Gas-phase fragmentation of protonated mono-N-methylated peptides. Analogy with solution-phase acid-catalyzed hydrolysis

Fragmentation of protonated peptides with a single N-methylated residue was studied by low-energy collision-induced dissociation (CID) and the effects of the N-alkylation on the fragmentation were evaluated. Peptides with an N-terminal N-alkylated amino acid behave similarly to regular peptides except for an increased stability of the protonated molecular ion due to the increased proton affinity. On the other hand, the N-alkylation of an internal amino acid residue has very distinct effect on fragmentation. It causes activation of the amide bond on the C-terminal side of the N-alkylated residue resulting in preferential cleavage of this bond and formation of corresponding b ions. This is in a sharp contrast to the effect of a natural N-alkylated amino acid, proline, which activates its N-terminal amide bond providing abundant y ions upon CID. Both peptides with Ac-N-methylamino acid N-terminus and with an internal N-methylated amino acid exhibit the former type of fragmentation. A fragmentation mechanism is proposed that explains the observed effects based on fragmentation of model peptide analogs and isotopically labeled peptides. It was found that an interaction between carbonyl groups of neighboring amide moieties is an important factor in the formation of the b ion with a structure of a protonated N-methyloxazolone. AM1 calculations suggest that the stability of this ion favors its formation in the CID of N-methylated peptides. It was also shown that an incorporation of a basic site outside the peptide backbone does not affect the course of fragmentation of the peptides with an internal N-alkylamino acid. These observations provide support for the ‘mobile proton’ model for the initial stage of protonated peptide fragmentation in the low-energy CID. The observed phenomenon is analogous to the solution-phase acid-catalyzed hydrolysis of these peptides.