Comparing Mass Spectrometric Characteristics of Peptides and Peptoids—2†

Abstract

The high-energy collision-induced dissociation (CID) spectra of the [M+H]+ and [M-H]- ions of substance P fragment 6–11, the retropeptide and the corresponding peptoid and retropeptoid were compared. The CID spectra of the [M+H]+ ion of the corresponding (retro)peptide and (retro)peptoid exhibit both B- and Y″-type sequence ions at identical m/z-values. The differences in the relative abundances of these sequence ions, however, can be related to structural characteristics of the compounds. The fragmentation behaviour of the N-substituted immonium ions differs from that of the immonium ions derived from common amino acids by showing a preferential loss of a CH2=NH imine molecule. This dominant fragmentation reaction is suppressed in the CID spectrum of the N-substituted glutamine immonium ion in favour of a less energy demanding cyclization reaction involving the loss of NH3. The CID spectra of the [M-H]- ions of both peptides and peptoids show C-type ions, which appeared to be more abundant in the spectra of the peptides than in those of the peptoids. C-Terminal ″Z- and Y-type ions are characteristic of the peptides, whereas the peptoid spectra show relatively abundant N-terminal ″B-type ions. Both [M+H]+ and [M-H]- ion CID spectra show loss of amino acid-specific side-chains, which occurs as radical loss in the case of peptides and as molecular loss in peptoids. © 1997 by John Wiley & Sons, Ltd.