:03:56] Quant Extracting 468.5 to 472.5 m/z (7.1910176 to 100.80056 min) [13:03:56] Quant Extracting 472.5 to 476.5 m/z (7.2383394 to 88.47207 min) [13:03:56] Quant Extracting 476.5 to 480.5 m/z (7.3877096 to 88.029816 min) [13:03:56] Quant Extracting 480.5 to 484.5 m/z (5.8239565 to 88.22527 min) [13:03:56] Quant Extracting 484.5 to 488.5 m/z (7.1427794 to 90.92208 min) [13:03:56] Quant Extracting 488.5 to 492.5 m/z (7.1427794 to 86.51692 min) [13:03:56] Quant Extracting 492.5 to 496.5 m/z (7.143394 to 86.56425 min) [13:03:57] Quant Extracting 496.5 to 500.5 m/z (7.143394 to 89.10861 min) [13:03:57] Quant Extracting 500.5 to 504.5 m/z (7.2345977 to 88.61985 min) [13:03:57] Quant Extracting 504.5 to 508.5 m/z (7.1440043 to 92.197075 min) [13:03:57] Quant Extracting 508.5 to 512.5 m/z (7.1451945 to 93.667496 min) [13:03:57] Quant Extracting 512.5 to 516.5 m/z (7.1451945 to 92.63086 min) [13:03:57] Quant Extracting 516.5 to 520.5 m/z (7.14581 to 92.10092 min) [13:03:57] Quant Extracting 520.5 to 524.5 m/z (6.1684356 to 92.06573 min) [13:03:57] Quant Extracting 524.5 to 528.5 m/z (7.1464243 to 91.71061 min) [13:03:57] Quant Extracting 528.5 to 532.5 m/z (7.1464243 to 89.014885 min) [13:03:57] Quant Extracting 532.5 to 536.5 m/z (7.14704 to 93.717255 min) [13:03:58] Quant Extracting 536.5 to 540.5 m/z (7.14704 to 92.787766 min) [13:03:58] Quant Extracting 540.5 to 544.5 m/z (7.1476564 to 96.02295 min) [13:03:58] Quant Extracting 544.5 to 548.5 m/z (7.1476564 to 91.66111 min) [13:03:58] Quant Extracting 548.5 to 552.5 m/z (7.1482706 to 96.712234 min) [13:03:58] Quant Extracting 552.5 to 556.5 m/z (7.1482706 to 94.26131 min) [13:03:58] Quant Extracting 556.5 to 560.5 m/z (7.148887 to 92.46187 min) [13:03:58] Quant Extracting 560.5 to 564.5 m/z (6.71067 to 97.79309 min) [13:03:58] Quant Extracting 564.5 to 568.5 m/z (8.274328 to 92.8375 min) [13:03:58] Quant Extracting 568.5 to 572.5 m/z (7.1495028 to 92.24929 min) [13:03:58] Quant Extracting 572.5 to 576.5 m/z (7.150118 to 92.496124 min) [13:03:58] Quant Extracting 576.5 to 580.5 m/z (7.150118 to 97.597046 min) [13:03:59] Quant Extracting 580.5 to 584.5 m/z (7.1507325 to 94.409706 min) [13:03:59] Quant Extracting 584.5 to 588.5 m/z (7.1507325 to 93.478195 min) [13:03:59] Quant Extracting 588.5 to 592.5 m/z (7.151349 to 94.852005 min) [13:03:59] Quant Extracting 592.5 to 596.5 m/z (7.151349 to 92.73388 min) [13:03:59] Quant Extracting 596.5 to 600.5 m/z (7.242566 to 92.25175 min) [13:03:59] Quant Extracting 600.5 to 604.5 m/z (7.151963 to 94.55913 min) [13:03:59] Quant Extracting 604.5 to 608.5 m/z (7.15258 to 97.05855 min) [13:03:59] Quant Extracting 608.5 to 612.5 m/z (7.2431803 to 93.774185 min) [13:03:59] Quant Extracting 612.5 to 616.5 m/z (7.1531954 to 99.85737 min) [13:03:59] Quant Extracting 616.5 to 620.5 m/z (7.2029166 to 94.901726 min) [13:04:00] Quant Extracting 620.5 to 624.5 m/z (12.254529 to 96.292816 min) [13:04:00] Quant Extracting 624.5 to 628.5 m/z (7.1538105 to 93.62537 min) [13:04:00] Quant Extracting 628.5 