Descriptive review of current NMR-based metabolomic data analysis packages.

CIBERES, CIBER Enfermedades Respiratorias, Departartamento Quimica-Fisica II, Facultad Farmacia, Universidad Complutense de Madrid, Madrid, Spain CIBERES, CIBER Enfermedades Respiratorias, CAI de Resonancia Magnetica, Universidad Complutense de Madrid, Madrid, Spain CIBERES, CIBER Enfermedades Respiratorias, Fundacion Jimenez Diaz – CAPIO, Madrid, Spain Departamento de Ingenieria Rural, ETSI Agronomos, Universidad Politecnica de Madrid, Madrid, Spain

[1]  I. Wilson,et al.  High resolution "ultra performance" liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. , 2005, Journal of proteome research.

[2]  W. Dietrich,et al.  Fast and precise automatic baseline correction of one- and two-dimensional nmr spectra , 1991 .

[3]  Ian D. Wilson,et al.  HIGH RESOLUTION PROTON MAGNETIC RESONANCE SPECTROSCOPY OF BIOLOGICAL FLUIDS , 1989 .

[4]  K. Wüthrich,et al.  IFLAT—A New Automatic Baseline-Correction Method for Multidimensional NMR Spectra with Strong Solvent Signals , 1995 .

[5]  I. Schuppe-Koistinen,et al.  Peak alignment of NMR signals by means of a genetic algorithm , 2003 .

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

[7]  P J Sadler,et al.  Use of high-resolution proton nuclear magnetic resonance spectroscopy for rapid multi-component analysis of urine. , 1984, Clinical chemistry.

[8]  T. Lundstedt,et al.  Chapter 6 – Chemometrics Techniques for Metabonomics , 2007 .

[9]  Matej Oresic,et al.  MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data , 2006, Bioinform..

[10]  Barbara L. Smith,et al.  Evaluating human breast ductal carcinomas with high-resolution magic-angle spinning proton magnetic resonance spectroscopy. , 1998, Journal of magnetic resonance.

[11]  R. J. O. Torgrip,et al.  A note on normalization of biofluid 1D 1H-NMR data , 2008, Metabolomics.

[12]  S. Watkins,et al.  Focused metabolomic profiling in the drug development process: advances from lipid profiling. , 2005, Current opinion in chemical biology.

[13]  M B.  AMERICAN CHEMICAL SOCIETY. , 1881, Science.

[14]  J. Davis.  Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .

[15]  J. Lindon,et al.  Scaling and normalization effects in NMR spectroscopic metabonomic data sets. , 2006, Analytical chemistry.

[16]  F. V. D. van den Berg,et al.  1H nuclear magnetic resonance-based metabolomic characterization of wines by grape varieties and production areas. , 2008, Journal of agricultural and food chemistry.

[17]  Jacco D. van Beek,et al.  matNMR: A flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab® , 2007 .

[18]  Douglas B. Kell,et al.  Metabolomics and Machine Learning: Explanatory Analysis of Complex Metabolome Data Using Genetic Programming to Produce Simple, Robust Rules , 2004, Molecular Biology Reports.

[19]  S. Papson,et al.  “Model” , 1981 .

[20]  Johan Trygg,et al.  K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space , 2008, BMC Bioinformatics.

[21]  Gerald A. Pearson,et al.  A general baseline-recognition and baseline-flattening algorithm , 1977 .

[22]  Erik Johansson,et al.  Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm) , 2004, Analytical and bioanalytical chemistry.

[23]  Xinjie Zhao,et al.  Strategy for metabonomics research based on high-performance liquid chromatography and liquid chromatography coupled with tandem mass spectrometry. , 2005, Journal of chromatography. A.

[24]  Royston Goodacre,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2006 .

[25]  E Holmes,et al.  Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks. , 2001, Chemical research in toxicology.

[26]  Steffen Neumann,et al.  Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements , 2008, BMC Bioinformatics.

[27]  Han Min Woo,et al.  Mass spectrometry based metabolomic approaches in urinary biomarker study of women's cancers. , 2009, Clinica chimica acta; international journal of clinical chemistry.

[28]  E. Johansson,et al.  Multi- and Megavariate Data Analysis: Finding and Using Regularities in Metabonomics Data , 2005 .

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

[30]  David M. Rocke,et al.  Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis , 2008, BMC Bioinformatics.

[31]  K. W. Cattermole.  The Fourier Transform and its Applications , 1965 .

[32]  George G. Lorentz,et al.  Deferred Bernstein polynomials , 1951 .

[33]  John C. Lindon,et al.  Pattern recognition methods and applications in biomedical magnetic resonance , 2001 .

