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

Global chemical effects of the microbiome include new bile-acid conjugations

(2020) Robert A. Quinn et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Feature-based molecular networking in the GNPS analysis environment

(2020) Louis-Félix Nothias et al.   NATURE METHODS

Structure Annotation of All Mass Spectra in Untargeted Metabolomics

(2019) Ivana Blaženović et al.   ANALYTICAL CHEMISTRY

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

(2019) Kai Dührkop et al.   NATURE METHODS

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms

(2019) Hiroshi Tsugawa et al.   NATURE METHODS

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

(2019) Madeleine Ernst et al.   Metabolites

CANPA: Computer-Assisted Natural Products Anticipation

(2019) Alexander E. Fox Ramos et al.   ANALYTICAL CHEMISTRY

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.

(2019) Madeleine Ernst et al.   Frontiers in Plant Science

Hybrid Search: A Method for Identifying Metabolites Absent from Tandem Mass Spectrometry Libraries

(2019) Brian T. Cooper et al.   ANALYTICAL CHEMISTRY

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

(2019) Peters et al.   Metabolites

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

Advances in computational metabolomics and databases deepen the understanding of metabolisms

(2018) Hiroshi Tsugawa   CURRENT OPINION IN BIOTECHNOLOGY

Propagating annotations of molecular networks using in silico fragmentation

(2018) Ricardo R. da Silva et al.   PLoS Computational Biology

PubChem chemical structure standardization

(2018) Volker D. Hähnke et al.   Journal of Cheminformatics

Identification of small molecules using accurate mass MS/MS search

(2017) Tobias Kind et al.   MASS SPECTROMETRY REVIEWS

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy

(2017) Robert A. Quinn et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Critical Assessment of Small Molecule Identification 2016: automated methods

(2017) Emma L. Schymanski et al.   Journal of Cheminformatics

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

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Global chemical analysis of biology by mass spectrometry

(2017) Alexander A. Aksenov et al.   Nature Reviews Chemistry

Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets

(2017) Dinesh Kumar Barupal et al.   Scientific Reports

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

(2016) Hendrik Treutler et al.   ANALYTICAL CHEMISTRY

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

(2016) Pierre-Marie Allard et al.   ANALYTICAL CHEMISTRY

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software

(2016) Hiroshi Tsugawa et al.   ANALYTICAL CHEMISTRY

Fast metabolite identification with Input Output Kernel Regression

(2016) Céline Brouard et al.   BIOINFORMATICS

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

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

(2016) Hannes L Röst et al.   NATURE METHODS

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Maria Vinaixa et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

Fragmentation trees reloaded

(2016) Sebastian Böcker et al.   Journal of Cheminformatics

Deep learning

(2015) Yann LeCun et al.   NATURE

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Euphorbia Diterpenes: Isolation, Structure, Biological Activity, and Synthesis (2008–2012)

(2014) Andrea Vasas et al.   CHEMICAL REVIEWS

Evolutionary bursts inEuphorbia(Euphorbiaceae) are linked with photosynthetic pathway

(2014) James W. Horn et al.   EVOLUTION

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

A molecular phylogeny and classification of the largely succulent and mainly African Euphorbia subg. Athymalus (Euphorbiaceae)

(2014) Jess A. Peirson et al.   TAXON

Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea

(2013) Lars Ridder et al.   ANALYTICAL CHEMISTRY

Phylogenetics, morphological evolution, and classification of Euphorbia subgenus Euphorbia

(2013) Brian L. Dorsey et al.   TAXON

A worldwide molecular phylogeny and classification of the leafy spurges, Euphorbia subgenus Esula (Euphorbiaceae)

(2013) Ricarda Riina et al.   TAXON

Identifying the Unknowns by Aligning Fragmentation Trees

(2012) Florian Rasche et al.   ANALYTICAL CHEMISTRY

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

Studies on the fragmentation pathways of ingenol esters isolated from Euphorbia esula using IT-MSn and Q-TOF-MS/MS methods in electrospray ionization mode

(2012) Min Yang et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

Automated compound classification using a chemical ontology

(2012) Claudia Bobach et al.   Journal of Cheminformatics

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

(2011) M. Askenazi et al.   NUCLEIC ACIDS RESEARCH

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization

(2008) H. P. Benton et al.   ANALYTICAL CHEMISTRY

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS