Proteomics

Discovery and definition of non-canonical phosphorylation

Gemma Hardman , Simon Perkins , Philip Brownridge, Christopher J. Clarke , Dominic P. Byrne, Amy E. Campbell , Anton Kalyuzhnyy , Ashleigh Myall , Patrick A. Eyers , Andrew R. Jones and Claire E. Eyers (2019) Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation [PUBMED] [PDF] [Abstract...]

Detailed protein analysis of the rat MUP complex

Guadalupe Gómez-Baena, Stuart D. Armstrong, Josiah O. Halstead, Mark Prescott, Sarah A. Roberts, Lynn McLean, Jonathan M. Mudge, Jane L. Hurst & Robert J. Beynon (2019) Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus. [PUBMED] [PDF] [Abstract...]

Proteomics of hippocampus in elipepsy

Karen Tse, Dean Hammond, Deborah Simpson, Robert J Beynon, Edward Beamer, Michael Tymianski, Michael W Salter, Graeme J Sills, Thimmasettappa Thippeswamy (2019) The impact of postsynaptic density 95 blocking peptide (Tat‐NR2B9c) and an iNOS inhibitor (1400W) on proteomic profile of the hippocampus in C57BL/6J mouse model of kainate‐induced epileptogenesis [PUBMED] [PDF] [Abstract...]

Role of RNA polymerase III through proteomics

Roza Szatkowska, Manuel Garcia-Albornoz,*, Katarzyna Roszkowska, Stephen W. Holman, Emil Furmanek, Simon J. Hubbard, Robert J. Beynon and Malgorzata Adamczyk (2019) Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1 [PUBMED] [PDF] [Abstract...]

Heparin binding proteome

Quentin M. Nunes, Dunhao Su, Philip J. Brownridge, Deborah M. Simpson, Changye Sun, Yong Li, Thao P. Bui, Xiaoying Zhang, Wei Huang, Daniel J. Rigden, Robert J. Beynon, Robert Sutton, David G. Fernig (2019) The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis [PUBMED] [PDF] [Abstract...]

Secretome analysis of cancer cells

J. Dinesh Kumar, Iman Aolymat, Laszlo Tiszlavicz, Zita Reisz, Hanan M. Garalla, Rob Beynon, Deborah Simpson, Graham J. Dockray and Andrea Varro (2019) Chemerin acts via CMKLR1 and GPR1 to stimulate migration and invasion of gastric cancer cells: putative role of decreased TIMP-1 and TIMP-2 [PUBMED] [PDF] [Abstract...]

Proteomics in craniopharyngioma

John R. Apps · Gabriela Carreno · Jose Mario Gonzalez‐Meljem · Scott Haston · Romain Guiho ·Julie E. Cooper · Saba Manshaei · Nital Jani · Annett Hlsken · Benedetta Pettorini · Robert J. Beynon · Deborah M. Simpson · Helen C. Fraser · Ying Hong · Shirleen Hallang · Thomas J. Stone1 · Alex Virasami · Andrew M. Donson · David Jones · Kristian Aquilina · Helen Spoudeas1· Abhijit R. Joshi · Richard Grundy · Lisa C. D. Storer · Márta Korbonits · David A. Hilton · Kyoko Tossell · Selvam Thavaraj · Mark A. Ungless · Jesus Gil1 · Rolf Buslei · Todd Hankinson · Darren Hargrave · Colin Goding · Cynthia L. Andoniadou · Paul Brogan · Thomas S. Jacques · Hywel J. Williams · Juan Pedro Martinez‐Barbera (2018) Tumour compartment transcriptomics demonstrates the activation of in ammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identi es the MAPK/ERK pathway as a novel therapeutic target. [PUBMED] [PDF] [Abstract...]

Proteostasis of heat shock

Andrew F. Jarnuczak, Manuel Garcia Albornoz, Claire E. Eyers, Christopher M. Grant, Simon J. Hubbard (2018) A quantitative and temporal map of proteostasis during heat shock in Saccharomyces cerevisiae. [PDF] [PUBMED] [Abstract...]

Kinases in spindle assembly

Bury L, Coelho PA, Simeone A, Ferries S, Eyers CE, Eyers PA, Zernicka-Goetz M, Glover DM. (2017) Plk4 and Aurora A cooperate in the initiation of acentriolar spindle assembly in mammalian oocytes. [PDF] [PUBMED] [Abstract...]

