Oxidative stress arises when cellular defenses against molecular oxygen and its by-products (reactive oxygen species; ROS) are overcome leading to covalent modification of lipids, DNA, and protein. Redox-based modification of proteins Can be conveniently studied by proteomic analysis using two-dimensional electrophoresis (2D SDS-PAGE). Despite some technical shortcomings, this technique allows rapid and quantitative analysis of paired samples, the visualization of discrete protein spots, and provides a robust platform for subsequent analysis and identification of specific proteins. Exposure to oxidative stress introduces a wide range of reversible or irreversible alterations to amino acid side chains. These include carbonylation, glutathionylation, formation of mixed disulphides, effects on disulphide bridge patterns, ubiquitinylation, and racemization. Identification of proteins targeted for specific modification adds a deeper dimension to the dissection of effects of oxidative stress on the proteome with potentially far-reaching implications. This article describes key methodologies now available for identification of redox-based modifications in proteins separated by 2D SDS-PAGE. (c) 2006 Elsevier Inc, All rights reserved.