skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Bioinformatics: The Next Frontier of Metabolomics

Journal Article · · Analytical Chemistry
DOI:https://doi.org/10.1021/ac5040693· OSTI ID:1167049
 [1];  [1];  [1];  [1]
  1. Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California 92037, United States

Sponsoring Organization:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
Grant/Contract Number:
AC0205CH11231; FG02-07ER64325
OSTI ID:
1167049
Journal Information:
Analytical Chemistry, Journal Name: Analytical Chemistry Vol. 87 Journal Issue: 1; ISSN 0003-2700
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 82 works
Citation information provided by
Web of Science

References (92)

Advances in metabolite identification journal August 2011
The Application of Isotopes to the Study of Intermediary Metabolism journal March 1938
MOLECULAR BIOLOGY: NIH Molecular Libraries Initiative journal November 2004
Toward Global Metabolomics Analysis with Hydrophilic Interaction Liquid Chromatography–Mass Spectrometry: Improved Metabolite Identification by Retention Time Prediction journal November 2011
Analyzing time series gene expression data journal May 2004
Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses journal June 2014
Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example journal August 2009
Metabolomic Profiling Reveals Mitochondrial-Derived Lipid Biomarkers That Drive Obesity-Associated Inflammation journal June 2012
Global reconstruction of the human metabolic network based on genomic and bibliomic data journal January 2007
After the feature presentation: technologies bridging untargeted metabolomics and biology journal August 2014
Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism journal July 2013
A Plasma Long‐Chain Acylcarnitine Predicts Cardiovascular Mortality in Incident Dialysis Patients journal November 2013
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes journal October 2005
MetPA: a web-based metabolomics tool for pathway analysis and visualization journal July 2010
Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling journal November 2010
RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data journal June 2014
Elemental formula annotation of polar and lipophilic metabolites using 13 C, 15 N and 34 S isotope labelling, in combination with high-resolution mass spectrometry journal July 2011
XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data journal June 2012
OpenMS – An open-source software framework for mass spectrometry journal March 2008
KEGG: Kyoto Encyclopedia of Genes and Genomes journal January 1999
Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods journal September 2014
apLCMS—adaptive processing of high-resolution LC/MS data journal May 2009
An Estimation of Acetic acid Formation in the rat journal June 1945
Characterization of Differential Cocaine Metabolism in Mouse and Rat through Metabolomics-Guided Metabolite Profiling journal October 2012
MassBank: a public repository for sharing mass spectral data for life sciences journal July 2010
Predicting Network Activity from High Throughput Metabolomics journal July 2013
The Elements of Statistical Learning book January 2009
Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics journal January 2009
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity journal January 2012
13 C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research journal August 2009
Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia journal November 2011
GMD@CSB.DB: the Golm Metabolome Database journal December 2004
Metabolomics and first-trimester prediction of early-onset preeclampsia journal March 2012
Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry journal January 2006
An accelerated workflow for untargeted metabolomics using the METLIN database journal September 2012
Acidosis induces reprogramming of cellular metabolism to mitigate oxidative stress journal January 2013
XCMS 2 : Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization journal July 2008
A study on retention “projection” as a supplementary means for compound identification by liquid chromatography–mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments journal September 2011
Peak Aggregation as an Innovative Strategy for Improving the Predictive Power of LC-MS Metabolomic Profiles journal February 2014
Metabolome Analysis of Biosynthetic Mutants Reveals a Diversity of Metabolic Changes and Allows Identification of a Large Number of New Compounds in Arabidopsis     journal June 2008
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data journal May 2010
MetaboAnalyst: a web server for metabolomic data analysis and interpretation journal May 2009
A Computer Program for Classifying Plants journal October 1960
The Edinburgh human metabolic network reconstruction and its functional analysis journal January 2007
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS: Metabolic flux profiling in E.���coli journal March 2003
XCMS:  Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification journal February 2006
Metabolomic profiling of regulatory lipid mediators in sputum from adult cystic fibrosis patients journal July 2012
Development of Ecom 50 and Retention Index Models for Nontargeted Metabolomics: Identification of 1,3-Dicyclohexylurea in Human Serum by HPLC/Mass Spectrometry journal April 2012
MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach journal June 2014
Analysis and Quantitation of Ceramide book January 2002
Glycerolipid and cholesterol ester analyses in biological samples by mass spectrometry journal November 2011
Accurate Mass Liquid Chromatography/Mass Spectrometry on Quadrupole Orthogonal Acceleration Time-of-Flight Mass Analyzers Using Switching between Separate Sample and Reference Sprays. 2. Applications Using the Dual-Electrospray Ion Source journal May 2001
Radiation Metabolomics. 4. UPLC-ESI-QTOFMS-Based Metabolomics for Urinary Biomarker Discovery in Gamma-Irradiated Rats journal April 2011
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data journal July 2010
Reactome knowledgebase of human biological pathways and processes journal January 2009
Metabolite profiling and beyond: approaches for the rapid processing and annotation of human blood serum mass spectrometry data journal April 2013
xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data journal January 2013
X 13 CMS: Global Tracking of Isotopic Labels in Untargeted Metabolomics journal January 2014
Metabolomic data streaming for biology-dependent data acquisition journal June 2014
Reconstruction of biochemical networks in microorganisms journal December 2008
On the Utilization of Acetic acid for Cholesterol Formation journal October 1942
Fatty Acid Labeling from Glutamine in Hypoxia Can Be Explained by Isotope Exchange without Net Reductive Isocitrate Dehydrogenase (IDH) Flux journal October 2013
PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis journal April 2011
Simple data-reduction method for high-resolution LC–MS data in metabolomics journal December 2009
Chemometrics in Metabonomics journal February 2007
Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data journal February 2012
LC‐MS‐MS Analysis of Neutral Eicosanoids book October 2007
Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin journal January 2012
A View from Above: Cloud Plots to Visualize Global Metabolomic Data journal December 2012
CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets journal December 2011
Metabolic fingerprint of Gestational Diabetes Mellitus journal May 2014
Investigations into the accuracy and precision obtainable on accurate mass measurements on a quadrupole orthogonal acceleration time-of-flight mass spectrometer using liquid chromatography as sample introduction journal January 2003
isoMETLIN: A Database for Isotope-Based Metabolomics journal September 2014
N-methylnicotinamide and nicotinamide N-methyltransferase are associated with microRNA-1291-altered pancreatic carcinoma cell metabolome and suppressed tumorigenesis journal August 2014
In Vivo 15N-Enrichment of Metabolites in Suspension Cultured Cells and Its Application to Metabolomics journal August 2006
A methodology for automated comparative analysis of metabolite profiling data journal February 2003
Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study journal March 2013
A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics journal July 2004
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal November 2003
High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole 13 C Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas journal December 2008
Azelaic and pimelic acids: Metabolic intermediates or artefacts? journal March 1992
Microbial Metabolomics with Gas Chromatography/Mass Spectrometry journal January 2006
Metabolomic profiling of serum in the progression of Alzheimer's disease by capillary electrophoresis-mass spectrometry: CE and CEC journal October 2014
MolFind: A Software Package Enabling HPLC/MS-Based Identification of Unknown Chemical Structures journal September 2012
Quantification and Mass Isotopomer Profiling of α-Keto Acids in Central Carbon Metabolism journal February 2014
ChEBI: a database and ontology for chemical entities of biological interest journal December 2007
Constructing a mass measurement error surface to improve automatic annotations in liquid chromatography/mass spectrometry based metabolomics: Automatic annotations in LC/MS-based metabolomics journal October 2013
MeltDB: a software platform for the analysis and integration of metabolomics experiment data journal September 2008
Identification of Urinary Biomarkers Useful for Distinguishing a Difference in Mechanism of Toxicity in Rat Model of Cholestasis journal September 2009
HMDB 3.0—The Human Metabolome Database in 2013 journal November 2012
MetFusion: integration of compound identification strategies: MetFusion journal February 2013
Diverse mechanisms of growth inhibition by luteolin, resveratrol, and quercetin in MIA PaCa-2 cells: a comparative glucose tracer study with the fatty acid synthase inhibitor C75 journal March 2011

Similar Records

Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement
Journal Article · Wed Mar 24 00:00:00 EDT 2021 · Journal of the World Aquaculture Society · OSTI ID:1167049

Metabolomic data streaming for biology-dependent data acquisition
Journal Article · Mon Jun 09 00:00:00 EDT 2014 · Nature Biotechnology · OSTI ID:1167049

Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses
Journal Article · Mon Jun 16 00:00:00 EDT 2014 · Analytical Chemistry · OSTI ID:1167049

Related Subjects