Research interests
When you measure what you are speaking about and express it in numbers, you know something about it,
but when you cannot express it in numbers your knowledge is of a meagre and unsatisfactory kind.
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(Lord Kelvin, early 20th century)
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Current research interests: Metabolomics
Rick's research goals focus on the systems biology investigations of microbial and mammalian systems,
specifically the application of metabolomics to these disciplines and the development of analytical
instrumentation and methodologies to fulfill these goals.
Metabolomics is focussed on the holistic and data-driven investigation of the quantitative collection
of low molecular weight organic and inorganic compounds present in biological systems. This collection
of endogenous and exogenous metabolites is defined as the metabolome. Endogenous metabolites can be
biochemically synthesized or catabolised within the system and exogenous metabolites are acquired from
the external environment (for example, food nutrients and drugs) or from co-habiting species (for example,
gut microbiome). A range of experimental strategies are employed to investigate the metabolome including
metabolic profiling (untargeted analysis), targeted analysis and metabolite fingerprinting, each with
different advantages and disadvantages. Both the intracellular and extracellular (metabolic footprint)
metabolomes can be investigated to increase our understanding of biological systems. Metabolomes are
physically and chemically complex and challenging to investigate.
My research goals involve the development of workflows (or metabolomic pipelines), instrumental
technologies and analytical methodologies to enable the detailed and reproducible investigation
of microbial and mammalian metabolomes, so to increase the biological and mechanistic understanding
of these systems. Biological systems studied include baker's yeast Saccharomyces cerevisiae
and mammals. The workflows extend from sampling of metabolomes to sample preparation, acquisition of
analytical data, processing of raw data and the conversion of data to biological knowledge. No single
analytical platform can detect all metabolites and the application of multiple platforms is recommended.
My expertise has allowed me to develop and exploit a range of mass spectrometric platforms for the
investigation of metabolomes including gas chromatography-time of flight-mass spectrometry (GC-ToF-MS),
comprehensive GCxGC-ToF-MS, direct infusion mass spectrometry (DIMS) and Ultra Performance Liquid
Chromatography-mass spectrometry (UPLC-MS). These technologies have been developed to produce valid
and reproducible datasets for both short-term and long-term metabolomic studies. I work with
Professor Douglas Kell in MCISB and previously in the
Bioanalytical Sciences group. My research interests include:
1. Systems biology investigation of baker's yeast Saccharomyces cerevisiae
At the Manchester Centre for Integrative Systems Biology (MCISB) we are developing new systems
biology-focused experimental and computational technologies to investigate and quantitatively
model the metabolism of baker's yeast, Saccharomyces cerevisiae. This involves the
development of mathematical models, acquisition of experimental data and the integrated fusion
of models and data in an iterative relationship to construct, test and validate quantitative
metabolic models. My role is focussed on the development, validation and application of targeted
analytical methodologies to provide the absolute quantification of metabolites present in the
intracellular and metabolic footprints of yeast under defined and reproducible growth conditions
(a typical example can be seen here).
Previous research with Professor Douglas Kell and
Dr Irena Spasic involved a large-scale metabolic
footprint investigation of single gene deletant mutants of S. cerevisiae.
2. Development and exploitation of mass spectrometric technologies for metabolomic investigations
As an analytical chemist my primary objective is to apply technological platforms to provide
reproducible and 'fit for purpose' data for research goals. At Manchester (and previously at
The University of Sheffield) I am developing mass spectrometric platforms for metabolic profiling
and metabolite fingerprinting. These have included optimisation of analytical platforms to
maximise the number of metabolites detected and development of methodologies that provide
reproducible data appropriate for studying small changes in metabolic profiles. The introduction
of new analytical technologies including GC-TOF-MS, comprehensive GCxGC-TOF-MS, UPLC and the
Orbitrap mass spectrometer (all applied at Manchester) have enabled researchers to detect and
identify larger fractions of a range of metabolomes. A separate problem being addressed at
Manchester is the identification of metabolites, essential to allow the conversion of analytical
data to biological knowledge. Identification of metabolites can be performed using a number of
different approaches, including the development of mass spectral libraries with authentic
standards and elucidation of metabolite identifications from accurate mass, isotope patterns
and fragmentation mass spectra. We are currently constructing GC-EI-TOF-MS retention index/mass
spectral libraries employing LECO GC-ToF-MS instruments and retention time/accurate mass/CID
fragmentation libraries employing UPLC coupled to a LTQ/Orbitrap hybrid mass spectrometer.
