Comparative embrane extraction methods for identifying membrane proteome of SW900 squamous lung Cancer cell line

Abstract

Although several methods for extracting and handling membrane proteins for proteomics experiments have been reported, the direct comparison of different methods has never been clarified for the identifying membrane proteome in lung cancer cell lines. This study was purposed to find a protocol suitable for membrane protein extraction and to identify the membrane proteome in lung cancer. Three detergent-based extraction methods including sequential detergent extraction using Triton X-100 and digitonin, Mem-PER Eukaryotic membrane protein extraction kit and sucrose gradient ultracentrifugation were used to enrich the membrane proteins from SW900 squamous lung cancer cell line. The membrane protein profiles separated by SDS-PAGE and two-dimensional electrophoresis (2-DE) were compared. Mem-PER Eukaryotic membrane protein extraction kit was our preferable method which showed the highest number of protein spots, compared to the other methods, and the good resolution of membrane protein separation on the prote n profile. The three membrane protein profiles from three extraction methods showed 73 matched protein spots, in which 15 membrane proteins were successfully identified by MALDI-TOF MS and MS/MS analyses and served as membrane proteome which played an important role in squamous lung cancer.