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We present a detailed analysis of the relative yields in dissociation products of doubly protonated polypeptide cations obtained via electron capture dissociation (ECD). These experimental studies are complemented by molecular dynamics force field modelling, using the AMBER force field, to correlate with putative gas-phase conformations for these peptides. It is shown that the highest gas-phase basicity amino acid residue (i.e. arginine) is included in all the charged fragments. This is of particular use in determining the primary structure tryptic digest peptides, which will ordinarily posses a high basicity C-terminal residue (i.e. arginine or lysine). Further, these results suggest that the relative ECD dissociation pattern is related to the secondary structure of the peptide. In particular, the ECD fragmentation pattern in gonadatropin releasing hormone (GnRH) variants appears to depend on whether a beta-turn or an extended alpha-helical structure is formed. In the peptide bradykinin, modelling suggests that the C-terminal arginine engages in much more extended solvation of the backbone than the N-terminal arginine. This strongly correlates with the observed dominance of c over z fragments. This work forms the first attempt at a systematic qualitative correlation of the low-energy structures of modelled gas-phase polypeptides, and their corresponding ECD dissociation pattern.
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