Hi Skyline Team,
I decided to add to this very old thread to report an observation that I made. I recently had to build a spectral library from an .msf file without q-values in it (similar situation as for Lars who opened this thread). This did not work when I was entering 0 as a value for the cutoff score, as recommended here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries
Instead, I was getting the lengthy error message reported below. However, it worked perfectly fine with a cutoff score of 1. This also makes more sense to me, as q-value cutoff of 1 means to take everything, while cutoff 0 would mean expecting perfection, as Skyline (23.0.9) itself also advised me:
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Skyline-daily
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Score threshold 1 for Percolator q-value will include all identifications. Percolator q-value scores indicate the probability that an identification is incorrect.
Are you sure you want to continue?
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OK Cancel
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Could it be that the cutoff value recommendation for the case of missing q-values should be updated? Here the lengthy error message:
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Skyline-daily
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ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file E25D105-19-235-16.msf
Command-line: C:\Users\Roman Sakson\AppData\Local\Apps\2.0\HKY1Z9MN.AMP\61TQ9EAM.84P\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\BlibBuild -s -A -H -o -i Test -S "C:\Users\Roman Sakson\AppData\Local\Temp\tmpC28D.tmp" "C:\Users\Roman Sakson\Desktop\Test.redundant.blib"
Working directory: F:\DGMS\DGMS_Skyline_Participants\DGMS_Skyline_Participants\Skyline_Data\Spectral_Libraries\MSF
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OK More Info
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System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file E25D105-19-235-16.msf
Command-line: C:\Users\Roman Sakson\AppData\Local\Apps\2.0\HKY1Z9MN.AMP\61TQ9EAM.84P\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\BlibBuild -s -A -H -o -i Test -S "C:\Users\Roman Sakson\AppData\Local\Temp\tmpC28D.tmp" "C:\Users\Roman Sakson\Desktop\Test.redundant.blib"
Working directory: F:\DGMS\DGMS_Skyline_Participants\DGMS_Skyline_Participants\Skyline_Data\Spectral_Libraries\MSF
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 180
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 430
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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Best wishes,
Roman