AbstractExposure to DNA‐damaging agents can activate cell cycle checkpoint and DNA repair processes to ensure genetic integrity. Such exposures also can affect the transcription of many genes required for these processes. In the budding yeast Saccharomyces cerevisiae, changes of global gene expression as a result of a DNA‐damaging agent were previously identified by using DNA chip technology. DNA microarray analysis is a powerful tool for identifying genes whose expressions are changed in response to environmental changes. Transcriptional levels, however, do not necessarily reflect cellular protein levels. Green fluorescent protein (GFP) has been widely used as a reporter of gene expression and subcellular protein localization. We have used 4156 yeast strains expressing full‐length, chromosome‐tagged GFP fusion proteins to monitor changes of protein levels in response to the DNA‐damaging agent, methyl methanesulphonate (MMS). Through flow cytometry, we identified 157 proteins whose levels were increased at least three‐fold following treatment with MMS. Of 157 responsible genes, transcriptions of 57 were previously not known to be induced by MMS. Immunoblot experiments with tandem affinity‐tagged yeast strains under the same experimental conditions confirmed these newly found proteins as inducible. These results suggest, therefore, that the 57 protein expressions are regulated by different mechanisms, such as post‐translational modifications, and not by transcriptional regulation. Copyright © 2007 John Wiley & Sons, Ltd.