to 632.5 m/z (7.154426 to 96.32565 min) [13:04:00] Quant Extracting 632.5 to 636.5 m/z (7.154426 to 97.50452 min) [13:04:00] Quant Extracting 636.5 to 640.5 m/z (7.1550417 to 95.442085 min) [13:04:00] Quant Extracting 640.5 to 644.5 m/z (10.511795 to 96.915085 min) [13:04:00] Quant Extracting 644.5 to 648.5 m/z (9.543322 to 95.49058 min) [13:04:00] Quant Extracting 648.5 to 652.5 m/z (11.094175 to 96.27612 min) [13:04:00] Quant Extracting 652.5 to 656.5 m/z (7.246874 to 95.76231 min) [13:04:00] Quant Extracting 656.5 to 660.6 m/z (14.58421 to 97.40772 min) [13:04:00] Quant Extracting 660.6 to 664.6 m/z (7.307964 to 95.39499 min) [13:04:01] Quant Extracting 664.6 to 668.6 m/z (19.3323 to 96.17872 min) [13:04:01] Quant Extracting 668.6 to 672.6 m/z (11.786402 to 95.152214 min) [13:04:01] Quant Extracting 672.6 to 676.6 m/z (7.157502 to 96.96483 min) [13:04:01] Quant Extracting 676.6 to 680.6 m/z (16.136282 to 98.339165 min) [13:04:01] Quant Extracting 680.6 to 684.6 m/z (9.5936575 to 99.66563 min) [13:04:01] Quant Extracting 684.6 to 688.6 m/z (7.249346 to 95.20136 min) [13:04:01] Quant Extracting 688.6 to 692.6 m/z (7.158733 to 96.526 min) [13:04:01] Quant Extracting 692.6 to 696.6 m/z (7.2499614 to 100.75145 min) [13:04:01] Quant Extracting 696.6 to 700.6 m/z (7.3538237 to 96.279816 min) [13:04:01] Quant Extracting 700.6 to 704.6 m/z (7.262152 to 100.75206 min) [13:04:01] Quant Extracting 704.6 to 708.6 m/z (7.250577 to 99.9634 min) [13:04:02] Quant Extracting 708.6 to 712.6 m/z (7.1605783 to 100.80056 min) [13:04:02] Quant Extracting 712.6 to 716.6 m/z (12.405939 to 97.85205 min) [13:04:02] Quant Extracting 716.6 to 720.6 m/z (9.328831 to 100.1613 min) [13:04:02] Quant Extracting 720.6 to 724.6 m/z (13.569297 to 99.37458 min) [13:04:02] Quant Extracting 724.6 to 728.6 m/z (11.099713 to 95.32612 min) [13:04:02] Quant Extracting 728.6 to 732.6 m/z (7.1618094 to 96.33364 min) [13:04:02] Quant Extracting 732.6 to 736.6 m/z (14.783606 to 99.521706 min) [13:04:02] Quant Extracting 736.6 to 740.6 m/z (15.85046 to 100.755135 min) [13:04:02] Quant Extracting 740.6 to 744.6 m/z (8.969425 to 99.129616 min) [13:04:02] Quant Extracting 744.6 to 748.6 m/z (7.16304 to 99.129616 min) [13:04:02] Quant Extracting 748.6 to 752.6 m/z (21.083715 to 97.85513 min) [13:04:03] Quant Extracting 752.6 to 756.6 m/z (9.211842 to 95.84406 min) [13:04:03] Quant Extracting 756.6 to 760.6 m/z (22.875158 to 95.64677 min) [13:04:03] Quant Extracting 760.6 to 764.6 m/z (15.042586 to 100.75755 min) [13:04:03] Quant Extracting 764.6 to 768.6 m/z (12.023118 to 96.77674 min) [13:04:03] Quant Extracting 768.6 to 772.6 m/z (7.2555013 to 99.4501 min) [13:04:03] Quant Extracting 772.6 to 776.6 m/z (12.072626 to 94.42448 min) [13:04:03] Quant Extracting 776.6 to 780.6 m/z (18.953957 to 98.005714 min) [13:04:03] Quant Extracting 780.6 to 784.6 m/z (19.923346 to 97.78038 min) [13:04:03] Quant Extracting 784.6 to 788.6 m/z (8.389688 to 97.75896 min) [13:04:04] Quant Extracting 788.6 to 792.6 m/z (13.236509 to 100.36474 