Generalized adaptive intelligent binning of multiway data.

NMR metabolic fingerprinting methods almost exclusively rely upon the use of one-dimensional (1D) 1H NMR data to gain insights into chemical differences between two or more experimental classes. While 1D 1H NMR spectroscopy is a powerful, highly informative technique that can rapidly and nondestructively report details of complex metabolite mixtures, it suffers from significant signal overlap that hinders interpretation and quantification of individual analytes. Two-dimensional (2D) NMR methods that report heteronuclear connectivities can reduce spectral overlap, but their use in metabolic fingerprinting studies is limited. We describe a generalization of Adaptive Intelligent binning that enables its use on multidimensional datasets, allowing the direct use of nD NMR spectroscopic data in bilinear factorizations such as principal component analysis (PCA) and partial least squares (PLS).

[1]  John C. Lindon,et al.  Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids , 2000 .

[2]  John W. Eaton,et al.  GNU Octave Manual Version 3 , 2008 .

[3]  Yi-Zeng Liang,et al.  Monte Carlo cross‐validation for selecting a model and estimating the prediction error in multivariate calibration , 2004 .

[4]  Peyman Eshghi,et al.  Dimensionality choice in principal components analysis via cross-validatory methods , 2014 .

[5]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[6]  Robert Powers,et al.  Multivariate Analysis in Metabolomics. , 2012, Current Metabolomics.

[7]  Mark de Berg,et al.  Computational geometry: algorithms and applications , 1997 .

[8]  Age K. Smilde,et al.  UvA-DARE ( Digital Academic Repository ) Assessment of PLSDA cross validation , 2008 .

[9]  Robert Powers,et al.  Negative impact of noise on the principal component analysis of NMR data. , 2006, Journal of magnetic resonance.

[10]  Elena Tsiporkova,et al.  NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. , 2008, Analytical chemistry.

[11]  Wojtek J. Krzanowski,et al.  Cross-Validation in Principal Component Analysis , 1987 .

[12]  William J. Astle,et al.  A Bayesian Model of NMR Spectra for the Deconvolution and Quantification of Metabolites in Complex Biological Mixtures , 2011, 1105.2204.

[13]  Mark Harrison,et al.  Adaptive binning: An improved binning method for metabolomics data using the undecimated wavelet transform , 2007 .

[14]  Márcia M. C. Ferreira,et al.  Optimized bucketing for NMR spectra: Three case studies , 2013 .

[15]  Robert Powers,et al.  MVAPACK: A Complete Data Handling Package for NMR Metabolomics , 2014, ACS chemical biology.

[16]  Arthur G. Palmer,et al.  Sensitivity improvement in proton-detected two-dimensional heteronuclear relay spectroscopy , 1991 .

[17]  Paul A. Keifer,et al.  Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity , 1992 .

[18]  H. Senn,et al.  Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. , 2006, Analytical chemistry.

[19]  Michael L. Raymer,et al.  Dynamic adaptive binning: an improved quantification technique for NMR spectroscopic data , 2011, Metabolomics.

[20]  Johan Trygg,et al.  CV‐ANOVA for significance testing of PLS and OPLS® models , 2008 .

[21]  R. A. van den Berg,et al.  Centering, scaling, and transformations: improving the biological information content of metabolomics data , 2006, BMC Genomics.

[22]  J. Trygg,et al.  Evaluation of the orthogonal projection on latent structure model limitations caused by chemical shift variability and improved visualization of biomarker changes in 1H NMR spectroscopic metabonomic studies. , 2005, Analytical chemistry.

[23]  U. Edlund,et al.  Visualization and interpretation of OPLS models based on 2D NMR data , 2008 .

[24]  Cheng Zheng,et al.  Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection , 2011, Bioinform..

[25]  Michael L. Raymer,et al.  Gaussian binning: a new kernel-based method for processing NMR spectroscopic data for metabolomics , 2008, Metabolomics.

[26]  U. Edlund,et al.  Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models. , 2008, Analytical chemistry.

[27]  A. Majumdar,et al.  A Comprehensive Discussion of HSQC and HMQC Pulse Sequences , 2004 .

[29]  Age K. Smilde,et al.  Principal Component Analysis , 2003, Encyclopedia of Machine Learning.

[30]  Ian T. Jolliffe,et al.  Principal Component Analysis , 2002, International Encyclopedia of Statistical Science.

[31]  Erik Alm,et al.  The correspondence problem for metabonomics datasets , 2009, Analytical and bioanalytical chemistry.

[32]  R. Rai,et al.  Fast and accurate quantitative metabolic profiling of body fluids by nonlinear sampling of 1H–13C two-dimensional nuclear magnetic resonance spectroscopy. , 2012, Analytical chemistry.

[33]  S. Wold,et al.  Orthogonal projections to latent structures (O‐PLS) , 2002 .

[34]  Jouni Uitto,et al.  Comparison of 1D and 2D NMR spectroscopy for metabolic profiling. , 2008, Journal of proteome research.

[35]  Haiping Lu,et al.  A survey of multilinear subspace learning for tensor data , 2011, Pattern Recognit..

[36]  A. Motta,et al.  Monitoring real-time metabolism of living cells by fast two-dimensional NMR spectroscopy. , 2010, Analytical chemistry.