AIM: To investigate the protein patterns of bone marrow mesenchymal stem cells(MSCs) induced by 5-azacytidine and Shuanglong Formula(Radix et Rhizoma Ginseng,Radix et Rhizoma Salviae Miltiorrhizae) and molecular mechanism of induced differentiation was discussed at the level of proteome. METHODS: MSCs extracted from Chinese miniswine were induced by 5-azacytidine and Shuanglong Formula.Proteins were separated by two-dimensional gel electrophoresis,and were detected by silver staining method.The image was analyzed by PDQuest software,and the intensities of spots in the gels were used to quantify the expressions of proteins.Proteins of interest were chosen for in-gel digestion and MALDI-TOF-MS analysis,and then further identified by peptide mass fingerprinting(PMF). RESULTS: 16 altered proteins were identified by PMF and their regulation might be caused by the addition of medicate sera containing the active components of Shuanglong Formula.The effects of medicated sera containing Shuanglong Formula on the induced-differentiation could be discussed from the regulated expression of functional proteins; CONCLUSION: Shuanglong Formula may promote the 5-azacytidine-induced differentiation of bone marrow MSCs in vitro,and our study indicate that proteomics can be used for the analysis of molecular mechanism for different cell process.