3. Investigation of the metabolomes of "healthy" and "diseased" humans
The metabolome is an ideal system to investigate the phenotypes of humans. At Manchester we are
studying the variability observed in the metabolomes of healthy individuals and the disease-independent
changes caused by diet, gender, age and lifestyle (as investigated in the
HUSERMET project). We are also investigating
differences in metabolic profiles associated with diseases including pre-eclampsia and heart disease.
These differences can be applied to define risk factors or as prognostic or diagnostic biomarkers of
disease and also enable a mechanistic model of disease to be deduced. Both serum/plasma and urine are
investigated. I work closely with a number of researchers at Manchester including Drs David Broadhurst
and Marie Brown.
My professional Curriculum Vitae can be seen here.
Publications
Reviews
Dunn, W. B. (2008)
Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes.
Physical Biology, 5, 011001
Samuel, J-l., Schaub, M.C., Zaugg, M., Mamas, M., Dunn, W.B. et al. (2008)
Genomics in cardiac metabolism.
Cardiovascular research, in press
Ellis, D. I., W. B. Dunn, et al. (2007)
Metabolic fingerprinting as a diagnostic tool.
Pharmacogenomics, 8, 1243-1266
Dunn, W.B., Bailey, N.J.C. and Johnson, H.E. (2005)
Measuring the metabolome: current analytical technologies.
Analyst, 130, 606-625
Dunn, W.B. and Ellis, D.I. (2005)
Metabolomics: current analytical platforms and methodologies.
TrAC: Trends Analytical Chemistry, 24, 285-294
Kell, D.B., Brown, M., Davey, H.M., Dunn, W.B., Spasic, I and Oliver, S.G. (2005)
Metabolic footprinting and systems biology: The medium is the message.
Nature Reviews Microbiology, 3, 557-565
Brown, M., Dunn, W.B., Ellis et al. (2005)
A metabolome pipeline: from concept to data to knowledge.
Metabolomics, 1, 39-51
Goodacre, R., Vaidyanathan, S., et al. (2004)
Metabolomics by numbers: acquiring and understanding global metabolite data.
Trends Biotechnology, 24, 245-253
Microbial metabolomics
MacKenzie, D.A., Defernez, M., Dunn, W.B. et al. (2008)
Relatedness of clinical, probiotic and commercial isolates of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics.
Yeast, in press
Peiris, D., Dunn, W.B., Brown, M., Kell, D.B. and Hedger, J. (2008)
Metabolite profiles of interacting mycelial fronts differ for the wood decay basidiomycete fungi Stereum hirsutum,
Coprinus micaceus and Coprinus disseminatus.
Metabolomics, 4, 52-62
Castrillo JI, Zeef LA, et al. (2007)
Growth control of the eukaryote cell: a systems biology study in yeast.
Journal of Biology, 6, art 4
Pope, G.A., Mackenzie, D.A., et al. (2007)
Metabolic footprinting as a tool for discriminating between brewing yeasts.
Yeast, 24, 667-679
Mammalian metabolomics
Heazell, A.E.P., Brown, M., Dunn, W.B. et al. (2008)
Analysis of the Metabolic Footprint and Tissue Metabolome of Placental Villous Explants Cultured at Different Oxygen Tensions Reveals Novel Redox Biomarkers.
Placenta, in press
Kenny LC, Broadhurst D, Brown M, Dunn WB, et al. (2008)
Detection and Identification of Novel Metabolomic Biomarkers in Preeclampsia.
Reproductive Sciences, 15, 591-598
Dunn, W. B., Broadhurst, D., et al. (2008)
A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols.
Int J Epidemiol, 37, i23-i30.
Dunn, W.B., Broadhurst, D.I., et al. (2007)
Serum metabolomics reveals many novel metabolic markers of heart failure, including pseudouridine and 2-oxoglutarate.
