Improving the depth of coverage in membrane proteomic studies through the use of lipid-based protein immobilization technology in parallel with methanol-facilitated solubilisationElectronic supplementary information (ESI) available: Plasma membrane protein identifications from human bone marrow mesenchymal stem cells (Table S1) and human dermal fibroblasts (Table S2). See DOI: 10.1039/b9ay00267g

Lipid-based protein immobilization (LPI) technology is a platform recently developed to facilitate shotgun membrane proteomic studies based on a nanotechnology framework. Proteoliposomes are generated from a membrane protein preparation. These proteoliposomes are immobilized onto an LPI chip and then subjected to proteolysis. The proteolytic peptides are then subjected to LC/MS analysis after fractionation by SCX chromatography. The focus of this study was to evaluate how the depth of coverage of the membrane proteome of a particular cell type varied as a function of the sample preparation method used. Human dermal fibroblasts (hDFs) and human bone marrow mesenchymal stem cells (BM-hMSCs) were subjected to membrane proteomic studies using two different sample preparation methods: LPI technology and methanol-facilitated solubilisation. The number of membrane proteins that could be identified from hDFs and BM-hMSCs using LC/MS was greater using LPI technology than it was using methanol-facilitated solubilisation. However, the number of membrane protein identifications that could be made for both hDFs and BM-hMSCs increased by ∼50% when both sample preparation methods were used in parallel and the MS/MS data was convolved together. Therefore, LPI technology is a very useful technology for high-throughput shotgun membrane proteomic studies. However, in order to maximize the depth of membrane proteome coverage that can be attained for a given cell type, it is necessary to use multiple sample preparation methods in concert. Lipid-based protein immobilization (LPI) technology is used to characterize the membrane proteome of bone marrow mesenchymal stem cells and human dermal fibroblasts.