Data Processing Methods: Fourier and Beyond
Vladislav Orekhov
Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, 40530 Gothenburg, Box 465, Sweden
Corresponding Author
Search for more papers by this authorPawel Kasprzak
Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Banacha 2C, Poland
Search for more papers by this authorKrzysztof Kazimierczuk
Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Banacha 2C, Poland
Search for more papers by this authorVladislav Orekhov
Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, 40530 Gothenburg, Box 465, Sweden
Corresponding Author
Search for more papers by this authorPawel Kasprzak
Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Banacha 2C, Poland
Search for more papers by this authorKrzysztof Kazimierczuk
Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Banacha 2C, Poland
Search for more papers by this authorP.K. Madhu
Search for more papers by this authorG. Rajalakshmi
Search for more papers by this authorAbstract
This chapter presents a compact overview of both practical and rigorously mathematical aspects of modern NMR signal processing. It discusses the properties of the Fourier transform (FT), which will be later useful to explain the effects of the experimental imperfections and signal processing procedures. The fast FT algorithm, used to calculate the discrete FT requires the same number of points in the input and output. However, one can increase the number of spectral points to any desired value by zero filling , that is, extending the free induction decay by adding artificial data points equal to zero at the end. The quadrature detection in one-dimensional spectra is realized through the acquisition of the two modulations, interpreted as real and imaginary parts of a complex NMR signal. The Projection Theorem is a powerful tool, useful in accelerating NMR experiments of dimensionality three and more.
References
- Szántay , C. ( 2007 ). NMR and the uncertainty principle: how to and how not to interpret homogeneous line broadening and pulse nonselectivity. I. The fundamentals. Concepts. Magn. Reson. Part A Bridg. Educ. Res . . ISSN 15466086.
- Bartholdi , E. and Ernst , R.R. ( 1973 ). Fourier spectroscopy and the causality principle . J. Magn. Reson. (1969) , 11 ( 1 ): 9 – 19 . ISSN 00222364.
- Mayzel , M. , Kazimierczuk , K. and Orekhov , V.Y. ( 2014 ). The causality principle in the reconstruction of sparse NMR spectra . Chem. Comm. 50 ( 64 ): 8947 – 8950 . 10.1039/c4cc03047h . ISSN 1364548X.
- Nyquist , H. Certain topics in telegraph transmission theory . Trans. Electr. Electron. Eng. 47 ( 2 ): 617 – 644 . 10.1109/5.989875 . ISSN 00189219.
-
Cooley , J.W.
and
Tukey , J.W.
1965
. An algorithm for the machine calculation of complex fourier series.
Math. Comput
. 19 (90): 297.
10.2307/2003354
. ISSN 00255718.
10.2307/2003354 Google Scholar
- States , D.J. , Haberkorn , R.A. and Ruben , D.J. ( 1982 ). A 2D NMR experiment with pure absorption phase in four quadrants . J. Magn. Res. , 48 : 286 – 292 .
- Palmer III , A.G. , Cavanagh , J. , Wright , P.E. , Rance, M . and ( 1991 ). Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation nmr spectroscopy . J. Magn. Reson. (1969), 93 ( 1 ): 151 – 170 . ISSN 0022-2364.
- Marion , D. and Wthrich , K. ( 1983 ). Application of phase sensitive two-dimensional correlated spectroscopy (cosy) for measurements of 1h-1h spin-spin coupling constants in proteins . Biochem. Biophys. Res. Commun. 113 ( 3 ): 967 – 74 .
- Marion , D. , Ikura , M. , Tschudin , R. and Bax , A.D. ( 1989 ). Rapid recording of 2d nmr spectra without phase cycling. application to the study of hydrogen exchange in proteins . J. Magn. Reson. 85 ( 2 ): 393 – 399 .
- Coggins , B.E. , Venters , R.A. and Zhou , P. ( 2010 ). Radial sampling for fast NMR: Concepts and practices over three decades . Prog. Nucl. Magn. Reson. Spectrosc. 57 ( 4 ): 381 – 419 . 10.1016/j.pnmrs.2010.07.001 . ISSN 1873-3301.
