MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is widely used in proteomics studies. Hundreds of proteins extracted from a biological sample can be separated and visualized on a 2D-PAGE gel. The interpretation of protein expression levels relies on the comparison of areas and intensities of the corresponding protein spots in 2D-PAGE gel images. However, determination of protein spot areas by the manual selection method is time-consuming and error-prone. The purpose of this research is to develop a highly automated program for the simultaneous detection and quantification of protein spots across a large number of 2D-PAGE protein gel images by using MATLAB image processing toolbox. This program will enhance the potential of using 2D-PAGE technique as a high throughput quantitative protein expression study tool. We developed MatGel, a simple and efficient program for protein spot area detection and intensity quantification from 2D-PAGE protein gel images. MatGel can detect and output the areas and mean intensities of corresponding protein spots across a large number of 2D-PAGE gel images simultaneously. Users also have options to adjust preferences at each step of image analysis. Basic knowledge with MATLAB programming language is required to run the program.•We developed MATLAB program MatGel to automate the determination of protein spots on 2D-PAGE protein gel images.•MatGel can analyze a large number of 2D-PAGE gel images simultaneously to minimize human errors.•MatGel is flexible and easy to use.