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Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis.

Jones FK, Hardman GE, Ferries S, Eyers CE, Pisconti A.

Methods Mol Biol. 2019;1889:301-317. doi: 10.1007/978-1-4939-8897-6_18.


Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells.

Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA.

Sci Signal. 2018 Sep 25;11(549). pii: eaat7951. doi: 10.1126/scisignal.aat7951.


New tools for carbohydrate sulfation analysis: heparan sulfate 2-O-sulfotransferase (HS2ST) is a target for small-molecule protein kinase inhibitors.

Byrne DP, Li Y, Ramakrishnan K, Barsukov IL, Yates EA, Eyers CE, Papy-Garcia D, Chantepie S, Pagadala V, Liu J, Wells C, Drewry DH, Zuercher WJ, Berry NG, Fernig DG, Eyers PA.

Biochem J. 2018 Aug 14;475(15):2417-2433. doi: 10.1042/BCJ20180265.


New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors.

Byrne DP, Li Y, Ngamlert P, Ramakrishnan K, Eyers CE, Wells C, Drewry DH, Zuercher WJ, Berry NG, Fernig DG, Eyers PA.

Biochem J. 2018 Aug 14;475(15):2435-2455. doi: 10.1042/BCJ20180266.


DNA Binding and Phosphorylation Regulate the Core Structure of the NF-κB p50 Transcription Factor.

Vonderach M, Byrne DP, Barran PE, Eyers PA, Eyers CE.

J Am Soc Mass Spectrom. 2019 Jan;30(1):128-138. doi: 10.1007/s13361-018-1984-0. Epub 2018 Jun 5. Erratum in: J Am Soc Mass Spectrom. 2019 Feb 11;:.


A quantitative and temporal map of proteostasis during heat shock in Saccharomyces cerevisiae.

Jarnuczak AF, Albornoz MG, Eyers CE, Grant CM, Hubbard SJ.

Mol Omics. 2018 Feb 1;14(1):37-52. doi: 10.1039/c7mo00050b. Epub 2018 Jan 16.


Understanding protein-drug interactions using ion mobility-mass spectrometry.

Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA.

Curr Opin Chem Biol. 2018 Feb;42:167-176. doi: 10.1016/j.cbpa.2017.12.013. Epub 2018 Jan 11. Review.


Plk4 and Aurora A cooperate in the initiation of acentriolar spindle assembly in mammalian oocytes.

Bury L, Coelho PA, Simeone A, Ferries S, Eyers CE, Eyers PA, Zernicka-Goetz M, Glover DM.

J Cell Biol. 2017 Nov 6;216(11):3571-3590. doi: 10.1083/jcb.201606077. Epub 2017 Sep 28.


Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer.

Ferries S, Perkins S, Brownridge PJ, Campbell A, Eyers PA, Jones AR, Eyers CE.

J Proteome Res. 2017 Sep 1;16(9):3448-3459. doi: 10.1021/acs.jproteome.7b00337. Epub 2017 Aug 11.


Local protein kinase A action proceeds through intact holoenzymes.

Smith FD, Esseltine JL, Nygren PJ, Veesler D, Byrne DP, Vonderach M, Strashnov I, Eyers CE, Eyers PA, Langeberg LK, Scott JD.

Science. 2017 Jun 23;356(6344):1288-1293. doi: 10.1126/science.aaj1669.


DOSCATs: Double standards for protein quantification.

Bennett RJ, Simpson DM, Holman SW, Ryan S, Brownridge P, Eyers CE, Colyer J, Beynon RJ.

Sci Rep. 2017 Apr 3;7:45570. doi: 10.1038/srep45570.


Bottom-Up Elucidation 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.

Anal Chem. 2017 Apr 18;89(8):4540-4549. doi: 10.1021/acs.analchem.6b04998. Epub 2017 Apr 6.


Label-Free Discovery Array Platform for the Characterization of Glycan Binding Proteins and Glycoproteins.

Gray CJ, Sánchez-Ruíz A, Šardzíková I, Ahmed YA, Miller RL, Reyes Martinez JE, Pallister E, Huang K, Both P, Hartmann M, Roberts HN, Šardzík R, Mandal S, Turnbull JE, Eyers CE, Flitsch SL.

Anal Chem. 2017 Apr 18;89(8):4444-4451. doi: 10.1021/acs.analchem.6b04122. Epub 2017 Mar 30.


KinView: a visual comparative sequence analysis tool for integrated kinome research.

McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N.

Mol Biosyst. 2016 Nov 15;12(12):3651-3665.


Dynamic phosphorylation of RelA on Ser42 and Ser45 in response to TNFα stimulation regulates DNA binding and transcription.

Lanucara F, Lam C, Mann J, Monie TP, Colombo SA, Holman SW, Boyd J, Dange MC, Mann DA, White MR, Eyers CE.

Open Biol. 2016 Jul;6(7). pii: 160055. doi: 10.1098/rsob.160055.


Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics.

