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Skyline support PD 2.1 result files?

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Skyline support PD 2.1 result files? xicao  2016-03-05 08:53
 
Hi,

I am wondering if Skyline support PD 2.1 result files? When I tried building a peptide library, if I loaded pdResult file, I got the error message:
System.IO.IOException: ERROR: Ziv_3_02232016-(01).pdResult
ERROR:

   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status, TextWriter writer) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 109
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 53
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, ProgressStatus& status, String[]& ambiguous) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 166
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 128

If I loaded msf file, eventually I got a message to tell me no peptide matched the filter settings, even though I set the cutoff score as 0 (see attachment).

Thanks,

Xing-Jun
 
 
Brendan MacLean responded:  2016-03-06 11:26
Hi Xing-Jun,
Hopefully you will soon hear from Kaipo on looking at your .pdResult file, since we believe Skyline can handle PD 2.1 results like this. That has been tested. So, it must be something specific to your file, and, yes, the message could be improved.

The PD.PNG message you have posted is simply telling you the number of PROTEINS (not peptides) for which Skyline could not find any peptide spectrum matches in your library. This is quite common when import a full organism FASTA file after building your library, and the function of discarding this matchless proteins was added after seeing so many cases where Skyline documents filled up with empty proteins containing no valid targets, because they lacked spectra in the library.

You can just OK this message, and then use View > Spectral Libraries to look at the actual contents of the spectral library Skyline built from your MSF file. I don't really recommend 0 as a scoring cut-off, but that is up to you.

Hope this helps to clarify. We'll be in touch about the pdResult issue.

Thanks for posting to the Skyline support board.

--Brendan
 
xicao responded:  2016-03-06 17:49
Hi Brendan,

Thank you for the reply in the weekend.

I used SequetHT in PD to search, and used 1% FDR to filter the result. I could not load pdResult file, so I tried loading msf file. When I set any value as cutoff score, the pop-up window told me that there was no q value in the file, so it stopped and closed. I had to set 0 for this msf file, and I had to load the whole database since I don't know what proteins were there. When the error message came out, next, Skyline stopped and closed without any saving, so I could not use View to see the contents.

Another question, if pdResult works, do I still need to set cutoff score?

Thanks,

Xing-Jun
 
Kaipo Tamura responded:  2016-03-07 12:09
Hi Xing-Jun,
You should set a cutoff score for pdResult files, it will filter out the PSMs by q-value. I will need your pdResult file to debug the issue further, I will contact you through email about it.

Thanks,
Kaipo
 
Fabian responded:  2017-09-05 02:11
Hi,
i have a similar issue with pdResult files (PD 2.1).
Trying to load a PD library in skyline(Cut-off score is set to 0) results in:

                                      ERROR: no such column: qValue
                                      ERROR

The issue may arise from the preceeding workflow, trying to import msf files in skyline, which were used for the library in PD, results in:

                                      ERROR: reading file 'filename.msf'

The workflow is such that different raw files were searched with Byonic, resulting in several msf files which were combined in PD 2.1.

Thanks,

Fabian
 
Kaipo Tamura responded:  2017-09-05 10:50
Hi Fabian,
Would you mind uploading a sample of a file with the problem to https://skyline.ms/files.url

Thanks,
Kaipo
 
Fabian responded:  2017-09-06 08:28
Dear Kaipo,

thank you so much for your fast response.

I uploaded two files:

a pdResult file: 043_KORA_JDRF_HeavyPeptidesinPlasma
and a msf file: 025_human_blood_cell_batch1_3xLEM7953


Best regards

Fabian
 
Kaipo Tamura responded:  2017-09-11 12:41
Hi Fabian,
This issue should be fixed if you update Skyline (the pdResult file may still not work until the next version of Skyline-daily is released).

Thanks,
Kaipo