MFragger EasyPQP library.tsv to populate Skyline target list

MFragger EasyPQP library.tsv to populate Skyline target list Tomas Vaisar  2023-09-18 06:26

Hi All,
Is there a way to populate Skyline target list with the library generated by MSFragger/EasyPQP (library.tsv)?


Nick Shulman responded:  2023-09-18 16:02
What does a "library.tsv" file look like? Can you post an example file?
Files which are less than 50MB can be attached to this support request. You can upload larger files here:

The usual way to get peptides into the document would be with the "Edit > Insert > Peptides" menu item, but it sounds like your library.tsv file might have more information in it than just the peptide sequence.
-- Nick
Tomas Vaisar responded:  2023-09-18 16:15
Hi Nick,
The library.tsv from MSFragger/EasyPQP has lot more info - it has retention times, fragment ions and intensities. I uploaded example into the files.url you sent.

Nick Shulman responded:  2023-09-18 18:57
I think you are just supposed to do:
File > Import > Transition List
and point Skyline at that library.tsv file.

A window will come up which allows you to specify how the columns in your .tsv file map to things that Skyline understands.
Skyline also seems to notice that there are retention times in there and offers to create an iRT library and also notices that there are intensities and offers to create a spectral library for the document.
-- Nick