Focus: Peptide fragmentation: Why Are a3 Ions Rarely Observed?

It has been determined experimentally that a3 ions are generally not observed in the tandem mass spectroscopic (MS/MS) spectra of b3 ions. This is in contrast to other bn ions, which often have the corresponding an ion as the base peak in their MS/MS spectra. Although this might suggest a different structure for b3 ions compared to that of other bn ions, theoretical calculations indicate the conventional oxazolone structure to be the lowest energy structure for the b3 ion of AAAAR, as it is for other bn ions of this peptide. However, it has been determined theoretically that the a3 ion is lower in energy than other an ions, relative to the corresponding b ions. Furthermore, the a3 - > b2 transition structure (TS) is lower in energy than other an - > bn-1 TSs of AAAAR, compared with the corresponding b ions. Consequently, it is suggested that the b3 ion does fragment to the a3 ion, but that the a3 ion then immediately fragments (to b2 and a3*) because of the excess internal energy arising from its relatively low energy and the facile a3 - > b2 reaction. That is why a3 ions are not observed in the MS/MS spectra of b3 ions.