Mass spectrometry
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...]
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...]
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...]
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...]
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...]
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...]
Stoichiometry of histidine kinases by mass spectrometry
Lauren J Tomlinson, Alice K M Clubbs Coldron , Patrick A Eyers, Claire E Eyers (2020) Determination of Phosphohistidine Stoichiometry in Histidine Kinases by Intact Mass Spectrometry. [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...]
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...]
Connective tissue protein turnover
Howard Choi, Deborah Simpson, Ding Wang, Mark Prescott, Andrew A Pitsillides, Jayesh Dudhia, Peter D Clegg, Peipei Ping, Chavaunne T Thorpe (2020) Heterogeneity of proteome dynamics between connective tissue phases of adult tendon. [PDF] [PUBMED] [DOI] [Abstract...]
Redox control of protein kinases
Dominic P Byrne, Safal Shrestha , Martin Galler, Min Cao, Leonard A Daly, Amy E Campbell, Claire E Eyers, Elizabeth A Veal, Natarajan Kannan Patrick A Eyers (2020) Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity. [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...]
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...]
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...]
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...]
MUPs shape the volatile odours of mice
Roberts SA, Prescott MC, Davidson AJ, McLean L, Beynon RJ, Hurst JL. (2018) Individual odour signatures that mice learn are shaped by involatile major urinary proteins (MUPs). [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...]
Using ion mobility MS to understand drug:protein interactions
Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA (2018). Understanding protein-drug interactions using ion mobility-mass spectrometry. [PDF] [PUBMED] [Abstract...]
Nextgen QconCATs - MEERCAT!
Takemori N, Takemori A, Tanaka Y, Endo Y, Hurst JL, Gómez-Baena G, Harman VM, Beynon RJ. (2017) MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. [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...]
A new lipocalin, fully sequenced, from bank voles
Loxley GM, Unsworth J, Turton MJ, Jebb A, Lilley KS, Simpson DM, Rigden DJ, Hurst JL, Beynon RJ. (2017) Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. [PDF] [PUBMED]
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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...]
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...]
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...]
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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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...]
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...]
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...]
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...]
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...]
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...]
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...]
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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MUP complexity and analytical challenges
Beynon RJ, Armstrong SD, Gómez-Baena G, Lee V, Simpson D, Unsworth J, Hurst JL. (2014) The complexity of protein semiochemistry in mammals. [PUBMED][PDF] [Abstract...]
Rats have MUPs too - but different!
Gómez-Baena G, Armstrong SD, Phelan MM, Hurst JL, Beynon RJ. (2014). The major urinary protein system in the rat. [PUBMED][PDF] [Abstract...]
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...]
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...]
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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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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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...]
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...]
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...]
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...]
EF2 kinase regulation
Knebel, Axel, Haydon, Claire E., Morrice, Nick, Cohen, Philip. 2002. Stress-induced regulation of eukaryotic elongation factor 2 kinase by SB 203580-sensitive and-insensitive pathways. Biochemical Journal 367: 525. [PUBMED] [Abstract...]