1990 Ph.D. ‘The Expression of Glycogen Phosphorylase in Normal and Abnormal Mouse Skeletal Muscle’ Department of Biochemistry, University of Liverpool
1985 B.Sc. Honours (Class 2:1) in Applied Biochemistry, University of Salford
Postdoctoral Research Assistant,
LabA, Centre for Proteome Research
Institute of Integrative Biology
University of Liverpool,
Crown Street
Liverpool L69 7ZB
Tel: +44 151 794 5344
Email: dsimpson[at]liv.ac.uk
About me
I graduated from the University of Salford with a degree in Applied Biochemistry in 1985. During my degree course I had a 12 month industrial placement at Higson’s Brewery in Liverpool. It was an exciting time to be there as a new lager plant was being installed and was commissioned the same year. In addition to the quality control analyses I was involved in the development of a new product.
Following my degree course I was fortunate to be offered a PhD project by the then Dr Rob Beynon to work in his lab on a project funded by the Muscular Dystrophy Group of GB and Northern Ireland. I was awarded my doctorate on’ The Expression of Glycogen Phosphorylase in Normal and Abnormal Mouse Skeletal muscle’ in 1989. The cofactor of the enzyme pyridoxal phosphate was employed as a specific label to measure the rate of degradation of the enzyme in vivo in muscle wasting conditions such as denervation-induced muscle atrophy and muscular dystrophy. Radiolabelled pyridoxine (vitamin B6) was used to label the precursor pool and phosphorylase-bound label was resolved from that associated with other proteins and free label by affinity and size-exclusion chromatography.
My first position as a Research Associate was an MRC-funded project ‘A novel and non-invasive method for measurement of the turnover of muscle glycogen phosphorylase’. This project extended the work of my PhD project and involved the chemical synthesis of stable isotope-labelled vitamin B6 to determine the kinetics of vitamin B6 assimilation and glycogen phosphorylase turnover in individual animals by non-invasive means (urinanalysis) enabling application to both experimental animals and humans. The project involved the implementation of GC/MS into the laboratory and the establishment of protocols for the isolation and derivatisation of urinary vitamin B6 metabolites.
My return to work in 2000 following a career break of eight years coincided with Prof Beynon’s return to Liverpool in the School of Veterinary Science. I once again became a member of Rob’s research group the ‘Protein Function Group’ which was now a proteomics group. Technology had moved on somewhat since I had last been in the lab and it was a steep learning curve to get up to speed. My first position was a 2 year Wellcome Trust funded project in which comparative 2-D gel analysis in conjunction with mass spectrometry was utilised to define the differential response of Cambridge and North Rondaldsay sheep to copper challenge. On this project I had the privilege of working with Dr Susan Haywood, a Veterinary Pathologist with considerable knowledge and expertise on North Rondaldsay sheep.
Following this project I moved into the realms of quantitative proteomics focussing on the provision of a novel solution to the absolute quantification of proteins using QconCAT technology. Artificial genes consisting of a concatenated series of peptides, QconCATs, are expressed in Ecoli. Two or more peptides act as signature quantification or Q-peptides for one protein enabling multiplexed absolute quantification. Part of this BBSRC-funded project was the design and deployment of a QconCAT for absolute quantification of mouse urinary proteins (MUPs). Building on the success of QconCATs for multiplexed absolute quantification of proteins I was part of a multi-disciplinary project funded by the BBSRC on the dynamics and function of the NF-κB signalling system. For this project I designed and deployed QconCATs to quantify NF-κB proteins and their inhibitors using MRM methodology.
I am currently funded by the BBSRC working on a part-time basis. I collaborate with colleagues from other departments within the university and work on a variety of projects where proteomics solutions can be used to answer biological questions.
Publications
I graduated from the University of Salford with a degree in Applied Biochemistry in 1985. During my degree course I had a 12 month industrial placement at Higson’s Brewery in Liverpool. It was an exciting time to be there as a new lager plant was being installed and was commissioned the same year. In addition to the quality control analyses I was involved in the development of a new product.
Following my degree course I was fortunate to be offered a PhD project by the then Dr Rob Beynon to work in his lab on a project funded by the Muscular Dystrophy Group of GB and Northern Ireland. I was awarded my doctorate on’ The Expression of Glycogen Phosphorylase in Normal and Abnormal Mouse Skeletal muscle’ in 1989. The cofactor of the enzyme pyridoxal phosphate was employed as a specific label to measure the rate of degradation of the enzyme in vivo in muscle wasting conditions such as denervation-induced muscle atrophy and muscular dystrophy. Radiolabelled pyridoxine (vitamin B6) was used to label the precursor pool and phosphorylase-bound label was resolved from that associated with other proteins and free label by affinity and size-exclusion chromatography.
