Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

2025/09/15 by Adriano Rutz, Wout Bittremieux, Robin Schmid +3 · 1 voice
Biochemistry, Genetics and Molecular Biology · Computer Science · Medicine · #Computational Drug Discovery Methods #Metabolomics and Mass Spectrometry Studies #Microbial Natural Products and Biosynthesis

paper · pdf · doi:10.1039/d5np00034c

openalex publication_date 2025/09/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

Covering: up to 2025This review explores the potential of bioinformatics and chemoinformatics tools to advance the exploration of natural extracts libraries (NELs). Although metabolomics has become a term used routinely in natural product (NP) research, the field remains focused on individual molecules or small sets of compounds, which restricts scalability. This narrow focus is mirrored in the computational handling of generated data, limiting broader insights. By challenging the traditional molecule-first paradigm-a framework historically shaped by practical constraints-we present our vision of using computational approaches to unlock the full potential of NELs, now and in the future.

Citations

• Natural products in drug discovery: advances and opportunities
• MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation
• Effective data visualization strategies in untargeted metabolomics
• A universal language for finding mass spectrometry data patterns
• Discovery of metabolites prevails amid in-source fragmentation
• Microflow Liquid Chromatography Coupled to Multinozzle Electrospray Ionization for Improved Lipidomics Coverage of 3D Clear Cell Renal Cell Carcinoma
• COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database

Discussions

• 🔓Take a look in our latest issue at a #OpenAccess review from @adafede.bsky.social, @mehdibeni.bsky.social et al. exploring the potential of bioinformatics and chemoinformatics tools to advance the e [bsky, 4 points, 0 comments]

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