Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology

J.W. Allwood, C.H. de Vos, A. Moing, C. Deborde, A. Erban, J. Kopka, R. Goodacre, R.D. Hall

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

49 Citations (Scopus)

Abstract

The "metabolome" comprises the entire complement of small molecules in a plant or any other organism. It represents the ultimate phenotype of cells, deduced from the perturbation of gene expression and the modulation of protein function, as well as environmental cues. Extensive advances over the past decade, regarding the high-throughput (HTP) nature of "omics" research, have given birth to the expectation that a type of "systems level" overview may soon be possible. Having such a global overview of the molecular organization of a plant in the context of a particular set of genetic or environmental conditions, be it at cell, organ, or whole plant level, would clearly be very powerful. Currently, we are far from achieving this goal; however, within our hands, plant metabolomics is an HTP and informative "omics" approach to both sample generation and data generation, as well as raw data preprocessing, statistical analysis, and biological interpretation. Within this chapter, we aim to describe the great attention given to experimental design to ensure that the correct sample set and control are included and to, thereby, enable reliable statistical analysis of the data. For as comprehensive metabolite coverage as possible, we advocate the use of multiparallel approaches; thus, we describe a step-by-step standardized method for Nuclear magnetic resonance spectroscopy, as well as discussing with reference to standardized methodologies the techniques of gas chromatography-time of flight/mass spectrometry, and liquid chromatography mass spectrometry.
Original languageEnglish
Title of host publicationMethods in Systems Biology
EditorsD. Jameson, M. Verma, H. V. Westerhoff
Pages299-336
DOIs
Publication statusPublished - 2011

Publication series

NameMethods in Enzymology
Number500

Fingerprint

Mass spectrometry
Throughput
Liquid chromatography
Metabolites
Gene expression
Gas chromatography
Design of experiments
Nuclear magnetic resonance spectroscopy
Statistical methods
Modulation
Molecules
Proteins
Metabolomics
Systems Biology
Statistical Data Interpretation

Keywords

  • chromatography-mass-spectrometry
  • minimum reporting standards
  • arabidopsis-thaliana
  • gas-chromatography
  • liquid-chromatography
  • functional genomics
  • tomato fruit
  • metabolite profiles
  • magnetic-resonance
  • sample preparation

Cite this

Allwood, J. W., de Vos, C. H., Moing, A., Deborde, C., Erban, A., Kopka, J., ... Hall, R. D. (2011). Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology. In D. Jameson, M. Verma, & H. V. Westerhoff (Eds.), Methods in Systems Biology (pp. 299-336). (Methods in Enzymology; No. 500). https://doi.org/10.1016/B978-0-12-385118-5.00016-5
Allwood, J.W. ; de Vos, C.H. ; Moing, A. ; Deborde, C. ; Erban, A. ; Kopka, J. ; Goodacre, R. ; Hall, R.D. / Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology. Methods in Systems Biology. editor / D. Jameson ; M. Verma ; H. V. Westerhoff. 2011. pp. 299-336 (Methods in Enzymology; 500).
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Allwood, JW, de Vos, CH, Moing, A, Deborde, C, Erban, A, Kopka, J, Goodacre, R & Hall, RD 2011, Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology. in D Jameson, M Verma & HV Westerhoff (eds), Methods in Systems Biology. Methods in Enzymology, no. 500, pp. 299-336. https://doi.org/10.1016/B978-0-12-385118-5.00016-5

Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology. / Allwood, J.W.; de Vos, C.H.; Moing, A.; Deborde, C.; Erban, A.; Kopka, J.; Goodacre, R.; Hall, R.D.

Methods in Systems Biology. ed. / D. Jameson; M. Verma; H. V. Westerhoff. 2011. p. 299-336 (Methods in Enzymology; No. 500).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

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Allwood JW, de Vos CH, Moing A, Deborde C, Erban A, Kopka J et al. Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology. In Jameson D, Verma M, Westerhoff HV, editors, Methods in Systems Biology. 2011. p. 299-336. (Methods in Enzymology; 500). https://doi.org/10.1016/B978-0-12-385118-5.00016-5