Composite figure describing the different fractions isolated and analyzed after photoaffinity labeling. (A) After photoaffinity labeling, DC-Raji cells were lysed and the membrane fraction (M) was isolated from the cytosolic fraction (S) by centrifugation as described in “Methods” for separation of proteins. Samples from both fractions were subjected to Western affinity staining with streptavidin-HRP for the identification of the biotin-containing fraction. (B) The membrane fraction of APC was solubilized in solubilization buffer, and the biotinylated proteins were isolated by affinity capture using streptavidin-agarose beads. Ten bands were subjected to digestion/tandem MS identification. An arrow indicates the identified band containing ATP synthase. The distribution of the peptides was as follows: DC-Raji cells (2 bands): band 1, 18 peptides of ATP synthase β-chain, 10 unique 15 peptides of ATP synthase α-chain, 9 unique. Altogether, 12 unique peptides of ATP synthase β-chain (19 total). Band 2, 9 peptides of ATP synthase β-chain, 9 unique, 6 peptides of ATP synthase α-chain, 5 unique. Altogether, 9 unique peptides of ATP synthase α-chain (14 total). DCs (2 bands): band 1, 38 peptides of ATP synthase β-chain, 15 unique 11 peptides of ATP synthase α-chain, 8 unique. Altogether, 14 unique peptides of ATP synthase β-chain (43 total). Band 2, 5 peptides of ATP synthase β-chain, 3 unique 24 peptides of ATP synthase α-chain, 14 unique. Altogether, 15 unique peptides of ATP synthase α-chain (35 total). Vimentin was also highly represented in those DC samples. (C) The membrane fraction was solubilized and subjected to 2D electrophoresis as described in “Methods” for separation of proteins. ATP synthase was identified in the spots indicated by an arrow. Peptides recovered (4 spots): 519 peptides of ATP synthase β-chain, 24 unique.