[HTML][HTML] 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 …

Advanced methods for natural products discovery: bioactivity screening, dereplication, metabolomics profiling, genomic sequencing, databases and informatic tools …

SP Gaudêncio, E Bayram, L Lukić Bilela, M Cueto… - Marine drugs, 2023 - mdpi.com
Natural Products (NP) are essential for the discovery of novel drugs and products for
numerous biotechnological applications. The NP discovery process is expensive and time …

CFM-ID 4.0: more accurate ESI-MS/MS spectral prediction and compound identification

F Wang, J Liigand, S Tian, D Arndt, R Greiner… - Analytical …, 2021 - ACS Publications
In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for
identifying and annotating metabolites. As this typically involves matching a given MS …

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 …

High-confidence structural annotation of metabolites absent from spectral libraries

MA Hoffmann, LF Nothias, M Ludwig… - Nature …, 2022 - nature.com
Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but,
typically, only a small fraction of spectra can be matched. Previous in silico methods search …

Tandem mass spectrum prediction for small molecules using graph transformers

A Young, H Röst, B Wang - Nature Machine Intelligence, 2024 - nature.com
Tandem mass spectra capture fragmentation patterns that provide key structural information
about molecules. Although mass spectrometry is applied in many areas, the vast majority of …

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

K Dührkop, M Fleischauer, M Ludwig, AA Aksenov… - Nature …, 2019 - nature.com
Mass spectrometry is a predominant experimental technique in metabolomics and related
fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 …

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 …

METLIN: a technology platform for identifying knowns and unknowns

C Guijas, JR Montenegro-Burke… - Analytical …, 2018 - ACS Publications
METLIN originated as a database to characterize known metabolites and has since
expanded into a technology platform for the identification of known and unknown …

Nontarget screening with high resolution mass spectrometry in the environment: ready to go?

J Hollender, EL Schymanski, HP Singer, PL Ferguson - 2017 - ACS Publications
The vast, diverse universe of organic pollutants is a formidable challenge for environmental
sciences, engineering, and regulation. Nontarget screening (NTS) based on high resolution …