Figure 1. Quantitative proteomics... | Rockefeller University Press

Figure 1.

Quantitative proteomics identifies a role of UBXD8 in regulating peroxisome protein abundance. (A) Volcano plot of the (−log10-transformed P value versus the log2-transformed ratio of UBXD8 KO to WT) proteins identified from HeLa 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 Supplementary Dataset in Ganji et al. (2023). Peroxisomal proteins (green-filled), important for biogenesis (blue outlines) and metabolism (red outlines), are highlighted. This dataset has been previously published (Ganji et al., 2023) and is reanalyzed here. (B) Schematic pathways regulating peroxisome abundance and function with highlighted TMT proteomics hits. (C) Peroxisomal proteins identified in A show reduced expression in UBXD8 KO compared with WT HeLa and HEK293T cells by immunoblot. (D) Quantification of C. ****P < 0.0001, N = 3, unpaired t test. Source data are available for this figure: SourceData F1.

Quantitative proteomics identifies a role of UBXD8 in regulating peroxisome protein abundance. (A) Volcano plot of the (−log₁₀-transformed P value versus the log₂-transformed ratio of UBXD8 KO to WT) proteins identified from HeLa 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 Supplementary Dataset in Ganji et al. (2023). Peroxisomal proteins (green-filled), important for biogenesis (blue outlines) and metabolism (red outlines), are highlighted. This dataset has been previously published (Ganji et al., 2023) and is reanalyzed here. (B) Schematic pathways regulating peroxisome abundance and function with highlighted TMT proteomics hits. (C) Peroxisomal proteins identified in A show reduced expression in UBXD8 KO compared with WT HeLa and HEK293T cells by immunoblot. (D) Quantification of C. ****P < 0.0001, N = 3, unpaired t test. Source data are available for this figure: SourceData F1.