Focus: MS/MS Peptide Identification: Research Article

Journal of The American Society for Mass Spectrometry

, Volume 23, Issue 4, pp 594-601

First online:

Fragmentation Reactions of b5 and a5 Ions Containing Proline—The Structures of a5 Ions

  • Alex G. HarrisonAffiliated withDepartment of Chemistry, University of Toronto Email author 


A detailed study has been made of the b5 and a5 ions derived from the amides H-Ala-Ala-Ala-Ala-Pro-NH2, H-Ala-Ala-Ala-Pro-Ala-NH2, and H-Ala-Ala-Pro-Ala-Ala-NH2. From quasi-MS3 experiments it is shown that the product ion mass spectra of the three b5 ions are essentially identical, indicating macrocyclization/reopening to produce a common mixture of intermediates prior to fragmentation. This is in agreement with numerous recent studies of sequence scrambling in b ions. By contrast, the product ion mass spectra for the a5 ions show substantial differences, indicating significant differences in the mixture of structures undergoing fragmentation for these three species. The results are interpreted in terms of a mixture of classical substituted iminium ions as well as protonated C-terminal amides formed by cyclization/rearrangement as reported recently for a4 ions (Bythell, Maître , Paizs, J . Am. Chem. Soc. 2010, 132, 14761–14779). Novel fragment ions observed upon fragmentation of the a5 ions are protonated H-Pro-NH2 and H-Pro-Ala-NH2 which arise by fragmentation of the amides. The observation of these products provides strong experimental evidence for the cyclization/rearrangement reaction to form amides and shows that it also applies to a5 ions.

Key words

b5 ion structures a5 Ion structures Tandem mass spectrometry