There is a need for improved appreciation of the importance of genome-wide mRNA and protein expression measurements and their role in understanding translation and in relation to genome-wide mathematical frameworks for gene expression regulation. We investigated the use of a high-density microarray technique for mRNA expression analysis and a two-dimensional protein electrophoresis–tandem mass spectrometry method for protein analysis to monitor changes in gene expression. We applied these analytical tools in the context of an environmental perturbation of Escherichia coli cells—the addition of varying amounts of IPTG. We also tested the application of these tools to the study of a genetic perturbation of Escherichia coli cells—the ability of certain strains to hypersecrete the hemolysin protein. We observed a lack of correspondence between mRNA and protein expression profiles. Although our data do not include measurements on all expressed genes (because the ability to measure protein expression profiles is limiting), we observed that the qualitative and quantitative behavior of the measurements of a subset of expressed genes is similar to the behavior of the entire system. The change in observed average mRNA and protein amplification factors for 77 and 52 genes coincided with the observed change in mRNA amplification factor for the entire system. Furthermore, we found that the use of relative changes in expression could be used to elucidate mechanisms of gene expression regulation for the system studied, even when measurements were made on a small subset of the system. © 2003 Wiley Periodicals, Inc.