Two-dimensional gel electrophoresis (2D gels) is an essential quantitative proteomics technique that is frequently used to study differences between samples of clinical relevance. Although considered to have a low throughput, 2D gels can separate thousands of proteins in one gel, making it a good complementary method to MS-based protein quantification. The main drawback of the technique is the tendency of large and hydrophobic proteins such as membrane proteins to precipitate in the isoelectric focusing step. Furthermore, tests using different programs with distinct algorithms for 2D-gel analysis have shown inconsistent ratio values. The aim here is therefore to provide a discussion of algorithms described for the analysis of 2D gels.
