Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids

With over 3000 representatives, the monoterpene indole alkaloids (MIAs) class is among the most diverse families of plant natural products. The MS/MS spectral space exploration of these complex compounds using chemoinformatic and computational mass spectrometry tools offers a valuable opportunity to...

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Vydáno v:Journal of cheminformatics Ročník 17; číslo 1; s. 62 - 15
Hlavní autoři: Szwarc, Sarah, Rutz, Adriano, Lee, Kyungha, Mejri, Yassine, Bonnet, Olivier, Hazni, Hazrina, Jagora, Adrien, Mbeng Obame, Rany B., Noh, Jin Kyoung, Otogo N’Nang, Elvis, Alaribe, Stephenie C., Awang, Khalijah, Bernadat, Guillaume, Choi, Young Hae, Courdavault, Vincent, Frederich, Michel, Gaslonde, Thomas, Huber, Florian, Kam, Toh-Seok, Low, Yun Yee, Poupon, Erwan, van der Hooft, Justin J. J., Kang, Kyo Bin, Le Pogam, Pierre, Beniddir, Mehdi A.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Cham Springer International Publishing 28.04.2025
BioMed Central Ltd
Springer Nature B.V
Chemistry Central Ltd. and BioMed Central
BMC
Témata:
Alkaloids
Biological products
Chemical Sciences
Chemistry
Chemistry and Materials Science
Complex compounds
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Computer Graphics and Computer-Aided Design
Computer Science
Computer Science Applications
Datasets
Discovery and exploration
Documentation and Information in Chemistry
Expert knowledge
Family
Fragmentation
Human health sciences
Indoles
Library and Information Sciences
Mass spectrometry
Mass spectroscopy
Missing in action
Monoterpene indole alkaloids
MS/MS
Natural products
Outer space
Pharmacie, pharmacologie & toxicologie
Pharmacy, pharmacology & toxicology
Physical and Theoretical Chemistry
Plant extracts
Query
Scaffold
Sciences de la santé humaine
Signatures
Similarity
Software
Space exploration
Spectra
Theoretical and Computational Chemistry
Workflow
Mississippi
Massachusetts
Expert knowledge
Scaffold
Query
Similarity
MS/MS
Monoterpene indole alkaloids
ISSN:1758-2946, 1758-2946
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Popis
Shrnutí:With over 3000 representatives, the monoterpene indole alkaloids (MIAs) class is among the most diverse families of plant natural products. The MS/MS spectral space exploration of these complex compounds using chemoinformatic and computational mass spectrometry tools offers a valuable opportunity to extract and share chemical insights from this emblematic family of natural products (NPs). In this work, we first present a substantially updated version of the MIADB, a database now containing 422 MS/MS spectra of MIAs that has been uploaded to the GNPS library versus 172 initial entries. We then introduce an innovative workflow that leverages hundreds of fragmentation spectra to support the FAIRification, extraction and dissemination of chemical knowledge. This workflow aims at the extraction of spectral patterns matching finely defined MIA skeletons. These extracted signatures can then be queried against complex biological extract datasets using MassQL. By applying this strategy to an LC-MS/MS dataset of 75 plant extracts, our results demonstrated the efficiency of this approach in identifying the diversity of MIA skeletons present in the analyzed samples. Additionally, our work enabled the digitization of structural data for diverse MIA skeletons by converting them into machine-readable formats and thereby enhancing their dissemination for the scientific community. Scientific contribution A comprehensive investigation of the monoterpene indole alkaloid chemical space, aiming to highlight skeleton-dependent fragmentation similarity trends and to generate valuable spectrometric signatures that could be used as queries. Graphical Abstract
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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scopus-id:2-s2.0-105003763854
ISSN:1758-2946
1758-2946
DOI:10.1186/s13321-025-01009-0