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Analytical and statistical approaches to metabolomics research
Abstract
Metabolomics, the global profiling of metabolites in different living systems, has experienced a rekindling of interest partially due to the improved detection capabilities of the instrumental techniques currently being used in this area of biomedical research. The analytical methods of choice for the analysis of metabolites in search of disease biomarkers in biological specimens, and for the study of various low molecular weight metabolic pathways include NMR spectroscopy, GC/MS, CE/MS, and HPLC/MS. Global metabolite analysis and profiling of two different sets of data results in a plethora of data that is difficult to manage or interpret manually because of their subtle differences. Multivariate statistical methods and pattern-recognition programs were developed to handle the acquired data and to search for the discriminating features between data acquired from two sample sets, healthy and diseased. Metabolomics have been used in toxicology, plant physiology, and biomedical research. In this paper, we discuss various aspects of metabolomic research including sample collection, handling, storage, requirements for sample analysis, peak alignment, data interpretation using statistical approaches, metabolite identification, and finally recommendations for successful analysis.
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“Briefly, NMR is robust, nondestructive, and quantitative but has a relatively low sensitivity, which narrows its coverage of the food metabolome to predominant nutrients, sugars, and microbial metabolites present at millimolar to micromolar concentrations.”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [113]
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Dumas, M., Canlet, C., André, F., Vercauteren, J., & Paris, A. (2002) · Analytical Chemistry · doi:10.1021/ac0156870 · Cited by 65
WERF, M. J. V. D., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T., Portais, J., Wittmann, C., Hooks, M. A., Tomassini, A., Oldiges, M., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0080-4 · Cited by 61
Proposed reporting requirements for the description of NMR-based metabolomics experiments
Rubtsov, D. V., JENKINS, H. A., Ludwig, C., Easton, J. M., Viant, M. R., Günther, U. L., Griffin, J. L., & Hardy, N. W. (2007) · Metabolomics · doi:10.1007/s11306-006-0040-4 · Cited by 57
Sample treatments prior to capillary electrophoresis–mass spectrometry
Hernández‐Borges, J., Borges‐Miquel, T. M., Rodríguez‐Delgado, M. Á., & Cifuentes, A. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.10.070 · Cited by 55
Analysis of nucleic acid constituents by on‐line capillary electrophoresis‐mass spectrometry
Willems, A. V., Deforce, D. L. D., Peteghem, C. H. V., & Bocxlaer, J. F. V. (2005) · Electrophoresis · doi:10.1002/elps.200410278 · Cited by 53
Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling
Ding, J., Sorensen, C. M., Zhang, Q., Jiang, H., Jaitly, N., Livesay, E. A., Shen, Y., Smith, R. D., & Metz, T. (2007) · Analytical Chemistry · doi:10.1021/ac070080q · Cited by 52
Sandusky, P. O., & Raftery, D. (2005) · Analytical Chemistry · doi:10.1021/ac0510890 · Cited by 52
Automated screening for metabolites in complex mixtures using 2D COSY NMR spectroscopy
Xi, Y., de Ropp, J. S., Viant, M. R., Woodruff, D. L., & Yu, P. (2006) · Metabolomics · doi:10.1007/s11306-006-0036-0 · Cited by 52
Correcting ligands, metabolites, and pathways
Ott, M. A., & Vriend, G. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-517 · Cited by 51
Balayssac, S., Delsuc, M., Gilard, V., Prigent, Y., & Malet‐Martino, M. (2008) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2008.09.022 · Cited by 49
Bertram, H. C., Malmendal, A., Petersen, B. O., Madsen, J. C., Pedersen, H., Nielsen, N. C., Hoppe, C., Mølgaard, C., Michaelsen, K. F., & Duus, J. Ø. (2007) · Analytical Chemistry · doi:10.1021/ac070928a · Cited by 48
Improvements in Complex Mixture Analysis by NMR: DQF-COSY iDOSY
Newman, J. M., & Jerschow, A. (2007) · Analytical Chemistry · doi:10.1021/ac061760g · Cited by 44
Comparison of different search engines using validated MS/MS test datasets
Boutilier, K., Ross, M. M., Podtelejnikov, A. V., Orsi, C., Taylor, R., Taylor, P. P., & Figeys, D. (2004) · Analytica Chimica Acta · doi:10.1016/j.aca.2004.04.047 · Cited by 43
Tomita, M., & Nishioka, T. (2005) · Springer eBooks · doi:10.1007/4-431-28055-3 · Cited by 41
Validation of a urine metabolome fingerprint in dog for phenotypic classification
Viant, M. R., Ludwig, C., Rhodes, S., Günther, U. L., & Allaway, D. (2007) · Metabolomics · doi:10.1007/s11306-007-0092-0 · Cited by 41
