Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve

Proteomics is an increasingly powerful technology that can provide in-depth insights into entire proteomes and their variation upon disease. Large-scale proteomics today enables identification and measurement of changes of thousands of proteins from minute amount of tissues. Here, we provide a proteomic profile of three distinct parts of the murine nerve system: cerebellum, spinal cord, and sciatic nerve. We focus on membrane proteins as the key regulators of neural transmission and memory. Rat tissues were homogenized and extracted to remove nonmembrane proteins and the resulting membranes were solubilized with detergents. Proteins were fractionated by size exclusion chromatography, depleted for detergents, digested and analyzed by LC-MS/MS using the LTQ-Orbitrap instrument. With the application of stringent identification criteria, in total, 4124 proteins were identified. Of these proteins, 3528, 3290, and 1649 were mapped to cerebellum, spinal cord, and sciatic nerve, respectively, allowing in-depth mapping of neurotransmitter receptors, ion channels, and transporter proteins. This work is the most in-depth proteomic analysis of nerve tissues to date and provides the first unbiased insights into the proteomes of anatomically and functionally distinct parts of the membrane proteome of the central and peripheral nerve systems. The methods applied here can be directly applied to studying nerve systems and their disorders.