pepxml-mzXML import from PEAKS no longer works | dkueltz | 2021-12-08 10:29 | |||||||||||||||||||||||||||
Hi, My lab has used Skyline for many years to import pepxml (and corresponding mzXML) generated by PEAKS and it always worked well until very recently when I get the error pasted below. Importing pepxml + mzML from MSfragger still works well. I wonder whether the pepxml + mzXML import function in Skyline has changed? Could you please look at the error below and let me know how to fix it such that my lab can continue to use our pipeline of generating spec libs from PEAKS DDA data? Thanks much, Dietmar --------------------------- Skyline --------------------------- ERROR: peptides.pep.xml(line 22656): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type ERROR: Command-line: C:\Users\dkueltz\AppData\Local\Apps\2.0\8JR1V559.JCC\KOCQGHPK.M36\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i test6 -S "C:\Users\dkueltz\AppData\Local\Temp\tmpB6D.tmp" "D:\Spectral-Libraries\test6.redundant.blib" Working directory: F:\EAM0021-24_Oremo_V8-AmBic_60min\PEAKS-to-Skyline\PEAKS10Pro_Oremo_V8-AmBic_Histones_PEAKS PTM_35 --------------------------- OK More Info --------------------------- System.IO.IOException: ERROR: peptides.pep.xml(line 22656): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type ERROR: Command-line: C:\Users\dkueltz\AppData\Local\Apps\2.0\8JR1V559.JCC\KOCQGHPK.M36\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i test6 -S "C:\Users\dkueltz\AppData\Local\Temp\tmpB6D.tmp" "D:\Spectral-Libraries\test6.redundant.blib" Working directory: F:\EAM0021-24_Oremo_V8-AmBic_60min\PEAKS-to-Skyline\PEAKS10Pro_Oremo_V8-AmBic_Histones_PEAKS PTM_35 at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 142 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157 --------------------------- |
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