Skyline-daily (64-bit) 21.0.9.139 (6dbba07d9) cannot load the library.tsv file from EasyPQP

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Skyline-daily (64-bit) 21.0.9.139 (6dbba07d9) cannot load the library.tsv file from EasyPQP fcyu  2021-06-02
 

The library.tsv file from EasyPQP is in OpenSWATH format. But when loading it in Skyline, it says "the file F:\dev\msfragger\test_skyline\library.tsv is not a supported spectral library file format.". According to https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild, it should support OpenSWATH tsv file.

I put an example of library.tsv in the attachment. Could you please take a look when you have time?

Thanks,

Fengchao

 
 
Kaipo responded:  2021-06-02

Hi Fengchao,

This doesn't look like the OpenSWATH files we have seen in the past. Normally we expect these columns:

  • filename
  • RT
  • FullPeptideName
  • Charge
  • m/z
  • decoy
  • aggr_Peak_Area
  • aggr_Fragment_Annotation
  • m_score

and optionally these ones:

  • ProteinName
  • leftWidth
  • rightWidth

Additionally, to build spectral libraries, Skyline requires results files that have some type of probability scores (e.g. q-values) and a way to map results to a spectrum file (e.g. filename and scan number). If you have that information, it should be possible to generate a generic ssl file (https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec input and output file formats) that can be used to build a library.

Thanks,
Kaipo