Mass spectrometry
New preprint on the nuts and bolts of SCOPE2
Aleksandra A Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht, David H Perlman, Nikolai Slavov (2021) Multiplexed single-cell proteomics using SCoPE2 doi: https://doi.org/10.1101/2021.03.12.435034
This article is a preprint and has not been certified by peer review [PDF] [DOI] [Abstract...]
This article is a preprint and has not been certified by peer review [PDF] [DOI] [Abstract...]
Single cell proteomics on macrophages
Harrison Specht, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller and Nikolai Slavov (2021) Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 Genome Biol 22(1):50. doi: 10.1186/s13059-021-02267-5. [PDF] [PUBMED] [DOI] [Abstract...]
First 'zap the crap', now 'Fry the fly': REIMS for insect identification
Iris Wagner, Natalie I. Koch, Joscelyn Sarsby, Nicola White, Tom A. R. Price, Sam Jones, Jane L. Hurst, Robert J. Beynon, (2020) The application of rapid evaporative ionisation mass spectrometry (REIMS) in the analysis of Drosophila species – a potential new tool in entomology [PDF] [PUBMED] [DOI] [Abstract...]
Plasticity of the mouse seminal vesical fluid proteome
Helen L Bayram, Catarina Franco, Philip Brownridge, Amy J Claydon, Natalie Koch, Jane L Hurst, Robert J Beynon, Paula Stockley (2020) Social status and ejaculate composition in the house mouse [PDF] [PUBMED] [DOI] [Abstract...]
Ion mobility to evaluate ligand binding to proteins
Lauren J Tomlinson, Claire E Eyers (2020) Ion Mobility-Mass Spectrometry to Evaluate the Effects of Protein Modification or Small Molecule Binding on Protein Dynamics. [PDF] [PUBMED] [DOI] [Abstract...]
MS from gels, top down or bottom up
Ayako Takemori, David S Butcher, Victoria M Harman, Philip Brownridge, Keisuke Shima, Daisuke Higo, Jun Ishizaki, Hitoshi Hasegawa, Junpei Suzuki, Masakatsu Yamashita, Joseph A Loo, Rachel R Ogorzalek Loo, Robert J Beynon, Lissa C Anderson, Nobuaki Takemori (2020) PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry [PDF] [PUBMED] [DOI] [Abstract...]
REIMS for the analysis of bacterial protein production
Joscelyn Sarsby, Lynn McLean, Victoria M Harman, Robert J Beynon (2019) Monitoring recombinant protein expression in bacteria by rapid evaporative ionisation mass spectrometry. [PDF] [PUBMED] [DOI] [Abstract...]
Methodology for hunting histidine phosphorylation
Gemma Hardman and Claire E. Eyers (2020) High-Throughput Characterization of Histidine Phosphorylation Sites Using UPAX and Tandem Mass Spectrometry. [PDF] [PUBMED] [DOI] [Abstract...]
Using proteomics to explore 'pseudogene' expression
Ian Goodhead, Frances Blow, Philip Brownridge, Margaret Hughes, John Kenny, Ritesh Krishna, Lynn McLean, Pisut Pongchaikul, Rob Beynon and Alistair C. Darby (202o) Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont [PDF] [PUBMED] [DOI] [Abstract...]
SILAC Phosphoproteomics
Dominic P Byrne, Christopher J Clarke, Philip J Brownridge, Anton Kalyuzhnyy, Simon Perkins, Amy Campbell, David Mason, Andrew R Jones, Patrick A Eyers, Claire E Eyers (2020) Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics [PUBMED] [PDF] [DOI] [Abstract...]
Zap the crap! Using REIMS to obtain valuable information from animal faeces
Davidson NB, Koch NI, Sarsby J, Jones E, Hurst JL, Beynon RJ. (2019) Rapid identification of species, sex and maturity by mass spectrometric analysis of animal faeces. [PUBMED] [PDF] [Abstract...]
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] [DOI]
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Proteomics in craniopharyngioma
John R. Apps · Gabriela Carreno · Jose Mario Gonzalez‐Meljem · Scott Haston · Romain Guiho ·Julie E. Cooper · Saba Manshaei · Nital Jani · Annett Hölsken · 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...]
Enhanced ability in phosphosite localisation
Ferries S, Perkins S, Brownridge PJ, Campbell A, Eyers PA, Jones AR, Eyers CE. (2017) Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer. [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 Wnęk, Gavin Laing, Graeme Hickey, Lynn McLean, Robert J. Beynon & Enitan D. Carrol (2017) Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis. [PDF] [PUBMED]
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New insights into protein kinase A action
Smith FD, Esseltine JL, Nygren PJ, Veesler D, Byrne DP, Vonderach M, Strashnov I, Eyers CE, Eyers PA, Langeberg LK, Scott JD. (2017) Local protein kinase A action proceeds through intact holoenzymes. [PUBMED] [PDF] [Abstract...]
