LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine
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TLDR
MAVEN as mentioned in this paper is an open-source software program for interactive processing of LC-MS-based metabolomics data, which enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data.Abstract:
MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis.read more
Citations
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Journal ArticleDOI
Multivariate Analysis in Metabolomics.
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TL;DR: The use of multivariate analysis for metabolomics is discussed, as well as common pitfalls and misconceptions, and spectral features contributing most to variation or separation are identified for further analysis.
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Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy
Lukas F. Mager,Regula Burkhard,Nicola Pett,Noah C. A. Cooke,Kirsty Brown,Hena R. Ramay,Seungil Paik,John Stagg,Ryan A. Groves,Marco Gallo,Ian A. Lewis,Markus B. Geuking,Kathy D. McCoy +12 more
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Journal ArticleDOI
Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development
Jared R. Mayers,Chen Wu,Chen Wu,Clary B. Clish,Peter Kraft,Margaret E. Torrence,Brian P. Fiske,Chen Yuan,Ying Bao,Mary K. Townsend,Shelley S. Tworoger,Shawn M. Davidson,Thales Papagiannakopoulos,Annan Yang,Talya L. Dayton,Shuji Ogino,Shuji Ogino,Meir J. Stampfer,Edward Giovannucci,Zhi Rong Qian,Douglas A. Rubinson,Jing Ma,Howard D. Sesso,John Michael Gaziano,John Michael Gaziano,Barbara B. Cochrane,Simin Liu,Jean Wactawski-Wende,JoAnn E. Manson,Michael Pollak,Alec C. Kimmelman,Amanda Souza,Kerry A. Pierce,Thomas J. Wang,Robert E. Gerszten,Charles S. Fuchs,Charles S. Fuchs,Matthew G. Vander Heiden,Brian M. Wolpin,Brian M. Wolpin +39 more
TL;DR: It is suggested that increased whole-body protein breakdown is an early event in development of PDAC, and elevated plasma levels of branched-chain amino acids (BCAAs) are associated with a greater than twofold increased risk of future pancreatic cancer diagnosis.
Journal ArticleDOI
Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers
Jared R. Mayers,Margaret E. Torrence,Laura V. Danai,Thales Papagiannakopoulos,Shawn M. Davidson,Matthew R. Bauer,Allison N. Lau,Brian W. Ji,Purushottam D. Dixit,Aaron M. Hosios,Alexander Muir,Christopher R. Chin,Elizaveta Freinkman,Tyler Jacks,Brian M. Wolpin,Dennis Vitkup,Matthew G. Vander Heiden +16 more
TL;DR: In this article, the authors argue that tissue of origin is an important determinant of how cancers satisfy their metabolic requirements, and that tissue context defines cancer dependence on specific metabolic pathways is unknown, but despite the same initiating events, these tumors use branched chain amino acids (BCAAs) differently.
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Metabolite concentrations, fluxes, and free energies imply efficient enzyme usage
Junyoung O. Park,Sara A. Rubin,Yi-Fan Xu,Yi-Fan Xu,Daniel Amador-Noguez,Jing Fan,Tomer Shlomi,Joshua D. Rabinowitz +7 more
TL;DR: Across metabolism, the observed conservation of metabolite concentrations and ΔG are substantially conserved, and that most substrate (but not inhibitor) concentrations exceed the associated enzyme binding site affinity.
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