Best Practices in NMR Metabolomics: Current State

Robert Powers¹, Erik R Andersson², Amanda L Bayless³, Robert B Brua⁴, Mario C Chang⁵, Leo L Cheng⁶, Chaevien S Clendinen⁷, Darcy Cochran¹, Valérie Copié⁸, John R Cort⁷, Alexandra A Crook¹, Hamid R Eghbalnia⁹, Anthony Giacalone⁶, Goncalo J Gouveia¹⁰, Jeffrey C Hoch⁹, Micah J Jeppesen¹, Amith S Maroli¹, Matthew E Merritt⁵, Wimal Pathmasiri¹¹, Heidi E Roth¹, Anna Rushin⁵, Isin T Sakallioglu¹, Saurav Sarma¹², Tracey B Schock³, Lloyd W Sumner¹², Panteleimon Takis¹³, Mario Uchimiya¹⁴, David S Wishart¹⁵; Metabolomics Association of North America (MANA), NMR Special Interest Group; Metabolomics Quality Assurance & Quality Control Consortium (mQACC), NMR Technology Group

Affiliations

¹ Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
² Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA.
³ National Institute of Standards and Technology (NIST), Chemical Sciences Division, Charleston, SC 29412, USA.
⁴ Environment and Climate Change Canada, National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, Saskatchewan S7N 3H5, Canada.
⁵ Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32611, USA.
⁶ Department of Pathology and Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁷ Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
⁸ Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA.
⁹ Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
¹⁰ Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, Maryland, 20850, USA.
¹¹ Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
¹² University of Missouri, Department of Biochemistry, MU Metabolomics Center, Bond Life Sciences Center, Interdisciplinary Plant Group, Columbia, MO 65211, USA.
¹³ Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK.
¹⁴ Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
¹⁵ Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.

PMID: 40237011
PMCID: PMC11999570
DOI: 10.1016/j.trac.2023.117478

Best Practices in NMR Metabolomics: Current State

Robert Powers et al. Trends Analyt Chem. 2024 Feb.

. 2024 Feb:171:117478.

doi: 10.1016/j.trac.2023.117478. Epub 2023 Dec 12.

Authors

Affiliations

¹ Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
² Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA.
³ National Institute of Standards and Technology (NIST), Chemical Sciences Division, Charleston, SC 29412, USA.
⁴ Environment and Climate Change Canada, National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, Saskatchewan S7N 3H5, Canada.
⁵ Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32611, USA.
⁶ Department of Pathology and Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁷ Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
⁸ Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA.
⁹ Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
¹⁰ Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, Maryland, 20850, USA.
¹¹ Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
¹² University of Missouri, Department of Biochemistry, MU Metabolomics Center, Bond Life Sciences Center, Interdisciplinary Plant Group, Columbia, MO 65211, USA.
¹³ Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK.
¹⁴ Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
¹⁵ Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.

PMID: 40237011
PMCID: PMC11999570
DOI: 10.1016/j.trac.2023.117478

Abstract

A literature survey was conducted to identify current practices used by NMR metabolomics investigators when conducting and reporting their metabolomics studies. A total of 463 papers from 2020 and 80 papers from 2010 were selected from PubMed and were manually analyzed by a team of investigators to assess the extent and completeness of the experimental procedures and protocols reported. A significant number of the papers did not report on essential experimental details, incompletely stated which statistical methods were used, improperly applied supervised multivariate statistical analyses, or lacked validation of statistical models. A large diversity of protocols and software were identified, which suggests a lack of consensus and a relatively limited use of commonly agreed upon standards for conducting and reporting NMR metabolomics studies. The overall intent of the survey is to inform and encourage the NMR metabolomics community to develop and adopt best-practices for the field.

Keywords: Best Practices; Literature survey; Metabolomics; NMR.

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