Recently, the proteomic analysis has become an ideal tool to study the structure and function of platelets. We proposed a nano-liquid chromatography (nano-LC) technique coupled off-line with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) for rat platelet proteome analysis. In this study, we attempted to analyze the rat platelet proteome in two different subcellular fractions: cytosol and membrane. Platelet-rich plasma was collected from healthy rats. The platelet samples were extracted with Subcellular Proteome Extraction Kit to collect subcellular compartments. For further investigations, platelet lysate, cytosol and membrane fractions were used. Enzymatic digestion of proteins was performed using Filter Aided Sample Preparation method with trypsin as a proteolytic enzyme. Tryptic peptides were analyzed using nano-LC-MALDI-TOF/TOF-MS. Platelet proteins identification was performed using the Mascot engine. We identified 238 proteins in the platelet lysate, 210 in the cytosol, and 148 in the membrane fraction. Among them, 45 were unique for platelet lysate, 55 for cytosol, and 34 for the membrane fraction. The gene ontology analysis showed that there were differences in the proteome of cytosol and membrane fractions related to the molecular functions, i.e. coagulative activity. Our results may suggest that the membrane or cytosol location of the proteins with coagulative activity may be responsible for the acute or delayed platelet response to an agonist. The nano-LC-MALDI-TOF/TOF-MS method can be used for identifying proteins of subcellular fraction in rat platelets.