Literature DB >> 21848333

Deconvolution of chemical mixtures with high complexity by NMR consensus trace clustering.

Kerem Bingol1, Rafael Brüschweiler.   

Abstract

Identification and quantification of analytes in complex solution-state mixtures are critical procedures in many areas of chemistry, biology, and molecular medicine. Nuclear magnetic resonance (NMR) is a unique tool for this purpose providing a wealth of atomic-detail information without requiring extensive fractionation of the samples. We present three new multidimensional-NMR based approaches that are geared toward the analysis of mixtures with high complexity at natural (13)C abundance, including approaches that are encountered in metabolomics. Common to all three approaches is the concept of the extraction of one-dimensional (1D) consensus spectral traces or 2D consensus planes followed by clustering, which significantly improves the capability to identify mixture components that are affected by strong spectral overlap. The methods are demonstrated for covariance (1)H-(1)H TOCSY and (13)C-(1)H HSQC-TOCSY spectra and triple-rank correlation spectra constructed from pairs of (13)C-(1)H HSQC and (13)C-(1)H HSQC-TOCSY spectra. All methods are first demonstrated for an eight-compound metabolite model mixture before being applied to an extract from E. coli cell lysate.

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Year:  2011        PMID: 21848333      PMCID: PMC3244875          DOI: 10.1021/ac201464y

Source DB:  PubMed          Journal:  Anal Chem        ISSN: 0003-2700            Impact factor:   6.986


  35 in total

1.  Covariance nuclear magnetic resonance spectroscopy.

Authors:  Rafael Brüschweiler; Fengli Zhang
Journal:  J Chem Phys       Date:  2004-03-15       Impact factor: 3.488

Review 2.  The role of analytical sciences in medical systems biology.

Authors:  Jan van der Greef; Paul Stroobant; Rob van der Heijden
Journal:  Curr Opin Chem Biol       Date:  2004-10       Impact factor: 8.822

3.  Covariance NMR spectroscopy by singular value decomposition.

Authors:  Nikola Trbovic; Serge Smirnov; Fengli Zhang; Rafael Brüschweiler
Journal:  J Magn Reson       Date:  2004-12       Impact factor: 2.229

4.  Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets.

Authors:  Olivier Cloarec; Marc-Emmanuel Dumas; Andrew Craig; Richard H Barton; Johan Trygg; Jane Hudson; Christine Blancher; Dominique Gauguier; John C Lindon; Elaine Holmes; Jeremy Nicholson
Journal:  Anal Chem       Date:  2005-03-01       Impact factor: 6.986

5.  Quantitative analysis of blood plasma metabolites using isotope enhanced NMR methods.

Authors:  G A Nagana Gowda; Fariba Tayyari; Tao Ye; Yuliana Suryani; Siwei Wei; Narasimhamurthy Shanaiah; Daniel Raftery
Journal:  Anal Chem       Date:  2010-09-29       Impact factor: 6.986

6.  Quantification of metabolites from two-dimensional nuclear magnetic resonance spectroscopy: application to human urine samples.

Authors:  Ratan Kumar Rai; Pratima Tripathi; Neeraj Sinha
Journal:  Anal Chem       Date:  2009-12-15       Impact factor: 6.986

7.  Web server suite for complex mixture analysis by covariance NMR.

Authors:  Fengli Zhang; Steven L Robinette; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  Magn Reson Chem       Date:  2009-12       Impact factor: 2.447

8.  A shortcut to identifying small molecule signals that regulate behavior and development in Caenorhabditis elegans.

Authors:  Chirag Pungaliya; Jagan Srinivasan; Bennett W Fox; Rabia U Malik; Andreas H Ludewig; Paul W Sternberg; Frank C Schroeder
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-03       Impact factor: 11.205

9.  Quantitative covariance NMR by regularization.

Authors:  Yanbin Chen; Fengli Zhang; David Snyder; Zhehong Gan; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  J Biomol NMR       Date:  2007-03-10       Impact factor: 2.582

10.  HMDB: the Human Metabolome Database.

Authors:  David S Wishart; Dan Tzur; Craig Knox; Roman Eisner; An Chi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; Mike Lewis; Marie-Aude Coutouly; Ian Forsythe; Peter Tang; Savita Shrivastava; Kevin Jeroncic; Paul Stothard; Godwin Amegbey; David Block; David D Hau; James Wagner; Jessica Miniaci; Melisa Clements; Mulu Gebremedhin; Natalie Guo; Ying Zhang; Gavin E Duggan; Glen D Macinnis; Alim M Weljie; Reza Dowlatabadi; Fiona Bamforth; Derrick Clive; Russ Greiner; Liang Li; Tom Marrie; Brian D Sykes; Hans J Vogel; Lori Querengesser
Journal:  Nucleic Acids Res       Date:  2007-01       Impact factor: 16.971

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  21 in total

1.  Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server.

Authors:  Kerem Bingol; Da-Wei Li; Bo Zhang; Rafael Brüschweiler
Journal:  Anal Chem       Date:  2016-12-06       Impact factor: 6.986

Review 2.  Can NMR solve some significant challenges in metabolomics?

Authors:  G A Nagana Gowda; Daniel Raftery
Journal:  J Magn Reson       Date:  2015-08-18       Impact factor: 2.229

Review 3.  Emerging new strategies for successful metabolite identification in metabolomics.

Authors:  Kerem Bingol; Lei Bruschweiler-Li; Dawei Li; Bo Zhang; Mouzhe Xie; Rafael Brüschweiler
Journal:  Bioanalysis       Date:  2016-02-26       Impact factor: 2.681

4.  TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database.

Authors:  Kerem Bingol; Fengli Zhang; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  Anal Chem       Date:  2012-10-11       Impact factor: 6.986

Review 5.  Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods.

Authors:  Kerem Bingol; Rafael Brüschweiler
Journal:  Curr Opin Biotechnol       Date:  2016-08-20       Impact factor: 9.740

6.  Carbon backbone topology of the metabolome of a cell.

Authors:  Kerem Bingol; Fengli Zhang; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2012-05-17       Impact factor: 15.419

7.  Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures.

Authors:  Da-Wei Li; Cheng Wang; Rafael Brüschweiler
Journal:  J Biomol NMR       Date:  2017-06-01       Impact factor: 2.835

8.  Use of Charged Nanoparticles in NMR-Based Metabolomics for Spectral Simplification and Improved Metabolite Identification.

Authors:  Bo Zhang; Mouzhe Xie; Lei Bruschweiler-Li; Kerem Bingol; Rafael Brüschweiler
Journal:  Anal Chem       Date:  2015-07-01       Impact factor: 6.986

Review 9.  Multidimensional approaches to NMR-based metabolomics.

Authors:  Kerem Bingol; Rafael Brüschweiler
Journal:  Anal Chem       Date:  2013-11-22       Impact factor: 6.986

10.  Quantitative analysis of metabolic mixtures by two-dimensional 13C constant-time TOCSY NMR spectroscopy.

Authors:  Kerem Bingol; Fengli Zhang; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  Anal Chem       Date:  2013-06-17       Impact factor: 6.986

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