Diastereomeric differentiation of norbornene amino acid peptides by electrospray ionization tandem mass spectrometry

Abstract A new class of diastereomeric pairs of non‐natural amino acid peptides derived from butyloxycarbonyl (Boc‐)protected cis‐ (2 S, 3 R )‐ and trans‐ (2 S ,3 S ) ‐β ‐norbornene amino acids including a monomeric pair have been investigated by electrospray ionization (ESI) tandem mass spectrometry using quadrupole time‐of‐flight (Q‐TOF) and ion‐trap mass spectrometers. The protonated cis ‐BocN‐ β ‐nbaa (2 S ,3 R ) (1) ( β nbaa =  β ‐norbornene amino acid) eliminates the Boc group to form [M+H–Boc+H] + , whereas an additional ion [M+H–C 4 H 8 ] + is formed from trans ‐BocN‐ β ‐nbaa (2 S ,3 S ) (2). Similarly, it is observed that the peptide diastereomers (di‐, tri‐ and tetra‐), with cis ‐BocN‐ β ‐nbaa (2 S ,3 R )‐ at the N‐terminus, initially eliminate the Boc group to form [M+H–Boc+H] + which undergo further fragmentation to give a set of product ions that are different for the peptides with trans ‐BocN‐ β ‐nbaa (2 S ,3 S )‐ at the N‐terminus. Thus the Boc group fragments differently depending on the configuration of the amino acid present at the N‐terminus. It is also observed that the peptide bond cleavage in these peptides is less favoured and most of the product ions are formed due to retro‐Diels‐Alder fragmentation. Interestingly, sodium‐cationized peptide diastereomers mainly yield a series of retro‐Diels‐Alder fragment ions which are different for each diastereomer as they are formed starting from [M+Na–Boc+H] + in peptides with cis ‐BocN‐ β ‐nbaa (2 S ,3 R )‐ at the N‐terminus, and [M+Na–C 4 H 8 ] + in peptides with trans ‐BocN‐ β ‐nbaa (2 S ,3 S )‐ at the N‐terminus. All these results clearly indicate that these diastereomeric pairs of peptides yield characteristic product ions which help distinguish the isomers. Copyright © 2009 John Wiley & Sons, Ltd.