New to Skyline: Searching for specific MS2 ions

New to Skyline: Searching for specific MS2 ions irahman2  2019-06-10


I am a new user to Skyline, and would like some help to do some MS2 searching/filtering.

To explain the experimental setup: I have a bait peptide that has a reactive group that can covalently crosslink with C-H/C-X bonds on the target molecule. I would like to search through all the MS2 spectra for known daughter ions of my bait peptide so I can identify the precursor mass that corresponds to some adduct. I have a hunch that the peptide is actually binding to some lipid molecule if that is helpful.

Is Skyline an appropriate software to do this kind of searching, or are there other programs I should look into?

Thank you!

Brian Pratt responded:  2019-06-10

It's important to understand that Skyline is for targeted mass spec - it assumes that you already have some idea of what you're looking for. It's not a search tool per se. But, it can be used for identifying expected transitions that don't perform well, which is more or less what you're describing.

You'd have to come up with a transition list containing precursors for all the various combinations of crosslinks and ionizing adducts that you suspect are in play, each with the same set of expected fragment ions. With that, Skyline could help you rule out the precursors that don't look promising based on poor chromatogram extraction at the MS2 level.

Good luck with your research!

Brian Pratt