[34]  Mark R Viant,et al.  International NMR-based environmental metabolomics intercomparison exercise. , 2009, Environmental science & technology.

[35]  Peak‐finding partial least squares for the analysis of 1H NMR spectra , 2006 .

[36]  Guangji Wang,et al.  Metabolomic investigation into variation of endogenous metabolites in professional athletes subject to strength-endurance training. , 2009, Journal of applied physiology.

[37]  John C. Lindon,et al.  The handbook of metabonomics and metabolomics , 2007 .

[38]  Joel G Pounds,et al.  A study of spectral integration and normalization in NMR-based metabonomic analyses. , 2005, Journal of pharmaceutical and biomedical analysis.

[39]  J. L. Izquierdo-García,et al.  A metabonomic approach to evaluate COPD in a model of cigarette smoke exposure in mice , 2010, Metabolomics.

[40]  M. Tomita,et al.  Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. , 2003, Journal of proteome research.

[41]  R. Goodacre,et al.  Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis , 2003, Springer US.

[42]  Manuel Desco,et al.  A novel R-package graphic user interface for the analysis of metabonomic profiles , 2009, BMC Bioinformatics.

[43]  David M. Rocke,et al.  A general-purpose baseline estimation algorithm for spectroscopic data. , 2010, Analytica chimica acta.

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

[45]  J. Nicholson,et al.  High‐resolution 1H and 1H‐13C magic angle spinning NMR spectroscopy of rat liver , 2000, Magnetic resonance in medicine.

[46]  Paul H. Gamache,et al.  Metabolomic applications of electrochemistry/Mass spectrometry , 2004, Journal of the American Society for Mass Spectrometry.

[47]  Golotvin,et al.  Improved baseline recognition and modeling of FT NMR spectra , 2000, Journal of magnetic resonance.

[48]  Richard G. Brereton,et al.  Applied Chemometrics for Scientists , 2007 .

[49]  Douglas B. Kell,et al.  Functional Genomics Via Metabolic Footprinting: Monitoring Metabolite Secretion by Escherichia Coli Tryptophan Metabolism Mutants Using FT–IR and Direct Injection Electrospray Mass Spectrometry , 2003, Comparative and functional genomics.

[50]  Manuel Martín-Pastor,et al.  A new general-purpose fully automatic baseline-correction procedure for 1D and 2D NMR data. , 2006, Journal of magnetic resonance.

[51]  Chen Wen-xue,et al.  Metabonomic Characterization of The Low-grade Human Astrocytomas and Meningiomas Using Magic-angle Spinning 1H Nuclear Magnetic Resonance Spectroscopy and Principal Component Analysis , 2008 .

[52]  W. Cho,et al.  Metabolomics and biomarker discovery: NMR spectral data of urine and hepatotoxicity by carbon tetrachloride, acetaminophen, and d-galactosamine in rats , 2008, Metabolomics.

[53]  Ping Liu,et al.  Metabonomic study of aristolochic acid-induced nephrotoxicity in rats. , 2006, Journal of proteome research.

[54]  Qi Zhao,et al.  HiRes - a tool for comprehensive assessment and interpretation of metabolomic data , 2006, Bioinform..

[55]  D. E. Brown.  Fully Automated Baseline Correction of 1D and 2D NMR Spectra Using Bernstein Polynomials , 1995 .

[56]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[57]  Elaine Holmes,et al.  Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. , 2008, Journal of proteome research.

[58]  S. D. Jong.  SIMPLS: an alternative approach to partial least squares regression , 1993 .

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

[60]  I. Campbell,et al.  Human erythrocyte metabolism studies by 1H spin echo NMR , 1977, FEBS letters.

[61]  David S. Wishart,et al.  MetaboAnalyst: a web server for metabolomic data analysis and interpretation , 2009, Nucleic Acids Res..

[62]  T. Ebbels,et al.  Recursive segment-wise peak alignment of biological (1)h NMR spectra for improved metabolic biomarker recovery. , 2009, Analytical chemistry.

[63]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[64]  B. Karlberg,et al.  New modes of data partitioning based on PARS peak alignment for improved multivariate biomarker/biopattern detection in 1H-NMR spectroscopic metabolic profiling of urine , 2006, Metabolomics.

[65]  J. Utzinger,et al.  Metabolic Profiling of an Echinostoma caproni Infection in the Mouse for Biomarker Discovery , 2008, PLoS neglected tropical diseases.

[66]  Alan Hutson,et al.  Detection of epithelial ovarian cancer using 1H‐NMR‐based metabonomics , 2005, International journal of cancer.

