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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 intensiti...

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Detalles Bibliográficos
Autores principales: Tiwari, Alka, Williams, W. Paul, Shan, Xueyan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703371/
https://www.ncbi.nlm.nih.gov/pubmed/36451780
http://dx.doi.org/10.1016/j.mex.2022.101930
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author Tiwari, Alka
Williams, W. Paul
Shan, Xueyan
author_facet Tiwari, Alka
Williams, W. Paul
Shan, Xueyan
author_sort Tiwari, Alka
collection PubMed
description 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.
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spelling pubmed-97033712022-11-29 MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images Tiwari, Alka Williams, W. Paul Shan, Xueyan MethodsX Method Article 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. Elsevier 2022-11-21 /pmc/articles/PMC9703371/ /pubmed/36451780 http://dx.doi.org/10.1016/j.mex.2022.101930 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Method Article
Tiwari, Alka
Williams, W. Paul
Shan, Xueyan
MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title_full MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title_fullStr MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title_full_unstemmed MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title_short MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images
title_sort matgel: a matlab program for quantitative analysis of 2d polyacrylamide electrophoresis (2d-page) protein gel images
topic Method Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703371/
https://www.ncbi.nlm.nih.gov/pubmed/36451780
http://dx.doi.org/10.1016/j.mex.2022.101930
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