Secondary interactions affecting the dissociation patterns of arginine-containing peptide ions

An explanation is proposed for the dominance of arginine in the dissociation patterns of peptides. Experiments measuring the kinetic energy lost by parent ions of a number of arginine-containing peptides in the formation of particular product ions provide a means of gauging the amount of energy required to observe the dissociation. It is proposed that the higher amounts of energy needed to observe dissociation adjacent to an arginine residue are due to secondary interactions between the arginine sidechain and an adjacent amino acid. The appearance of the (b(n-1) + OH) ion in the MS/MS spectra of many arginine-containing peptides and data acquired on a quadrupole ion trap help support these findings. We further suggest that the differences in the dissociation between peptides with arginine and those without may be due to the predominance of different reaction mechanisms, i.e. charge-remote versus charge-directed.