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In recent years, a wide variety of proteomic approaches using gel electrophoresis and mass spectrometry has been developed to detect post-translational modifications. Mitochondria are often a focus of these studies due to their important role in cellular function. Many of their crucial transport and oxidative-phosphorylation functions are performed by proteins residing in the inner and outer membranes of the mitochondria. Although proteomic technologies have greatly enhanced our understanding of regulation in cellular processes, analysis of membrane proteins has lagged behind that of soluble proteins. Herein, we present techniques to facilitate the detection of post-translational modifications of mitochondrial membrane proteins including the isolation of resident membranes as well as electrophoretic and immunological-based methods for identification of post-translational modifications.