Collision-induced dissociations of deprotonated dipeptide methyl esters containing serine or threonine

The collision-induced mass spectra (MS/MS) of (M - H)^- ions derived from dipeptide methyl esters containing serine or threonine lack the characteristic backbone cleavage of the underivatized peptides (which provide primary sequencing data). Instead, competitive fragmentation occurs through the ester and α-side chain functions. For example, Ser methyl esters lose both CH₂O (from the side chain) and MeOH (MeO comes from the methyl ester). Isomeric dipeptides may be differentiated by competitive fragmentations; for example [Gly Ser(OMe) - H]^- fragments first by loss of CH₂O, while [Ser Gly(OMe) - H]^-, in contrast, shows initial elimination of MeOH. The structures of the product ions in these spectra have been probed by deuterium labelling and MS/MS/MS studies.