Journal de protéomique et bioinformatique
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Fractional Precipitation of Plasma Proteome by Ammonium Sulphate:Case Studies in Leukemia and Thalassemia

Sutapa Saha, Suchismita Halder, Dipankar Bhattacharya, Debasis Banerjee and Abhijit Chakrabarti

Human plasma proteome is a comprehensive source of disease biomarkers. However, the >10 orders-wide dynamic concentration range of its constituent proteins necessitates depletion of abundant proteins from plasma prior to biomarker discovery. Our objective has been to develop a simple method that would deplete the most abundant proteins e.g. albumin and immunoglobulins, effectively facilitating identification of differentially regulated proteins in plasma samples. We employed ammonium sulphate based pre-fractionation of plasma followed by twodimensional gel electrophoresis (2DGE) for comparison of normal proteins with those from the plasma samples of the patients, after identification of proteins by MALDI-TOF/TOF tandem mass spectrometry. Fractional precipitation of the plasma samples by 20% ammonium sulphate from raw plasma doubled the number of protein spots after 2DGE and led to identification of 87 unique proteins, including several low-abundance proteins. Case studies done with fractional precipitation of the plasma samples of patients suffering from hematological diseases e.g. leukemia and thalassemia indicate the utility of such pre-fractionation in the detection of differentially regulated proteins.