When I search DIA mzML files using FragPipe, and import the interact-*_rankX.pep.xml
files to Skyline, there is an error:
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Skyline-daily
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ERROR: No spectra were found for the new library.
Command-line: C:\Users\yufe\AppData\Local\Apps\2.0\181WWENP.RYH\PWGEADGY.2C2\skyl..tion_e4141a2a22107248_0015.0001_9a4bb3d7cf8a899e\BlibBuild -s -A -H -o -c 0.95 -i 1 -S "C:\Users\yufe\AppData\Local\Temp\tmp9D35.tmp" "F:\msfraggerdia\1.redundant.blib"
Working directory: F:\msfraggerdia
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OK More Info
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System.IO.IOException: ERROR: No spectra were found for the new library.
Command-line: C:\Users\yufe\AppData\Local\Apps\2.0\181WWENP.RYH\PWGEADGY.2C2\skyl..tion_e4141a2a22107248_0015.0001_9a4bb3d7cf8a899e\BlibBuild -s -A -H -o -c 0.95 -i 1 -S "C:\Users\yufe\AppData\Local\Temp\tmp9D35.tmp" "F:\msfraggerdia\1.redundant.blib"
Working directory: F:\msfraggerdia
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 149
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157
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When I search the raw files using FragPipe, and import the interact-*_rankX.pep.xml
files to Skyline, everything works well.
The difference between using mzML files and raw files is that, with raw files, FragPipe will generate _uncalibrated.mgf
files which will be used by Skyline during importing. Also please note that the there is a _rankX
suffix in the interact-*_rankX.pep.xml
file.
If you want some data to reproduce it, here (https://www.dropbox.com/sh/qc3z8ive4vh5wt7/AABnlEQvqNjysOG2bixl-2wwa?dl=1) it is.
Thank in advance for your help,
Fengchao