Metabolomics, 3, 413-426
Underwood, B.R., Broadhurst, D., Dunn, W.B., Ellis, D.I., Michell, A.W., Vacher, C., Mosedale, D.E., Kell, D.B., Barker, R.A., Grainger, D.J. and Rubinsztein, D.C. (2006)
Huntington disease patients and transgenic mice have similar pro-catabolic serum metabolite profiles,
Brain, 129, 877-886
Kenny, L.C., Dunn, W.B., et al. (2005)
Novel biomarkers for preeclampsia detected using metabolomics and machine learning,
Metabolomics, 1, 227
Instrument and methodology development
Dunn, W.B., Broadhurst, D., et al. (2008)
Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system.
J. Chromat. B, in press
Winder, C.L., Dunn, W.B., et al. (2008)
Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites.
Anal Chem., 80, 2939-48
Lu, H., W. B. Dunn, et al. (2008)
Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS.
Trac-Trends in Analytical Chemistry, 27, 215-227
O’Hagan, S.O., Dunn, W.B., et al. (2007)
Closed-loop, multiobjective optimization of two-dimensional gas chromatography/mass spectrometry for serum metabolomics.
Analytical Chemistry, 79, 464-476
Spasic, I., Dunn, W.B., Velarde, G., Tseng, A., Jenkins, H., Hardy, N., Oliver, S.G. and Kell, D.B. (2006)
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics.
BMC Bioinformatics, 7, 281
Vaidyanathan, S., Jones, D., Broadhurst, D., Ellis, J., Jenkins, T., Dunn, W.B., Hayes, A., Burton, N., Oliver, S.G., Kell, D.B. and Goodacre, R. (2005)
A laser desorption ionization mass spectrometry approach for high throughput metabolomics.
Metabolomics, 1, 243-250
Dunn, W.B., Overy, S. and Quick, W.P., (2005)
Evaluation of Automated Electrospray-TOF Mass Spectrometry for Metabolite Fingerprinting.
Metabolomics, 1, 137-148
O’Hagan, S., Dunn, W.B., et al. (2005)
Closed-loop, multiobjective optimization of analytical instrumentation:
gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations.
Anal. Chem, 77, 290-303
Relevant websites
The websites and publications detailed below are not intended to be comprehensive, are not in any
specific order of preference and are provided as an initial portal to the subjects of metabolomics
and mass spectrometry.
Rick's list of recommended reading can be seen here.
Metabolomics and Systems Biology at Manchester
Professor Douglas Kell's group website
Manchester Centre for Integrative Systems Biology
The HUSERMET project
Laboratory for Bioanalytical Spectroscopy
Portals to Metabolomics and Chemistry
The Metabolomics Society
The Royal Society of Chemistry
Metabolomics journal
The Golm Metabolome Database
The Metabolomics Fiehn Lab
Metabolomics at The Scripps Centre for Mass Spectrometry
The Human Metabolome Database including DrugBank and FoodDB
MetRO at Rothamsted
Quantitative Biology and Bioinformatics (Matej Orešić)
MassBank.jp
Comprehensive Yeast Genome Database
KEGG
Reactome
BioCyc
InChI
ChEBI
PubChem
ChemSpider
Mass Spectrometry Instrument Manufacturers
LECO
Anatune Ltd
Waters
Bruker
Agilent's metabolomics lab
Applied Biosystems
ThermoFisher Electron
ThermoFisher Electron
Mass spectrometry based websites
British Mass Spectrometry Society
American Society for Mass Spectrometry
Michael Barber Centre for Mass Spectrometry at The University of Manchester
Spectroscopy Now
i-mass
Ion source
AMDIS (Automated Mass Spectral Deconvulotion and Identification Software)
XCMS
List of accurate atomic weights and isotope information
Other websites
School of Chemistry, University of Manchester
Manchester Interdisciplinary Biocentre
BBSRC
EPSRC
UoM webmail
UoM mail manager
Google
Trainline
Animal and Plant Sciences, University of Sheffield
Interests
Good ale and food, sport, Sheffield United FC season ticket holder, walking, gardening.
Campaign for Real Ale
Everything to learn about Sheffield (UK)
Sheffield United FC (greatest football club ever!)
SUFC Annie's Song
Yorkshire County Cricket Club
Everything to learn about Manchester (UK)
Peak District National Park
Walks in The Peak District
Photos of the Peak District
Lake District National Park
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Photos of the Lake District
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Walks in the Yorkshire Dales
Photos of the Yorkshire Dales
Snowdonia National park
Walks in the Snowdonia National Park
Pictures of the Snowdonia National Park
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Rock Tavern
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Trainline
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Meerkats
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