Contact details

Paul Benton

Research

Paul Benton is a Graduate Student at Imperial College London under the Faculty of Medicine. Previously working at the Scripps Research Institute in La Jolla California as a Reseach Programmer, his research ranged from work on METLIN and the development of XCMS. He started developing xcms in early 2008 and later that year published XCMS². XCMS² allows for the automation of metabolite identification through high accuracy tandem mass spectrometry data. As Paul notes "structural characterization of metabolites ... is commonly the most time-consuming aspect of metabolomics." This step of automation will speed up the analysis of the large datasets being generated and hopefully allow for an increase in biomarker discovery.

Currently, Paul is involved with the COMET2 study and metabonomic experiments. This work is concentrating on the reproducibility of different techniques that are used in metabonomics and metabolomics. "This work will give us tangible results on how much error we have in the system" says Paul. This is important in any study, but even more so in these large ‘omic’ type experiments. Once these numbers are available Paul wants to use temporal metabolic profiles for forecasting of diseases states and estimation of cell to cell variability.

Publications

H. P. Benton, D. M. Wong, S. A. Trauger and G. Siuzdak --XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal. Chem., 2008, 80 (16), pp 6382–6389 "

William M. Edmands, Florian Geier, Paul Benton, Elaine Holmes and Nigel J. Gooderham "Toxicology 262 (1) 2009 pp11"
Oscar Yanes, Julie Clark, Diana M Wong, Gary J Patti, Antonio Sanchez-Ruiz,H Paul Benton, Sunia A Trauger, Caroline Desponts, Sheng Ding and Gary Siuzdak. -- Metabolic oxidation regulates embryonic stem cell differentiation. Nature Chemical Biology 2010, 6, pp 411–417

H Paul Benton, Elizabeth J Want, Timothy M D Ebbels -- Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data. Bioinformatics. 2010 Oct 1;26(19):2488-9.
H. Paul Benton, Elizabeth Want, Hector C. Keun, Alexander Amberg, Robert S. Plumb, Francoise Goldfain-Blanc, Bernhard Walther, Michael D. Reily, John C. Lindon, Elaine Holmes, Jeremy K. Nicholson, and Timothy M. D. Ebbels -- Intra- and Interlaboratory Reproducibility of Ultra Performance Liquid Chromatography–Time-of-Flight Mass Spectrometry for Urinary Metabolic Profiling. Anal. Chem., 2012, 84 (5), pp 2424–2432

Talks

XCMS and XCMS^2 - Identification of metabolites - Metabolomics Short course - TSRI- 2008
Metabolite Identification with XCMS - XCMS workshop - ASMS - 2009
Taking XCMS to higher levels - XCMS day course - MetaboMeeting - 2009
Taking XCMS to higher levels - Cheminformatics with R - EBI Hinxton - May 2010 http://www.ebi.ac.uk/industry/Workshops/CheminformaticsR170510.html
Gap Correction of LC-MS datasets - BioC - Manchester UK - December 2011
Advance data processing using XCMS - Metabolomics short course - Imperial College - every June & October 2008 - 2012