C:\DIA-NN\2.3.1>set ROOTFOLDER=E:\Shubham\DIANN\results C:\DIA-NN\2.3.1>set SKYLINEFOLDER=C:\DIA-NN\2.3.1 C:\DIA-NN\2.3.1>set SKYLINEFILEBASE=Batch1234_colon_full2_diann3_skyline C:\DIA-NN\2.3.1>del E:\Shubham\DIANN\results\Batch1234_colon_full2_diann3_skyline.* "C:\DIA-NN\2.3.1>set SKYLINEEXEC=""C:\DIA-NN\2.3.1\SkylineRunner.exe""" "C:\DIA-NN\2.3.1>""C:\DIA-NN\2.3.1\SkylineRunner.exe"" --timestamp --dir=E:\Shubham\DIANN\results --overwrite --new=Batch1234_colon_full2_diann3_skyline.sky --import-search-cutoff-score=0 --import-search-add-mods --import-search-file=""E:\Shubham\DIANN\results\Batch1234_colon_full2_diann3-lib.parquet.skyline.speclib"" --pep-max-missed-cleavages=2 --pep-min-length=6 --pep-max-length=50 --pep-exclude-nterminal-aas=0 --tran-precursor-ion-charges=""1,2,3,4"" --tran-product-ion-charges=""1,2"" --tran-product-ion-types=""y,b,p"" --tran-product-start-ion=""ion 3"" --tran-product-end-ion=""last ion"" --tran-product-clear-special-ions --library-match-tolerance=10ppm --library-product-ions=12 --library-min-product-ions=4 --library-pick-product-ions=filter --full-scan-precursor-analyzer=centroided --full-scan-precursor-isotopes=Count --full-scan-precursor-threshold=3 --full-scan-precursor-res=20 --full-scan-product-analyzer=centroided --full-scan-product-res=20 --ims-library-res=20 --full-scan-rt-filter=ms2_ids --full-scan-rt-filter-tolerance=2 --instrument-min-mz=50 --instrument-max-mz=2000 --full-scan-acquisition-method=DIA --full-scan-isolation-scheme=""Results only"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_070_DIA_Slot2-5_1_4248.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_076_DIA_Slot2-11_1_4254.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_067_DIA_Slot2-2_1_4245.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_077_DIA_Slot2-12_1_4255.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_066_DIA_Slot2-1_1_4244.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_048_DIA_Slot1-40_1_4229.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_040_DIA_Slot1-32_1_4221.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_029_DIA_Slot1-21_1_4210.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_006_DIA_Slot1-4_1_4193.d"" --import-file=""E:\Shubham\diaData\20250605_Stanford-Snyder_004_DIA_Slot1-2_1_4191.d"" --import-search-exclude-library-sources --import-fasta=""E:\Shubham\DIANN\lib\2025-01-04-contam-A002014015_vep.fasta.fas"" --associate-proteins-shared-peptides=DuplicatedBetweenProteins" [2026/01/16 01:40:32] File Batch1234_colon_full2_diann3_skyline.sky opened. Transition Settings -- Filter changed "Settings > Transition Settings -- Filter > Peptide Ion charges changed from ""1"" to ""1, 2""" "Settings > Transition Settings -- Filter > Ion types changed from ""p"" to ""y, b, p""" "Settings > Transition Settings -- Filter > Product ion selection start changed from ""m/z > precursor"" to ""ion 3""" "Settings > Transition Settings -- Filter > Product ion selection end changed from ""3 ions"" to ""last ion""" Settings > Transition Settings -- Filter > Special ions: removed all "Transition Settings -- Instrument > Max m/z changed to ""2000""" "Settings > Transition Settings -- Instrument > Max m/z changed from ""1500"" to ""2000""" Transition Settings -- Library changed "Settings > Transition Settings -- Library > Ion match tolerance changed from ""0.5"" m/z to ""10"" ppm" "Settings > Transition Settings -- Library > Minimum product ions changed from ""0"" to ""4""" "Settings > Transition Settings -- Library > Product ions changed from ""3"" to ""12""" "Settings > Transition Settings -- Library > Pick changed from ""From filtered ion charges and types"" to ""From filtered product ions""" Transition Settings -- Full-Scan changed "Settings > Transition Settings -- Full-Scan > Acquisition method changed from ""None"" to ""DIA""" "Settings > Transition Settings -- Full-Scan > Isolation scheme changed from Missing to ""Results only""" "Settings > Transition Settings -- Full-Scan > Isolation scheme > Isolation width is ""Results""" Settings > Transition Settings -- Full-Scan > Isolation scheme > Prespecified isolation windows is Empty "Settings > Transition Settings -- Full-Scan > Product mass analyzer changed from ""None"" to ""Centroided""" "Settings > Transition Settings -- Full-Scan > Mass accuracy changed from Missing to ""20""" "Settings > Transition Settings -- Full-Scan > Retention time filter length changed from ""5"" to ""2""" "Peptide Settings -- Digestion > Max missed cleavages changed to ""2""" "Settings > Peptide Settings -- Digestion > Max missed cleavages changed from ""0"" to ""2""" Peptide Settings -- Filter changed "Settings > Peptide Settings -- Filter > Exclude N-terminal AAs changed from ""25"" to ""0""" "Settings > Peptide Settings -- Filter > Min length changed from ""8"" to ""6""" "Settings > Peptide Settings -- Filter > Max length changed from ""25"" to ""50""" [2026/01/16 01:40:35] Enabling extraction based on spectral library ion mobility values. [2026/01/16 