Proteome profiling of U2OS cell line in response to a prenylphenol antibiotic isolated from a phytopathogenic fungus. Proteomics is a novel molecular profiling technology. It is mainly concerned with determining the structure, expression, localization, biochemical activity, interactions, and cellular roles of any proteins. Clinical research hopes to benefit from proteomics in the identification of new drug targets and the development of new diagnostic markers. Better to understand the mechanisms by which ascofuranone (AF), an isoprenoid antibiotic, regulates physiological or pathological events and induces responses in the pharmacological treatment of cancer, we performed differential analysis of the human osteosarcoma cells U2OS proteomes in response to this agent. The U2OS cell proteomes with and without treatment with AF were compared using two-dimensional electrophoresis, matrix-assisted laser desorption/ionization mass spectrometry, and bioinformatics. The largest differences in protein expression were observed for hydroxyindole O-methyltransferase, syntaxin-binding protein 1, the matrix metalloproteinase (MMP)-2, urokinase receptor, and endothelial protein C receptor. Changes in expression and activity of some selected proteins were confirmed by Western blotting, zymography, and reverse transcription-polymerase chain reaction analysis. In particular, we observed downregulated tumor growth related-proteins such as MMP-2 and endothelial protein C receptor. According to these results, AF might be useful as a potent chemotherapeutic agent.