Why Are a3 Ions Rarely Observed?

It has been determined experimentally that a(3) ions are generally not observed in the tandem mass spectroscopic (MS/MS) spectra of b(3) ions. This is in contrast to other b(n) ions, which often have the corresponding a(n) ion as the base peak in their MS/MS spectra. Although this might suggest a different structure for b(3) ions compared to that of other b(n) ions, theoretical calculations indicate the conventional oxazolone structure to be the lowest energy structure for the b(3) ion of AAAAR, as it is for other b(n) ions of this peptide. However, it has been determined theoretically that the a(3) ion is lower in energy than other a(n) ions, relative to the corresponding b ions. Furthermore, the a(3) -> b(2) transition structure (TS) is lower in energy than other a(n) -> b(n-1) TSs of AAAAR, compared with the corresponding b ions. Consequently, it is suggested that the b(3) ion does fragment to the a(3) ion, but that the a(3) ion then immediately fragments (to b(2) and a(3)(*)) because of the excess internal energy arising from its relatively low energy and the facile a(3) -> b(2) reaction. That is why a(3) ions are not observed in the MS/MS spectra of b(3) ions. (J Am Soc Mass Spectrom 2008, 19, 1764-1770) (c) 2008 American Society for Mass Spectrometry