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Bittremieux W, Avalon NE, Thomas SP, Kakhkhorov SA, Aksenov AA, Gomes PWP, Aceves CM, Caraballo-Rodríguez AM, Gauglitz JM, Gerwick WH, Huan T, Jarmusch AK, Kaddurah-Daouk RF, Kang KB, Kim HW, Kondić T, Mannochio-Russo H, Meehan MJ, Melnik AV, Nothias LF, O'Donovan C, Panitchpakdi M, Petras D, Schmid R, Schymanski EL, van der Hooft JJJ, Weldon KC, Yang H, Xing S, Zemlin J, Wang M, Dorrestein PC. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat Commun 2023; 14:8488. [PMID: 38123557 PMCID: PMC10733301 DOI: 10.1038/s41467-023-44035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
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Affiliation(s)
- Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020, Antwerpen, Belgium.
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sydney P Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sarvar A Kakhkhorov
- Laboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, 100174, Uzbekistan
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Rima F Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, 27701, USA
- Department of Medicine, Duke University, Durham, NC, 27710, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, 27710, USA
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Goyang, 10326, Korea
| | - Todor Kondić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, 14800-901, Brazil
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexey V Melnik
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Louis-Felix Nothias
- Université Côte d'Azur, CNRS, ICN, Nice, France
- Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, Nice, France
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, 72076, Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92507, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Heejung Yang
- Laboratory of Natural Products Chemistry, College of Pharmacy, Kangwon National University, Chuncheon, 24341, Korea
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, 92507, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
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