The Whereabouts of 2D Gels in Quantitative Proteomics

TL;DR

This paper reviews the role of 2D gel electrophoresis in quantitative proteomics, focusing on detection methods and data analysis to improve sample comparison accuracy.

Contribution

It provides a critical examination of various detection techniques and data analysis challenges in 2D gel-based quantitative proteomics.

Findings

Different detection methods have unique advantages and limitations.

Data analysis critically impacts quantitative accuracy.

2D gels remain valuable for large sample series.

Abstract

Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using 2D gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of 2D gels is performed.