Many compounds fail in the later stages of drug development because of unexpected toxicity or poor efficacy. Therefore, a greater understanding of drug properties is needed at an earlier stage in the development pipeline. Proteomics can generate expression signatures from cells or tissues treated with a compound for target identification and validation, and for delineating the mechanism of action of compounds. Proteomic signatures can also be used in the identification and optimization of lead compounds by correlations with efficacy or a specific toxicity. The ultimate aim is to use changes in proteomic patterns to understand how drugs exert their effects at the molecular level.