A review of blind source separation in NMR spectroscopy.

Fourier transform is the data processing naturally associated to most NMR experiments. Notable exceptions are Pulse Field Gradient and relaxation analysis, the structure of which is only partially suitable for FT. With the revamp of NMR of complex mixtures, fueled by analytical challenges such as metabolomics, alternative and more apt mathematical methods for data processing have been sought, with the aim of decomposing the NMR signal into simpler bits. Blind source separation is a very broad definition regrouping several classes of mathematical methods for complex signal decomposition that use no hypothesis on the form of the data. Developed outside NMR, these algorithms have been increasingly tested on spectra of mixtures. In this review, we shall provide an historical overview of the application of blind source separation methodologies to NMR, including methods specifically designed for the specificity of this spectroscopy.

[1]  M. Nilsson,et al.  Speedy component resolution: an improved tool for processing diffusion-ordered spectroscopy data. , 2008, Analytical chemistry.

[2]  John M. Walker,et al.  Metabolic Profiling , 2011, Methods in Molecular Biology.

[3]  M. Nilsson,et al.  Diffusion NMR and trilinear analysis in the study of reaction kinetics. , 2009, Chemical communications.

[4]  N. Garti,et al.  New insights into silica-based NMR "chromatography". , 2011, Journal of magnetic resonance.

[5]  Adam A Colbourne,et al.  Local covariance order diffusion-ordered spectroscopy: a powerful tool for mixture analysis. , 2011, Journal of the American Chemical Society.

[6]  M. Nilsson,et al.  Resolving natural product epimer spectra by matrix-assisted DOSY. , 2011, Organic & biomolecular chemistry.

[7]  Lutgarde M. C. Buydens,et al.  Robust DOSY NMR data analysis , 2007 .

[8]  Eric Moulines,et al.  A blind source separation technique using second-order statistics , 1997, IEEE Trans. Signal Process..

[9]  M. Nilsson,et al.  Matrix‐assisted diffusion‐ordered spectroscopy: mixture resolution by NMR using SDS micelles , 2010, Magnetic resonance in chemistry : MRC.

[10]  Mathias Nilsson,et al.  The DOSY Toolbox: a new tool for processing PFG NMR diffusion data. , 2009, Journal of magnetic resonance.

[11]  Rafael Brüschweiler,et al.  Deconvolution of chemical mixtures with high complexity by NMR consensus trace clustering. , 2011, Analytical chemistry.

[12]  Aapo Hyvärinen,et al.  Fast and robust fixed-point algorithms for independent component analysis , 1999, IEEE Trans. Neural Networks.

[13]  P. Paatero,et al.  Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values† , 1994 .

[14]  Charles S. Johnson,et al.  Diffusion-ordered two-dimensional nuclear magnetic resonance spectroscopy , 1992 .

[15]  M. Nilsson,et al.  Simple proton spectra from complex spin systems: pure shift NMR spectroscopy using BIRD. , 2011, Angewandte Chemie.

[16]  Adam A Colbourne,et al.  Decoupling two-dimensional NMR spectroscopy in both dimensions: pure shift NOESY and COSY. , 2012, Angewandte Chemie.

[17]  Jean-Francois Cardoso,et al.  Blind signal separation: statistical principles , 1998, Proc. IEEE.

[18]  Mattias Rantalainen,et al.  Statistical correlation and projection methods for improved information recovery from diffusion-edited NMR spectra of biological samples. , 2007, Analytical chemistry.

[19]  S. Caldarelli,et al.  Determination of labile chiral supramolecular ion pairs by chromatographic NMR spectroscopy. , 2013, Angewandte Chemie.

[20]  R. Brüschweiler,et al.  Covariance nuclear magnetic resonance spectroscopy. , 2004, The Journal of chemical physics.

[21]  Rafael Brüschweiler,et al.  NMR in Metabolomics and Natural Products Research: Two Sides of the Same Coin , 2011, Accounts of chemical research.

[22]  D. Gauguier,et al.  Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. , 2005, Analytical chemistry.

[23]  Ivica Kopriva,et al.  Blind separation of analytes in nuclear magnetic resonance spectroscopy and mass spectrometry: sparseness-based robust multicomponent analysis. , 2010, Analytical chemistry.

[24]  A. Yilmaz,et al.  Metabolic profiling based on two-dimensional J-resolved 1H NMR data and parallel factor analysis. , 2011, Analytical chemistry.

[25]  A. Bax,et al.  Two-dimensional nuclear magnetic resonance spectroscopy. , 1986, Science.

[26]  Rafael Brüschweiler,et al.  Robust deconvolution of complex mixtures by covariance TOCSY spectroscopy. , 2007, Angewandte Chemie.

[27]  Chih-Jen Lin,et al.  On the Convergence of Multiplicative Update Algorithms for Nonnegative Matrix Factorization , 2007, IEEE Transactions on Neural Networks.