01:40:35] Changing ion mobility spectral library resolving power to 20. [2026/01/16 01:40:35] Creating spectral library from files: [2026/01/16 01:40:35] Batch1234_colon_full2_diann3-lib.parquet.skyline.speclib [2026/01/16 01:40:36] Loading library [2026/01/16 01:40:37] Building binary cache for Batch1234_colon_full2_diann3_skyline.blib library [2026/01/16 01:40:59] 100% "[2026/01/16 01:41:02] 99% - Loading Batch1234_colon_full2_diann3_skyline.blib library," [2026/01/16 01:41:02] 100% [2026/01/16 01:41:02] Adding 4 modifications. [2026/01/16 01:41:02] Importing FASTA file 2025-01-04-contam-A002014015_vep.fasta.fas... [2026/01/16 01:41:06] 0% [2026/01/16 01:41:11] Adding protein ENSP00000028008.5 284 proteins and 25 peptides added [2026/01/16 01:41:14] Adding protein ENSP00000193391.6 807 proteins and 53 peptides added [2026/01/16 01:41:18] Adding protein ENSP00000217043.3 1613 proteins and 131 peptides added [2026/01/16 01:41:22] 1% - Adding protein ENSP00000222718.5:p.Pro73Ser 112 proteins and 168 peptides added [2026/01/16 01:41:24] Adding protein ENSP00000233954.1:p.Glu398Asp 172 proteins and 320 peptides added [2026/01/16 01:41:28] 2% - Adding protein ENSP00000243077.3:p.Val3182Ala 204 proteins and 353 peptides added [2026/01/16 01:41:41] Adding protein ENSP00000249700.4:p.Pro63Ala 249 proteins and 439 peptides added [2026/01/16 01:41:44] 3% - Adding protein ENSP00000252999.3:p.Val1900Met 292 proteins and 613 peptides added [2026/01/16 01:41:49] Adding protein ENSP00000255616.7:p.Gln65Arg 312 proteins and 656 peptides added [2026/01/16 01:42:01] Adding protein ENSP00000258341.3:p.Phe386Leu 331 proteins and 677 peptides added [2026/01/16 01:42:26] 4% - Adding protein ENSP00000261169.6 345 proteins and 727 peptides added [2026/01/16 01:42:56] Adding protein ENSP00000261835.3 370 proteins and 756 peptides added [2026/01/16 01:43:18] 5% - Adding protein ENSP00000262467.5:p.Thr246Ser 395 proteins and 817 peptides added [2026/01/16 01:43:24] Adding protein ENSP00000263202.9:p.Val115Ile 413 proteins and 835 peptides added [2026/01/16 01:43:40] Adding protein ENSP00000264042.3:p.Ala861_Pro862insAspArgLysSerValValThrArgLeuGluLysGluLysTrpMetLeuAspLeuAsnSerAlaIleGlnAlaAlaLysSerGlyGlyAspThrAla 422 proteins and 845 peptides added [2026/01/16 01:43:46] Adding protein ENSP00000264668.2:p.Lys377Arg 441 proteins and 864 peptides added [2026/01/16 01:43:51] 6% - Adding protein ENSP00000265362.3:p.Ile334Val 456 proteins and 880 peptides added [2026/01/16 01:43:55] Adding protein ENSP00000267488.4 473 proteins and 901 peptides added [2026/01/16 01:44:16] Adding protein ENSP00000269499.4:p.Glu211Gly 488 proteins and 928 peptides added [2026/01/16 01:44:41] 7% - Adding protein ENSP00000273859.3:p.Ser1389Thr 502 proteins and 976 peptides added [2026/01/16 01:45:16] Adding protein ENSP00000278886.6:p.Lys1200Asn 545 proteins and 1028 peptides added [2026/01/16 01:45:41] Adding protein ENSP00000282276.6:p.Arg12Cys 580 proteins and 1067 peptides added [2026/01/16 01:45:47] 8% - Adding protein ENSP00000286639.6 608 proteins and 1110 peptides added [2026/01/16 01:46:11] Adding protein ENSP00000291182.3:p.Ala616Ser 632 proteins and 1148 peptides added [2026/01/16 01:46:16] 9% - Adding protein ENSP00000295488.3:p.Gln99dup 639 proteins and 1167 peptides added [2026/01/16 01:46:36] Adding protein ENSP00000296702.5:p.Asn850_Glu875dup 660 proteins and 1191 peptides added [2026/01/16 01:46:58] 10% - Adding protein ENSP00000298784.1:p.Gly698= 676 proteins and 1229 peptides added [2026/01/16 01:47:08] Adding protein ENSP00000300714.3:p.Ser210Pro 704 proteins and 1260 peptides added [2026/01/16 01:47:14] Adding protein ENSP00000302344.7:p.Glu287Ala 727 proteins and 1287 peptides added [2026/01/16 01:47:28] 11% - Adding protein ENSP00000304072.5:p.Glu287Gly 759 proteins and 1328 peptides added [2026/01/16 01:47:32] Adding protein ENSP00000306121.8:p.Phe701Ser 787 proteins and 1380 peptides added [2026/01/16 01:47:35] Adding protein ENSP00000308165.7:p.Ala107Pro 815 proteins and 1442 peptides added [2026/01/16 01:47:42] 12% - Adding protein ENSP00000310301.6:p.Leu59= 842 proteins and 1476 peptides added [2026/01/16 01:47:56] Adding protein ENSP00000312222.4:p.Ser790Asn 863 proteins and 1522 peptides added [2026/01/16 01:48:04] Adding protein ENSP00000313851.10:p.Lys20Asn 882 proteins and 1553 peptides added [2026/01/16 01:48:09] 13% - Adding protein ENSP00000316032.7:p.Thr261_Ser262insThrGlyThrThrThrGlyLeuPheGlySerSerProAlaThrSerSerAlaThrGlyLeuPheSerSerSerThrThrAsnSerGlyPheAlaTyrGlyGlnAsnLysThrAlaPheGlyThr 935 proteins and 1631 peptides added [2026/01/16 01:48:20] Adding protein ENSP00000318111.6:p.Leu402= 959 proteins and 1655 peptides added [2026/01/16 01:48:30] 14% - Adding protein ENSP00000320794.4:p.Glu1355Gly 994 proteins and 1790 peptides added [2026/01/16 01:48:39] Adding protein ENSP00000323071.4:p.Arg57Cys 1019 proteins and 1831 peptides added [2026/01/16 01:48:46] Adding protein ENSP00000324323.5 1062 proteins and 1906 peptides added [2026/01/16 01:48:51] 