Proteomics suppporting supramolecular studies
M. Faulkner, J. Rodriguez-Ramos, G. F. Dykes, S. V. Owen, S. Casella, D. Simpson, R. Beynon and L. Liu (2017) Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes [PUBMED] [PDF] [Abstract...]
Bottom up analysis of glycosidic bond stereochemistry
Gray CJ, Schindler B, Migas LG, Pičmanová M, Allouche AR, Green AP, Mandal S, Motawia MS, Sánchez-Pérez R, Bjarnholt N, Møller BL, Rijs AM, Barran PE, Compagnon I, Eyers CE, Flitsch SL. (2017) Bottom-Up Elucidation of Glycosidic Bond Stereochemistry. [PUBMED] [PDF]
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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...]
Double standards in proteomics
Richard J. Bennett, Deborah M. Simpson, Stephen W. Holman, Sheila Ryan, Philip Brownridge, Claire E. Eyers, John Colyer, Robert J. Beynon (2017) DOSCATs: Double standards for protein quantification [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...]
MUP variation in mouse subspecies
Hurst JL, Beynon RJ, Armstrong SD, Davidson AJ, Roberts SA, Gómez-Baena G, Smadja CM, Ganem G. (2017) Molecular heterogeneity in major urinary proteins of Mus musculus subspecies: potential candidates involved in speciation. [PDF] [PUBMED] [Abstract...]
Ion mobility for glycan analysis
Gray CJ, Thomas B, Upton R, Migas LG, Eyers CE, Barran PE, Flitsch SL. (2016) Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. [PUBMED] [PDF] [Abstract...]
Complexity of RelA phosphorylation
Lanucara F, Lam C, Mann J, Monie TP, Colombo SA, Holman SW, Boyd J, Dange MC, Mann DA, White MR, Eyers CE. (2016) Dynamic phosphorylation of RelA on Ser42 and Ser45 in response to TNFα stimulation regulates DNA binding and transcription. [PDF] [PUBMED] [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...]
Quantitative analysis of the yeast 'chaperome'
Rebecca J. Mackenzie, Craig Lawless [2], Stephen W. Holman, Karin Lanthaler, Robert J. Beynon, Chris M. Grant, Simon J. Hubbard and Claire E. Eyers (2106) Absolute protein quantification of the yeast chaperome under conditions of heat shock [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...]
Review of ion mobility MS for glycan sequencing
Gray CJ, Thomas B, Upton R, Migas LG, Eyers CE, Barran PE, Flitsch SL. (2016) Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. [Abstract...]
Genetics of individual MUP variation
Sheehan MJ, Lee V, Corbett-Detig R, Bi K, Beynon RJ, Hurst JL, Nachman MW. (2016) Selection on Coding and Regulatory Variation Maintains Individuality in Major Urinary Protein Scent Marks in Wild Mice. [PUBMED] [PDF] [Abstract...]
QconCATs in equine wound healing
Bundgaard L, Bendixen E, Sørensen MA, Harman VM, Beynon RJ, Petersen LJ, Jacobsen S. (2016) A selected reaction monitoring based analysis of acute phase proteins in interstitial fluids from experimental equine wounds healing by secondary intention. [PUBMED] [PDF] [Abstract...]
Of mice, mups and mass spectrometry
Robert J. Beynon, Stuart D. Armstrong, Amy J. Claydon, Amanda J. Davidson, Claire E. Eyers, James I. Langridge, Guadalupe Gómez-Baena, Victoria M. Harman, Jane L. Hurst, Victoria Lee, Lynn McLean, Rebecca Pattison, Sarah A. Roberts, Deborah M. Simpson, Jenny Unsworth, Matthias Vonderach, Jonathan Williams and Yvonne E. Woolerton (2015) Mass spectrometry for structural analysis and quantification of the Major Urinary Proteins of the house mouse. [PDF] [NotEvenIndexedInPubmed?] [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...]
Genetic programming for peptide 'flyability'
Wedge, David C., Gaskell, Simon J., Hubbard, Simon J., Kell, Douglas B., Lau, King Wai, Eyers, Claire. 2007. Peptide detectability following ESI mass spectrometry: prediction using genetic programming. Presented at Proceedings of the 9th annual conference on Genetic and evolutionary computation [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...]
