IRMPD spectroscopy b2 ions from protonated tripeptides with 4-aminomethyl benzoic acid residues

Collision-induced dissociation (CID) of the peptide alanine-4-aminomethylbenzoic acid-glycine, A(AMBz)G generates a prominent b2 ion despite a previous report [E.R. Talaty, T.J. Cooper, S.M. Osburn, M.J. Van Stipdonk, Collision-induced dissociation of protonated tetrapeptides containing β-alanine, γ-aminobutyric acid, ɛ-aminocaproic acid or 4-aminomethylbenzoic acid residues, Rapid Commun. Mass Spectrom. 20 (2006) 3443–3455.] which showed that incorporation of the aromatic amino acid into a peptide sequence inhibits generation of bn ions formed by cleavage to the immediate C-terminal side of the residue. Infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations suggest that the b2 ion generated from A(AMBz)G has an acylium structure. The b2 ion generated from (AMBz)AG, in which the aromatic residue is situated at the amino-terminus, is instead a conventional oxazolone.

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► Infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations used to study fragmentation of peptides that contain 4-aminomethylbenzoic acid residues.
► Dominant product ion from protonated AAG, A(AMBz)G and (AMBz)AG is b2+.
► IRMPD and DFT calculations suggest that the b2 ion generated from A(AMBz)G has an acylium structure while b2 ion from (AMBz)AG is instead a conventional oxazolone.