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Export the library retention time for matched peptides in document grid

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Export the library retention time for matched peptides in document grid chiyy  2026-02-04 17:18
 

Hi Skyline team, are you aware about the ways to export the retention time provided in library for every matched peptide (the number red framed in the attached figure)? I looked through the document list and I am not sure which is the right one to export. Thank you very much for your help.
 
 
Nick Shulman responded:  2026-02-04 19:25

I think there is no way to export those retention times from Skyline but you could potentially read them from the library yourself.
BiblioSpec spectral libraries (.blib) are SQLite databases.

If you have the program sqlite3.exe, the following command would list all the peptides and the retention time of the best spectrum:

sqlite3.exe mylibrary.blib -cmd ".mode csv" "SELECT peptideModSeq, retentionTime FROM RefSpectra;"

If you wanted to know the retention times of the peptide in all of the files that it was found in, you would need to use a query which joined the RefSpectra, RetentionTimes, and SpectrumSourceFiles tables:

sqlite3.exe mylibrary.blib  -cmd ".mode csv" "SELECT rs.peptideModSeq, rt.RetentionTime, ssf.FileName FROM RefSpectra rs INNER JOIN RetentionTimes rt ON rs.Id = rt.RefSpectraId INNER JOIN SpectrumSourceFiles ssf ON rt.SpectrumSourceId = ssf.id;"

-- Nick
 
chiyy responded:  2026-02-04 19:59

Thanks Nick! This works pefectly.