Label-free proteomic analysis of the hydrophobic membrane protein complement in articular chondrocytes: a technique for identification of membrane biomarkers.

CONTEXT There is insufficient knowledge about the chondrocyte membranome and its molecular composition. OBJECTIVE To develop a Triton X-114 based separation technique using nanoLC-MS/MS combined with shotgun proteomics to identify chondrocyte membrane proteins. MATERIALS AND METHODS Articular chondrocytes from equine metacarpophalangeal joints were separated into hydrophobic and hydrophilic fractions; trypsin-digested proteins were analysed by nanoLC-MS/MS. RESULTS A total of 315 proteins were identified. The phase extraction method yielded a high proportion of membrane proteins (56%) including CD276, S100-A6 and three VDAC isoforms. DISCUSSION Defining the chondrocyte membranome is likely to reveal new biomarker targets for conventional and biological drug discovery.