Backbone and side-chain specific dissociations of z ions from non-tryptic peptides

Backbone z-type fragment ions formed by electron-transfer dissociation (ETD) of doubly protonated peptides AAHAL, AHDAL, and AHADL were subjected to collisional activation and their dissociation products were studied by ETD-CID-MS(3) and MS(4). Electron structure theory calculations were performed to elucidate ion structures and reaction mechanisms. All z ions showed competitive eliminations of C(3)H(7) and C(4)H(8) from the C-terminal Leu side chain. The energetics and kinetics of these dissociations were studied computationally for the z(4) ion from AAHAL, and optimized structures are reported for several intermediates and transition states. RRKM calculations on the combined B3LYP and PMP2/6-311++G(2d,p) potential energy surface provided unimolecular rate constants that closely reproduced the experimental branching ratios for C(3)H(7) and C(4)H(8) eliminations. Mechanisms were also studied for the loss of CO(2) from z ions generated by ETD of AHDAL and AHADL and for a specific radical-induced Asp-C(alpha)-CO backbone cleavage. CID of the z ions under study did not produce any fragment ions that would indicate cascade backbone dissociations triggered by the radical sites. In contrast, the majority of backbone dissociations occurred at bonds that were remote from the radical sites (spin-remote dissociations) and were triggered by proton migrations that were analogous to those considered for standard peptide ion fragmentations.