Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Wout Bittremieux (), Nicole E. Avalon, Sydney P. Thomas, Sarvar A. Kakhkhorov, Alexander A. Aksenov, Paulo Wender P. Gomes, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M. Gauglitz, William H. Gerwick, Tao Huan, Alan K. Jarmusch, Rima F. Kaddurah-Daouk, Kyo Bin Kang, Hyun Woo Kim, Todor Kondić, Helena Mannochio-Russo, Michael J. Meehan, Alexey V. Melnik, Louis-Felix Nothias, Claire O’Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L. Schymanski, Justin J. J. van der Hooft, Kelly C. Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang and Pieter C. Dorrestein ()
Additional contact information
Wout Bittremieux: University of Antwerp
Nicole E. Avalon: University of California San Diego
Sydney P. Thomas: University of California San Diego
Sarvar A. Kakhkhorov: Center for Advanced Technologies
Alexander A. Aksenov: University of California San Diego
Paulo Wender P. Gomes: University of California San Diego
Christine M. Aceves: The Scripps Research Institute
Andrés Mauricio Caraballo-Rodríguez: University of California San Diego
Julia M. Gauglitz: University of California San Diego
William H. Gerwick: University of California San Diego
Tao Huan: University of British Columbia
Alan K. Jarmusch: University of California San Diego
Rima F. Kaddurah-Daouk: Duke University School of Medicine
Kyo Bin Kang: Sookmyung Women’s University
Hyun Woo Kim: Dongguk University
Todor Kondić: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Helena Mannochio-Russo: University of California San Diego
Michael J. Meehan: University of California San Diego
Alexey V. Melnik: University of Connecticut
Louis-Felix Nothias: CNRS, ICN
Claire O’Donovan: Wellcome Genome Campus
Morgan Panitchpakdi: University of California San Diego
Daniel Petras: University of California San Diego
Robin Schmid: University of California San Diego
Emma L. Schymanski: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Justin J. J. van der Hooft: University of California San Diego
Kelly C. Weldon: University of California San Diego
Heejung Yang: Kangwon National University
Shipei Xing: University of California San Diego
Jasmine Zemlin: University of California San Diego
Mingxun Wang: University of California Riverside
Pieter C. Dorrestein: University of California San Diego

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-44035-y

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