Fig. 3

Hydrogen peroxide treatment of wild-type yeast cells. a Carbonylation of proteins in wild-type cells treated with 1 mM H₂O₂ for 30 min was analysed by immunoblotting with anti-DNP antibody or quantified by spectrophotometry. Mean ± SEM, n = 3, *P-value < 0.05; two-sided, paired t-test DNP(H), 2,4-dinitrophenyl(hydrazine). b Volcano plot showing H₂O₂-dependent changes in protein abundance. In total, 3,116 unique proteins and 61 protein groups were quantified. Shaded areas highlight proteins with an average fold change of ≥ 2 (average log₁₀ ratio = ± 0.3) and a P-value < 0.05 (−log₁₀P-value > 1.3; n = 3, two-sided t-test). Dark grey, regulated proteins with the GO term ‘response to oxidative stress’ and/or ‘oxidoreductase activity’. c Wild-type cells were grown in fermentative medium at 28 °C and when indicated treated with 1 mM H₂O₂ for 30 min. Samples were analysed by immunoblotting. *Unspecific band. d Left: volcano plot showing difference in average % oxidation (H₂O₂-treated minus untreated samples) for 4,341 unique cysteine-containing peptides plotted against −log₁₀P-value highlighting unique cysteine-containing peptides with significantly increased oxidation levels (dark grey, P-value < 0.05, n = 3, ANOVA). Lines indicate difference in average % oxidation > 7 and a P-value of 0.05 (−log₁₀ = 1.3). Right: zoom-in of the region highlighted in the volcano plot. Peptides of proteins annotated with the GO term ‘ribonucleoprotein complex’ are highlighted (dark grey). e GO term enrichment analysis of proteins with significantly increased oxidation levels. P-values after Benjamini–Hochberg FDR (< 0.05) correction were plotted against their corresponding GO terms from the three main domains (cellular component, molecular function and biological process). For each GO term, the number of proteins is shown