Extended Data Fig. 1: Proteomic analysis.

A proteomic time-course experiment recorded by SWATH-MS⁶ was re-analysed with a new spectral library and a recent version of Spectronaut (Biognosys) software, increasing the depth of the proteomic analysis. a, Principal component analysis shows that proteome profiles of H₂O₂-exposed Δtpo1 yeast⁶ are more different from the wild type than that of a Tpo1p-overexpressing strain and that there is a metabolic adaptation in the lysine pathway. Numbers indicate time points (in minutes) after the oxidative insult. b, Gene Ontology (GO) enrichment analysis shows that a number of biosynthetic processes are significantly enriched in proteins differentially expressed between wild-type and Δtpo1 yeast upon exposure to H₂O₂. Most of the GO terms that are significantly enriched belong to processes that are typically seen to be activated upon treatment with H₂O₂, including oxidation–reduction processes, cell cycle, nucleotide synthesis and ribosome⁴³. Metabolic processes affected include carbohydrate- and amino acid metabolism, including two GO terms specific for the lysine pathway. Significance of enrichment over base frequency was calculated using a binomial test⁴⁴, and P values (red line) were corrected for false discovery rate using Bonferroni (blue) or Benjamini–Hochberg (green) correction. n = 5.