q-value issue when attempting to build library from .pdresult

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q-value issue when attempting to build library from .pdresult monica lane  2018-02-09 12:52
 
Hi Skyline team,

I'm attempting build spectral library from Proteome Discoverer 2.2 search result (Mascot search node in workflow and consensus workflow nodes that calculate q-values at PSM, peptide and protein level). I'm using the .pdresult file but getting following message from Skyline (in both Skyline v 4.1.0.11714 and Skyline Daily v 4.1.1.11756):

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:
ERROR: reading file Heavy_peptide_pool_2X_013118_2.pdResult

   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in c:\proj\skyline_4_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in c:\proj\skyline_4_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 125



Do you have a workaround or fix so that I don't have to set cut-off to zero?

Thank you!
 
 
Kaipo Tamura responded:  2018-02-11 11:46
Hi,
Would you mind uploading the pdResult file to: https://skyline.ms/files.url
so I can have a look at it?

Thanks,
Kaipo
 
Kaipo Tamura responded:  2018-02-23 13:53
Hi Monica,
I've added support for this and it will be available in the next release of Skyline-daily.

Thanks,
Kaipo