ArticleNature communications2021
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment.
Abstract read
In one paragraph
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers.
0numbers the graph read from it
0cells of the map it votes in
173citing 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
173 citing papers in PubMed.
- Annotating Tandem Mass Spectra in Metabolomics with DreaMS and MassSpecGym.Methods in molecular biology (Clifton, N.J.) · 2027Article
- eCOMET: an R package for evaluating metabolic diversity and enrichment from LC-MS/MS data to test ecological hypotheses from individuals to ecosystems.The New phytologist · 2026Article
- Integrated molecular networking-guided discovery of antimicrobial secondary metabolites fromRSC advances · 2026Article
- Observational
- Chemical Ontogeny in Plants: Developmental Dynamics of Specialized Metabolism and Implications for Ecology, Quality Control, and Bioprospecting.Plants (Basel, Switzerland) · 2026Review
- Biosynthesis of pathogen-induced hydroxylated tryptamine derivatives in barley.Plant physiology · 2026Article
- Tandyukisins K-P, New Decalin Polyketides fromAntibiotics (Basel, Switzerland) · 2026Article
- Discovery of VEGFR-2 Inhibitors From Leonurus japonicus via Integrated Genetic Authentication, Molecular Networking, and In Silico Analysis.Archiv der Pharmazie · 2026Article
- LC-HRMS and Molecular Networking for Non-Targeted Screening of Emerging Contaminants in Cosmetics: Workflow, Applications, and Regulatory Challenges.Molecules (Basel, Switzerland) · 2026Review
- Ordering molecular diversity in untargeted metabolomics via molecular community networking.Cell reports methods · 2026Article
- Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021-2025).Analytical chemistry · 2026Review
- Direct Capture Methods Reveal Extensive Organohalide Chemical Space in Marine Environments.Marine drugs · 2026Article
- Chimpanzee-Guided Discovery of a Non-Native Bioactive Plant.Animals : an open access journal from MDPI · 2026Article
- A polarity-based two-dimensional LC-MS/MS distribution strategy combined with ion identity molecular networking for enhanced metabolite annotation in Astragalus Radix species.Analytical and bioanalytical chemistry · 2026Article
- Characterization of Atrasentan Metabolic Pathway in Human Liver Microsomes Using Feature-Based Molecular Networking.Pharmaceutics · 2026Article
- Inducible CRISPRi enables efficient and high-fidelity genome editing in Streptomyces.Nucleic acids research · 2026Article
- Lipid Class Prediction from MS1 Data using Gaussian Graphical Models.Analytical chemistry · 2026Article
- Chemical Profiling of Aboveground and Underground Parts ofMolecules (Basel, Switzerland) · 2026Article
- From Target-Nontarget to Nontarget Screening: A Review on Screening Methods for Organic Pollutants Based on High-Resolution Mass Spectrometry.Environment & health (Washington, D.C.) · 2026Review
- Structural determination of natural products at speeds and scale of high-throughput screening.Natural product reports · 2026Review
113 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
45 authors.
Robin Schmid *Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Daniel Petras *Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-6561-3022
Louis-Félix Nothias *Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Mingxun WangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0001-7647-6097
Allegra T AronSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Annika JagelsInstitute of Food Chemistry, University of Münster, Münster, Germany.
Hiroshi TsugawaRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0002-2015-3958
Johannes RainerInstitute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.ORCID http://orcid.org/0000-0002-6977-7147
Mar Garcia-AloyInstitute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.ORCID http://orcid.org/0000-0002-1330-6610
Kai DührkopChair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany.ORCID http://orcid.org/0000-0002-9056-0540
Ansgar KorfInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.ORCID http://orcid.org/0000-0002-2769-2460
Tomáš PluskalInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.ORCID http://orcid.org/0000-0002-6940-3006
Zdeněk KameníkInstitute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.ORCID http://orcid.org/0000-0002-5363-0597
Alan K JarmuschSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-2228-6308
Andrés Mauricio Caraballo-RodríguezSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Kelly C WeldonSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-1064-8153
Melissa Nothias-EspositoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Alexander A AksenovSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-9445-2248
Anelize BauermeisterSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Andrea Albarracin OrioIRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina.ORCID http://orcid.org/0000-0002-4722-1439
Carlismari O GrundmannSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-2799-3527
Fernando VargasSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Irina KoesterScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-1571-882X
Julia M GauglitzSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Emily C GentrySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-0016-8132
Yannick HövelmannInstitute of Food Chemistry, University of Münster, Münster, Germany.
