An Integrative Analysis Program for Two-dimensional Gel Electrophoresis

Abstract

Two-dimensional gel electrophoresis (2DE) is one of the most popular way to separate thousands of proteins simultaneously with quantification. To analyze the position of each gel spot containing the protein profile, i.e. protein isoelectric point (pI) and molecular weight (Mw), several computer assisted tools are suggested, including MELANIE and PDQuest. Those softwares provide various and performant methods for image processing and spot detection, but their handling is time-consuming and requires the assistance of user guide manual. In this study, we propose an automatic gel image processing program with a friendly graphic user interface based on MATLAB®. Our tool not only processes spots detection, including preprocessing of noise and distortion of the data, but also provides an automatic association to the corresponding reference spot of the dataset, or landmarks. The latest operation is also called the ‘landmark matching’ process. In this paper we present an example of application of our integrative analysis program with to the data set of human leukemia. We think that this program will be able to gently assist biologist in the analysis of high-throughput proteomics.