Literature DB >> 22200565

Deterministic schedules for robust and reproducible non-uniform sampling in multidimensional NMR.

Matthew T Eddy1, David Ruben, Robert G Griffin, Judith Herzfeld.   

Abstract

We show that a simple, general, and easily reproducible method for generating non-uniform sampling (NUS) schedules preserves the benefits of random sampling, including inherently reduced sampling artifacts, while removing the pitfalls associated with choosing an arbitrary seed. Sampling schedules are generated from a discrete cumulative distribution function (CDF) that closely fits the continuous CDF of the desired probability density function. We compare random and deterministic sampling using a Gaussian probability density function applied to 2D HSQC spectra. Data are processed using the previously published method of Spectroscopy by Integration of Frequency and Time domain data (SIFT). NUS spectra from deterministic sampling schedules were found to be at least as good as those from random schedules at the SIFT critical sampling density, and significantly better at half that sampling density. The method can be applied to any probability density function and generalized to greater than two dimensions.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 22200565      PMCID: PMC3257378          DOI: 10.1016/j.jmr.2011.12.002

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


  28 in total

1.  Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction.

Authors:  Alan S Stern; Kuo-Bin Li; Jeffrey C Hoch
Journal:  J Am Chem Soc       Date:  2002-03-06       Impact factor: 15.419

2.  Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy.

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Am Chem Soc       Date:  2004-05-26       Impact factor: 15.419

3.  Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction.

Authors:  David Rovnyak; Dominique P Frueh; Mallika Sastry; Zhen-Yu J Sun; Alan S Stern; Jeffrey C Hoch; Gerhard Wagner
Journal:  J Magn Reson       Date:  2004-09       Impact factor: 2.229

4.  Fast reconstruction of four-dimensional NMR spectra from plane projections.

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Biomol NMR       Date:  2004-04       Impact factor: 2.835

5.  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

6.  A proton-detected 4D solid-state NMR experiment for protein structure determination.

Authors:  Matthias Huber; Sebastian Hiller; Paul Schanda; Matthias Ernst; Anja Böckmann; René Verel; Beat H Meier
Journal:  Chemphyschem       Date:  2011-02-15       Impact factor: 3.102

7.  High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition.

Authors:  Vitali Tugarinov; Lewis E Kay; Ilghiz Ibraghimov; Vladislav Yu Orekhov
Journal:  J Am Chem Soc       Date:  2005-03-02       Impact factor: 15.419

8.  Application of nonlinear sampling schemes to COSY-type spectra.

Authors:  P Schmieder; A S Stern; G Wagner; J C Hoch
Journal:  J Biomol NMR       Date:  1993-09       Impact factor: 2.835

9.  Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling.

Authors:  David Rovnyak; Claudiu Filip; Boris Itin; Alan S Stern; Gerhard Wagner; Robert G Griffin; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2003-03       Impact factor: 2.229

10.  Indirect covariance NMR spectroscopy.

Authors:  Fengli Zhang; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2004-10-20       Impact factor: 15.419

View more
  10 in total

1.  Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies.

Authors:  Sivakumar Paramasivam; Christopher L Suiter; Guangjin Hou; Shangjin Sun; Melissa Palmer; Jeffrey C Hoch; David Rovnyak; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2012-06-18       Impact factor: 2.991

2.  Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR.

Authors:  Melissa R Palmer; Broc R Wenrich; Phillip Stahlfeld; David Rovnyak
Journal:  J Biomol NMR       Date:  2014-03-29       Impact factor: 2.835

3.  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

4.  Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins.

Authors:  Mark J Bostock; Daniel J Holland; Daniel Nietlispach
Journal:  J Biomol NMR       Date:  2012-07-26       Impact factor: 2.835

5.  Subrandom methods for multidimensional nonuniform sampling.

Authors:  Bradley Worley
Journal:  J Magn Reson       Date:  2016-06-09       Impact factor: 2.229

6.  Pitfalls in compressed sensing reconstruction and how to avoid them.

Authors:  Alexandra Shchukina; Paweł Kasprzak; Rupashree Dass; Michał Nowakowski; Krzysztof Kazimierczuk
Journal:  J Biomol NMR       Date:  2016-11-11       Impact factor: 2.835

7.  Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy.

Authors:  Eugenio Daviso; Matthew T Eddy; Loren B Andreas; Robert G Griffin; Judith Herzfeld
Journal:  J Biomol NMR       Date:  2013-01-19       Impact factor: 2.835

8.  Deterministic multidimensional nonuniform gap sampling.

Authors:  Bradley Worley; Robert Powers
Journal:  J Magn Reson       Date:  2015-10-23       Impact factor: 2.229

9.  Sampling scheme and compressed sensing applied to solid-state NMR spectroscopy.

Authors:  Eugene C Lin; Stanley J Opella
Journal:  J Magn Reson       Date:  2013-10-01       Impact factor: 2.229

10.  Evaluation of Non-Uniform Sampling 2D 1H-13C HSQC Spectra for Semi-Quantitative Metabolomics.

Authors:  Bo Zhang; Robert Powers; Elizabeth M O'Day
Journal:  Metabolites       Date:  2020-05-16
  10 in total

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