Proteomics analysis to identify novel TFEB-interacting proteins during lysosomal damage. (A) Strategy for interactome analysis of TFEB::mNG. Samples of WT and ATG7 KO HeLa cells stably expressing TFEB::mNG were collected at the indicated time points after 1 mM LLOMe treatment (0 h: untreated control), and subjected to IP followed by MS. (B) Volcano plot of the proteins enriched in WT HeLa cells treated with LLOMe for 1 h relative to WT controls (green circle in E) (n = 3 biologically independent samples). The green square indicates that the log₂ ratio is >0.4. (C) Volcano plot of the proteins enriched in ATG7 KO HeLa cells treated with LLOMe for 1 h relative to ATG7 KO controls (red circle in E) (n = 3 biologically independent samples). The red square indicates that the log₂ ratio is >0.4. (D) Volcano plot of the proteins enriched in WT HeLa cells treated with LLOMe for 3 h relative to ATG7 KO HeLa cells treated with LLOMe for 3 h (blue circle in E) (n = 3 biologically independent samples). The blue square shows that the log₂ ratio is >0.4. (E) Venn diagram showing overlap between three sets of proteins in B–D. Fifty-two proteins are enriched under ATG conjugation system–independent TFEB activation. IP, immunoprecipitation.