Quantitative proteomics of WT and UBXD8 KO cells identifies loss of peroxisomal proteins. (A) Volcano plot of the (−log₁₀-transformed P value versus the log₂-transformed ratio of UBXD8 KO to WT) proteins identified from HEK293T cells. n = 3 biologically independent samples for each genotype. P values were determined by empirical Bayesian statistical methods (two-tailed t test adjusted for multiple comparisons using Benjamini–Hochberg’s correction method) using the LIMMA R package; for parameters, individual P values, and q values, see Ganji et al. (2023) for dataset. Peroxisomal proteins are shown in green-filled circles. Outlines indicate proteins involved in biogenesis (blue) and metabolism (red). (B) Correlation of two HEK293T UBXD8 KO clones used for TMT analysis. (C) Bubble plot representing significantly enriched GO clusters identified from TMT proteomics of CRISPR UBXD8 KO (black) and WT (blue) cells. The size of the circle indicates the number of genes identified in each cluster. (D) RT-qPCR assessment of different peroxisomal transcripts in WT and UBXD8 KO cells. N = 3 independent experiments. The graph shows the mean and std.dev. NS: not significant, *P < 0.05, **P < 0.01, ***P < 0.001, Student’s unpaired t test.