Doctoral Training Centre in Cell & Proteomic Technologies

Publications

Names highlighted in bold are DTC students.

2015

• Y. Berezovskaya, M. Porrini, C. Nortcliffe, P.E. Barran, The use of ion mobility mass spectrometry to assist protein design: a case study on zinc finger fold versus coiled coil interactions, Analyst. (2015). doi:10.1039/C4AN00427B
• C. Nortcliffe, L.G. Migas, X. Liu, H.T. Ngo, K. a. Jolliffe, P.E. Barran, The potential of ion mobility mass spectrometry for tuning synthetic host guest systems: A case study using novel zinc(II)dipicolylamine anion sensors, Int. J. Mass Spectrom. (2015) 1–9. doi:10.1016/j.ijms.2015.07.030.
• R. Beveridge, A.S. Phillips, L. Denbigh, H.M. Saleem, C.E. MacPhee, P.E. Barran, Relating gas phase to solution conformations: Lessons from disordered proteins, Proteomics. 15 (2015) 2872–2883. doi:10.1002/pmic.201400605.
• A.S. Phillips, A.F. Gomes, J.M.D. Kalapothakis, J.E. Gillam, J. Gasparavicius, F.C. Gozzo, et al., Conformational dynamics of α-synuclein: insights from mass spectrometry, Analyst. 140 (2015) 3070–3081. doi:10.1039/C4AN02306D.
• AR. Healy, DR. Houston, L. Remnant, AS Huart, V. Brychtova, MM. Maslon, O. Meers, P. Muller, A. Krejci, EA. Blackburn, B. Vojtesek, L. Hernychova, MD. Walkinshaw, NJ. Westwood and TR. Hupp, Discovery of a novel ligand that modulates the protein-protein interactions of AAA+ superfamily oncoprotein reptin, Chem. Sci., 2015, 6, 3109 (2015).
• Lewis, E. E.L., Child, H. W., Hursthouse, A., Stirling, D., McCully, M., Paterson, D., Mullin, M., and Berry, C. C. (2015) The influence of particle size and static magnetic fields on the uptake of magnetic nanoparticles into three dimensional cell-seeded collagen gel cultures. Journal of Biomedical Materials Research Part B: Applied Biomaterials, (doi:10.1002/jbm.b.33302)

2014

2013

• L. Ma, K. Chen, D.J. Clarke, C.P. Nortcliffe, G.G. Wilson, J.M. Edwardson, et al., Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats., Nucleic Acids Res. (2013) 1–11. doi:10.1093/nar/gkt176
• Reynolds PM, Pedersen RH, Stormonth-Darling, J, Dalby, MJ, Riehle, MO, & Gadegaard, N. Label-free segmentation of Co-cultured cells on a nanotopographical gradient. Nano letters, 13(2), 570–6 (2013).
• Tsimbouri PM, Gadegaard N, Burgess KV, White K, Reynolds PM, Herzyk P, Oreffo RC, & Dalby MJ. Nanotopographical effects on mesenchymal stem cell morphology and phenotype. Journal of Cellular Biochemistry, September 2013; DOI: 10.1002/jcb.24673
• Cappell J, Burgess K, Fewou S, McGonigal R, Barrie J, Willison H, and Burchmore R, “Novel Lipidomic Methods for the Investigation of Gangliosides in Development and Disease”. Lipids, Cellular and Molecular Biology of. Waterville Valley, NH, July 2013
• Gray TA, Murray E, Nowicki MW, Remnant L, Scherl A, Muller P, Vojtesek B, Hupp TR.  Development of a fluorescent monoclonal antibody-based assay to measure the allosteric effects of synthetic peptides on self-oligomerization of AGR2 protein.Protein Sci. 2013 Sep;22(9):1266-78.
• Chevet, E., Fessart, D., Delom, F., Mulot, A., Vojtesek, B., Hrstka, R., Murray, E., Gray, T., & Hupp, T. 2013. Emerging roles for the pro-oncogenic anterior gradient-2 in cancer development. Oncogene. 2013 May 16;32(20):2499-509.
• Reynolds, PM, Pedersen, RH, Dalby, MJ, Riehle, MO, & Gadegaard, N. Co-culture Separation and Assembly by Nanotopographical Persuasion of Cells. Society for Biomaterials Annual Meeting and Exposition, Boston, USA, April 2013. (oral)