New paper on CSF proteomics in paediatric meningitis

Guadalupe Gómez-Baena, Richard J. Bennett, Carmen Martínez-Rodríguez, Małgorzata Wnk, Gavin Laing, Graeme Hickey, Lynn McLean, Robert J. Beynon & Enitan D. Carrol (2017) Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis. [PDF] [PUBMED]

[Abstract...]

Proteomics to identify galectin binding partners

Colomb F, Wang W, Simpson D, Zafar M, Beynon R, Rhodes JM, Yu LG. (2017) Galectin-3 interacts with the cell surface glycoprotein CD146 (MCAM, MUC18) and induces secretion of metastasis-promoting cytokines from vascular endothelial cells. [PDF] [PUBMED] [Abstract...]

Label free approaches to glycan and glycoprotein analysis

Gray CJ, Sánchez-Ruiz A, Šardzíková I, Ahmed YA, Miller RL, Reyes Martinez JE, Pallister E, Huang K, Both P, Hartmann M, Roberts HN, Šardzik R, Mandal S, Turnbull JE, Eyers CE, Flitsch SL. (2016) Label-Free Discovery Array Platform for the Characterization of Glycan Binding Proteins and Glycoproteins. [PDF] [PUBMED] [Abstract...]

Tools for kinome research

McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N. (2016) KinView: a visual comparative sequence analysis tool for integrated kinome research. [PUBMED] [PDF] [Abstract...]

Improving the quality of turnover measurement

Stephen W. Holman, Dean E. Hammond, Deborah M. Simpson, John Waters, Jane L. Hurst and Robert J. Beynon (2016) Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM MS). [PUBMED] [PDF] [Abstract...]

Proteome dynamics in a non-model species - the challenges!

Hammond DE, Claydon AJ, Simpson DM, Edward D, Stockley P, Hurst JL, Beynon RJ. (2016) Proteome Dynamics: Tissue Variation in the Kinetics of Proteostasis in Intact Animals. [PUBMED] [PDF] [Abstract...]

Proteomics of dystrophic muscle

Arecco N, Clarke CJ, Jones FK, Simpson DM, Mason D, Beynon RJ, Pisconti A. (2016) Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation. [PDF] [PUBMED] [Abstract...]

Proteomics of ocular cancer secretomes reveal malignancy potential

Angi, M., Kalirai, H, Prendegast, S., Simpson, D.M., Hammond, D.E., Madigan, M. C., Beynon, R.J. & Coupland, S.E. (2016) Proteomic analysis of uveal melanoma secretome reveals novel biological insights and potential biomarkers. [PDF] [PUBMED] [Abstract...]

Proteomics and protein moonlighting

Beynon RJ, Hammond D, Harman V, Woolerton Y. (2014) The role of proteomics in studies of protein moonlighting. [PUBMED][PDF]
[Abstract...]

QconCAT compared to label-free for plasma proteins

Kramer G, Woolerton , van Straalen JP, Vissers JP, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JM. (2015) Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. [PUBMED][PDF] [Abstract...]

Proteome plasticity in sperm competition

Ramm SA, Edward DA, Claydon AJ, Hammond DE, Brownridge, Hurst JL, Beynon RJ, Stockley P. (2015) Sperm competition risk drives plasticity in seminal fluid composition. [PUBMED] [PDF] [Abstract...]

It is worth adding DMSO to the mobile phase?

Dominika Strzeleckaa, Stephen W. Holman, Claire E. Eyers (2015) Evaluation of dimethyl sulfoxide (DMSO) as a mobile phase additive during top 3 label-free quantitative proteomics. [PDF] [PUBMED] [Abstract...]

Chaperone networks in yeast

Jarnuczak, A., Eyers, C. E., Schwartz, J.-M., Grant, C.M. & Hubbard, S. J. (2015) Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae. [PUBMED][PDF] [Abstract...]

Ion mobility review

Lanucara F, Holman SW, Gray CJ, Eyers CE. (2014) The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. [PDF] [PUBMED] [Abstract...]

MS for identification of PTMs

Eyers, Claire E., Gaskell, Simon J. 2008. Mass spectrometry to identify posttranslational modifications. Wiley Encyclopedia of Chemical Biology. [Abstract...]