min) [13:04:04] Quant Extracting 792.6 to 796.6 m/z (13.865961 to 95.69713 min) [13:04:04] Quant Extracting 796.6 to 800.6 m/z (14.789097 to 99.23255 min) [13:04:04] Quant Extracting 800.6 to 804.6 m/z (18.181087 to 96.5819 min) [13:04:04] Quant Extracting 804.6 to 808.6 m/z (16.644096 to 96.83111 min) [13:04:04] Quant Extracting 808.6 to 812.6 m/z (16.872433 to 95.65165 min) [13:04:04] Quant Extracting 812.6 to 816.6 m/z (13.0917845 to 100.16926 min) [13:04:04] Quant Extracting 816.6 to 820.6 m/z (23.512218 to 98.055504 min) [13:04:04] Quant Extracting 820.6 to 824.6 m/z (14.159556 to 96.04504 min) [13:04:04] Quant Extracting 824.6 to 828.6 m/z (15.323156 to 100.76247 min) [13:04:04] Quant Extracting 828.6 to 832.6 m/z (25.59633 to 100.71114 min) [13:04:05] Quant Extracting 832.6 to 836.6 m/z (24.289371 to 95.52962 min) [13:04:05] Quant Extracting 836.6 to 840.6 m/z (18.183546 to 100.763084 min) [13:04:05] Quant Extracting 840.6 to 844.6 m/z (11.012663 to 96.09361 min) [13:04:05] Quant Extracting 844.6 to 848.6 m/z (20.607233 to 98.79611 min) [13:04:05] Quant Extracting 848.6 to 852.6 m/z (14.502664 to 100.76431 min) [13:04:05] Quant Extracting 852.6 to 856.6 m/z (16.538044 to 96.0475 min) [13:04:05] Quant Extracting 856.6 to 860.6 m/z (23.173662 to 100.21964 min) [13:04:05] Quant Extracting 860.6 to 864.6 m/z (28.020739 to 98.79735 min) [13:04:05] Quant Extracting 864.6 to 868.6 m/z (21.931715 to 99.09214 min) [13:04:05] Quant Extracting 868.6 to 872.6 m/z (26.277555 to 100.76554 min) [13:04:05] Quant Extracting 872.6 to 876.6 m/z (25.746452 to 97.667656 min) [13:04:05] Quant Extracting 876.6 to 880.7 m/z (32.480762 to 100.62369 min) [13:04:06] Quant Extracting 880.7 to 884.7 m/z (31.705639 to 96.36911 min) [13:04:06] Quant Extracting 884.7 to 888.7 m/z (25.213518 to 96.73864 min) [13:04:06] Quant Extracting 888.7 to 892.7 m/z (28.7502 to 96.98201 min) [13:04:06] Quant Extracting 892.7 to 896.7 m/z (21.336761 to 100.71664 min) [13:04:06] Quant Extracting 896.7 to 900.7 m/z (19.447733 to 98.847694 min) [13:04:06] Quant Extracting 900.7 to 904.7 m/z (27.15255 to 99.48729 min) [13:04:06] Quant Extracting 904.7 to 908.7 m/z (28.848196 to 99.82933 min) [13:04:06] Quant Extracting 908.7 to 912.7 m/z (21.871338 to 98.75028 min) [13:04:06] Quant Extracting 912.7 to 916.7 m/z (27.788078 to 95.17187 min) [13:04:06] Quant Extracting 916.7 to 920.7 m/z (33.887592 to 95.56284 min) [13:04:06] Quant Extracting 920.7 to 924.7 m/z (37.474926 to 96.54442 min) [13:04:06] Quant Extracting 924.7 to 928.7 m/z (27.687593 to 98.3588 min) [13:04:07] Quant Extracting 928.7 to 932.7 m/z (10.050297 to 100.80056 min) [13:04:07] Quant Extracting 932.7 to 936.7 m/z (37.765915 to 99.73317 min) [13:04:07] Quant Extracting 936.7 to 940.7 m/z (37.52339 to 97.672585 min) [13:04:07] Quant Extracting 940.7 to 944.7 m/z (34.4225 to 97.82258 min) [13:04:07] Quant Extracting 944.7 to 948.7 m/z (37.186497 to 99.88377 min) [13:04:07] Quant Extracting 948.7 to 952.7 m/z (35.732155 to 100.37705 min) [13:04:07] Quant