Jarnuczak AF, Lee DC, Lawless C, Holman SW, Eyers CE, Hubbard SJ.

J Proteome Res. 2016 Sep 2;15(9):2945-59. doi: 10.1021/acs.jproteome.6b00048. Epub 2016 Aug 8.


cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry.

Byrne DP, Vonderach M, Ferries S, Brownridge PJ, Eyers CE, Eyers PA.

Biochem J. 2016 Oct 1;473(19):3159-75. doi: 10.1042/BCJ20160648. Epub 2016 Jul 21.


Human CDK18 promotes replication stress signaling 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.

Nucleic Acids Res. 2016 Oct 14;44(18):8772-8785. Epub 2016 Jul 5.


Absolute protein quantification of the yeast chaperome under conditions of heat shock.

Mackenzie RJ, Lawless C, Holman SW, Lanthaler K, Beynon RJ, Grant CM, Hubbard SJ, Eyers CE.

Proteomics. 2016 Aug;16(15-16):2128-40. doi: 10.1002/pmic.201500503. Epub 2016 Jul 22.


Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis.

Gray CJ, Thomas B, Upton R, Migas LG, Eyers CE, Barran PE, Flitsch SL.

Biochim Biophys Acta. 2016 Aug;1860(8):1688-709. doi: 10.1016/j.bbagen.2016.02.003. Epub 2016 Feb 22. Review.


RePLiCal: A QconCAT Protein for Retention Time Standardization in Proteomics Studies.

Holman SW, McLean L, Eyers CE.

J Proteome Res. 2016 Mar 4;15(3):1090-102. doi: 10.1021/acs.jproteome.5b00988. Epub 2016 Feb 2.


Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.

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.

Mol Cell Proteomics. 2016 Apr;15(4):1309-22. doi: 10.1074/mcp.M115.054288. Epub 2016 Jan 10.


Focus on Quantitative Proteomics.

Lilley KS, Beynon RJ, Eyers CE, Hubbard SJ.

Proteomics. 2015 Sep;15(18):3101-3. doi: 10.1002/pmic.201570163. No abstract available.


Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer.

Gonzalez-Sanchez MB, Lanucara F, Hardman GE, Eyers CE.

Int J Mass Spectrom. 2014 Jun 15;367:28-34.


Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae.

Jarnuczak AF, Eyers CE, Schwartz JM, Grant CM, Hubbard SJ.

Proteomics. 2015 Sep;15(18):3126-39. doi: 10.1002/pmic.201400527. Epub 2015 Apr 10.


The Tribbles 2 (TRB2) pseudokinase binds to ATP and autophosphorylates in a metal-independent manner.

Bailey FP, Byrne DP, Oruganty K, Eyers CE, Novotny CJ, Shokat KM, Kannan N, Eyers PA.

Biochem J. 2015 Apr 1;467(1):47-62. doi: 10.1042/BJ20141441.


Eukaryotic elongation factor 2 kinase activity is controlled by multiple inputs from oncogenic signaling.

Wang X, Regufe da Mota S, Liu R, Moore CE, Xie J, Lanucara F, Agarwala U, Pyr Dit Ruys S, Vertommen D, Rider MH, Eyers CE, Proud CG.

Mol Cell Biol. 2014 Nov 15;34(22):4088-103. doi: 10.1128/MCB.01035-14. Epub 2014 Sep 2.


Peptide scrambling during collision-induced dissociation is influenced by N-terminal residue basicity.

Chawner R, Holman SW, Gaskell SJ, Eyers CE.

J Am Soc Mass Spectrom. 2014 Nov;25(11):1927-38. doi: 10.1007/s13361-014-0968-y. Epub 2014 Aug 19.


Probing the exposure of the phosphate group in modified amino acids and peptides by ion-molecule reactions with triethoxyborane in Fourier transform ion cyclotron resonance mass spectrometry.

Lanucara F, Fornarini S, Eyers CE, Crestoni ME.

Rapid Commun Mass Spectrom. 2014 May 30;28(10):1107-16. doi: 10.1002/rcm.6884.


The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics.

Lanucara F, Holman SW, Gray CJ, Eyers CE.

Nat Chem. 2014 Apr;6(4):281-94. doi: 10.1038/nchem.1889. Review.


Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing.

Both P, Green AP, Gray CJ, Sardzík R, Voglmeir J, Fontana C, Austeri M, Rejzek M, Richardson D, Field RA, Widmalm G, Flitsch SL, Eyers CE.

Nat Chem. 2014 Jan;6(1):65-74. doi: 10.1038/nchem.1817. Epub 2013 Dec 8. Erratum in: Nat Chem. 2014 Apr;6(4):368.


Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue.

Lanucara F, Lee DC, Eyers CE.

J Am Soc Mass Spectrom. 2014 Feb;25(2):214-25. doi: 10.1007/s13361-013-0770-2. Epub 2013 Dec 3.


Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides.

Gonzalez-Sanchez MB, Lanucara F, Helm M, Eyers CE.