Proteomics of myeloma line in protien free medium

de la Luz-Hernández, Kathya R., Rojas-del Calvo, Luis, Victores-Sarasola, Svieta, Lage-Castellanos, Agustín, Eyers, Claire, Hart, Sarah, Castellanos-Serra, Lila, Castillo-Vitlloch, Adolfo, Gaskell, Simon. 2008. Proteomic analysis of the adaptation of the host NS0 myeloma cell line to a protein-free medium. Biotecnología Aplicada 24: y04. [Abstract...]

Lysine acetylation of histones

Fraga, Mario F., Ballestar, Esteban, Villar-Garea, Ana, Boix-Chornet, Manuel, Espada, Jesus, Schotta, Gunnar, Bonaldi, Tiziana, Haydon, Claire, Ropero, Santiago, Petrie, Kevin. 2005. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature genetics 37: 391-400. [PUBMED] [Abstract...]

PTM's by MS

Schweppe, Rebecca E., Haydon, Claire E., Lewis, Timothy S., Resing, Katheryn A., Ahn, Natalie G. 2003. The characterization of protein post-translational modifications by mass spectrometry. Accounts of chemical research 36: 453-461. [PUBMED] [Abstract...]

Unblocking the sink

Lanucara F, Chi Hoo Lee D, Eyers CE. (2013) Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C-Terminal Residue. [PDF][PUBMED] [Abstract...]

Quantification of proteins in the human osteoarthritic secretome

Peffers MJ, Beynon RJ, Clegg PD. (2013) Absolute quantification of selected proteins in the human osteoarthritic secretome. [PDF][PUBMED] [Abstract...]

Whole animal protein turnover studies

Claydon, A.J., Thom, M.D., Hurst, J.L. & Beynon, R.J. (2011) Protein turnover: measurement of proteome dynamics by whole animal metabolic labelling with stable isotope labelled amino acids. Proteomics 12:1194-1206 [PUBMED][PDF] [Abstract...]

Asymetric equalisation with combinatorial beads

Jenny Rivers, Chris Hughes, Thérèse McKenna, Yvonne Woolerton, Johannes P. C. Vissers, James I. Langridge and Robert J. Beynon (2011) Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library [PUBMED] [PDF]
[Abstract...]

Yeast complex proteomics

Drummond, S., Hildyard, J., Firczuk, H., Reamtong, O., Li, N.,Kannambath, S., Claydon, A., Beynon, R., Eyers, C.E. McCarthy, J.E.G (2011) Diauxic shift-dependent relocalization of decapping activators Dhh1 and Pat1 to polysomal complexes. [PUBMED][PDF] [Abstract...]

Strategies for dynamic SILAC

Claydon, A & Beynon R (2011) Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC [PUBMED] [PDF] [Abstract...]

Unkind cuts - proteolysis and proteomics

Brownridge, P. & Beynon, R.J. (2011) The importance of the digest: proteolysis and absolute quantification in proteomics. [PUBMED] [PDF] [Abstract...]

Global proteome quantification: dreams or reality?

Brownridge, P., Holman, S.W., Gaskell, S.J., Grant, C., Harman, V.M., Lanthaler, K., Lawless, C., O’cualain, R., Sims, P., Watkins, R & Beynon, R.J. (2011) Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics, 11, 2957-2970 [PUBMED][PDF] [Abstract...]

Derivatization for proteomics

Brancia, F.L., Butt, A., Beynon, R.J., Hubbard, S.J., Gaskell, S.J. & Oliver, S.G. (2001) A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics. Electrophoresis, 22, 552-559 [PUBMED] [PDF] [Abstract...]

Chromatographic separation at the protein level

Butt, A., Davison, M.D., Smith, G.J., Young, J.A., Gaskell, S.J., Oliver, S.G. & Beynon, R.J. (2001) Chromatographic separations as a prelude to two-dimensional electrophoresis in proteomics analysis. Proteomics, 1, 42-53. [PUBMED] [PDF] [Abstract...]

Stable isotope labelling for identification

Pratt, J. M., Robertson, D. H., Gaskell, S. J., Riba-Garcia, I., Hubbard, S. J., Sidhu, K., Oliver, S. G., Butler, P., Hayes, A., Petty, J. & Beynon, R. J. (2002). Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting. Proteomics 2, 157-63. [PUBMED] [PDF] [Abstract...]