Extracting 952.7 to 956.7 m/z (32.051903 to 96.37464 min) [13:04:07] Quant Extracting 956.7 to 960.7 m/z (31.518042 to 95.27178 min) [13:04:07] Quant Extracting 960.7 to 964.7 m/z (39.70583 to 100.80056 min) [13:04:07] Quant Extracting 964.7 to 968.7 m/z (27.303288 to 98.85324 min) [13:04:07] Quant Extracting 968.7 to 972.7 m/z (29.385872 to 100.80056 min) [13:04:07] Quant Extracting 972.7 to 976.7 m/z (30.45371 to 98.119125 min) [13:04:08] Quant Extracting 976.7 to 980.7 m/z (29.047426 to 99.736244 min) [13:04:08] Quant Extracting 980.7 to 984.7 m/z (19.356865 to 100.80056 min) [13:04:08] Quant Extracting 984.7 to 988.7 m/z (15.820453 to 100.08412 min) [13:04:08] Quant Extracting 988.7 to 992.7 m/z (34.038013 to 96.74663 min) [13:04:08] Quant Extracting 992.7 to 996.7 m/z (38.78642 to 96.597244 min) [13:04:08] Quant Extracting 996.7 to 1000.7 m/z (42.279045 to 100.80056 min) [13:04:08] Quant Extracting 1000.7 to 1004.7 m/z (16.112293 to 91.10856 min) [13:04:08] Attempted extraction for: 48640, found 48640 [13:04:08] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_01.mzML (48640 entries)... [13:04:08] Writing 48640 peptides to entries table... [13:04:11] Writing 48640 peptides to peptidequants table... [13:04:14] Finished writing to Encyclopedia ELIB at Wed Jul 17 13:04:14 BST 2024 [13:04:15] Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML: Number of global peptides: 48640 vs local peptides: 45338 [13:04:15] Reading Percolator Results from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML... [13:04:15] Extracting Spectral Data for 45338 Peptides from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML... [13:04:16] Wrote 41494 RT alignment points for Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML [13:04:16] Number of global peptides: 48640 vs local peptides: 45338 [13:04:16] Found additional 0 globally detected peptides without scores in the individual run. Adding those into the list for re-extraction. [13:04:16] Parsed features and scores for 48640 peptides. [13:04:16] Extracting 48640 peptides... [13:04:16] Quant Extracting 396.4 to 400.4 m/z (7.328947 to 78.24973 min) [13:04:16] Quant Extracting 400.4 to 404.4 m/z (5.2280536 to 80.450294 min) [13:04:16] Quant Extracting 404.4 to 408.4 m/z (7.1349926 to 81.91802 min) [13:04:16] Quant Extracting 408.4 to 412.4 m/z (4.347999 to 81.57463 min) [13:04:16] Quant Extracting 412.4 to 416.4 m/z (5.8169026 to 87.00602 min) [13:04:16] Quant Extracting 416.4 to 420.4 m/z (5.962843 to 82.06273 min) [13:04:17] Quant Extracting 420.4 to 424.4 m/z (7.1362233 to 85.517525 min) [13:04:17] Quant Extracting 424.4 to 428.4 m/z (7.2739277 to 85.09614 min) [13:04:17] Quant Extracting 428.4 to 432.4 m/z (7.1863046 to 83.33652 min) [13:04:17] Quant Extracting 432.4 to 436.4 m/z (7.136839 to 81.82189 min) [13:04:17] Quant Extracting 436.4 to 440.5 m/z (7.137454 to 85.44085 min) [13:04:17] Quant Extracting 440.5 to 444.5 m/z (7.137454 to 85.24608 min) [13:04:17] Quant Extracting 444.5 to 448.5 m/z (7.1380696 