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  • Brief Communication
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Enhancing untargeted metabolomics using metadata-based source annotation

Nature Biotechnology volume 40, pages 1774–1779 (2022)Cite this article

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An Author Correction to this article was published on 18 October 2023

This article has been updated

Abstract

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.

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Fig. 1: The concept of an RDD-based analysis workflow.
Fig. 2: RDD with food reference data.

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Data availability

The following files are available in addition to the Global FoodOmics mzXML files on https://massive.ucsd.edu under MSV000084900: metadata as a.txt; an image repository with between one and six images per food item that was sampled; table of FDR-based parameters; full size PDF of sleep restriction and circadian misalignment study; food reference data molecular network (excerpts found in Fig. 1). A metadata dictionary can also be accessed here: https://docs.google.com/spreadsheets/d/1Ebn-TgMWEkd_7KOw9TCRvHGPsE7dGjVCr7dg28pwbmM/edit#gid=727944641. The accessions numbers to the raw metabolomics data files available via Supplementary Table 2. The GNPS-based molecular networking analyses jobs used in this study can be accessed online at the following links: sleep and circadian study (MSV000083759, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=e0bf255bcb2e492bb0be3be1a691b5fb, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6fe434761daf4f9da540cf1fd90b3985, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=9a90bd12f51e453e968656e6458e0da4); centenarian (MSV000084591, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=8895b6e3445546c4a5bc3a726a920227, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=981c9a7d39f742bda296d52f856981e5); impact of diet on rheumatoid arthritis (MSV000084556, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=0794151fce2c4c18a7a0aa3a09140169); LP infant (MSV000083462, MSV000083463, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a7b222466ef844e69cdbd9835d2f6c39, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c756a9dfb5c34a2a8655f88114edf0a8, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=4a322e640bb644068030949267fb4ea9); children with medical complexity (MSV000084610, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=df24423835a341969342c2086b46275a); american gut (MSV000081981, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=4884483bcffe4f269819858c3fd4faef); fermented food consumption (MSV000081171, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=5cca39e0ebab4066a56e41ded48b4466); Malawi legume supplement (MSV000081486, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=93ba727aa9234727a73ae7860b2af3ca); Rotarix vaccine response (MSV000084218, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=08e9b9e048f04ac4b416e574a073e8e6); IBD_1 (MSV000082431; https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=ec08eed8f186430d893c63111409baf4); IBD_individual (MSV000079115, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=fad746939afd4184975a296436aebfb7); IBD_seed (MSV000082221, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=907f2e0b7878417dbdb4c83f0df0e83a); IBD_biobank (MSV000079777, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a79fbd4c96124209adfd0ef84cb56dec); IBD_2 (MSV000084775, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=07f855658c5342458045032ea70fc526); IBD_200 (MSV000084908, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=55bef02250d744eb97c6040c379cbfb4); Alzheimer’s disease (MSV000085256, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=aac78e9d23b84194ab2f768cb685c636); Alzheimer’s disease serum (MSV000086270, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=570aacf2244948c7afa590631de5d345); omnivore versus vegan (MSV000086989, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=74089e95b8df41b2af7c289869dc866f); COVID-19 (MSV000085505, MSV000085537, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=9cbcb6b46fe24826bc56c9e893d0bd2b); IBD_biopsy (MSV000082220, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a83a279dad154f9ca7b549d40ce117ba); gout (MSV000084908, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=55bef02250d744eb97c6040c379cbfb4); adult saliva (MSV000083049, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6dd6e5b1cf454d67b8a2b3c151c18f4a); legume supplementation (MSV000084663, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=93ba727aa9234727a73ae7860b2af3ca); tomato seedling (MSV000083353, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=3b6020d7034045c39969631894ae4c22); food only (MSV000084900, https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=d5adba7f67cc402396e9ba7cd85ce52b). Networking parameters were set on the basis of the MOLECULAR-LIBRARYSEARCH-FDR workflow on GNPS with the following task IDs: GFOP3500, a7bf6cc3f91d466bab923f2268d6f4fc; sleep deprivation, b55ab4004ed342d7b4ed1c488e935998; sleep study, 78bbfed8574748d1a77dc7c2f1a44d39; sleep study_SSF_test, b55ab4004ed342d7b4ed1c488e935998; centenarian, 265a9553c69e47499cca3de056b43178; centenarian_SSF_test, 265a9553c69e47499cca3de056b43178; American gut, aee5dde3b2f84079a264e68ec981487e; fermented food consumption, a44d1b2e1b9d4612974d0b85021675a7; Malawi legume supplement, de7b55f8adaa4ad9b2a8430e30435bf3; children with medical complexity, f27243af071b43ab90d846bda959fc1c; Rotarix vaccine response, a2e02e3f97a54ca08e3866cc60f8d42b; impact of diet on rheumatoid arthritis, 62b8754e761549f3b94ffae83d7ab95a; LP infant, 532aba2ad3644fadba0e6e7ea063c7ee; IBD_1, bb10b1ce90a24f3a9cef1e85e88c3882; IBD_biopsy, c4cfda90933b4842a7154f5f2def139d; IBD_individual, 3ce8cc636ae944848b4ada322aaf12fe; IBD_seed, ebbb715fc605457ba5f7e910b79d6177; IBD_biobank, 9465c34cf5444e12b89318b1fb363714; IBD_2, 983fa9271136404fb5743b44a6a109f0; IBD_200, e5acf5726722486caa897b2b07d402e8; Alzheimer’s disease, 658103164325425981c097cecba840b0; Alzheimer’s disease serum, 67516099b37647f2a9c91f890366bef3; omnivore versus vegan, ba974d08cab04f77aaacdb7828baada6; gout, a478f419ae824378aa02e5e1b310cad2; adult saliva, 32980f95dbd5437aaa9e15d05c7246bb; LP infant, 8bfbdc1bf38c418fb223306cd42af897; LP infant, 3e414e13a4394bb78c07f7ca7f4d1be3; legume supplementation, 2ca007303b9c4bb3820f392b996eba27; COVID-19 Brazil, d16eb32276c84bdb9c35c5872e97a986; Tomato seedling, f1c9cd79e0e94c66a367b6816b149750.

