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Abstract: Computerization is necessary to build the database of chromatography coupled mass spectrometric analytical data. On the basis of this proteomic data we can identify the proteins as biomarkers which are expressing dissimilarity between healthy and disease condition. Affinity chromatography is one of the fastest liquid chromato-graphic methods for the separation and purification of biomolecules due to its high molecular specificity. Proteomics and the tools used to identify and understand the biochemistry of proteins and pathways are in a new stage of development and evaluation. In this article the computation of chromatography coupled mass spectrometric data is reviewed highlighting the role of affinity chromatography. C itation: Allam Appa Rao, Computational approach of protein analysis using affinity chromatography: application to proteomics, African Journal of Pure and Applied Chemistry Vol. 1 (1), pp. 001-007, 2007.