TY - CHAP
T1 - Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology
AU - Allwood, J.W.
AU - de Vos, C.H.
AU - Moing, A.
AU - Deborde, C.
AU - Erban, A.
AU - Kopka, J.
AU - Goodacre, R.
AU - Hall, R.D.
N1 - Allwood, J. William De Vos, Ric C. H. Moing, Annick Deborde, Catherine Erban, Alexander Kopka, Joachim Goodacre, Royston Hall, Robert D.
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
KW - chromatography-mass-spectrometry
KW - minimum reporting standards
KW - arabidopsis-thaliana
KW - gas-chromatography
KW - liquid-chromatography
KW - functional genomics
KW - tomato fruit
KW - metabolite profiles
KW - magnetic-resonance
KW - sample preparation
U2 - 10.1016/B978-0-12-385118-5.00016-5
DO - 10.1016/B978-0-12-385118-5.00016-5
M3 - Chapter
SN - 9780123851185
T3 - Methods in Enzymology
SP - 299
EP - 336
BT - Methods in Systems Biology
A2 - Jameson, D.
A2 - Verma, M.
A2 - Westerhoff, H. V.
ER -