Import all peptides option using SkylineCmd

Import all peptides option using SkylineCmd jpaezpae  2021-02-23

Hello everyone,

I am trying to import a spectral library and add to the document all peptides in such library.

I am aware that using the GUI, this task can be accomplished by going to View > Spectral Libraries > Library > "<Add...>" > {add the library} > {click on the Add All... button} and it "just works" but I trying to use the command line interface for skyline and don't know exactly how to do this and cant seem to find any CLI flag for it.

As a workaround I think I could generate a transition list from my .sptxt by parsing all peptide names, duplicating precursor mass as a column and filtering the peaks that match y and b ions ... But I really feel like there should be a easier version.

Highly appreciating all of your help
Kindest wishes,

Nick Shulman responded:  2021-02-23

As far as I can tell there is no commandline command to do the exact equivalent of "Add All" from the Spectral Library Viewer.

You can do "--import-fasta" which often results in the same thing as adding from the spectral library viewer.

When you do "--import-fasta" you will sometimes be missing some of the peptides that are in your spectral library, even if you are using the same FASTA file as you performed your peptide search against. The peptides that you end up missing are the ones where Skyline does not believe they could have been produced based on the enzyme specified as "Settings > Peptide Settings > Digestion".

You should make it so that "Pick Peptides Matching > Library" is selected at "Settings > Peptide Settings > Library" so that Skyline will know that you only want the peptides in your FASTA file that can also be found in your library.

-- Nick