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Journal of Experimental Botany 2006 57(7):1493-1499; doi:10.1093/jxb/erj141
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© The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

RESEARCH PAPER

Methods of quantitative proteomics and their application to plant organelle characterization

Kathryn S Lilley1,* and Paul Dupree1

1Department of Biochemistry, University of Cambridge, Building 0, Downing Site, Cambridge CB2 1QW, UK

*To whom correspondence should be addressed. E-mail: k.s.lilley{at}bioc.cam.ac.uk

Many cell biologists wish to know the subcellular localization of proteins of interest. Proteomics methods have the potential to describe the entire protein content of organelles. However, practical limitations in organelle isolation and analysis of low abundance proteins have meant that organelle proteomics has had, until recently, only limited success. Some examples of quantitative proteomic methods and their use in the study of plant organelle proteomes are discussed here. It is concluded that 2D-difference gel electrophoresis (2D-DIGE) as well as differential isotope tagging strategies coupled to non-gel-based LC-MS are proving useful in this area of research.

Key words: 2D-DIGE, 2D-PAGE, endoplasmic reticulum, Golgi apparatus, isotope labelling, LOPIT, organelle fractionation, quantitative proteomics, PCA, PLS-DA


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