This is the first report where hexafluoroisopropanol (HFIP) was used to induce the coacervation of lipid components in natural cell membranes that would concomitantly result in solubilization, extraction, and enrichment of hydrophobic proteins (e.g., integral membrane proteins, IMP) into the coacervate phase, and extraction of hydrophilic proteins in a separate aqueous phase. The incorporation of this innovative approach in the proteomics workflow would allow the fractionation of proteins in separate aqueous and coacervate phases and would also eliminate the need for using surfactants. Subsequently, proteins can be identified by the bottom-up proteomics approach where samples were digested in solution after phase separation. Yeast cell wall proteins, anchored membrane proteins, and proteins related to some regulatory activities were mostly found in the aqueous-rich phase. On the other hand, most integral membrane proteins, proteins involved in metabolic processes, and proteins responsible for ions or drug binding were identified in the coacervate phase. The detergent-free, facile, and rapid process of natural lipid coacervation increased the number of identified proteins by 8% (vs no-phase separation experiment). The identification of all IMPs and organelle IMPs was improved by 13% and 29%, respectively. In addition, 25% more low-abundance proteins (less than 20 ppm) were identified.
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