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Many algorithms are available for quantitative and qualitative analysis of protein spot in gel electrophoresis images and majority of the these algorithms use geometric and image processing techniques to match protein spots. These algorithms do not take into consideration the electrophoretic mobility of the proteins and they only match similar protein spots rather than matching similar proteins. The approach presented in this paper uses a novel technique based on electrophoretic mobility to match protein spots between source and target images. The algorithm identifies the protein spot in the target image which lies on the same line of path as it is in the source image. A shape matching algorithm using Generalized Hough Transform and Canny Edge Detection method is used to determine the shape variance. The method describes here gives an accuracy of 90% or more to identify the same or similar proteins from the target image. Finally, a dedicated target based database has been created to store a set of finite values of an element spot for correlating the 3D protein structure.