Oxidation and modification of protein cysteines can have profound effects on protein structure and function. Using tubulin and microtubule-associated proteins (MAP) tau and MAP2 as examples, this chapter summarizes methods employed to characterize total cysteine modification using thiol-specific reagent 5-iodoacetamido-fluorescein labeling. Western blot analysis of peroxynitrite-damaged tubulin under nonreducing conditions reveals the formation of higher molecular weight dimers and tetramers. Disulfides in microtubule proteins are substrates for both the thioredoxin reductase system and the glutaredoxin/glutathione reductase system. The yield of disulfides formed by peroxynitrite anion is quantitated by monitoring the oxidation of NADPH, a cofactor required by the thioredoxin reductase system. Treatment of proteins with S-nitrosothiols, including S-nitrosoglutathione and S-nitroso-N-acetyl penicillamine, can yield either disulfides or protein S-nitrosation. In the case of tubulin, both types of cysteine modification were detected.