to 87.251274 min) [13:04:17] Quant Extracting 448.5 to 452.5 m/z (4.252419 to 83.534004 min) [13:04:17] Quant Extracting 452.5 to 456.5 m/z (7.1386843 to 84.21843 min) [13:04:17] Quant Extracting 456.5 to 460.5 m/z (7.1386843 to 85.73672 min) [13:04:17] Quant Extracting 460.5 to 464.5 m/z (6.2133303 to 87.34935 min) [13:04:18] Quant Extracting 464.5 to 468.5 m/z (7.327993 to 87.25251 min) [13:04:18] Quant Extracting 468.5 to 472.5 m/z (7.139916 to 100.77177 min) [13:04:18] Quant Extracting 472.5 to 476.5 m/z (7.236676 to 88.42759 min) [13:04:18] Quant Extracting 476.5 to 480.5 m/z (7.3351045 to 88.08681 min) [13:04:18] Quant Extracting 480.5 to 484.5 m/z (5.7237997 to 88.18605 min) [13:04:18] Quant Extracting 484.5 to 488.5 m/z (7.1411467 to 90.82909 min) [13:04:18] Quant Extracting 488.5 to 492.5 m/z (7.1411467 to 86.470795 min) [13:04:18] Quant Extracting 492.5 to 496.5 m/z (7.1417623 to 86.57003 min) [13:04:18] Quant Extracting 496.5 to 500.5 m/z (7.1417623 to 89.11606 min) [13:04:18] Quant Extracting 500.5 to 504.5 m/z (7.1423717 to 88.52871 min) [13:04:18] Quant Extracting 504.5 to 508.5 m/z (7.1423717 to 92.2028 min) [13:04:19] Quant Extracting 508.5 to 512.5 m/z (7.143561 to 93.622604 min) [13:04:19] Quant Extracting 512.5 to 516.5 m/z (7.143561 to 92.59991 min) [13:04:19] Quant Extracting 516.5 to 520.5 m/z (7.144176 to 92.007965 min) [13:04:19] Quant Extracting 520.5 to 524.5 m/z (6.1668954 to 92.05587 min) [13:04:19] Quant Extracting 524.5 to 528.5 m/z (7.1447897 to 91.61973 min) [13:04:19] Quant Extracting 528.5 to 532.5 m/z (7.1447897 to 89.02234 min) [13:04:19] Quant Extracting 532.5 to 536.5 m/z (7.145404 to 93.576546 min) [13:04:19] Quant Extracting 536.5 to 540.5 m/z (7.145404 to 92.84078 min) [13:04:19] Quant Extracting 540.5 to 544.5 m/z (7.1460204 to 96.03242 min) [13:04:19] Quant Extracting 544.5 to 548.5 m/z (7.1460204 to 91.568146 min) [13:04:20] Quant Extracting 548.5 to 552.5 m/z (7.146635 to 96.62303 min) [13:04:20] Quant Extracting 552.5 to 556.5 m/z (7.146635 to 94.21754 min) [13:04:20] Quant Extracting 556.5 to 560.5 m/z (7.1472483 to 92.44984 min) [13:04:20] Quant Extracting 560.5 to 564.5 m/z (6.9052663 to 97.70389 min) [13:04:20] Quant Extracting 564.5 to 568.5 m/z (8.078052 to 92.89218 min) [13:04:20] Quant Extracting 568.5 to 572.5 m/z (7.147864 to 92.15818 min) [13:04:20] Quant Extracting 572.5 to 576.5 m/z (7.148479 to 92.451065 min) [13:04:20] Quant Extracting 576.5 to 580.5 m/z (7.148479 to 97.50968 min) [13:04:20] Quant Extracting 580.5 to 584.5 m/z (7.1490927 to 94.41734 min) [13:04:20] Quant Extracting 584.5 to 588.5 m/z (7.128758 to 93.52951 min) [13:04:20] Quant Extracting 588.5 to 592.5 m/z (7.1497083 to 94.80885 min) [13:04:20] Quant Extracting 592.5 to 596.5 m/z (7.129375 to 92.70296 min) [13:04:21] Quant Extracting 596.5 to 600.5 m/z (7.1912107 to 92.172775 min) [13:04:21] Quant Extracting 600.5 to 604.5 m/z (7.1503224 to 94.66538 min) [13:04:21] Quant Extracting 604.5 to 608.5 m/z (7.150938 to 97.018265 min) [13:04:21] Quant