[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 analytical and informatic strategies for metabolite annotation in untargeted metabolomics

Y Cai, Z Zhou, ZJ Zhu - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics is
constantly challenged by large-scale and unambiguous metabolite annotation in complex …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

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 …

The Chemistry Development Kit (CDK) v2. 0: atom ty**, depiction, molecular formulas, and substructure searching

EL Willighagen, JW Mayfield, J Alvarsson… - Journal of …, 2017 - Springer
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source
cheminformatics toolkit, providing data structures to represent chemical concepts along with …

Fully automated unconstrained analysis of high-resolution mass spectrometry data with machine learning

DA Boiko, KS Kozlov, JV Burykina… - Journal of the …, 2022 - ACS Publications
Mass spectrometry (MS) is a convenient, highly sensitive, and reliable method for the
analysis of complex mixtures, which is vital for materials science, life sciences fields such as …

Recent advances in proteomics and metabolomics in plants

S Yan, R Bhawal, Z Yin, TW Thannhauser… - Molecular Horticulture, 2022 - Springer
Over the past decade, systems biology and plant-omics have increasingly become the main
stream in plant biology research. New developments in mass spectrometry and …

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 …

Natural products targeting strategies involving molecular networking: different manners, one goal

AEF Ramos, L Evanno, E Poupon, P Champy… - Natural product …, 2019 - pubs.rsc.org
Covering: up to 2019 Landmark advances in bioinformatics tools have recently enhanced
the field of natural products research, putting today's natural product chemists in the …