Fragmentation reactions of some peptide b3 ions: an energy-resolved study.

The fragmentation reactions of b3 ions of nominal structure AAAoxa, YAAoxa, AYAoxa and AAYoxa have been studied as a function of collision energy, allowing the construction of breakdown graphs expressing in a qualitative way the energy dependence of the fragmentation reactions. The primary fragmentation reactions of the AAAoxa b3 ion involve formation of the a3* (a3-NH3) ion and the b2 ion, with the latter becoming the dominant product at higher internal energies. For both YAAoxa and AYAoxa b3 ions the pathway to a3* is relatively minor with formation of b2 the dominant primary fragmentation reaction. For the AAYoxa b3 ion, in addition to a3*, abundant formation of the tyrosine (Y) iminium ion is observed with only minor formation of the b2 ion. The results support and expand upon the detailed mechanism of fragmentation of b3 ions proposed by Cooper et al. (J. Am. Soc. Mass Spectrom. 2006; 17: 1654).