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foreign goal of this experimental strategy is to resolve the distinct functional assemblies a protein may be involved in through blue native polyacrylamide gel electrophoresis fractionation of affinity purified protein complexes and mass spectrometry correlation profiling this method can help add organizational information to the protein lists generated by Affinity purification massive spectrometry experiments the main advantages of this procedure are that it is simple to perform as good resolution and entails little more work than conventional gel C msms this protocol is optimized for the purification of protein complexes from 200 to 500 million cells expressing endogenous levels of a flag-tagged protein after thawing the cell pellet as described in the text protocol add five milliliters of ice cold lysis buffer containing dtt and protease Inhibitors to the cell suspension and swirl to mix incubate the suspension on ice for 10 minutes transfer the cell suspension to a cold dow
