PROTEOMICS Volume 6, Issue 4 , Pages 1237 - 1249 Research Article Potential biomarkers for ischemic heart damage identified in mitochondrial proteins by comparative proteomics Nari Kim, Youngsuk Lee, Hyungkyu Kim, Hyun Joo, Jae Boum Youm, Won Sun Park, Mohamad Warda, Dang Van Cuong, Jin Han, Dr. * Mitochondrial Signaling Laboratory, Department of Physiology and Biophysics, College of Medicine, Cardiovascular and Metabolic Diseases Research Center, Biohealth Products Research Center, Inje University, Busan, Korea email: Jin Han (phyhanj@ijnc.inje.ac.kr) *Correspondence to Jin Han, Mitochondrial Signaling Laboratory, Department of Physiology and Biophysics, College of Medicine, Cardiovascular and Metabolic Disease Center, Biohealth Products Research Center, Inje University, 633-165 Gaegeum-Dong, Busanjin-Gu, Busan 614-735, Korea Fax: +82-51-894-5714 Keywords Cardiac marker ?Ischemia-reperfusion ?Ischemic preconditioning ?MALDI-TOF-MS ?Mitochondria ?2-DE Abstract We used proteomics to detect regional differences in protein expression levels from mitochondrial fractions of control, ischemia-reperfusion (IR), and ischemic preconditioned (IPC) rabbit hearts. Using 2-DE, we identified 25 mitochondrial proteins that were differentially expressed in the IR heart compared with the control and IPC hearts. For three of the spots, the expression patterns were confirmed by Western blotting analysis. These proteins included 3-hydroxybutyrate dehydrogenase, prohibitin, 2-oxoglutarate dehydrogenase, adenosine triphosphate synthases, the reduced form of nicotinamide adenine dinucleotide (NADH) oxidoreductase, translation elongation factor, actin alpha, malate dehydrogenase, NADH dehydrogenase, pyruvate dehydrogenase and the voltage-dependent anion channel. Interestingly, most of these proteins are associated with the mitochondrial respiratory chain and energy metabolism. The successful use of multiple techniques, including 2-DE, MALDI-TOF-MS and Western blotting analysis demonstrates that proteomic analysis provides appropriate means for identifying cardiac markers for detection of ischemia-induced cardiac injury.