Proteomics
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This article is a preprint and has not been certified by peer review [PDF] [DOI] [Abstract...]
This article is a preprint and has not been certified by peer review [PDF] [DOI] [Abstract...]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...]
CSF proteomics in bacterial meningitis
Emma C Wall, Philip Brownridge, Gavin Laing, Vanessa S Terra, Veronica Mlozowa, Brigitte Denis, Mulinda Nyirenda, Theresa Allain, Elisa Ramos-Sevillano, Enitan Carrol, Andrea Collins, Stephen B Gordon, David G Lalloo, Brendan Wren, Robert Beynon, Robert S Heyderman, Jeremy S Brown (2020) CSF Levels of Elongation Factor Tu Is Associated With Increased Mortality in Malawian Adults With Streptococcus pneumoniae Meningitis Front Cell Infect Microbiol doi: 10.3389/fcimb.2020.603623. eCollection 2020. [PDF][PUBMED][DOI] [Abstract...]
PhosphoLFQ of NF-kB/RelA in DNA damage
Amy E Campbell, Caterina Ferraz Franco, Ling-I Su, Emma K Corbin, Simon Perkins, Anton Kalyuzhnyy, Andrew R Jones, Philip J Brownridge, Neil D Perkins, Claire E Eyers (2021) Temporal modulation of the NF-κB RelA network in response to different types of DNA damage Biochem J doi: 10.1042/BCJ20200627. Online ahead of print. [Abstract...]
Norovirus mode of action
Myra Hosmillo , Jia Lu, Michael R McAllaster, James B Eaglesham, Xinjie Wang, Edward Emmott, Patricia Domingues, Yasmin Chaudhry, Tim J Fitzmaurice, Matthew Kh Tung, Marc Dominik Panas, Gerald McInerney, Nicolas Locker, Craig B Wilen, Ian G Goodfellow (2020) Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation [PDF] [PUBMED] [DOI] [Abstract...]
Using stable isotopes to track sperm competition
Paula Stockley, Catarina Franco, Amy J. Claydon, Amanda Davidson, Dean E. Hammond, Philip J. Brownridge, Jane L. Hurst, and Robert J. Beynon (2020) Revealing mechanisms of mating plug function under sexual selection. [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...]
Novel proteolytic events in SARS-Cov-2 infection
Bjoern Meyer, Jeanne Chiaravalli, Philip Brownridge, Dominic P. Byrne, Leonard A. Daly, Fabrice Agou, Claire E. Eyers, Patrick A. Eyers, Marco Vignuzzi, Edward Emmott (2020) Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing [DOI] [PDF] [Abstract...]
The COVID-19 MS coalition
Weston Struwe, Edward Emmott, Melanie Bailey, Michal Sharon, Andrea Sinz, Fernando J Corrales, Kostas Thalassinos, Julian Braybrook, Clare Mills, Perdita Barran, COVID-19 MS Coalition (2020) The COVID-19 MS Coalition-accelerating diagnostics, prognostics, and treatment. [PDF] [PUBMED] [DOI] [Abstract...]
Temporal proteomics of herpes virus infection
Timothy K Soh, Colin T R Davies, Julia Muenzner, Leah M Hunter, Henry G Barrow, Viv Connor, Clément R Bouton, Cameron Smith, Edward Emmott, Robin Antrobus, Stephen C Graham, Michael P Weekes, Colin M Crump(2020) Temporal Proteomic Analysis of Herpes Simplex Virus 1 Infection Reveals Cell-Surface Remodeling via pUL56-Mediated GOPC Degradation. [PDF] [PUBMED] [DOI] [Abstract...]
Using QconCATs to establish protein complex stoichiometry
Mengru Yang, Deborah M Simpson, Nicolas Wenner, Philip Brownridge, Victoria M Harman, Jay C D Hinton, Robert J Beynon, Lu-Ning Liu (2020) Decoding the stoichiometric composition and organisation of bacterial metabolosomes [PDF] [PUBMED] [DOI] [Abstract...]
Regulation of Aurora A by CoASH
Yugo Tsuchiya, Dominic P Byrne, Selena G Burgess, Jenny Bormann, Jovana Baković, Yueyang Huang, Alexander Zhyvoloup, Bess Yi Kun Yu, Sew Peak-Chew, Trang Tran, Fiona Bellany, Alethea B Tabor, Aw Edith Chan, Lalitha Guruprasad, Oleg Garifulin, Valeriy Filonenko, Matthias Vonderach, Samantha Ferries, Claire E Eyers, John Carroll, Mark Skehel, Richard Bayliss , Patrick A Eyers, Ivan Gout (2020) Covalent Aurora A regulation by the metabolic integrator coenzyme A. [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...]
An unusual marsupial urinary lipocalin - vulpeculin
Grace M. Loxley, David O. Hooks, Aristotelis Antonopoulos, Anne Dell, Stuart M. Haslam, Wayne L. Linklater, Jane L. Hurst and Robert J. Beynon (2020) Vulpeculin: a novel and abundant lipocalin in the urine of the common brushtail possum, Trichosurus vulpecula. Open Biology Open Biol. 10: 200218. http://dx.doi.org/10.1098/rsob.200218 [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...]
