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Creating & naming spectral libraries from ssl files via command line

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Creating & naming spectral libraries from ssl files via command line Jonas Becker  2024-11-13 10:18
 

Dear Skyline Team and Community,

I'm generating spectral libraries from ssl files via the command line tool with the following (simplified) code:

"D:\Software\Skyline\SkylineRunner.exe" ^
--in="tool_comparison.sky" ^
--import-search-file="results_tool1.ssl" ^
--out="tool_comparison.sky

How can I set the name of the generated spectral library? Currently, it is automatically named "tool_comparison.blib". Is there any option to assign a name or have it named after the ssl file (i.e. "results_tool1.blib")?

Additionally I receive the following warning: "Warning: Unable to locate results file 'results_tool1.mgf'". This does not seem to cause any major error for my analysis, nevertheless it would be nice to understand why this is happening. The mgf file is in the same folder as the ssl file and naming in the ssl file is correct.

Thanks in advance! Cheers
Jonas
 
 
Nick Shulman responded:  2024-11-13 13:45
When you import peptide search results, the library is always given the same name as the Skyline document.
You can import peptide search results in the user interface using the menu item "File > Import > Peptide Search" or with the "--import-search-file" command line argument.
Importing peptide search results is different from building a spectral library, which is the thing that you can do in the user interface using the "Build" button on the "Library" tab at "Settings > Peptide Settings".

I do not see any command line argument to tell Skyline to build a spectral library. The reason for this might be that Skyline uses BlibBuild.exe and BlibFilter.exe to build the library and it would be straightforward to do that yourself.

If you wanted to build a library called "mylibrary.blib" from "results_tool1.ssl" you could execute the following two commands:
BlibBuild.exe -H results_tool1.ssl mylibrary.redundant.blib
BlibFilter.exe -b true mylibrary.redundant.blib mylibrary.blib

BlibBuild.exe and BlibFilter.exe can be found in the same folder as the Skyline executable (i.e. Skyline.exe or Skyline-daily.exe).

I am not sure where the warning "Unable to locate results file 'results_tool1.mgf'" might be coming from. If you send me your files I could try to figure it out.
Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick