Targeted chemotherapy is a new approach for the treatment of cancer, which may prevent undesired side effects occurring in the “classical” treatment with free anticancer drugs. The combination of chemotherapeutic agents (e.g. Daunorubicin) with a targeting moiety which recognizes tumor specific or highly expressed receptors on cancer cells (e.g. gonadotropin-releasing hormone (GnRH) derivatives) might provide efficient anticancer drugs with minimal systemic toxicity. Oxime bond-linked [4Lys(Ac)]-GnRH-III(Dau=Aoa) bioconjugate represents a promising drug delivery system with potential applications in targeted cancer chemotherapy. Valuable information for understanding the drug action mechanism (which is crucial for its therapeutic applications) can be provided by the global analysis of the cellular protein alterations. The proteins expressed in cells under given conditions such as chemotherapeutic treatment can be identified and characterized by proteomics approaches. The major goal of the present study is to compare the protein expression profile of untreated MCF-7 human breast and HT-29 human colon cancer cells with that of cancer cells treated with free daunorubicin and [4Lys(Ac)]-GnRH-III(Dau=Aoa) bioconjugate.