Mass spectrometry-based metabolomics in microbiome investigations

A Bauermeister, H Mannochio-Russo… - Nature Reviews …, 2022 - nature.com
Microbiotas are a malleable part of ecosystems, including the human ecosystem.
Microorganisms affect not only the chemistry of their specific niche, such as the human gut …

Mining genomes to illuminate the specialized chemistry of life

MH Medema, T de Rond, BS Moore - Nature Reviews Genetics, 2021 - nature.com
All organisms produce specialized organic molecules, ranging from small volatile chemicals
to large gene-encoded peptides, that have evolved to provide them with diverse cellular and …

Feature-based molecular networking in the GNPS analysis environment

LF Nothias, D Petras, R Schmid, K Dührkop, J Rainer… - Nature …, 2020 - nature.com
Molecular networking has become a key method to visualize and annotate the chemical
space in non-targeted mass spectrometry data. We present feature-based molecular …

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

K Dührkop, LF Nothias, M Fleischauer, R Reher… - Nature …, 2021 - nature.com
Metabolomics using nontargeted tandem mass spectrometry can detect thousands of
molecules in a biological sample. However, structural molecule annotation is limited to …

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

AT Aron, EC Gentry, KL McPhail, LF Nothias… - Nature protocols, 2020 - nature.com
Abstract Global Natural Product Social Molecular Networking (GNPS) is an interactive online
small molecule–focused tandem mass spectrometry (MS2) data curation and analysis …

Natural product drug discovery in the artificial intelligence era

FI Saldívar-González, VD Aldas-Bulos… - Chemical …, 2022 - pubs.rsc.org
Natural products (NPs) are primarily recognized as privileged structures to interact with
protein drug targets. Their unique characteristics and structural diversity continue to marvel …

Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking

Z Zhou, M Luo, H Zhang, Y Yin, Y Cai, ZJ Zhu - Nature Communications, 2022 - nature.com
Liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics allows
to measure both known and unknown metabolites in the metabolome. However, unknown …

Ecology and genomics of Actinobacteria: new concepts for natural product discovery

DA van Bergeijk, BR Terlouw, MH Medema… - Nature Reviews …, 2020 - nature.com
Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic
versatility. They produce most of the clinically used antibiotics and a plethora of other natural …

Software tools and approaches for compound identification of LC-MS/MS data in metabolomics

I Blaženović, T Kind, J Ji, O Fiehn - Metabolites, 2018 - mdpi.com
The annotation of small molecules remains a major challenge in untargeted mass
spectrometry-based metabolomics. We here critically discuss structured elucidation …

Artificial intelligence for natural product drug discovery

MW Mullowney, KR Duncan, SS Elsayed… - Nature Reviews Drug …, 2023 - nature.com
Developments in computational omics technologies have provided new means to access
the hidden diversity of natural products, unearthing new potential for drug discovery. In …