15% - Adding protein ENSP00000326253.4 1090 proteins and 1939 peptides added [2026/01/16 01:49:16] Adding protein ENSP00000328277.6:p.Ala67Val 1099 proteins and 2005 peptides added [2026/01/16 01:49:46] Adding protein ENSP00000330805.6:p.Ser193Asn 1154 proteins and 2122 peptides added [2026/01/16 01:49:56] 16% - Adding protein ENSP00000333674.7:p.His558Arg 1188 proteins and 2252 peptides added [2026/01/16 01:50:02] Adding protein ENSP00000334714.4:p.Asn2401Ser 1207 proteins and 2277 peptides added [2026/01/16 01:50:26] 17% - Adding protein ENSP00000337290.4:p.Ser875Pro 1235 proteins and 2321 peptides added [2026/01/16 01:50:56] Adding protein ENSP00000339445.5:p.Ala902Val 1264 proteins and 2389 peptides added [2026/01/16 01:51:26] Adding protein ENSP00000340554.6:p.Lys23783Arg 1279 proteins and 2414 peptides added [2026/01/16 01:51:53] 18% - Adding protein ENSP00000341151.7 1292 proteins and 2441 peptides added [2026/01/16 01:52:16] Adding protein ENSP00000341930.2:p.Pro261Leu 1306 proteins and 2482 peptides added [2026/01/16 01:52:40] Adding protein ENSP00000343535.4:p.Gln5Arg 1328 proteins and 2552 peptides added [2026/01/16 01:53:01] Adding protein ENSP00000343764.6:p.Lys1201Glu 1344 proteins and 2568 peptides added [2026/01/16 01:53:36] Adding protein ENSP00000343930.3:p.Ala100Thr 1363 proteins and 2587 peptides added [2026/01/16 01:53:52] 19% - Adding protein ENSP00000344855.3 1415 proteins and 2693 peptides added [2026/01/16 01:54:17] Adding protein ENSP00000346372.2:p.Leu484Pro 1432 proteins and 2715 peptides added [2026/01/16 01:54:44] Adding protein ENSP00000347188.6:p.Ala232Thr 1505 proteins and 2859 peptides added [2026/01/16 01:55:06] 20% - Adding protein ENSP00000348498.3:p.Lys2521_Ser2522insArgThrArgLys 1542 proteins and 2903 peptides added [2026/01/16 01:55:26] Adding protein ENSP00000349213.4:p.Val996Ala 1594 proteins and 3025 peptides added [2026/01/16 01:55:36] Adding protein ENSP00000349903.3:p.Lys295Arg 1610 proteins and 3062 peptides added [2026/01/16 01:55:51] 21% - Adding protein ENSP00000350719.3:p.Trp4001Gln 1671 proteins and 3173 peptides added [2026/01/16 01:56:30] Adding protein ENSP00000351697.3:p.Ser788Gly 1705 proteins and 3213 peptides added [2026/01/16 01:56:56] Adding protein ENSP00000352154.5:p.Gln22270Arg 1726 proteins and 3235 peptides added [2026/01/16 01:57:09] Adding protein ENSP00000352572.5:p.Leu1616Met 1730 proteins and 3243 peptides added [2026/01/16 01:57:13] Adding protein ENSP00000353114.4:p.Pro1562Leu 1756 proteins and 3288 peptides added [2026/01/16 01:57:22] 22% - Adding protein ENSP00000353646.5:p.Ile229Val 1783 proteins and 3413 peptides added [2026/01/16 01:57:56] Adding protein ENSP00000354508.3:p.Gln3642His 1796 proteins and 3430 peptides added [2026/01/16 01:58:31] Adding protein ENSP00000354943.5:p.Val160Ala 1815 proteins and 3510 peptides added [2026/01/16 01:59:06] 23% - Adding protein ENSP00000355465.1:p.Asn883Ser 1834 proteins and 3546 peptides added [2026/01/16 01:59:46] Adding protein ENSP00000355960.3:p.Cys764Tyr 1840 proteins and 3561 peptides added [2026/01/16 02:00:21] Adding protein ENSP00000356379.4:p.Ile2428Phe 1849 proteins and 3578 peptides added [2026/01/16 02:01:01] 24% - Adding protein ENSP00000357198.3:p.Glu1369Gly 1883 proteins and 3616 peptides added [2026/01/16 02:01:41] Adding protein ENSP00000357905.3:p.Tyr1537Ser 1899 proteins and 3633 peptides added [2026/01/16 02:02:21] 25% - Adding protein ENSP00000358747.3:p.Val576Ala 1906 proteins and 3643 peptides added [2026/01/16 02:02:51] Adding protein ENSP00000359660.3:p.Ala28Thr 1943 proteins and 3681 peptides added [2026/01/16 02:03:26] Adding protein ENSP00000360431.2:p.Thr1777Ile 1964 proteins and 3711 peptides added [2026/01/16 02:03:51] 26% - Adding protein ENSP00000361289.4:p.Phe24Leu 1973 proteins and 3724 peptides added [2026/01/16 02:04:31] Adding protein ENSP00000362006.4:p.Glu6311Lys 1986 proteins and 3744 peptides added [2026/01/16 02:05:11] 27% - Adding protein ENSP00000362580.3:p.Ala234= 2024 proteins and 3804 peptides added [2026/01/16 02:05:51] Adding protein ENSP00000363193.3:p.Tyr283_His318dup 2072 proteins and 3872 peptides added [2026/01/16 02:06:26] Adding protein ENSP00000363832.2:p.Ile1283Val 2104 proteins and 3922 peptides added [2026/01/16 02:07:01] 28% - Adding protein ENSP00000364678.4:p.Ser1057Arg 2110 proteins and 3930 peptides added [2026/01/16 02:07:36] Adding protein ENSP00000365588.3:p.Ser1540Pro 2115 proteins and 3940 peptides added [2026/01/16 02:08:11] 29% - Adding protein ENSP00000366475.3:p.Asn317Ser 2135 proteins and 3960 peptides added [2026/01/16 02:08:46] Adding protein ENSP00000367263.4:p.Glu2605_Val2620del 2165 proteins and 4178 peptides added [2026/01/16 02:09:21] Adding protein ENSP00000368349.3:p.Trp1084Arg 2202 proteins and 4450 peptides added [2026/01/16 02:10:01] 30% - Adding protein ENSP00000368755.3:p.Gly127Ala 2216 proteins and 4494 peptides added [2026/01/16 02:10:36] Adding protein ENSP00000369126.3 2227 proteins and 4505 peptides added [2026/01/16 02:11:06] Adding protein ENSP00000370034.3:p.Asn799Tyr 2275 proteins and 4599 peptides added [2026/01/16 02:11:41] 31% - Adding protein ENSP00000371462.1:p.Ala1708Thr 2287 proteins and 4620 peptides added [2026/01/16 02:12:11] Adding protein ENSP00000372613.3 2303 proteins and 4648 peptides added [2026/01/16 02:12:46] Adding protein ENSP00000374212.2:p.Val1590Ala 2337 proteins and 4689 peptides added [2026/01/16 02:13:21] 32% - Adding protein ENSP00000375863.2:p.Thr804= 2369 proteins and 4723 peptides added [2026/01/16 02:14:01] Adding protein ENSP00000376814.3:p.Ile92_Gly121dup 2379 proteins and 4738 peptides added [2026/01/16 02:14:36] 33% - Adding protein ENSP00000377529.2 2400 proteins and 4778 peptides added [2026/01/16 02:15:16] Adding protein ENSP00000378260.3:p.Ile593_Arg594insLeuIleSerGluMetAspIleLysGlnGlnLysLysMetPheLysLysIle 2434 proteins and 4813 peptides added [2026/01/16 02:15:56] Adding protein ENSP00000379053.3:p.Arg496Ser 2457 proteins and 4857 peptides added [2026/01/16 02:16:31] 34% - Adding protein ENSP00000379709.2:p.Leu1703Phe 2498 proteins and 5029 peptides added [2026/01/16 02:17:11] Adding protein ENSP00000380785.2:p.Arg656Pro 2519 proteins and 5057 peptides added [2026/01/16 02:17:46] 35% - Adding protein ENSP00000381604.1:p.Leu166Pro 2532 proteins and 5122 peptides added [2026/01/16 02:18:21] Adding protein ENSP00000382292.2 2603 proteins and 5257 peptides added [2026/01/16 02:19:01] Adding protein ENSP00000382779.1 2604 proteins and 5259 peptides added [2026/01/16 02:19:36] Adding protein ENSP00000384204.3:p.Leu366_Leu396dup 2626 proteins and 5287 peptides added [2026/01/16 02:20:16] 36% - Adding protein ENSP00000384845.1:p.Arg121_Thr147dup 2632 proteins and 5293 peptides added [2026/01/16 02:20:51] Adding protein ENSP00000385852.2:p.Ala259Val 2658 proteins and 5372 peptides added [2026/01/16 02:21:26] 37% - Adding protein ENSP00000386512.1:p.Glu2012Gly 2669 proteins and 5385 peptides added [2026/01/16 02:21:56] Adding protein ENSP00000386881.3:p.Cys1006Ser 2682 proteins and 5404 peptides added [2026/01/16 02:22:31] Adding protein ENSP00000387641.2:p.Ala1225Thr 2692 proteins and 5420 peptides added [2026/01/16 02:23:06] 38% - Adding protein ENSP00000388475.1:p.Asp397= 2744 proteins and 5523 peptides added [2026/01/16 02:23:46] Adding protein ENSP00000390158.2:p.Glu3722Asp 2767 proteins and 5572 peptides added [2026/01/16 02:24:21] 39% - Adding protein ENSP00000391765.1 2788 proteins and 5617 peptides added [2026/01/16 02:25:01] Adding protein ENSP00000392336.2:p.Ile31885Met 2794 proteins and 5625 peptides added [2026/01/16 02:25:41] Adding protein ENSP00000392812.1:p.Ser408Cys 2803 proteins and 5634 peptides added [2026/01/16 02:26:16] 40% - Adding protein ENSP00000393723.2 2842 proteins and 5683 peptides added [2026/01/16 02:26:51] Adding protein ENSP00000394672.2:p.Asn22527Asp 2878 proteins and 5721 peptides added [2026/01/16 02:27:31] Adding protein ENSP00000394672.2:p.Trp18319Arg 2878 proteins and 5721 peptides added [2026/01/16 02:28:11] Adding protein ENSP00000395538.1:p.Arg1998= 2904 proteins and 5780 peptides added [2026/01/16 02:28:51] 41% - Adding protein ENSP00000396576.2:p.Thr660Ala 2918 proteins and 5804 peptides added [2026/01/16 02:29:31] Adding protein ENSP00000396805.3:p.Leu16944Ile 2924 proteins and 5810 peptides added [2026/01/16 02:30:06] Adding protein ENSP00000396955.2:p.Val89Met 2929 proteins and 5815 peptides added [2026/01/16 02:30:46] Adding protein ENSP00000398481.2:p.Glu798Val 2967 proteins and 5853 peptides added [2026/01/16 02:31:26] 42% - Adding protein ENSP00000399994.3 2985 proteins and 5911 peptides added [2026/01/16 02:32:01] Adding protein ENSP00000401197.2:p.Asp36His 3027 proteins and 6012 peptides added [2026/01/16 02:32:40] 43% - Adding protein ENSP00000402049.1 3057 proteins and 6060 peptides added [2026/01/16 02:33:21] Adding protein ENSP00000403208.2:p.Asp410Tyr 3061 proteins and 6069 peptides added [2026/01/16 02:33:56] 44% - Adding protein ENSP00000404475.2:p.Phe196Leu 3078 proteins and 6096 peptides added [2026/01/16 02:34:31] Adding protein ENSP00000405517.2:p.Arg8554Cys 3092 proteins and 6116 peptides added [2026/01/16 02:35:11] Adding protein ENSP00000405517.2:p.Thr31933Ala 3092 proteins and 6116 peptides added [2026/01/16 02:35:51] Adding protein ENSP00000406661.1:p.Glu149Gln 3108 proteins and 6156 peptides added [2026/01/16 02:36:26] 45% - Adding protein ENSP00000408004.2:p.Ala22364Pro 3135 proteins and 6382 peptides added [2026/01/16 02:37:06] Adding protein ENSP00000408004.2:p.Ser16147Thr 3135 proteins and 6382 peptides added [2026/01/16 02:37:41] Adding protein ENSP00000409080.2 3155 proteins and 6424 peptides added [2026/01/16 02:38:16] Adding protein ENSP00000410083.1:p.Thr162Ala 3175 proteins and 6447 peptides added [2026/01/16 02:38:56] 46% - Adding protein ENSP00000411459.1:p.Arg573Cys 3187 proteins and 6478 peptides added [2026/01/16 02:39:31] Adding protein ENSP00000412864.2:p.Thr2290_Thr2291insLysHisThr 3199 proteins and 6572 peptides added [2026/01/16 