Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Open accessAbstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Bioactivity-based molecular networking approaches have been successful in guiding the isolation of novel compounds with specific activity, such as antibacterial or antiviral activity.
“These approaches have been successful in guiding the isolation of novel compounds with specific activity (e.g., antibacterial or antiviral).”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [52]
In Molecular Explorer (page not provided), molecular networking guided the purification of a previously undescribed stenothricin analog, which was subsequently found active against a specific bacterial cell type. The paper does not describe bioactivity-based selection guiding that isolation or an antiviral example. (LLM, conf=0.85)
Experimental — accuracy not yet measuredMassbank, Massbank of North America, and GNPS are key active public MS/MS spectral library resources within the natural products field that include in aggregate 587,213 experimental MS/MS reference spectra.
“Massbank,161 Massbank of North America, and GNPS52 are key active public MS/MS spectral library resources within the natural products field that include in aggregate 587 213 experimental MS/MS reference spectra.”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [52]
The GNPS Spectral Libraries section identifies GNPS as a publicly searchable MS/MS reference library relevant to natural products, supporting the citation’s identification of GNPS. It does not report an aggregate of 587,213 spectra across MassBank, MassBank of North America, and GNPS; the Introduction instead reports a combined GNPS-searchable catalog of over 221,000 reference spectra. (LLM, conf=0.84)
Experimental — accuracy not yet measuredAnalog search techniques expand on the library search by facilitating the putative identification of new molecules related to known natural products.
“Analog search techniques,52 also called hybrid search,162 expand on the library search by facilitating the putative identification of new molecules that are related to known natural products.”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [52]
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Mass spectrometry searches using MASST
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Self-citationAssembling the Community-Scale Discoverable Human Proteome
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Self-citationMSNovelist: de novo structure generation from mass spectra
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Self-citationBile salt hydrolase/aminoacyltransferase shapes the microbiome
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Self-citationReDU: a framework to find and reanalyze public mass spectrometry data
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Mass Spectrometry‐Based Untargeted Plant Metabolomics
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Self-citationSiderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut
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Self-citationAnnotating metabolite mass spectra with domain-inspired chemical formula transformers
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Native mass spectrometry-based metabolomics identifies metal-binding compounds
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Self-citationTowards nutrition with precision: unlocking biomarkers as dietary assessment tools
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Review: Metabolomics as a Prediction Tool for Plants Performance under Environmental Stress
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Host and microbiota metabolic signals in aging and longevity
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Self-citationThe confluence of big data and evolutionary genome mining for the discovery of natural products
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Vitale, G. A., Geibel, C., Minda, V., Wang, M., Aron, A. T., & Petras, D. (2024) · Natural Product Reports · doi:10.1039/d3np00050h · Cited by 66 · see citing works
Self-citationBottromycins - biosynthesis, synthesis and activity
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Self-citationIntegrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery
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Self-citationHeterologous production of cyanobacterial compounds
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Decoding the Foodome: Molecular Networks Connecting Diet and Health
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Native metabolomics for mass spectrometry-based siderophore discovery.
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Native Metabolomics Unveils Suomilide Analogs with Potent Trypsin Inhibitory Activity
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- Authors
- Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W.-T., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., Kersten, R. D., Pace, L. A., Quinn, R. A., Duncan, K. R., Hsu, C.-C., Floros, D. J., Gavilan, R. G., Kleigrewe, K., Northen, T., Dutton, R. J., Parrot, D., Carlson, E. E., Aigle, B., Michelsen, C. F., Jelsbak, L., Sohlenkamp, C., Pevzner, P., Edlund, A., McLean, J., Piel, J., Murphy, B. T., Gerwick, L., Liaw, C.-C., Yang, Y.-L., Humpf, H.-U., Maansson, M., Keyzers, R. A., Sims, A. C., Johnson, A. R., Sidebottom, A. M., Sedio, B. E., Klitgaard, A., Larson, C. B., Boya P, C. A., Torres-Mendoza, D., Gonzalez, D. J., Silva, D. B., Marques, L. M., Demarque, D. P., Pociute, E., O'Neill, E. C., Briand, E., Helfrich, E. J. N., Granatosky, E. A., Glukhov, E., Ryffel, F., Houson, H., Mohimani, H., Kharbush, J. J., Zeng, Y., Vorholt, J. A., Kurita, K. L., Charusanti, P., McPhail, K. L., Nielsen, K. F., Vuong, L., Elfeki, M., Traxler, M. F., Engene, N., Koyama, N., Vining, O. B., Baric, R., Silva, R. R., Mascuch, S. J., Tomasi, S., Jenkins, S., Macherla, V., Hoffman, T., Agarwal, V., Williams, P. G., Dai, J., Neupane, R., Gurr, J., Rodríguez, A. M. C., Lamsa, A., Zhang, C., Dorrestein, K., Duggan, B. M., Almaliti, J., Allard, P.-M., Phapale, P., Nothias, L.-F., Alexandrov, T., Litaudon, M., Wolfender, J.-L., Kyle, J. E., Metz, T. O., Peryea, T., Nguyen, D.-T., VanLeer, D., Shinn, P., Jadhav, A., Müller, R., Waters, K. M., Shi, W., Liu, X., Zhang, L., Knight, R., Jensen, P. R., Palsson, B. Ø., Pogliano, K., Linington, R. G., Gutiérrez, M., Lopes, N. P., Gerwick, W. H., Moore, B. S., Dorrestein, P. C., & Bandeira, N.
