Plant metabolomics: large-scale phytochemistry in the functional genomics era Lloyd W. Sumner, Pedro Mendes, Richard A. Dixon Abstract: Metabolomics, or the large-scale phytochemical analysis of plants, is reviewed in relation to functional genomics and systems biology. The historical development of metabolite profiling into today's comprehensive metabolomics approach is provided. Technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry, are surveyed. The critical role of bioinformatics and various methods of data visualization are summarized, and the future role of metabolomics in plant science is assessed. Keywords: Metabolomics; Metabolic profiling; Metabolite profiling; Analytical instrumentation; Mass spectrometry; MS; Bioinformatics; Metabolite databases; Medicago truncatula Contents: 2. The metabolome; 3. Bioinformatics; 4. Applications of metabolomics to plant systems; 5. Future perspectives. Introduction: Recent advances in technology have revolutionized the visualization and querying of biological systems. Advances in genetics and automated nucleotide sequencing have enabled the large-scale physical mapping and sequencing of over twenty genomes, including Arabidopsis thaliana, rice, and humans. Expressed sequence tag (EST) sequencing and mRNA profiling using microarrays or serial analysis of gene expression (SAGE) now allow for comprehensive analysis of the transcriptome. Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics and systems biology. Functional genomics seeks to decipher unknown gene function. The functions of many genes revealed in large-scale sequencing projects can be inferred through nucleotide similarity with gene sequences of known function. However, there still remains a large number of predicted open reading frames (ORFs) that have no assigned function based on similarity. Thus, empirical methods of functional determination are required. Functional elucidation of genes can be pursued through the systematic perturbation of gene expression followed by quantitative and qualitative analyses of gene expression products including mRNA, protein, and now metabolite levels. Genetic perturbations can be achieved by mutations caused by chemicals or ionizing radiation, or by integration of foreign DNA sequences leading to either over- or under-expression of genes. Once expression has been altered, expression products are quantified through various profiling approaches and the resultant changes are assessed to infer gene function. Function may also be deciphered through analysis of co-responses. Systems biology is similar to functional genomics in its approach, but is slightly different in its objectives. Systems biology encompasses a holistic approach to the study of biology and the objective is to simultaneously monitor all biological processes operating as an integrated system. Through the study of systems, one can begin to visualize how individual pathways or metabolic networks are interconnected. This approach is based on solid theoretical frameworks and uses computer modeling to explain experimental observations. ItPlant metabolomics: large-scale phytochemistry in the functional genomics era Lloyd W. Sumner, Pedro Mendes, Richard A. Dixon Abstract: Metabolomics, or the large-scale phytochemical analysis of plants, is reviewed in relation to functional genomics and systems biology. The historical development of metabolite profiling into today's comprehensive metabolomics approach is provided. Technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry, are surveyed. The critical role of bioinformatics and various methods of data visualization are summarized, and the future role of metabolomics in plant science is assessed. Keywords: Metabolomics; Metabolic profiling; Metabolite profiling; Analytical instrumentation; Mass spectrometry; MS; Bioinformatics; Metabolite databases; Medicago truncatula Contents: 2. The metabolome; 3. Bioinformatics; 4. Applications of metabolomics to plant systems; 5. Future perspectives. Introduction: Recent advances in technology have revolutionized the visualization and querying of biological systems. Advances in genetics and automated nucleotide sequencing have enabled the large-scale physical mapping and sequencing of over twenty genomes, including Arabidopsis thaliana, rice, and humans. Expressed sequence tag (EST) sequencing and mRNA profiling using microarrays or serial analysis of gene expression (SAGE) now allow for comprehensive analysis of the transcriptome. Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics and systems biology. Functional genomics seeks to decipher unknown gene function. The functions of many genes revealed in large-scale sequencing projects can be inferred through nucleotide similarity with gene sequences of known function. However, there still remains a large number of predicted open reading frames (ORFs) that have no assigned function based on similarity. Thus, empirical methods of functional determination are required. Functional elucidation of genes can be pursued through the systematic perturbation of gene expression followed by quantitative and qualitative analyses of gene expression products including mRNA, protein, and now metabolite levels. Genetic perturbations can be achieved by mutations caused by chemicals or ionizing radiation, or by integration of foreign DNA sequences leading to either over- or under-expression of genes. Once expression has been altered, expression products are quantified through various profiling approaches and the resultant changes are assessed to infer gene function. Function may also be deciphered through analysis of co-responses. Systems biology is similar to functional genomics in its approach, but is slightly different in its objectives. Systems biology encompasses a holistic approach to the study of biology and the objective is to simultaneously monitor all biological processes operating as an integrated system. Through the study of systems, one can begin to visualize how individual pathways or metabolic networks are interconnected. This approach is based on solid theoretical frameworks and uses computer modeling to explain experimental observations. It