Finding and using diagnostic ions in collision induced crosslinked peptide fragmentation spectra

Crosslinking mass spectrometry (XL-MS) has emerged as a powerful tool in its own right for the investigation of protein structures and interactions. Utilizing standard shotgun MS mass spectrometry equipment and specialized database search software, crosslinked peptide-pairs can be identified and directly translated into distance constraints for protein structure and protein-protein interaction investigations. Whereas the gas-phase dissociation behavior of linear peptides is well understood, less is however known about the gas-phase dissociation behavior of crosslinked peptides. In this work, we set out to expose the behavior of commonly used non-cleavable and gas-phase cleavable crosslinking reagents using synthetic peptides to establish mechanistic insights. We describe that crosslinked peptide pairs generate specific fragmentation patterns and diagnostic ions under HCD and CID fragmentation conditions, distinct from mono-linked peptide and non-modified peptides. We discuss in detail the resulting diagnostic ions that can help distinguishing linear peptides from mono-linked and crosslinked peptide pairs and how that may be used to further increase the efficiency of XL-MS analysis.