Biochem Soc Trans. 2013 Aug;41(4):1089-95. doi: 10.1042/BST20130072. Review.


Enzymatic reactions on immobilised substrates.

Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL.

Chem Soc Rev. 2013 Aug 7;42(15):6378-405. doi: 10.1039/c3cs60018a. Review.


The nitrosated bile acid DNA lesion O6-carboxymethylguanine is a substrate for the human DNA repair protein O6-methylguanine-DNA methyltransferase.

Senthong P, Millington CL, Wilkinson OJ, Marriott AS, Watson AJ, Reamtong O, Eyers CE, Williams DM, Margison GP, Povey AC.

Nucleic Acids Res. 2013 Mar 1;41(5):3047-55. doi: 10.1093/nar/gks1476. Epub 2013 Jan 17.


A novel approach to the analysis of SUMOylation with the independent use of trypsin and elastase digestion followed by database searching utilising consecutive residue addition to lysine.

Chicooree N, Griffiths JR, Connolly Y, Tan CT, Malliri A, Eyers CE, Smith DL.

Rapid Commun Mass Spectrom. 2013 Jan 15;27(1):127-34. doi: 10.1002/rcm.6425.


Dual purpose S-trityl-linkers for glycoarray fabrication on both polystyrene and gold.

Wehner JW, Weissenborn MJ, Hartmann M, Gray CJ, Šardzík R, Eyers CE, Flitsch SL, Lindhorst TK.

Org Biomol Chem. 2012 Nov 28;10(44):8919-26. doi: 10.1039/c2ob26118a.


The N-methylated peptide SEN304 powerfully inhibits Aβ(1-42) toxicity by perturbing oligomer formation.

Amijee H, Bate C, Williams A, Virdee J, Jeggo R, Spanswick D, Scopes DI, Treherne JM, Mazzitelli S, Chawner R, Eyers CE, Doig AJ.

Biochemistry. 2012 Oct 23;51(42):8338-52. doi: 10.1021/bi300415v. Epub 2012 Oct 12.


Formation of carbohydrate-functionalised polystyrene and glass slides and their analysis by MALDI-TOF MS.

Weissenborn MJ, Wehner JW, Gray CJ, Sardzík R, Eyers CE, Lindhorst TK, Flitsch SL.

Beilstein J Org Chem. 2012;8:753-62. Epub 2012 May 21.


QconCAT standard for calibration of ion mobility-mass spectrometry systems.

Chawner R, McCullough B, Giles K, Barran PE, Gaskell SJ, Eyers CE.

J Proteome Res. 2012 Nov 2;11(11):5564-72. doi: 10.1021/pr3005327. Epub 2012 Oct 9.


The use of selected reaction monitoring in quantitative proteomics.

Holman SW, Sims PF, Eyers CE.

Bioanalysis. 2012 Jul;4(14):1763-86. doi: 10.4155/BIO.12.126. Review.


Top-down mass spectrometry for the analysis of combinatorial post-translational modifications.

Lanucara F, Eyers CE.

Mass Spectrom Rev. 2013 Jan-Feb;32(1):27-42. doi: 10.1002/mas.21348. Epub 2012 Jun 20. Review.


Proposal for a common nomenclature for peptide fragment ions generated following sequence scrambling during collision-induced dissociation.

Chawner R, Gaskell SJ, Eyers CE.

Rapid Commun Mass Spectrom. 2012 Jan 30;26(2):205-6. doi: 10.1002/rcm.5294. No abstract available.


Mass spectrometric-based quantitative proteomics using SILAC.

Lanucara F, Eyers CE.

Methods Enzymol. 2011;500:133-50. doi: 10.1016/B978-0-12-385118-5.00008-6.


Quantification of proteins and their modifications using QconCAT technology.

Carroll KM, Lanucara F, Eyers CE.

Methods Enzymol. 2011;500:113-31. doi: 10.1016/B978-0-12-385118-5.00007-4.


Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach.

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn WB, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007633. doi: 10.1074/mcp.M111.007633. Epub 2011 Sep 19.


CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches.

Eyers CE, Lawless C, Wedge DC, Lau KW, Gaskell SJ, Hubbard SJ.

Mol Cell Proteomics. 2011 Nov;10(11):M110.003384. doi: 10.1074/mcp.M110.003384. Epub 2011 Aug 3.


Diauxic shift-dependent relocalization of decapping activators Dhh1 and Pat1 to polysomal complexes.

Drummond SP, Hildyard J, Firczuk H, Reamtong O, Li N, Kannambath S, Claydon AJ, Beynon RJ, Eyers CE, McCarthy JE.

Nucleic Acids Res. 2011 Sep 1;39(17):7764-74. doi: 10.1093/nar/gkr474. Epub 2011 Jun 28.


Analysis of post-translational modifications by LC-MS/MS.

Johnson H, Eyers CE.

Methods Mol Biol. 2010;658:93-108. doi: 10.1007/978-1-60761-780-8_5. Review.


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