Literature DB >> 28332026

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

Sven G Hyberts1, Scott A Robson1, Gerhard Wagner2.   

Abstract

Non-Uniform Sampling has the potential to exploit the optimal resolution of high-field NMR instruments. This is not possible in 3D and 4D NMR experiments when using traditional uniform sampling due to the long overall measurement time. Nominally, uniformly sampled time domain data acquired to a maximum evolution time tmax can be extended to high resolution via a virtual maximum evolution time t*max while extrapolating with linear prediction or iterative soft thresholding (IST). At the high resolution obtainable with extrapolation of US data, however, the accuracy of peak positions is compromised as observed when comparing inter- and intra-residue peaks in a 3D HNCA experiment. However, the accuracy of peak positions is largely improved by spreading the same number of acquired time domain data points non-uniformly over a larger evolution time to an optimal tmax followed by extrapolation to a total t*max and processing the data with an appropriate reconstruction method, such as hmsIST. To explore the optimum value of experimentally measured tmax to be reached non-uniformly with a given number of sampling points we have created test situations of time-equivalent experiments and evaluate sensitivity and accuracy of peak positions. Here we use signal-to-maximum-noise ratio as the decisive measure of sensitivity. We find that both sensitivity and resolution are optimal when PoissonGap sampling to a tmax of about ½*T2*. Digital resolution is further enhanced by extrapolating the range of acquired time domain data to 2*T2* but without measuring experimental points beyond ½*T2*.

Entities:  

Keywords:  Iterative soft threshold reconstruction; NUS; Non-uniform sampling; Protein backbone chemical shift assignments; Reduced time multidimensional NMR spectroscopy

Mesh:

Year:  2017        PMID: 28332026      PMCID: PMC5614452          DOI: 10.1007/s10858-017-0103-z

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


  28 in total

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Authors:  Eriks Kupce; Ray Freeman
Journal:  J Magn Reson       Date:  2005-04       Impact factor: 2.229

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Authors:  David Rovnyak; Mark Sarcone; Ze Jiang
Journal:  Magn Reson Chem       Date:  2011-07-12       Impact factor: 2.447

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

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

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Authors:  Sven G Hyberts; Scott A Robson; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2012-12-29       Impact factor: 2.835

8.  Carbon Isotopomer Analysis with Non-Unifom Sampling HSQC NMR for Cell Extract and Live Cell Metabolomics Studies.

Authors:  Sujin Lee; He Wen; Yong Jin An; Jin Wook Cha; Yoon-Joo Ko; Sven G Hyberts; Sunghyouk Park
Journal:  Anal Chem       Date:  2016-12-27       Impact factor: 6.986

9.  Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data.

Authors:  Sven G Hyberts; Koh Takeuchi; Gerhard Wagner
Journal:  J Am Chem Soc       Date:  2010-02-24       Impact factor: 15.419

10.  High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN.

Authors:  Brian E Coggins; Pei Zhou
Journal:  J Biomol NMR       Date:  2008-10-14       Impact factor: 2.835

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1.  Non-uniform sampling in biomolecular NMR.

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Journal:  J Biomol NMR       Date:  2017-06-15       Impact factor: 2.835

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

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3.  Nonuniform sampling in multidimensional NMR for improving spectral sensitivity.

Authors:  Matthew A Zambrello; Adam D Schuyler; Mark W Maciejewski; Frank Delaglio; Irina Bezsonova; Jeffrey C Hoch
Journal:  Methods       Date:  2018-03-06       Impact factor: 3.608

4.  Characterizing Protein Hydration Dynamics Using Solution NMR Spectroscopy.

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Review 5.  Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins.

Authors:  Haribabu Arthanari; Koh Takeuchi; Abhinav Dubey; Gerhard Wagner
Journal:  Curr Opin Struct Biol       Date:  2019-07-19       Impact factor: 6.809

6.  The influence of the probability density function on spectral quality in nonuniformly sampled multidimensional NMR.

Authors:  Matthew A Zambrello; D Levi Craft; Jeffrey C Hoch; David Rovnyak; Adam D Schuyler
Journal:  J Magn Reson       Date:  2019-12-20       Impact factor: 2.229

7.  Reducing the measurement time of exact NOEs by non-uniform sampling.

Authors:  Parker J Nichols; Alexandra Born; Morkos A Henen; Dean Strotz; David N Jones; Frank Delaglio; Beat Vögeli
Journal:  J Biomol NMR       Date:  2020-09-03       Impact factor: 2.582

8.  Mixed pyruvate labeling enables backbone resonance assignment of large proteins using a single experiment.

Authors:  Scott A Robson; Koh Takeuchi; Andras Boeszoermenyi; Paul W Coote; Abhinav Dubey; Sven Hyberts; Gerhard Wagner; Haribabu Arthanari
Journal:  Nat Commun       Date:  2018-01-24       Impact factor: 14.919

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Journal:  Nat Commun       Date:  2018-06-07       Impact factor: 14.919

10.  Improving the sensitivity of FT-NMR spectroscopy by apodization weighted sampling.

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Journal:  J Biomol NMR       Date:  2019-05-02       Impact factor: 2.835

  10 in total

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