Enhancing untargeted metabolomics using metadata-based source annotation

Julia M Gauglitz; Kiana A West; Wout Bittremieux; Candace L Williams; Kelly C Weldon; Morgan Panitchpakdi; Francesca Di Ottavio; Christine M Aceves; Elizabeth Brown; Nicole C Sikora; Alan K Jarmusch; Cameron Martino; Anupriya Tripathi; Michael J Meehan; Kathleen Dorrestein; Justin P Shaffer; Roxana Coras; Fernando Vargas; Lindsay DeRight Goldasich; Tara Schwartz; MacKenzie Bryant; Gregory Humphrey; Abigail J Johnson; Katharina Spengler; Pedro Belda-Ferre; Edgar Diaz; Daniel McDonald; Qiyun Zhu; Emmanuel O Elijah; Mingxun Wang; Clarisse Marotz; Kate E Sprecher; Daniela Vargas-Robles; Dana Withrow; Gail Ackermann; Lourdes Herrera; Barry J Bradford; Lucas Maciel Mauriz Marques; Juliano Geraldo Amaral; Rodrigo Moreira Silva; Flavio Protasio Veras; Thiago Mattar Cunha; Rene Donizeti Ribeiro Oliveira; Paulo Louzada-Junior; Robert H Mills; Paulina K Piotrowski; Stephanie L Servetas; Sandra M Da Silva; Christina M Jones; Nancy J Lin; Katrice A Lippa; Scott A Jackson; Rima Kaddurah Daouk; Douglas Galasko; Parambir S Dulai; Tatyana I Kalashnikova; Curt Wittenberg; Robert Terkeltaub; Megan M Doty; Jae H Kim; Kyung E Rhee; Julia Beauchamp-Walters; Kenneth P Wright Jr; Maria Gloria Dominguez-Bello; Mark Manary; Michelli F Oliveira; Brigid S Boland; Norberto Peporine Lopes; Monica Guma; Austin D Swafford; Rachel J Dutton; Rob Knight; Pieter C Dorrestein

doi:10.1038/s41587-022-01368-1

Enhancing untargeted metabolomics using metadata-based source annotation

Nat Biotechnol. 2022 Dec;40(12):1774-1779. doi: 10.1038/s41587-022-01368-1. Epub 2022 Jul 7.

Authors

Julia M Gauglitz^#^{1

2}, Kiana A West^#^{1

2}, Wout Bittremieux^#^{1

2}, Candace L Williams³, Kelly C Weldon^{1

2

4}, Morgan Panitchpakdi^{1

2}, Francesca Di Ottavio¹, Christine M Aceves^{1

2}, Elizabeth Brown^{2

5}, Nicole C Sikora^{1

2}, Alan K Jarmusch^{1

2}, Cameron Martino^{4

6

7}, Anupriya Tripathi^{2

5

6}, Michael J Meehan^{1

2}, Kathleen Dorrestein^{1

2}, Justin P Shaffer⁶, Roxana Coras⁸, Fernando Vargas^{1

2

5}, Lindsay DeRight Goldasich⁶, Tara Schwartz⁶, MacKenzie Bryant⁶, Gregory Humphrey⁶, Abigail J Johnson⁹, Katharina Spengler¹, Pedro Belda-Ferre^{4

6}, Edgar Diaz⁶, Daniel McDonald⁶, Qiyun Zhu⁶, Emmanuel O Elijah^{1

2}, Mingxun Wang^{1

2}, Clarisse Marotz⁶, Kate E Sprecher^{10

11}, Daniela Vargas-Robles¹², Dana Withrow¹⁰, Gail Ackermann⁶, Lourdes Herrera¹³, Barry J Bradford¹⁴, Lucas Maciel Mauriz Marques¹⁵, Juliano Geraldo Amaral¹⁶, Rodrigo Moreira Silva¹⁷, Flavio Protasio Veras¹⁵, Thiago Mattar Cunha¹⁵, Rene Donizeti Ribeiro Oliveira¹⁸, Paulo Louzada-Junior¹⁸, Robert H Mills^{1

2

6

19}, Paulina K Piotrowski²⁰, Stephanie L Servetas²⁰, Sandra M Da Silva²⁰, Christina M Jones²⁰, Nancy J Lin²⁰, Katrice A Lippa²⁰, Scott A Jackson²⁰, Rima Kaddurah Daouk^{21

22

23}, Douglas Galasko²⁴, Parambir S Dulai²⁵, Tatyana I Kalashnikova²⁶, Curt Wittenberg²⁶, Robert Terkeltaub^{8

27}, Megan M Doty^{6

28}, Jae H Kim²⁹, Kyung E Rhee⁶, Julia Beauchamp-Walters³⁰, Kenneth P Wright Jr¹⁰, Maria Gloria Dominguez-Bello³¹, Mark Manary³², Michelli F Oliveira³³, Brigid S Boland²⁵, Norberto Peporine Lopes¹⁷, Monica Guma⁸, Austin D Swafford⁴, Rachel J Dutton⁵, Rob Knight^{34

35

36

37

38}, Pieter C Dorrestein^{39

40

41

42

43}

Affiliations

¹ Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
³ Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA.
⁴ Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
⁵ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
⁶ Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁷ Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
⁸ Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
⁹ Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
¹⁰ Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
¹¹ Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA.
¹² Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela.
¹³ Department of Pediatrics, Billings Clinic, Billings, MT, USA.
¹⁴ Department of Animal Science, Michigan State University, East Lansing, MI, USA.
¹⁵ Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
¹⁶ Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil.
¹⁷ NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
¹⁸ Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
¹⁹ Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
²⁰ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
²¹ Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA.
²² Department of Medicine, Duke University, Durham, NC, USA.
²³ Duke Institute of Brain Sciences, Duke University, Durham, NC, USA.
²⁴ Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
²⁵ Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
²⁶ Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
²⁷ San Diego VA Healthcare System, San Diego, CA, USA.
²⁸ Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA.
²⁹ Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
³⁰ Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³¹ Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
³² Department of Pediatrics, Washington University, St. Louis, MO, USA.
³³ Department of Medicine, University of California San Diego, La Jolla, CA, USA.
³⁴ Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
³⁵ Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
³⁶ Department of Medicine, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
³⁷ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
³⁸ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
³⁹ Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴⁰ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴¹ Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴² Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴³ Department of Pharmacology, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.

^# Contributed equally.

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.

Enhancing untargeted metabolomics using metadata-based source annotation

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