Literature DB >> 31292847

Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps.

Robert L Blum1, Jared Rovny1, J Patrick Loria2,3, Sean E Barrett4.   

Abstract

Many of the ubiquitous experiments of biomolecular NMR, including [Formula: see text], [Formula: see text], and CEST, involve acquiring repeated 2D spectra under slightly different conditions. Such experiments are amenable to acceleration using non-uniform sampling spectral reconstruction methods that take advantage of prior information. We previously developed one such technique, an iterated maps method (DiffMap) that we successfully applied to 2D NMR spectra, including [Formula: see text] relaxation dispersion data. In that prior work, we took a top-down approach to reconstructing the 2D spectrum with a minimal number of sparse samples, reaching an undersampling fraction that appeared to leave some room for improvement. In this study, we develop an in-depth understanding of the action of the DiffMap algorithm, identifying the factors that cause reconstruction errors for different undersampling fractions. This improved understanding allows us to formulate a bottom-up approach to finding the lowest number of sparse samples required to accurately reconstruct individual spectral features with DiffMap. We also discuss the difficulty of extending this method to reconstructing many peaks at once, and suggest a way forward.

Entities:  

Keywords:  DiffMap; Difference map; Nonuniform sampling; Reconstruction; Sparse sampling

Year:  2019        PMID: 31292847     DOI: 10.1007/s10858-019-00262-4

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


  32 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.  Phase retrieval by iterated projections.

Authors:  Veit Elser
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  2003-01       Impact factor: 2.129

3.  Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets.

Authors:  Jan Stanek; Wiktor Koźmiński
Journal:  J Biomol NMR       Date:  2010-04-07       Impact factor: 2.835

Review 4.  Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy.

Authors:  Arthur G Palmer; Francesca Massi
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

5.  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

6.  Analysis of non-uniformly sampled spectra with multi-dimensional decomposition.

Authors:  Vladislav Yu Orekhov; Victor A Jaravine
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-02-24       Impact factor: 9.795

7.  Interpolating and extrapolating with hmsIST: seeking a tmax for optimal sensitivity, resolution and frequency accuracy.

Authors:  Sven G Hyberts; Scott A Robson; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2017-03-22       Impact factor: 2.835

8.  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

9.  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

10.  Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation.

Authors:  George P Lisi; Allen A Currier; J Patrick Loria
Journal:  Front Mol Biosci       Date:  2018-02-06
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  2 in total

1.  Non-Uniform Sampling in NMR Spectroscopy and the Preservation of Spectral Knowledge in the Time and Frequency Domains.

Authors:  Manpreet Kaur; Callie M Lewis; Aaron Chronister; Gabriel S Phun; Leonard J Mueller
Journal:  J Phys Chem A       Date:  2020-06-18       Impact factor: 2.781

2.  Accelerating 2D NMR relaxation dispersion experiments using iterated maps.

Authors:  Jared Rovny; Robert L Blum; J Patrick Loria; Sean E Barrett
Journal:  J Biomol NMR       Date:  2019-07-06       Impact factor: 2.835

  2 in total

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