Two-dimensional remains one of the main experimental approaches in proteome analysis. However, comigration of protein leads to several limitations: lack of accuracy in protein identification, impaired comparative quantification, and PTM detection. We have optimized a third additional step of in-gel separation to alleviate comigration associated drawbacks. Spot resolution is strikingly improved following this simple and rapid method and the positive impact on protein and peptide identification from MS/MS data, on the analysis of relative changes in protein abundance, and on the detection of PTM is described.
Colignon, B., Raes, M., Dieu, M., Delaive, E., & Mauro, S. (2013). Evaluation of three-dimensional gel electrophoresis to improve quantitative profiling of complex proteomes. Proteomics, 13(14), 2077-2082. https://doi.org/10.1002/pmic.201200494