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,
Sebastian