Unable to build PEPTIDE spectral library using .pep.xml and .mzxml files downloded together from PEAKS 11 | ciaranmc 28 | 2024-06-05 11:51 | |||||||||||||||||||||||||||||||||
Dear Skyline supporters, I am attempting to build a spectral library using pep.xml and .mzXML files downsloded from PEAKS 11 (derived from DDA run on TimTOF, filtered for MS2 peptides at 1% FDR) However, despite rerunning my peaks analysis to try again, I am repeatedly met with the skyline error included below (which suggest discrepancy between the pep.xml and mzXML files). Both files were exported from PEAKS at the same time and from the same PEAKs database search (so they should be compatible). Please let me know if you have any suggestions, thanks! Cheers, Ciaran --------------------------- Skyline --------------------------- ERROR: index 3128 out of range in mzXML file '.\C240501_C.elegans_Lib_100ng_17min_dda_141.d.mzxml' Command-line: C:\Users\ciara\AppData\Local\Apps\2.0\7GXGT77K.ABK\AJO9DCLR.Z52\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\BlibBuild -s -A -H -v warn -o -i P -S "C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_142\P.redundant202406050814.stdin.txt" "C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_142\P.redundant.blib" Working directory: C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_141 --------------------------- OK More Info --------------------------- System.IO.IOException: ERROR: index 3128 out of range in mzXML file '.\C240501_C.elegans_Lib_100ng_17min_dda_141.d.mzxml' Command-line: C:\Users\ciara\AppData\Local\Apps\2.0\7GXGT77K.ABK\AJO9DCLR.Z52\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\BlibBuild -s -A -H -v warn -o -i P -S "C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_142\P.redundant202406050814.stdin.txt" "C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_142\P.redundant.blib" Working directory: C:\Users\ciara\Dropbox\KU_Leuven\1_Prohormone_convertase_project\Skyline\2024.06.05_initial_spectral_library\Peptide_library_ran_seperately\Peptide_library_141 at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_23_1\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 181 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_23_1\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 433 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161 --------------------------- |
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