Journal ArticleDOI
Gas chromatography mass spectrometry–based metabolite profiling in plants
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A detailed protocol for gas chromatography mass spectrometry (GC-MS)-based metabolite profiling that offers a good balance of sensitivity and reliability, being considerably more sensitive than NMR and more robust than liquid chromatography–linked mass spectromaetry.Abstract:
The concept of metabolite profiling has been around for decades, but technical innovations are now enabling it to be carried out on a large scale with respect to the number of both metabolites measured and experiments carried out. Here we provide a detailed protocol for gas chromatography mass spectrometry (GC-MS)-based metabolite profiling that offers a good balance of sensitivity and reliability, being considerably more sensitive than NMR and more robust than liquid chromatography-linked mass spectrometry. We summarize all steps from collecting plant material and sample handling to derivatization procedures, instrumentation settings and evaluating the resultant chromatograms. We also define the contribution of GC-MS-based metabolite profiling to the fields of diagnostics, gene annotation and systems biology. Using the protocol described here facilitates routine determination of the relative levels of 300-500 analytes of polar and nonpolar extracts in approximately 400 experimental samples per week per machine.read more
Citations
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Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry
TL;DR: A detailed protocol for large-scale untargeted metabolomics of plant tissues, based on reversed phase liquid chromatography coupled to high-resolution mass spectrometry (LC-QTOF MS) of aqueous methanol extracts is described.
Journal ArticleDOI
NMR-based metabolomic analysis of plants.
TL;DR: This protocol is particularly suited for the analysis of secondary metabolites such as phenolic compounds and for primary metabolites, and is rapid; it takes not more than 30 min for sample preparation and a further 10 min for NMR spectrum acquisition.
Journal ArticleDOI
Metabolomics for Functional Genomics, Systems Biology, and Biotechnology
Kazuki Saito,Fumio Matsuda +1 more
TL;DR: The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana and can be used for the identification of genes involved in specific pathways in crops and medicinal plants.
Journal ArticleDOI
The use of metabolomics to dissect plant responses to abiotic stresses
TL;DR: In this review, the analytical methods used for plant metabolomics are introduced and their use in studies related to the metabolic response to water, temperature, light, nutrient limitation, ion and oxidative stresses are described.
Journal ArticleDOI
Quality control for plant metabolomics: reporting MSI‐compliant studies
Oliver Fiehn,Gert Wohlgemuth,Martin Scholz,Tobias Kind,Do Yup Lee,Yun Lu,Stephanie Michelle Moon,Basil J. Nikolau +7 more
TL;DR: This work exemplifies how metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype can be reported by using a small case study.
References
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Journal ArticleDOI
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
TL;DR: An LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching, and is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples.
Journal ArticleDOI
Metabolite profiling for plant functional genomics.
Oliver Fiehn,Joachim Kopka,Peter Dörmann,Thomas Altmann,Richard N. Trethewey,Lothar Willmitzer +5 more
TL;DR: The use of metabolite profiling is described as a new tool for a comparative display of gene function and has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly.
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GMD@CSB.DB: the Golm Metabolome Database
Joachim Kopka,Nicolas Schauer,Stephan Krueger,Claudia Birkemeyer,Björn Usadel,Eveline Bergmüller,Peter Dörmann,Wolfram Weckwerth,Yves Gibon,Mark Stitt,Lothar Willmitzer,Alisdair R. Fernie,Dirk Steinhauser +12 more
TL;DR: GD, The Golm Metabolome Database is presented, an open access metabolome database, which provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds.
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Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry.
TL;DR: Although the method represents a compromise for a wide range of metabolites in terms of extraction, chemical modification and GC-MS analysis, for 25 metabolites analysed in detail the recoveries were found to be within the generally accepted range of 70-140%.
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Plant metabolomics: large-scale phytochemistry in the functional genomics era
TL;DR: The critical role of bioinformatics and various methods of data visualization are summarized and the future role of metabolomics in plant science assessed.