Reporting Standards & Protocols

The variety and complexity of omics data mean that interpretation of results is often difficult without knowledge of a number of experimental factors. The subtleties of instrumental setup and the ontologies used to describe both experiments and profile components have often led to a reporting of variable quality and completeness. In the transcriptomics community, the development of the Minimum Information About a Microarray Experiment (MIAME) has promoted the use of a set of parameters that can be easily interpreted and can be verified independently and has served as a useful framework for experimental description, especially when the deposition of data to central community archives is considered. CSM are involved in several efforts to improve various aspects of reporting and protocol use across the metabolic profiling, chemometrics and systems biology communities.

The standard protocols for biofluid collection, storage and analysis that have been developed in CSM continue to be published in leading journals and serve as a reference for those seeking to establish metabonomics as a component in their own studies.

Key Recent Publications

Beckonert O, Keun HC, Ebbels TM, Bundy J, Holmes E, Lindon JC, Nicholson JK. 2007. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2(11):2692-703.

Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TWM, Fiehn O, Goodacre R, Griffin JL and others. 2007. Proposed minimum reporting standards for chemical analysis. Metabolomics 3(3):211-21.

Morrison N, Bearden D, Bundy JG, Collette T, Currie F, Davey MP, Haigh NS, Hancock D, Jones OAH, Rochfort S and others. 2007. Standard reporting requirements for biological samples in metabolomics experiments: environmental context. Metabolomics 3(3):203-10.

Teahan O, Gamble S, Holmes E, Waxman J, Nicholson JK, Bevan C, Keun HC. 2006. Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem 78(13):4307-18.