Phytochemistry Reviews

, Volume 7, Issue 3, pp 479–497 | Cite as

Plant metabolomics: analytical platforms and integration with functional genomics

  • Jillian M. Hagel
  • Peter J. Facchini


As the final downstream product of the genome, the plant metabolome is a highly complex, dynamic assortment of primary and secondary compounds. Although technological platforms to study genomes, transcriptomes and even proteomes are presently available, methods to pursue genuine metabolomics have not yet been developed due to the extensive chemical diversity of plant primary and secondary metabolites. No single analytical method can accurately survey the entire metabolome. However, recent technical, chemometric and bioinformatic advances promise to enhance our global understanding of plant metabolism. Separation-based mass spectrometry (MS) approaches, such as gas (GC) or liquid chromatography (LC)-MS, are relatively inexpensive, highly sensitive and provide excellent identifying capacity. However, Fourier transform-ion cyclotron resonance (FT-ICR)-MS is better suited for rapid, high-throughput applications and is currently the most sensitive method available. Unlike MS-based analyses, nuclear magnetic resonance (NMR) spectroscopy provides a large amount of information regarding molecular structure, and novel software innovations have facilitated the unequivocal identification and absolute quantification of compounds within composite samples. Due to the size and complexity of metabolomics datasets, numerous chemometric methods are used to extract and display systematic variation. Coupled with pattern recognition techniques and plant-specific metabolite databases, broad-scope metabolite analyses have emerged as functional genomics tools for novel gene discovery and functional characterization. In this review, key metabolomics technologies are compared and the applications of FT-ICR-MS and NMR to the study of benzylisoquinoline alkaloid metabolism in opium poppy are discussed.


Chemometrics Mass spectrometry Metabolite analysis Nuclear magnetic resonance Opium poppy 



Atmospheric pressure chemical ionization




Capillary electrophoresis


Chemical Abstract Service


Collision induced dissociation


Direct injection mass spectrometry


Electrospray ionization


Expressed sequence tag


Free induction decay


Fourier transform-ion cyclotron resonance


Gas chromatography


Hierarchical cluster analysis


High performance liquid chromatography


Internal mass calibrant


Liquid chromatography


Mass spectrometry


Tandem mass spectrometry


Matrix-assisted laser desorption/ionization


Nuclear magnetic resonance


Orthogonal partial least squares discriminatory analysis


Partial least squares discriminatory analysis


Photodiode array detection


Principle component analysis


Self-organized mapping


Solid phase extraction





Program research support is provided by a Natural Sciences and Engineering Research Council of Canada Discovery Grant to PJF.


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© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.Department of Biological SciencesUniversity of CalgaryCalgaryCanada

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