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Multiple Testing and Pattern Recognition in 2-DE Proteomics

  • Sebastien C. CarpentierEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1384)

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.

Key words

2-DE Multivariate statistics Protein correlations Clustering Protein isoforms 

Notes

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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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Biosystems, Faculty of Bioscience EngineeringK.U. LeuvenLeuvenBelgium
  2. 2.SYBIOMA: Facility for Systems Biology Based Mass SpectrometryLeuvenBelgium

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