Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation.

The low-energy collision-induced dissociation reactions of a series of multiply-protonated peptides have been investigated by tandem mass spectrometry. It is known that doubly-protonated tryptic peptides undergo facile fragmentation yielding redundant sequence information. The present work has shown that this fortunate circumstance seems likely to be the exception rather than the rule. The presence of additional basic residues, at positions other than the C-terminus, complicates the spectra. The most important such complication discovered in the present work involves wholesale transfer of one or two residues from the C-terminal end of a doubly-charged b fragment to the side chain of a lysine residue located near the N-terminus, resulting in mass shifts of the products of subsequent second-stage fragmentations. Other examples of the participation of the flexible lysine side chain are suggested but could not be confirmed to the same extent. The role of Coulombic repulsion in facilitating fragmentation has been explored via investigations of triply- and quadruply-protonated basic peptides bearing one charge for every three or four amino acid residues. Such species yielded almost no sequence information under low-energy collision conditions, due to the localization of the ionizing protons on highly basic sites rather than on the peptide backbone. It is proposed that collisionally activated mobilization of protons from the basic sites, where they are originally located upon formation, to the backbone is a necessary condition for structurally useful fragmentation to occur. It was not possible, on the basis of the present work, to deduce mechanistic generalizations and predictive schemes which would permit structural interpretations of such fragment spectra for unknown peptides.