- Affiliations
- University of California San Diego (US)
- Stanford University (US)
- Scripps Institution of Oceanography (US)
- Sirenas (United States) (US)
- Salk Institute for Biological Studies (US)
- San Diego State University (US)
- Lawrence Berkeley National Laboratory (US)
- Harvard University (US)
- Université Rennes 1 (FR)
- University of Minnesota (US)
- Dynamique des Génomes et Adaptation Microbienne (FR)
- Technical University of Denmark (DK)
- Universidad Nacional Autónoma de México (MX)
- J. Craig Venter Institute (US)
- University of California, Los Angeles (US)
- ETH Zurich (CH)
- University of Illinois Chicago (US)
- National Sun Yat-sen University (TW)
- University of Münster (DE)
- Victoria University of Wellington (NZ)
- Indiana University Bloomington (US)
- Smithsonian Tropical Research Institute (PA)
- Universidade Federal de Mato Grosso do Sul (BR)
- Universidade de São Paulo (BR)
- Centre National de la Recherche Scientifique (FR)
- University of Notre Dame (US)
- University of California, Santa Cruz (US)
- Oregon State University (US)
- University of California, Berkeley (US)
- Florida International University (US)
- University of North Carolina at Chapel Hill (US)
- Helmholtz Institute for Pharmaceutical Research Saarland (DE)
- University of Hawaiʻi at Mānoa (US)
- University of Geneva (CH)
- European Molecular Biology Laboratory (DE)
- Pacific Northwest National Laboratory (US)
- National Center for Advancing Translational Sciences (US)
- Chinese Academy of Sciences (CN)
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (PA)
- ORCID
- Wang, Mingxun
- Carver, Jeremy J
- Phelan, Vanessa V
- Sanchez, Laura M
- Garg, Neha
- Peng, Yao
- Watrous, Jeramie
- Kapono, Clifford A
- Porto, Carla
- Bouslimani, Amina
- Melnik, Alexey V
- Meehan, Michael J
- Liu, Wei-Ting
- Crüsemann, Max
- Boudreau, Paul D
- Kersten, Roland D
- Pace, Laura A
- Quinn, Robert A
- Duncan, Katherine R
- Hsu, Cheng-Chih
- Floros, Dimitrios J
- Gavilan, Ronnie G
- Kleigrewe, Karin
- Northen, Trent
- Dutton, Rachel J
- Parrot, Delphine
- Carlson, Erin E
- Aigle, Bertrand
- Jelsbak, Lars
- Sohlenkamp, Christian
- Pevzner, Pavel
- Edlund, Anna
- McLean, Jeffrey
- Piel, Jörn
- Murphy, Brian T
- Gerwick, Lena
- Liaw, Chih-Chuang
- Humpf, Hans-Ulrich
- Keyzers, Robert A
- Sidebottom, Ashley M
- Sedio, Brian E
- Klitgaard, Andreas
- Torres-Mendoza, Daniel
- Gonzalez, David J
- Silva, Denise B
- Marques, Lucas M
- Demarque, Daniel P
- O'Neill, Ellis C
- Briand, Enora
- Helfrich, Eric J N
- Granatosky, Eve A
- Glukhov, Evgenia
- Houson, Hailey
- Mohimani, Hosein
- Kharbush, Jenan J
- Vorholt, Julia A
- Kurita, Kenji L
- Charusanti, Pep
- McPhail, Kerry L
- Nielsen, Kristian Fog
- Vuong, Lisa
- Traxler, Matthew F
- Engene, Niclas
- Koyama, Nobuhiro
- Vining, Oliver B
- Baric, Ralph
- Silva, Ricardo R
- Mascuch, Samantha J
- Tomasi, Sophie
- Agarwal, Vinayak
- Williams, Philip G
- Neupane, Ram
- Rodríguez, Andrés M C
- Zhang, Chen
- Duggan, Brendan M
- Almaliti, Jehad
- Allard, Pierre-Marie
- Phapale, Prasad
- Alexandrov, Theodore
- Litaudon, Marc
- Wolfender, Jean-Luc
- Kyle, Jennifer E
- Metz, Thomas O
- Peryea, Tyler
- Shinn, Paul
- Jadhav, Ajit
- Müller, Rolf
- Waters, Katrina M
- Shi, Wenyuan
- Liu, Xueting
- Zhang, Lixin
- Knight, Rob
- Jensen, Paul R
- Palsson, Bernhard Ø
- Pogliano, Kit
- Linington, Roger G
- Gutiérrez, Marcelino
- Lopes, Norberto P
- Gerwick, William H
- Dorrestein, Pieter C
- Bandeira, Nuno
- Venue
- Nature Biotechnology
- Published
- 2016-08
- Volume
- 34
- Issue
- 8
- Pages
- 828-837
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC5321674
- OpenAlex
- W2504691963