- Hassanieh , H. , Mayzel , M. , Shi , L. , Katabi , D. and Orekhov , V.Y. ( 2015 ). Fast multi-dimensional NMR acquisition and processing using the sparse FFT . J. Biomol. NMR , 63 ( 1 ): 9 – 19 . 10.1007/s10858-015-9952-5 . ISSN 15735001.
-
Pustovalova , Y.
,
Mayzel , M.
and
Orekhov , V.Y.
(
2018
).
XLSY: Extra-Large NMR Spectroscopy
.
Angew. Chem.
130
(
43
):
14239
–
14241
.
10.1002/ange.201806144
. ISSN 1521-3757.
10.1002/ange.201806144 Google Scholar
- Nagayama , K. , Bachmann , P. , Wuthrich , K. and Ernst , R.R. ( 1978 ). The use of cross-sections and of projections in two-dimensional NMR spectroscopy . J. Magn. Reson. (1969) 31 ( 1 ): 133 – 148 . 10.1016/0022-2364(78)90176-2 . ISSN 00222364.
- Szyperski , T. , Wider , G. , Bushweller , J.H. and Wuethrich , K. ( 1993 ). Reduced Dimensionality in Triple-Resonance NMR Experiments . J. Am. Chem. Soc. 115 ( 20 ): 9307 – 9308 . 10.1021/ja00073a064 . ISSN 15205126.
- Hiller , S. , Fiorito , F. , Wüthrich , K. and Wider , G. ( 2005 ). Automated projection spectroscopy (APSY) . Proc. Natl. Acad. Sci. U.S.A. 102 ( 31 ): 10876 – 10881 . 10.1073/pnas.0504818102 . ISSN 00278424.
- Barna , J.C.J. , Laue , E.D. , Mayger , M.R. , Skilling , J. and Worrall , S.J.P. ( 1987 ). Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments . J. Magn. Reson. (1969) 73 ( 1 ): 69 – 77 . 10.1016/0022-2364(87)90225-3 . ISSN 00222364.
- Hoch , J.C. and Stern , A. ( 1996 ). NMR Data Processing . Wiley-Liss . ISBN 0471039004.
- Kazimierczuk , K. and Orekhov , V. ( 2015 ). Non-uniform sampling: Post-Fourier era of NMR data collection and processing . Magn. Reson. Chem. 53 ( 11 ): 921 – 926 . 10.1002/mrc.4284 . URL http://www.ncbi.nlm.nih.gov/pubmed/26290057 . ISSN 1097458X.
- Kazimierczuk , K. and Orekhov , V.Y. ( 2012 ). A comparison of convex and non-convex compressed sensing applied to multidimensional NMR . J. Magn. Reson. 223: 1 – 10 . 10.1016/j.jmr.2012.08.001 . ISSN 10907807.
- Kazimierczuk , K. and Orekhov , V.Y. ( 2011 ). Accelerated NMR spectroscopy by using compressed sensing . Angew. Chem. Int. Ed. Engl. 50 ( 24 ): 556 – 5559 . ISSN 1521-3773.
- Holland , D.J. , Bostock , M.J. , Gladden , L.F. and Nietlispach , D. ( 2011 ). Fast multidimensional NMR spectroscopy using compressed sensing . Angew. Chem. Int. Ed. Engl. 50 ( 29 ): 6548 – 6551 . ISSN 1521-3773.
- Hyberts , S.G. , Milbradt , A.G. , Wagner , A.B. , Arthanari , H. and Wagner , G. (2012). Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling . J. Biomol. NMR 52 : 1–13, 2012 . ISSN 0925-2738.
- Sun , S. , Gill , M. , Li , Y. , Huang , M. and Byrd , R.A. ( 2015 ). Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms . J. Biomol. NMR 62 ( 1 ): 105 – 17 . 10.1007/s10858-015-9923-x . ISSN 1573-5001.
- Kazimierczuk , K. and Orekhov , V.Y. ( 2012 b). A comparison of convex and non-convex compressed sensing applied to multidimensional NMR . J. Magn. Reson. 223 ( 0 ): 1 – 10 . 10.1016/j.jmr.2012.08.001 . ISSN 10907807.