02:40:11] 47% - Adding protein ENSP00000414287.2:p.Val499Ala 3210 proteins and 6584 peptides added [2026/01/16 02:40:46] Adding protein ENSP00000415407.2:p.Ala676Val 3228 proteins and 6606 peptides added [2026/01/16 02:41:26] 48% - Adding protein ENSP00000416757.3:p.Lys1047Gln 3242 proteins and 6638 peptides added [2026/01/16 02:42:01] Adding protein ENSP00000417397.1:p.Gly701Arg 3298 proteins and 7378 peptides added [2026/01/16 02:42:41] Adding protein ENSP00000417405.1 3361 proteins and 8699 peptides added [2026/01/16 02:43:21] Adding protein ENSP00000417498.3:p.His4066Pro 3405 proteins and 9604 peptides added [2026/01/16 02:44:06] Adding protein ENSP00000417498.3:p.Val2659Leu 3461 proteins and 10780 peptides added [2026/01/16 02:44:41] Adding protein ENSP00000417657.1:p.Pro3846Leu 3520 proteins and 12017 peptides added [2026/01/16 02:45:26] Adding protein ENSP00000417722.1:p.Ala3038Thr 3571 proteins and 13047 peptides added [2026/01/16 02:46:01] 49% - Adding protein ENSP00000417722.1:p.Thr2142Ala 3640 proteins and 14496 peptides added [2026/01/16 02:46:36] Adding protein ENSP00000418306.1:p.Ala1240Ser 3682 proteins and 14983 peptides added [2026/01/16 02:47:11] Adding protein ENSP00000418306.1:p.Thr1390Ala 3753 proteins and 16474 peptides added [2026/01/16 02:47:46] Adding protein ENSP00000419269.1 3803 proteins and 17044 peptides added [2026/01/16 02:48:26] 50% - Adding protein ENSP00000419798.1:p.Asp2979Val 3835 proteins and 17646 peptides added [2026/01/16 02:49:06] Adding protein ENSP00000419798.1:p.Thr1487Met 3885 proteins and 18696 peptides added [2026/01/16 02:49:41] Adding protein ENSP00000419989.1:p.Glu953Gln 3943 proteins and 19872 peptides added [2026/01/16 02:50:16] Adding protein ENSP00000419989.1:p.Thr525Ala 3999 proteins and 21048 peptides added [2026/01/16 02:50:56] Adding protein ENSP00000420243.1:p.Asp2115Val 4035 proteins and 21762 peptides added [2026/01/16 02:51:36] Adding protein ENSP00000420243.1:p.Thr1086Ser 4083 proteins and 22770 peptides added [2026/01/16 02:52:11] Adding protein ENSP00000420439.1:p.Gln3805His 4148 proteins and 23973 peptides added [2026/01/16 02:52:46] Adding protein ENSP00000420439.1:p.Thr2443Arg 4198 proteins and 25023 peptides added [2026/01/16 02:53:26] 51% - Adding protein ENSP00000421216.1:p.Thr2290_Thr2291insIleThrValPheValGlnThrProAsnLeuGluGlyProGlyValSerValLysGluHisThr 4229 proteins and 25465 peptides added [2026/01/16 02:54:06] Adding protein ENSP00000422377.1:p.Ala44Thr 4250 proteins and 25486 peptides added [2026/01/16 02:54:41] 52% - Adding protein ENSP00000423458.1 4281 proteins and 25568 peptides added [2026/01/16 02:55:16] Adding protein ENSP00000424940.3:p.Ala491Thr 4294 proteins and 25587 peptides added [2026/01/16 02:55:56] 53% - Adding protein ENSP00000426130.1 4319 proteins and 25681 peptides added [2026/01/16 02:56:31] Adding protein ENSP00000427567.1:p.Pro726Ser 4344 proteins and 25734 peptides added [2026/01/16 02:57:06] 54% - Adding protein ENSP00000428981.1 4375 proteins and 25771 peptides added [2026/01/16 02:57:41] 55% - Adding protein ENSP00000431012.1:p.Ser59Asn 4425 proteins and 25880 peptides added [2026/01/16 02:58:16] 56% - Adding protein ENSP00000432322.1 4457 proteins and 25952 peptides added [2026/01/16 02:58:46] Adding protein ENSP00000433468.1:p.Gly190Asp 4500 proteins and 26018 peptides added [2026/01/16 02:59:26] 57% - Adding protein ENSP00000434355.1 4544 proteins and 26098 peptides added [2026/01/16 03:00:01] Adding protein ENSP00000434586.1:p.Leu14565Pro 4588 proteins and 26180 peptides added [2026/01/16 03:00:41] Adding protein ENSP00000435442.1 4612 proteins and 26217 peptides added [2026/01/16 03:01:16] 58% - Adding protein ENSP00000436803.1:p.Arg616Lys 4675 proteins and 26320 peptides added [2026/01/16 03:01:56] Adding protein ENSP00000437303.2:p.Ala3980Pro 4700 proteins and 26368 peptides added [2026/01/16 03:02:31] 59% - Adding protein ENSP00000439479.1:p.Phe615Ser 4763 proteins and 26457 peptides added [2026/01/16 03:03:16] Adding protein ENSP00000440857.1:p.Ile283_Gln295dup 4820 proteins and 26532 peptides added [2026/01/16 03:03:56] 60% - Adding protein ENSP00000441929.1:p.Pro2260Thr 4833 proteins and 26546 peptides added [2026/01/16 03:04:36] Adding protein ENSP00000443439.1 4867 proteins and 26604 peptides added [2026/01/16 03:05:11] 61% - Adding protein ENSP00000445163.1:p.Phe961Leu 4887 proteins and 26630 peptides added [2026/01/16 03:05:46] Adding protein ENSP00000447170.1:p.Ala202Thr 4913 proteins and 26681 peptides added [2026/01/16 03:06:31] 62% - Adding protein ENSP00000449215.1:p.Ala548Thr 4939 proteins and 26749 peptides added [2026/01/16 03:07:06] 63% - Adding protein ENSP00000450945.2:p.Glu100Gly 4982 proteins and 26946 peptides added [2026/01/16 03:07:46] Adding protein ENSP00000452015.2:p.His159Leu 5010 proteins and 27042 peptides added [2026/01/16 03:08:21] Adding protein ENSP00000452825.2:p.Glu432Asp 5031 proteins and 27091 peptides added [2026/01/16 03:09:01] 64% - Adding protein