[28]  Lutgarde M. C. Buydens,et al.  Assessment of techniques for DOSY NMR data processing , 2003 .

[29]  Stphane Mallat,et al.  A Wavelet Tour of Signal Processing, Third Edition: The Sparse Way , 2008 .

[30]  Alexander Kraskov,et al.  Least-dependent-component analysis based on mutual information. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[31]  S. Jacobsson,et al.  Enhanced multivariate analysis by correlation scaling and fusion of LC/MS and 1H NMR data , 2007 .

[32]  Rute Almeida,et al.  dAMUSE - A new tool for denoising and blind source separation , 2005, Digit. Signal Process..

[33]  Y. Nishiyama,et al.  (13)C Solid-state NMR chromatography by magic angle spinning (1)H T(1) relaxation ordered spectroscopy. , 2010, Journal of magnetic resonance.

[34]  Jack Xin,et al.  Nonnegative Sparse Blind Source Separation for NMR Spectroscopy by Data Clustering, Model Reduction, and 1 Minimization , 2012, SIAM J. Imaging Sci..

[35]  A. J. Shaka,et al.  Processing DOSY spectra using the regularized resolvent transform. , 2003, Journal of magnetic resonance.

[36]  José Domingo Salazar,et al.  Application of a Bayesian deconvolution approach for high-resolution (1)H NMR spectra to assessing the metabolic effects of acute phenobarbital exposure in liver tissue. , 2010, Analytical chemistry.

[37]  R. Bro PARAFAC. Tutorial and applications , 1997 .

[38]  Automated CORE, RECORD, and GRECORD processing of multi-component PGSE NMR diffusometry data , 2012, European Biophysics Journal.

[39]  Rafael Brüschweiler,et al.  Multidimensional approaches to NMR-based metabolomics. , 2014, Analytical chemistry.

[40]  Richard A. Harshman,et al.  Foundations of the PARAFAC procedure: Models and conditions for an "explanatory" multi-model factor analysis , 1970 .

[41]  Alexander Kraskov,et al.  Monte Carlo Algorithm for Least Dependent Non-Negative Mixture Decomposition , 2006, Analytical chemistry.

[42]  Angela M. Gronenborn,et al.  NMR of Proteins , 1993 .

[43]  R. Harshman,et al.  PARAFAC: parallel factor analysis , 1994 .

[44]  K. Zangger,et al.  Homonuclear Broadband-Decoupled NMR Spectra , 1997 .

[45]  S. Viel,et al.  Enhanced diffusion-edited NMR spectroscopy of mixtures using chromatographic stationary phases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  H. Sebastian Seung,et al.  Algorithms for Non-negative Matrix Factorization , 2000, NIPS.

[47]  Patrik O. Hoyer,et al.  Non-negative sparse coding , 2002, Proceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing.

[48]  Bruno Torrésani,et al.  Effective processing of pulse field gradient NMR of mixtures by blind source separation. , 2013, Analytical chemistry.

[49]  P. Griffiths,et al.  Global Least-Squares Analysis of Large, Correlated Spectral Data Sets: Application to Component-Resolved FT-PGSE NMR Spectroscopy , 1996 .

[50]  Lucas C. Parra,et al.  Recovery of constituent spectra using non-negative matrix factorization , 2003, SPIE Optics + Photonics.

[51]  Rafael Brüschweiler,et al.  Simultaneous de novo identification of molecules in chemical mixtures by doubly indirect covariance NMR spectroscopy. , 2010, Journal of the American Chemical Society.

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

[53]  S. Opella,et al.  Shiftless nuclear magnetic resonance spectroscopy. , 2008, The Journal of chemical physics.

[54]  Yulia B. Monakhova,et al.  Independent components in spectroscopic analysis of complex mixtures , 2010, 1009.0534.

[55]  Pierre Comon,et al.  Handbook of Blind Source Separation: Independent Component Analysis and Applications , 2010 .

[56]  P. Comon Independent Component Analysis , 1992 .

[57]  A. J. Shaka,et al.  Postprocessing and sparse blind source separation of positive and partially overlapped data , 2011, Signal Process..

[58]  Andrzej Cichocki,et al.  Adaptive Blind Signal and Image Processing - Learning Algorithms and Applications , 2002 .

[59]  Patrik O. Hoyer,et al.  Non-negative Matrix Factorization with Sparseness Constraints , 2004, J. Mach. Learn. Res..

[60]  M. Nilsson,et al.  Isomer resolution by micelle-assisted diffusion-ordered spectroscopy. , 2009, Analytical chemistry.

[61]  S. Caldarelli,et al.  Maximum-quantum (MaxQ) NMR for the speciation of mixtures of phenolic molecules. , 2011, Chemical communications.

