Abstract: In Post-Genome Era, Functional Genomic becomes a major research field. Two-Dimensional Electrophoresis (abbreviated as 2-DE) technique is a central technique for analyzing proteins. The final process and goal of this technique is to compare different experimental data and construct a database for querying. In this article, we present a query system, based on the R-Tree index technique, to support the regional searching function. With the regional searching ability, researchers may retrieve all the 2-DE images consisting of protein molecules in a given region. The process of the proposed system consists of two phases, one for extracting the regional properties of proteins, the other for constructing the R-Tree.