Standardization in Metabolomics Experiments
A discussion forum of the Metabolomics Society for best practice in reporting metabolomics experiments 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 fundamental and translational research. Large laboratories are moving towards the acquisition of datasets with 1000s of samples, while smaller labs are beginning to work together to tackle large problems, such as species metabolomes. 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. Furthermore, the re-use of data may have significant financial savings, avoiding laboratories from acquiring data on common model organisms, and instead cross comparing their data with archived studies. 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. Without this information it is impossible to assess whether two studies can be compared. 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.
The first reporting requirements
Resulting from these efforts were agreements to write draft documents on 'Reporting standards in Metabolomics' that aimed at reaching a consensus and that might therefore serve as guideline for researchers, journals, funding and scientific organizations, vendors and regulatory bodies. This culminated in the publication of a number of reporting requirements for different types of study as well as an over-arching article detailing the overall framework: The metabolomics standards initiative. MSI Board Members, Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. Nat Biotechnol. 2007 Aug;25(8):846-8. The metabolomics standards initiative is also described at: http://link.springer.com/article/10.1007/s11306-007-0070-6 along with a number of the specific guidelines for particular types of experiments.
The scope of these efforts was to identify, develop and disseminate best practice in the reporting of metabolomics experiments. The aim was not be to prescribe how to do metabolomics experiments but to formulate a minimum of reporting standards that describe the experiments. Consequently, in the documents there is 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 specify the data identified as necessary for complete and comprehensive reporting in a range of identified contexts, such as submission to academic journals. These requirements have been adopted by a number of journals including Metabolomics, the Nature journals and BMC journals.
There are currently a number of issues aimed at developing these standards further and adopting them across the research community.
MetaboLights: is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. www.ebi.ac.uk/metabolights
ISAtab: The open source ISA metadata tracking tools helps to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Built around the 'Investigation' (the project context), 'Study' (a unit of research) and 'Assay' (analytical measurement) general-purpose Tabular format, the ISA tools helps provide a rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable. The tool is based on standard ontology for a range of biological approaches, including the MSI initiative. http://isa-tools.org
COSMOS- COordination Of Standards In MetabOlomicS is a FP7 EU Initiative bringing together leading researchers and bioinformaticians of the European metabolomics community, members of the Metabolomics Society, instrument and software vendors along with other stakeholders worldwide. The aim is to develop a robust data infrastructure for metabolomics data representation and exchange, to support workflows for a broad range of metabolomics applications. http://cosmos-fp7.eu
The metabolomics standards initiative. MSI Board Members, Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. Nat Biotechnol. 2007 Aug;25(8):846-8.
The metabolomics standards initiative (MSI). Oliver Fiehn, Don Robertson, Jules Griffin, Mariet van der Werf, Basil Nikolau, Norman Morrison, Lloyd W. Sumner, Roy Goodacre, Nigel W. Hardy, Chris Taylor, Jennifer Fostel, Bruce Kristal, Rima Kaddurah-Daouk, Pedro Mendes, Ben van Ommen, John C. Lindon & Susanna-Assunta Sansone, Metabolomics Volume 3, Issue 3 , pp 175-178
Toward interoperable bioscience data. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Nat Genet. 2012 Jan 27;44(2):121-6.
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C. Nucleic Acids Res. 2013 Jan;41(Database issue):D781-6.
For information on working groups and progress please go to http://msi-workgroups.sourceforge.net