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Optimal use of genome sequences and gene-expression resources requires powerful phenotyping platforms, including those for systematic analysis of metabolite composition. The most used technologies for metabolite profiling, including mass spectral, nuclear magnetic resonance and enzyme-based approaches, have various advantages and disadvantages, and problems can arise with reliability and the interpretation of the huge datasets produced. These | Opinion Metabolite profiling in plant biology platforms and destinations Joachim Kopka Alisdair Fernie Wolfram Weckwerth Yves Gibon and Mark Stitt Address Max-Planck Institute of Molecular Plant Physiology Am Muhlenberg 1 14476 Golm Germany. Correspondence Mark Stitt. E-mail stitt@mpimp-golm.mpg.de Published 18 May 2004 Genome Biology 2004 5 109 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2004 5 6 109 2004 BioMed Central Ltd Abstract Optimal use of genome sequences and gene-expression resources requires powerful phenotyping platforms including those for systematic analysis of metabolite composition. The most used technologies for metabolite profiling including mass spectral nuclear magnetic resonance and enzyme-based approaches have various advantages and disadvantages and problems can arise with reliability and the interpretation of the huge datasets produced. These techniques will be useful for answering important biological questions in the future. The challenge Genes and genomes can be routinely sequenced the resulting information stored accessed and analyzed and organisms with altered gene expression produced. Use of these resources requires powerful phenotyping platforms including approaches for the systematic analysis of metabolite composition. Whereas the chemistry of nucleic acids is relatively simple and uniform there are tens of thousands of metabolites with an immense range of types of structure. This has led to a plethora of different extraction separation and detection systems for different groups of metabolically important compounds. Researchers have typically measured a handful of metabolites chosen on the basis of assumptions about what was relevant and the technical capacity of their laboratory. But now in parallel with the development of genome-wide gene-expression arrays there has been a shift to an unbiased approach to metabolite analysis. It is helpful to distinguish between .
