Drug-induced toxicities can result in stopping preclinical development of a compound, or even in the withdrawal of compounds once they are marketed. What is lacking is a means of identifying early in the drug discovery process the potential safety liabilities of compounds. By the time a compound is tested in vivo, it is usually too late to change the compound profile and remove the toxicity. Testing compounds in in vitro cellular models is a widely used approach that can help identify potential toxicities, but this approach is limited by the endpoints that are measured. Compounds that are cytotoxic can be identified easily but there are many other in vivo toxicities for which in vitro correlates are not known. In this work, we have treated HepG2 liver cells with compounds known to cause liver toxicity, and profiled the resulting protein changes using SILAC mass spectrometry. We analyzed the results using a systems biology approach which identified biological networks associated with compound toxicity. Application of this approach to a wider range of compounds will be important in helping to build a proteomic database that can be utilized to catalog toxicity profiles.