- Cited by
- 4,629
- References
- 66
- Citations by year
- 2026: 670 · 2025: 719 · 2024: 625 · 2023: 576 · 2022: 519 · 2021: 542 · 2020: 364 · 2019: 293 · 2018: 165 · 2017: 124 · 2016: 24 · 2015: 2 · 2012: 1
- FWCI
- 104.95
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion)
- Helmholtz Centre for Ocean Research Kiel (GEOMAR) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea) (submittedVersion, other-oa)
- HZI (Helmholtz Centre for Infection Research) (submittedVersion, other-oa)
- Strathprints: The University of Strathclyde institutional repository (University of Strathclyde) (submittedVersion, other-oa)
- HAL (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- HZI (Helmholtz Centre for Infection Research) (submittedVersion, cc-by-nc-sa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1010816, CAREER)
- U.S. Department of Defense (W81XWH, W81XWH1310171, W81XWH-13)
- Smithsonian Institution
- U.S. Department of Health and Human Services
- Research Corporation for Science Advancement
- University of California Institute for Mexico and the United States (CN-12-552)
- United States - Israel Binational Agricultural Research and Development Fund (FI-494-13)
- Villum Fonden (VKR023113, 00007262)
- Indian National Science Academy
- European Commission (301244)
- Deutscher Akademischer Austauschdienst
- Deutsche Forschungsgemeinschaft
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (149025, 116262, 50265, 146200, 200020)
- Fundação de Amparo à Pesquisa do Estado de São Paulo (2013/16496-5, 2014/50265/3, 2012/18031-7, 2014/, 14/50265-3, 2014/01651-8, 2014/01884-2, 2014/18052-0)
- National Natural Science Foundation of China (31125002, 81102369)
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Consejo Nacional de Ciencia y Tecnología (CN-12-552)
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (306385/2011-2)
- Novo Nordisk
- Ministry of Science and Technology, Taiwan (MOST-103)
- Danmarks Frie Forskningsfond
- Augustinus Fonden
- Novo Nordisk Fonden (NNF10CC1016517)
- Key Laboratory of Micro-Systems and Micro-Structures Manufacturing, Ministry of Education, Harbin Institute of Technology
- National Institutes of Health (HHSN272200800060C, 1s10rr029121-01, NIH T32, W81XWH, 5r01de020102-10, 5r21ai085540-02)
- Oregon Sea Grant, Oregon State University (#NA10OAR4170059)
- Japan Society for the Promotion of Science (15K07867)
- Ciência sem Fronteiras
- National Institute of General Medical Sciences (R01GM095373, R01GM097509, P41GM103484, K01GM103809, F32GM089044, T32GM075762, R01GM094802, R01GM085770, K12GM068524)
- National Institute of Allergy and Infectious Diseases (R01AI095125, R21 AI085540, U19AI106772, HHSN272200800060C, AI106772, U01AI124316)
- Fogarty International Center (U01TW006634, U19TW007401, U01TW007401)
- National Institute of Diabetes and Digestive and Kidney Diseases (T32DK007202)
- National Institute of Dental and Craniofacial Research (R01-DE020102, K99DE024543, R00DE024543, R01DE023810)
- National Center for Research Resources (UL1RR031980, S10-RR029121)
- National Center for Complementary and Integrative Health (U41AT008718)
- FP7 People: Marie-Curie Actions (FP7-PEOPLE-2011-IOF)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- natural products, GNPS, tandem mass spectrometry, spectral annotation, data reanalysis, natural product database
- MeSH terms
- Biological Products, Database Management Systems, Mass Spectrometry, Information Storage and Retrieval, Information Dissemination, Internationality, Databases, Chemical, Data Curation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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