Radical Stability Directs Electron Capture and Transfer Dissociation of [beta]-Amino Acids in Peptides

We report on the characteristics of the radical-ion-driven dissociation of a diverse array of [beta]-amino acids incorporated into [alpha]-peptides, as probed by tandem electron-capture and electron-transfer dissociation (ECD/ETD) mass spectrometry. The reported results demonstrate a stronger ECD/ETD dependence on the nature of the amino acid side chain for [beta]-amino acids than for their [alpha]-form counterparts. In particular, only aromatic (e.g., [beta]-Phe), and to a substantially lower extent, carbonyl-containing (e.g., [beta]-Glu and [beta]-Gln) amino acid side chains, lead to NC[beta] bond cleavage in the corresponding [beta]-amino acids. We conclude that radical stabilization must be provided by the side chain to enable the radical-driven fragmentation from the nearby backbone carbonyl carbon to proceed. In contrast with the cleavage of backbones derived from [alpha]-amino acids, ECD of peptides composed mainly of [beta]-amino acids reveals a shift in cleavage priority from the NC[beta] to the C[alpha]C bond. The incorporation of CH2 groups into the peptide backbone may thus drastically influence the backbone charge solvation preference. The characteristics of radical-driven [beta]-amino acid dissociation described herein are of particular importance to methods development, applications in peptide sequencing, and peptide and protein modification (e.g., deamidation and isomerization) analysis in life science research.