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Human bone marrow stromal cells (BMSCs) have been hailed as a promising source for cell therapy and tissue regeneration due to its multipotent nature. Bone marrow stromal cells differentiate into various tissues at the cues from its surrounding. Proteomics is a powerful tool to elucidate cellular mechanisms. The present study established a reproducible protocol to display the complete qualitative 2-D protein map of BMSCs. Results showed the standard optimization of the 2-D protein mapping at pH 3-10 with 60 μg protein loading in freshly isolated mononuclear cells, cultured BMSCs (P0) and BMSCs (P2). This protocol could be further used, along with identification of differentially expressed protein by mass spectrometry, for thorough understanding of the molecular events involved, which would enable a better control of the various differentiation processes of BMSCs.