Using quantitative proteomics in chromatin-enriched fractions, we have identified changes in the cellular response of cells lacking Sgs1, the yeast RecQ-like DNA helicase involved in homologous recombination. Primarily, we have identified upregulation of antioxidant enzymes such as Sod2 and Tsa1, compared to the wildtype cells. This analysis identifies an oxidative stress phenotype in cells lacking Sgs1.