Dissociation mechanisms and implication for the presence of multiple conformations for peptide ions with arginine at the C‐terminus: time‐resolved photodissociation study

Time‐resolved photodissociation (PD) patterns of singly protonated peptides with arginine at the C‐terminus (C‐arg peptide ions) have been used to classify the dissociation channels into two categories, i.e. high‐energy channels generating v, w and x and low‐energy ones generating b, y and z. x + 1 formed by C_α? CO cleavage seems to be the intermediate ion in high‐energy channels just as a + 1 is for N‐arg peptide ions. Difference in time‐resolved pattern indicates that the two sets of channels, high‐ and low‐energy ones, are not in direct competition. Noncompetitive dissociation is also indicated by the observation of anomalous effect of matrix used in matrix‐assisted laser desorption ionization, a cooler matrix generating more high‐energy product ions both in spontaneous dissociation and in PD. Results from detailed investigation suggest that the two sets of channels start from two (or more) different conformations. Copyright © 2010 John Wiley & Sons, Ltd.