Global proteomics of carbon source metabolism in Saccharomyces
M Garcia-Albornoz 1, S W Holman, T Antonisse, P Daran-Lapujade, B Teusink, R J Beynon, S J Hubbard (2020) A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. [PDF] [PUBMED] [DOI] [Abstract...]
Using proteomics to identify targets for schistosomiasis
Leandro X Neves, R Alan Wilson, Philip Brownridge, Victoria M Harman, Stephen W Holman, Robert J Beynon, Claire E Eyers, Ricardo DeMarco, William Castro-Borges (2020) Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni Pinpoints Secreted Proteins for Vaccine Development. [PDF] [PUBMED] [DOI] [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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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...]
Proteomics of canine ligament progenitors
Katie J Lee, Eithne J. Comerford, Deborah M. Simpson, Peter D. Clegg, and Elizabeth G Canty-Laird (2019) Identification and characterisation of canine ligament progenitor cells and their extracellular matrix niche [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...]
Myoblast phosphoproteomics
Fiona K. Jones, Gemma E. Hardman, Samantha Ferries, Claire E. Eyers, and Addolorata Pisconti (2019) Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis . [PUBMED] [PDF] [Abstract...]
Caught in a trap - proteomics of NETS
Elinor A. Chapman, Max Lyon, Deborah Simpson, David Mason, RobertJ.Beynon, RobertJ.Moots and HelenL.Wright (2019) Caught in a Trap? Proteomic Analysis of Neutrophil Extracellular Traps in Rheumatoid Arthritis and Systemic Lupus Erythematosus [PUBMED] [PDF] [Abstract...]
Synovial fluid proteomes
James R. Anderson, Aibek Smagul, Deborah Simpson, Peter D. Clegg, Luis M. Rubio-Martinez, Mandy J. Peffers (2019) The synovial fluid proteome differentiates between septic and nonseptic articular pathologies. [PUBMED] [PDF] [Abstract...]
Using protemics to define MMP7 processing
Garalla HM, Lertkowit N, Tiszlavicz L, Reisz Z, Holmberg C, Beynon R, Simpson D, Varga A, Kumar JD, Dodd S, Pritchard DM, Moore AR, Rosztóczy AI, Wittman T, Simpson A, Dockray GJ, Varro A. (2018) Matrix metalloproteinase (MMP)-7 in Barrett's esophagus and esophageal adenocarcinoma: expression, metabolism, and functional significance. [PUBMED] [PDF] [Abstract...]
SIDLS: stable isotope labelling for secretome dynamics
Hammond DE, Kumar JD, Raymond L, Simpson DM, Beynon RJ, Dockray GJ, Varro A. (2018) Stable Isotope Dynamic Labeling of Secretomes (SIDLS) Identifies Authentic Secretory Proteins Released by Cancer and Stromal Cells. [PDF] [PUBMED] [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 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...]
Deep discovery of novel phosphorylation sites
Gemma Hardman, Simon Perkins, Zheng Ruan, Natarajan Kannan, Philip Brownridge, Dominic P Byrne, Patrick A Eyers, Andrew R Jones (2017) Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics [PDF] [BIORXIV] [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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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...]
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...]
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...]
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...]
Proteomics of a marine organism
María del Carmen Muñoz-Marín, Guadalupe Gómez-Baena, Jesús Díez, Robert J. Beynon, David González-Ballester. Mikhail V. Zubkov and José M. García-Fernández (2017) Glucose Uptake in Prochlorococcus: Diversity of Kinetics and Effects on the Metabolism [PDF] [OA] [Abstract...]
Complete de novo sequencing of a mouse lemur protein
Jennifer Unsworth, Grace M. Loxley, Amanda Davidson, Jane L. Hurst, Guadalupe Gómez-Baena, Nicholas I. Mundy, Robert J. Beynon, Elke Zimmermann & Ute Radespiel. (2017) Characterisation of urinary WFDC12 in small nocturnal basal primates, mouse lemurs (Microcebus spp.) [PDF] [PUBMED] [Abstract...]
Connective tissue proteomics
Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD (2016). Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition. [PUBMED] [PDF] [Abstract...]
The F factor! F for 'flyability'!
Jarnuczak AF, Lee DC, Lawless C, Holman SW, Eyers CE, Hubbard SJ. (2016) Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. [PDF][PUBMED]
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The joys of running a training course!
A short article, written for the Biochemist, explaining the role of the Society in training provision and our experiences of running the Quantitative Proteomics Course [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...]
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...]
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...]
Replical: engineered protein for improved proteomics workflows
Holman SW, McLean L, Eyers CE. (2016) RePLiCal: A QconCAT Protein for Retention Time Standardization in Proteomics Studies. [PUBMED] [PDF] [Abstract...]
Sperm proteomes, gone large
Bayram HL, Claydon AJ, Brownridge PJ, Hurst JL, Mileham A, Stockley P, Beynon RJ, Hammond DE.(2016) Cross-species proteomics in analysis of mammalian sperm proteins. [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...]
SRM data standards
Da Qi, Craig Lawless, Johan Teleman,Fredrik Levander, Stephen W. Holman, Simon Hubbard and Andrew Jones (2015) The representation of selected-reaction monitoring data in the mzQuantML data standard. [PUBMED][PDF] [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...]
Proteomics and protein moonlighting
Beynon RJ, Hammond D, Harman V, Woolerton Y. (2014) The role of proteomics in studies of protein moonlighting. [PUBMED][PDF]
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QconCAT for equine acute phase proteins
Bundgaard L, Jacobsen S, Dyrlund TF, Sørensen MA, Harman VM, Beynon RJ, Brownridge PJ, Petersen LJ, Bendixen E. (2014) Development of a method for absolute quantification of equine acute phase proteins using concatenated peptide standards and selected reaction monitoring. [PUBMED][PDF]
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Proteomics of myofibroblasts
Balabanova S, Holmberg C, Steele I, Ebrahimi B, Rainbow L, Burdyga T, McCaig C, Tiszlavicz L, Lertkowit N, Giger OT, Oliver S, Prior I, Dimaline R, Simpson D, Beynon R, Hegyi P, Wang TC, Dockray GJ, Varro A. (2014) The neuroendocrine phenotype of gastric myofibroblasts and its loss with cancer progression. [PDF] [PUBMED] [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...]
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...]
Who's got the biggest workload? Analysis of chaperone abundance and workload
Brownridge P, Lawless C, Payapilly AB, Lanthaler K, Holman SW, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. Quantitative analysis of chaperone network throughput in budding yeast (2012). [PUBMED][PDF] [Abstract...]
A degrading synthesis of proteome turnover research!
Claydon, A.C. & Beynon, R.J. (2012) Proteome dynamics: revisiting turnover with a global perspective. [PUBMED][PDF] [Abstract...]
QconCATs for mastitis research
Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Røntved CM, Aebersold R, Moritz RL, Bendixen E. (2012) Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis. [PUBMED][PDF] [Abstract...]
Dynamic sperm labelling
Claydon AJ, Ramm SA, Pennington A, Hurst JL, Stockley P, Beynon R. (2012) Heterogenous turnover of sperm and seminal vesicle proteins in the mouse revealed by dynamic metabolic labeling. [PUBMED][PDF] [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...]
Extending Progenesis to embrace SILAC and Hi3
Qi, D., Brownridge, P., Xia, D., Mackay, K., Gonzalez-Galarza, F.F., Kenyani, J., Harman, V., Beynon, R.J. & Jones, A.R. (2012) A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS OMICS [PUBMED] [PDF] [Abstract...]
Designing QconCATs for a mammalian pathway
Simpson, D.M. & Beynon, R.J. (2012) QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification. [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]
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Positional proteomics and MetAP-2 substrates
Thomas B. Sundberg, Nicole Darricarrere, Pasquale Cirone, Xia Li, Lucy McDonald, Xue Mei, Christopher J. Westlake, Diane C. Slusarski, Robert J. Beynon, and Craig M. Crews (2011) Disruption of Wnt Planar Cell Polarity Signaling by Aberrant Accumulation of the MetAP-2 Substrate Rab37. [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...]
Quantification of a metabolic pathway
Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn W, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ. (2011) Absolute quantification of a metabolic pathway in yeast: deployment of a complete QconCAT approach. [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...]
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...]
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...]
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...]
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...]
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...]
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...]
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...]
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, AgustÃn, 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. BiotecnologÃa Aplicada 24: y04. [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...]
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...]
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...]
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...]
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...]
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...]
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...]
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...]
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...]
A proteomics workbench?
Beynon, R.J. (2004) Specification of a proteomics workbench. Comparative and Functional Genomics 5, 52-55 [PUBMED] [PDF] [Abstract...]
Sequential exoproteolysis is not valid as a structural probe
Beynon, R.J. (2004) Sequential exoproteolysis as a structural probe: a cautionary note. J. Mass. Spec. 39, 188-192. [PUBMED] [PDF] [Abstract...]
Proteomics of copper effects in Ronaldsay sheep
Simpson, D.M., Beynon, R.J., Robertson, D.H.L., Loughran, M.J. & Haywood, S. (2004) Copper associated liver disease: a proteomics study of copper challenge in a sheep model. Proteomics 4, 524-536. [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...]
Prevention of proteolysis
Beynon RJ, Oliver S. (2004) Avoidance of proteolysis in extracts. Methods Mol Biol. 244:75-84. [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...]
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...]
iMAC for phosphorylation sites
Haydon, Claire E., Eyers, Patrick A., Aveline-Wolf, Lauren D., Resing, Katheryn A., Maller, James L., Ahn, Natalie G. 2003. Identification of novel phosphorylation sites on Xenopus laevis Aurora A and analysis of phosphopeptide enrichment by immobilized metal-affinity chromatography. Molecular & Cellular Proteomics 2: 1055-1067. [PUBMED] [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...]
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...]