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

Adriano Rutz; Wout Bittremieux; Robin Schmid; Olivier Cailloux; Justin J.J. van der Hooft; Mehdi A. Beniddir

doi:10.1039/d5np00034c

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

Adriano Rutz^*, Wout Bittremieux, Robin Schmid, Olivier Cailloux, Justin J.J. van der Hooft, Mehdi A. Beniddir^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

2 Citations (Scopus)

Abstract

Covering: up to 2025 This 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.

Original language	English
Journal	Natural Product Reports
DOIs	https://doi.org/10.1039/d5np00034c
Publication status	E-pub ahead of print - 2025

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10.1039/d5np00034cLicence: CC BY-NC

https://edepot.wur.nl/703291Licence: CC BY-NC

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

abstract = "Covering: up to 2025 This 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.",

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doi = "10.1039/d5np00034c",

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T1 - Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration

T2 - current status, challenges, and opportunities

AU - Rutz, Adriano

AU - Bittremieux, Wout

AU - Schmid, Robin

AU - Cailloux, Olivier

AU - van der Hooft, Justin J.J.

AU - Beniddir, Mehdi A.

PY - 2025

Y1 - 2025

N2 - Covering: up to 2025 This 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.

AB - Covering: up to 2025 This 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.

U2 - 10.1039/d5np00034c

DO - 10.1039/d5np00034c

M3 - Article

AN - SCOPUS:105018480883

SN - 0265-0568

JO - Natural Product Reports

JF - Natural Product Reports

ER -

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

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