Perspective: use and reuse of NMR-based metabolomics data: what works and what remains challenging

Goncalo Jorge Gouveia; Thomas Head; Leo L Cheng; Chaevien S Clendinen; John R Cort; Xiuxia Du; Arthur S Edison; Candace C Fleischer; Jeffrey Hoch; Nathaniel Mercaldo; Wimal Pathmasiri; Daniel Raftery; Tracey B Schock; Lloyd W Sumner; Panteleimon G Takis; Valérie Copié; Hamid R Eghbalnia; Robert Powers

doi:10.1007/s11306-024-02090-6

Perspective: use and reuse of NMR-based metabolomics data: what works and what remains challenging

Metabolomics. 2024 Mar 13;20(2):41. doi: 10.1007/s11306-024-02090-6.

Authors

Goncalo Jorge Gouveia^{1

2}, Thomas Head^{1

3}, Leo L Cheng^{1

4}, Chaevien S Clendinen^{1

5}, John R Cort^{1

6}, Xiuxia Du^{1

7}, Arthur S Edison^{1

8}, Candace C Fleischer^{1

9}, Jeffrey Hoch^{1

10}, Nathaniel Mercaldo^{1

11}, Wimal Pathmasiri^{1

12}, Daniel Raftery^{1

13}, Tracey B Schock^{1

14}, Lloyd W Sumner^{1

15}, Panteleimon G Takis^{1

16

17}, Valérie Copié^{1

18}, Hamid R Eghbalnia^{1

10}, Robert Powers^{19

20}

Affiliations

¹ Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada.
² Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA.
³ University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
⁴ Department of Pathology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
⁶ Earth and Biological Sciences Directorate, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
⁷ Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9291 University City Blvd, Charlotte, NC, 28223, USA.
⁸ Department of Biochemistry, University of Georgia, Athens, GA, USA.
⁹ Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA.
¹⁰ Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06030-3305, USA.
¹¹ Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹² Department of Nutrition, School of Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
¹³ Department of Anesthesia and Pain Medicine, University of Washington, Seattle, WA, 98109, USA.
¹⁴ Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA.
¹⁵ Department of Biochemistry, MU Metabolomics Center, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA.
¹⁶ Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK.
¹⁷ Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK.
¹⁸ Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA.
¹⁹ Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada. rpowers3@unl.edu.
²⁰ Department of Chemistry, Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE, 68588-0304, USA. rpowers3@unl.edu.

PMID: 38480600
DOI: 10.1007/s11306-024-02090-6

Abstract

Background: The National Cancer Institute issued a Request for Information (RFI; NOT-CA-23-007) in October 2022, soliciting input on using and reusing metabolomics data. This RFI aimed to gather input on best practices for metabolomics data storage, management, and use/reuse.

Aim of review: The nuclear magnetic resonance (NMR) Interest Group within the Metabolomics Association of North America (MANA) prepared a set of recommendations regarding the deposition, archiving, use, and reuse of NMR-based and, to a lesser extent, mass spectrometry (MS)-based metabolomics datasets. These recommendations were built on the collective experiences of metabolomics researchers within MANA who are generating, handling, and analyzing diverse metabolomics datasets spanning experimental (sample handling and preparation, NMR/MS metabolomics data acquisition, processing, and spectral analyses) to computational (automation of spectral processing, univariate and multivariate statistical analysis, metabolite prediction and identification, multi-omics data integration, etc.) studies.

Key scientific concepts of review: We provide a synopsis of our collective view regarding the use and reuse of metabolomics data and articulate several recommendations regarding best practices, which are aimed at encouraging researchers to strengthen efforts toward maximizing the utility of metabolomics data, multi-omics data integration, and enhancing the overall scientific impact of metabolomics studies.

Keywords: Best practices; Mass spectrometry; Metabolomics; NMR; Use and reuse of metabolomics datasets.

Publication types

Review

MeSH terms

Automation
Magnetic Resonance Imaging*
Magnetic Resonance Spectroscopy / methods
Mass Spectrometry / methods
Metabolomics* / methods