Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics View Full Text


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Article Info

DATE

2009-07-24

AUTHORS

J. William Allwood, Alexander Erban, Sjaak de Koning, Warwick B. Dunn, Alexander Luedemann, Arjen Lommen, Lorraine Kay, Ralf Löscher, Joachim Kopka, Royston Goodacre

ABSTRACT

The application of gas chromatography-mass spectrometry (GC-MS) to the 'global' analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project's (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC-MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GCxGC-TOF/MS was compared with 1 dimensional GC-TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise. More... »

PAGES

479-496

References to SciGraph publications

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  • 2007-08-25. Proposed minimum reporting standards for data analysis in metabolomics in METABOLOMICS
  • 2004-09. Metabolite profiling: from diagnostics to systems biology in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2007-09-06. A roadmap for the establishment of standard data exchange structures for metabolomics in METABOLOMICS
  • 2008-08-27. Metabolomic analysis of the interaction between plants and herbivores in METABOLOMICS
  • 2007. Nonsupervised Construction and Application of Mass Spectral and Retention Time Index Libraries From Time-of-Flight Gas Chromatography-Mass Spectrometry Metabolite Profiles in METABOLOMICS
  • 1986. Principal Component Analysis in NONE
  • 2007-04-24. A comparative study of amino acid measurement in leaf extracts by gas chromatography-time of flight-mass spectrometry and high performance liquid chromatography with fluorescence detection in METABOLOMICS
  • 2000-11. Metabolite profiling for plant functional genomics in NATURE BIOTECHNOLOGY
  • 2006-06-27. Gas chromatography mass spectrometry–based metabolite profiling in plants in NATURE PROTOCOLS
  • 2004-12-06. A proposed framework for the description of plant metabolomics experiments and their results in NATURE BIOTECHNOLOGY
  • 1999-02. Variation in sugar levels and invertase activity in mature fruit representing a broad spectrum of Cucumis melo genotypes in GENETIC RESOURCES AND CROP EVOLUTION
  • 2007-04-05. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry in NATURE PROTOCOLS
  • 2006-01-01. Chemometrics in Metabolomics — An Introduction in PLANT METABOLOMICS
  • 2007-08-23. Minimum reporting standards for plant biology context information in metabolomic studies in METABOLOMICS
  • 2007-09-12. Proposed minimum reporting standards for chemical analysis in METABOLOMICS
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    DOI

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    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20376177


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    22 schema:description The application of gas chromatography-mass spectrometry (GC-MS) to the 'global' analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project's (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC-MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GCxGC-TOF/MS was compared with 1 dimensional GC-TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise.
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    31 GC-TOF/MS
    32 GCxGC-TOF/MS
    33 MS
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    37 analysis method
    38 analysis of metabolites
    39 analytical method variants
    40 applications
    41 aspects
    42 assessment
    43 chromatography-mass spectrometry
    44 comparison
    45 complex matrices
    46 complex samples
    47 comprehensive GCxGC-TOF/MS
    48 data
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    51 data-rich profiles
    52 database
    53 dataset
    54 development
    55 dimensional GC-TOF/MS
    56 equal performance
    57 exemplary dataset
    58 experiments
    59 fast gas
    60 features
    61 flight mass spectrometry
    62 further investigation
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    67 identical models
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    72 major metabolite features
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    75 metabolite features
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    79 method
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    86 performance
    87 plant metabolomics
    88 preparation
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