Extracting 608.5 to 612.5 m/z (7.1918263 to 93.68135 min) [13:04:21] Quant Extracting 612.5 to 616.5 m/z (7.1515512 to 99.71741 min) [13:04:21] Quant Extracting 616.5 to 620.5 m/z (7.1515512 to 94.95889 min) [13:04:21] Quant Extracting 620.5 to 624.5 m/z (12.252651 to 96.23586 min) [13:04:21] Quant Extracting 624.5 to 628.5 m/z (7.152166 to 93.63121 min) [13:04:21] Quant Extracting 628.5 to 632.5 m/z (7.152781 to 96.13785 min) [13:04:22] Quant Extracting 632.5 to 636.5 m/z (7.1324525 to 97.462616 min) [13:04:22] Quant Extracting 636.5 to 640.5 m/z (7.2022815 to 95.35468 min) [13:04:22] Quant Extracting 640.5 to 644.5 m/z (10.51048 to 96.873146 min) [13:04:22] Quant Extracting 644.5 to 648.5 m/z (9.299252 to 95.50002 min) [13:04:22] Quant Extracting 648.5 to 652.5 m/z (11.043232 to 96.285614 min) [13:04:22] Quant Extracting 652.5 to 656.5 m/z (7.1546264 to 95.69612 min) [13:04:22] Quant Extracting 656.5 to 660.6 m/z (14.485251 to 97.37803 min) [13:04:22] Quant Extracting 660.6 to 664.6 m/z (7.2566266 to 95.35332 min) [13:04:22] Quant Extracting 664.6 to 668.6 m/z (19.281315 to 96.1882 min) [13:04:22] Quant Extracting 668.6 to 672.6 m/z (11.626722 to 95.061226 min) [13:04:23] Quant Extracting 672.6 to 676.6 m/z (7.155856 to 96.7297 min) [13:04:23] Quant Extracting 676.6 to 680.6 m/z (16.085264 to 98.34859 min) [13:04:23] Quant Extracting 680.6 to 684.6 m/z (9.49537 to 99.57643 min) [13:04:23] Quant Extracting 684.6 to 688.6 m/z (7.1570864 to 95.16108 min) [13:04:23] Quant Extracting 688.6 to 692.6 m/z (7.1570864 to 96.53548 min) [13:04:23] Quant Extracting 692.6 to 696.6 m/z (7.1986094 to 100.758896 min) [13:04:23] Quant Extracting 696.6 to 700.6 m/z (7.450778 to 96.22042 min) [13:04:23] Quant Extracting 700.6 to 704.6 m/z (7.210803 to 100.759514 min) [13:04:23] Quant Extracting 704.6 to 708.6 m/z (7.158316 to 100.02012 min) [13:04:23] Quant Extracting 708.6 to 712.6 m/z (7.1589303 to 100.77177 min) [13:04:24] Quant Extracting 712.6 to 716.6 m/z (12.356836 to 97.8142 min) [13:04:24] Quant Extracting 716.6 to 720.6 m/z (9.207964 to 100.11999 min) [13:04:24] Quant Extracting 720.6 to 724.6 m/z (13.470511 to 99.48268 min) [13:04:24] Quant Extracting 724.6 to 728.6 m/z (11.185283 to 95.266464 min) [13:04:24] Quant Extracting 728.6 to 732.6 m/z (7.1601605 to 96.29747 min) [13:04:24] Quant Extracting 732.6 to 736.6 m/z (14.878583 to 99.49257 min) [13:04:24] Quant Extracting 736.6 to 740.6 m/z (15.8486 to 100.76259 min) [13:04:24] Quant Extracting 740.6 to 744.6 m/z (8.968077 to 99.139015 min) [13:04:24] Quant Extracting 744.6 to 748.6 m/z (7.202303 to 99.190384 min) [13:04:24] Quant Extracting 748.6 to 752.6 m/z (21.034039 to 97.816666 min) [13:04:24] Quant Extracting 752.6 to 756.6 m/z (9.066119 to 95.75487 min) [13:04:25] Quant Extracting 756.6 to 760.6 m/z (23.068756 to 95.75487 min) [13:04:25] Quant Extracting 760.6 to 764.6 m/z (14.9282875 to 100.765 min) [13:04:25] Quant Extracting 764.6 to 768.6 m/z (12.021241 to 96.73703 min) [13:04:25] Quant Extracting 768.6 to 772.6 