Formation of (bn-1+H2O) ions by collisional activation of MALDI-formed peptide [M+H]+ ions in a QqTOF mass spectrometer

Collisional activation of [M + H](+) parent ions from peptides of n amino acid residues may yield a rearrangement that involves loss of the C-terminal amino acid residue to produce (b(n-1) + H2O) daughters. We have studied this reaction by a retrospective examination of the m/z spectra of two collections of data. The first set comprised 398 peptides from coat protein digests of a number of plant viruses by various enzymes, where conditions in the tryptic digests were chosen so as to produce many missed cleavages. In this case, a large effect was observed - 323 (b(n-1) + H2O) daughter ions (similar to 81%), including 185 (similar to 46%) "strong" decays with ratios (b(n-1) + H2O)/ (b(n-1)) > 1. The second set comprised 1200 peptides, all from tryptic digests, which were carried out under more stringent conditions, resulting in relatively few missed cleavages. Even here, 190 (b(n-1) + H2O) ions (similar to 16%) were observed, including 87 (> 7%) "strong" decays, so the effect is still appreciable. The results suggest that the tendency for (b(n-1) + H2O) ion formation is promoted by the protonated side chain of a non-C-terminal basic amino acid residue, in the order arginine >> lysine >= histidine, and that its (non-C-terminal) position is not critical. The results can be interpreted by a mechanism in which hydrogen bonding between the protonated side chain and the (n - 1) carbonyl oxygen facilitates loss of the C-terminal amino acid residue to give a product ion having a carboxyl group at the new C-terminus.