ArticleNature methods2020
Feature-based molecular networking in the GNPS analysis environment.
Abstract read
In one paragraph
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 793 papers.
0numbers the graph read from it
0cells of the map it votes in
793citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
793 citing papers in PubMed.
- Annotating Tandem Mass Spectra in Metabolomics with DreaMS and MassSpecGym.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles.Gut microbes · 2026Article
- Lipidomic profiling of PEX11β knockout T-REx 293 cells reveals lipid shifts suggesting potential metabolic perturbations.Biochemistry and biophysics reports · 2026Article
- Environmental drivers of metabolomic profiles within and between cryptic lineages of Montastraea cavernosa, the great star coral.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Antibiotic-producing microorganisms: taxonomic diversity, screening strategies, and emerging and underexploited antibacterial targets.Archives of microbiology · 2026Review
- Integrated molecular networking-guided discovery of antimicrobial secondary metabolites fromRSC advances · 2026Article
- Integrated sensory evaluation and feature-based molecular networking elucidate flavor improvement and associated metabolites in dark tea fermented byFood chemistry: X · 2026Article
- Article
- Article
- Chemical Game Theory: Linking Metabolite Diversity, Biosynthetic Architecture, and Realized Payoffs.Molecules (Basel, Switzerland) · 2026Article
- DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.Plant communications · 2026Article
- Evaluation of Indigenous Bacillus Strains from Asian Fermented Foods for Probiotic Properties.Probiotics and antimicrobial proteins · 2026Article
- Structure-guided parameter optimization of feature-based molecular networking for DIA-HRMS screening of antihistamines in cosmetics.Analytical and bioanalytical chemistry · 2026Article
- Chemical Ontogeny in Plants: Developmental Dynamics of Specialized Metabolism and Implications for Ecology, Quality Control, and Bioprospecting.Plants (Basel, Switzerland) · 2026Review
- Molecular-networking-based characterization of cytotoxic metabolites produced by the cyanobacterium Nostoc edaphicum CCNP1411.Molecular diversity · 2026Article
- MetaboAnnotate: An AI-powered Multiagent Framework for Integrating Annotation Tools for Untargeted Metabolomics.Analytical chemistry · 2026Article
- Coral metabolomic diversity is associated with restoration success.Scientific reports · 2026Article
- Integrated GNPS Molecular Networking and Network Pharmacology Uncover Methylophiopogonanone B as a Novel Anti-Inflammatory Agent From Polygonatum cyrtonema Hua Targeting the SRC-PI3K-Akt Pathway.Biomedical chromatography : BMC · 2026Article
- Component Analysis and Mechanism Exploration of Fangji Dihuang Decoction in Treating Ischemic Stroke With Homotherapy for Heteropathy Based on Molecular Networking and Network Pharmacology.Biomedical chromatography : BMC · 2026Article
- Biosynthesis of pathogen-induced hydroxylated tryptamine derivatives in barley.Plant physiology · 2026Article
733 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
62 authors.
Louis-Félix Nothias *Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Daniel Petras *Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-6561-3022
Robin Schmid *Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Kai DührkopChair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.ORCID http://orcid.org/0000-0002-9056-0540
Johannes RainerInstitute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.ORCID http://orcid.org/0000-0002-6977-7147
Abinesh SarvepalliSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Ivan ProtsyukStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Madeleine ErnstSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Hiroshi TsugawaRIKEN Center for Sustainable Resource Science, Yokohama, Japan.ORCID http://orcid.org/0000-0002-2015-3958
Markus FleischauerChair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.ORCID http://orcid.org/0000-0001-7557-0831
Fabian AichelerApplied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Alexander A AksenovSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9445-2248
Oliver AlkaApplied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Pierre-Marie AllardDepartment of Phytochemistry and Bioactive Natural Products, University of Geneva, Geneva, Switzerland.
Aiko BarschBruker Daltonics, Bremen, Germany.
Xavier CachetEquipe PNAS, UMR 8038 CiTCoM CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Paris, France.ORCID http://orcid.org/0000-0001-9150-1932
Andres Mauricio Caraballo-RodriguezSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5499-2728
Ricardo R Da SilvaCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Tam DangCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3602-1917
Neha GargSchool of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
Julia M GauglitzSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Alexey GurevichCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.ORCID http://orcid.org/0000-0002-5855-3519
Giorgis IsaacWaters Corporation, Milford, MA, USA.