m/z (7.20415 to 99.48695 min) [13:04:25] Quant Extracting 772.6 to 776.6 m/z (12.021857 to 94.43211 min) [13:04:25] Quant Extracting 776.6 to 780.6 m/z (18.952425 to 98.015175 min) [13:04:25] Quant Extracting 780.6 to 784.6 m/z (19.922606 to 97.819695 min) [13:04:25] Quant Extracting 784.6 to 788.6 m/z (8.435163 to 97.72936 min) [13:04:25] Quant Extracting 788.6 to 792.6 m/z (13.331801 to 100.275475 min) [13:04:25] Quant Extracting 792.6 to 796.6 m/z (13.817175 to 95.75852 min) [13:04:26] Quant Extracting 796.6 to 800.6 m/z (14.787262 to 99.24199 min) [13:04:26] Quant Extracting 800.6 to 804.6 m/z (18.276405 to 96.597855 min) [13:04:26] Quant Extracting 804.6 to 808.6 m/z (16.579826 to 96.787445 min) [13:04:26] Quant Extracting 808.6 to 812.6 m/z (16.921045 to 95.66111 min) [13:04:26] Quant Extracting 812.6 to 816.6 m/z (13.139807 to 100.22599 min) [13:04:26] Quant Extracting 816.6 to 820.6 m/z (23.55852 to 98.1169 min) [13:04:26] Quant Extracting 820.6 to 824.6 m/z (14.110154 to 96.05453 min) [13:04:26] Quant Extracting 824.6 to 828.6 m/z (15.395585 to 100.76993 min) [13:04:26] Quant Extracting 828.6 to 832.6 m/z (25.548676 to 100.71862 min) [13:04:26] Quant Extracting 832.6 to 836.6 m/z (24.289629 to 95.514175 min) [13:04:26] Quant Extracting 836.6 to 840.6 m/z (18.229223 to 100.77054 min) [13:04:27] Quant Extracting 840.6 to 844.6 m/z (10.863888 to 96.05637 min) [13:04:27] Quant Extracting 844.6 to 848.6 m/z (20.653831 to 98.65562 min) [13:04:27] Quant Extracting 848.6 to 852.6 m/z (14.450238 to 100.77177 min) [13:04:27] Quant Extracting 852.6 to 856.6 m/z (16.680305 to 96.056984 min) [13:04:27] Quant Extracting 856.6 to 860.6 m/z (23.173372 to 100.281006 min) [13:04:27] Quant Extracting 860.6 to 864.6 m/z (27.923979 to 98.75605 min) [13:04:27] Quant Extracting 864.6 to 868.6 m/z (21.867638 to 99.101524 min) [13:04:27] Quant Extracting 868.6 to 872.6 m/z (26.229845 to 100.77177 min) [13:04:27] Quant Extracting 872.6 to 876.6 m/z (25.696026 to 97.62981 min) [13:04:27] Quant Extracting 876.6 to 880.7 m/z (32.48147 to 100.62425 min) [13:04:27] Quant Extracting 880.7 to 884.7 m/z (31.75642 to 96.30401 min) [13:04:27] Quant Extracting 884.7 to 888.7 m/z (25.213312 to 96.69734 min) [13:04:28] Quant Extracting 888.7 to 892.7 m/z (28.653307 to 97.04099 min) [13:04:28] Quant Extracting 892.7 to 896.7 m/z (21.336178 to 100.724106 min) [13:04:28] Quant Extracting 896.7 to 900.7 m/z (19.44642 to 98.906685 min) [13:04:28] Quant Extracting 900.7 to 904.7 m/z (27.104462 to 99.544685 min) [13:04:28] Quant Extracting 904.7 to 908.7 m/z (28.848177 to 99.79149 min) [13:04:28] Quant Extracting 908.7 to 912.7 m/z (21.967468 to 98.85837 min) [13:04:28] Quant Extracting 912.7 to 916.7 m/z (27.742163 to 95.12813 min) [13:04:28] Quant Extracting 916.7 to 920.7 m/z (33.839294 to 95.52151 min) [13:04:28] Quant Extracting 920.7 to 924.7 m/z (37.328915 to 96.55387 min) [13:04:28] Quant Extracting 924.7 to 928.7 m/z (27.638708 to 99.10582 min) [13:04:28] Quant Extracting 928.7 to 932.7 m/z (9.952045 