This invention teaches a computerized method for use in data acquisition and manipulation of two-dimensional patterns in the fields of medicine, astronomy, chemistry, biology and biotechnology. The invention teaches an interactive computerized method for matching visual patterns of polypeptide spots in two-dimensional (2-D) gel electrophoretogram solubilized into polypeptide constituents that are separated by electrophoresis. The computerized method manipulates spot pixel coordinates using staged coordinate transformation techniques on spot markers and unknown study spots to reduce gel preparation distortions and allows a user to produce matching results in a manner that compares the transformed spot data using either a single reference gel or multiple reference gels approach for producing the matching results. The method also includes a spot matching verification step and a step to extract potentially mis-matched spots from reported matching results. The user can also resolve contradictions and perform spot matching analysis using isoelectric focusing (PI), and molecular weight (MW) dimensional separation data.