Effect of phenylalanine on the fragmentation of deprotonated peptides

Abstract

The fragmentation reactions of a variety of deprotonated dipeptides and tripeptides containing phenylalanine have been studied using energy-resolved collision-induced dissociation, isotopic labeling and MS/MS/MS experiments. The benzyl α-group has a substantial effect on the fragmentation reactions observed. When the phenylalanine is in the C-terminal position of dipeptides or tripeptides a major fragmentation reaction is elimination of neutral cinnamic acid to from a deprotonated amino acid amide (c 1 ion) for dipeptides and a deprotonated dipeptide amide (c 2 ion) for tripeptides. Fragmentation of the [M − H] − ions of tripeptides with phenylalanine in the central position also results in substantial formation of the deprotonated amide of the N-terminal amino acid residue. When the phenylalanine residue is in the N-terminal position elimination of C 7H 8 from the [M − H − CO 2] − ion and formation of the benzyl anion become important fragmentation pathways. Sequence ions frequently observed are the y 1 ions, ″b 2 ions and a 3-N t ions.