An investigation of fragmentation mechanisms of doubly protonated tryptic peptides.

Peptides formed as reaction products, of specific hydrolysis of proteins by trypsin, are characterized by a basic residue (Arg or Lys) at the C-terminus, which facilitates formation of abundant [M + 2H]2+ ions under electrospray or ionspray conditions. These doubly charged ions readily dissociate upon collisional activation to y" and b fragment ions which are mass complements of one another. The suggestion that these fragments are formed by direct charge-separation dissociations must contend with the observation that the y" intensities are generally appreciably larger than those of their b counterparts. However, it is shown that this can be accounted for by a greater susceptibility of the b ions to undergo further dissociation to smaller fragments such as immonium ions. In addition no evidence could be found to support alternative mechanisms, including dissociative electron capture, for which equal intensities of the two fragment ion series are not obligatory. Initial protonation at the N-terminus was shown to be required for formation of these [M + 2H]2+ ions via its suppression by mono-acetylation at the N-terminus. These findings, and others concerning formation of [y"']2+ fragments, are consistent with extensions of published mechanisms for formation of b and of y" fragments from singly protonated peptides, via charge-site-induced cleavages and intramolecular proton transfers between nitrogen atoms, respectively.