Abstract
Metabolomics is a new genomics approach that aims at measuring all or a subset of metabolites in the cell. Several approaches to plant metabolomics are currently used in plant research. These include targeted analysis, metabolite profiling, and metabolic fingerprinting. Metabolic fingerprinting, unlike metabolite profiling, does not aim at separating or identifying all the metabolites present in the sample, but rather generates a fingerprint that characterizes a specific metabolic state of the plant system under investigation. This chapter describes the implementation of metabolic fingerprinting approach using gas chromatography coupled to mass spectrometry (GC-MS) and discriminant function analysis combined with genetic algorithm (GA-DFA). This approach enables the identification of specific metabolites that are biologically relevant, and which may go undetected if direct infusion-based fingerprinting approaches were used due to the sample complexity and matrix suppression effects.
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References
Shulaev, V. (2006) Metabolomics technology and bioinformatics. Brief. Bioinform. 7, 128–139.
Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., Davletova, S., et al. (2004) When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol. 134, 1683–1696.
Roessner, U., Wagner, C., Kopka, J., Trethewey, R. N., Willmitzer, L. (2000) Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23, 131–142.
Krishnan, P., Kruger, N. J., Ratcliffe, R. G. (2005) Metabolite fingerprinting and profiling in plants using NMR. J. Exp. Bot. 56, 255–265.
Goodacre, R., York, E. V., Heald, J. K., Scott, I. M. (2003) Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry. Phytochemistry 62, 859–863.
Johnson, H. E., Broadhurst, D., Goodacre, R., Smith, A. R. (2003) Metabolic fingerprinting of salt-stressed tomatoes. Phytochemistry 62, 919–928.
Shulaev, V., Cortes, D., Miller, G., Mittler, R. (2008) Metabolomics for plant stress response. Physiol. Plant. 132, 199–208.
Kováts, E. (1958) Gas-chromatographische charakterisierung organischer verbindungen. Teil 1: retentionsindices aliphatischer halogenide, alkohole, aldehyde und ketone. Helv. Chim. Acta 41, 1915–1932.
Jarvis, R.M. and Goodacre, R. (2005) Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data. Bioinformatics 21, 860–868.
Mendes, P. (2006) Available from: http://mendes.vbi.vt.edu/tiki-index.php?page=ometer.
Schweer, H. (1982) Gas chromatography–mass spectrometry of aldoses as O-methoxime, O-2-methyl-2-propoxime and O-n-butoxime pertrifluoroacetyl derivatives on OV-225 with methylpropane as ionization agent: II. Hexoses. J. Chrom. A 236, 361–367.
Henriques, I. D., Aga, D. S., Mendes, P., O’Connor, S. K., Love, N. G. (2007) Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals. Environ. Sci. Technol. 41, 3945–3951.
Acknowledgments
This work was funded by National Science Foundation grant 03122857 as part of the Arabidopsis 2010 Project.
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Shuman, J.L., Cortes, D.F., Armenta, J.M., Pokrzywa, R.M., Mendes, P., Shulaev, V. (2011). Plant Metabolomics by GC-MS and Differential Analysis. In: Pereira, A. (eds) Plant Reverse Genetics. Methods in Molecular Biology, vol 678. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-682-5_17
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DOI: https://doi.org/10.1007/978-1-60761-682-5_17
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