ENSP00000453664.1:p.Ser290delinsArgHisGlnLeuGlnProAspGlySerLeuValIleSerArgValAlaValGluAspGlyGlyPheTyrThrCysValAlaPheAsnGlyGlnAspArgAspGlnArgTrpValGlnLeuArgValLeuGlyAsp 5039 proteins and 27112 peptides added [2026/01/16 03:09:41] 65% - Adding protein ENSP00000454990.2:p.Thr1611Met 5076 proteins and 27190 peptides added [2026/01/16 03:10:26] Adding protein ENSP00000455507.2:p.Pro674Thr 5095 proteins and 27226 peptides added [2026/01/16 03:11:06] Adding protein ENSP00000456353.1 5103 proteins and 27258 peptides added [2026/01/16 03:11:46] 66% - Adding protein ENSP00000457555.2:p.Ser513Pro 5110 proteins and 27278 peptides added [2026/01/16 03:12:26] 67% - Adding protein ENSP00000461629.3:p.Glu621= 5170 proteins and 27365 peptides added [2026/01/16 03:13:01] 68% - Adding protein ENSP00000463531.1 5190 proteins and 27396 peptides added [2026/01/16 03:13:41] Adding protein ENSP00000464837.1 5214 proteins and 27425 peptides added [2026/01/16 03:14:16] Adding protein ENSP00000465570.1:p.Met14168Thr 5234 proteins and 27475 peptides added [2026/01/16 03:14:51] 69% - Adding protein ENSP00000466340.2 5255 proteins and 27503 peptides added [2026/01/16 03:15:31] Adding protein ENSP00000467872.1 5296 proteins and 27572 peptides added [2026/01/16 03:16:06] 70% - Adding protein ENSP00000470248.1:p.Gly485Asp 5335 proteins and 27667 peptides added [2026/01/16 03:16:41] 71% - Adding protein ENSP00000472953.1:p.Ala895Thr 5356 proteins and 27731 peptides added [2026/01/16 03:17:11] 72% - Adding protein ENSP00000476295.1 5411 proteins and 27796 peptides added [2026/01/16 03:17:51] 73% - Adding protein ENSP00000478190.1 5433 proteins and 27824 peptides added [2026/01/16 03:18:26] Adding protein ENSP00000479094.1:p.Val672Gly 5463 proteins and 27873 peptides added [2026/01/16 03:19:06] Adding protein ENSP00000480220.1 5496 proteins and 27920 peptides added [2026/01/16 03:19:41] 74% - Adding protein ENSP00000481058.2 5508 proteins and 27935 peptides added [2026/01/16 03:20:16] Adding protein ENSP00000482233.1:p.Phe2999_Pro3004dup 5531 proteins and 27980 peptides added [2026/01/16 03:20:56] 75% - Adding protein ENSP00000483235.1:p.Pro108His 5550 proteins and 28015 peptides added [2026/01/16 03:21:31] Adding protein ENSP00000484472.1:p.Ala2631_Ala2633del 5581 proteins and 28053 peptides added [2026/01/16 03:22:06] 76% - Adding protein ENSP00000485513.1:p.Ala295Ser 5594 proteins and 28089 peptides added [2026/01/16 03:22:46] Adding protein ENSP00000486712.1:p.Leu55= 5639 proteins and 28439 peptides added [2026/01/16 03:23:21] Adding protein ENSP00000488294.1 5683 proteins and 28653 peptides added [2026/01/16 03:23:56] 77% - Adding protein ENSP00000489551.2:p.Ser1250Thr 5726 proteins and 28710 peptides added [2026/01/16 03:24:31] Adding protein ENSP00000489969.1:p.Pro37Ser 5742 proteins and 28755 peptides added [2026/01/16 03:25:11] 78% - Adding protein ENSP00000490704.1 5748 proteins and 28802 peptides added [2026/01/16 03:25:43] Adding protein ENSP00000491921.1:p.His1237_Tyr1238dup 5802 proteins and 28859 peptides added [2026/01/16 03:26:16] 79% - Adding protein ENSP00000493389.1 5824 proteins and 28882 peptides added [2026/01/16 03:26:51] Adding protein ENSP00000494030.1 5830 proteins and 28892 peptides added [2026/01/16 03:27:31] 80% - Adding protein ENSP00000494751.1:p.Ile508Thr 5845 proteins and 28944 peptides added [2026/01/16 03:28:06] Adding protein ENSP00000495537.1:p.Gly566Glu 5860 proteins and 28983 peptides added [2026/01/16 03:28:41] 81% - Adding protein ENSP00000496203.1 5893 proteins and 29047 peptides added [2026/01/16 03:29:11] Adding protein ENSP00000496893.1:p.Met903Ile 5909 proteins and 29136 peptides added [2026/01/16 03:29:51] 82% - Adding protein ENSP00000497552.1:p.Gly86Val 5930 proteins and 29162 peptides added [2026/01/16 03:30:31] Adding protein ENSP00000498014.1:p.Gly1777_Gly1778dup 5942 proteins and 29174 peptides added [2026/01/16 03:31:06] Adding protein ENSP00000498627.1:p.Val66Leu 5968 proteins and 29204 peptides added [2026/01/16 03:31:41] 83% - Adding protein ENSP00000499216.1:p.Ala2052Val 5974 proteins and 29214 peptides added [2026/01/16 03:32:21] Adding protein ENSP00000499407.1 5974 proteins and 29214 peptides added [2026/01/16 03:32:56] Adding protein ENSP00000499737.1 5974 proteins and 29214 peptides added [2026/01/16 03:33:31] 84% - Adding protein ENSP00000500245.1:p.Gly1069Ser 5977 proteins and 29218 peptides added [2026/01/16 03:34:11] Adding protein ENSP00000500937.1:p.Gly1090Ser 5986 proteins and 29234 peptides added [2026/01/16 03:34:46] Adding protein ENSP00000501367.2:p.Ala996Thr 6011 proteins and 29277 peptides added [2026/01/16 03:35:26] 85% - Adding protein ENSP00000502030.1:p.Glu446_Tyr447dup 6037 proteins and 29420 peptides added [2026/01/16 03:36:01] Adding protein ENSP00000502449.1:p.Lys257_Lys258insProIleGlyProAspAspAlaIleAspAlaLeuSerSerAspPheThrCysGlySerProThrAlaAlaGlyLysLysThrGluLysGluGluSerThrGluValLeuLysAlaGlnSerAlaGlyThrLys 6057 proteins and 29543 peptides added [2026/01/16 03:36:41] 86% - Adding protein ENSP00000502966.1:p.Asn1002Ser 6087 