Analyzing the hydrophobic proteome of the antarctic archaeon Methanococcoides burtonii using differential solubility fractionation.

Proteomic studies have proven useful for studying the Antarctic archaeon Methanococcoides burtonii; however, little has been learned about the hydrophobic and membrane proteins, despite knowledge of their biological importance. In this study, new methods were developed to analyze and maximize the coverage of the hydrophobic proteome. Central to the analysis was a differential solubility fractionation (DSF) procedure using n-octyl-beta-D-glucopyranoside. The study achieved a significant increase (330) in the total number of known expressed proteins. From 612 identified, 185 were predicted to contain transmembrane domains or be associated with the membrane and 190 to be hydrophobic. The DSF procedure increased the efficacy of identifying membrane proteins by up to 169% and was economical, requiring far fewer runs (12% of machine time) to analyze the proteome compared to procedures without DSF. The analysis of peptide spectral counts enabled the assessment of growth temperature specific proteins. This semiquantitative analysis was particularly useful for identifying low abundance proteins unable to be quantified using labeling strategies. The proteogenomic analysis of the newly identified proteins revealed many cellular processes not previously associated with adaptation of the cell. This DSF-based approach is likely to benefit proteomic analyses of hydrophobic proteins for a broad range of biological systems.