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.
Fiehn
Oliver
O
Davis Genome Center, University of California, Davis, CA 95616, USA. ofiehn@ucdavis.edu
Wohlgemuth
Gert
G
Scholz
Martin
M
Kind
Tobias
T
Lee
Do Yup
DY
Lu
Yun
Y
Moon
Stephanie
S
Nikolau
Basil
B
D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002138:Calibration; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods / Q000592:standards; D005838:Genotype; D008660:Metabolism; D012275:Oryza / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010936:Plant Extracts / Q000032:analysis / Q000302:isolation & purification / Q000592:standards; D018515:Plant Leaves / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011786:Quality Control; D015203:Reproducibility of Results; D013025:Glycine max / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D010936:Plant Extracts