Bibliospec not recognize modification from PLGS file | jcaceresvergara | 2022-12-02 | |||||||||||||||||||||||||||||||||||||||||
I'm trying to create a library from a peptide search made using PLGS. I get the error at the end. It does not appear to understand the modification I set, I try to change the final_fragment.csv file or add the modification to my skyline file but nothing seems to work. can you help me with this? The modification should be a loss of' -2HS' variable on cysteine. I'm attaching my final_fragment.csv file. --------------------------- Skyline-daily --------------------------- ERROR: The modification 'Dehydroalanine+C(4)' on line 1429 is not recognized. Supported modifications include: "12C d0", "13C", "13C N15", "13C d9", "1H d0", "2H d8", "Acetyl", "Amidation", "Biotin", "C-Mannosyl", "Carbamidomethyl", "Carbamyl", "Carboxymethyl", "DUPLEX_TANDEM_MASS_TAG126", "DUPLEX_TANDEM_MASS_TAG127", "Deamidation", "Dehydration", "Dimethyl", "Farnesyl", "Flavin-adenine", "Formyl", "Gamma-carboxyglutamic", "Geranyl-geranyl", "Glycation", "Hydroxyl", "ICAT-C", "ICAT-C13C(9)", "ICAT-D", "ICAT-D 2H(8)", "ICAT-G", "ICAT-G 2H(8)", "ICAT-H", "ICAT-H13(6)", "Isobaric 114", "Isobaric 115", "Isobaric 116", "Isobaric 117", "Isobaric 8plex 113", "Isobaric 8plex 114", "Isobaric 8plex 115", "Isobaric 8plex 116", "Isobaric 8plex 117", "Isobaric 8plex 118", "Isobaric 8plex 119", "Isobaric 8plex 121", "Lipoyl", "Methyl", "Myristoyl", "N-Glycosylation", "NATIVE_TANDEM_MASS_TAG126", "NATIVE_TANDEM_MASS_TAG127", "NIPCAM", "O-GlcNAc", "O-Glycosylation", "O18", "O18 label at both C-terminal oxygens", "Oxidation", "Palmitoyl", "Phosphopantetheine", "Phosphoryl", "Propionamide", "Pyridoxal", "Pyrrolidone", "S-pyridylethyl", "SILAC 13C(1) 2H3", "SILAC 13C(3)", "SILAC 13C(3) 15N(1)", "SILAC 13C(4) 15N(1)", "SILAC 13C(5)", "SILAC 13C(6)", "SILAC 13C(6) 15N(2)", "SILAC 13C(6) 15N(4)", "SILAC 13C(8) 15N(2)", "SILAC 13C(9)", "SILAC 13C(9) 15N(1)", "SILAC 15N(2) 2H(9)", "SILAC 15N(4)", "SIXPLEX_TANDEM_MASS_TAG126", "SIXPLEX_TANDEM_MASS_TAG127", "SIXPLEX_TANDEM_MASS_TAG128", "SIXPLEX_TANDEM_MASS_TAG129", "SIXPLEX_TANDEM_MASS_TAG130", "SIXPLEX_TANDEM_MASS_TAG131", "SMA", "Sulfo", "Trimethyl". ERROR: reading file 20221122 C418U_iRT MSE JC_LC-05_IA_final_fragment.csv Command-line: C:\Users\jcaceresvergara\AppData\Local\Apps\2.0\T0VY925W.HAY\GJ5BNRYZ.4Y7\skyl..tion_e4141a2a22107248_0016.0002_c984fd7cba69179e\BlibBuild -s -A -H -o -i lib -S "C:\Users\jcaceresvergara\AppData\Local\Temp\tmp6856.tmp" "D:\lib.redundant.blib" Working directory: C:\Users\jcaceresvergara\Downloads\PLGS Search Results\PLGS Search Results\Trypsin\20221122 C418U_iRT MSE JC_LC-05_20221202133552 --------------------------- OK More Info --------------------------- System.IO.IOException: ERROR: The modification 'Dehydroalanine+C(4)' on line 1429 is not recognized. Supported modifications include: "12C d0", "13C", "13C N15", "13C d9", "1H d0", "2H d8", "Acetyl", "Amidation", "Biotin", "C-Mannosyl", "Carbamidomethyl", "Carbamyl", "Carboxymethyl", "DUPLEX_TANDEM_MASS_TAG126", "DUPLEX_TANDEM_MASS_TAG127", "Deamidation", "Dehydration", "Dimethyl", "Farnesyl", "Flavin-adenine", "Formyl", "Gamma-carboxyglutamic", "Geranyl-geranyl", "Glycation", "Hydroxyl", "ICAT-C", "ICAT-C13C(9)", "ICAT-D", "ICAT-D 2H(8)", "ICAT-G", "ICAT-G 2H(8)", "ICAT-H", "ICAT-H13(6)", "Isobaric 114", "Isobaric 115", "Isobaric 116", "Isobaric 117", "Isobaric 8plex 113", "Isobaric 8plex 114", "Isobaric 8plex 115", "Isobaric 8plex 116", "Isobaric 8plex 117", "Isobaric 8plex 118", "Isobaric 8plex 119", "Isobaric 8plex 121", "Lipoyl", "Methyl", "Myristoyl", "N-Glycosylation", "NATIVE_TANDEM_MASS_TAG126", "NATIVE_TANDEM_MASS_TAG127", "NIPCAM", "O-GlcNAc", "O-Glycosylation", "O18", "O18 label at both C-terminal oxygens", "Oxidation", "Palmitoyl", "Phosphopantetheine", "Phosphoryl", "Propionamide", "Pyridoxal", "Pyrrolidone", "S-pyridylethyl", "SILAC 13C(1) 2H3", "SILAC 13C(3)", "SILAC 13C(3) 15N(1)", "SILAC 13C(4) 15N(1)", "SILAC 13C(5)", "SILAC 13C(6)", "SILAC 13C(6) 15N(2)", "SILAC 13C(6) 15N(4)", "SILAC 13C(8) 15N(2)", "SILAC 13C(9)", "SILAC 13C(9) 15N(1)", "SILAC 15N(2) 2H(9)", "SILAC 15N(4)", "SIXPLEX_TANDEM_MASS_TAG126", "SIXPLEX_TANDEM_MASS_TAG127", "SIXPLEX_TANDEM_MASS_TAG128", "SIXPLEX_TANDEM_MASS_TAG129", "SIXPLEX_TANDEM_MASS_TAG130", "SIXPLEX_TANDEM_MASS_TAG131", "SMA", "Sulfo", "Trimethyl". ERROR: reading file 20221122 C418U_iRT MSE JC_LC-05_IA_final_fragment.csv Command-line: C:\Users\jcaceresvergara\AppData\Local\Apps\2.0\T0VY925W.HAY\GJ5BNRYZ.4Y7\skyl..tion_e4141a2a22107248_0016.0002_c984fd7cba69179e\BlibBuild -s -A -H -o -i lib -S "C:\Users\jcaceresvergara\AppData\Local\Temp\tmp6856.tmp" "D:\lib.redundant.blib" Working directory: C:\Users\jcaceresvergara\Downloads\PLGS Search Results\PLGS Search Results\Trypsin\20221122 C418U_iRT MSE JC_LC-05_20221202133552 at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\pwiz\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 161 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 412 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161 --------------------------- |
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