Over the past decade, understanding of the structure and function of membrane proteins has advanced significantly as well as how their detailed characterization can be approached experimentally. Detergents have played significant roles in this effort. They serve as tools to isolate, solubilize, and manipulate membrane proteins for subsequent biochemical and physical characterization. Combination of detergents and various separation methods coupled with mass spectrometry technology e.g. MALDI-TOF/TOF and nano-HPLC-ESI-Q-TOF/MS/MS is now possible to examine the expression of membrane proteins. This study for establishing separation methods of membrane proteins on two modified gel-electrophoresis (16-BAC and BN-PAGE subsequently with SDS-PAGE) could make it likely that the components of membranes become increasingly amenable to identification and characterization. To study the structure (complexes) and function of membrane proteins, we must first pre-fractionate enriched membrane proteins, or isolate and purify membrane complexes. Such proteins can be solubilized by high-salt solutions or detergents, which have affinity both for hydrophobic groups and for water. Due to a preponderance of binding detergents over hydrophobic regions, when integral proteins are exposed on aqueous solution, these protein molecules are prevented from aggregation and maintained their native conformation. Subsequently, diverse kinds of eletrophoretic analysis combined with mass spectrometry have been applied with site specific (tripsin, chymotrypsin, CNBr and Asp-N) enzymes. The final goal is to enable high-throughput analysis of ion-channel proteins and major neurotransmitter receptor complexes within central nervous system by an electrophoretic method allowing quantification with subsequent unambiguous protein identification.