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Abstract

Electrospray ionization ion trap mass spectrometry has been used to distinguish three pairs of positional isomers of a new series of N-blocked hybrid peptides derived from repeats of phenylalanine(D)-β3-h-valine/β3-h-valine-phenylalanine(D) (FβV/βVF) non-natural amino acids. MSn of protonated isomeric peptides produces characteristic fragmentation involving the peptide backbone, the Boc group and the side chain. FβV-peptides can be distinguished from βVF-peptides by the loss of R-OH from [M+H−Boc+H]+, which is either of relatively low abundance or totally absent for the latter peptides. In contrast, βVF-peptides show abundant Mannich base characteristic ions by the elimination of ammonia, and imine due to a retro-Mannich cleavage. This fragmentation is absent for FβV-peptides. When β-valine is at the C-terminus, abundant bmath image ions are produced. This is ascribed to the probable formation of a stable diketopiperazine structure, and this has been supported by the loss of H2O and CO in the CID spectra of bmath image ions. The hybrid dipeptide acids have also been distinguished in negative ion mass spectrometry. Copyright © 2007 John Wiley & Sons, Ltd.