Proposal for a common nomenclature for peptide fragment ions generated following sequence scrambling during collision-induced dissociation.

Figure 1. (A) The b5 ion is generated by collision induced dissociation resulting in formation of the oxazolone ring through attack of the oxygen lone pair on the newly formed terminal carbonyl group. (B) N-terminal nucleophilic attack of the oxazolone ring to form the macrocycle. (C) The resultant macrocyclic intermediate undergoes ring opening to give sequence scrambled b5 ions. N.B. Numbering of the peptide bonds is performed for the initial sequence and the order maintained throughout the scrambling pathway. This numbering system enables not only the scrambled product, but also the fragmentation pathway from which it was derived to be assigned. Bond 0 is that formed by N-terminal nucleophilic attack of the oxazolone ring. Ring opening at this position results in reformation of the original sequence. 20 Dear Editor,