Alan K JarmuschSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2228-6308
Zdeněk KameníkInstitute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
Kyo Bin KangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3290-1017
Nikolas KesslerBruker Daltonics, Bremen, Germany.
Irina KoesterSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-1571-882X
Ansgar KorfInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Audrey Le GouellecUniv. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France.ORCID http://orcid.org/0000-0002-4905-3854
Marcus LudwigChair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.ORCID http://orcid.org/0000-0001-9981-2153
Christian Martin HCentro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.
Laura-Isobel McCallDepartment of Chemistry and Biochemistry, Department of Microbiology and Plant Biology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.
Jonathan McSaylesNonlinear Dynamics, Milford, MA, USA.
Sven W MeyerBruker Daltonics, Bremen, Germany.
Hosein MohimaniComputational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
Mustafa MorsyDepartment of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA.
Oriane MoyneUniv. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France.ORCID http://orcid.org/0000-0002-0475-6177
Steffen NeumannBioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, Germany.
Heiko NeuwegerBruker Daltonics, Bremen, Germany.
Ngoc Hung NguyenSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Melissa Nothias-EspositoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Julien PaoliniLaboratoire de Chimie des Produits Naturels, UMR CNRS SPE, Université de Corse Pascal Paoli, Corte, France.
Vanessa V PhelanSkaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Denver, Aurora, CO, USA.
Tomáš PluskalWhitehead Institute for Biomedical Research, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6940-3006
Robert A QuinnDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
Simon RogersSchool of Computing Science, University of Glasgow, Glasgow, UK.ORCID http://orcid.org/0000-0003-3578-4477
Bindesh ShresthaWaters Corporation, Milford, MA, USA.
Anupriya TripathiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Justin J J van der HooftSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9340-5511
Fernando VargasSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5847-2439
Kelly C WeldonSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Michael WittingResearch Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, München, Germany.ORCID http://orcid.org/0000-0002-1462-4426
Heejung YangCollege of Pharmacy, Kangwon National University, Chuncheon-si, Republic of Korea.ORCID http://orcid.org/0000-0001-5986-9024
Zheng ZhangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Florian ZubeilBruker Daltonics, Bremen, Germany.
Oliver KohlbacherApplied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0003-1739-4598
Sebastian BöckerChair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.ORCID http://orcid.org/0000-0002-9304-8091
Theodore AlexandrovSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9464-6125
Nuno BandeiraSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8385-3655
Mingxun WangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.ORCID http://orcid.org/0000-0001-7647-6097
Pieter C DorresteinSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.ORCID http://orcid.org/0000-0002-3003-1030
Funding
Project 4 - Mechanistic studies on the role of the gut microbiome in models for Alzheimer's diseaseU19AG063744 · NIA · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Rima F Kaddurah-Daouk · 2019 to 2026
$54.1MTrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET · 2012 to 2018
$8.7MUnified Computation Tools for Natural Products ResearchR01GM107550 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI COTTRELL, GARRISON W, GERWICK, WILLIAM HENRY · 2013 to 2025
$8.2MDiscovering novel small molecule antibiotics from complex microbial communities by integrating computational mass spectrometry and metagenome miningDP2GM137413 · NIGMS · CARNEGIE-MELLON UNIVERSITY · PI MOHIMANI, HOSEIN · 2019 to 2019
$2.2MCharacterizing Natural Product Mediated Microbial InteractionsR35GM128690 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI PHELAN, VANESSA V · 2018 to 2022
$1.9MMassIVE.quant: a curated and scalable community resource for quantitative proteomicsR01LM013115 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BANDEIRA, NUNO · 2019 to 2022
$1.3MAdvancing data and metadata standards for proteomics mass spectraR24GM127667 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC · 2017 to 2019
$1.2MThe Interactive Metabolome of Polymicrobial BiofilmsK01GM103809 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI PHELAN, VANESSA V · 2012 to 2016
$647kReuse of Public Metabolomics DataR03CA211211 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DORRESTEIN, PIETER C · 2016 to 2016
$155kNCI NIH HHS R03 CA211211NIA NIH HHS U19 AG063744NIGMS NIH HHS DP2 GM137413NIGMS NIH HHS K01 GM103809NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM107550NIGMS NIH HHS R24 GM127667NIGMS NIH HHS R35 GM128690NLM NIH HHS R01 LM013115
Abstract
Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
Indexed as
Mass SpectrometryBiological ProductsComputational BiologyDatabases, FactualMetabolomicsSoftwareBiological Products
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.