 2012

• Gawthorne, J.A., Reddick, L.E., Akpunarlieva, S.N., Beckham, K.S.H., Christie, J.M., Alto, N.M., Gabrielsen, M., and Roe, A.J. (2012) Express Your LOV: An Engineered Flavoprotein as a Reporter for Protein Expression and Purification. PLoS ONE 7(12): e52962. doi:10.1371/journal.pone.0052962
• Cappell J, Burgess K, Fewou S, McGonigal R, Barrie J, Willison H, and Burchmore R, “Novel Mass Spectrometry Based Lipidomics Methods for the Investigation of Gangliosides in Mouse Models of Guillain-Barré Syndrome”. Warwick Mass spectrometry 60/80 Conference. Warwick, UK, December 2012. (Student Poster Prize)
• P. Monica Tsimbouri, Rebecca J. McMurray, Karl V. Burgess, Enateri V. Alakpa, Paul M. Reynolds, Kate Murawski, Emmajayne Kingham, Richard O.C. Oreffo, Nikolaj Gadegaard & Matthew J. Dalby. Using nanotopography and metabolomics to identify biochemical effectors of multipotency. 2012 Nov 27;6(11):10239-49 (doi: 10.1021/nn304046m)
• Dalby, M.J., Macintyre, A., Roberts, J.N., Yang, J., Lee, L.L.C.Y., Tsimbouri, P.M., and McNamara, L.E. (2012) 3D patterned agarose hydrogels for investigation of precursor cells in differentiation and chemoattraction. Nanomedicine, 7 (1). pp. 17-21. ISSN 1743-5889 (doi:10.2217/nnm.11.172)
• Dennison, A., Edgar, J., Winters, D., Yoon, S. H., Huang, Y., Li, Y., Walton, A.,  Mackay, C.L., Goodlett, D.R., Langridge-Smith, P. Development and Application of Surface Acoustic Wave Nebulisation for Top-Down Protein Fragmentation. 60^th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, 2012.
• Dalby, M.J., Macintyre, A., Roberts, J.N., Yang, J., Lee, L.C.Y., Tsimbouri, P.M., and McNamara, L.E. (2012) Nanosubstrates to illustrate differential adhesion mechanisms to fibronectin and vitronectin. Nanomedicine, 7 (1). pp. 17-21. ISSN 1743-5889 (doi:10.2217/nnm.11.172)
• Kanwar N, Roberts GA, Cooper LP, Dawson A, Blakely GW and Dryden DTF, Mapping Charge-Function Relationships of a DNA Mimic (poster). Honorable mention at CSHL, Bacteria Archaea and Phage conference, 2012
• Roberts GA, Stephanou AS, Kanwar N, Dawson A, Cooper LP, Chen K, Nutley M, Cooper A, Blakely GW and Dryden DTF. Exploring the DNA mimicry of the Ocr protein of phage T7. Nucleic Acids Res. 2012 Sep 1;40(16)
• Cappell J. et al. “Investigating Ganglioside GM2 in Acute Canine Polyradiculoneuritus”. 9^th EMSG Symposium. Ardgour House, West Scotland, September 2012
• Reynolds PM, Pedersen RH, Reihle MO, Gadegaard N. A Dual Gradient Assay for the Parametric Analysis of Cell-Surface Interactions. Small 8 (16): 2541-2547(2012)
• Pedersen RH, Reynolds PM, Stormonth-Darling J, Dalby M, Reihle MO, Gadegaard N. Nanostructured topographical gradient patterns for cell-surface interaction studies, MNE Toulouse 2012 (poster)
• Reynolds PM, Pedersen RH, Stormonth-Darling J, Gadegaard N. Development of a dual step etch process for fabrication of enhanced depth range microgradients, MNE Toulouse 2012 (poster)
• Gray TA, Al-Sammam K, Murray E, Hernychova L, Hrstka R & Hupp TR. Using Engineered Isogenic Cell Models and Quantitative Proteomics to Unravel How Anterior Gradient-2 Promotes Oncogenic Activity. 3rd RECAMO joint meeting. Role of p53, MDM2, AGR2/3 and Ubiquitin/Chaperone system in Tumour Biology, Brno, Czech Republic, 24-27th September 2012
• E., V., Alakpa, V., Jayawarna, K.,Burgess, R., Ulijn & M., J., Dalby. Development of biomaterials for cellular differentiation using a metabolomics approach. Journal of tissue engineering & regenerative medicine. 2012; 6 (Supplement 1); 238.3rd TERMIS World Congress. 5th – 8th September, 2012. Vienna, Austria
• Cappell J, Burgess K, Fewou S, Galban-Horcajo F, Gannon S, Willison H, and Burchmore R, “Application of Proteomic Methodologies to Lipid Research”. EuPA 2012 Scientific Congress; new horizons and applications for proteomics. Glasgow, UK, July 2012
• E., V., Alakpa, V., Jayawarna, K.,Burgess, R., Ulijn & M., J., Dalby. Elucidating cellular reaction to biomaterial substrates using a metabolomics approach. European Cell & Materials Journal. 2011; 22 (supplement 3);18. Tissue & Cell Engineering Society Annual Meeting. 19th – 21st July, 2011. University of Leeds, UK
• E., V., Alakpa, V., Jayawarna, K., Burgess, R., Ulijn & M., J., Dalby. Characterisation of peptide biomaterials & innate metabolites that direct stem cell differentiation in vitro. EuPA/BSPR Proteomics congress. 9th – 12th July, 2012. Glasgow Royal Concert Hall, Glasgow, UK
• Gray TA & Hupp TR. Deconstructing the Role of Anterior Gradient-2 Protein Expression Utilising Synthetically Engineered Cell Lines and Quantitative Mass Spectrometry. New Horizons and Applications for Proteomics, European Proteomics Association/British Society for Proteome Research, Glasgow Royal Concert Hall, Glasgow, 9-12 July 2012
• E., V., Alakpa, V., Jayawarna, K., Burgess, R., Ulijn & M., J., Dalby. Tissue & Cell Engineering Society Annual Meeting. 4th – 6th July, 2012. University of Liverpool, UK* Characterisation of peptide biomaterials & innate metabolites that direct stem cell differentiation in vitro. European Cell & Materials Journal. 2012; 23 (supplement 4); 50.

