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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1774-1779 |
| Number of pages | 6 |
| Journal | Nature biotechnology |
| Volume | 40 |
| Issue number | 12 |
| DOIs | |
| State | Published - Dec 2022 |
| Externally published | Yes |
ASJC Scopus subject areas
- Applied Microbiology and Biotechnology
- Bioengineering
- Molecular Medicine
- Biotechnology
- Biomedical Engineering
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In: Nature biotechnology, Vol. 40, No. 12, 12.2022, p. 1774-1779.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Enhancing untargeted metabolomics using metadata-based source annotation
AU - Gauglitz, Julia M.
AU - West, Kiana A.
AU - Bittremieux, Wout
AU - Williams, Candace L.
AU - Weldon, Kelly C.
AU - Panitchpakdi, Morgan
AU - Di Ottavio, Francesca
AU - Aceves, Christine M.
AU - Brown, Elizabeth
AU - Sikora, Nicole C.
AU - Jarmusch, Alan K.
AU - Martino, Cameron
AU - Tripathi, Anupriya
AU - Meehan, Michael J.
AU - Dorrestein, Kathleen
AU - Shaffer, Justin P.
AU - Coras, Roxana
AU - Vargas, Fernando
AU - Goldasich, Lindsay De Right
AU - Schwartz, Tara
AU - Bryant, MacKenzie K.
AU - Humphrey, Gregory
AU - Johnson, Abigail J.
AU - Spengler, Katharina
AU - Belda-Ferre, Pedro
AU - Diaz, Edgar
AU - McDonald, Daniel
AU - Zhu, Qiyun
AU - Elijah, Emmanuel O.
AU - Wang, Mingxun
AU - Marotz, Clarisse
AU - Sprecher, Kate E.
AU - Vargas-Robles, Daniela
AU - Withrow, Dana
AU - Ackermann, Gail
AU - Herrera, Lourdes
AU - Bradford, Barry J.
AU - Marques, Lucas Maciel Mauriz
AU - Amaral, Juliano Geraldo
AU - Silva, Rodrigo Moreira
AU - Veras, Flavio Protasio
AU - Cunha, Thiago Mattar
AU - Oliveira, Rene Donizeti Ribeiro
AU - Louzada-Junior, Paulo
AU - Mills, Robert H.
AU - Piotrowski, Paulina K.
AU - Servetas, Stephanie L.
AU - Da Silva, Sandra M.
AU - Jones, Christina M.
AU - Lin, Nancy J.
AU - Lippa, Katrice A.
AU - Jackson, Scott A.
AU - Daouk, Rima Kaddurah
AU - Galasko, Douglas
AU - Dulai, Parambir S.
AU - Kalashnikova, Tatyana I.
AU - Wittenberg, Curt
AU - Terkeltaub, Robert
AU - Doty, Megan M.
AU - Kim, Jae H.
AU - Rhee, Kyung E.
AU - Beauchamp-Walters, Julia
AU - Wright, Kenneth P.
AU - Dominguez-Bello, Maria Gloria
AU - Manary, Mark
AU - Oliveira, Michelli F.
AU - Boland, Brigid S.
AU - Lopes, Norberto Peporine
AU - Guma, Monica
AU - Swafford, Austin D.
AU - Dutton, Rachel J.
AU - Knight, Rob
AU - Dorrestein, Pieter C.
N1 - Funding Information: 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.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. 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. Funding Information: 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. Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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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UR - http://www.scopus.com/inward/citedby.url?scp=85133629409&partnerID=8YFLogxK
U2 - 10.1038/s41587-022-01368-1
DO - 10.1038/s41587-022-01368-1
M3 - Article
C2 - 35798960
AN - SCOPUS:85133629409
SN - 1087-0156
VL - 40
SP - 1774
EP - 1779
JO - Nature biotechnology
JF - Nature biotechnology
IS - 12
ER -