A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments

Lindon, 2000, Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids, Concepts Magn Reson, 12, 289, 10.1002/1099-0534(2000)12:5<289::AID-CMR3>3.0.CO;2-W Fiehn, 2002, Metabolomics—the link between genotypes and phenotypes, Plant Mol Biol, 48, 155, 10.1023/A:1013713905833 Lindon, 2007 Clayton, 2006, Pharmaco-metabonomic phenotyping and personalized drug treatment, Nature, 440, 1073, 10.1038/nature04648 Clayton, 2009, Pharmacometabonomic identification of a significant host–microbiome metabolic interaction affecting human drug metabolism, Proc Natl Acad Sci U S A, 106, 14728, 10.1073/pnas.0904489106 Everett, 2013, Pharmacometabonomics and personalized medicine, Ann Clin Biochem, 50, 523, 10.1177/0004563213497929 Everett, 2015, Pharmacometabonomics in humans: a new tool for personalized medicine, Pharmacogenomics, 16, 737, 10.2217/pgs.15.20 Beckonert, 2007, Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts, Nat Protoc, 2, 2692, 10.1038/nprot.2007.376 Dunn, 2015, Molecular phenotyping of a UK population: defining the human serum metabolome, Metabolomics, 11, 9, 10.1007/s11306-014-0707-1 Craig, 2006, Scaling and normalization effects in NMR spectroscopic metabonomic data sets, Anal Chem, 78, 2262, 10.1021/ac0519312 Bylesjo, 2006, OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification, J Chemometr, 20, 341, 10.1002/cem.1006 Dona, 2014, Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping, Anal Chem, 86, 9887, 10.1021/ac5025039 Posma, 2012, Subset Optimization by Reference Matching (STORM): an optimized statistical approach for recovery of metabolic biomarker structural information from H-1 NMR spectra of biofluids, Anal Chem, 84, 10694, 10.1021/ac302360v Bouatra, 2013, The human urine metabolome, PLoS One, 8, 10.1371/journal.pone.0073076 Emwas, 2013, NMR-based metabolomics in human disease diagnosis: applications, limitations, and recommendations, Metabolomics, 9, 1048, 10.1007/s11306-013-0524-y Emwas, 2015, Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review, Metabolomics, 11, 872, 10.1007/s11306-014-0746-7 Teahan, 2006, Impact of analytical bias in metabonomic studies of human blood serum and plasma, Anal Chem, 78, 4307, 10.1021/ac051972y Pinto, 2014, Human plasma stability during handling and storage: impact on NMR metabolomics, Analyst, 139, 1168, 10.1039/C3AN02188B Izquierdo-Garcia, 2011, Descriptive review of current NMR-based metabolomic data analysis packages, Prog Nucl Magn Reson Spectrosc, 59, 263, 10.1016/j.pnmrs.2011.02.001 Want, 2010, Global metabolic profiling procedures for urine using UPLC–MS, Nat Protoc, 5, 1005, 10.1038/nprot.2010.50 Fonville, 2010, Evaluation of full-resolution J-resolved 1H NMR projections of biofluids for metabonomics information retrieval and biomarker identification, Anal Chem, 82, 1811, 10.1021/ac902443k Ludwig, 2010, Two-dimensional J-resolved NMR Spectroscopy: review of a key methodology in the metabolomics toolbox, Phytochem Anal, 21, 10.1002/pca.1186 Cui, 2008, Metabolite identification via the Madison metabolomics consortium database, Nat Biotechnol, 26, 162, 10.1038/nbt0208-162 Tulpan, 2011, MetaboHunter: an automatic approach for identification of metabolites from H-1-NMR spectra of complex mixtures, BMC Bioinforma, 12, 10.1186/1471-2105-12-400 van der Hooft, 2013, Structural elucidation of low abundant metabolites in complex sample matrices, Metabolomics, 9, 1009, 10.1007/s11306-013-0519-8 van der Hooft, 2011, A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC–MS-SPE-NMR, Magn Reson Chem, 49, S55, 10.1002/mrc.2833 Jacob, 2013, An efficient spectra processing method for metabolite identification from H-1-NMR metabolomics data, Anal Bioanal Chem, 405, 5049, 10.1007/s00216-013-6852-y Wishart, 2011, Advances in metabolite identification, Bioanalysis, 3, 1769, 10.4155/bio.11.155 Dunn, 2013, Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics, Metabolomics, 9, S44, 10.1007/s11306-012-0434-4 Watson, 2013, A rough guide to metabolite identification using high resolution liquid chromatography mass spectrometry in metabolomic profiling in metazoans, Comput Struct Biotechnol J, 4, e201301005, 10.5936/csbj.201301005 Peironcely, 2013, Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics, Anal