[67]  I Martínez-Pérez,et al.  Genetic programming for classification and feature selection: analysis of 1H nuclear magnetic resonance spectra from human brain tumour biopsies , 1998, NMR in biomedicine.

[68]  Therese E. Malliavin,et al.  An NMR assignment module implemented in the Gifa NMR processing program , 1998, Bioinform..

[69]  Henrik Antti,et al.  Spectral editing and pattern recognition methods applied to high-resolution magic-angle spinning 1H nuclear magnetic resonance spectroscopy of liver tissues. , 2003, Analytical biochemistry.

[70]  Wen Wu,et al.  Peak Alignment of Urine NMR Spectra Using Fuzzy Warping , 2006, J. Chem. Inf. Model..

[71]  M. Rantalainen,et al.  Kernel‐based orthogonal projections to latent structures (K‐OPLS) , 2007 .

[72]  M. Saraste,et al.  FEBS Lett , 2000 .

[73]  Zhirong Zhang,et al.  Development of rat urinary HPLC-UV profiling for metabonomic study on Liuwei Dihuang Pills. , 2009, Journal of pharmaceutical and biomedical analysis.

[74]  Ad Bax,et al.  Baseline distortion in real-Fourier-transform NMR spectra , 1988 .

[75]  Karl-Heinz Ott,et al.  Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. , 2003, Phytochemistry.

[76]  Pei Wang,et al.  Bioinformatics Original Paper a Suite of Algorithms for the Comprehensive Analysis of Complex Protein Mixtures Using High-resolution Lc-ms , 2022 .

[77]  T. Veenstra,et al.  The Use of Urine Proteomic and Metabonomic Patterns for the Diagnosis of Interstitial Cystitis and Bacterial Cystitis , 2004, Disease markers.

[78]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[79]  Qing Yang,et al.  Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases. , 2004, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[80]  R. Hewer,et al.  Applying biofluid 1H NMR-based metabonomic techniques to distinguish between HIV-1 positive/AIDS patients on antiretroviral treatment and HIV-1 negative individuals. , 2006, Journal of pharmaceutical and biomedical analysis.

[81]  Ruedi Aebersold,et al.  A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry*S , 2005, Molecular & Cellular Proteomics.

[82]  C. Braak,et al.  Comments on the PLS kernel algorithm , 1994 .

[83]  A. B. Robinson,et al.  Quantitative analysis of urine vapor and breath by gas-liquid partition chromatography. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Bhupinder S. Dayal,et al.  Improved PLS algorithms , 1997 .

[85]  Tao Wang,et al.  Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis , 2009, BMC Bioinformatics.

[86]  John C. Lindon,et al.  Metabonomics in toxicity assessment , 2005 .

[87]  G. Willems,et al.  A robust Hotelling test , 2002 .

[88]  Julie Wilson,et al.  Novel feature selection method for genetic programming using metabolomic 1H NMR data , 2006 .

[89]  D. Stephenson,et al.  Automated analysis of high-resolution NMR spectra. II. Illustrative applications of the computer program DAVINS , 1980 .

[90]  Johan Trygg,et al.  Chemometrics in metabonomics. , 2007, Journal of proteome research.

[91]  S. Wold,et al.  A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: Theory and algorithm , 1994 .

[92]  Sirish L. Shah,et al.  Analysis of metabolomic data using support vector machines. , 2008, Analytical chemistry.

[93]  E Holmes,et al.  High‐resolution magic angle spinning 1H NMR spectroscopic studies on intact rat renal cortex and medulla , 1999, Magnetic resonance in medicine.

[94]  R. Bro,et al.  Quantitative analysis of NMR spectra with chemometrics. , 2008, Journal of magnetic resonance.

[95]  P J Lisboa,et al.  Assessment of statistical and neural networks methods in NMR spectral classification and metabolite selection , 1998, NMR in biomedicine.

[96]  Knut Reinert,et al.  OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.

[97]  J C Lindon,et al.  Pattern recognition analysis of high resolution 1H NMR spectra of urine. A nonlinear mapping approach to the classification of toxicological data , 1990, NMR in biomedicine.

[98]  R. Gentleman,et al.  Classification Using Generalized Partial Least Squares , 2005 .

[99]  A. Heuer,et al.  A new method for suppressing baseline distortions in FT NMR , 1989 .

[100]  J. Trygg.  O2‐PLS for qualitative and quantitative analysis in multivariate calibration , 2002 .

[101]  Changguo Tang.  An Analysis of Baseline Distortion and Offset in NMR Spectra , 1994 .