Fig. 6

Sub-organelle level molecular context map of the mitochondria. a Mitochondrion can be divided to four compartments, namely to the outer mitochondrial membrane (dark green), inner mitochondrial space (light green), inner mitochondrial membrane (gray) and the mitochondrial matrix (yellow). b The three mitochondrial proteins, TOM20, SCO1 and PDK1, used for generation of the mitochondrial sub-organelle molecular context map, with their PPI network obtained from the BioID (key: the interacting proteins are colored according to their corresponding bait mitochondrial location. Known (blue), newly identified (red) and prey-prey (black dashed line) interactions are color-coded). c Confocal microscopy analysis fails to provide sub-organelle level information of mitochondrial protein, whereas MS microscopy allows assigning the proteins within mitochondrial compartments. Confocal microscopy (HC PL APO 93×/1.30 GLYC motCORR) was applied to observe the mitochondrial localization MAC-tagged mitochondrial proteins. The MAC-tagged bait proteins are visualized with anti-HA immunostaining (green), nucleus with DAPI (blue), and mitochondria by co-transfection with pDsRed-Mito vector (red), Scale bar: 10 μm. The MS microscopy analysis and the resulting polar plots assign the mitochondrial proteins to their corresponding mitochondrial compartments. The color assigned to each sub-organelle location is based on the annotation frequency (green: 0.75–1; yellow: 0.5–0.75; pink: 0–0.5)