Stable Isotope–Assisted Plant Metabolomics: Combination of Global and Tracer-Based Labeling for Enhanced Untargeted Profiling and Compound Annotation

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

Stable Isotope-Assisted Plant Metabolomics: Investigation of Phenylalanine-Related Metabolic Response in Wheat Upon Treatment With the Fusarium Virulence Factor Deoxynivalenol

(2019) Maria Doppler et al.   Frontiers in Plant Science

Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data

(2017) Bertrand Rochat   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

(2016) Hendrik Treutler et al.   ANALYTICAL CHEMISTRY

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Using the knowns to discover the unknowns: MS-based dereplication uncovers structural diversity in 17-hydroxygeranyllinalool diterpene glycoside production in the Solanaceae

(2016) Sven Heiling et al.   PLANT JOURNAL

Novel Approach for High-Throughput Metabolic Screening of Whole Plants by Stable Isotopes

(2016) Lisa Maria Dersch et al.   PLANT PHYSIOLOGY

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

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

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

CHANGES IN WHOLE-PLANT METABOLISM DURING GRAIN-FILLING STAGE IN SORGHUM BICOLOR L. (MOENCH) GROWN UNDER ELEVATED CO2 AND DROUGHT

(2015) Amanda Pereira de Souza et al.   PLANT PHYSIOLOGY

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

Untargeted Profiling of Tracer-Derived Metabolites Using Stable Isotopic Labeling and Fast Polarity-Switching LC–ESI-HRMS

(2014) Bernhard Kluger et al.   ANALYTICAL CHEMISTRY

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

(2014) Emma L. Schymanski et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

GC–MS based targeted metabolic profiling identifies changes in the wheat metabolome following deoxynivalenol treatment

(2014) Benedikt Warth et al.   Metabolomics

Metabolite identification: are you sure? And how do your peers gauge your confidence?

(2014) Darren J. Creek et al.   Metabolomics

Metabolomics: What You See is What You Extract

(2014) Young Hae Choi et al.   PHYTOCHEMICAL ANALYSIS

Metabolomics as a Potential Chemotaxonomical Tool: Application in the Genus Vernonia Schreb

(2014) Maria Elvira Poleti Martucci et al.   PLoS One

A novel stable isotope labelling assisted workflow for improved untargeted LC–HRMS based metabolomics research

(2013) Christoph Bueschl et al.   Metabolomics

Exploring the Arabidopsis sulfur metabolome

(2013) Katharina Gläser et al.   PLANT JOURNAL

Stable Isotope-Assisted Metabolomics for Network-Wide Metabolic Pathway Elucidation

(2012) Darren J. Creek et al.   ANALYTICAL CHEMISTRY

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

An accelerated workflow for untargeted metabolomics using the METLIN database

(2012) Ralf Tautenhahn et al.   NATURE BIOTECHNOLOGY

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

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

Metabolism and Growth inArabidopsisDepend on the Daytime Temperature but Are Temperature-Compensated against Cool Nights

(2012) Eva-Theresa Pyl et al.   PLANT CELL

Integrated Metabolo-Proteomic Approach to Decipher the Mechanisms by Which Wheat QTL (Fhb1) Contributes to Resistance against Fusarium graminearum

(2012) Raghavendra Gunnaiah et al.   PLoS One

Liquid chromatography–mass spectrometry based global metabolite profiling: A review

(2011) Georgios A. Theodoridis et al.   ANALYTICA CHIMICA ACTA

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Elemental formula annotation of polar and lipophilic metabolites using13C,15N and34S isotope labelling, in combination with high-resolution mass spectrometry

(2011) Patrick Giavalisco et al.   PLANT JOURNAL

An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research

(2011) Wen-Ping Chen et al.   Proteome Science

Metabolic engineering of the plant primary–secondary metabolism interface

(2010) Asaph Aharoni et al.   CURRENT OPINION IN BIOTECHNOLOGY

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

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

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

13C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

(2009) Patrick Giavalisco et al.   ANALYTICAL CHEMISTRY

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS