Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)
Open accessAbstract
There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at http://msi-workgroups.sourceforge.net/ or http://Msi-workgroups-feedback@lists.sourceforge.net. Further, community input related to this document can also be provided via this electronic forum.
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Most reported substances were level 3 identifications or putatively characterized compound classes according to the Metabolomics Standards Initiative.
“Despite most of the reported substances being ‘level 3’ identifications, or belonging to ‘putatively characterized compound classes’ (focusing on their accurate mass and spectral similarity to known compounds) [44], according to the Metabolomics Standards Initiative [45]”
From Pharmacometabolomics Study of Sulfamethoxazole and Trimethoprim in Kidney Transplant Recipients: Real-World Metabolism and Urinary Excretion (2025) · cites this paper as [45]
An extension of the metabolomics standard initiative guidelines was used to assign annotation level confidence.
“An extension of the metabolomics standard initiative guidelines was used to assign annotation level confidence82,83.”
From An iPSC-derived astrocyte model of fragile X syndrome exhibits dysregulated cholesterol homeostasis (2023) · cites this paper as [82]
No standard currently exists for reporting chemical identification of biomarkers in metabolomic studies.
“In addition, no standard yet exists to report chemical identification of biomarkers in metabolomic studies (110).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [110]
The Metabolomics Standards Initiative launched by the Metabolomics Society has already had significant impact on reporting formats in metabolomics.
“The Metabolomics Standards Initiative (MSI) launched by the Metabolomics Society is an example of such an initiative, and the MSI has already had significant impact on reporting formats in metabolomics (110, 188).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [110]
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- Authors
- Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W.-M., Fiehn, O., Goodacre, R., Griffin, J. L., Hankemeier, T., Hardy, N., Harnly, J., Higashi, R., Kopka, J., Lane, A. N., Lindon, J. C., Marriott, P., Nicholls, A. W., Reily, M. D., Thaden, J. J., & Viant, M. R.
- Affiliations
- Noble Research Institute (US)
- Sanofi (Germany) (DE)
- University of Nottingham (GB)
- Rothamsted Research (GB)
- National Center for Toxicological Research (US)
- University of Louisville (US)
- Max Planck Society (DE)
- University of Manchester (GB)
- University of Cambridge (GB)
- Leiden University (NL)
- Aberystwyth University (GB)
- Agricultural Research Service (US)
- Imperial College London (GB)
- RMIT University (AU)
- GlaxoSmithKline (United Kingdom) (GB)
- Pfizer (United States) (US)
- University of Arkansas for Medical Sciences (US)
- University of Birmingham (GB)
- ORCID
- Venue
- Metabolomics
- Published
- 2007-09-12
- Volume
- 3
- Issue
- 3
- Pages
- 211-221
- ISSN
- 1573-3882 (ISSN-L)
- 1573-3890
- PMC
- PMC3772505
- OpenAlex
- W1611854178
- Cited by
- 5,368
- References
- 14
- Citations by year
- 2026: 823 · 2025: 552 · 2024: 513 · 2023: 457 · 2022: 471 · 2021: 506 · 2020: 468 · 2019: 368 · 2018: 263 · 2017: 206 · 2016: 177 · 2015: 155 · 2014: 128 · 2013: 99 · 2012: 39
- FWCI
- 11.93
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Metabolomics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Rothamsted Repository (Rothamsted Repository) (submittedVersion)
- RMIT Research Repository (RMIT University Library) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Figshare (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Institutes of Health (Y01 OD001298)
- Biotechnology and Biological Sciences Research Council (BB/D525121/1, BB/C519038/1, BB/D006422/1, BBS/E/C/00004559)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- minimum reporting standards, chemical analysis, sample preparation, quality control, metabolite identification, data preprocessing, mass spectrometry, NMR spectroscopy, metadata
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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