Literature DB >> 21316276

Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

Yoav Shrot1, Lucio Frydman.   

Abstract

A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 21316276      PMCID: PMC5040485          DOI: 10.1016/j.jmr.2011.01.017

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  18 in total

Review 1.  Maximum entropy reconstruction, spectrum analysis and deconvolution in multidimensional nuclear magnetic resonance.

Authors:  J C Hoch; A S Stern
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

2.  Adiabatic single scan two-dimensional NMR spectrocopy.

Authors:  Philippe Pelupessy
Journal:  J Am Chem Soc       Date:  2003-10-08       Impact factor: 15.419

3.  Interlaced Fourier transformation of ultrafast 2D NMR data.

Authors:  Mor Mishkovsky; Lucio Frydman
Journal:  J Magn Reson       Date:  2005-04       Impact factor: 2.229

4.  Fast acquisition of NMR spectra using Fourier transform of non-equispaced data.

Authors:  Dominique Marion
Journal:  J Biomol NMR       Date:  2005-06       Impact factor: 2.835

5.  Sparse MRI: The application of compressed sensing for rapid MR imaging.

Authors:  Michael Lustig; David Donoho; John M Pauly
Journal:  Magn Reson Med       Date:  2007-12       Impact factor: 4.668

6.  Two-dimensional Fourier transform of arbitrarily sampled NMR data sets.

Authors:  Krzysztof Kazimierczuk; Wiktor Koźmiński; Igor Zhukov
Journal:  J Magn Reson       Date:  2006-02-20       Impact factor: 2.229

Review 7.  Spatial encoding strategies for ultrafast multidimensional nuclear magnetic resonance.

Authors:  Yoav Shrot; Lucio Frydman
Journal:  J Chem Phys       Date:  2008-02-07       Impact factor: 3.488

8.  NMR data processing using iterative thresholding and minimum l(1)-norm reconstruction.

Authors:  Alan S Stern; David L Donoho; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2007-08-03       Impact factor: 2.229

9.  Single-scan 2D Hadamard NMR spectroscopy.

Authors:  Assaf Tal; Boaz Shapira; Lucio Frydman
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

10.  Spatial/spectral encoding of the spin interactions in ultrafast multidimensional NMR.

Authors:  Yoav Shrot; Lucio Frydman
Journal:  J Chem Phys       Date:  2009-12-14       Impact factor: 3.488

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  14 in total

1.  Accurate scoring of non-uniform sampling schemes for quantitative NMR.

Authors:  Phillip C Aoto; R Bryn Fenwick; Gerard J A Kroon; Peter E Wright
Journal:  J Magn Reson       Date:  2014-07-02       Impact factor: 2.229

2.  Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.

Authors:  Christopher L Suiter; Sivakumar Paramasivam; Guangjin Hou; Shangjin Sun; David Rice; Jeffrey C Hoch; David Rovnyak; Tatyana Polenova
Journal:  J Biomol NMR       Date:  2014-04-22       Impact factor: 2.835

3.  Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.

Authors:  Amir Seginer; Gregory L Olsen; Lucio Frydman
Journal:  J Biomol NMR       Date:  2016-09-28       Impact factor: 2.835

4.  Spatially selective heteronuclear multiple-quantum coherence spectroscopy for biomolecular NMR studies.

Authors:  Bharathwaj Sathyamoorthy; David M Parish; Gaetano T Montelione; Rong Xiao; Thomas Szyperski
Journal:  Chemphyschem       Date:  2014-04-30       Impact factor: 3.102

5.  Efficient 31 P band inversion transfer approach for measuring creatine kinase activity, ATP synthesis, and molecular dynamics in the human brain at 7 T.

Authors:  Jimin Ren; A Dean Sherry; Craig R Malloy
Journal:  Magn Reson Med       Date:  2016-11-20       Impact factor: 4.668

6.  A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection.

Authors:  Shangjin Sun; Si Yan; Changmiao Guo; Mingyue Li; Jeffrey C Hoch; John C Williams; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2012-11-12       Impact factor: 2.991

7.  A new approach to compressed sensing for NMR.

Authors:  Alan S Stern; Jeffrey C Hoch
Journal:  Magn Reson Chem       Date:  2015-08-10       Impact factor: 2.447

8.  Accelerating multidimensional NMR and MRI experiments using iterated maps.

Authors:  Merideth A Frey; Zachary M Sethna; Gregory A Manley; Suvrajit Sengupta; Kurt W Zilm; J Patrick Loria; Sean E Barrett
Journal:  J Magn Reson       Date:  2013-09-21       Impact factor: 2.229

Review 9.  The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Authors:  James B McAlpine; Shao-Nong Chen; Andrei Kutateladze; John B MacMillan; Giovanni Appendino; Andersson Barison; Mehdi A Beniddir; Maique W Biavatti; Stefan Bluml; Asmaa Boufridi; Mark S Butler; Robert J Capon; Young H Choi; David Coppage; Phillip Crews; Michael T Crimmins; Marie Csete; Pradeep Dewapriya; Joseph M Egan; Mary J Garson; Grégory Genta-Jouve; William H Gerwick; Harald Gross; Mary Kay Harper; Precilia Hermanto; James M Hook; Luke Hunter; Damien Jeannerat; Nai-Yun Ji; Tyler A Johnson; David G I Kingston; Hiroyuki Koshino; Hsiau-Wei Lee; Guy Lewin; Jie Li; Roger G Linington; Miaomiao Liu; Kerry L McPhail; Tadeusz F Molinski; Bradley S Moore; Joo-Won Nam; Ram P Neupane; Matthias Niemitz; Jean-Marc Nuzillard; Nicholas H Oberlies; Fernanda M M Ocampos; Guohui Pan; Ronald J Quinn; D Sai Reddy; Jean-Hugues Renault; José Rivera-Chávez; Wolfgang Robien; Carla M Saunders; Thomas J Schmidt; Christoph Seger; Ben Shen; Christoph Steinbeck; Hermann Stuppner; Sonja Sturm; Orazio Taglialatela-Scafati; Dean J Tantillo; Robert Verpoorte; Bin-Gui Wang; Craig M Williams; Philip G Williams; Julien Wist; Jian-Min Yue; Chen Zhang; Zhengren Xu; Charlotte Simmler; David C Lankin; Jonathan Bisson; Guido F Pauli
Journal:  Nat Prod Rep       Date:  2018-07-13       Impact factor: 13.423

Review 10.  Ultrafast 2D NMR: an emerging tool in analytical spectroscopy.

Authors:  Patrick Giraudeau; Lucio Frydman
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2014       Impact factor: 10.745

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