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Identification of bioactive metabolites using activity metabolomics

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

(2019) Hiroshi Tsugawa et al.   NATURE METHODS

CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

(2019) Oriol Senan et al.   BIOINFORMATICS

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

(2019) Xavier Domingo-Almenara et al.   ANALYTICAL CHEMISTRY

Advancing untargeted metabolomics using data-independent acquisition mass spectrometry technology

(2019) Ruohong Wang et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Method to Calculate the Retention Index in Hydrophilic Interaction Liquid Chromatography Using Normal Fatty Acid Derivatives as Calibrants

(2019) Quan-Fei Zhu et al.   ANALYTICAL CHEMISTRY

OUP accepted manuscript

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Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition

(2018) Tobias Bruderer et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

A Survey of Orbitrap All Ion Fragmentation Analysis Assessed by an R MetaboList Package to Study Small-Molecule Metabolites

(2018) Enrique Sentandreu et al.   CHROMATOGRAPHIA

Challenges, progress and promises of metabolite annotation for LC–MS-based metabolomics

(2018) Romanas Chaleckis et al.   CURRENT OPINION IN BIOTECHNOLOGY

HMDB 4.0: the human metabolome database for 2018

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

MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition

(2016) Hao Li et al.   ANALYTICAL CHEMISTRY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

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

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

PredRet: Prediction of Retention Time by Direct Mapping between Multiple Chromatographic Systems

(2015) Jan Stanstrup et al.   ANALYTICAL CHEMISTRY

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

(2015) Tomas Cajka et al.   ANALYTICAL CHEMISTRY

Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods

(2015) Daniel Abate-Pella et al.   JOURNAL OF CHROMATOGRAPHY A

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

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

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

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InChI, the IUPAC International Chemical Identifier

(2015) Stephen R Heller et al.   Journal of Cheminformatics

RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data

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New Biomarkers of Coffee Consumption Identified by the Non-Targeted Metabolomic Profiling of Cohort Study Subjects

(2014) Joseph A. Rothwell et al.   PLoS One

An Untargeted Metabolomic Workflow to Improve Structural Characterization of Metabolites

(2013) Igor Nikolskiy et al.   ANALYTICAL CHEMISTRY

Comparison of Information-Dependent Acquisition, SWATH, and MSAll Techniques in Metabolite Identification Study Employing Ultrahigh-Performance Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry

(2013) Xiaochun Zhu et al.   ANALYTICAL CHEMISTRY

LC-MS alignment in theory and practice: a comprehensive algorithmic review

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Analysis of 136 Pesticides in Avocado Using a Modified QuEChERS Method with LC-MS/MS and GC-MS/MS

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Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

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Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

(2012) Warwick B. Dunn et al.   Metabolomics

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

ChemSpider: An Online Chemical Information Resource

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Metabolic profiling of the fission yeast S. pombe: quantification of compounds under different temperatures and genetic perturbation

(2009) Tomáš Pluskal et al.   Molecular BioSystems

Interferences and contaminants encountered in modern mass spectrometry

(2008) Bernd O. Keller et al.   ANALYTICA CHIMICA ACTA