Svetlana A KalininaInstitute of Food Chemistry, University of Münster, Münster, Germany.
Matthew A PendergraftScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4415-7651
Morgan PanitchpakdiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Richard TehanDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
Audrey Le GouellecUniv. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France.ORCID http://orcid.org/0000-0002-4905-3854
Gajender AletiDepartment of Psychiatry, University of California San Diego, San Diego, CA, USA.
Helena Mannochio RussoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Birgit ArndtInstitute of Food Chemistry, University of Münster, Münster, Germany.
Florian HübnerInstitute of Food Chemistry, University of Münster, Münster, Germany.
Heiko HayenInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Hui ZhiDivision of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Manuela RaffatelluDivision of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6487-4215
Kimberly A PratherScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Lihini I AluwihareScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Sebastian BöckerChair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany.ORCID http://orcid.org/0000-0002-9304-8091
Kerry L McPhailDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.ORCID http://orcid.org/0000-0003-2076-1002
Hans-Ulrich HumpfInstitute of Food Chemistry, University of Münster, Münster, Germany.ORCID http://orcid.org/0000-0003-3296-3058
Uwe KarstInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Pieter C DorresteinSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA. pdorrestein@ucsd.edu.ORCID http://orcid.org/0000-0002-3003-1030
Funding
TrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 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
$8.2MC3-Dependent Intracellular Killing in Innate Immunity and Bacterial PathogenesisR01AI145325 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NIZET, VICTOR, RAFFATELLU, MANUELA · 2019 to 2023
$3.1MModulation of Protein Biogenesis and Secretion by Natural Product Translocon LigandsR01GM132649 · NIGMS · OREGON STATE UNIVERSITY · PI ISHMAEL, JANE E, MCPHAIL, KERRY LEIGH · 2019 to 2024
$2.0MNutritional immunity during Salmonella infectionR01AI126277 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RAFFATELLU, MANUELA · 2016 to 2020
$1.9MDevelopment of siderophore-based vaccines against non-typhoidal Salmonella infectionR01AI114625 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NOLAN, ELIZABETH M, RAFFATELLU, MANUELA · 2015 to 2019
$1.9MNutritional immunity during Salmonella infectionR37AI126277 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Manuela Raffatellu · 2023 to 2026
$1.8MResearch Training in Natural Product Complementary and Integrative Health - Diversity Supplement to T32 Predoctoral Training GrantT32AT010131 · NCCIH · OREGON STATE UNIVERSITY · PI TAIFO MAHMUD, RICHARD B VAN BREEMEN · 2020 to 2026
$1.8MHarnessing iron acquisition to hinder enterobacterial pathogenesisR56AI114625 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NOLAN, ELIZABETH M, RAFFATELLU, MANUELA · 2022 to 2022
$400kReuse of Public Metabolomics DataR03CA211211 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DORRESTEIN, PIETER C · 2016 to 2016
$155kNCCIH NIH HHS T32 AT010131NCI NIH HHS R03 CA211211NIAID NIH HHS R01 AI114625NIAID NIH HHS R01 AI126277NIAID NIH HHS R01 AI145325NIAID NIH HHS R37 AI126277NIAID NIH HHS R56 AI114625NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM107550NIGMS NIH HHS R01 GM132649
Abstract
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
Indexed as
Metabolic Networks and PathwaysAnimalsComputational BiologyInternetIonsMass SpectrometryMetabolomicsMolecular StructureReproducibility of ResultsSoftwareIons
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
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.