Cleavage of the amide bond of protonated dipeptides

Dissociation of the amide bond of protonated dipeptides is investigated using quantum chemical and RRKM calculations, via exploring linear free energy relationships and performing MS/MS experiments. Our studies suggest that fragmentation of protonated dipeptides at the amide bond is dominated by the a(1)-y(1) pathway. Based on the proton affinities of the N- and C-terminal fragments the ally, ion abundance ratio can be approximated considering a linear free energy relationship. To assist such discussions the PAs of a large number of imines are determined using reliable quantum chemical calculations. The energetics and kinetics of the a(1)-y(1) pathways of H-Ser-Ala-OH, H-Val-Ala-OH, H-Val-Phe-OH, and H-Thr-Phe-OH are explored to rationalize differences between the MS/MS spectra of these peptides. The effect of increasing collision energy on the ally, ion abundance ratio is investigated for protonated H-Tyr-Ile-OH. It is shown that kinetic shifts are mainly responsible for lack of observable [MH-CO](+) peak in the MS/MS spectra of the majority of protonated peptides.