Details of Group leader - Prof Roy Goodacre
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Post: Professor of Biological Chemistry Phone: +44 (0)161 306 4480 Email: roy.goodacre@manchester.ac.uk Website: Click Me |
Research The research theme in our group is predominantly directed towards developing metabolomic and proteomic technologies for the rapid accurate characterisation of biological systems. There are four main themes in our research group which overlap considerably and details of these are given below… |
Current Research
Metabolomics
Our strategy is to use a hierarchical approach where metabolic fingerprinting using Fourier transform infrared (FT-IR) spectroscopy is used to screen biological samples prior to more in depth mass spectrometry-based approached; as detailed in (Plant J. 46 (2006) 351-368).
Highlights include: we were the first to demonstrate that electrospray ionization mass spectrometry (ESI-MS) can be used for the reproducible characterisation of bacteria (FEMS Microbiol. Lett. 176 (1999) 17-24; Anal. Chem. 73 (2001) 4134-4144), an approach that has since been developed further using flow-injection ESI-MS for high throughput metabolic profiling (JASMS 13 (2002) 118-128). We have also very recently been developing laser desorption ionisation-MS for the same purpose (Metabolomics 1 (2005) 243-250; RCMS 20 (2006) 1192-1198).
Raman spectroscopy
We are developing a variety of Raman spectroscopic approaches (including near IR, deep UV, and surface enhanced Raman scattering) for the identification of bacterial pathogens and for the characterization and understanding of bacterial, yeast, plant and animal systems.
We were the first to show that surface enhanced Raman scattering (SERS) could be made reproducible enough to allow the discrimination of bacteria (Anal. Chem. 76 (2004) 40-47) including the possibility of single-cell measurements (Anal. Chem. 76 (2004) 5198-5202), and that quantitative measurements of microbial metabolites is possible (Analyst 130 (2005) 1019-1026). For UV resonance Raman (UVRR) spectroscopy we demonstrated that this method could be readily used for taxonomic purposes (Anal. Chem. 76 (2004) 585-591) as well as being able to predict the quantitative antibiotic mode-of-action and increase our understanding of the effect antimicrobials have on cells (Anal. Chem. 77 (2005) 2901-2906).
Machine learning
We are continually developing a variety of chemometric methods, and in the past have worked with artificial neural networks (Nature 359 (1992) 594) and partial least squares (Anal. Chem. 66 (1994) 1070-1085). More recently we want more understanding from our modelling and so have moved towards algorithms based on evolutionary computational approaches and in particular genetic algorithms (GAs). We have developed GAs (a) for variable selection for spectroscopic analysis (b) to perform baseline correction and spectral pre-processing (Bioinformatics 21 (2005) 860-868), and (c) to tune ESI-MS for discovering optimal conditions for protein analysis (Anal. Chem. 75 (2003) 6679-6686). We have also produced PyChem (Python + Chemometrics), an application for multivariate analysis (Bioinformatics 2006 in press). This is a easy to use graphical interface to chemometric algorithms that is available for both Windows XP and LINUX users and can be downloaded via http://www.pychem.org.uk/.
Spatial metabolomics and proteomics
The ability to collect ’omics data as a function of space (as well as time) will be hugely beneficial to increasing our knowledge of complex biological systems. Currently we are investigating the vibrational spectroscopic approaches of FT-IR and Raman for giving metabolite information, and MALDI-MS for spatial location of proteins. Watch this space for more details…
Service & Awards
- 2004: Recipient of the Third Professor S. Ramaseshan Distinguished Lecture. Presented by AstraZeneca Research Foundation India, Bangalore, India.
- 2005: Awarded the RSC’s Industrially-Sponsored Award in Bioanalytical Chemistry.
- 2006: Member of Systematics & Evolution Group Committee, Society for General Microbiology.
- 2006: Member of Biochemical Society - Theme Panel VI on Biotechnology and Bioinformatics.
- Editor-in-chief of Metabolomics.
- Editorial board of Journal of Analytical and Applied Pyrolysis.
- Founding director of the Metabolomics Society
Funding
BBSRC - EPSRC - Home Office - Royal Society of Chemistry - Shimadzu Biotech - Stiefel Laboratories (UK) Ltd.
Recent Publications
- Winder, C.L., Gordon, S.V., Dale, J., Hewinson, R.G. & Goodacre, R., Metabolic fingerprints of Mycobacterium bovis cluster with molecular type: implications for genotype-phenotype links., Microbiology, 152, 2757-2765, 2006.
- Hollywood, K., Brison, D.R. & Goodacre, R., Metabolomics: current technologies and future trends., Proteomics, 6, 4716-4723, 2006.
- Vaidyanathan, S., Gaskell, S. & Goodacre R., Matrix suppressed laser desorption ionization mass spectrometry and its suitability for metabolome analyses., Rapid Communications in Mass Spectrometry, 20, 1192-1198, 2006.
- López-Díez, E.C., Winder, C.L., Ashton, L., Currie, F. & Goodacre, R., Monitoring the mode of action of antibiotics using Raman spectroscopy: investigating sub-inhibitory effects of amikacin on Pseudomonas aeruginosa., Analytical Chemistry, 77, 2901-2906, 2006.
- Jarvis, R.M. & Goodacre, R., Genetic algorithm optimisation for pre-processing and variable selection of spectroscopic data., Bioinformatics, 21, 860-868, 2005.
- Brown, D.M., Zeef, L., Ellis, J., Goodacre, R. & Turner, S.R., Identification of novel genes involved in secondary cell wall formation using expression profiling and reverse genetics., Plant Cell, 17, 2281-2295, 2005.
- Vaidyanathan, S., Kell, D.B. & Goodacre, R., Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: influence of instrumental settings and implications for proteomics., Analytical Chemistry, 76, 5024-5032, 2004.
- Jarvis, R.M. and Goodacre, R., Rapid discrimination of bacteria using surface enhanced Raman spectroscopy., Analytical Chemistry, 76, 40-47, 2004.