Objective  To identify the proteins related to ischemia in the mitochondia of cerebral cortex.   Methods  Totally 7 adult male SD rats were inflicted by middle cerebral artery occlusion (MCAO) for 6 h with nylon monofilament. Another 7 rats served as normal control. Then cerebral cortex were collected and mitochondria were extracted and purified. After 2-dimensional electrophoresis and PDQuest for gel image analysis

the MS/MS of the peptides from the differential proteins digested by tripsin were analyzed by HPLC-Chip/MS and the original data were pre-processed by Spectrum Mill then search

ed in NCBInr database.   Results  Specific protein spots were identified as TUC-4b

CKB

HS1 binding protein

mitochondrial ribosomal protein S27

dihydrolipoamide dehydrogenase

malate dehydrogenase

isocitrate dehydrogenase(NAD+) alpha

dihydrolipoamide S-acetyltransferase

cytochrome c oxidase subunit Vla

succinate-coenzyme A ligase

ubiquinol-cytochrome c reductase core protein

ATP synthase beta subunit

heat shock 70×10

3

protein

heat shock 60×10

3

protein

acyl-coenzyme A dehydrogenase family.  Conclusion  Cerebebral ischemia affects the proteins related to cerebral cortex mitochondria

which suggests that these proteins may be correlated with the energy metabolism and apoptosis of mitochondria.