Identification of global proteome changes upon rapalog-induced tethering of WIPI2 to the mitochondrial outer membrane in wild-type or NIX/BNIP3 DKO HeLa cells

We aimed to identify proteins that would be turned over upon artificial tethering of WIPI2 to the mitochondrial surface upon rapalog treatment, using the FIS1-FRB plus FKBP-GFP-WIPI2 tethering system. We had previously observed that this induces mitophagy based on flow cytometry analysis of the mt-mKeima probe. Here, we aimed to identify which proteins are degraded upon 24 h Rapalog treatment and verified whether there was an enrichment of mitochondrial proteins being selectively turned over by mitophagy under these conditions in wild-type and NIX/BNIP3 double-knockout HeLa cells.