Ubiquinone (UQ), also known as “coenzyme Q” is an essential player in the mitochondrial respiratory electron transport chain as well as a lipid-soluble antioxidant in eukaryotic cells. In this study, we attempted to identify the proteins involved in the pathway by which the exogenous UQ is taken up and accumulated in mitochondria through chemical biology approaches. This project contains MS and MS/MS analysis of the proteins which were specifically labeled by the photo-reactive ubiquinone analogue.