- Mobli , M. , Maciejewski , M.W. , Gryk , M.R. and Hoch , J.C. ( 2007 ). Automatic maximum entropy spectral reconstruction in NMR . J. Biomol. NMR , 39 ( 2 ): 133 – 139 . 10.1007/s10858-007-9180-8 . ISSN 09252738.
- Matsuki , Y. , Eddy , M.T. and Herzfeld , J. ( 2009 April). Spectroscopy by Integration of Frequency and Time Domain Information for Fast Acquisition of High-Resolution Dark Spectra . J. Am. Chem. Soc. 131 ( 13 ): 4648 – 4656 . 10.1021/ja807893k . ISSN 1520-5126.
- Orekhov , V.Y. and Jaravine , V.A. ( 2011 ). Analysis of non-uniformly sampled spectra with multi-dimensional decomposition . Prog. Nucl. Magn. Reson. Spectrosc. 59 ( 3 ): 271 – 292 . 10.1016/j.pnmrs.2011.02.002 . ISSN 00796565.
- Qu , X. , Mayzel , M. , Cai , J.F. , Chen , Z. and Orekhov , V. ( 2015 ). Accelerated NMR spectroscopy with low-rank reconstruction . Angew. Chem. Int. Ed. 54 ( 3 ): 852 – 854 . 10.1002/anie.201409291 . ISSN 15213773.
- Hansen , D.F. ( 2019 ). Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra . J. Biomol. NMR 73 ( 10-11 ): 577 – 585 . 10.1007/s10858-019-00265-1 . ISSN 15735001.
- Qu , X. , Huang , Y. , Lu , H. , Qiu , T. , Guo , D. , Agback , T. , Orekhov , V. and Chen , Z. ( 2019 ). Accelerated nuclear magnetic resonance spectroscopy with deep learning . Angew. Chem. 59 ( 26 ): 10297 – 10300 . 10.1002/anie.201908162 . ISSN 0044-8249.
-
Karunanithy , G.
and
Hansen , D.F.
(
2020
). FID-net: a versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling.
J. Biomol. NMR
75:
1
–
19
.
10.1007/s10858-021-00366-w
. ISSN 1573-5001.
10.1007/s10858-021-00366-w Google Scholar
- Stanek , J. and Koźmiński , W. ( 2010 ). Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets . J. Biomol. NMR , 47 ( 1 ): 65 – 77 . 10.1007/s10858-010-9411-2 . ISSN 09252738.
- Ying , J. , Delaglio , F. , Torchia , D.A. and Bax , A. ( 2017 ). Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data . J. Biomol. NMR 68 ( 2 ): 101 – 118 . 10.1007/s10858-016-0072-7 . ISSN 15735001.
- Kazimierczuk , K. , Zawadzka , A. and Koźmiński , W. ( 2009 ). Narrow peaks and high dimensionalities: exploiting the advantages of random sampling . J. Magn. Reson. 197 ( 2 ): 219 – 228 . 10.1016/j.jmr.2009.01.003 .
- Motáčková , V. , Nováček , J. , Zawadzka-Kazimierczuk , A. , Kazimierczuk , K. , Žídek, L., Šanderová, H., Krásný, L., Koźmiński, W. and Sklenář, V. ( 2010 November). Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J. Biomol. NMR 48 ( 3 ): 169 – 177 .
- Kosiński , K. , Stanek , J. , Górka , M.J. , Żerko , S. and Koźmiński , W. ( 2017 ). Reconstruction of non-uniformly sampled five-dimensional NMR spectra by signal separation algorithm . J. Biomol. NMR 68 ( 2 ): 129 – 138 .
- Morris , G.A. , Barjat , H. and Home , T.J. ( 1997 ). Reference deconvolution methods . Prog. Nucl. Magn. Reson. Spectr. 31 ( 2-3 ): 197 – 257 . 10.1016/S0079-6565(97)00011-3 . ISSN 00796565.