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

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

Research output: Contribution to journalArticlepeer-review

97 Citations (Scopus)


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: 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.
Original languageEnglish
Pages (from-to)479-496
Number of pages18
Issue number4
Publication statusPublished - Dec 2009


  • Metabolomics
  • GC–MS
  • GC×GC–MS
  • Inter-laboratory reproducibility
  • Rice
  • Melon
  • Broccoli


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