Structure of anionic c-type peptide fragments elucidated by IRMPD spectroscopy

In contrast to protonated peptides, collision-induced dissociation of deprotonated peptides is known to yield abundant c- and z-type fragments, in addition to typical a-, b- and y-type ions. Here we investigate the isomeric structures of short anionic c-type peptide fragments using IR photodissociation spectroscopy. As for all N-terminal fragments of deprotonated peptides, an important structural question concerns the site of deprotonation, as no C-terminal COOH group is present in these products. Comparison of the experimental action spectra with spectra computed for several candidate structures suggests that the c1 and c2 ions investigated have linear peptide structures with a C-terminal C(O)NH2 amide group. Competition between deprotonation on the peptide bond nitrogen atom, forming an amidate anion, and on the residue side chain, depending on its gas-phase acidity, is observed.

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► First IR spectra for anionic c-type peptide fragments.
► Comparison between experimental and DFT computed spectra suggests linear peptide structures with C-terminal amide group.
► Deprotonation sites identified: competition between peptide bond nitrogen atom and side chain depending on residue.