Code availability

The code generated during this study is available at https://github.com/DorresteinLaboratory/GlobalFoodomics.

Change history

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Acknowledgements

Funding sources: we thank the Crohn’s & Colitis foundation #675191, U19 AG063744 01, R01AG061066, 1 DP1 AT010885, P30 DK120515, Office of Naval Research MURI grant N00014-15-1-2809 and NIH/NCATS Colorado CTSA Grant UL1TR002535, the Emch Fund and C&D Fund. This work was also supported in part by the Chancellor’s Initiative in the Microbiome and Microbial Sciences and by Illumina through reagent donation and by Danone Nutricia Research in partnership with the Center for Microbiome Innovation at UCSD. We would like to thank E. Sayyari, D. S. Nguyen, E. Wolfe and K. Sanders for sample processing, and J. DeReus for data handling, processing, and maintaining the computational infrastructure. J.P.S. was supported by SD IRACDA (5K12GM068524-17), and in part by USDA-NIFA (2019-67013-29137) and the Einstein Institute GOLD project (R01MD011389). R.C. and M.G. were supported by the Krupp Endowed Fund; R.C. was also supported by a UCSD Rheumatic Diseases Research Training Grant from the NIH/NIAMS (T32AR064194). VA Research Service, NIH/NIAMS AR060772 and AR075990 to R.T., R.H.M. was supported through a UCSD training grant from the NIH/NIDDK Gastroenterology Training Program (T32 DK007202). The Brazilian National Council for Scientific and Technological Development (CNPq)-Brazil (245954/2012) to M.F.O. and FAPESP (2014/50265-3) to N.P.L. D.W. was supported by NIH/NHLBI Training Grant (NIH T32 HL149646). K.S. was supported by a PROMOS fund (DAAD). W.B. is a postdoctoral researcher of the Research Foundation–Flanders (FWO). R.J.D. was supported by NIH DP2 AT010401-01. We thank R. da Silva for his feedback and early bioinformatics analysis for the Global FoodOmics project. We further acknowledge all the individuals that contributed samples as well as companies and organizations that have donated samples: D. Vargas, Townshend’s Tea Company, BDK Kombucha, Oregonian Tonic, Squirrel & Crow, Venissimo cheese, Fermenter’s Club San Diego, Good Neighbor Gardens, Sprouts Farmers Market, Ralphs, Whole Foods, Julian Ciderworks and San Diego Zoo and Safari Park. Specifically thank you to A. Durant for coordinating sampling at Fermentation Festivals and the wonderful staff at San Diego Zoo Wildlife Alliance for coordinating and helping with sample collection: M. Gaffney, E. Galindo, K. Kerr, A. Fidgett, J. Stuart, D. Tanciatco, and L. Pospychala. NIST would like to acknowledge The Institute for the Advancement of Food and Nutrition Sciences (IAFNS) microbiome committee for providing support for the development of standardized fecal materials. Funding for the ADMC (Alzheimer’s Disease Metabolomics Consortium, led by Dr R.K.-D. at Duke University) was provided by the National Institute on Aging grants 1U01AG061359-01 and R01AG046171, a component of the Accelerating Medicines Partnership for AD (AMP-AD) Target Discovery and Preclinical Validation Project (https://www.nia.nih.gov/research/dn/ampad-target-discovery-and-preclinical-validation-project) and the National Institute on Aging grant RF1 AG0151550, a component of the M2OVE-AD Consortium (Molecular Mechanisms of the Vascular Etiology of AD Consortium, https://www.nia.nih.gov/news/decoding-molecular-tiesbetween-vascular-disease-and-alzheimer). Additional support was provided by the following NIA grants: (1RF1AG058942-01 and 3U01 AG024904-09S4). Data collection and sharing for the ADNI was supported by National Institutes of Health Grant U01 AG024904. ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimer’s Association; Alzheimer’s Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol-Myers Squibb Company; CereSpir, Inc.; Cogstate; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO Ltd; Janssen Alzheimer Immunotherapy Research & Development, LLC; Johnson & Johnson Pharmaceutical Research & Development LLC; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer’s Therapeutic Research Institute at the University of Southern California. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California. UCSD Academic Senate Research/Bridge Grant. Eunice Kennedy Shriver National Institute of Child Health and Human Development K12-HD000850.

Author information

Author notes

  1. These authors contributed equally: Julia M. Gauglitz, Kiana A. West, Wout Bittremieux.

Authors and Affiliations

  1. Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA

    Julia M. Gauglitz, Kiana A. West, Wout Bittremieux, Kelly C. Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M. Aceves, Nicole C. Sikora, Alan K. Jarmusch, Michael J. Meehan, Kathleen Dorrestein, Fernando Vargas, Katharina Spengler, Emmanuel O. Elijah, Mingxun Wang, Robert H. Mills & Pieter C. Dorrestein

  2. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA

    Julia M. Gauglitz, Kiana A. West, Wout Bittremieux, Kelly C. Weldon, Morgan Panitchpakdi, Christine M. Aceves, Elizabeth Brown, Nicole C. Sikora, Alan K. Jarmusch, Anupriya Tripathi, Michael J. Meehan, Kathleen Dorrestein, Fernando Vargas, Emmanuel O. Elijah, Mingxun Wang, Robert H. Mills & Pieter C. Dorrestein

  3. Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA

    Candace L. Williams

  4. Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA

    Kelly C. Weldon, Cameron Martino, Pedro Belda-Ferre, Austin D. Swafford, Rob Knight & Pieter C. Dorrestein

