A proposed framework for the description of plant metabolomics experiments and their results (original) (raw)
References
- Quackenbush, J. Data standards for 'omic' science. Nat. Biotechnol. 22, 613–614 (2004).
Article CAS Google Scholar - Brazma, A. et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29, 365–371 (2001).
Article CAS Google Scholar - Spellman, P.T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, research0046.0041–0046.0049 (2002).
Article Google Scholar - Brazma, A. et al. ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68–71 (2003).
Article CAS Google Scholar - Killion, P.J., Sherlock, G. & Iyer, V.R. The Longhorn Array Database (LAD): An open-source, MIAME compliant implementation of the Stanford Microarray database (SMD). BMC Bioinformatics 4, 32 (2003). http://biomedcentral.com/1471-2105/4
Google Scholar - Editorial. Microarray standards at last. Nature 419, 323 (2002).
- Glueck, S.B. & Dzau, V.J. Our new requirement for MIAME standards. Physiol. Genomics 13, 1–2 (2003).
Article Google Scholar - Oliver, S. On the MIAME standards and central repositories, of microarray. Comp. Funct. Genomics 4, 1 (2003).
Article CAS Google Scholar - Taylor, C.F. et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol. 21, 247–254 (2003).
Article CAS Google Scholar - Booch, G., Rumbaugh, J. & Jacobson, I. The Unified Modeling Language User Guide (Addison-Wesley, Reading, MA, 1999).
Google Scholar - Orchard, S., Hermjakob, H. & Apweiler, R. The proteomics standards initiative. Proteomics 3, 1374–1376 (2003).
Article CAS Google Scholar - Orchard, S. et al. Common interchange of standards for proteomics data: public availability of tools and schema. Proteomics 4, 490–491 (2004).
Article CAS Google Scholar - Fiehn, O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genomics 2, 155–168 (2001).
Article CAS Google Scholar - Fiehn, O. Metabolomics—the link between genotypes and phenotypes. Plant Mol. Biol. 48, 155–171 (2002).
Article CAS Google Scholar - Fiehn, O. & Weckwerth, W. Deciphering metabolic networks. Eur. J. Biochem. 270, 579–588 (2003).
Article CAS Google Scholar - Goodacre, R., Vaidyanathan, S., Dunn, W.B., Harrigan, G.G. & Kell, D.B. Metabolomics by numbers:acquiring and understanding global metabolite data. Trends Biotechnol. 22, 245–252 (2004).
Article CAS Google Scholar - Harrigan, G.G. & Goodacre, R. (eds.) Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (Kluwer Academic Publishers, Boston, 2003).
Book Google Scholar - Mendes, P. Emerging bioinformatics for the metabolome. Brief. Bioinform. 3, 134–145 (2002).
Article CAS Google Scholar - Oliver, S.G., Winson, M.K., Kell, D.B. & Baganz, F. Systematic functional analysis of the yeast genome. Trends Biotechnol. 16, 373–378 (1998).
Article CAS Google Scholar - Raamsdonk, L.M. et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19, 45–50 (2001).
Article CAS Google Scholar - Roessner, U. et al. Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11–29 (2001).
Article CAS Google Scholar - Roessner, U., Wagner, C., Kopka, J., Trethewey, R.N. & Willmitzer, L. Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23, 131–142 (2000).
Article CAS Google Scholar - Sumner, L.W., Mendes, P. & Dixon, R.A. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62, 817–836 (2003).
Article CAS Google Scholar - Weckwerth, W. Metabolomics in systems biology. Annu. Rev. Plant Biol. 54, 669–689 (2003).
Article CAS Google Scholar - Hall, R. et al. Plant metabolomics: the missing link in functional genomics strategies (Meeting report). Plant Cell 14, 1437–1440 (2002).