2011

• Gray, T.A., MacLaine, N.J., Michie, C.O., Bouchalova, P., Murray, E., Howie, J., Hrstka, R., Maslon, M.M., Nenutil, R., Vojtesek, B., Langdon, S., Hayward, L., Gourley, C., & Hupp, T.R. 2012. Anterior Gradient-3: a novel biomarker for ovarian cancer that mediates cisplatin resistance in xenograft models. J.Immunol.Methods, 378, (1-2) 20-32
• Chevet, E., Fessart, D., Delom, F., Mulot, A., Vojtesek, B., Hrstka, R., Murray, E., Gray, T., & Hupp, T. 2012. Emerging roles for the pro-oncogenic anterior gradient-2 in cancer development. Oncogene (e-publication ahead of print)
• Reynolds PM, Pedersen RH, Reihle MO, Gadegaard N. Fabrication of 3D high throughput cell screening topographies using plasma polymerised gradients as a secondary etch mask, MNE Berlin 2011 (poster)
• Gray TA & Hupp TR. Anterior Gradient Proteins 2 & 3, Understanding Subcellular Distribution Related to Function and Determining the Role in Protein Maturation. 2nd RECAMO joint meeting, Role of p53, MDM2, AGR2/3 and Ubiquitin/Chaperone System in Tumour Biology, Brno, Czech Republic, 10-13th October 2011
• Cappell J, “Novel Analytical Technologies for Investigation Lipid-Protein Interactions in Autoimmune Neuropathies”. 8^th EMSG Symposium. Ardgour House, West Scotland, September 2011
• Thurlow SE, Goodwin R, Langridge-Smith P and Mackay CL. Using Imaging Mass Spectrometry to Examine the Effects of Nifurtimox on Mouse Brain Tissue, MSBM Dubrovnik 2011
• Cappell J, Gannon S, Sandison M, Galban-Horcajo G, Pitt A, Willison H, and Burchmore R, “Application of Array Technology to Investigating Glycolipid Immunology”.
• Thurlow SE, Goodwin R, Langridge-Smith P and Mackay CL. A comparison of Time-of-flight and Fourier Transform Instruments for Mass Spectrometry Imaging (poster), MSBM Dubrovnik 2011
• Kanwar N, Dawson A, Stephanou AS, Roberts GA, Blakely GW, and Dryden DTF. The interplay between Ocr and Type I restriction modification systems (poster). Runner-up prize at YLS Protein Evolution symposium, 2011
• Thurlow SE, Reboud J, Wilson R and Cooper JM. Using Surface Acoustic Waves for Mammalian Cell Transfection (Poster). Awarded prize at PGBioMed conference.
• Karim M, Clarke DJ, Pchelintsev N, Adams P, Langridge-Smith P and Mackay CL. Characterizing Global Histone Modifications in Senescent Cells by FT-ICR MS
• Gray T, Murray E and Hupp T. Deciphering the Role of Linear Motif Peptides Influencing the Dynamic Interactome of the Anterior Gradient Family of Proteins.  Peptide Arrays as Tools for the Study of Protein-Protein Interactions, Charles Darwin House, London, 15-16 March 2011
• Gray TA & Hupp TR. AGR2 and AGR3: Similarities & Divergences.  1st International AGR2 Workshop, Edinburgh, 3 March 2011
• Preece D, Warren R, Evans RML, Gibson GM, Padgett MJ, Cooper JM and Tassieri M, 2011, Optical tweezers: wideband microrhealology, Journal of Optics: special issue, 13 (4)
• Cappell J, Karim M, Goodwin R. Meeting report on the 7th Exploratory Measurement Science Group meeting. Bioanalysis, 2011, 3(1)