  5. Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA

    Elizabeth Brown, Anupriya Tripathi, Fernando Vargas & Rachel J. Dutton

  6. Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA

    Cameron Martino, Anupriya Tripathi, Justin P. Shaffer, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Pedro Belda-Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Clarisse Marotz, Gail Ackermann, Robert H. Mills, Megan M. Doty, Kyung E. Rhee, Rob Knight & Pieter C. Dorrestein

  7. Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA

    Cameron Martino

  8. Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Roxana Coras, Robert Terkeltaub & Monica Guma

  9. Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA

    Abigail J. Johnson

  10. Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA

    Kate E. Sprecher, Dana Withrow & Kenneth P. Wright Jr

  11. Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA

    Kate E. Sprecher

  12. Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela

    Daniela Vargas-Robles

  13. Department of Pediatrics, Billings Clinic, Billings, MT, USA

    Lourdes Herrera

  14. Department of Animal Science, Michigan State University, East Lansing, MI, USA

    Barry J. Bradford

  15. Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil

    Lucas Maciel Mauriz Marques, Flavio Protasio Veras & Thiago Mattar Cunha

  16. Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil

    Juliano Geraldo Amaral

  17. NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil

    Rodrigo Moreira Silva & Norberto Peporine Lopes

  18. Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil

    Rene Donizeti Ribeiro Oliveira & Paulo Louzada-Junior

  19. Department of Pharmacology, University of California San Diego, La Jolla, CA, USA

    Robert H. Mills & Pieter C. Dorrestein

  20. Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA

    Paulina K. Piotrowski, Stephanie L. Servetas, Sandra M. Da Silva, Christina M. Jones, Nancy J. Lin, Katrice A. Lippa & Scott A. Jackson

  21. Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA

    Rima Kaddurah Daouk

  22. Department of Medicine, Duke University, Durham, NC, USA

    Rima Kaddurah Daouk

  23. Duke Institute of Brain Sciences, Duke University, Durham, NC, USA

    Rima Kaddurah Daouk

  24. Department of Neurosciences, University of California San Diego, La Jolla, CA, USA

    Douglas Galasko

  25. Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Parambir S. Dulai & Brigid S. Boland

  26. Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA

    Tatyana I. Kalashnikova & Curt Wittenberg

  27. San Diego VA Healthcare System, San Diego, CA, USA

    Robert Terkeltaub

  28. Division of Neonatology, Department of Pediatrics, Kapi’olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA

    Megan M. Doty

  29. Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA

    Jae H. Kim

  30. Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA

    Julia Beauchamp-Walters

  31. Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA

    Maria Gloria Dominguez-Bello

  32. Department of Pediatrics, Washington University, St. Louis, MO, USA

    Mark Manary

  33. Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Michelli F. Oliveira & Rob Knight

  34. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA

    Rob Knight

  35. Department of Bioengineering, University of California San Diego, La Jolla, CA, USA

    Rob Knight

Authors
  1. Julia M. Gauglitz
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Contributions

