Proteome coverage after simultaneous proteo-metabolome liquid-liquid extraction

Proteo-metabolomics is essential in systems biology and simultaneous proteo-metabolome extraction by liquid-liquid extraction (SPM-LLE) allows extraction of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE it must be solubilized for quantitative proteomics. Solubilization and proteome extraction is a critical factor in the information that can be obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea with respect to proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated the extent to which the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were very similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants (SDC, SDS) for quantitative proteomics is better when the proteome was extracted by direct cell lysis and not from an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet and by direct cell lysis.