Standardization in Metabolomics Experiments

A discussion forum of the Metabolomics Society for drafting a document on best practice, reporting and data exchange

Comprehensive analysis of metabolic responses (Metabolomics and Metabonomics) has been made possible and useful with the advent of modern computational and analytical tools in the 1990’s. In conjunction with sequenced genomes and online access to a wealth of medical and biological information, today metabolomics is applied to both clinical trials and fundamental research. In analogy to proteomic or transcriptomic experiments, a great richness in data is acquired in global metabolic studies.

Potentially, such data could be re-used by other researchers using different bioinformatics or chemometric techniques. However, standards are lacking that guide researchers to report in detail how data were actually acquired, which experimental designs were used, and how data were processed and structured to eventually reason scientific conclusions. Furthermore, the flexibility of metabolism and the need for validation of disease biomarkers or biochemical events across different diseases requires comparison of different metabolomic datasets between laboratories and beyond specific techniques. However, without establishment of a common ontology and structure how metabolomic data should be reported, comparisons will be disabled despite the willingness of most researchers to report details on experimental procedures and other metadata.

Therefore, metabolomic researchers have undertaken great efforts in standardizing reporting structures culminating in two larger research papers (Lindon J.C. et al. Nat. Biotechnol. 2005, 23, 833-838 , Jenkins H. et al. Nat. Biotechnol. 2004, 22, 1601-1605) and two discussion conferences in summer 2005, MetaboMeeting 1.0 in Cambridge, U.K. and the Metabolomics Standards workshop hosted by the NIH/NIDDK in Bethesda, USA.

Resulting from these efforts were agreements to write a draft document on ‘Reporting standards in Metabolomics’ that aims at reaching a consensus and that might therefore serve as guideline for researchers, journals, funding and scientific organizations, vendors and regulatory bodies.

Scope

The scope of these efforts will be to identify, develop and disseminate best practice in all aspects of metabolomics. The aim will not be to prescribe how to do metabolomics experiments but to formulate a minimum of reporting standards that describe the experiments. Consequently, there will be no attempt to restrict or dictate specific practices but to develop better descriptors to support the dissemination and re-use of metabolomic data. Such reporting standards will specify the data identified as necessary for complete and comprehensive reporting in a range of identified contexts, such as submission to academic journals. Data exchange standards will be developed to provide a technical vehicle which meets or exceeds the requirements of reporting standards.

Recent papers

Fiehn O, Kristal B, v Ommen B, Sumner LW, Sansone SA, Taylor C, Hardy N, Kaddurah-Daouk R (2006) Establishing Reporting Standards for Metabolomic and Metabonomic Studies: A Call for Participation. OMICS 10, 158-163

Castle LA, Fiehn O, Kaddurah-Daouk R, Lindon JC (2006) Metabolomics standards workshop and the development of international standards for reporting metabolomics experimental results. Brief. Bioinformatics 7, 159-165

More Information

For information on working groups and progress please go to http://msi-workgroups.sourceforge.net/