Multi-stage collisionally-activated decomposition in an ion trap for identification of sequences, structures and bn → bn-1 fragmentation pathways of protonated cyclic peptides

Cyclic penta-, hexa- and heptapeptides have been designed, synthesized and their fragmentations induced by multi-stage tandem mass spectrometry have been studied. Under low-energy collisionally-activated decomposition (CAD), the protonated cyclic peptides mainly dissociate via ring opening pathways and the corresponding b(n) -> b(n-1) pathways to form several sets of b ions as oxazolone rings (and b(1) ions as aziridinone rings). Through repeated observation of these b ions in multistep CAD experiments, accurate sequencing and head-to-tail ring structure of cyclic peptides can be determined. The mistaken assignments of these b ions can be avoided by this sequencing method. Semi-empirical molecular orbital calculations have been utilized to provide insight into the proposed dissociation mechanism. In addition, for cyclic peptides that include an Asn residue, the nitrogen of the Asn side chain is observed to be preferentially protonated, which can induce a unique ring-opening pathway with a loss of ammonia that competes with the conventional ring opening pathway.