Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
Open accessAbstract
Mass spectrometry (MS) techniques, because of their sensitivity and selectivity, have become methods of choice to characterize the human metabolome and MS-based metabolomics is increasingly used to characterize the complex metabolic effects of nutrients or foods. However progress is still hampered by many unsolved problems and most notably the lack of well established and standardized methods or procedures, and the difficulties still met in the identification of the metabolites influenced by a given nutritional intervention. The purpose of this paper is to review the main obstacles limiting progress and to make recommendations to overcome them. Propositions are made to improve the mode of collection and preparation of biological samples, the coverage and quality of mass spectrometry analyses, the extraction and exploitation of the raw data, the identification of the metabolites and the biological interpretation of the results.
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Untargeted metabolomics-based methods are time-consuming and require complex sample preparation steps, including extraction, purification, and sometimes derivatization or modification of metabolites.
“Although these methods have significant advantages for the identification of marker compounds, these techniques are time-consuming, and complex sample preparation steps are needed, including extraction, purification of samples, and in some instances, the derivatization/modification of metabolites [13].”
From Rapid metabolic fingerprinting with the aid of chemometric models to identify authenticity of natural medicines: Turmeric, Ocimum, and Withania somnifera study (2023) · cites this paper as [13]
The Sampling strategy for metabolomics section (page unavailable) describes complex extraction and necessary protein removal for blood samples; the Mass spectrometry for metabolomics section (page unavailable) describes derivatization for some GC–MS and RPLC–MS analyses. The paper does not establish that untargeted methods generally require purification or are time-consuming: its explicit time estimate concerns supervised data processing, not sample preparation, and it also describes LC–MS as allowing fast analysis. (LLM, conf=0.86)
Experimental — accuracy not yet measuredNMR is robust, nondestructive, and quantitative but has relatively low sensitivity, limiting its coverage of the food metabolome to predominant nutrients, sugars, and microbial metabolites at millimolar to micromolar concentrations.
“Briefly, NMR is robust, nondestructive, and quantitative but has a relatively low sensitivity, which narrows its coverage of the food metabolome to predominant nutrients, sugars, and microbial metabolites present at millimolar to micromolar concentrations.”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [112]
Several training workshops on metabolomics and nutrition were supported by the Nutrigenomics Organization.
“Several training workshops on metabolomics and nutrition were supported by the Nutrigenomics Organization (112).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [112]
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The food metabolome: a window over dietary exposure
Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.076133 · Cited by 519 · see citing works
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“Although circulating concentrations of amino acids are subject to homeostatic control (3) they are also affected by diet, metabolism, lifestyle and genetic factors (4).”
Self-citationImpact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
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bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis
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Self-citationThe complex links between dietary phytochemicals and human health deciphered by metabolomics
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Self-citationECMDB: the E-coli Metabolome Database
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Khan, S., Rai, A. K., Singh, A., Singh, S., Dubey, B. K., Lal, R. K., Negi, A. S., Birse, N., Trivedi, P. K., Elliott, C. T., et al. (2023) · Journal of Pharmaceutical Analysis · doi:10.1016/j.jpha.2023.04.018 · Cited by 34 · see citing works
“…these methods have signi fi cant advantages for the iden-ti fi cation of marker compounds, these techniques are time-consuming, and complex sample preparation steps are needed, including extraction, puri fi cation of samples, and in some instances, the derivatization/modi fi cation of metabolites [13].”
Method
- Authors
- Scalbert, A., Brennan, L., Fiehn, O., Hankemeier, T., Kristal, B. S., van Ommen, B., Pujos-Guillot, E., Verheij, E., Wishart, D., & Wopereis, S.
- Affiliations
- Unité de Nutrition Humaine (FR)
- University College Dublin (IE)
- University of California, Davis (US)
- Leiden University (NL)
- Brigham and Women's Hospital (US)
- University of Alberta (CA)
- Corresponding author
- Scalbert, Augustin
- ORCID
- Venue
- Metabolomics
- Published
- 2009-06-12
- Volume
- 5
- Issue
- 4
- Pages
- 435-458
- ISSN
- 1573-3882 (ISSN-L)
- 1573-3890
- PMC
- PMC2794347
- OpenAlex
- W2142923621
- Cited by
- 565
- References
- 159
- Citations by year
- 2026: 19 · 2025: 18 · 2024: 17 · 2023: 17 · 2022: 38 · 2021: 30 · 2020: 33 · 2019: 42 · 2018: 37 · 2017: 37 · 2016: 44 · 2015: 42 · 2014: 38 · 2013: 54 · 2012: 43
- FWCI
- 13.30
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Metabolomics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- HAL (submittedVersion)
- TNO Repository (submittedVersion)
- Repository hosted by TU Delft Library (TU Delft) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- National Institute on Aging (R01AG025872, R01AG028996)
- National Cancer Institute (R01CA102536)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK040561)
- National Institute of Environmental Health Sciences (U01ES016048)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- mass spectrometry-based metabolomics, human metabolome, dietary intervention, metabolite identification, sample collection and preparation, metabolite extraction, data analysis, method standardization
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