Literature DB >> 24488481

A fast NMR method for resonance assignments: application to metabolomics.

Shivanand M Pudakalakatti1, Abhinav Dubey, Garima Jaipuria, U Shubhashree, Satish Kumar Adiga, Detlef Moskau, Hanudatta S Atreya.   

Abstract

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled ((12)C) or (13)C-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D [(13)C, (1)H] HSQC-TOCSY, (2) 2D (1)H-(1)H TOCSY and (3) 2D (13)C-(1)H HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D [(13)C, (1)H] HSQC-TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete (1)H and (13)C assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.

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Year:  2014        PMID: 24488481     DOI: 10.1007/s10858-014-9814-6

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  29 in total

Review 1.  Radial sampling for fast NMR: Concepts and practices over three decades.

Authors:  Brian E Coggins; Ronald A Venters; Pei Zhou
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-07-30       Impact factor: 9.795

Review 2.  Next-generation genomics: an integrative approach.

Authors:  R David Hawkins; Gary C Hon; Bing Ren
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242

3.  Molecular structure from a single NMR sequence (fast-PANACEA).

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Magn Reson       Date:  2010-07-08       Impact factor: 2.229

4.  Enhanced covariance spectroscopy from minimal datasets.

Authors:  Yanbin Chen; Fengli Zhang; Wolfgang Bermel; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2006-12-13       Impact factor: 15.419

5.  Molecular structure from a single NMR experiment.

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Am Chem Soc       Date:  2008-07-22       Impact factor: 15.419

6.  Multiple parallel 2D NMR acquisitions in a single scan.

Authors:  Kevin J Donovan; Eriks Kupče; Lucio Frydman
Journal:  Angew Chem Int Ed Engl       Date:  2013-03-04       Impact factor: 15.336

Review 7.  Applications of non-uniform sampling and processing.

Authors:  Sven G Hyberts; Haribabu Arthanari; Gerhard Wagner
Journal:  Top Curr Chem       Date:  2012

8.  NMR studies of preimplantation embryo metabolism in human assisted reproductive techniques: a new biomarker for assessment of embryo implantation potential.

Authors:  Shivanand M Pudakalakatti; Shubhashree Uppangala; Fiona D'Souza; Guruprasad Kalthur; Pratap Kumar; Satish Kumar Adiga; Hanudatta S Atreya
Journal:  NMR Biomed       Date:  2012-06-19       Impact factor: 4.044

9.  A covariance NMR toolbox for MATLAB and OCTAVE.

Authors:  Timothy Short; Leigh Alzapiedi; Rafael Brüschweiler; David Snyder
Journal:  J Magn Reson       Date:  2010-12-05       Impact factor: 2.229

Review 10.  Isotope enhanced approaches in metabolomics.

Authors:  G A Nagana Gowda; Narasimhamurthy Shanaiah; Daniel Raftery
Journal:  Adv Exp Med Biol       Date:  2012       Impact factor: 2.622

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  9 in total

Review 1.  NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry.

Authors:  Andrew N Lane; Teresa W-M Fan
Journal:  Arch Biochem Biophys       Date:  2017-03-02       Impact factor: 4.013

2.  A new broadband homonuclear mixing pulse for NMR with low applied power.

Authors:  Paul Coote; Kendra E Leigh; Tsyr-Yan Yu; Navin Khaneja; Gerhard Wagner; Haribabu Arthanari
Journal:  J Chem Phys       Date:  2014-07-14       Impact factor: 3.488

Review 3.  Holistic Analysis Enhances the Description of Metabolic Complexity in Dietary Natural Products.

Authors:  Charlotte Simmler; Daniel Kulakowski; David C Lankin; James B McAlpine; Shao-Nong Chen; Guido F Pauli
Journal:  Adv Nutr       Date:  2016-01       Impact factor: 8.701

Review 4.  Applications of NMR spectroscopy to systems biochemistry.

Authors:  Teresa W-M Fan; Andrew N Lane
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2016-02-06       Impact factor: 9.795

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.  Mitochondrial responses to extreme environments: insights from metabolomics.

Authors:  Katie A O'Brien; Julian L Griffin; Andrew J Murray; Lindsay M Edwards
Journal:  Extrem Physiol Med       Date:  2015-05-04

7.  Unraveling the association between genetic integrity and metabolic activity in pre-implantation stage embryos.

Authors:  Fiona D'Souza; Shivanand M Pudakalakatti; Shubhashree Uppangala; Sachin Honguntikar; Sujith Raj Salian; Guruprasad Kalthur; Renu Pasricha; Divya Appajigowda; Hanudatta S Atreya; Satish Kumar Adiga
Journal:  Sci Rep       Date:  2016-11-17       Impact factor: 4.379

8.  Spent embryo culture medium metabolites are related to the in vitro attachment ability of blastocysts.

Authors:  Fiona D'Souza; Shubhashree Uppangala; Gitanjali Asampille; Sujith Raj Salian; Guruprasad Kalthur; Riccardo Talevi; Hanudatta S Atreya; Satish Kumar Adiga
Journal:  Sci Rep       Date:  2018-11-19       Impact factor: 4.379

Review 9.  The metaRbolomics Toolbox in Bioconductor and beyond.

Authors:  Jan Stanstrup; Corey D Broeckling; Rick Helmus; Nils Hoffmann; Ewy Mathé; Thomas Naake; Luca Nicolotti; Kristian Peters; Johannes Rainer; Reza M Salek; Tobias Schulze; Emma L Schymanski; Michael A Stravs; Etienne A Thévenot; Hendrik Treutler; Ralf J M Weber; Egon Willighagen; Michael Witting; Steffen Neumann
Journal:  Metabolites       Date:  2019-09-23
  9 in total

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