Differentiation of three pairs of Boc-β,γ- and γ,β-hybrid peptides by electrospray ionization tandem mass spectrometry

A new series of Boc-N-beta(3)(,) gamma(4)-/gamma(4), beta(3)-isomeric hybrid peptides (containing repeats of beta(3)-Caa and gamma(4)-Caa's, Caa = C-linked carbo beta(3)-/gamma(4)-amino acids derived from D-xylose) have been differentiated by both positive and negative ion electrospray ionization (ESI) ion-trap and high resolution quadrupole time-of-flight/tandem mass spectrometry (Q-TOF MS/MS). MSn of protonated isomeric peptides and [M + H - Boc + H](+) produce characteristic fragmentation involving the peptide backbone, the Boc-group, and the side chain. The positional isomers are differentiated from one another by the presence of y(n)(+), b(n)(+), and other fragment ions of different m/z values. It is observed that the peptides with beta-Caa at the N-terminus produce extensive fragmentation, whereas gamma-Caa gave rise to much less fragmentation. Peptides with gamma-Caa at the N-terminus lose NH3, whereas this process is absent for the carbopepticles with beta-Caa at the N-terminus. Two pairs of dipeptide diastereomers are clearly differentiated by the collision-induced dissociation (CID) of their protonated molecules. The loss of 2-methylprop-1-ene is more pronounced for Boc-NH-(R)-beta-Caa-(R)-gamma-Caa-OCH3 (6) and Boc-NH-(R)-gamma-Caa-(R)-beta-Caa-OCH3 (12), whereas it is insignificant or totally absent for its protonated diastereomeric pair Boc-NH-(S)-beta-Caa-(S)-gamma-Caa-OCH3 (1) and Boc-NH-(S)-gamma-Caa-(S)-beta-Caa-OCH3 (7). Further, ESI negative ion tandem mass spectrometry has also been found to lie useful for differentiating these isomeric peptide acids. Copyright (C) 2008 John Wiley & Sons, Ltd.