2010

• Roberts J, Burchmore R, Ulijn R and Dalby M. The Use of Enzymes to Control Stem Cell Differentiation. Surface Science of Biologically Important Interfaces (SSBI), University of Ulster, October 2010.
• Gray T. Defining the Role of Intrinsically Disordered Linear Domains in Signal Transduction. 1st RECAMO joint meeting, 3rd joint meeting on the Rolw of p53, MDM2, AGR2/3 and Ubiquitin/Chaperone System in Tumour Biology, Brno, Czech Republic, 27-29 December 2010
• Nicholson J, Hupp TR. The molecular dynamics of MDM2. Cell Cycle 2010 May 12;9(10)
• Stokes AA, Clarke DJ, Weidt S, Langridge-Smith P, Mackay CL.  Top-down protein sequencing by CID and ECD using desorption electrospray ionisation (DESI) and high-field FTICR mass spectrometry.  Int J Mass Spec 289 (1):54-57 (2010)
• Heron SR, Wilson R, Shaffer SA, Goodlett DR & Cooper JM. Surface acoustic wave nebulization of peptides as a microfluidic interface for mass spectrometry. Anal Chem, 10.1021/ac100372c (2010). Apr 5. [Epub ahead of print]
• Goodwin RJ, Lang AM, Allingham H, Borén M, Pitt AR. Stopping the clock on proteomic degradation by heat treatment at the point of tissue excision. Proteomics. 2010 May;10(9):1751-61
• Stokes AA. RASOR Lab-On-A-Chip Symposium, The University of Glasgow; March 2010. Poster: Development and Integration of Digital Microfluidics with Mass Spectrometry
• Vincent I, Scotcher J, Burchmore R. Meeting Report: Sixth Exploratory Measurement Science Group symposium  Expert Review of Proteomics, February 2010, 7(1): 19-20 (2010)
• Tassieri M, Gibson GM, Evans RML, Yao AM, Warren R, Padgett MJ, and Cooper JM. Measuring storage and loss moduli using optical tweezers: Broadband microrheology Phys. Rev. E 81, 026308 (2010)
• Clarke DJ, Stokes AA, Langridge-Smith P and Mackay CL. Online Quench-Flow Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Elucidating Kinetic and Chemical Enzymatic Reaction Mechanisms. Anal. Chem. (2010), DOI: 10.1021/ac9026302

