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