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 …

The re-emergence of natural products for drug discovery in the genomics era

AL Harvey, RA Edrada-Ebel, RJ Quinn - Nature reviews drug discovery, 2015 - nature.com
Natural products have been a rich source of compounds for drug discovery. However, their
use has diminished in the past two decades, in part because of technical barriers to …

Identification of small molecules using accurate mass MS/MS search

T Kind, H Tsugawa, T Cajka, Y Ma, Z Lai… - Mass spectrometry …, 2018 - Wiley Online Library
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS
spectra from screening small molecules in fields such as environmental analysis, drug …

Bioactivity-based molecular networking for the discovery of drug leads in natural product bioassay-guided fractionation

LF Nothias, M Nothias-Esposito… - Journal of natural …, 2018 - ACS Publications
It is a common problem in natural product therapeutic lead discovery programs that despite
good bioassay results in the initial extract, the active compound (s) may not be isolated …

Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities

LK Caesar, R Montaser, NP Keller… - Natural product reports, 2021 - pubs.rsc.org
Covering: 2010 to 2021 Organisms in nature have evolved into proficient synthetic chemists,
utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of …

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication

PM Allard, T Péresse, J Bisson, K Gindro… - Analytical …, 2016 - ACS Publications
Dereplication represents a key step for rapidly identifying known secondary metabolites in
complex biological matrices. In this context, liquid-chromatography coupled to high …

Current approaches and challenges for the metabolite profiling of complex natural extracts

JL Wolfender, G Marti, A Thomas, S Bertrand - Journal of Chromatography …, 2015 - Elsevier
Metabolite profiling is critical in many aspects of the life sciences, particularly natural product
research. Obtaining precise information on the chemical composition of complex natural …

Propagating annotations of molecular networks using in silico fragmentation

RR da Silva, M Wang, LF Nothias… - PLoS computational …, 2018 - journals.plos.org
The annotation of small molecules is one of the most challenging and important steps in
untargeted mass spectrometry analysis, as most of our biological interpretations rely on …

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

T Netzker, J Fischer, J Weber, DJ Mattern… - Frontiers in …, 2015 - frontiersin.org
Microorganisms form diverse multispecies communities in various ecosystems. The high
abundance of fungal and bacterial species in these consortia results in specific …

Dereplication strategies in natural product research: How many tools and methodologies behind the same concept?

J Hubert, JM Nuzillard, JH Renault - Phytochemistry Reviews, 2017 - Springer
The development of new drugs will certainly benefit from an ever improving knowledge of
the living beings chemistry. However, identification of drugable molecules within the …