Similarity behween condensed phase and gas phase chemistry: Fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics

Amino acid residues containing thioethers are easily oxidized during protei n purification, derivatization, and/or digestion. For instance, oxidation o f methionine residues in proteins during SDS-PAGE is commonly observed. Und er low energy collision induced dissociation this gives rise to a second se ries of fragment ion of lower abundance that are shifted by -64 Da when com pared to the oxidized methionine-containing fragments. We report here that alkylated cysteine residues can be found in their oxidized form too, indica ting that the oxidation of thioethers can occur during and following protei n digestion and not only during SDS-PAGE or reduction and alkylation. Colli sion induced dissociation experiments on the singly- and multiply-charged s pecies reveals that these peptides preferentially undergo elimination react ions that forms a dehydroalanine from the oxidized, alkylated cysteine resi due. This contrasts to the less abundant elimination reaction of peptides c ontaining oxidized methionines which cannot form an alpha,beta -unsaturated compound, but parallels the condensed phased chemistry of sulfoxides. The masses of both precursor and product ions are shifted such that these pepti des cannot be identified in database searches with current algorithms. Inco rporation of this fragmentation pattern is important for the isotope-coded affinity tag approach since this method is based on peptides containing cys teine residues. (C) 2000 American Society for Mass Spectrometry.