Enhancing Membrane Protein Identification Using a Simplified, Centrifugation and Detergent-based Membrane Extraction Approach

Membrane proteins may act as transporters, receptors, enzymes and adhesion-anchors, accounting for nearly 70% of pharmaceutical drug targets. Difficulties in efficient enrichment, extraction and solubilization still exist because of their relatively low abundance and poor solubility. A simplified membrane protein extraction approach with advantages of user-friendly sample processing procedures, good repeatability and significant effectiveness was developed in the current research for enhancing enrichment and identification of membrane proteins. The approach combining centrifugation and detergent along with LC-MS/MS successfully identified higher proportion of membrane proteins, integral proteins and transmembrane proteins in membrane fraction (76.6%, 48.1%, and 40.6%) than in total cell lysate (41.6%, 16.4%, and 13.5%), and tended to capture membrane proteins with high degree of hydrophobicity and number of transmembrane domains as 486 out of 2106 (23.0%) had GRAVY>0 in membrane fraction, 488 out of 2106 (23.1%) had TMs ≥2. It also provided for improved identification of membrane proteins as more than 60.6% of the commonly-identified membrane proteins in two cell samples were better identified in membrane fraction with higher sequence coverage.