Both nitric oxide and hydrogen peroxide, as well as their respective metabolites (reactive nitrogen or oxygen species), participate in a variety of cellular redox processes and have become well recognized as messengers in cellular signal transduction. One important mechanism by which cellular redox-based signaling occurs is reversible oxidation of cysteine residues in the presence of low concentrations of these oxidants. SNitrosothiols (RSNO) and sulfenic acids (RSOH) are thought to be two of the most common cysteine modifications, and formation of these species reversibly alters protein function. Protein oxidation is studied to a lesser extent than lipid and DNA oxidation in part because of a lack of sensitive, stable, readily detectable markers for tracking these unstable intermediates. We addressed the specificity of current RSNO detection methods, including the Biotin Switch Technique, using a mutated C165S alkyl hydroperoxide reductase (AhpC) enzyme from Salmonella typhimurium. Through both SDS PAGE and MS-based methods, we showed that the thiol alkylating agents used during this assay had an unexpected cross-reactivity with our model sulfenic acid, and in all cases formed covalent sulfoxide products. This cross-reactivity suggests that the Biotin Switch Technique may quantify both -SNO and -SOH versions of our enzyme, questioning the reliability of this assay. We also report the development of new chemical probes for the detection of Snitrosothiols and sulfenic acids. Using the water-soluble phosphine, tris(4,6-dimethyl-3-sulfonatophenyl)phosphine trisodium salt hydrate (TXPTS), we covalently labeled S-nitrosated cysteine, glutathione, and C165S AhpC. A combination of NMR and MS techniques reveals that these reactions produce covalent S-alkylphosphonium ion adducts (with S-P connectivity), TXPTS oxide, and a TXPTS-derived aza-ylide. Mechanistically, this reaction may proceed through an S-substituted aza-ylide or the direct displacement of nitroxyl from the RSNO group. This work provides a new means for detecting and quantifying S-nitrosated species in solution and highlights the role of triaryl phosphines as a new tools to elucidate the role of S-nitrosothiols in nitric oxide metabolism. The synthesis of novel dimedone-based chemical probes for the detection of protein sulfenic acids are also presented. These probes all contain a dimedone-based 1,3-cyclohexadione core, which covalently binds RSOHs, and reporter tags such as biotin for affinity capture and fluorescent labels for visual detection of cellular sulfenic acids. The application of these new chemical probes has improved our understanding of the role of sulfenicacid formation in a variety of cellular processes. These new probes have been used to monitor protein oxidation events in models of the immune response, angiogenesis, and cancer signaling pathways and have enhanced our understanding of the biological roles of hydrogen peroxide and other cellular ROS in signal transduction.