2009

• Clarke DJ, Stokes AA, Langridge-Smith P, Mackay CL. Development of a Microfluidic Quench-Flow Interface Compatible with ESI-FT-ICR-MS for the Characterisation of Enzyme Mechanisms. 57th ASMS Conference on Mass Spectrometry. Philadelphia, USA, 2009. (poster)
• Fourtouna A, Murray E, Nicholson J, Dryden D, Hupp T. AGR2 as a novel drug target for Activation of the P53 pathway in Cancer: Peptide Aptamers Targeting AGR2 Stimulate the Nuclear Import of p53. Current Chemical Biology 3(2): 124-137, May 2009
• Stokes AA. 4th Annual RASOR Conference, Stirling Management Centre, Stirling University; December 2009. Talk: Development and Integration of Digital Microfluidics with Mass Spectrometry
• Smith H, Peggie M, Campbell DG, Vandermoere F, Carrick E, Philip Cohen P.  Inaugural Article: Identification of the phosphorylation sites on the E3 ubiquitin ligase Pellino that are critical for activation by IRAK1 and IRAK4.  PNAS 2009 Mar 24;106(12):4584-90. (epub March 5) (2009)
• Goodwin R, McBride M, Allingham H, Lang AM, Pitt A. A Quantitative and Qualitative Proteomic Study of Hypertension using a Congenic Rat Model. 6th BSPR/EBI Proteomics Meeting, Hinxton, UK, 2009. (poster)
• Warren R. Microrheology: a tool for studying protein-protein interactions. BSPR Nanoproteomics Workshop, Hinxton, UK, July 2009. (oral)
• Stokes AA. Edinburgh Chemical Biology PhD Meeting, Firbush; April 2009. Poster:  Development of Automated Protein Identification by nLC EWOD DESI FT-ICR ECD MS/MS
• Stokes AA, Li Y, Parkes W, Clarke DJ, Langridge-Smith P, Mackay CL, Walton AJ. Development of Multiplexed Protein Separation and Identification Using Digital Microfluidics and Mass Spectrometry. 57th ASMS Conference on Mass Spectrometry. Philadelphia, USA, 2009. (poster)
• Scotcher J, Clarke DJ, Weidt S, Nikolova P, Hupp T, Sadler PJ, Langridge-Smith P, Mackay CL. Redox-Regulation of p53: Identifying Redox Modifications by Top-Down FT-ICR Mass Spectrometry. 57th ASMS Conference on Mass Spectrometry. Philadelphia, USA, 2009. (poster)
• Nicholson J,  Murray E,  Barran P, Scherl A & Hupp T.  Characterisation and Development of an AGR2 Binding Peptide Aptamer and Proteomic Methods for Investigating Protein-Protein Interaction Inhibitors.  East Midlands Proteomics Conference, Nottingham Trent, November 2009, (oral - winner of best short talk)
• Pitt A, Tan KY, Gannon S, Cumming S, Goodwin R, McKenna E. Protein interaction arrays: joining the dots for protein interactions. 6th BSPR/EBI Proteomics Meeting, Hinxton, UK, 2009 (oral)
• Stokes AA. EPSRC DTC Showcase, Royal Society, London, February 2009. Poster: Doctoral Training Centre in Cell and Proteomic Technologies: Current Research Themes. Poster: Doctoral Training Centre in Cell and Proteomic Technologies: MRes Proteomics Technologies.
• Stokes AA. 57th ASMS Conference on Mass Spectrometry, Philadelphia; May 2009. Poster:  Development of Digital Microfluidics for Low-Volume Multiplexed Sample Handling in Biological Mass Spectrometry
• Stokes AA. 6th EMSG Symposium, Ardgour September 2009. Talk: "Development and Integration of Digital Microfluidics with Mass Spectrometry."

