Gel-based detection of protein S-nitrosothiols has relied on the biotin-switch method. This method attempts to replace the nitroso group with a biotin label to allow detection and isolation of S-nitrosated proteins and has been used extensively in the literature. This chapter describes a modification of this method that differs from the original in two major ways. First, it uses a combination of copper ions and ascorbate to achieve selective reduction of the S-nitrosothiol. Second, it replaces the biotin label with fluorescent cyanine dyes in order to directly observe the modified proteins in-gel and perform comparative studies using difference gel electrophoresis analysis in two dimensions.