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‐β 3 , γ 4 ‐/γ 4 , β 3 ‐isomeric hybrid peptides (containing repeats of β 3 ‐Caa and γ 4 ‐Caa's, Caa = C‐linked carbo β 3 ‐/γ 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). MS n 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 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 NH 3 , 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‐OCH 3 (6) and Boc‐NH‐(R)‐γ‐Caa‐(R)‐β‐Caa‐OCH 3 (12), whereas it is insignificant or totally absent for its protonated diastereomeric pair Boc‐NH‐(S)‐β‐Caa‐(S)‐γ‐Caa‐OCH 3 (1) and Boc‐NH‐(S)‐γ‐Caa‐(S)‐β‐Caa‐OCH 3 (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.