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Metabolite profiling: from diagnostics to systems biology

Abstract

The concept of metabolite profiling has been around for several decades, but only recent technical innovations have allowed metabolite profiling to be carried out on a large scale — with respect to both the number of metabolites measured and the number of experiments carried out. As a result, the power of metabolite profiling as a technology platform for diagnostics, and the research areas of gene-function analysis and systems biology, is now beginning to be fully realized.

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Figure 1: The trade-off between metabolic coverage and the quality of metabolic analysis.
Figure 2: Overexpression and metabolite profiling at the transgenomic level.

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Acknowledgements

The authors thank O. Schmitz for assistance in the preparation of figure 2. Software used in the preparation of figure 2 was provided by OmniViz Inc.

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Correspondence to Alisdair R. Fernie.

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FURTHER INFORMATION

AMDIS

BRENDA enzyme database

GenMAPP

Kyoto Encyclopedia of Genes and Genomes

MapMan

Max-Planck-Institut für Molekulare Pflanzenphysiologie

Metabolon

metanomics

Paradigm Genetics

Glossary

CHEMOMETRIC

The application of statistical and computer methods to data analysis in chemistry and related scientific fields.

ECOTYPE

The smallest taxonomic subdivision of an ecospecies, which consists of populations that have adapted to a particular set of environmental conditions.

ELECTROSPRAY IONIZATION

To analyse compounds effectively by mass spectrometry, they must be ionized in the gas phase. Electrospray is the most widely used atmospheric-pressure ionization technique for the sensitive, comprehensive analysis of polar and ionic compounds. Using electrospray, a strong electric field is applied to the liquid sample stream, which is then nebulized and desolvated with the assistance of a high-temperature gas flow to produce gas-phase ions.

HIERARCHICAL CLUSTER ANALYSIS

An agglomerative statistical method that finds clusters of observations within a data set. It allows the grouping of individuals on the basis of the similarity in their properties.

ION SUPPRESSION

The common term that is given to a range of phenomena that can occur during the ionization of complex mixtures. An important component of this is the competition between co-eluting compounds for ionization energy, which can lead to varying degrees of ionization of any individual compounds.

PRINCIPAL COMPONENT ANALYSIS

A statistical tool in which an orthogonal coordinate system, with axes that are ordered in terms of the amount of variance in a dataset, is produced. This allows the separation of individuals on the basis of differences in their properties and can also be used to evaluate the properties that contribute the most to these separations.

QUADRUPOLE TECHNOLOGY

A quadrupole mass filter consists of four parallel metal rods. Two opposite rods have a DC voltage and the other two have an AC voltage. The applied voltages affect the trajectory of ions that travel down the flight path that is centred between the four rods, such that only ions of a certain mass-to-charge ratio pass through the quadrupole filter and all other ions are thrown out of their original path. A mass spectrum is obtained by monitoring the ions that pass through the quadrupole filter as the voltages on the rods are varied.

SUBSTANTIAL EQUIVALENCE TESTING

The concept of substantial equivalence embodies the idea that organisms that are used as foods or as food sources can serve as a basis for comparison when assessing the safety of human consumption of a food or food component that has been modified or is new.

SUPERVISED GROUPING APPROACH

A method that requires training with known data sets in which the types of groups expected are predefined before being applied to experimental data.

UNSUPERVISED GROUPING APPROACH

A method that does not require training with known data sets and that generates groups on the basis of the data structure in the experimental data.

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Fernie, A., Trethewey, R., Krotzky, A. et al. Metabolite profiling: from diagnostics to systems biology. Nat Rev Mol Cell Biol 5, 763–769 (2004). https://doi.org/10.1038/nrm1451

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