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 (bn−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 (bn−1 + H2O) daughter ions (∼81%), including 185 (∼46%) “strong” decays with ratios (bn−1 + H2O)/(bn−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 (bn−1 + H2O) ions (∼16%) were observed, including 87 (> 7%) “strong” decays, so the effect is still appreciable. The results suggest that the tendency for (bn−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.