to 100.77177 min) [13:04:28] Quant Extracting 932.7 to 936.7 m/z (37.66937 to 99.704094 min) [13:04:28] Quant Extracting 936.7 to 940.7 m/z (37.37968 to 97.71599 min) [13:04:29] Quant Extracting 940.7 to 944.7 m/z (34.422894 to 97.78126 min) [13:04:29] Quant Extracting 944.7 to 948.7 m/z (37.186775 to 99.89323 min) [13:04:29] Quant Extracting 948.7 to 952.7 m/z (35.58675 to 100.485054 min) [13:04:29] Quant Extracting 952.7 to 956.7 m/z (32.107414 to 96.360916 min) [13:04:29] Quant Extracting 956.7 to 960.7 m/z (31.325203 to 95.23045 min) [13:04:29] Quant Extracting 960.7 to 964.7 m/z (39.559566 to 100.77177 min) [13:04:29] Quant Extracting 964.7 to 968.7 m/z (27.254078 to 98.911606 min) [13:04:29] Quant Extracting 968.7 to 972.7 m/z (29.385962 to 100.77177 min) [13:04:29] Quant Extracting 972.7 to 976.7 m/z (30.406843 to 98.029945 min) [13:04:29] Quant Extracting 976.7 to 980.7 m/z (28.997967 to 99.69839 min) [13:04:29] Quant Extracting 980.7 to 984.7 m/z (19.306505 to 100.77177 min) [13:04:29] Quant Extracting 984.7 to 988.7 m/z (15.800776 to 100.04221 min) [13:04:29] Quant Extracting 988.7 to 992.7 m/z (33.941765 to 96.75427 min) [13:04:30] Quant Extracting 992.7 to 996.7 m/z (38.690105 to 96.658066 min) [13:04:30] Quant Extracting 996.7 to 1000.7 m/z (42.084534 to 100.77177 min) [13:04:30] Quant Extracting 1000.7 to 1004.7 m/z (16.013647 to 91.01552 min) [13:04:30] Attempted extraction for: 48640, found 48640 [13:04:30] Writing Encyclopedia ELIB from Inst-Exploris480_Date-2024JUL09_Evts-_Meth-90min_DIA_Cond-50cm_02.mzML (48640 entries)... [13:04:30] Writing 48640 peptides to entries table... [13:04:32] Writing 48640 peptides to peptidequants table... [13:04:35] Finished writing to Encyclopedia ELIB at Wed Jul 17 13:04:35 BST 2024 [13:04:35] Writing global target/decoy peptides: 48640/2465, pi0: 0.177637 [13:04:36] Writing global target/decoy proteins: 5831/58 [13:04:48] Getting source files... [13:04:48] Found 4 data files [13:04:48] 10000 records processed... [13:04:49] 20000 records processed... [13:04:49] 30000 records processed... [13:04:49] 40000 records processed... [13:04:49] 50000 records processed... [13:04:49] 60000 records processed... [13:04:49] 70000 records processed... [13:04:50] 80000 records processed... [13:04:50] 90000 records processed... [13:04:50] 100000 records processed... [13:04:50] 110000 records processed... [13:04:50] 120000 records processed... [13:04:50] 130000 records processed... [13:04:51] 140000 records processed... [13:04:51] 150000 records processed... [13:04:51] 160000 records processed... [13:04:51] 170000 records processed... [13:04:51] 180000 records processed... [13:04:51] 190000 records processed... [13:04:52] Finished processing 194464 records, found 48616 quantitative unique peptides. Writing reports... [13:04:52] Inconsistent number of fragments in 23891 of 48616 peptides [13:04:52] Finished writing peptide report for 190640 unique peptides! [13:04:52] Finished writing protein report for 5829 protein groups! Search done.