Pathways to Immonium Ions in the Fragmentation of Protonated Peptides

The pathways leading to the formation of immonium (An) ions in the fragmentation of protonated peptides were investigated using metastable ion studies, including kinetic energy release measurements, and low-energy collision-induced dissociation studies. In addition to the established pathway Bn→An+CO, it is shown that B2 ions, in suitable circumstances, fragment directly to A1 ions. In addition, metastable ion studies show that A1 ions can be formed directly from protonated di- and tripeptides most likely by concerted elimination of CO and an amino acid or smaller peptide. A2 ions can be formed directly from protonated dipeptides in part through the sequential loss of H2O+CO, although kinetic energy release measurements suggest direct elimination of HCOOH also may be occurring. Internal immonium ions are shown to originate by further fragmentation of An ions and by further fragmentation of Yn″ ions.