Error importing Percolator v3.05 xml

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Error importing Percolator v3.05 xml damon barbacci22098  2021-01-19
 
I receive the following error when I try to import Percolator pep xml output into SkyLine.

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Skyline
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ERROR: boost::filesystem::directory_iterator::construct: The system cannot find the path specified: "../sequest/"
ERROR:
ERROR: reading file 2021012_MSB50697A.perc.xml

Command-line: C:\Users\dbarbacci\AppData\Local\Apps\2.0\LY2EZ3ML.RV9\JVPER9HM.HDE\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0.95 -i MSB50697_98A -K -S "C:\Users\dbarbacci\AppData\Local\Temp\tmpFB5A.tmp" "S:\Process Dev\Analytical Team\Damon Barbacci\MSBioworks_HUD01_HCP\MSB50697_98A.redundant.blib"
Working directory: S:\Process Dev\Analytical Team\Damon Barbacci\MSBioworks_HUD01_HCP
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OK More Info
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System.IO.IOException: ERROR: boost::filesystem::directory_iterator::construct: The system cannot find the path specified: "../sequest/"
ERROR:
ERROR: reading file 2021012_MSB50697A.perc.xml

Command-line: C:\Users\dbarbacci\AppData\Local\Apps\2.0\LY2EZ3ML.RV9\JVPER9HM.HDE\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0.95 -i MSB50697_98A -K -S "C:\Users\dbarbacci\AppData\Local\Temp\tmpFB5A.tmp" "S:\Process Dev\Analytical Team\Damon Barbacci\MSBioworks_HUD01_HCP\MSB50697_98A.redundant.blib"
Working directory: S:\Process Dev\Analytical Team\Damon Barbacci\MSBioworks_HUD01_HCP
   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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damon barbacci22098 responded:  2021-01-19

Example file small enough for upload that gives same error.

 
Nick Shulman responded:  2021-01-19
When you are building a spectral library from a .perc.xml file, there are a lot of other files that you need to have there as well.

BiblioSpec also needs the .sqt files, and well as the spectrum files that were searched (.ms2, .cms2, or I think it can handle other file types like .mzML).

I am not sure exactly where all those files need to be relative to the .perc.xml. The error that you are seeing "cannot find the path ../sequest" happened because BiblioSpec was looking around for the .sqt files and could not find it. If BiblioSpec had found the .sqt files in the same directory as the .perc.xml files, it would not have felt that it needed to find a directory called "../sequest".

This web page tells you what additional files BiblioSpec needs to be able to find, depending on which type of search results you are using:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

-- Nick
 
damon barbacci22098 responded:  2021-01-19
Thanks for the quick reply. Bibliospec lists the .ms2 or .cms2 file type. With this data I used .mgf files for the Comet searches. Is there a way to specify an mgf file instead of an ms2? As of now the Skyline just crashes without options to look for alternate file types.

If not, I will convert my RAW file to ms2 format using pwiz.

Thanks!
 
Nick Shulman responded:  2021-01-19
I believe when reading Percolator results, BiblioSpec really does need to be able to find "ms2" or "cms2" files.

With other sorts of search results, BiblioSpec is willing to use whatever type of spectrum files it is able to find (".mzML", ".mzXML", and I think even ".raw" in most cases), but for Percolator results, it looks like it needs something that ends in "...ms2".

-- Nick
 
matt.chambers42 responded:  2021-01-19
Note that perc.xml is not pepXML, it is percolator's non-standard XML format. BiblioSpec does support it but like Nick said it requires SQT and only supports ms2/cms2/bms2/pms2 extensions for reading the spectra. If you can use pepXML instead that would be better (and it supports reading far more input formats). Adding MGF support to the perc.xml reader might be a little tricky but it shouldn't be too hard.

The sequest directory_iterator error you're getting indicates a bug though. You should be getting an error that says it didn't find the file with one of the supported extensions.

The easiest way forward for you at the moment is to use pwiz to convert the MGF to MS2. You shouldn't need to go back to the RAW file.