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JXB Advance Access published online on March 21, 2006
Journal of Experimental Botany, doi:10.1093/jxb/erj130
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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
Received April 10, 2005
Accepted January 23, 2006

Plant Proteomics Special Issue Article

Arabidopsis thaliana proteomics: from proteome to genome

Sacha Baginsky 1 * and Wilhelm Gruissem 1

1 Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland

* To whom correspondence should be addressed.
Sacha Baginsky, E-mail: sacha.baginsky{at}ipw.biol.ethz.ch


  Abstract

Proteomics has become an important approach for investigating cellular processes and network functions. Significant improvements have been made during the last few years in technologies for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. As proteomics technologies advance and become more widely accessible, efforts of cataloguing and quantifying full proteomes are underway to complement other genomics approaches, such as RNA and metabolite profiling. Of particular interest is the application of proteome data to improve genome annotation and to include information on post-translational protein modifications with the annotation of the corresponding gene. This type of analysis requires a paradigm shift because amino acid sequences must be assigned to peptides without relying on existing protein databases. In this review, advances and current limitations of full proteome analysis are briefly highlighted using the model plant Arabidopsis thaliana as an example. Strategies to identify peptides are also discussed on the basis of MS/MS data in a protein database-independent approach.

Keywords: Analysis; Arabidopsis thaliana; proteomics.
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