Quality control for plant metabolomics: Reporting MSI-compliant studies

Oliver Fiehn, Gert Wohlgemuth, Martin Scholz, Tobias Kind, Do Yup Lee, Yun Lu, Stephanie Moon, Basil Nikolau

Research output: Contribution to journalArticlepeer-review

413 Scopus citations


The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study - the metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.

Original languageEnglish (US)
Pages (from-to)691-704
Number of pages14
JournalPlant Journal
Issue number4
StatePublished - Feb 2008


  • Abiotic stress
  • BinBase
  • GC/MS
  • SetupX
  • Standard operating procedure
  • Wounding

ASJC Scopus subject areas

  • Plant Science


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