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Importing libraries in Skyline with no Q-value

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Importing libraries in Skyline with no Q-value lars kristensen  2017-07-04 05:03
 
Is there a workaround to import libraries in Skyline from a Proteome Discoverer 2.1 Sequest HT search without q-values from Percolator (e.g. because the number of hits were too few for the Percolator node to calculate a q-value due to the use of a small database)?
I tried to set the cut off score to 0 but it still required the q-values.
I’m using the latest version of Skyline (64-bit) 3.7.0.10940.

My aim is to quantify PRTC peptides in a HeLa background. Performing a PD 2.1 serch using parameters to identify both HeLa and PRTC peptides will result i q-values allowing me to import the identified PRTC peptides/fragments. However, only a few of the PRTC peptides are identified this way.

I have tried to make two separate searches, one optimized for HeLa and one optimized for PRTC and then combine them by creating a multiconsensus report. I checked that the PRTC peptides were indeed in the multiconsensus report. When I used this PD result file to create a library in Skyline I could create a library in Skyline without an error presumably because there were q-values in the PD result file. However only one PRTC peptide matched the spectral library (presumably because the PRTC peptides were not associated with a q-value and the single match was a random event.
 

Thank you very much for any assistance
Kind regards
Lars, lars.kristensen@thermofisher.com
 
 
Kaipo Tamura responded:  2017-07-05 12:21
Hi Lars,
Would you mind sharing the file here so I can look into the problem: https://skyline.ms/files.url

Thanks,
Kaipo
 
roman sakson responded:  2023-07-17 13:19
Hi Skyline Team,

I decided to add to this very old thread to report an observation that I made. I recently had to build a spectral library from an .msf file without q-values in it (similar situation as for Lars who opened this thread). This did not work when I was entering 0 as a value for the cutoff score, as recommended here:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries

Instead, I was getting the lengthy error message reported below. However, it worked perfectly fine with a cutoff score of 1. This also makes more sense to me, as q-value cutoff of 1 means to take everything, while cutoff 0 would mean expecting perfection, as Skyline (23.0.9) itself also advised me:

---------------------------
Skyline-daily
---------------------------
Score threshold 1 for Percolator q-value will include all identifications. Percolator q-value scores indicate the probability that an identification is incorrect.

Are you sure you want to continue?
---------------------------
OK Cancel
---------------------------


 Could it be that the cutoff value recommendation for the case of missing q-values should be updated? Here the lengthy error message:

---------------------------
Skyline-daily
---------------------------
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: reading file E25D105-19-235-16.msf

Command-line: C:\Users\Roman Sakson\AppData\Local\Apps\2.0\HKY1Z9MN.AMP\61TQ9EAM.84P\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\BlibBuild -s -A -H -o -i Test -S "C:\Users\Roman Sakson\AppData\Local\Temp\tmpC28D.tmp" "C:\Users\Roman Sakson\Desktop\Test.redundant.blib"
Working directory: F:\DGMS\DGMS_Skyline_Participants\DGMS_Skyline_Participants\Skyline_Data\Spectral_Libraries\MSF
---------------------------
OK More Info
---------------------------
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: reading file E25D105-19-235-16.msf

Command-line: C:\Users\Roman Sakson\AppData\Local\Apps\2.0\HKY1Z9MN.AMP\61TQ9EAM.84P\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\BlibBuild -s -A -H -o -i Test -S "C:\Users\Roman Sakson\AppData\Local\Temp\tmpC28D.tmp" "C:\Users\Roman Sakson\Desktop\Test.redundant.blib"
Working directory: F:\DGMS\DGMS_Skyline_Participants\DGMS_Skyline_Participants\Skyline_Data\Spectral_Libraries\MSF
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_23_1\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 180
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_23_1\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 430
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161
---------------------------

Best wishes,
Roman