Homeostatic Signature of Anabolic Steroids in Cattle Using 1H−13C HMBC NMR Metabonomics
Dumas, M., Canlet, C., Vercauteren, J., André, F., & Paris, A. (2005) · Journal of Proteome Research · doi:10.1021/pr0500556 · Cited by 38
Zhang, F., Bruschweiler‐Li, L., & Robinette, S. L. (2008) · Analytical Chemistry · doi:10.1021/ac801116u · Cited by 34
Evaluating Low-Intensity Unknown Signals in Quantitative Proton NMR Mixture Analysis
Weljie, A. M., Newton, J., Jirik, F. R., & Vogel, H. J. (2008) · Analytical Chemistry · doi:10.1021/ac8012362 · Cited by 31
Baykal, A. T., Jain, M. R., & Hong Li, A. (2008) · Metabolomics · doi:10.1007/s11306-008-0125-3 · Cited by 29
Validation of a urine metabolome fingerprint in dog for phenotypic classification
Viant, M. R., Ludwig, C., Rhodes, S., Günther, U. L., & Allaway, D. (2009) · Metabolomics · doi:10.1007/s11306-009-0172-4 · Cited by 28
2D NMR metabonomic analysis: a novel method for automated peak alignment
Zheng, M., Lü, P., Liu, Y., Pease, J. H. B., Usuka, J., Liao, G., & Peltz, G. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm427 · Cited by 27
Metabolic analysis of human biological fluids by 1H NMR spectroscopy
Kolokolova, T. N., Savel’ev, O. Y., & Sergeev, N. M. (2008) · Journal of Analytical Chemistry · doi:10.1134/s1061934808020020 · Cited by 26
Two-Dimensional Correlation Analysis of Nuclear Magnetic Resonance Metabonomics Data
Šašić, S. (2008) · Applied Spectroscopy · doi:10.1366/000370208785284439 · Cited by 20
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HORA suite: a database and software for human metabolomics
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Korfmacher, W. A. (2006) · Current Drug Metabolism · doi:10.2174/138920006777697945 · Cited by 8
Flagged first, then by citations
1 of the 133 references couldn’t be matched to a known paper.
Research works printed but not linked: 6
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Cited by
Sorted by citations
Global metabolic profiling of animal and human tissues via UPLC-MS
Want, E. J., Masson, P., Michopoulos, F., Wilson, I. D., Theodoridis, G. A., Plumb, R. S., Shockcor, J. P., Loftus, N. J., Holmes, E. C., & Nicholson, J. K. (2012) · Nature Protocols · doi:10.1038/nprot.2012.135 · Cited by 1,647
The food metabolome: a window over dietary exposure
Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.076133 · Cited by 519
Advances in structure elucidation of small molecules using mass spectrometry
Kind, T., & Fiehn, O. (2010) · Bioanalytical reviews · doi:10.1007/s12566-010-0015-9 · Cited by 508
Targeted Metabolomics for Biomarker Discovery
Griffiths, W. J., Koal, T., Wang, Y., Kohl, M., Enot, D. P., & Deigner, H. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.200905579 · Cited by 418
Foodomics: MS‐based strategies in modern food science and nutrition
Herrero, M., Simó, C., García‐Cañas, V., Ibáñez, E., & Cifuentes, A. (2011) · Mass Spectrometry Reviews · doi:10.1002/mas.20335 · Cited by 397
Metadata
- Authors
- Issaq, H. J., Van, Q. N., Waybright, T. J., Muschik, G. M., & Veenstra, T. D.
- Affiliations
- National Cancer Institute (US)
- Venue
- Journal of Separation Science
- Publisher
- Wiley
- Published
- 2009-06-30
- Volume
- 32
- Issue
- 13
- Pages
- 2183-2199
- ISSN
- 1615-9306 (ISSN-L)
- 1615-9314
- OpenAlex
- W2103773262
- Cited by
- 227
- References
- 133
- Citations by year
- 2026: 4 · 2025: 12 · 2024: 8 · 2023: 7 · 2022: 6 · 2021: 11 · 2020: 4 · 2019: 17 · 2018: 6 · 2017: 7 · 2016: 11 · 2015: 15 · 2014: 27 · 2013: 22 · 2012: 18
- FWCI
- 1.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Separation Science (publishedVersion)
- PubMed (publishedVersion)
- DigitalCommons-Cedarville (Cedarville University) (submittedVersion)
- Funders
- National Cancer Institute, National Institutes of Health (HHSN261200800001E)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Engineering › Biomedical Engineering › Advanced Chemical Sensor Technologies
- Physical Sciences › Chemistry › Analytical Chemistry › Spectroscopy and Chemometric Analyses
- Keywords
- metabolomics, multivariate analysis, pattern recognition, disease biomarkers, metabolite profiling, sample collection and storage, peak alignment, metabolite identification, NMR spectroscopy, gas chromatography-mass spectrometry, HPLC-MS, capillary electrophoresis-mass spectrometry, toxicology, plant physiology
- MeSH terms
- Chromatography, High Pressure Liquid, Humans, Gas Chromatography-Mass Spectrometry, Software, Specimen Handling, Biomarkers, Electrophoresis, Capillary, Nuclear Magnetic Resonance, Biomolecular, Biomedical Research, Metabolomics
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