Defining membrane proteomes is fundamental to our understanding of many physiological and pathophysiological processes. Their separation and identification is hence a key issue in basic and biomedical research. Due to their hydrophobic character, few high-resolution techniques for separation are available for qualitative and quantitative approaches. For gel-based methods, the two-dimensional 16-BAC/SDS-PAGE is the method of choice. This technique separates proteins in the first dimension using an acidic buffer system and the cationic detergent benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and in the second dimension by SDS-PAGE. Here, we describe a detailed protocol for the separation of proteins by 16-BAC/SDS-PAGE.
