Abstract
After separation through two-dimensional gel electrophoresis (2-DE), several hundreds of individual protein abundances can be quantified in a cell population or sample tissue. However, gel-based proteomics has the reputation of being a slow and cumbersome art. But art is not dead! While 2-DE may no longer be the tool of choice in high-throughput differential proteomics, it is still very effective to identify and quantify protein species caused by genetic variations, alternative splicing, and/or PTMs. This chapter reviews some typical statistical exploratory and confirmatory tools available and suggests case-specific guidelines for (1) the discovery of potentially interesting protein spots, and (2) the further characterization of protein families and their possible PTMs.
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Acknowledgements
The author would like to thank Annick De Troyer and Anne-Catherine Vanhove for technical assistance. Prof. Etienne Waelkens and his group (Laboratory of Protein Phosphorylation and Proteomics, KU Leuven), are gratefully acknowledged for the MALDI-TOF/TOF measurements. Financial support from “CIALCA” and the Bioversity International project “ITC characterization” (research projects financed by the Belgian Directorate-General for Development Cooperation (DGDC)) is gratefully acknowledged.
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Carpentier, S.C. (2016). Multiple Testing and Pattern Recognition in 2-DE Proteomics. In: Marengo, E., Robotti, E. (eds) 2-D PAGE Map Analysis. Methods in Molecular Biology, vol 1384. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3255-9_13
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DOI: https://doi.org/10.1007/978-1-4939-3255-9_13
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