Investigation of apparent mass deviations in electrospray ionization tandem mass spectrometry of a benzophenone-labeled peptide

In a previous study utilizing benzophenone‐based topological probes to study conformationally dependent changes in mouse muscle nicotinic acetylcholine receptor (nAChR) topology, electrospray ionization tandem mass spectrometric (ESI‐MS/MS) analysis led to a consistent −2.0 Da mass deviation from expected values. In the present study a synthetic peptide, corresponding to nAChR α1 subunit residues 130–139, was photolabeled. MS/MS analysis of this peptide using an ion trap confirmed the previously observed mass deviation, associated only with fragment ions that contain the incorporated benzophenone moiety. Analysis of peak profiles for the photolabeled ions does not indicate the typical ‘peak fronting’ that produces a mass shift when labile ions are prematurely ejected from the ion trap. Rather, hydrogen/deuterium (H/D) exchange experiments support the hypothesis that a chemical rearrangement involving phenyl migration and ketone formation has formed an unexpected oxidized peptide, with molecular mass 2 Da less than that expected, that is isolated for collision‐induced dissociation in the ion trap together with the predicted precursor due to the broad ion isolation window specified. Copyright © 2003 John Wiley & Sons, Ltd.