ArticleProceedings of the National Academy of Sciences of the United States of America2015
Searching molecular structure databases with tandem mass spectra using CSI:FingerID.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 518 papers.
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Who cites it
518 citing papers in PubMed.
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- 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
- Reduced organic nitrogen compounds dominate the toxicity of PMScience advances · 2026Article
- Times are changing but order matters: transferable prediction of small-molecule liquid chromatography retention times.Nature methods · 2026Article
- Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpa.Plant, cell & environment · 2026Article
- Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Environmental Contaminants in Surface Snow Samples Made from Reclaimed Water at a Ski Resort: A Mass Spectrometry Analysis.ACS environmental Au · 2026Article
- Metabolite correlation networks reveal complex phenotypes of adaptation-driving mutations.Nature communications · 2026Article
- DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.Plant communications · 2026Article
- Structure-guided parameter optimization of feature-based molecular networking for DIA-HRMS screening of antihistamines in cosmetics.Analytical and bioanalytical chemistry · 2026Article
- South Brazilian Amber Propolis: Chemical Profile, and Antioxidant, Antimicrobial and Antileukemic Activities.Molecules (Basel, Switzerland) · 2026Article
- Mass Spectrometry-Based Chromatographic and Computational Workflows for Biomarker and Therapeutic Target Discovery: A Comprehensive Review.Biomedical chromatography : BMC · 2026Review
- Metabolomic and biochemometric profiling of Tecoma stans with mechanistic insights of its in vitro cytotoxic activity.Scientific reports · 2026Article
- From known chemical space to unannotated metabolites: a cluster-guided retention-time driven framework for biologically informed annotation.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Multi-Platform Metabolomics for Fraud Detection in Spices and Botanical Food Supplements: From Fingerprint Acquisition to Decision-Grade Evidence.Molecules (Basel, Switzerland) · 2026Review
- Foundation Models for Liquid Chromatography-High-Resolution Mass Spectrometry: A New Era beyond Labeled Datasets.Analytical chemistry · 2026Article
- Protocol for untargeted LC-MS/MS metabolomics annotation and differential abundance analysis using the SIRIUS Python client.STAR protocols · 2026Article
458 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin.
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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.