Competing gas-phase fragmentation pathways of asparagine-, glutamine-, and lysine-containing protonated dipeptides

Abstract

The fragmentation chemistry of protonated H–Val–Asn–OH, H–Val–Gln–OH and H–Val–Lys–OH is investigated in this work by means of modeling and density functional theory calculations. Former experimental studies indicate that the ratio of a1 and y1 ions cannot be explained by considering the proton affinities of the corresponding dissociating species on the a1–y1 pathway, while the fragmentation of other dipeptides can be understood in this way. We demonstrate that considering the correct PA value for H–Asn–OH eliminates the deviation observed for H–Val–Asn–OH. The larger than expected a1/y1 ratio of H–Val–Gln–OH is explained by considering the dissociation kinetics of the proton-bound dimers formed on the a1–y1 pathway and competition of the deamidation and a1–y1 channels. For H–Val–Lys–OH, it is proposed that a1 ions are indeed formed from one of the primary products, protonated H–Val–Cap–OH.