Article CAS Google Scholar - van der Greef, J., van der Heiiden, R. & Verheij, E.R. The role of mass spectrometry in system biology: data processing and identification strategies in metabolomics. in Advances in Mass Spectrometry, vol. 16. (eds. Ashcroft, A.E., Brenton, G. & Monaghan, J.J.) 145–165 (Elsevier, Amsterdam, 2004).
Google Scholar - Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
Article CAS Google Scholar - Krieger, C.J. et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32, D438–D442 (2004).
Article CAS Google Scholar - Mueller, L.A., Zhang, P. & Rhee, S.Y. AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiol. 132, 453–460 (2003).
Article CAS Google Scholar - Harris, M.A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 Special Issue, D258–D261 (2004).
Article CAS Google Scholar - Nicholson, J.K., Lindon, J.C. & Homes, E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181–1189 (1999).
Article CAS Google Scholar - Bino, R.J. et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9, 418–425 (2004).
Article CAS Google Scholar - Stein, S.E. & Scott, D.R. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5, 859–866 (1994).
Article CAS Google Scholar - McLafferty, F.W., Zhang, M-Y., Stauffer, D.B. & Loh, S.Y. Comparison of algorithms and databases for matching unknown mass spectra. J. Am. Soc. Mass Spectrom. 9, 92–95 (1998).
Article CAS Google Scholar - Xirasagar, S. et al. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 20, 2004–2015 (2004).
Article CAS Google Scholar - Lampen, P. et al. An extension to the JCAMP-DX standard file format, JCAMP-DX V.5.01 (IUPAC Recommendations 1999). Pure Appl. Chem. 71, 1549–1556 (1999).
Article CAS Google Scholar - Griffiths, P.R. & de Haseth, J.A. Fourier Transform Infrared Spectrometry, vol. 83 (John Wiley & Sons, Chichester, England, 1986).
Google Scholar - Allen, J.K. et al. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 21, 692–696 (2003).
Article CAS Google Scholar - Smedsgaard, J. Terverticillate penicillia studied by direct electrospray mass spectrometric profiling of crude extracts: II. Database and identification. Biochemical Systematics and Ecology 25, 65–71 (1997).
Article CAS Google Scholar - Smedsgaard, J. & Frisvad, J.C. Using direct electrospray mass spectrometry in taxonomy and secondary metabolite profiling of crude fungal extracts. J Microbiol. Methods 25, 5–17 (1996).
Article CAS Google Scholar
Acknowledgements
The authors gratefully acknowledge the United Kingdom Food Standards Agency (under the G02006 project), the United Kingdom Biotechnology and Biological Sciences Research Council (particularly under the HiMet project) and the United Kingdom Engineering and Physical Sciences Research Council for support of their work in metabolomics. We would also like to thank personnel at the United Kingdom Institute of Grassland and Environmental Research and delegates at the 1st, 2nd and 3rd International Plant Metabolomics Conferences for many useful discussions.