Chem, 85, 3576, 10.1021/ac303218u Kertesz, 2009, Database searching for structural identification of metabolites in complex biofluids for mass spectrometry-based metabonomics, Bioanalysis, 1, 10.4155/bio.09.145 Theodoridis, 2011, Mass spectrometry-based holistic analytical approaches for metabolite profiling in systems biology studies, Mass Spectrom Rev, 30, 884, 10.1002/mas.20306 Kind, 2010, Advances in structure elucidation of small molecules using mass spectrometry, Bioanal Rev, 2, 23, 10.1007/s12566-010-0015-9 Claridge, 2009 Williams, 2008 Keeler, 2010 Gunther, 2013 Pearce, 2008, Robust algorithms for automated chemical shift calibration of 1D H-1 NMR spectra of blood serum, Anal Chem, 80, 7158, 10.1021/ac8011494 Farrant, 1994, Internal temperature calibration for H-1-NMR spectroscopy studies of blood-plasma and other biofluids, NMR Biomed, 7, 243, 10.1002/nbm.1940070508 Fan, 2008, Structure-based profiling of metabolites and isotopomers by NMR, Prog Nucl Magn Reson Spectrosc, 52, 69, 10.1016/j.pnmrs.2007.03.002 Schaller, 1995, New parameters for predicting H-1-NMR chemical-shifts of protons attached to carbon-atoms, Anal Chim Acta, 312, 95, 10.1016/0003-2670(95)00106-A Reich HJ. Web-based NMR information, 2015, http://www.chem.wisc.edu/areas/reich/chem605/index.htm Brown, 1985, A short set of C-13 NMR correlation tables, J Chem Educ, 62, 209, 10.1021/ed062p209 Wishart, 2013, HMDB 3.0—the human metabolome database in 2013, Nucleic Acids Res, 41, D801, 10.1093/nar/gks1065 Mestrelab Research MNova NMR Software. v 10.0.0, 2015, http://mestrelab.com/software/mnova/nmr/ ChemAxon's NMR Predictor in MarvinSketch, Marvin 6.1.1, 2013, ChemAxon (http://www.chemaxon.com). Bremser, 1985, Expectation ranges Of C-13 NMR Chemical-Shifts, Magn Reson Chem, 23, 271, 10.1002/mrc.1260230413 Breitmaier, 1979 Breitmaier, 1987 Wehrli, 1988 Kalinowski, 1988 Everett, 1984, Spin-Echo H-1-NMR spectroscopy — a new method for studying penicillin metabolism, J Chem Soc Chem Commun, 14, 894, 10.1039/c39840000894 Connor, 1994, High-resolution H-1-NMR spectroscopic studies of the metabolism and excretion of ampicillin in rats and amoxicillin in rats and man, J Pharm Pharmacol, 46, 128, 10.1111/j.2042-7158.1994.tb03755.x Everett, 1979, Homonuclear and heteronuclear coupling in 5′-Amp as probed by 2-dimensional proton nuclear magnetic-resonance spectroscopy, J Am Chem Soc, 101, 6776, 10.1021/ja00516a061 Leverence, 2007, Signal suppression/enhancement in HPLC-ESI-MS/MS from concomitant medications, Biomed Chromatogr, 21, 1143, 10.1002/bmc.863 Keun, 2002, Analytical reproducibility in H-1 NMR-based metabonomic urinalysis, Chem Res Toxicol, 15, 1380, 10.1021/tx0255774 Barton, 2008, High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study, Int J Epidemiol, 37, i31, 10.1093/ije/dym284 Tomlins, 1998, High resolution (1)H NMR spectroscopic studies on dynamic biochemical processes in incubated human seminal fluid samples, Biochim Biophys Acta Gen Subj, 1379, 367, 10.1016/S0304-4165(97)00116-5 Mercier, 2011, Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra, J Biomol NMR, 49, 307, 10.1007/s10858-011-9480-x Malagon, 2015, The phenotype of a knockout mouse identifies flavin-containing monooxygenase 5 (FMO5) as a regulator of metabolic ageing, Biochem Pharmacol, 96, 267, 10.1016/j.bcp.2015.05.013 Viant, 2003, Improved methods for the acquisition and interpretation of NMR metabolomic data, Biochem Biophys Res Commun, 310, 943, 10.1016/j.bbrc.2003.09.092 Bain, 1994, Artifacts in 2-dimensional NMR, Prog Nucl Magn Reson Spectrosc, 26, 59, 10.1016/0079-6565(94)80004-9 Le Guennec, 2014, Evaluation of fast 2D NMR for metabolomics, Anal Chem, 86, 5946, 10.1021/ac500966e Davis, 1985, Assignment of complex 'H NMR spectra via wo-dimensional homonuclear Hartmann–Hahn spectroscopy, J Am Chem Soc, 107, 2820, 10.1021/ja00295a052 Wishart, 2009, Computational strategies for metabolite identification in metabolomics, Bioanalysis, 1, 10.4155/bio.09.138 Lindon, 2001, Pattern recognition methods and applications in biomedical magnetic resonance, Prog Nucl Magn Reson Spectrosc, 39, 1, 10.1016/S0079-6565(00)00036-4 Wold, 1996, Hierarchical multiblock PLS and PC models for easier model interpretation and as an alternative to