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J Biomol NMR. 2017 Jun;68(2):101-118. doi: 10.1007/s10858-016-0072-7. Epub 2016 Nov 19.

Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data.

Author information

1
Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. jinfaying@niddk.nih.gov.
2
Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA.
3
National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
4
Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. bax@nih.gov.

Abstract

Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.

KEYWORDS:

4D NMR; Linear prediction; Multi-dimensional NMR; NUS; Non-uniform sampling; Sampling scheme; Sparse sampling; Spectral reconstruction

PMID:
27866371
PMCID:
PMC5438302
DOI:
10.1007/s10858-016-0072-7
[Indexed for MEDLINE]
Free PMC Article

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