ArticleNature communications2023
MS2Query: reliable and scalable MS
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
50 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.Plant communications · 2026Article
- FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data.ACS measurement science au · 2026Article
- Foundation Models for Liquid Chromatography-High-Resolution Mass Spectrometry: A New Era beyond Labeled Datasets.Analytical chemistry · 2026Article
- Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles.Nature communications · 2026Article
- Benchmarking MS/MS Featurization Strategies for Machine Learning-Driven Metabolite Structure Annotation.Journal of the American Society for Mass Spectrometry · 2026Article
- Characterizing the effect of short wavelengths on the floral flavonoid metabolome of medicinal cannabis using a comparative computational metabolomics workflow.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra.ACS omega · 2026Article
- Structural determination of natural products at speeds and scale of high-throughput screening.Natural product reports · 2026Review
- Molecular Design with Artificial Intelligence: Progress and Perspectives for Small Molecules.Chemical reviews · 2026Review
- Cross ionization mode chemical similarity prediction between tandem mass spectra in metabolomics.Nature communications · 2026Article
- Stress-Induced Plant Specialized Metabolism: Signaling, Multi-Omics Integration, and Plant-Derived Antimicrobial Metabolites to Combat Antimicrobial Resistance.Plants (Basel, Switzerland) · 2026Review
- ChemEmbed: a deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings.Briefings in bioinformatics · 2026Article
- LC-MS Data Processing Using OpenMS.Methods in molecular biology (Clifton, N.J.) · 2026Article
- An Integrative Omics and Network Pharmacology Approach to Evaluate the Antiulcer Activity ofACS omega · 2025Article
- Untargeted metabolomics approaches challenge the nutri-score FOPNL system in soluble cocoa products.NPJ science of food · 2025Article
- Recent Advances in Implementation of Machine Learning for Environmental Nontarget Identification.Environment & health (Washington, D.C.) · 2025Review
- Creation of an Open-Access High-Resolution Tandem Mass Spectral Library of 1000 Food Toxicants.Analytical chemistry · 2025Article
- A large language model for deriving spectral embeddings for accurate compound identification in mass spectrometry.Communications chemistry · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge of metabolite annotation and identification. Only few metabolites have an annotated spectrum in spectral libraries; hence, searching only for exact library matches generally returns a few hits. An attractive alternative is searching for so-called analogues as a starting point for structural annotations; analogues are library molecules which are not exact matches but display a high chemical similarity. However, current analogue search implementations are not yet very reliable and relatively slow. Here, we present MS2Query, a machine learning-based tool that integrates mass spectral embedding-based chemical similarity predictors (Spec2Vec and MS2Deepscore) as well as detected precursor masses to rank potential analogues and exact matches. Benchmarking MS2Query on reference mass spectra and experimental case studies demonstrate improved reliability and scalability. Thereby, MS2Query offers exciting opportunities to further increase the annotation rate of metabolomics profiles of complex metabolite mixtures and to discover new biology.
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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.