Metabolite profiling: from diagnostics to systems biology

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.

[1]  H. Sauter,et al.  Metabolic profiling of plants: a new diagnostic technique , 1991 .

[2]  R. A. Zeeuw,et al.  HPLC-UV ATMOSPHERIC-PRESSURE IONIZATION MASS-SPECTROMETRIC DETERMINATION OF THE DOPAMINE-D2 AGONIST N-0923 AND ITS MAJOR METABOLITES AFTER OXIDATIVE-METABOLISM BY RAT-LIVER, MONKEY LIVER, AND HUMAN LIVER-MICROSOMES , 1993 .

[3]  H. Kacser,et al.  The control of flux. , 1995, Biochemical Society transactions.

[4]  M. Jacob,et al.  Screening blood spots for inborn errors of metabolism by electrospray tandem mass spectrometry with a microplate batch process and a computer algorithm for automated flagging of abnormal profiles. , 1997, Clinical chemistry.

[5]  S. Fields,et al.  A biochemical genomics approach for identifying genes by the activity of their products. , 1999, Science.

[6]  Stephen E. Stein,et al.  An Integrated Method for Spectrum Extraction and Compound Identification from GC/MS Data , 1999 .

[7]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[8]  S. Stein,et al.  Deconvolution gas chromatography/mass spectrometry of urinary organic acids--potential for pattern recognition and automated identification of metabolic disorders. , 1999, Rapid communications in mass spectrometry : RCM.

[9]  S. Stein An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data , 1999 .

[10]  R. Trethewey,et al.  Metabolic profiling: a Rosetta Stone for genomics? , 1999, Current opinion in plant biology.

[11]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[12]  E Holmes,et al.  NMR spectroscopy based metabonomic studies on the comparative biochemistry of the kidney and urine of the bank vole (Clethrionomys glareolus), wood mouse (Apodemus sylvaticus), white toothed shrew (Crocidura suaveolens) and the laboratory rat. , 2000, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[13]  B. Palsson,et al.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.

[14]  Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. , 2001, The Plant cell.

[15]  Thomas Linke,et al.  Visualizing plant metabolomic correlation networks using clique-metabolite matrices , 2001, Bioinform..

[16]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[17]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[18]  N Aranìbar,et al.  Automated mode-of-action detection by metabolic profiling. , 2001, Biochemical and biophysical research communications.

[19]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[20]  Ute Roessner,et al.  Metabolic Profiling Allows Comprehensive Phenotyping of Genetically or Environmentally Modified Plant Systems , 2001, Plant Cell.

[21]  J. Pawliszyn,et al.  Verapamil drug metabolism studies by automated in-tube solid phase microextraction. , 2002, Journal of pharmaceutical and biomedical analysis.

[22]  Nigel W. Hardy,et al.  Plant Metabolomics , 2002, The Plant Cell Online.

[23]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[24]  J. Nicholson,et al.  Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics , 2002, Nature Medicine.

[25]  Min Pan,et al.  Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Meiler,et al.  Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra. , 2002, Journal of the American Chemical Society.

[27]  Lloyd W Sumner,et al.  Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer. , 2002, Phytochemistry.

[28]  D. Goodenowe,et al.  Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. , 2002, Omics : a journal of integrative biology.

[29]  J Bruce German,et al.  Metabolomics and biochemical profiling in drug discovery and development. , 2002, Current opinion in molecular therapeutics.

[30]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[31]  Esther J Kok,et al.  Comparative safety assessment for biotech crops. , 2003, Trends in biotechnology.

[32]  Fernando Carrari,et al.  Metabolic Profiling of Transgenic Tomato Plants Overexpressing Hexokinase Reveals That the Influence of Hexose Phosphorylation Diminishes during Fruit Development , 2003, Plant Physiology.

[33]  J. Thornton,et al.  A structure-based anatomy of the E.coli metabolome. , 2003, Journal of molecular biology.

[34]  Manor Askenazi,et al.  Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains , 2003, Nature Biotechnology.

[35]  D. Kell,et al.  High-throughput classification of yeast mutants for functional genomics using metabolic footprinting , 2003, Nature Biotechnology.

[36]  Jian Yang,et al.  Metabolomics spectral formatting, alignment and conversion tools (MSFACTs) , 2003, Bioinform..

[37]  R. Brereton,et al.  Evaluation of chemometric methods for determining the number and position of components in high-performance liquid chromatography detected by diode array detector and on-flow 1H nuclear magnetic resonance spectroscopy , 2003 .

[38]  I. Wilson,et al.  Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism , 2003, Nature Reviews Drug Discovery.

[39]  B. Matuszewski,et al.  Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. , 2003, Analytical chemistry.

[40]  Partha S. Vasisht Computational Analysis of Microarray Data , 2003 .

[41]  M. Tomita,et al.  Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. , 2003, Journal of proteome research.

[42]  J. Kopka,et al.  Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. , 2003, Phytochemistry.

[43]  HPLC-NMR-MS: past, present and future. , 2003, Drug discovery today.

[44]  R. Goodacre,et al.  Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis , 2003, Springer US.

[45]  W. Weckwerth Metabolomics in systems biology. , 2003, Annual review of plant biology.

[46]  J. Selbig,et al.  Parallel analysis of transcript and metabolic profiles: a new approach in systems biology , 2003, EMBO reports.

[47]  J. Haselden,et al.  Use of liquid chromatography/time-of-flight mass spectrometry and multivariate statistical analysis shows promise for the detection of drug metabolites in biological fluids. , 2003, Rapid communications in mass spectrometry : RCM.

[48]  Marcus Fehr,et al.  In Vivo Imaging of the Dynamics of Glucose Uptake in the Cytosol of COS-7 Cells by Fluorescent Nanosensors* , 2003, Journal of Biological Chemistry.

[49]  A. Aharoni,et al.  Terpenoid Metabolism in Wild-Type and Transgenic Arabidopsis Plants Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016253. , 2003, The Plant Cell Online.

[50]  Douglas B. Kell,et al.  Functional Genomics Via Metabolic Footprinting: Monitoring Metabolite Secretion by Escherichia Coli Tryptophan Metabolism Mutants Using FT–IR and Direct Injection Electrospray Mass Spectrometry , 2003, Comparative and functional genomics.

[51]  Karl-Heinz Engel,et al.  A methodology for automated comparative analysis of metabolite profiling data , 2003 .

[52]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[53]  O. Fiehn Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[54]  D. Kell Metabolomics and systems biology: making sense of the soup. , 2004, Current opinion in microbiology.