Application Notes

Application Notes

Quality Control for Plant Metabolomics: Reporting MSI-compliant Studies

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.

From – The Plant Journal (2008) 53, 691-704

Oliver Fiehn1,* , Gert Wohlgemuth1 , Martin Scholz1 , Tobias Kind1 , Do Yup Lee1 , Yun Lu1 , Stephanie Moon2 and Basil Nikolau2

1Davis Genome Center, University of California, Davis, CA 95616, USA, and

2Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA