Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling.

Journal of Biomolecular NMR
Sven G HybertsGerhard Wagner

Abstract

The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would match the resolution power of modern high-field instruments. Thus, many alternative sampling and transformation schemes have been proposed. Their common challenges are the suppression of the artifacts due to the non-uniformity of the sampling schedules, the preservation of the relative signal amplitudes, and the computing time needed for spectra reconstruction. Here we present a fast implementation of the Iterative Soft Thresholding approach (istHMS) that can reconstruct high-resolution non-uniformly sampled NMR data up to four dimensions within a few hours and make routine reconstruction of high-resolution NUS 3D and 4D spectra convenient. We include a graphical user interface for generating sampling schedules with the Poisson-Gap method and an estimation of optimal evolution times based on molec...Continue Reading

References

Jul 1, 1991·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·H Suzuki, J Toriwaki
Jan 1, 1994·Methods in Enzymology·J W Peng, G Wagner
Aug 26, 1998·Journal of Magnetic Resonance·V A MandelshtamA J Shaka
Jun 30, 2001·Journal of Biomolecular NMR·P ZhouG Wagner
Nov 13, 2003·Journal of the American Chemical Society·Eriks Kupce, Ray Freeman
Feb 3, 2004·Journal of Biomolecular NMR·Vitali Tugarinov, Lewis E Kay
Jul 21, 2004·Journal of Magnetic Resonance·Jianhan ChenVladimir A Mandelshtam
Sep 29, 2004·Journal of Biomolecular NMR·D RovnyakG Wagner
Feb 24, 2005·Journal of the American Chemical Society·Vitali TugarinovVladislav Yu Orekhov
Mar 23, 2005·Journal of Magnetic Resonance·Eriks Kupce, Ray Freeman
Aug 29, 2007·Journal of Magnetic Resonance·Alan S SternJeffrey C Hoch
Sep 8, 2007·Journal of Magnetic Resonance·Krzysztof KazimierczukIgor Zhukov
Oct 31, 2007·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·Michael LustigJohn M Pauly
Dec 14, 2007·Proteins·David J WiltonMike P Williamson
Mar 1, 2008·Journal of Magnetic Resonance·Krzysztof KazimierczukWiktor Koźmiński
Oct 15, 2008·Journal of Biomolecular NMR·Brian E Coggins, Pei Zhou
Mar 17, 2009·Journal of the American Chemical Society·Yoh MatsukiJudith Herzfeld
Apr 22, 2009·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Michael TingAlfred O Hero
Sep 10, 2009·Journal of the American Chemical Society·Sebastian HillerVladislav Y Orekhov
Apr 8, 2010·Journal of Biomolecular NMR·Jan Stanek, Wiktor Koźmiński
Jun 1, 2010·Nature Structural & Molecular Biology·Antoine GautierDaniel Nietlispach
Mar 8, 2011·Nature Structural & Molecular Biology·Alexander G MilbradtGerhard Wagner
May 4, 2011·Angewandte Chemie·Krzysztof Kazimierczuk, Vladislav Yu Orekhov
Jun 8, 2011·Angewandte Chemie·Daniel J HollandDaniel Nietlispach
Jul 29, 2011·Topics in Current Chemistry·Sven G HybertsGerhard Wagner

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Citations

Nov 1, 2011·Journal of Biomolecular NMR·Maayan GalGerhard Wagner
Jul 27, 2012·Journal of Biomolecular NMR·Mark J BostockDaniel Nietlispach
Jan 1, 2013·Journal of Biomolecular NMR·Sven G HybertsGerhard Wagner
Dec 24, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·J MitchellE J Fordham
Oct 9, 2013·Analytical Chemistry·Ichrak ToumiStefano Caldarelli
Jan 9, 2013·Journal of the American Chemical Society·Franz HagnGerhard Wagner
Feb 19, 2014·Progress in Nuclear Magnetic Resonance Spectroscopy·Dominique P Frueh
Sep 7, 2014·Journal of Biomolecular NMR·ShengQi XiangAdam Lange
Sep 5, 2014·Journal of Biomolecular NMR·Bharathwaj SathyamoorthyHashim Al-Hashimi
Feb 22, 2016·Journal of Magnetic Resonance·Rupashree DassKrzysztof Kazimierczuk
Feb 6, 2016·Journal of Biomolecular NMR·Troels E Linnet, Kaare Teilum
Feb 20, 2016·Journal of Magnetic Resonance·Bradley Worley
Feb 8, 2016·Journal of Magnetic Resonance·Yulan LinLucio Frydman
Jul 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kendra E LeighHaribabu Arthanari
Jul 15, 2015·Proceedings of the National Academy of Sciences of the United States of America·Naotaka SekiyamaMélissa Léger-Abraham
Dec 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Joshua B BrettmannKatherine A Henzler-Wildman
Sep 11, 2012·Journal of Magnetic Resonance·Krzysztof Kazimierczuk, Vladislav Yu Orekhov
Jul 6, 2014·Journal of the American Chemical Society·Rasmus LinserGerhard Wagner
Sep 3, 2014·Journal of the American Chemical Society·Andrew J WommackElizabeth M Nolan
Nov 3, 2015·Journal of Magnetic Resonance·Bradley Worley, Robert Powers
Aug 1, 2015·Chemistry : a European Journal·Tatiana DidenkoKurt Wüthrich
Nov 26, 2015·Progress in Nuclear Magnetic Resonance Spectroscopy·Rachel W MartinKelsey A Collier
Aug 11, 2015·Magnetic Resonance in Chemistry : MRC·Alan S Stern, Jeffrey C Hoch
Jun 9, 2015·Magnetic Resonance in Chemistry : MRC·Adrien Le GuennecStefano Caldarelli
Aug 21, 2015·Magnetic Resonance in Chemistry : MRC·Krzysztof Kazimierczuk, Vladislav Orekhov
Sep 4, 2015·Magnetic Resonance in Chemistry : MRC·Philippe LesotOlivier Lafon
Jun 25, 2013·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Krzysztof KazimierczukWiktor Koźmiński
Jul 3, 2013·Chembiochem : a European Journal of Chemical Biology·Julien RocheAd Bax
Nov 26, 2015·Progress in Nuclear Magnetic Resonance Spectroscopy·Michał NowakowskiWiktor Koźmiński
Oct 29, 2014·Angewandte Chemie·Daniel J Holland, Lynn F Gladden
May 1, 2015·Magnetic Resonance in Chemistry : MRC·Carlos CobasFelipe Seoane
Nov 13, 2014·Angewandte Chemie·Xiaobo QuVladislav Orekhov
Jul 16, 2013·Current Opinion in Structural Biology·Dominique P FruehScott R Nichols
Mar 3, 2015·Analytical Chemistry·Luke W ArbogastJohn P Marino
May 16, 2015·Journal of Biomolecular NMR·ShengQi XiangRasmus Linser
Apr 23, 2015·The Journal of Physical Chemistry. B·Melissa R PalmerDavid Rovnyak
Feb 14, 2015·Journal of Biomolecular NMR·Takumi UedaIchio Shimada
Oct 22, 2013·Journal of Magnetic Resonance·Eugene C Lin, Stanley J Opella

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