Role of the sulfhydryl group on the gas phase fragmentation reactions of protonated cysteine and cysteine containing peptides

The gas phase fragmentation reactions of protonated cysteine and cysteine-containing peptides have been studied using a combination of collisional activation in a tandem mass spectrometer and ab initio calculations [at the MP2(FC)/6-31G*//HF/6-31G* level of theory]. There are two major competing dissociation pathways for protonated cysteine involving: (i) loss of ammonia, and (ii) loss of the elements of [CH₂O₂]. MS/MS, MS/MS of selected ions formed by collisional activation in the electrospray ionization source as well as ab initio calculations have been carried out to determine the mechanisms of these reactions. The ab initio results reveal that the most stable [M + H − NH₃]⁺ isomer is an episulfonium ion (A), whereas the most stable [M + H − CH₂O₂]⁺ isomer is an immonium ion (B). The effect of the position of the cysteine residue on the fragmentation reactions of the [M + H]⁺ ions of all the possible simple dipeptide and tripeptide methyl esters containing one cysteine (where all other residues are glycine) has also been investigated. When cysteine is at the N-terminal position, NH₃ loss is observed, although the relative abundance of the resultant [M + H − NH₃]⁺ ion decreases with increasing peptide size. In contrast, when cysteine is at any other position, water loss is observed. The proposed mechanism for loss of H₂O is in competition with those channels leading to the formation of structurally relevant sequence ions.