Intact mass proteomics

Hayter J.R., Robertson, D.H.L., Gaskell, S.J. & Beynon, R.J. (2003) Proteome analysis of intact proteins in complex mixtures. Mol. Cell. Proteomics 2, 85-95 [PUBMED] [PDF] [Abstract...]

A proteomics workbench?

Beynon, R.J. (2004) Specification of a proteomics workbench. Comparative and Functional Genomics 5, 52-55 [PUBMED] [PDF] [Abstract...]

Proteomics of tissue samples

McLean, L., Doherty, M.K., Deeming, C.D. & Beynon, R.J. (2004) A proteome analysis of the subcutaneous gel in avian hatchlings. Mol. Cell. Proteomics 3, 250-256 [PUBMED] [PDF] [Abstract...]

Proteomics of growing muscle

Doherty, M.K., McLean, L., Hayter, J.R., Pratt, J.M,, Robertson, D.H.L., El-Sahfei, A.E., Gaskell, S.J. & Beynon, R.J. (2004) The proteome of chicken skeletal muscle: changes in soluble protein expression during growth in a layer strain. Proteomics 4, 2082-2093 [PUBMED] [PDF] [Abstract...]

Metabolic labelling in proteomics

Beynon RJ, Pratt J.M. (2005) Metabolic labelling of proteins for proteomics. Mol Cell Proteomics. 4, 857-872 [PUBMED] [PDF] [Abstract...]

Proteome dynamics review

Beynon RJ.(2005) The dynamics of the proteome: strategies for measuring protein turnover on a proteome-wide scale. Brief Funct Genomic Proteomic. 3, 382-390 [PUBMED] [PDF] [Abstract...]

First paper on dynamic SILAC in intact animals

Doherty, M.K., Whitehead, C., McCormack, H., Gaskell, S.J. & Beynon, R.J. (2005) Proteome dynamics in complex organisms: using stable isotopes to monitor individual protein turnover rates. Proteomics 5, 522-533 [PUBMED] [PDF] [Abstract...]

Identification of an atypical male-specific MUP in mouse urine

Armstrong, S.D., Robertson, D.H.L., Cheetham, S.A., Hurst, J.L. & Beynon, R.J. (2005) Structural and functional differences in isoforms of Major Urinary Proteins: a male specific protein that preferentially binds a male pheromone. Biochem. J. 391, 343-350 [PUBMED] [PDF] [Abstract...]

Copper toxicity in sheep

Haywood, S. Simpson, D.M, Ross, G. & Beynon, R.J. (2005) The unique response of North Ronaldsay sheep to copper challenge compared with Cambridge sheep: oxidative stress, mitochondrial damage and hepatic stellate cell activation. J. Comp. Path.133, 114-127 [PUBMED] [PDF] [Abstract...]

Peptide map drawing tool

Beynon, R.J. (2005) A simple tool for drawing proteolytic peptide maps. Bioinformatics 21, 674-675 [PUBMED] [PDF] [Abstract...]

Proteasome proteolysis

Hayter JR, Doherty MK, Whitehead C, McCormack H, Gaskell SJ & Beynon RJ. (2005) The subunit structure and dynamics of the 20S proteasome in chicken skeletal muscle. Mol. Cell. Proteomics. 4, 1370-1381 [PUBMED] [PDF] [Abstract...]

First paper describing QconCAT

Beynon, R.J., Doherty, M.K., Pratt, J.M. & Gaskell, S.J. (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides rates. Nature Methods 2, 587-589 [PUBMED] [PDF [Abstract...]

Muscle proteomics: anabolic agent effects

Burniston JG, McLean L, Beynon RJ, Goldspink DF.   (2007) Anabolic effects of a non-myotoxic dose of the beta(2)-adrenergic receptor agonist clenbuterol on rat plantaris muscle. Muscle & Nerve. 35, 217-223 [PUBMED] [PDF] [Abstract...]

