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. 2022 Oct 20;13:6212. doi: 10.1038/s41467-022-33951-0

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — 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.