MSfragger splib to blib?

MSfragger splib to blib? dkueltz  2021-05-31


I wonder if there is a way to convert MSfragger generated splib to blib for use in skyline? I tried generating blib in skyline from MSfragger mzml, pepxml and calibrated.mgf output files but only get blibs that have proteins but 0 peptides/ precursors. and transitions - this seems similar to a previous thread report where the upgrade of Skyline 19 to 20 was reported to fail in including precursor spectra in the speclib. ANy suggestins would be appreciated.


Nick Shulman responded:  2021-05-31
This is the page that lists which type of files you need in order to build a BiblioSpec spectral library from different types of peptide search results:

That page says that for msfragger you need pepxml files.

It sounds like something isn't working right. Can you send us your pepxml and mzml files (If you'd like you could include your mgf and raw files too)? You can upload those files here:

Which other support request are you referring to? I found this support request which kind of sounds similar to the description you gave:
That support request looks like it was talking about something which was eventually fixed.

-- Nick
dkueltz responded:  2021-06-01
Hi Nick,

Never mind - building a speclib in Skyline works flawless when using msfragger pepxml and mgf files generated from dda raw data.

Thanks much,