Perfluorinated alcohol induced coacervates as extraction media for proteomic analysis

We describe a novel method for using hexafluoroisopropanol (HFIP) induced coacervates with a variety of surfactants to extract proteins from a yeast whole cell lysate and conduct a global proteomic investigation on the extracted proteins. Yeast whole cell lysates were prepared and proteins were extracted using two workflows: 1) Proteins were extracted into the coacervate generated from the mixture of HFIP, surfactant, and cell lysate. 2) Proteins were extracted from cell lysate using a surfactant solution, and HFIP was added to the supernatant to generate a coacervate phase with concentrated proteins. Both initial extractions were followed by a modified filter-aided sample preparation (FASP) cleanup. The methodology yields significant protein concentrations in the coacervate phase (2-3 orders of magnitude increase in concentration) and an increase in proteome sequence coverage (+5%), membrane proteins identifications (+50%), and identification of proteins from low abundance cellular subfractions (>10% of total IDs).