Myocardial ischemia and reperfusion injury (MI/R) can be related to leukocyte activation with subsequent release of cytokines and oxygen derived free radicals. Activation of the complement system has been implicated in the pathogenesis of myocardial ischemia and reperfusion injury. Inflammatory injury will subsequently result in cellular activation and protein synthesis. In the present study we analyzed the myocardial protein expression and its pattern following myocardial ischemia and reperfusion, with and without complement inhibition with the synthetic serine protease inhibitor Futhan/nafamstat mesilate (FUT-175) known to inhibit classical and alternative complement pathway in a rabbit model of myocardial ischemia and reperfusion (60 min I+180 min R). FUT-175 significantly reduced myocardial necrosis, i.e. creatine kinase release which were analyzed for the three groups (p<0.05). Similarly, histological analysis demonstrated preservation of myocardial tissue injury and reduced leukocyte accumulation following FUT-175 treatment. Further, the myocardial protein expression was analyzed by two-dimensional gel electrophoresis following MI/R in the different groups. The protein patterns were evaluated by means of MELANIE III, a computer assisted gel analysis system. The biochemical identification of the proteins of interest was, achieved using nanohigh-performance liquid chromatography/electrospray ionization-tandem mass spectrometry. On average, 509 +/- 25 protein spots were found on the gels. A pattern of 480 spots with identical positions was found on every gel of five animals of each group. We analyzed ten spots which were significantly altered (i.e., in eight spots we observed decreased protein expression and in two spots we observed increased expression, vehicle vs. sham), by using mass spectrometry. Superoxide dismutase precursor and alphaB-crystallin were identified. We compared sham group vs. vehicle group and vehicle group vs. FUT-175 treated animals. Expression of the two identified proteins decreased by half the amount in the vehicle group when compared to sham treated animals. Treatment with FUT-175 preserved significantly superoxide dismutase precursor and alphaB-crystallin protein expression when compared to vehicle animals. The results present marked differences in myocardial protein expression after ischemia and reperfusion and following treatment with the complement inhibitor FUT-175. Our results illustrate the application of proteomics to discover possible new therapeutic targets or to detect unexpected effects of pharmacological inhibitors.