The oxidation of the sulfhydryl group in cysteine to sulfenic acid, sulfinic acid, and sulfonic acid in proteins is important in a number of enzymatic processes. In this study we examined the fragmentation of four peptides containing cysteine, cysteine sulfinic acid (Cys-SO 2 H), and cysteine sulfonic acid (Cys-SO 3 H) in an ion-trap mass spectrometer. Our results show that the presence of a Cys-SO 2 H in a peptide leads to preferential cleavage of the amide bond at the C-terminal side of the oxidized cysteine residue. The results are important for the determination of the site of the cysteine oxidation and might be useful for the sequencing of cysteine-containing peptides. (J Am Soc Mass Spectrom 2004, 15, 697-702)