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JXB Advance Access originally published online on March 30, 2006
Journal of Experimental Botany 2006 57(7):1529-1535; doi:10.1093/jxb/erj157
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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

Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidopsis thaliana

Stefanie Wienkoop1 and Wolfram Weckwerth2,*

1Proteome Factory AG, Dorotheenstr. 94, D-10117 Berlin, Germany
2Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany

*To whom correspondence should be addressed. E-mail: weckwerth{at}mpimp-golm-mpg.de

The plant system is a highly dynamic structure on all molecular levels, transcripts, proteins, and metabolites. Thus, protein analysis has to cope with a highly dynamic range of concentrations. A severe problem is the detection of low-abundance proteins in the presence of housekeeping proteins. Basically three approaches are facilitated to measure protein abundance in a comprehensive manner: 2DE and one- or multi-dimensional shotgun proteomics, with or without stable-isotope labelling. These comparative techniques allow for the identification of altered protein levels compared with a reference state. However, they are limited to the analysis of medium/high-abundance proteins. Using stable-isotope dilution techniques it is possible to target the quantitative analysis to low-abundance proteins and to measure absolute concentrations of proteins. Based on multi-dimensional non-gel shotgun proteomics in Arabidopis thaliana, a list of tryptic peptides comprising >1000 proteins was generated. A strategy for quantitative plant proteomics is proposed using this master-list for selecting signature peptides of proteins. To prove the concept, a liquid chromatography–high-resolution triple quadrupole multiple reaction monitoring–mass spectrometry technique is described to determine the absolute amount of a low-abundance sucrose synthase isoform out of an ultra-complex A. thaliana protein extract.

Key words: Absolute quantitation, Arabidopsis, high resolution, linear ion trap, multiple reaction monitoring (MRM), plant, quantitative proteomics, relative quantitation, shotgun proteomics, single reaction monitoring (SRM), stable-isotope labelling, SUSY, triple quadrupole


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