4.8 Article

HERMES: a molecular-formula-oriented method to target the metabolome

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

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

Kai Duehrkop et al.

Summary: CANOPUS is a computational tool that uses a deep neural network to predict compound classes from fragmentation spectra, even for compounds lacking reference data. In evaluation, CANOPUS showed high prediction performance and outperformed other baseline methods. It has broad utility in investigating chemical diversity in plants and discovering natural products, providing biological insights at the compound class level.

NATURE BIOTECHNOLOGY (2021)

Article Chemistry, Analytical

Targeting unique biological signals on the fly to improve MS/MS coverage and identification efficiency in metabolomics

Kevin Cho et al.

Summary: The study demonstrates a simple data processing strategy to decrease the number of features for MS/MS analysis in LC/MS experiments by annotating non-biological contaminants and redundancies in real-time. Utilizing optimized collision energies results in more informative MS/MS patterns compared to using a single fixed collision energy. An overall workflow evaluation indicates that optimal fragmentation data can be obtained for over 90% of unique biological metabolites in a sample when features are annotated during acquisition and collision energies are selected using parallel mass spectrometry detection.

ANALYTICA CHIMICA ACTA (2021)

Review Chemistry, Multidisciplinary

Chemical Discovery in the Era of Metabolomics

Miriam Sindelar et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Biochemical Research Methods

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Allegra T. Aron et al.

NATURE PROTOCOLS (2020)

Article Computer Science, Artificial Intelligence

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

Marcus Ludwig et al.

NATURE MACHINE INTELLIGENCE (2020)

Article Chemistry, Analytical

Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics

Xavier Domingo-Almenara et al.

ANALYTICAL CHEMISTRY (2019)

Article Biochemical Research Methods

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

Kai Duhrkop et al.

NATURE METHODS (2019)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

Yannick Djoumbou-Feunang et al.

JOURNAL OF CHEMINFORMATICS (2019)

Article Biochemistry & Molecular Biology

HMDB 4.0: the human metabolome database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Metabolomics and Isotope Tracing

Cholsoon Jang et al.

Review Chemistry, Analytical

Annotation: A Computational Solution for Streamlining Metabolomics Analysis

Xavier Domingo-Almenara et al.

ANALYTICAL CHEMISTRY (2018)

Article Biochemical Research Methods

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Andrew Palmer et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

Jeremy P. Koelmel et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2017)

Letter Biochemical Research Methods

Systems biology guided by XCMS Online metabolomics

Tao Huan et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes L. Roest et al.

NATURE METHODS (2016)

Review Chemistry, Analytical

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

Maria Vinaixa et al.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2016)

Review Biochemical Research Methods

A roadmap for interpreting 13C metabolite labeling patterns from cells

Joerg M. Buescher et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

Review Biochemistry & Molecular Biology

Defining the Metabolome: Size, Flux, and Regulation

Nicola Zamboni et al.

MOLECULAR CELL (2015)

Article Biochemical Research Methods

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

Hiroshi Tsugawa et al.

NATURE METHODS (2015)

Article Chemistry, Analytical

Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods

Nathaniel Guy Mahieu et al.

ANALYTICAL CHEMISTRY (2014)

Article Biochemical Research Methods

LipidBlast in silico tandem mass spectrometry database for lipid identification

Tobias Kind et al.

NATURE METHODS (2013)

Letter Biotechnology & Applied Microbiology

A cross-platform toolkit for mass spectrometry and proteomics

Matthew C. Chambers et al.

NATURE BIOTECHNOLOGY (2012)

Article Biochemistry & Molecular Biology

LIPID MAPS online tools for lipid research

Eoin Fahy et al.

NUCLEIC ACIDS RESEARCH (2007)