The following publications from within the Department of Surgery and Cancer, form the basis of the experiments performed as part of the training courses we offer. We would recommend them as good introductory publications within the field of metabolic profiling. Publications from external organisations are also listed and form the pre-course reading materials.
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Journal articleWant EJ, Masson P, Michopoulos F, et al., 2013,
Global metabolic profiling of animal and human tissues via UPLC-MS
, NATURE PROTOCOLS, Vol: 8, Pages: 17-32, ISSN: 1754-2189- Author Web Link
- Cite
- Citations: 569
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Journal articleKamleh MA, Ebbels TMD, Spagou K, et al., 2012,
Optimizing the Use of Quality Control Samples for Signal Drift Correction in Large-Scale Urine Metabolic Profiling Studies
, ANALYTICAL CHEMISTRY, Vol: 84, Pages: 2670-2677, ISSN: 0003-2700- Author Web Link
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- Citations: 106
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Journal articleTheodoridis GA, Gika HG, Want EJ, et al., 2012,
Liquid chromatography-mass spectrometry based global metabolite profiling: A review
, ANALYTICA CHIMICA ACTA, Vol: 711, Pages: 7-16, ISSN: 0003-2670- Author Web Link
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- Citations: 373
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Journal articleKamburov A, Cavill R, Ebbels TMD, et al., 2011,
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
, BIOINFORMATICS, Vol: 27, Pages: 2917-2918, ISSN: 1367-4803- Author Web Link
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- Citations: 268
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Book chapterEbbels TMD, De Iorio M, 2011,
Statistical Data Analysis in Metabolomics
, Handbook of Statistical Systems Biology, Editors: Stumpf, Balding, Girolami, Publisher: Wiley, ISBN: 97811199706138 Statistical Data Analysis in Metabolomics Timothy MD Ebbels1 and Maria De Iorio2 1Department of Surgery and Cancer, Imperial College, London, UK 2Department of Epidemiology and Biostatistics, Imperial College, London, ...
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Journal articleVeselkov KA, Vingara LK, Masson P, et al., 2011,
Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery
, ANALYTICAL CHEMISTRY, Vol: 83, Pages: 5864-5872, ISSN: 0003-2700- Author Web Link
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- Citations: 211
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Journal articleCavill R, Kamburov A, Ellis JK, et al., 2011,
Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
, PLOS COMPUTATIONAL BIOLOGY, Vol: 7, ISSN: 1553-734X- Author Web Link
- Open Access Link
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- Citations: 72
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Journal articleSpagou K, Wilson ID, Masson P, et al., 2011,
HILIC-UPLC-MS for Exploratory Urinary Metabolic Profiling in Toxicological Studies
, ANALYTICAL CHEMISTRY, Vol: 83, Pages: 382-390, ISSN: 0003-2700- Author Web Link
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- Citations: 126
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Journal articleWant EJ, Wilson ID, Gika H, et al., 2010,
Global metabolic profiling procedures for urine using UPLC-MS
, NATURE PROTOCOLS, Vol: 5, Pages: 1005-1018, ISSN: 1754-2189- Author Web Link
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- Citations: 760
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Journal articleEbbels TMD, Cavill R, 2009,
Bioinformatic methods in NMR-based metabolic profiling
, PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, Vol: 55, Pages: 361-374, ISSN: 0079-6565- Author Web Link
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- Citations: 74
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Publications from external organisations
We would also recommend the following publications as further reading in the field of metabolic profiling.
General Metabolic Profiling
Fiehn, O. (2002). "Metabolomics--the link between genotypes and phenotypes." Plant Molecular Biology 48(1-2): 155-171.
NMR data pre-processing
Hoch, J. C. and A. S. Stern (1996). NMR Data Processing. New York, Wiley-Liss.
Aberg, K. M., E. Alm and R. J. Torgrip (2009). "The correspondence problem for metabonomics datasets." Anal Bioanal Chem 394(1): 151-162.
LC-MS data pre-processing
Pluskal, T., S. Castillo, A. Villar-Briones and M. Oresic (2010). "MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data." BMC Bioinformatics 11: 395.
Multivariate Analysis - Unsupervised
Bro, R. and A. K. Smilde (2014). "Principal component analysis." Analytical Methods 6(9): 2812-2831.
Multivariate Analysis - Supervised
Wold, S., M. Sjostrom and L. Eriksson (2001). "PLS-regression: a basic tool of chemometrics."
Chemometrics and Intelligent Laboratory Systems 58(2): 109-130.
Trygg, J. and S. Wold (2002). "Orthogonal projections to latent structures (O-PLS)." Journal of
Chemometrics 16(3): 119-128.
Trygg, J. and S. Wold (2003). "O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter." Journal of Chemometrics 17(1): 53-64.
Löfstedt, T. and J. Trygg (2011). "OnPLS—a novel multiblock method for the modelling of predictive and orthogonal variation." Journal of Chemometrics 25(8): 441-455.
Pathway Analysis
Khatri, P., M. Sirota and A. J. Butte (2012). "Ten years of pathway analysis: current approaches and outstanding challenges." PLoS Comput Biol 8(2): e1002375.
Xia, J. and D. S. Wishart (2010). "MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data." Nucleic Acids Res 38(Web Server issue): W71-77.
Metabolite Identification
Kuhl, C., R. Tautenhahn, C. Bottcher, T. R. Larson and S. Neumann (2012). "CAMERA: An integrated strategy for compound spectra extraction and annotation of LC/MS data sets." Analytical Chemistry 84(1): 283-289.
Kind, T., K.-H. Liu, D. Y. Lee, B. DeFelice, J. K. Meissen and O. Fiehn (2013). "LipidBlast in silico
tandem mass spectrometry database for lipid identification." Nat Meth 10(8): 755-758.