Error when importing iproph.pep.xml

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Error when importing iproph.pep.xml ztflaten  2020-12-07
 
Hello,

I am trying to build a spectral library with an iproph.pep.xml document I've generated and I keep running into various forms of this error
"---------------------------
Skyline
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ERROR: index 17017 out of range in mzXML file '.\P2.mzXML'

Command-line: C:\Users\pc\AppData\Local\Apps\2.0\5PYCWJGV.XX2\M6EMW1MM.TJV\skyl..tion_e4141a2a22107248_0014.0002_be619ba2d44825a4\BlibBuild -s -A -H -o -c 0.99 -i fragpipe_dda_2 -S "C:\Users\pc\AppData\Local\Temp\tmp79D2.tmp" "C:\Fragpipe_Skyline\fragpipe_dda_2.redundant.blib"
Working directory: C:\Fragpipe_Skyline
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OK More Info
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System.IO.IOException: ERROR: index 17017 out of range in mzXML file '.\P2.mzXML'

Command-line: C:\Users\pc\AppData\Local\Apps\2.0\5PYCWJGV.XX2\M6EMW1MM.TJV\skyl..tion_e4141a2a22107248_0014.0002_be619ba2d44825a4\BlibBuild -s -A -H -o -c 0.99 -i fragpipe_dda_2 -S "C:\Users\pc\AppData\Local\Temp\tmp79D2.tmp" "C:\Fragpipe_Skyline\fragpipe_dda_2.redundant.blib"
Working directory: C:\Fragpipe_Skyline
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 156
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I am not sure I understand what the error is telling me but I think it has to do with the location of the files it's trying to find (which are located in the same directory in a sub folder). I've tried moving files around in my directory but keep having issues, even when they are all in the same folder as the saved skyline document.

Thanks,

-Zach
 
 
Nick Shulman responded:  2020-12-07
That error is saying that your pep.xml file claims to have a spectrum match for spectrum #17017, but there aren't that many spectra in that mzXML file.

Are you sure that the P2.mzXML file that you have put in the same folder with your pep.xml file is the actual mzXML file that was searched? Maybe that mzXML file has had some spectra filtered out of it, and maybe you have a different mzXML or mzML file somewhere that has the right number of spectra in it.

By the way, here is a useful page which lists the peptide search engines which are supported by BiblioSpec and which files need to be provided:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

-- Nick