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Significance Interorganelle communication occurs at membrane contact sites via dynamic trafficking of diverse biomolecules between the two organelles. The mitochondria-associated membrane (MAM) is the most critical cellular contact site of mitochondria and endoplasmic reticulum. However, a proteomics method to profile in vivo components at the contact sites is still unavailable. Here, we introduce Contact-ID, a split-BioID method, which specifically biotinylates the proteins localized at MAM and the biotinylated sites are identified by mass spectrometry, thereby definitively disclosing the MAM proteome in live cells. As a result, we report 115 MAM-specific proteins with diverse functions (e.g., cholesterol metabolism and antiapoptosis process). We expect this method to be utilized to profile the local proteome at any organelle–membrane contact site in live cells.

Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation