Fig 1: The human lysosomal interactome.a PPIs identified in the XL-LC-MS/MS dataset. Lysosomal proteins (blue dots), non-lysosomal proteins (gray dots), and PPIs (gray lines) are indicated. b Matching of PPIs to the STRING database. c Numbers of proteins from distinct subcellular localizations interacting with lysosomal proteins. d, e Interaction networks of the V-ATPase (d) and the flotillin (e) complex. f Co-IP of ATP6V1D and FZD9 (n = 2). ATP6V1B2 and ATP6V1A1 are known members of the V-ATPase complex; LAMP2 is a lysosomal membrane protein. Control: empty beads. g Co-IPs of FLOT1, FLOT2, and GNB4 (n = 2). RRAGA is a lysosomal membrane-associated protein. Control: empty beads. h, i Site frequency distribution for identified FLOT1 (h) and FLOT2 (i) cross-links. Site frequency represents the percentage of cross-links detected in bins of 20 residues each. The region indicated by red dots represents the PHB domain. CY cytoplasm, CK cytoskeleton, NC nucleus, ER endoplasmic reticulum, GA Golgi apparatus, PM plasma membrane, LS lysosome, OT others, NK not known, IN input, SN supernatant, W wash, EL eluate, X empty lane. Source data are provided as a Source Data file.