|TIWARI, ALKA - Mississippi State University
|SHAN, XUEYAN - Mississippi State University
Submitted to: MethodsX
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2022
Publication Date: 11/21/2022
Citation: Tiwari, A., Williams, W.P., Shan, X. 2022. MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images. MethodsX. 9(101930):1-5. https://doi.org/10.1016/j.mex.2022.101930.
Interpretive Summary: Proteomics is a useful method of investigating gene expression. Two-dimensional gel electrophoresis is widely used in proteomics studies. Hundreds of proteins extracted from a biological sample can be separated and visualized on a single 2DE gel. The interpretation of protein expression levels relies on the comparison of areas and intensities of the corresponding protein spots in the 2DE gel images. Determination of protein spot areas by manual selection is time-consuming and error-prone. The purpose of this research was to develop an open-access and highly automated program for simultaneous detection and quantification of protein spots across a large number of 2DE protein gel images by using the MATLAB image processing toolbox. This program will enhance the potential of using 2DE technique as a high throughput quantitative protein expression study tool. A simple and efficient program for protein spot area detection and intensity quantification from 2DE protein gel images was developed. MatGel detects and outputs the area and mean intensities of corresponding protein spots across a large number of 2DE gel images simultaneously. These techniques will be useful in many types of proteomic studies. They are currently being used by USDA-ARS in investigating resistance to diseases and insect pests in maize.
Technical Abstract: Two-dimensional gel electrophoresis (2DE) has been widely used in proteomic studies for revealing differences in proteomic profiles among tissues of interest under different conditions. However, limitations in the capacity, accessibility, or expense of 2DE image analysis software packages restricted the adaptation of this technique as a high throughput quantitative study tool. In this research, we aimed to develop a user-friendly program for the detection and quantification of protein spots from unlimited number of 2DE protein gel images by using Matlab image processing toolbox. Result: We developed MatGel, a highly efficient and user friendly program for the analysis of 2DE gel images. MatGel analyzes and outputs the area and mean intensities of same protein spots across multiple 2DE gel images. A large number of 2DE gel images can be analyzed in a very short time. Users have freedom to check each step of gel image analysis and make corrections if errors occur. The step by step instructions of using MatGel are shown in the Supplementary Section. Availability and implementation: MatGel is written in programming language Matlab. The code is available at http://www.entomology.msstate.edu/associate.asp?id=111.