[62]  R. Y. Dong NMR Spectroscopy in Liquid Crystalline and Ordered Phases , 2012 .

[63]  C. F. Beckmann,et al.  Tensorial extensions of independent component analysis for multisubject FMRI analysis , 2005, NeuroImage.

[64]  M. Foroozandeh,et al.  Simultaneously Enhancing Spectral Resolution and Sensitivity in Heteronuclear Correlation NMR Spectroscopy , 2013, Angewandte Chemie.

[65]  J. Chang,et al.  Analysis of individual differences in multidimensional scaling via an n-way generalization of “Eckart-Young” decomposition , 1970 .

[66]  David A. Snyder,et al.  Generalized indirect covariance NMR formalism for establishment of multidimensional spin correlations. , 2009, The journal of physical chemistry. A.

[67]  I. Kopriva,et al.  Extraction of multiple pure component 1H and 13C NMR spectra from two mixtures: novel solution obtained by sparse component analysis-based blind decomposition. , 2009, Analytica chimica acta.

[68]  S. Caldarelli,et al.  Improved excitation uniformity in multiple‐quantum NMR experiments of mixtures , 2013, Magnetic resonance in chemistry : MRC.

[69]  N. Garti,et al.  High-resolution NMR "chromatography" using a liquids spectrometer. , 2008, Journal of magnetic resonance.

[70]  Jack Xin,et al.  A Recursive Sparse Blind Source Separation Method and Its Application to Correlated Data in NMR Spectroscopy of Biofluids , 2012, J. Sci. Comput..

[71]  Erkki Oja,et al.  Efficient Variant of Algorithm FastICA for Independent Component Analysis Attaining the CramÉr-Rao Lower Bound , 2006, IEEE Transactions on Neural Networks.

[72]  S. Caldarelli,et al.  Identification and quantification of EPA 16 priority polycyclic aromatic hydrocarbon pollutants by Maximum-Quantum NMR. , 2012, The Analyst.

[73]  M. Nilsson,et al.  Pure shift proton DOSY: diffusion-ordered 1H spectra without multiplet structure. , 2007, Chemical communications.

[74]  Rafael Brüschweiler,et al.  Web server based complex mixture analysis by NMR. , 2008, Analytical chemistry.

[75]  J. E. Tanner,et al.  Spin diffusion measurements : spin echoes in the presence of a time-dependent field gradient , 1965 .

[76]  S. Mallat A wavelet tour of signal processing , 1998 .

[77]  Pierre Comon,et al.  Independent component analysis, A new concept? , 1994, Signal Process..

[78]  Mathias Nilsson,et al.  Filter diagonalization method for processing PFG NMR data. , 2013, Journal of magnetic resonance.

[79]  Soo-Young Lee Blind Source Separation and Independent Component Analysis: A Review , 2005 .

[80]  J. Nuzillard,et al.  Model-free analysis of mixtures by NMR using blind source separation , 1998, Journal of magnetic resonance.

[81]  Daniel Raftery,et al.  "Add to subtract": a simple method to remove complex background signals from the 1H nuclear magnetic resonance spectra of mixtures. , 2012, Analytical chemistry.

[82]  Wady Naanaa,et al.  Blind source separation of positive and partially correlated data , 2005, Signal Process..

[83]  Mathias Nilsson,et al.  T1-diffusion-ordered spectroscopy: nuclear magnetic resonance mixture analysis using parallel factor analysis. , 2009, Analytical chemistry.

[84]  Rafael Brüschweiler,et al.  Covariance NMR spectroscopy by singular value decomposition. , 2004, Journal of magnetic resonance.

[85]  M. Nilsson,et al.  Resolving complex mixtures: trilinear diffusion data , 2014, Journal of biomolecular NMR.

[86]  Mathias Nilsson,et al.  Pure shift 1H NMR: a resolution of the resolution problem? , 2010, Angewandte Chemie.

[87]  M. Williamson,et al.  NMR of proteins. , 1993, Natural product reports.

[88]  M. Nilsson,et al.  Simultaneous enhancement of chemical shift dispersion and diffusion resolution in mixture analysis by diffusion-ordered NMR spectroscopy. , 2011, Chemical communications.

[89]  R. Brüschweiler,et al.  Spectral deconvolution of chemical mixtures by covariance NMR. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

[90]  M. Nilsson,et al.  Detection of Potential TNA and RNA Nucleoside Precursors in a Prebiotic Mixture by Pure Shift Diffusion-Ordered NMR Spectroscopy , 2013, Chemistry.

[91]  M. Nilsson,et al.  True chemical shift correlation maps: a TOCSY experiment with pure shifts in both dimensions. , 2010, Journal of the American Chemical Society.

[92]  T. Ebbels,et al.  Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts , 2007, Nature Protocols.