Proteomics of oxidative stress in mice

Aphrodite Vasilaki, Deborah Simpson, Francis McArdle, Lynne McLean, Robert J. Beynon, Holly Van Remmen, Arlan G. Richardson, Anne McArdle, John A Faulkner and Malcolm J. Jackson (2007) Formation of 3-nitrotyrosines in carbonic anhydrase III is a sensitive marker of oxidative stress in skeletal muscle PROTEOMICS – Clinical Applications 1: 362–372 [PDF] [Abstract...]

Proteomics and animal disease

Mary K. Doherty, Robert J. Beynon and Phillip D. Whitfield (2007) Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine PROTEOMICS – Clinical Applications 2: 135–141 [PDF] [Abstract...]

Proteomics of copper toxicity

Simpson, D. M., Mobasheri, A., Haywood, S. & Beynon, R. J. (2007) A proteomics study of the response of North Ronaldsay sheep to copper challenge. BMC Veterinary Research BMC Vet Res. 27, 36 [PUBMED][PDF] [Abstract...]

Mass spectrometry identification of proteins

Nominated in Faculty of 1000 by Harald Stenmark. McCullough, J., Row, P.E. Lorenzo, O, Doherty, M., Beynon, R.J., Clague, M.J. and Urbé, S (2006) Activation of the Endosome-Associated Ubiquitin Isopeptidase AMSH by STAM, a Component of the Multivesicular Body-Sorting Machinery Current Biology 16, 160-165.[PUBMED][PDF] [Abstract...]

Proteome dynamics

Doherty MK, Beynon RJ. (2006) Protein turnover on the scale of the proteome. Expert Rev Proteomics. 1, 97-110[PUBMED] [PDF] [Abstract...]

Proteome turnover: why is it not being studied?

Beynon, R.J. & Pratt, J.M. (2006) Strategies for measuring dynamics: the temporal component of proteomics. Methods Biochem Anal. 2006;49:15-25 [PUBMED] [Abstract...]

QconCAT protocols defined

Pratt, J.M., Simpson, D.M., Doherty, M.K., Rivers, J, Gaskell, S.J. Beynon , R.J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nature Protocols 1, 1029 - 1043 [PUBMED][PDF] [Abstract...]

Isolation of N-terminal peptides

Nominated in Faculty of 1000 by Ruedi Aebersold. McDonald, L. & Beynon, R.J. (2006) Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization. Nature Protocols 1, 1790 - 1798 [PUBMED] [PDF] [Abstract...]

Cauxin in big cat urine

McLean, L., Hurst, J.L., Gaskell, C.J., Lewis, J. C. M & Beynon, R.J. (2007) Characterization of Cauxin in the Urine of Domestic and Big Cats (2007) J. Chem. Ecol 3, 1997-2009 [PUBMED][PDF] [Abstract...]

Muscle proteomics

Burniston J G, McLean L, Beynon R J and Goldspink D F (2007) Anabolic effects of a non-myotoxic dose of the beta2-adrenergic receptor agonist clenbuterol on rat plantaris muscle. Muscle Nerve 35, 217-23 [PUBMED][PDF] [Abstract...]

Global cooling

Mclean, L., Young, I.S. Doherty, M.K., Robertson, D.H.L., Cossins, A.R., Gracey, A. Y., Beynon, R.J. & Whitfield, P.D. (2007) Global cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics Proteomics 7, 2667-2681 [PUBMED][PDF] [Abstract...]

Pre-eclampsia biomarkers

Myers JE, Hart S, Armstrong S, Mires GJ, Beynon R, Gaskell SJ, Baker PN. (2007) Evidence for multiple circulating factors in preeclampsia. Am J Obstet Gynecol. 196, 266.e1-6. [PUBMED][PDF] [Abstract...]

Absolute quantification by QconCAT

Rivers J, Simpson DM, Robertson DH, Gaskell SJ, Beynon RJ.(2007) Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol Cell Proteomics. 6, 1416-1427. [PUBMED][PDF] [Abstract...]

Avian Proteomics

Doherty, M.K., Mclean, L. & Beynon, R.J. (2007) Avian Proteomics: Advances, Challenges and New Technologies. Cytogenetic and Genome Research 117, 358-369.[PUBMED][PDF] [Abstract...]

FPGA acceleration of proteomics data processing

Bogdan I, Coca D, Rivers J, Beynon RJ. (2007) Hardware acceleration of processing of mass spectrometric data for proteomics.Bioinformatics. 23, 724-31.[PUBMED][PDF] [Abstract...]

