Quality control for plant metabolomics: reporting MSI-compliant studies
Article first published online: 4 FEB 2008
© 2008 The Authors
The Plant Journal
Volume 53, Issue 4, pages 691–704, February 2008
How to Cite
Fiehn, O., Wohlgemuth, G., Scholz, M., Kind, T., Lee, D. Y., Lu, Y., Moon, S. and Nikolau, B. (2008), Quality control for plant metabolomics: reporting MSI-compliant studies. The Plant Journal, 53: 691–704. doi: 10.1111/j.1365-313X.2007.03387.x
- Issue published online: 4 FEB 2008
- Article first published online: 4 FEB 2008
- Received 22 October 2007; revised 26 November 2007; accepted 27 November 2007.
- standard operating procedure;
- abiotic stress;
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.