Error generating spectral library from FragPipe in Skyline v20.1.0.31

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Error generating spectral library from FragPipe in Skyline v20.1.0.31 Chinmaya k  2020-02-13
 

Hello,

I have not been able to generate a spectral library in Skyline from FragPipe/MSFragger output. Please find the attached error file. The same error has also been reported recently as well. (https://skyline.ms/announcements/home/support/thread.view?rowId=43828)

I tried to generate a spectral library separately using BlibBuid.exe and it was also ended up with the same error. Please find the attached screenshot as well.

Is there any other way to rectify this and generate a Skyline compatible spectral library?

--
Chinmaya

 
 
matt.chambers42 responded:  2020-02-18

Hi Chinmaya,

This has been fixed but a new daily release has not yet been made that includes the fix. You can get the bleeding edge automated build (BiblioSpec.zip or SkylineTester.zip) from:
https://teamcity.labkey.org/viewLog.html?buildId=lastSuccessful&buildTypeId=bt209&tab=artifacts

Just unzip the BiblioSpec into your Skyline-daily directory, for example.

 
Chinmaya k responded:  2020-02-20

Hi Matt,

I did try using the standalone bleeding-edge BiblioSpec. But, neither it is showing an error like before nor the complete .blib file.

It is because the mzML file I have used in MSFragger was exported from Proteome Discoverer v2.2?

--
Chinmaya

 
matt.chambers42 responded:  2020-02-20

What do you get if you add "-v detail" to the command?

 
Chinmaya k responded:  2020-02-20

Hi Matt,

I did try with the above command. I can see all the PSMs in my .pep.xml file and later it will start looking for the PSM with a list scan number i.e. 626 in my case and it does not move ahead from these like before (Please find the attachment).

What might be the reason?

I could not upload the MSFragger output and mzML file in the file-sharing folder in Skyline. Is there any other way to share it with you, if you want to have a look?

--
Chinmaya

 
matt.chambers42 responded:  2020-02-21

Not sure what's going wrong there. Can you upload your pep.xml and mzML to:
https://skyline.ms/project/home/support/file sharing/begin.view?

 
Chinmaya k responded:  2020-02-21

Hi Matt,

I have added the files to the file sharing folder. It is named "MSFragger_Result_Spec_Lib.rar".

Let me know if you need more info.

--
Chinmaya

 
Chinmaya k responded:  2020-02-28

Hi Matt,

Any update on the above issue?

Were you able to figure out why the skyline or BiblioSpec is showing an error?

--
Chinmaya