FTICR resolution of similar mass proteins

Robertson DH, Wong SC, Beynon RJ, Hurst JL, Gaskell SJ. (2008) Observation of heterogeneous gene products by FT-ICR MS. J. Am. Soc. Mass Spectrom. 19, 103-110. [PUBMED][PDF] [Abstract...]

Structure and asparagine deamidation

Rivers J, McDonald L, Edwards IJ, Beynon RJ. (2008) Asparagine deamidation and the role of higher order protein structure. J. Proteome Res. 7, 921-7. [PUBMED][PDF] [Abstract...]

Proteomics and animal disease

Doherty, MK; Beynon, RJ; Whitfield, PD (2008): Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine. Proteomics: Clinical Applications 2, 135-141 [Abstract...]

Speeding up proteomics with hardware computing solutions

Bogdán IA, Rivers J, Beynon RJ, Coca D. (2008) High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting. Bioinformatics. 24, 1498-1502. [PUBMED][PDF] [Abstract...]

Designer genes for mass spectrometry

Eyers CE, Simpson DM, Wong SC, Beynon RJ, Gaskell SJ. (2008) QCAL-a Novel Standard for Assessing Instrument Conditions for Proteome Analysis. J Am Soc Mass Spectrom. 19, 1275-1280 [PUBMED][PDF] [Abstract...]

Biomarkers of ragwort poisoning in horses

Moore RE, Knottenbelt D, Matthews JB, Beynon RJ, Whitfield PD. (2008) Biomarkers for ragwort poisoning in horses: identification of protein targets.BMC Vet Res. 4:30. [PUBMED][PDF] [Abstract...]

Proteomics of HGF/EGF signalling

Hammond DE, Hyde R, Kratchmarova I, Beynon RJ, Blagoev B, Clague MJ. (2010) J Proteome Res. 9(5):2734-2742. Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks.[PUBMED][PDF] [Abstract...]

Acetone modifies peptides! Be careful if you're using acetone precipitation.

Simpson DM, Beynon RJ. (2010) Acetone precipitation of proteins and the modification of peptides. J Proteome Res. 9, 444-450 [PUBMED][PDF] [Abstract...]

Cross-species proteomics

Wright JC, Beynon RJ, Hubbard SJ. Cross species proteomics. (2010) Methods Mol Biol. 604:123-135 [PUBMED][PDF] [Abstract...]

Hardware accelerated proteomics

Coca D, Bogdan I, Beynon RJ. A high-performance reconfigurable computing solution for peptide mass fingerprinting. (2010) Methods Mol Biol. 604:163-185 [PUBMED][PDF] [Abstract...]

Phosphorylation stoichiometry

Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry (2009) Johnson H, Eyers CE, Eyers PA, Beynon RJ, Gaskell SJ. J Am Soc Mass Spectrom. 20, 2211-2220 [PUBMED][PDF] [Abstract...]

Proteomics and genome annotation

Wright, J.C., Sugden, D., Francis-McIntyre, S., Riba-Gacia, I., Gaskell, S.J., Grigoriev, I V., Baker, S.E., Beynon, R.J. & Hubbard, S.J. (2009)Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics. 10, 61 [PUBMED][PDF] [Abstract...]

Parasite proteomics

Smith, S.K., Nisbet, A.J., Meikle, L.I., Inglis, N.F., Sales, J., Beynon, R.J. & Matthews, J.B. (2010) Proteomic analysis of excretory/secretory products released by Teladorsagia circumcincta larvae early post-infection. Parasite Immunology 31, 10-19 [PUBMED][PDF] [Abstract...]

Dynamic SILAC for global assessment of proteome turnover

Doherty, M.K., Hammond, D., Clague, M. J., Gaskell, S.J. & Beynon, R.J. (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8, 104-112 [PUBMED] [PDF] [Abstract...]

Seminal vesicle protein evolution

Ramm, S.A., McDonald, L.M., Hurst, JL., Beynon, R.J. & Stockley, P.S. (2009) Comparative Proteomics Reveals Evidence for Evolutionary Diversification of Rodent Seminal Fluid and Its Functional Significance in Sperm Competition. Mol. Biol. Evol. 26, 189-198 [PUBMED] [PDF] [Abstract...]