proteins and 29587 peptides added [2026/01/16 03:37:16] Adding protein ENSP00000503792.1:p.Gly1126Val 6212 proteins and 29760 peptides added [2026/01/16 03:37:56] 87% - Adding protein ENSP00000504406.1 6307 proteins and 29889 peptides added [2026/01/16 03:38:31] Adding protein ENSP00000504976.1 6361 proteins and 29983 peptides added [2026/01/16 03:39:16] Adding protein ENSP00000505225.1:p.Pro744_Ala776dup 6378 proteins and 30000 peptides added [2026/01/16 03:39:56] 88% - Adding protein ENSP00000505384.1:p.Leu1881His 6392 proteins and 30014 peptides added [2026/01/16 03:40:31] Adding protein ENSP00000505517.1:p.Phe2491Leu 6399 proteins and 30021 peptides added [2026/01/16 03:41:11] Adding protein ENSP00000505859.1:p.Ser395Pro 6414 proteins and 30036 peptides added [2026/01/16 03:41:46] Adding protein ENSP00000506124.1:p.Ala405Pro 6426 proteins and 30048 peptides added [2026/01/16 03:42:21] 89% - Adding protein ENSP00000506486.1:p.Thr2481Ser 6439 proteins and 30061 peptides added [2026/01/16 03:43:01] Adding protein ENSP00000506726.1:p.Thr4298Arg 6449 proteins and 30071 peptides added [2026/01/16 03:43:41] Adding protein ENSP00000507112.1:p.Ser488Leu 6471 proteins and 30093 peptides added [2026/01/16 03:44:16] Adding protein ENSP00000507421.1:p.Ser2448Asn 6489 proteins and 30111 peptides added [2026/01/16 03:44:56] 90% - Adding protein ENSP00000507811.1:p.Ala1004Val 6512 proteins and 30134 peptides added [2026/01/16 03:45:36] Adding protein ENSP00000508029.1:p.Trp246Leu 6535 proteins and 30289 peptides added [2026/01/16 03:46:11] Adding protein ENSP00000508231.1:p.Glu1202Lys 6544 proteins and 30302 peptides added [2026/01/16 03:46:46] 91% - Adding protein ENSP00000508500.1:p.Glu980Asp 6578 proteins and 30352 peptides added [2026/01/16 03:47:21] Adding protein ENSP00000508936.1 6586 proteins and 30364 peptides added [2026/01/16 03:47:56] Adding protein ENSP00000509279.1:p.Glu519Gly 6613 proteins and 30393 peptides added [2026/01/16 03:48:31] 92% - Adding protein ENSP00000509586.1:p.Ala1351Thr 6634 proteins and 30421 peptides added [2026/01/16 03:49:01] Adding protein ENSP00000510003.1:p.Ala589Val 6638 proteins and 30430 peptides added [2026/01/16 03:49:36] Adding protein ENSP00000510454.1:p.Glu59delinsAspLeu 6682 proteins and 30503 peptides added [2026/01/16 03:50:11] 93% - Adding protein ENSP00000510708.1:p.Asn50Asp 6713 proteins and 30567 peptides added [2026/01/16 03:50:46] Adding protein ENSP00000511649.1:p.Thr1677Ile 6713 proteins and 30567 peptides added [2026/01/16 03:51:26] Adding protein ENSP00000512015.1:p.Ser2911Arg 6735 proteins and 30589 peptides added [2026/01/16 03:52:06] Adding protein ENSP00000512337.1:p.His402Tyr 6735 proteins and 30589 peptides added [2026/01/16 03:52:41] 94% - Adding protein ENSP00000512807.1:p.Asp237Asn 6751 proteins and 30605 peptides added [2026/01/16 03:53:16] Adding protein ENSP00000513330.1:p.Arg721Cys 6757 proteins and 30617 peptides added [2026/01/16 03:53:56] 95% - Adding protein ENSP00000513791.1:p.Arg69Trp 6773 proteins and 30635 peptides added [2026/01/16 03:54:36] Adding protein ENSP00000514331.1:p.Ile995= 6802 proteins and 30664 peptides added [2026/01/16 03:55:21] 96% - Adding protein ENSP00000514781.1:p.Cys269Arg 6820 proteins and 30682 peptides added [2026/01/16 03:56:01] Adding protein ENSP00000515196.2:p.Phe592Leu 6871 proteins and 30733 peptides added [2026/01/16 03:56:36] Adding protein ENSP00000515566.1:p.Lys594Asn 7089 proteins and 30952 peptides added [2026/01/16 03:57:11] 97% - Adding protein ENSP00000516056.1:p.Ala2419Thr 7141 proteins and 31008 peptides added [2026/01/16 03:57:51] Adding protein ENSP00000516442.1:p.Asn611Ile 7170 proteins and 31054 peptides added [2026/01/16 03:58:21] Adding protein ENSP00000516669.1:p.Ser157Phe 7201 proteins and 31105 peptides added [2026/01/16 03:58:56] 98% - Adding protein ENSP00000518363.1 7253 proteins and 31224 peptides added [2026/01/16 03:59:26] Adding protein ENSP00000518771.1:p.Gly2048Asp 7272 proteins and 31257 peptides added [2026/01/16 04:00:06] Adding protein ENSP00000518981.1:p.Val2466Ala 7290 proteins and 31314 peptides added [2026/01/16 04:00:41] 99% - Adding protein ENSP00000519250.1:p.Gly74Asp 7338 proteins and 31388 peptides added [2026/01/16 04:01:16] Adding protein ENSP00000520370.1:p.Arg8508Cys 7363 proteins and 31425 peptides added [2026/01/16 04:01:56] Adding protein ENSP00000520370.1:p.Thr31887Ala 7363 proteins and 31425 peptides added [2026/01/16 04:01:57] 100% - Adding protein sp|Q9NSB4|KRT82_HUMAN 7404 proteins and 31538 peptides added [2026/01/16 04:01:57] Associating peptides with proteins from FASTA file 2025-01-04-contam-A002014015_vep.fasta.fas [2026/01/16 04:03:12] 6% [2026/01/16 04:03:52] 12% [2026/01/16 04:04:36] 16% [2026/01/16 04:05:17] 21% [2026/01/16 04:05:57] 26% [2026/01/16 04:06:41] 31% [2026/01/16 04:07:17] 35% [2026/01/16 04:07:52] 40% [2026/01/16 04:08:32] 46% [2026/01/16 04:09:11] 52% [2026/01/16 04:09:46] 53% [2026/01/16 04:10:22] 55% [2026/01/16 04:10:57] 59% [2026/01/16 04:11:32] 64% [2026/01/16 04:12:12] 69% [2026/01/16 04:12:51] 74% [2026/01/16 04:13:27] 79% [2026/01/16 04:14:07] 85% [2026/01/16 04:14:47] 91% [2026/01/16 04:15:32] 96% [2026/01/16 04:15:32] 100% [2026/01/16 04:15:33] Applying parsimony options [2026/01/16 04:15:33] Creating protein targets and assigning their peptides [2026/01/16 04:15:33] [2026/01/16 04:15:33] [2026/01/16 04:16:12] [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 1. E:\Shubham\diaData\20250605_Stanford-Snyder_070_DIA_Slot2-5_1_4248.