ArticleJournal of cheminformatics2016
Fragmentation trees reloaded.
Article in Journal of cheminformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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Who cites it
94 citing papers in PubMed.
- Gut microbial metabolism of Flutamide attenuates its therapeutic efficacy against prostate cancer.Gut microbes · 2026Article
- Integrated metabolomics and DNA methylation signatures and their association with flare remission in SLE.Lupus science & medicine · 2026Article
- Protocol for untargeted LC-MS/MS metabolomics annotation and differential abundance analysis using the SIRIUS Python client.STAR protocols · 2026Article
- Interactive Software for Interpreting and Curating High-Resolution Electron Ionization Mass Spectra.Journal of mass spectrometry : JMS · 2026Article
- The Nematicide Tioxazafen Disrupts Proteasome Function via Cytochrome P450 Bioactivation.bioRxiv : the preprint server for biology · 2026Article
- Chimpanzee-Guided Discovery of a Non-Native Bioactive Plant.Animals : an open access journal from MDPI · 2026Article
- A Two-Layer Structural Key Framework for Linking Compound Identifiers and MS/MS Evidence in Spectral Database Curation.Metabolites · 2026Article
- Why machine learning fails at mass spectrometry for small molecules.Nature metabolism · 2026Article
- Structure-informed deep generation enables de novo metabolite annotation in untargeted metabolomics.Nature communications · 2026Article
- Fusarium infection in malting barley drives trichothecene transfer and transformation during brewing process, impacting beer safety and composition.Mycotoxin research · 2026Article
- Evaluation of MassFrontier, MetFrag, MS-FINDER, and SIRIUS for Metabolite Annotation Using an Experimental LC-HRMS Dataset.Biomedicines · 2026Article
- Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS.Nature biotechnology · 2026Article
- Predicting xenobiotic metabolism: a computational approach mining LC-MS/MS data with SIRIUS and BioTransformer.Archives of toxicology · 2026Article
- De Novo Structure Prediction from Tandem Mass Spectra: Algorithms, Benchmarks, and Limitations.Molecules (Basel, Switzerland) · 2026Review
- Amino acids and their metabolites as potential biochemical markers in postmortem vitreous humour.International journal of legal medicine · 2025Article
- Ipecac alkaloid biosynthesis in two evolutionarily distant plants.Nature chemical biology · 2025Article
- mineMS2: annotation of spectral libraries with exact fragmentation patterns.Journal of cheminformatics · 2025Article
- Longitudinal Fragment Profiles Based on Multi-Collision Energy Tandem Mass Spectra Improve the Accuracy of Metabolite Identification in Untargeted Metabolomics.Analytical chemistry · 2025Article
- Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry.bioRxiv : the preprint server for biology · 2025Article
- Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum.The Plant journal : for cell and molecular biology · 2025Article
34 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUntargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring).
resultsWe present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task.
conclusionSIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.
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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.