Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers

[Image: see text] Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N–C(α) bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c(3)- and c(4)-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000–1200 cm(–1) serves as an important diagnostic feature.