A new series of Boc-N-β3, γ4-/γ4, β3-isomeric hybrid peptides (containing repeats of β3-Caa and γ4-Caa's, Caa = C-linked carbo β3-/γ4-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 yn+, bn+, and other fragment ions of different m/z values. It is observed that the peptides with β-Caa at the N-terminus produce extensive fragmentation, whereas γ-Caa gave rise to much less fragmentation. Peptides with γ-Caa at the N-terminus lose NH3, whereas this process is absent for the carbopeptides with β-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)-β-Caa-(R)-γ-Caa-OCH3 (6) and Boc-NH-(R)-γ-Caa-(R)-β-Caa-OCH3 (12), whereas it is insignificant or totally absent for its protonated diastereomeric pair Boc-NH-(S)-β-Caa-(S)-γ-Caa-OCH3 (1) and Boc-NH-(S)-γ-Caa-(S)-β-Caa-OCH3 (7). Further, ESI negative ion tandem mass spectrometry has also been found to be useful for differentiating these isomeric peptide acids. Copyright © 2008 John Wiley & Sons, Ltd.