Abstract: The present invention relates to a transgenic animal in which APEX2 is specifically expressed in a mitochondrial matrix and to uses thereof. When the transgenic animal according to the present invention is used, it is possible to overcome the limitation of being susceptible to contamination with proteins derived from other organelles or other tissue cells in existing mitochondrial proteomic studies. Accordingly, mitochondrial matrix proteomic research with a high reliability is possible, tissue-specific mitochondrial matrix proteomics can easily be analyzed, and a wide range of applications are possible in basic life science research, drug development, and diagnostic research related to mitochondrial proteomics.