a Comparison of mitochondrial protein solubility in DNAJA3 and LONP1 knockdown cells. Cells were analyzed by Triton X-100 extraction and Western blotting. Note that the anti-DNAJA3 antibody recognizes a doublet, with both bands disappearing after DNAJA3 knockdown. NT: non-target. b, c Comparison of mass spectrometry data from three independent LONP1 knockdown, DNAJA3 (JA3) knockdown, CDDO alone and CDDO + cycloheximide (CHX)-treated mitochondria. LC-MS was used to identify proteins within detergent-insoluble pellets isolated from mitochondria. Clustered heatmap (b) and scatter plot (c) show the fold-change (compared to Ctrl) in insolubility of 445 mitochondrial proteins. d Venn diagram analysis of significantly aggregated proteins (at least 2-fold over control with a p-value <0.05) in LONP1-knockdown, CDDO alone and CDDO + CHX-treated mitochondria. Statistical analysis of proteins enriched in mitochondrial aggregates was performed using the LIMMA moderated two-tailed t-test.