Eyers
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...]
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...]
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...]
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...]
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 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...]
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...]
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...]
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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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...]
Protein sulfation enzymes are targeted by kinase inhibitors
Byrne DP, Li Y1, Ngamlert P, Ramakrishnan K, Eyers CE, Wells C, Drewry DH, Zuercher WJ, Berry NG, Fernig DG, Eyers PA. (2018) New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors. [PUBMED] [PDF] [Abstract...]
Enzymes for carbohydrate sulfation are targeted by kinase inhibitors
Dominic P. Byrne, Yong Li, Krithika Ramakrishnan, Igor L. Barsukov, Edwin A. Yates, Claire E. Eyers, Dulcé Papy-Garcia, Sandrine Chantepie, Vijayakanth Pagadala, Jian Liu, Carrow Wells, David H. Drewry, William J. Zuercher, Neil G. Berry, David G. Fernig and Patrick A. Eyers (2018) New tools for carbohydrate sulfation analysis: heparan sulfate 2-O-sulfotransferase (HS2ST) is a target for small-molecule protein kinase inhibitors [PDF] [PUBMED] [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...]
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...]
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 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...]
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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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...]
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...]
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...]
Role of CDK18 in replication stress signalling and genome stability
Barone G, Staples CJ, Ganesh A, Patterson KW, Bryne DP, Myers KN, Patil AA, Eyers CE, Maslen S, Skehel JM, Eyers PA, Collis SJ. (2016). Human CDK18 promotes replication stress signaling and genome stability. [PUBMED] [PDF] [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...]
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...]
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...]
The biggest absolute quantification study ever! A tale of 100 QconCATs for nearly 2,000 proteins
Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ. (2016) Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. [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...]
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...]
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...]
CaZIP phosphorylation
Eyers, Claire E., McNeill, Helen, Knebel, Axel, Morrice, Nick, Arthur, Simon J. C., Cuenda, Ana, Cohen, Philip. 2005. The phosphorylation of CapZ-interacting protein (CapZIP) by stress-activated protein kinases triggers its dissociation from CapZ. Biochemical Journal 389: 127. [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...]
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...]
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...]
Myosin light chain kinase phosphorylation site
Haydon, Claire E., Watt, Peter W., Morrice, Nick, Knebel, Axel, Gaestel, Matthias, Cohen, Philip. 2002. Identification of a phosphorylation site on skeletal muscle myosin light chain kinase that becomes phosphorylated during muscle contraction. Archives of Biochemistry and Biophysics 397: 224-231. [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...]
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...]