Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks

New Untargeted Metabolic Profiling Combining Mass Spectrometry and Isotopic Labeling: Application on Aspergillus fumigatus Grown on Wheat

(2013) Patricia M. Cano et al.   ANALYTICAL CHEMISTRY

Transcription factor NRF2 regulates miR-1 and miR-206 to drive tumorigenesis

(2013) Anju Singh et al.   JOURNAL OF CLINICAL INVESTIGATION

Contextual inhibition of fatty acid synthesis by metformin involves glucose-derived acetyl-CoA and cholesterol in pancreatic tumor cells

(2013) Mary Jo Cantoria et al.   Metabolomics

Pyrimidine homeostasis is accomplished by directed overflow metabolism

(2013) Marshall Louis Reaves et al.   NATURE

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

The Carbon Storage Regulator (Csr) System Exerts a Nutrient-Specific Control over Central Metabolism in Escherichia coli Strain Nissle 1917

(2013) Olga Revelles et al.   PLoS One

Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

(2013) A. C. Mosier et al.   mBio

Stable isotopic labelling-assisted untargeted metabolic profiling reveals novel conjugates of the mycotoxin deoxynivalenol in wheat

(2012) Bernhard Kluger et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Isotopic labeling-assisted metabolomics using LC–MS

(2012) C. Bueschl et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Subsecond Absolute Quantitation of Amine Metabolites Using Isobaric Tags for Discovery of Pathway Activation in Mammalian Cells

(2012) Wei Yuan et al.   ANALYTICAL CHEMISTRY

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

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

mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

(2012) Achuthanunni Chokkathukalam et al.   BIOINFORMATICS

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

(2012) Michael Weitzel et al.   BIOINFORMATICS

MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research

(2012) Christoph Bueschl et al.   BIOINFORMATICS

IDEOM: an Excel interface for analysis of LC–MS-based metabolomics data

(2012) Darren J. Creek et al.   BIOINFORMATICS

iMS2Flux – a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

(2012) C Hart Poskar et al.   BMC BIOINFORMATICS

Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells

(2012) Scott B Crown et al.   BMC Systems Biology

Mitochondrial Metabolism of Glucose and Glutamine Is Required for Intracellular Growth of Toxoplasma gondii

(2012) James I. MacRae et al.   Cell Host & Microbe

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

(2012) Warwick B. Dunn et al.   Metabolomics

Serine is a natural ligand and allosteric activator of pyruvate kinase M2

(2012) Barbara Chaneton et al.   NATURE

Addressing the current bottlenecks of metabolomics: Isotopic Ratio Outlier Analysis™, an isotopic-labeling technique for accurate biochemical profiling

(2012) Felice A de Jong et al.   Bioanalysis

Isotope labeling experiments in metabolomics and fluxomics

(2012) Sebastian Klein et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

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

PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis

(2011) Richard A. Scheltema et al.   ANALYTICAL CHEMISTRY

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

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

Toward Global Metabolomics Analysis with Hydrophilic Interaction Liquid Chromatography–Mass Spectrometry: Improved Metabolite Identification by Retention Time Prediction

(2011) Darren J. Creek et al.   ANALYTICAL CHEMISTRY

Riboneogenesis in Yeast

(2011) Michelle F. Clasquin et al.   CELL

Simplified absolute metabolite quantification by gas chromatography–isotope dilution mass spectrometry on the basis of commercially available source material

(2011) Oliver Vielhauer et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets

(2011) Andris Jankevics et al.   Metabolomics

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

(2011) B. R. B. Haverkorn van Rijsewijk et al.   Molecular Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger 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

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Stable isotope-resolved metabolomics and applications for drug development

(2011) Teresa W.-M. Fan et al.   PHARMACOLOGY & THERAPEUTICS

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

Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry

(2011) David P. Leader et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

TARDIS-based microbial metabolomics: time and relative differences in systems

(2011) Catherine L. Winder et al.   TRENDS IN MICROBIOLOGY

Advances in metabolite identification

(2011) David S Wishart   Bioanalysis

Metabolomic Analysis and Visualization Engine for LC−MS Data

(2010) Eugene Melamud et al.   ANALYTICAL CHEMISTRY

Nontargeted Elucidation of Metabolic Pathways Using Stable-Isotope Tracers and Mass Spectrometry

(2010) Karsten Hiller et al.   ANALYTICAL CHEMISTRY

High-Performance Isotope Labeling for Profiling Carboxylic Acid-Containing Metabolites in Biofluids by Mass Spectrometry

(2010) Kevin Guo et al.   ANALYTICAL CHEMISTRY

Targeted Metabolomics for Biomarker Discovery

(2010) William J. Griffiths et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

MetPA: a web-based metabolomics tool for pathway analysis and visualization

(2010) J. Xia et al.   BIOINFORMATICS

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

(2010) Warwick B. Dunn et al.   CHEMICAL SOCIETY REVIEWS

In vivo D2O labeling to quantify static and dynamic changes in cholesterol and cholesterol esters by high resolution LC/MS

(2010) Jose Castro-Perez et al.   JOURNAL OF LIPID RESEARCH

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

(2010) L. Cottret et al.   NUCLEIC ACIDS RESEARCH

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

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

Differential12C-/13C-Isotope Dansylation Labeling and Fast Liquid Chromatography/Mass Spectrometry for Absolute and Relative Quantification of the Metabolome

(2009) Kevin Guo et al.   ANALYTICAL CHEMISTRY

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

(2009) Lake-Ee Quek et al.   Microbial Cell Factories

Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM)

(2009) Teresa WM Fan et al.   Molecular Cancer

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics

(2009) R. Peyraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative metabolome analysis using liquid chromatography–high-resolution mass spectrometry

(2008) Patrick Kiefer et al.   ANALYTICAL BIOCHEMISTRY

High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole13C Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas

(2008) Patrick Giavalisco et al.   ANALYTICAL CHEMISTRY

Highly sensitive feature detection for high resolution LC/MS

(2008) Ralf Tautenhahn et al.   BMC BIOINFORMATICS

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

(2008) Bryson D Bennett et al.   Nature Protocols

Metabolic flux analysis inEscherichia coli by integrating isotopic dynamic and isotopic stationary13C labeling data

(2007) Jochen Schaub et al.   BIOTECHNOLOGY AND BIOENGINEERING