ArticlePLoS computational biology2018
Propagating annotations of molecular networks using in silico fragmentation.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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
158 citing papers in PubMed, 363 citations in OpenAlex.
- Molecular-networking-based characterization of cytotoxic metabolites produced by the cyanobacterium Nostoc edaphicum CCNP1411.Molecular diversity · 2026Article
- LC-HRMS and Molecular Networking for Non-Targeted Screening of Emerging Contaminants in Cosmetics: Workflow, Applications, and Regulatory Challenges.Molecules (Basel, Switzerland) · 2026Review
- Integrated volatile and non-volatile metabolomics reveal aroma chemotypes in Capsicum cultivars.Food chemistry: X · 2026Article
- Bioactivity-guided metabolomics reveals discriminant cytotoxic signatures in Siparuna guianensis.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Extensive variation between chromosomes of North American and European hop.Nature communications · 2026Article
- Repositioning Natural Products in Modern Drug Discovery: Technological Innovation, Systems Pharmacology, and Pathological Validation.International journal of molecular sciences · 2026Review
- Structural determination of natural products at speeds and scale of high-throughput screening.Natural product reports · 2026Review
- A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring.Nature protocols · 2026Review
- Chemical diversity and species differentiation in Brazilian Vanilla: insights from LC-HRMS/MS metabolomics.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associatedmSystems · 2026Article
- Silicone-Foam Passive Air Samplers for Combined Target and Nontarget Chemical Profiling and Toxicity Assessment of Airborne Exposomes.Environmental science & technology · 2026Article
- Discovery of pyridomycin derivatives as InhA inhibitors from actinomycetes through molecular networking and an In-House tandem mass library.Natural products and bioprospecting · 2026Article
- The undiscovered natural product potential of Actinomycetes.The Journal of antibiotics · 2026Article
- Breaking the boundaries of affinity selection-mass spectrometry: From ligand screening to target-ligand interaction insights.Journal of pharmaceutical analysis · 2026Review
- Large-Scale Metabolite Annotation in Untargeted Metabolomics Using MetDNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Molecular Networking in Cosmetic Analysis: A Review of Non-Targeted Profiling for Safety Hazards and Bioactive Compounds.Molecules (Basel, Switzerland) · 2025Review
- Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics.Nature communications · 2025Article
- Automated annotation of complex natural products using a modular fragmentation-based structure assembly (MFSA) strategy.Science advances · 2025Article
- Contact- and Water-Mediated Interactions With an Allelopathic Macroalga Drive Distinct Coral Microbiome and Metabolome.Environmental microbiology · 2025Article
- Effective data visualization strategies in untargeted metabolomics.Natural product reports · 2025Review
98 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
10 authors at 3 institutions in 3 countries.
Funding
Abstract
The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.