P.C.D., R.K.D., R.J.D., and J.M.G. conceptualized the idea. M.J.M., M.B., M.P., F.D.O., K.C.W., C.M.A., E.B., K.S., P.C.D., R.J.D., R.K.D., N.C.S., A.D.S., K.D., G.A., D.M.D., N.P.L., M.B., and J.M.G. collected FoodOmics samples and performed metadata curation. M.J.M, M.P., F.D.O., F.V., C.M.A., E.B., N.C.S., and J.M.G. performed FoodOmics sample processing and MS data acquisition. A.J.J., P.B.F., E.D., Q.Z., D.N., D.M., J.P.S., and J.M.G. curated Global FoodOmics metadata to match FNDDS. K.E.R., J.B.W., B.S.B., B.J.B., R.C., M.G.D.B., M.M.D., E.O.E., D.G., L.H., J.H.K., M.M., C.M., R.K., K.E.S., D.V.R., T.I.K., C.W., K.P.W.J., M.F.O., R.H.M., D.W., R.T., J.G.A., P.S.D., M.G., D.J.G., A.K.J., B.J.B., R.M.S., K.C.W., A.D.S., F.V., N.P.L., P.K.P., S.M.D.S., S.L.S., C.M.J., N.J.L., K.A.L., S.A.J., R.K.D. and J.M.G. provided samples, comparative dataset, and/or detailed metadata. L.M.M.M., T.M.C. performed COVID-19 patient and/or food sample preparation and analysis. P.L.J. was the physician responsible for the COVID-19 patients. R.D.R.O was the physician responsible for collecting the plasma from COVID-19 patients. F.P.V. was responsible for tabulation of COVID-19 patient data. M.P., J.M.G., T.S., M.G.D.B., L.D.R.G., G.H. prepared samples for food. M.W. supported GNPS computational infrastructure used in the study. C.L.W., W.B., A.K.J., K.A.W., E.S., A.T., N.P.L. and J.M.G. analyzed MS data. C.L.W., W.B., A.K.J., K.A.W., C.M., and J.M.G. generated figures. P.C.D., R.K., R.J.D., A.D.S., and J.M.G. supervised the work. P.C.D., R.K., C.L.W., K.A.W., W.B., and J.M.G. wrote the paper. All authors have contributed feedback and edits to the manuscript.

Corresponding authors

Correspondence to Rob Knight or Pieter C. Dorrestein.

Ethics declarations

Competing interests

B.S.B. has a research grant from Prometheus Biosciences and has received consulting fees from Pfizer. P.C.D. is on the scientific advisory board of Sirenas, Cybele Microbiome, Galileo, and founder and scientific advisor of Ometa Labs LLC and Enveda (with approval by UC San Diego). J.H.K. is a consultant for Medela and on the Board for Innara Health; he owns shares in Astarte Medical and Nicolette. M.G. has research grants from Pfizer and Novartis. P.S.D. has received research support and/or consulting from Takeda, Pfizer, Abbvie, Janssen, Prometheus, Buhlmann, Polymedco. R.J.D. is a consultant for and owns shares in Impossible Foods Inc., and is on the Scientific Advisory Panel of Boost Biomes. A.J.J. has received consulting fees from Abbott Nutrition and Corebiome. D.M. is a consultant for BiomeSense, Inc., has equity and receives income. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. D.G. is a consultant for Biogen, Fujirebio, vTv Therapeutics, Esai and Amprion and serves on a DSMB for Cognition Therapeutics. K.P.W. reports during the conduct of the study receiving research support from SomaLogic, Inc., consulting fees from or served as a paid member of scientific advisory boards for the Sleep Disorders Research Advisory Board–National Heart, Lung and Blood Institute, CurAegis Technologies, Philips, Inc., Circadian Therapeutics, Ltd. and Circadian Biotherapies Ltd. R.T. received a research grant from AstraZeneca Consulting, SOBI, Selecta, Horizon, Allena, AstraZeneca. A.D.S. and R.K. are directors at the Center for Microbiome Innovation at UC San Diego, which receives industry research funding for multiple microbiome initiatives, but no industry funding was provided for this project. R.K. is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant and scientific advisory board member for DayTwo, and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, and has equity and is a scientific advisory board member. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. M.W. is a co-founder of Ometa Labs LLC. K.D. is an inventor on a series of patents on the use of metabolomics for the diagnosis and treatment of central nervous system diseases and holds equity in Metabolon Inc., Chymia LLC and PsyProtix. The remaining authors declare no competing interests.

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Nature Biotechnology thanks Elaine Holmes and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1−3.

Reporting Summary

Supplementary Table 1

The metadata table for the foodomics project

Supplementary Table 2

Table of the study details of each of the 28 public projects

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Gauglitz, J.M., West, K.A., Bittremieux, W. et al. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 40, 1774–1779 (2022). https://doi.org/10.1038/s41587-022-01368-1

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