[93]  N. DiDonato,et al.  Independent component analysis applied to diffusion‐ordered spectroscopy: separating nuclear magnetic resonance spectra of analytes in mixtures , 2012 .

[94]  Seungjin Choi Blind Source Separation and Independent Component Analysis : A Review , 2004 .

[95]  Jon Clardy,et al.  Differential analysis of 2D NMR spectra: new natural products from a pilot-scale fungal extract library. , 2007, Angewandte Chemie.

[96]  Jerrold Meinwald,et al.  A new approach to natural products discovery exemplified by the identification of sulfated nucleosides in spider venom. , 2004, Journal of the American Chemical Society.

[97]  R Huo,et al.  Improved DOSY NMR data processing by data enhancement and combination of multivariate curve resolution with non-linear least square fitting. , 2004, Journal of magnetic resonance.

[98]  Rafael Brüschweiler,et al.  Theory of covariance nuclear magnetic resonance spectroscopy. , 2004, The Journal of chemical physics.

[99]  David A. Snyder,et al.  Non-negative matrix factorization of two-dimensional NMR spectra: application to complex mixture analysis. , 2008, The Journal of chemical physics.

[100]  Rafael Brüschweiler,et al.  Web server suite for complex mixture analysis by covariance NMR , 2009, Magnetic resonance in chemistry : MRC.

[101]  D. Armstrong,et al.  Micellar Effects on Molecular Diffusion: Theoretical and Chromatographic Considerations , 1986 .

[102]  Sebastiano Collino,et al.  Multivariate modeling strategy for intercompartmental analysis of tissue and plasma 1H NMR spectrotypes. , 2009, Journal of proteome research.

[103]  Erkki Oja,et al.  Independent component analysis: algorithms and applications , 2000, Neural Networks.

[104]  Peter Ladefoged,et al.  UCLA Working Papers in Phonetics, 23. , 1972 .

[105]  F. Asaro,et al.  Resolution of a nonionic surfactant oligomeric mixture by means of DOSY with inverse micelle assistance , 2011, Magnetic resonance in chemistry : MRC.

[106]  Chih-Jen Lin,et al.  Projected Gradient Methods for Nonnegative Matrix Factorization , 2007, Neural Computation.

[107]  C. Magon,et al.  Processing of high resolution magic angle spinning spectra of breast cancer cells by the filter diagonalization method. , 2012, The Analyst.

[108]  Rasmus Bro,et al.  Mathematical chromatography solves the cocktail party effect in mixtures using 2D spectra and PARAFAC , 2010 .

[109]  Rasmus Bro,et al.  Analysis of lipoproteins using 2D diffusion-edited NMR spectroscopy and multi-way chemometrics , 2005 .

[110]  L. Buydens,et al.  Diagnostic analysis of experimental artefacts in DOSY NMR data by covariance matrix of the residuals. , 2005, Journal of magnetic resonance.

[111]  W. Windig,et al.  Generalized Rank Annihilation Method Applied to a Single Multicomponent Pulsed Gradient Spin Echo NMR Data Set , 1996 .

[112]  J. Griffin,et al.  Time-domain Bayesian detection and estimation of noisy damped sinusoidal signals applied to NMR spectroscopy. , 2007, Journal of magnetic resonance.

[113]  M. Piotto,et al.  Non-uniformly sampled Maximum Quantum spectroscopy. , 2011, Journal of magnetic resonance.

[114]  N. Garti,et al.  NMR chromatography using microemulsion systems. , 2011, Langmuir : the ACS journal of surfaces and colloids.

[115]  Diffusion Ordered Nuclear Magnetic Resonance Spectroscopy: Principles and Applications , 1999 .

[116]  S. Caldarelli,et al.  Investigation of the chromatographic process via pulsed-gradient spin-echo nuclear magnetic resonance. Role of the solvent composition in partitioning chromatography. , 2006, Analytical chemistry.

[117]  Barak A. Pearlmutter,et al.  Blind Source Separation by Sparse Decomposition in a Signal Dictionary , 2001, Neural Computation.

[118]  W. Windig,et al.  Direct exponential curve resolution algorithm (DECRA): A novel application of the generalized rank annihilation method for a single spectral mixture data set with exponentially decaying contribution profiles , 1997 .

[119]  P. Stilbs RECORD processing - a robust pathway to component-resolved HR-PGSE NMR diffusometry. , 2010, Journal of magnetic resonance.

[120]  T. Malliavin,et al.  Maximum Entropy Processing of DOSY NMR Spectra , 1998 .

[121]  John C Lindon,et al.  Statistical spectroscopic tools for biomarker discovery and systems medicine. , 2013, Analytical chemistry.

[122]  Barak A. Pearlmutter,et al.  Blind source separation by sparse decomposition , 2000, SPIE Defense + Commercial Sensing.

[123]  E. Oja,et al.  Independent Component Analysis , 2013 .