ArticleAnalytical chemistry2025
Molecular Structure Discovery for Untargeted Metabolomics Using Biotransformation Rules and Global Molecular Networking.
Article in Analytical chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Computational metabolomics at scale: from open data to insight.Current opinion in biotechnology · 2026Review
- RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.Nucleic acids research · 2026Article
- Reaction-Guided Metabolomics Accelerates High-Throughput Annotation of Xenobiotic Metabolites for Human Exposome.Environmental science & technology · 2025Article
- Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics.Nature communications · 2025Article
- JESTR: Joint Embedding Space Technique for Ranking candidate molecules for the annotation of untargeted metabolomics data.Bioinformatics (Oxford, England) · 2025Article
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Abstract
Although untargeted mass spectrometry-based metabolomics is crucial for understanding life's molecular underpinnings, its effectiveness is hampered by low annotation rates of the generated tandem mass spectra. To address this issue, we introduce a novel data-driven approach, Biotransformation-based Annotation Method (BAM), that leverages molecular structural similarities inherent in biochemical reactions. BAM operates by applying biotransformation rules to known "anchor" molecules, which exhibit high spectral similarity to unknown spectra, thereby hypothesizing and ranking potential structures for the corresponding "suspect" molecule. BAM's effectiveness is demonstrated by its success in annotating query spectra in a global molecular network comprising hundreds of millions of spectra. BAM was able to assign correct molecular structures to 24.2% of examined anchor-suspect cases, thereby demonstrating remarkable advancement in metabolite annotation.
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