Enzyme turnover and metabolic regulation
Arden, C, Petrie, J.L., Tudhope, S.J., Al-Oanzi, Z., Claydon, A.J., Beynon, R.J., Towle, H.C. & Agius, L. (2011)Elevated glucose represses liver glucokinase and induces its regulatory protein to safeguard hepatic phosphate homeostasis [PUBMED][PDF] [Abstract...]
Scent of sensecence
Garratt, .M, Stockley, P., Armstrong, S.D., Beynon, R.J. & Hurst, J.L. (2011) The scent of senescence: sexual signalling and female preference in house mice. [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...]
Schistosome parasite QconCAT
Castro-Borgesa, W., Simpson, D.M., Dowlea, A., Curwen, R.S., Thomas-Oates, J., Beynon, R.J. & Wilson, A. R. (2011) Abundance of tegument surface proteins in the human blood fluke Schistosoma mansoni determined by QconCAT proteomics. [PUBMED][PDF] [Abstract...]
Strategies for dynamic SILAC
Claydon, A & Beynon R (2011) Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC [PUBMED] [PDF] [Abstract...]
The end of proteomics
Davidson GR, Armstrong SD, Beynon R (2011) Positional proteomics at the N-terminus as a means of proteome simplification. [PUBMED][PDF]
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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...]
MUP molecular heterogeneity
Robertson, D.H.L., Gaskell, S.J., Cox, K., Evershed, R.P. & Beynon, R.J. Molecular heterogeneity in the Major Urinary Proteins of the house mouse, Mus musculus (1996) Biochem. J. 316, 265-272 [PUBMED] [PDF] [Abstract...]
PLP to monitor phosphorylase turnover
Beynon, R.J., Leyland, D.M., Evershed, R.P., Edwards, R.H.T. & 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 [PUBMED] [PDF] [Abstract...]
Protein binding in chemical communication
Beynon, R.J., Robertson, D.H.L., Hubbard, S. J., Gaskell, S.J. & Hurst, J.L. (1999) The role of protein binding in chemical communication: major urinary proteins in the house mouse. in "Chemical Signals in Vertebrates" (R.E. Johnston, D. Müller-Schwarze and P.W.Sorensen eds) Plenum Press pp 137-147 [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...]
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...]
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...]
MUPs in an aboriginal mouse
Robertson, D.H.L., Hurst, J.L., Searle, J.B., Gunduz, I. & Beynon, R.J. (2007) Characterization and Comparison of Major Urinary Proteins from the House Mouse, Mus musculus domesticus, and the Aboriginal Mouse, Mus macedonicus. J. Chem. Ecol. 33, 613-630.[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...]
Urinary lipocalins
Beynon, RJ, Hurst, JL, Turton, MJ , Robertson, DHL , Armstrong, SD, Cheetham, SA, Simpson, D, MacNicoll, A, Humphries, RE (2008) Urinary lipocalins in rodenta: is there a generic model? Chemical Signals in Vertebrates 11, 37-49 [PDF] [Abstract...]
First paper on a systematic analysis of MUP expression
Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL. (2008) Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. [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...]
FTICR based quantification
Johnson, H., Wong, S C C, D M Simpson, R J Beynon, and S J Gaskell (2008) . Protein quantification by selective isolation and fragmentation of isotopic pairs using FT-ICR MS. J Am Soc Mass Spectrom 19, 973-977 [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...]
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...]
MUP variation in lab mouse strains
Cheetham SA, Smith AL, Armstrong SD, Beynon RJ, Hurst JL. (2009) Limited variation in the major urinary proteins of laboratory mice. Physiol Behav. 96, 253-261 [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...]
Even the smallest of hamsters have lipocalins in their urine.
Turton MJ, Robertson DH, Smith JR, Hurst JL, Beynon RJ. Roborovskin, a Lipocalin in the Urine of the Roborovski Hamster, Phodopus roborovskii. Chem Senses. 2010 Jun 24. [PUBMED][PDF] [Abstract...]
It is a truth, universally acknowledged, that a mouse in possession of darcin must be in want of a mate.
Nominated as 'Exceptional' by Etienne Joly in Faculty1000 Biology (http://f1000biology.com)
Roberts SA, Simpson, Armstrong, Davidson, Robertson, McLean, Beynon & Hurst JL (2010) Darcin: a male pheromone that stimulates female memory and sexual attraction to an individual male's odour. BMC Biology 8:75. [PUBMED][PDF] [Abstract...]
Roberts SA, Simpson, Armstrong, Davidson, Robertson, McLean, Beynon & Hurst JL (2010) Darcin: a male pheromone that stimulates female memory and sexual attraction to an individual male's odour. BMC Biology 8:75. [PUBMED][PDF] [Abstract...]