ArticleNature methods2021
DecoID improves identification rates in metabolomics through database-assisted MS/MS deconvolution.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A metabolomic signature of the APOE2 allele.GeroScience · 2023Pooled it
- Acute aerobic exercise reveals that FAHFAs distinguish the metabolomes of overweight and normal-weight runners.JCI insight · 2022Trial
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- ENVnet provides a global molecular resource of dissolved organic matter.Nature biotechnology · 2026Article
- Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites.Journal of the American Society for Mass Spectrometry · 2026Article
- Assessing the metabolomics "dark matter" by a detectable khipu model.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Decoding cancer across scales with metabolomics.Nature reviews. Cancer · 2026Review
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- Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry.Nature methods · 2026Article
- Review
- FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra.Nature communications · 2025Article
- Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics.Nature communications · 2025Article
- Longitudinal Fragment Profiles Based on Multi-Collision Energy Tandem Mass Spectra Improve the Accuracy of Metabolite Identification in Untargeted Metabolomics.Analytical chemistry · 2025Article
- Extracellular matrix repair and organization of chronic infected diabetic wounds treated with methacrylated chitosan-based hydrogels.Acta biomaterialia · 2025Article
- Article
- Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer.Nature methods · 2025Article
- Identification, Genome Characterization, and Growth Optimization ofMicroorganisms · 2025Article
- Integrating Metabolomics and Genomics to Uncover Antimicrobial Compounds inAntibiotics (Basel, Switzerland) · 2025Article
- A comprehensive review on computational metabolomics: Advancing multiscale analysis throughComputational and structural biotechnology journal · 2025Review
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Authors and funding
4 authors.
Funding
Abstract
Chimeric MS/MS spectra contain fragments from multiple precursor ions and therefore hinder compound identification in metabolomics. Historically, deconvolution of these chimeric spectra has been challenging and relied on specific experimental methods that introduce variation in the ratios of precursor ions between multiple tandem mass spectrometry (MS/MS) scans. DecoID provides a complementary, method-independent approach where database spectra are computationally mixed to match an experimentally acquired spectrum by using LASSO regression. We validated that DecoID increases the number of identified metabolites in MS/MS datasets from both data-independent and data-dependent acquisition without increasing the false discovery rate. We applied DecoID to publicly available data from the MetaboLights repository and to data from human plasma, where DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching. DecoID is compatible with any user-defined MS/MS database and provides automated searching for some of the largest MS/MS databases currently available.
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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.