Accelerated NMR spectroscopy with low-rank reconstruction.

Accelerated multi-dimensional NMR spectroscopy is a prerequisite for high-throughput applications, studying short-lived molecular systems and monitoring chemical reactions in real time. Non-uniform sampling is a common approach to reduce the measurement time. Here, a new method for high-quality spectra reconstruction from non-uniformly sampled data is introduced, which is based on recent developments in the field of signal processing theory and uses the so far unexploited general property of the NMR signal, its low rank. Using experimental and simulated data, we demonstrate that the low-rank reconstruction is a viable alternative to the current state-of-the-art technique compressed sensing. In particular, the low-rank approach is good in preserving of low-intensity broad peaks, and thus increases the effective sensitivity in the reconstructed spectra.

[1]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[2]  J. Skilling,et al.  Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments , 1987 .

[3]  C M Dobson,et al.  Protein Folding Monitored at Individual Residues During a Two-Dimensional NMR Experiment , 1996, Science.

[4]  Alan S. Stern,et al.  NMR Data Processing , 1996 .

[5]  P. Koehl LINEAR PREDICTION SPECTRAL ANALYSIS OF NMR DATA , 1999 .

[6]  V. Mandelshtam FDM: The Filter Diagonalization Method for Data Processing in NMR Experiments , 2001 .

[7]  E. Candès,et al.  Stable signal recovery from incomplete and inaccurate measurements , 2005, math/0503066.

[8]  Vladislav Yu Orekhov,et al.  Removal of a time barrier for high-resolution multidimensional NMR spectroscopy , 2006, Nature Methods.

[9]  K. Saxena,et al.  NMR Analysis of a Tau Phosphorylation Pattern , 2006 .

[10]  Emmanuel J. Candès,et al.  Exact Matrix Completion via Convex Optimization , 2009, Found. Comput. Math..

[11]  Masaki Mishima,et al.  Protein structure determination in living cells by in-cell NMR spectroscopy , 2009, Nature.

[12]  Emmanuel J. Candès,et al.  A Singular Value Thresholding Algorithm for Matrix Completion , 2008, SIAM J. Optim..

[13]  K. Kazimierczuk,et al.  Random sampling in multidimensional NMR spectroscopy. , 2010, Progress in nuclear magnetic resonance spectroscopy.

[14]  S. Hyberts,et al.  Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data. , 2010, Journal of the American Chemical Society.

[15]  Emmanuel J. Candès,et al.  Matrix Completion With Noise , 2009, Proceedings of the IEEE.

[16]  Lucio Frydman,et al.  Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications. , 2011, Journal of magnetic resonance.

[17]  V. Orekhov,et al.  Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. , 2011, Progress in nuclear magnetic resonance spectroscopy.

[18]  V. Orekhov,et al.  Accelerated NMR spectroscopy by using compressed sensing. , 2011, Angewandte Chemie.

[19]  Zuowei Shen,et al.  Robust Video Restoration by Joint Sparse and Low Rank Matrix Approximation , 2011, SIAM J. Imaging Sci..

[20]  L. Gladden,et al.  Fast multidimensional NMR spectroscopy using compressed sensing. , 2011, Angewandte Chemie.

[21]  Di Guo,et al.  Reconstruction of Self-Sparse 2D NMR Spectra from Undersampled Data in the Indirect Dimension† , 2011, Sensors.

[22]  Yi Ma,et al.  Robust principal component analysis? , 2009, JACM.

[23]  Paul Schanda,et al.  Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. , 2012, Journal of the American Chemical Society.

[24]  Justin P. Haldar,et al.  Image Reconstruction From Highly Undersampled $( {\bf k}, {t})$-Space Data With Joint Partial Separability and Sparsity Constraints , 2012, IEEE Transactions on Medical Imaging.

[25]  Gerhard Wagner,et al.  Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling , 2012, Journal of Biomolecular NMR.

[26]  François-Xavier Theillet,et al.  Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts , 2013, Nature Protocols.

[27]  Eugene C Lin,et al.  Sampling scheme and compressed sensing applied to solid-state NMR spectroscopy. , 2013, Journal of magnetic resonance.

[28]  S. Hyberts,et al.  Exploring signal-to-noise ratio and sensitivity in non-uniformly sampled multi-dimensional NMR spectra , 2013, Journal of biomolecular NMR.

[29]  Minh N. Do,et al.  Denoising MR Spectroscopic Imaging Data With Low-Rank Approximations , 2013, IEEE Transactions on Biomedical Engineering.

[30]  Krzysztof Kazimierczuk,et al.  Causality principle in reconstruction of sparse NMR spectra , 2014, Chemical communications.

[31]  Guangming Shi,et al.  Compressive Sensing via Nonlocal Low-Rank Regularization , 2014, IEEE Transactions on Image Processing.

[32]  Mark W Maciejewski,et al.  Nonuniform sampling and maximum entropy reconstruction in multidimensional NMR. , 2014, Accounts of chemical research.

[33]  Steve B. Jiang,et al.  Cine Cone Beam CT Reconstruction Using Low-Rank Matrix Factorization: Algorithm and a Proof-of-Principle Study , 2012, IEEE Transactions on Medical Imaging.

[34]  M. Mayzel,et al.  Time-resolved multidimensional NMR with non-uniform sampling , 2014, Journal of biomolecular NMR.

[35]  S. Caldarelli,et al.  Evaluation of fast 2D NMR for metabolomics. , 2014, Analytical chemistry.