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 2. E:\Shubham\diaData\20250605_Stanford-Snyder_076_DIA_Slot2-11_1_4254.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 3. E:\Shubham\diaData\20250605_Stanford-Snyder_067_DIA_Slot2-2_1_4245.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 4. E:\Shubham\diaData\20250605_Stanford-Snyder_077_DIA_Slot2-12_1_4255.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 5. E:\Shubham\diaData\20250605_Stanford-Snyder_066_DIA_Slot2-1_1_4244.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 6. E:\Shubham\diaData\20250605_Stanford-Snyder_048_DIA_Slot1-40_1_4229.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 7. E:\Shubham\diaData\20250605_Stanford-Snyder_040_DIA_Slot1-32_1_4221.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 8. E:\Shubham\diaData\20250605_Stanford-Snyder_029_DIA_Slot1-21_1_4210.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 9. E:\Shubham\diaData\20250605_Stanford-Snyder_006_DIA_Slot1-4_1_4193.d [2026/01/16 04:16:12] Adding results... [2026/01/16 04:16:12] 10. E:\Shubham\diaData\20250605_Stanford-Snyder_004_DIA_Slot1-2_1_4191.d [2026/01/16 04:16:12] [2026/01/16 04:16:47] Aligning retention times [2026/01/16 04:16:47] 100% [2026/01/16 04:34:47] [1] 10% [3] 10% [4] 10% [5] 10% [6] 10% [7] 10% [8] 10% [9] 10% [10] 10% [2026/01/16 04:35:57] [3] 10% [4] 10% [5] 10% [7] 10% [8] 10% [9] 10% [10] 10% [2026/01/16 04:37:07] [5] 10% [7] 10% [8] 10% [9] 10% [10] 10% [2026/01/16 04:37:47] [5] 10% [8] 10% [9] 10% [10] 10% [2026/01/16 04:38:22] [8] 10% [9] 10% [10] 10% [2026/01/16 04:39:07] [10] 10% [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_070_DIA_Slot2-5_1_4248.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_070_DIA_Slot2-5_1_4248.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_076_DIA_Slot2-11_1_4254.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_076_DIA_Slot2-11_1_4254.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_067_DIA_Slot2-2_1_4245.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_067_DIA_Slot2-2_1_4245.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_077_DIA_Slot2-12_1_4255.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_077_DIA_Slot2-12_1_4255.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_066_DIA_Slot2-1_1_4244.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_066_DIA_Slot2-1_1_4244.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_048_DIA_Slot1-40_1_4229.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_048_DIA_Slot1-40_1_4229.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_040_DIA_Slot1-32_1_4221.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_040_DIA_Slot1-32_1_4221.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_029_DIA_Slot1-21_1_4210.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_029_DIA_Slot1-21_1_4210.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_006_DIA_Slot1-4_1_4193.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_006_DIA_Slot1-4_1_4193.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] [2026/01/16 04:39:47] Error: Failed importing the results file E:\Shubham\diaData\20250605_Stanford-Snyder_004_DIA_Slot1-2_1_4191.d. [2026/01/16 04:39:47] Message: pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Shubham\diaData\20250605_Stanford-Snyder_004_DIA_Slot1-2_1_4191.d'. The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI ---> pwiz.Skyline.Model.Irt.IncompleteStandardException: The calculator fPop0059_1 requires at least 8 of its 10 standard peptides. The following 10 peptides are missing: ADHASSY AGGGRIDKPILK AKPKAAKPKKAAA DSTGHVG EIEKFDKS GSGGGGGGHGSY LPPYVSNM LSSNVTVSVTS SAKKKNKKGKTISL VHINAGPEI " at pwiz.Skyline.Model.Irt.RCalcIrt.ChooseRegressionPeptides(IEnumerable`1 peptides, Int32& minCount) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Irt\RCalcIrt.cs:line 153" at pwiz.Skyline.Model.Results.ChromCacheBuilder.RetentionTimePredictor.CreateConversion() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 848 " at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateRetentionTimeEquation(ChromDataProvider provider, IList`1 listChromData) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 479" at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 397 at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263 --- End of inner exception stack trace --- [2026/01/16 04:39:47] C:\DIA-NN\2.3.1>if 2 == 0 (start E:\Shubham\DIANN\results\Batch1234_colon_full2_diann3_skyline.sky ) C:\DIA-NN\2.3.1>pause Press any key to continue . . .