Software tools and approaches for compound identification of LC-MS/MS data in metabolomics
The annotation of small molecules remains a major challenge in untargeted mass
spectrometry-based metabolomics. We here critically discuss structured elucidation …
spectrometry-based metabolomics. We here critically discuss structured elucidation …
Accelerating metabolite identification in natural product research: toward an ideal combination of liquid chromatography–high-resolution tandem mass spectrometry …
Natural product research aims to characterize specialized metabolites from various living
organisms and assess their biological properties from either a chemical ecology or drug …
organisms and assess their biological properties from either a chemical ecology or drug …
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …
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
Mass spectrometry is a predominant experimental technique in metabolomics and related
fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 …
fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 …
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
Abstract Global Natural Product Social Molecular Networking (GNPS) is an interactive online
small molecule–focused tandem mass spectrometry (MS2) data curation and analysis …
small molecule–focused tandem mass spectrometry (MS2) data curation and analysis …
The Chemistry Development Kit (CDK) v2. 0: atom typing, depiction, molecular formulas, and substructure searching
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source
cheminformatics toolkit, providing data structures to represent chemical concepts along with …
cheminformatics toolkit, providing data structures to represent chemical concepts along with …
Topic modeling for untargeted substructure exploration in metabolomics
JJJ van Der Hooft, J Wandy… - Proceedings of the …, 2016 - National Acad Sciences
The potential of untargeted metabolomics to answer important questions across the life
sciences is hindered because of a paucity of computational tools that enable extraction of …
sciences is hindered because of a paucity of computational tools that enable extraction of …
Propagating annotations of molecular networks using in silico fragmentation
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 …
untargeted mass spectrometry analysis, as most of our biological interpretations rely on …
Natural products targeting strategies involving molecular networking: different manners, one goal
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 …
the field of natural products research, putting today's natural product chemists in the …
BUDDY: molecular formula discovery via bottom-up MS/MS interrogation
A substantial fraction of metabolic features remains undetermined in mass spectrometry
(MS)-based metabolomics, and molecular formula annotation is the starting point for …
(MS)-based metabolomics, and molecular formula annotation is the starting point for …