Author information
Author notes
- Janet Taylor
Present address: IGER, Plas Gogerddan, Aberystwyth, Ceredigion, Wales, UK, SY23 3EB
Authors and Affiliations
- Department of Computer Science, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, SY23 3DB, UK
Helen Jenkins, Nigel Hardy & Janet Taylor - Institute of Biological Sciences, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, SY23 3DB, UK
Manfred Beckmann, John Draper & Aileen R Smith - Max Planck Institute of Molecular Plant Physiology, Potsdam, 14424, Germany
Oliver Fiehn & Joachim Kopka - School of Chemistry, The University of Manchester, PO Box 88, Manchester, M60 1QD, UK
Royston Goodacre & Douglas B Kell - Plant Research International, POB 16, Wageningen, 6700 AA, The Netherlands
Raoul J Bino & Robert Hall - Centre for BioSystems Genomics, POB 98, Wageningen, 6700 AB
Raoul J Bino - AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
Geoffrey A Lane - Institute of Biological Chemistry and Center for Integrated Biotechnology, Washington State University, Pullman, 99164-6340, Washington, USA
B Markus Lange - Plant Cell Biotechnology Laboratory of KRIBB and NRL of Eugentech Inc.,, PO Box 115, Yuseong, 305-600, Daejeon, Korea
Jang R Liu - Virginia Bioinformatics Institute, Virginia Tech, 1880 Pratt Drive, Blacksburg, 24061, Virginia, USA
Pedro Mendes - Department of Biochemistry, Center for Designer Crops, W.M. Keck Metabolomics Research Laboratory, Biophysics and Molecular Biology, Iowa State University, Ames, 50011, Iowa, USA
Basil J Nikolau - School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Stephen G Oliver - Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Norman W Paton - Department of Plant Biology, The Arabidopsis Information Resource, Carnegie Institution of Washington, 260 Panama Street, Stanford, 94305, California, USA
Sue Rhee - Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, Victoria, 3010, Australia
Ute Roessner-Tunali - Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi-cho 1-33, Inage-ku, 263-8522, Chiba, Japan
Kazuki Saito - Technical University of Denmark, BioCentrum-DTU, Søltofts Plads Building 221, Kgs Lyngby, 2800, Denmark
Jørn Smedsgaard - The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, 73401, Oklahoma, USA
Lloyd W Sumner - John Innes Centre, Norwich Research Park, Colney, NR4 7UH, Norwich
Trevor Wang & Sean Walsh - Department of Genetics, Development and Cell Biology, 441 Bessey Hall, Iowa State University, Ames, 50011, Iowa, USA
Eve Syrkin Wurtele
Authors
- Helen Jenkins
You can also search for this author inPubMed Google Scholar - Nigel Hardy
You can also search for this author inPubMed Google Scholar - Manfred Beckmann
You can also search for this author inPubMed Google Scholar - John Draper
You can also search for this author inPubMed Google Scholar - Aileen R Smith
You can also search for this author inPubMed Google Scholar - Janet Taylor
You can also search for this author inPubMed Google Scholar - Oliver Fiehn
You can also search for this author inPubMed Google Scholar - Royston Goodacre
You can also search for this author inPubMed Google Scholar - Raoul J Bino
You can also search for this author inPubMed Google Scholar - Robert Hall
You can also search for this author inPubMed Google Scholar - Joachim Kopka
You can also search for this author inPubMed Google Scholar - Geoffrey A Lane
You can also search for this author inPubMed Google Scholar - B Markus Lange
You can also search for this author inPubMed Google Scholar - Jang R Liu
You can also search for this author inPubMed Google Scholar - Pedro Mendes
You can also search for this author inPubMed Google Scholar - Basil J Nikolau
You can also search for this author inPubMed Google Scholar - Stephen G Oliver
You can also search for this author inPubMed Google Scholar - Norman W Paton
You can also search for this author inPubMed Google Scholar - Sue Rhee
You can also search for this author inPubMed Google Scholar - Ute Roessner-Tunali
You can also search for this author inPubMed Google Scholar - Kazuki Saito
You can also search for this author inPubMed Google Scholar - Jørn Smedsgaard
You can also search for this author inPubMed Google Scholar - Lloyd W Sumner
You can also search for this author inPubMed Google Scholar - Trevor Wang
You can also search for this author inPubMed Google Scholar - Sean Walsh
You can also search for this author inPubMed Google Scholar - Eve Syrkin Wurtele
You can also search for this author inPubMed Google Scholar - Douglas B Kell
You can also search for this author inPubMed Google Scholar
Corresponding author
Correspondence toNigel Hardy.
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Rights and permissions
About this article
Cite this article
Jenkins, H., Hardy, N., Beckmann, M. et al. A proposed framework for the description of plant metabolomics experiments and their results.Nat Biotechnol 22, 1601–1606 (2004). https://doi.org/10.1038/nbt1041
- Published: 06 December 2004
- Issue Date: December 2004
- DOI: https://doi.org/10.1038/nbt1041