variable selection, J Chemometr, 10, 463, 10.1002/(SICI)1099-128X(199609)10:5/6<463::AID-CEM445>3.0.CO;2-L Wold, 2001, PLS-regression: a basic tool of chemometrics, Chemom Intell Lab Syst, 58, 109, 10.1016/S0169-7439(01)00155-1 Trygg, 2002, Orthogonal projections to latent structures (O-PLS), J Chemometr, 16, 119, 10.1002/cem.695 Holmes, 1994, Automatic data reduction and pattern recognition methods for analysis of 1H nuclear magnetic resonance spectra of human urine from normal and pathological states, Anal Biochem, 220, 284, 10.1006/abio.1994.1339 Holmes, 2000, Chemometric models for toxicity classification based on NMR spectra of biofluids, Chem Res Toxicol, 13, 471, 10.1021/tx990210t Trygg, 2007, Chemometrics in metabonomics, J Proteome Res, 6, 469, 10.1021/pr060594q Cloarec, 2005, Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets, Anal Chem, 77, 1282, 10.1021/ac048630x Fonville, 2010, The evolution of partial least squares models and related chemometric approaches in metabonomics and metabolic phenotyping, J Chemother, 24, 636 Zou, 2014, Statistical HOmogeneous cluster SpectroscopY (SHOCSY): an optimized statistical approach for clustering of 1H NMR spectral data to reduce interference and enhance robust biomarkers selection, Anal Chem, 86, 5308, 10.1021/ac500161k Cloarec, 2005, 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, Anal Chem, 77, 517, 10.1021/ac048803i Anderssen, 2006, Reducing over-optimism in variable selection by cross-model validation, Chemom Intell Lab Syst, 84, 69, 10.1016/j.chemolab.2006.04.021 Rubingh, 2006, Assessing the performance of statistical validation tools for megavariate metabolomics data, Metabolomics, 2, 53, 10.1007/s11306-006-0022-6 Szymańska, 2012, Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies, Metabolomics, 8, 3, 10.1007/s11306-011-0330-3 Golland, 2003, Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies, 330 Noda, 1993, Generalized 2-dimensional correlation method applicable to infrared, Raman, and other types of spectroscopy, Appl Spectrosc, 47, 1329, 10.1366/0003702934067694 Baker, 1990, A novel series of milbemycin antibiotics from streptomyces strain-E225.2. Isolation, characterization, structure elucidation and solution conformations, J Antibiot, 43, 1069, 10.7164/antibiotics.43.1069 Ashline, 1990, Isolation, structure elucidation, and synthesis of novel penicillin degradation products — Thietan-2-Ones, J Chem Soc Perkin Trans, 2, 1559, 10.1039/p29900001559 Ulrich, 2008, BioMagResBank, Nucleic Acids Res, 36, D402, 10.1093/nar/gkm957 Ludwig, 2012, Birmingham Metabolite Library: a publicly accessible database of 1-D H-1 and 2-D H-1 J-resolved NMR spectra of authentic metabolite standards (BML-NMR), Metabolomics, 8, 8, 10.1007/s11306-011-0347-7 2014 Sumner, 2007, Proposed minimum reporting standards for chemical analysis, Metabolomics, 3, 211, 10.1007/s11306-007-0082-2 Fiehn, 2007, The metabolomics standards initiative (MSI), Metabolomics, 3, 175, 10.1007/s11306-007-0070-6 Salek, 2013, The role of reporting standards for metabolite annotation and identification in metabolomic studies, GigaScience, 2, 13, 10.1186/2047-217X-2-13 Creek, 2014, Metabolite identification: are you sure? And how do your peers gauge your confidence?, Metabolomics, 10, 350, 10.1007/s11306-014-0656-8 Sumner, 2014, Proposed quantitative and alphanumeric metabolite identification metrics, Metabolomics, 10, 1047, 10.1007/s11306-014-0739-6 Daly, 2014, MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach, Bioinformatics, 30, 2764, 10.1093/bioinformatics/btu370 Everett, 2015, A new paradigm for known metabolite identification in metabonomics/metabolomics: metabolite identification efficiency, Comput Struct Biotechnol J, 13, 131, 10.1016/j.csbj.2015.01.002 Tang, 2013, Salting-out assisted liquid–liquid extraction for bioanalysis, Bioanalysis, 5, 1583, 10.4155/bio.13.117 Mushtaq, 2014, Extraction for metabolomics: access to the metabolome, Phytochem Anal, 25, 291, 10.1002/pca.2505 Gierth, 2015, Fast experiments for structure elucidation of small molecules: Hadamard NMR with multiple receivers, Magn Reson Chem, 10.1002/mrc.4292 Robinette, 2013, Statistical spectroscopic tools for biomarker discovery and systems medicine, Anal Chem, 85, 5297, 10.1021/ac4007254