My first position as a Research Associate was an MRC-funded project ‘A novel and non-invasive method for measurement of the turnover of muscle glycogen phosphorylase’. This project extended the work of my PhD project and involved the chemical synthesis of stable isotope-labelled vitamin B6 to determine the kinetics of vitamin B6 assimilation and glycogen phosphorylase turnover in individual animals by non-invasive means (urinanalysis) enabling application to both experimental animals and humans. The project involved the implementation of GC/MS into the laboratory and the establishment of protocols for the isolation and derivatisation of urinary vitamin B6 metabolites.
My return to work in 2000 following a career break of eight years coincided with Prof Beynon’s return to Liverpool in the School of Veterinary Science. I once again became a member of Rob’s research group the ‘Protein Function Group’ which was now a proteomics group. Technology had moved on somewhat since I had last been in the lab and it was a steep learning curve to get up to speed. My first position was a 2 year Wellcome Trust funded project in which comparative 2-D gel analysis in conjunction with mass spectrometry was utilised to define the differential response of Cambridge and North Rondaldsay sheep to copper challenge. On this project I had the privilege of working with Dr Susan Haywood, a Veterinary Pathologist with considerable knowledge and expertise on North Rondaldsay sheep.
Following this project I moved into the realms of quantitative proteomics focussing on the provision of a novel solution to the absolute quantification of proteins using QconCAT technology. Artificial genes consisting of a concatenated series of peptides, QconCATs, are expressed in Ecoli. Two or more peptides act as signature quantification or Q-peptides for one protein enabling multiplexed absolute quantification. Part of this BBSRC-funded project was the design and deployment of a QconCAT for absolute quantification of mouse urinary proteins (MUPs). Building on the success of QconCATs for multiplexed absolute quantification of proteins I was part of a multi-disciplinary project funded by the BBSRC on the dynamics and function of the NF-κB signalling system. For this project I designed and deployed QconCATs to quantify NF-κB proteins and their inhibitors using MRM methodology.
I am currently funded by the BBSRC working on a part-time basis. I collaborate with colleagues from other departments within the university and work on a variety of projects where proteomics solutions can be used to answer biological questions.
Publications
- Simpson, D.M. and Beynon, R.J. (2012) QconCATs use and performance in absolute quantification in proteomics. QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification. Anal. Bioanal. Chem. 404: 977-989
▪ Brownridge, P., Harman, V., Simpson, D.M. and Beynon, R.J. (2012) Absolute Multiplexed Protein Quantification Using QconCAT technology. Methods in Molecular Biology 893: 267-293.
▪ Carroll, K.M., Simpson D.M., Eyers C.E., Knight, C.G., Brownridge P., Dunn, W., Winder C.L., Lanthaler, K., Pir, P., Malys, N., Kell, D.B., Oliver, S.G., Gaskell, S.J. & Beynon, R.J. (2011) Absolute quantification of a metabolic pathway: deployment of a complete QconCAT approach. Mol. Cell. Proteomics M111.007633
▪ Castro-Borges, W., Simpson, D.M., Dowle, A., Curwen, R.S., Thomas-Oates, J., Beynon, R.J. and Wilson, R. A. (2011) Abundance of tegument surface proteins in the human bloodfluke Schistosoma mansoni determined by QconCAT proteomics. J. Proteomics 74: 1519-1533.
- Roberts, S.A., Simpson, D.M., Armstrong, S.D., Davidsom, A.J., Robertson, D.H., McLean, L., Beynon, R.J. and Hurst, J.L. (2010) Darcin: a male pheromone that stimulates female memory and sexual attraction to an individual male’s odour. BMC Biology. 8: 75-
- Simpson, D.M and Beynon, R.J (2010) Acetone precipitation and the modification of proteins. J.Proteome Res. 9: 444-450.
- Eyers, C., Simpson, D.M., Wong, C.C.S.., Beynon, R.J. and Gaskell, S. (2008) QCAL – a novel standard for assessing instrument conditions for proteome analysis. J. Am. Soc. Mass Spectrom. 19: 1275-1280.
- Johnson, H., Wong, C.C S., Simpson, D.M., Beynon, R.J. and Gaskell, S.J. (2008) Protein quantification by selective isolation and fragmentation of isotopic pairs using FT-ICR MS. J. Am. Soc. Mass Spectrom. 19: 973-977.
- Rivers, J., Simpson, D. M., Robertson, D. H., Gaskell, S. J. and Beynon, R. J. (2007). Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol. Cell. Proteomics 6: 1416-1427.