2008

• Li Y, Parkes W, Haworth LI, Stokes AA, Muir KR, Li P, Collin AJ, Hutcheon NG, Henderson R, Rae B, Walton AJ. Anodic Ta2O5 for CMOS compatible low voltage electrowetting-on-dielectric device fabrication, Solid-State Electronics, 52(9): 1382-1387, September (2008)
• Trinkle-Mulcahy L, Boulon S, Lam YW, Urcia R, Boisvert FM, Vandermoere F, Morrice NA, Swift S, Rothbauer U, Leonhardt H, Lamond A.  Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol. 183(2):223-39.  (2008)
• Ordureau A, Smith H, Windheim M, Peggie M, Carrick E, Morrice N, Cohen P.  The IRAK-catalysed activation of the E3 ligase function of Pellino isoforms induces the Lys(63)-linked polyubiquitination of IRAK1.  Biochem. J., 409, 43-52, (2008).
• Goodwin RJ, Lang AM, Allingham H, Pitt AR. Exploring the proteome by targeted mass spectrometry: Biomarker identification and spatial distribution at near cellular resolution. BMSS Annual Meeting, York, 2008.
• Goodwin RJ, Lang AM, Allingham H, Pitt AR. MALDI-MS imaging. 4th International Symposium on: The Enabling Role of MS and Related Techniques in the Health and Life Sciences 7-8 May at the Manchester Museum of Science and Industry (UK). 2008 (poster).
• Goodwin RJ, Lang AM, Allingham H, Pitt AR. MALDI-MSI. Is it more that just pretty pictures? Bruker User Meeting, York, 2008.
• Stokes AA, Galloway G, Li Y, Parkes W, Dryden D, Walton AJ, Langridge-Smith P, Mackay CL. Development of Automated Protein Identification by nLC EWOD DESI FT-ICR ECD MS/MS.  56th ASMS Conference on Mass Spectrometry, Denver, USA, 2008.
• Stokes AA. 3rd Annual RASOR Conference, Drymen; November 2008. Poster: Development of Automated Protein Identification by nLC EWOD DESI FT-ICR ECD MS/MS.
• Carrick E. Identification of Ubiquitination sites and Chain Architecture: The Hunt for Red K29. 7th HUPO World Congress, Amsterdam. 2008. (poster)
• Stokes AA. 5th EMSG Symposium, Ardgour November 2008. Poster: Development of Automated Protein Identification by nLC EWOD DESI FT-ICR ECD MS/MS. Talk: Development and Integration of Digital Microfluidics with Mass Spectrometry.

2007

• Goodwin RJ, Allingham H, Lang AM, Cobb S, Pitt AR. MALDI-MS imaging and small sample proteomics. 6th East Midlands Proteomics Workshop, Nottingham, UK, 2007.
• Li Y, Parkes W, Haworth LI, Stokes AA, Muir KR, Li P, Collin AJ, Hutcheon NG, Henderson R, Rae B, Walton AJ. Anodic Ta2O5 for CMOS Compatible Low Voltage Electrowetting-On-Dielectric Device Fabrication. European Solid-State Device Research Conference, 2007.
• Pitt A, Goodwin R, McKenna E, Mouls L, Tan KY, Kolch W. Applications of proteomics in translational research (Plenary). Society for Endocrinology BES 2007. 5-8 March 2007, Birmingham, UK, 2007.
• Tan KY, Kolch W, Pitt AR. Downstream of the receptor: protein interactions and crosstalk. MGPI Workshop: Breast Cancer and Proteomics, Cambridge, 2007.
• Tan KY, Kolch W, Pitt AR. Mapping RKIP Interactions in Signalling. RTK Consortium Meeting, Proteomics and Phosphoproteomics of RTK Signalling Networks, Hinxton, 2007.
• Stokes AA. 2nd Annual RASOR Conference, Polmont; 4th & 5th September 2007. Poster: Investigation of novel temperature-dependent fluorophores for fluorescence-lifetime imaging.
• Stokes AA. 4th EMSG Symposium, Ardgour; 22-26th October 2007. Talk: Design, Fabrication and Optimisation of a DESI Source for Mass Spectrometry.

2006

• Mackay CL, Weidt S, Carrick E, Lang AM, Kenicer J, Pommier Y, Hupp T, Langridge-Smith P, Ramsahoye B, Hayward RL. Electron Capture Dissociation and Electron Transfer Dissociation for Identification of p53 Dependent Histone Modifications Following Topoisomerase I Mediated DNA Damage. 54th ASMS Conference on Mass Spectrometry, Seattle, USA, 2006.