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Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra

[Image: see text] A new metabolomics database and query algorithm for the analysis of (13)C–(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new datab...

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Autores principales: Bingol, Kerem, Li, Da-Wei, Bruschweiler-Li, Lei, Cabrera, Oscar A., Megraw, Timothy, Zhang, Fengli, Brüschweiler, Rafael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340359/
https://www.ncbi.nlm.nih.gov/pubmed/25333826
http://dx.doi.org/10.1021/cb5006382
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author Bingol, Kerem
Li, Da-Wei
Bruschweiler-Li, Lei
Cabrera, Oscar A.
Megraw, Timothy
Zhang, Fengli
Brüschweiler, Rafael
author_facet Bingol, Kerem
Li, Da-Wei
Bruschweiler-Li, Lei
Cabrera, Oscar A.
Megraw, Timothy
Zhang, Fengli
Brüschweiler, Rafael
author_sort Bingol, Kerem
collection PubMed
description [Image: see text] A new metabolomics database and query algorithm for the analysis of (13)C–(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C–(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index. Our new HSQC database separately treats slowly exchanging isomers that belong to the same metabolite, which permits improved query in cases where lowly populated isomers are below the HSQC detection limit. The performance of our new database and query web server compares favorably with the one of existing web servers, especially for spectra of samples of high complexity, including metabolite mixtures from the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on average a 37% higher accuracy (true positive rate) and a 82% lower false positive rate, which makes it a useful tool for the rapid and accurate identification of metabolites from (13)C–(1)H HSQC spectra at natural abundance. This information can be combined and validated with NMR data from 2D TOCSY-type spectra that provide connectivity information not present in HSQC spectra.
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spelling pubmed-43403592015-10-21 Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra Bingol, Kerem Li, Da-Wei Bruschweiler-Li, Lei Cabrera, Oscar A. Megraw, Timothy Zhang, Fengli Brüschweiler, Rafael ACS Chem Biol [Image: see text] A new metabolomics database and query algorithm for the analysis of (13)C–(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C–(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index. Our new HSQC database separately treats slowly exchanging isomers that belong to the same metabolite, which permits improved query in cases where lowly populated isomers are below the HSQC detection limit. The performance of our new database and query web server compares favorably with the one of existing web servers, especially for spectra of samples of high complexity, including metabolite mixtures from the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on average a 37% higher accuracy (true positive rate) and a 82% lower false positive rate, which makes it a useful tool for the rapid and accurate identification of metabolites from (13)C–(1)H HSQC spectra at natural abundance. This information can be combined and validated with NMR data from 2D TOCSY-type spectra that provide connectivity information not present in HSQC spectra. American Chemical Society 2014-10-21 2015-02-20 /pmc/articles/PMC4340359/ /pubmed/25333826 http://dx.doi.org/10.1021/cb5006382 Text en Copyright © 2014 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Bingol, Kerem
Li, Da-Wei
Bruschweiler-Li, Lei
Cabrera, Oscar A.
Megraw, Timothy
Zhang, Fengli
Brüschweiler, Rafael
Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title_full Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title_fullStr Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title_full_unstemmed Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title_short Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of (13)C–(1)H HSQC Spectra
title_sort unified and isomer-specific nmr metabolomics database for the accurate analysis of (13)c–(1)h hsqc spectra
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340359/
https://www.ncbi.nlm.nih.gov/pubmed/25333826
http://dx.doi.org/10.1021/cb5006382
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