Fig. 1.

Experimental design for global profiling of peripheral membrane, integral membrane, and soluble proteins in highly pure yeast mitochondria. a Highly pure mitochondria were isolated from yeast cultures grown in the presence of either “light” (L) or “heavy” (H) amino acids (Arg, Lys). Protein extraction was performed based on sonication to separate membrane proteins (PEL_son) from soluble proteins (SN_son) or carbonate treatment, which results in a pellet containing integral membrane proteins (PEL_carb) and a supernatant with peripheral membrane and soluble proteins (SN_carb). Respective SN/PEL SILAC ratios were determined by LC-MS. carb, carbonate; son, sonication. b Exemplary SILAC results a for Tim proteins representing the three different protein classes analyzed, confirmed by immunoblotting