ArticleJournal of the American Society for Mass Spectrometry2024
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.
Article in Journal of the American Society for Mass Spectrometry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data.bioRxiv : the preprint server for biology · 2026Article
- A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring.Nature protocols · 2026Review
- OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and evidence for the antimicrobial thiazole alkaloid agrochelin II.Applied and environmental microbiology · 2026Article
- A Functional Metabolomics Framework to Track Microbiome Drug Metabolism.bioRxiv : the preprint server for biology · 2026Article
- The undiscovered natural product potential of Actinomycetes.The Journal of antibiotics · 2026Article
- Multiple Spectrum Alignment for Molecular Networking Exploration and Discovery.Journal of the American Society for Mass Spectrometry · 2026Article
- A resource to empirically establish drug exposure records directly from untargeted metabolomics data.Nature communications · 2025Article
- Effective data visualization strategies in untargeted metabolomics.Natural product reports · 2025Review
- Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry.bioRxiv : the preprint server for biology · 2025Article
- Multispectrum ModiFinder Site Localization Performance.Journal of the American Society for Mass Spectrometry · 2025Article
- Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum.The Plant journal : for cell and molecular biology · 2025Article
- Chemical clues to infection: A pilot study on the differential secondary metabolite production during the life cycle of selectedIMA fungus · 2025Article
- A complementary approach for detecting biological signals through a semi-automated feature selection tool.Frontiers in chemistry · 2024Article
- Analysis of plant metabolomics data using identification-free approaches.Applications in plant sciencesReview
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Authors and funding
12 authors.
Funding
Abstract
Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the reidentification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder which leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes this information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.
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Registered trials
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