Abstract
Positive and negative ion electrospray ionization (ESI) tandem mass spectral study of a new series of hybrid peptides, viz, BocN‐α,β‐peptides and BocN‐β,α‐peptides, synthesized from C‐linked carbo‐β^3^‐amino acids [Caa (S)] and L‐Ala has been carried out. The α,β‐peptides have been differentiated from β,α‐peptides by the collision‐induced dissociation (CID) of [M + H]^+^ and [M − H]^−^ ions in positive and negative ion ESI‐MS respectively. The fragment ion [M + H − C(CH~3~)~3~ + H]^+^ formed from [M + H]^+^ ions by the loss of 2‐methyl‐prop‐2‐ene in α,β‐peptides with L‐Ala at the N‐terminus is insignificant or totally absent for β,α‐peptides which have the Caa (S) at N‐terminus. The fragment ion [M − H‐C(CH~3~)~3~OH − HNCO]^−^ formed from [M − H]^−^ of β,α‐peptide acids is totally absent for α,β‐peptide acids. This has been attributed to the absence of the β‐methylene group in α,β‐peptides, and the participation of the β‐methylene group in the loss of HNCO in β,α‐peptide acids is confirmed by the deuteration experiments. The CID of [M + H‐Boc + H]^+^ ions of these peptides also produce characteristic fragmentation. In the CID spectra of α,β‐peptides, the b~n~^+^ ions and the resulting y~n~^+^ ions occur at a mass difference of 243 and 71 Da corresponding to the successive losses of Caa and L‐Ala, whereas a mass difference of 71 and 243 Da is observed for β,α‐peptides. In contrast to the CID of protonated peptides, the CID of [M − H]^−^ ions of the α,β‐ and β,α‐peptide acids do not give b~n~^−^ ions and show abundant z~n~^−^ ions. Further, a pair of diastereomeric dipeptide esters and acids have been distinguished by the CID of [M + H]^+^ ions. The loss of 2‐methyl‐prop‐2‐ene is more pronounced for Boc‐NH‐Caa(R)‐D‐Ala‐OCH~3~ (21) and Boc‐NH‐Caa(R)‐D‐Ala‐OH (23) with Caa (R) at the N‐terminus, whereas it is totally absent for Boc‐NH‐Caa (S)‐D‐Ala‐OCH~3~ (22) and Boc‐NH‐Caa(S)‐D‐Ala‐OH (24) peptides, which have Caa (S) at the N‐terminus. Thus, on the basis of our previous and present studies, we propose that the CID of [M + H]^+^ ions provides a simple and useful method for distinguishing the configuration of Caa (S or R) at the N‐terminus of BocN‐carbo β,α‐ and β,β‐dipeptides. Copyright © 2005 John Wiley & Sons, Ltd.