- Beynon, R.J., Hurst, J., Turton, M.J., Robertson, D.H.L., Armstrong, S.D., Cheetham, S.A., Simpson, D.M., MacNicholl, A. and Humphries, R. Urinary lipocalins in Rodentia: is there a generic model? (2007) In Chemical Signalling 11 (Springer) 37-51
- Vasilaki, A., Simpson, D., McArdle, F., McLean, L., Beynon, R.J., Remmen, H.V., Richardson, A.G., McArdle, A., Faulkner, J.A. and Jackson, M.J. (2007) Formation of 3-nitrotyrosines in carbonic anhydrase III is a sensitive marker of oxidative stress in skeletal muscle. Proteomics Clin. Appl. 1, 362-372.
- Simpson., D.M., Mobasheri, A., Haywood, S. and Beynon, R.J. (2006) A proteomics study of the response of North Ronaldsay sheep to copper challenge. BMC Vet. Res. 2:36
- Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J. and Beynon, R. J. (2006). Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nature protocols, 1, No. 2, 1-15.
- Haywood, S., Simpson, D.M., Ross, G. and Beynon, R.J. (2005) The greater susceptibility of North Ronaldsay sheep compared with Cambridge sheep to copper-induced oxidative stress, mitochondrial damage and hepatic stellate cell activation. J. Comp. Path.133, 114-127.
- Simpson, D.M., Beynon, R.J., Robertson, D.H.L., Loughran, M. and Haywood, S. (2004) Copper-associated liver disease: a proteomics study of copper challenge in a sheep model Proteomics 4, 524-536.
- Simpson, D.M, Beynon, R. J., Ross, G., Loughran, M. and Haywood, S. (2003). Copper toxicosis in sheep: a proteomics approach. Research in Veterinary Science, 74 Suppl A (44) p 15.
- Beynon, R.J., Leyland, D.M., Evershed, R.P., Edwards, R.H.T., and Coburn, S.P. (1996). Measurement of the turnover of glycogen phosphorylase by gas chromatography/mass spectrometry using stable isotope derivatives of pyridoxine (vitamin B6). Biochem. J. 317 ,613-619.
- Beynon, R.J., Bartram, C., Flannery, A., Evershed, R.P., Leyland, D.M., Hopkins, P., Toescu, V., Pheonix, J. and Edwards, R. H. T. (1996). Interrelationships between metabolism of glycogen phosphorylase and pyridoxal phosphate-implications in McArdles’s disease. Adv.Food Nutr. Res.40, 135-147. Academic Press.
- Beynon, R.J., Flannery, A., Edwards, R. H. T., Evershed, R.P. and Leyland, D.M. (1993). Degradation of glycogen phosphorylase in normal and abnormal skeletal muscle. In ;“Intracellular Protein Catabolism” (J. S. Bond and A. J. Barrett, eds), pp 157-162.
- Leyland, D.M., Evershed, R.P., Edwards, R.H.T. and Beynon, R.J. (1992). Application of GC/MS with selected ion monitoring to the urinanalysis of 4-pyridoxic acid. J. Chromatogr. Biomed. 581, 179-185.
- Leyland, D.M., and Beynon, R.J. (1991). The expression of glycogen phosphorylase in normal and dystrophic muscle. Biochem. J. 278, 113-117.
- Leyland, D.M., Turner, P.C., and Beynon, R.J. (1990). Effect of denervation on the expression of glycogen phosphorylase in mouse skeletal muscle. Biochem. J. 272, 231-237.
- Leyland, D.M., Turner, P.C., and Beynon, R.J. (1987). The expression of glycogen phosphorylase in normal and dystrophic mouse skeletal muscle. Biochem. Soc. Trans. 15, 881.
- Beynon, R.J., Armstrong, S.D., Gomez-Baena, G., Lee, V., Simpson, D., Unsworth, J. and Hurst, J.L. (2014) The complexity of protein semiochemistry in mammals. Biochemical Society Transactions 42 pp 837-845
- Balabanova, S., Holmberg. C., Steele, I., Ebrahimi, B., Rainbow, L., Burdyga, T., McCraig, C., Tiszlavicz, L., Lertkowit, N., Giger, O.T., Oliver, S., Prior, I., Dimaline, R., Simpson, D., Beynon, R., Hegyi, P., Wang, TC., Dockray, G.J. and Varro, A. (2014) The neuroendocrine phenotype of gastric myofibroblasts and its loss with cancer progression. Carcinogenesis (2014) 35 (8): 1798-1806.
- Phelan, M.M., McLean, L., Simpson, D.M., Hurst, J.L., Beynon, R.J. and Lian, L.Y. (2010) 1H, 15N and 13C resonance assignment of darcin, a mouse major urinary protein. Biomol. NMR Assign. 4 (2) 239-241.