Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

(2020) Allegra T. Aron et al.   Nature Protocols

ReDU: a framework to find and reanalyze public mass spectrometry data

(2020) Alan K. Jarmusch 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

Identification of bioactive metabolites using activity metabolomics

(2019) Markus M. Rinschen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2019) Hiroshi Tsugawa et al.   NATURE METHODS

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

(2019) Nils Hoffmann et al.   ANALYTICAL CHEMISTRY

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics

(2019) Xiaotao Shen et al.   Nature Communications

Filtering procedures for untargeted LC-MS metabolomics data

(2019) Courtney Schiffman et al.   BMC BIOINFORMATICS

Ontology-based metabolomics data integration with quality control

(2019) Patricia Buendia et al.   Bioanalysis

The microbiota regulate neuronal function and fear extinction learning

(2019) Coco Chu et al.   NATURE

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

(2019) Elliott J. Price et al.   PLANT JOURNAL

Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for “Precision Medicine and Pharmacometabolomics Task Group”—The Metabolomics Society Initiative)

(2018) Jennifer A. Kirwan et al.   CLINICAL CHEMISTRY

From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

(2018) T. Hautbergue et al.   NATURAL PRODUCT REPORTS

Metabolomics activity screening for identifying metabolites that modulate phenotype

(2018) Carlos Guijas et al.   NATURE BIOTECHNOLOGY

Microbiome metabolomics reveals new drivers of human liver steatosis

(2018) Nathalie M. Delzenne et al.   NATURE MEDICINE

Metabolomics 20 years on: what have we learned and what hurdles remain?

(2018) Saleh Alseekh et al.   PLANT JOURNAL

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation

(2017) Thomas De Vijlder et al.   MASS SPECTROMETRY REVIEWS

Genomewide landscape of gene–metabolome associations in Escherichia coli

(2017) Tobias Fuhrer et al.   Molecular Systems Biology

Systems biology guided by XCMS Online metabolomics

(2017) Tao Huan et al.   NATURE METHODS

Global metabolomics

(2017) Allison Doerr   NATURE METHODS

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

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

Improved batch correction in untargeted MS-based metabolomics

(2016) Ron Wehrens et al.   Metabolomics

Metabolomics: Small molecules, single cells

(2016) Marissa Fessenden   NATURE

Revealing disease-associated pathways by network integration of untargeted metabolomics

(2016) Leila Pirhaji et al.   NATURE METHODS

YMDB 2.0: a significantly expanded version of the yeast metabolome database

(2016) Miguel Ramirez-Gaona et al.   NUCLEIC ACIDS RESEARCH

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

Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals

(2016) Wei Chen et al.   Nature Communications

The WEIZMASS spectral library for high-confidence metabolite identification

(2016) Nir Shahaf et al.   Nature Communications

Genome-wide association study and targeted metabolomics identifies sex-specific association of CPS1 with coronary artery disease

(2016) Jaana A. Hartiala et al.   Nature Communications

Gut Microbiota Orchestrates Energy Homeostasis during Cold

(2015) Claire Chevalier et al.   CELL

ECMDB 2.0: A richer resource for understanding the biochemistry ofE. coli

(2015) Tanvir Sajed 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

Experiment design beyond gut feeling: statistical tests and power to detect differential metabolites in mass spectrometry data

(2014) Diana Trutschel et al.   Metabolomics

Synthetic lethal metabolic targeting of cellular senescence in cancer therapy

(2013) Jan R. Dörr et al.   NATURE

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

(2013) Zheng-Jiang Zhu et al.   Nature Protocols

KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities

(2013) Y. Nakamura et al.   PLANT AND CELL PHYSIOLOGY

Dissemination of metabolomics results: role of MetaboLights and COSMOS

(2013) Reza M Salek et al.   GigaScience

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

(2012) Dajana Vuckovic   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

MetaboLights: towards a new COSMOS of metabolomics data management

(2012) Christoph Steinbeck et al.   Metabolomics

An accelerated workflow for untargeted metabolomics using the METLIN database

(2012) Ralf Tautenhahn et al.   NATURE BIOTECHNOLOGY

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics

(2012) Vishal R Patel et al.   NATURE METHODS

ECMDB: The E. coli Metabolome Database

(2012) An Chi Guo et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

Metabolic priming by a secreted fungal effector

(2011) Armin Djamei et al.   NATURE

Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

(2011) Takayuki Tohge et al.   Nature Protocols

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Recommendations for Reporting Metabolite Data

(2011) A. R. Fernie et al.   PLANT CELL

From models to crop species: caveats and solutions for translational metabolomics

(2011) Takayuki Tohge   Frontiers in Plant Science

Fast sampling for quantitative microbial metabolomics

(2010) Walter M van Gulik   CURRENT OPINION IN BIOTECHNOLOGY

Solid phase extraction for removal of matrix effects in lipophilic marine toxin analysis by liquid chromatography-tandem mass spectrometry

(2009) Arjen Gerssen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Dual Labeling of Metabolites for Metabolome Analysis (DLEMMA): A New Approach for the Identification and Relative Quantification of Metabolites by Means of Dual Isotope Labeling and Liquid Chromatography−Mass Spectrometry

(2009) Liron Feldberg et al.   ANALYTICAL CHEMISTRY

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legumeLotus japonicus

(2009) DIEGO H. SANCHEZ et al.   PLANT CELL AND ENVIRONMENT

Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the Calvin cycle and other metabolic intermediates in Arabidopsis rosettes at different carbon dioxide concentrations

(2009) Stéphanie Arrivault et al.   PLANT JOURNAL

Analytical strategies for LC–MS-based targeted metabolomics

(2008) Wenyun Lu et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Metabolite identification via the Madison Metabolomics Consortium Database

(2008) Qiu Cui et al.   NATURE BIOTECHNOLOGY

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

(2008) Bryson D Bennett et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

(2008) Christian Gieger et al.   PLoS Genetics