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

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 a (1) and y (1) ions cannot be explained by considering the proton affinities of the corresponding dissociating species on the a (1)-y (1) 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 a (1)/y (1) ratio of H-Val-Gln-OH is explained by considering the dissociation kinetics of the proton-bound dimers formed on the a (1)-y (1) pathway and competition of the deamidation and a (1)-y (1) channels. For H-Val-Lys-OH, it is proposed that a (1) ions are indeed formed from one of the primary products, protonated H-Val-Cap-OH.