Having an error when importing FragPipe DIA interact.pep.xml files

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Having an error when importing FragPipe DIA interact.pep.xml files fcyu  2021-12-31
 

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

 
 
Nick Shulman responded:  2021-12-31
Fengchao,

Using the files from that DropBox link, what would I need to do differently to see different behavior in Skyline?

When I create a library from one of the "interact-*_rankX.pep.xml" files (specifically "interact-CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00004_NAT_rank1.pep.xml") I don't get the "No spectra were found" error message. This sounds like the "searched raw files" behavior.

Do you have at a different set of files which contains the peptide search results which you got when you searched mzML files?
-- Nick
 
fcyu responded:  2021-12-31
Hi Nick,

Thanks for your prompt reply.

I cannot reproduce the error now. Maybe something was wrong when I import it last time. Sorry for the false alarm.

Best,

Fengchao