To identify components of mitochondrial apoptotic foci, Flag-APEX2-tagged constructs targeting Bax, Bak, and Drp1 were generated. These constructs are designed to localize to foci at the mitochondrial outer membrane (MOM) during apoptosis. Following biotinylation with BP and H2O2, quantitative mass spectrometry was used to identify neighbouring proteins. Notably, the mitochondrial outer membrane (MOM) contains porins that allow the free diffusion of molecules, potentially resulting in the biotinylation of intermembrane space (IMS) and mitochondrial inner membrane (MIM)-resident proteins. To comprehensively analyse the protein composition of apoptotic foci, three independent quantitative mass spectrometry experiments were conducted. Each experiment involved comparing untreated (control) cells with apoptotic cells induced by staurosporine treatment. By utilizing APEX2-tagged constructs in live cells, the subcellular localization of proteins under both healthy and apoptotic conditions was preserved. Moreover, consistent biotinylation patterns were observed across all three constructs, validating the reliability of the approach for studying dynamic protein complexes in apoptosis.