Stability of peptide fragmentation patterns

Our study aims to determine the stability of fragmetnation patterns of peptides upon collision-induced dissociation (CID). Recent studies reported that for a minority of peptides, CID fragmentation leads to non-reproducible fragmentation spectra and therefore impaired identification. In order to study the fragmentation behavior, we first identified peptides that exhibit different fragmentation patterns. In order to reveal the cause, we selected a subset of the peptides and studied the dependency of abundance of distinct fragmentation patterns with collision energy settings and with of the isolation window.