Fig. 2.

High-throughput comparative analysis of the cysteine oxidation status of proliferating and senescent hTERT-RPE-1 cells using SILAC-iodoTMT. (A) Principal component analysis of the oxidation proportion values (n = 2595) quantified in all samples; the percentage indicates proportion of variability explained by principal components 1 (PC1) and 2 (PC2). (B) Distributions of the average oxidation proportion values of control and senescent cells depicted as a density plot. (C) Relative comparison of PRDX6 peptides with different modifications (iodoTMT-labeled or post-translationally modified by oxidation) between senescent and proliferating cells using the SILAC channel. Each dot represents a ratio from one biological replicate. Statistical analysis was performed using one-way ANOVA; pairwise comparisons relative to unmodified peptides were performed using Dunnett's test. Asterisks indicate statistical significance; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. (D) The volcano plot shows statistically significant differences between senescent and proliferating cells at the p-value (blue and red circles; two-sample t-test) and FDR level (blue and red triangles; Benjamini-Hochberg correction). (E-F) The cysteine residues of proteins were mapped to cellular compartments (GOCC; E) and biological processes (GOBP; F), and paired samples Wilcoxon test was performed with Benjamini-Hochberg correction. The red asterisk indicates Benjamini-Hochberg FDR < 0.05. The most representative examples were selected for visualization. (G) Selected examples of cysteine residues mapped to the two biological processes shown in (F). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)