A close-up photograph of stacks of academic publications

Publications

Hot off the press publications from the Centre for Proteome Research can be found here. For a full list of publications, please view the team's individual staff profiles.

2023

  • Huffman, R. G., Leduc, A., Wichmann, C., Di Gioia, M., Borriello, F., Specht, H., Derks, J., Khan, S., Khoury, L., Emmott, E., Petelski, A. A., Perlman, D. H., Cox, J., Zanoni, I. and Slavov, N. (2023). "Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics." Nature Methods 20(5): 714-722. DOI:  10.1038/s41592-023-01830-1.
  • Gatto, L., Aebersold, R., Cox, J., Demichev, V., Derks, J., Emmott, E., Franks, A. M., Ivanov, A. R., Kelly, R. T., Khoury, L., Leduc, A., MacCoss, M. J., Nemes, P., Perlman, D. H., Petelski, A. A., Rose, C. M., Schoof, E. M., Van Eyk, J., Vanderaa, C., Yates, J. R. and Slavov, N. (2023). "Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments." Nature Methods 20(3): 375-386. DOI:  10.1038/s41592-023-01785-3.
  • Maher, R. E., Barry, P. J., Emmott, E., Jones, A. M., Lin, L., McNamara, P. S., Smith, J. A. and Lord, R. W. (2023). "The influence of highly effective modulator therapies on the sputum proteome in cystic fibrosis." medRxiv: 2023.2004.2017.23288625. DOI:  10.1101/2023.04.17.23288625.
  • Venkat, A., Watterson, G., Byrne, D. P., O'Boyle, B., Shrestha, S., Gravel, N., Fairweather, E. E., Daly, L. A., Bunn, C., Yeung, W., Aggarwal, I., Katiyar, S., Eyers, C. E., Eyers, P. A. and Kannan, N. (2023). "Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases." bioRxiv. DOI:  10.1101/2023.03.29.534689.
  • Huffman, R. G., Leduc, A., Wichmann, C., Di Gioia, M., Borriello, F., Specht, H., Derks, J., Khan, S., Khoury, L., Emmott, E., Petelski, A. A., Perlman, D. H., Cox, J., Zanoni, I. and Slavov, N. (2023). "Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics." Nat Methods. DOI:  10.1038/s41592-023-01830-1.
  • Gatto, L., Aebersold, R., Cox, J., Demichev, V., Derks, J., Emmott, E., Franks, A. M., Ivanov, A. R., Kelly, R. T., Khoury, L., Leduc, A., MacCoss, M. J., Nemes, P., Perlman, D. H., Petelski, A. A., Rose, C. M., Schoof, E. M., Van Eyk, J., Vanderaa, C., Yates, J. R., 3rd and Slavov, N. (2023). "Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments." Nat Methods 20(3): 375-386. DOI:  10.1038/s41592-023-01785-3.
  • Byrne, D. P., Shrestha, S., Daly, L. A., Marensi, V., Ramakrishnan, K., Eyers, C. E., Kannan, N. and Eyers, P. A. (2023). "Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2." Biochem J 480(2): 141-160. DOI:  10.1042/BCJ20220474.
  • Gómez-Baena, G., Pounder, K. C., Halstead, J. O., Roberts, S. A., Davidson, A. J., Prescott, M., Beynon, R. J. and Hurst, J. L. (2023). "Unraveling female communication through scent marks in the Norway rat." Proc Natl Acad Sci U S A 120(25): e2300794120. DOI:  10.1073/pnas.2300794120
  • Neves, L. X., Wilson, R. A., Brownridge, P., Holman, S. W., Harman, V. M., Eyers, C. E., Beynon, R. J. and Castro-Borges, W. (2023). "Dissection of schistosome tissues under LC-MS compatible preservative conditions for quantitative proteomics." Rapid Commun Mass Spectrom: e9523. DOI:  10.1002/rcm.9523.
  • Ventura, I., Harman, V., Beynon, R. J. and Santos, R. (2023). "Glycoproteins Involved in Sea Urchin Temporary Adhesion." Mar Drugs 21(3). DOI:  10.3390/md21030145.
  • Wagner, I., Grigoraki, L., Enevoldson, P., Clarkson, M., Jones, S., Hurst, J. L., Beynon, R. J. and Ranson, H. (2023). "Rapid identification of mosquito species and age by mass spectrometric analysis." BMC Biol 21(1): 10. DOI:  10.1186/s12915-022-01508-8.
  • Rusilowicz, M., Newman, D. W., Creamer, D. R., Johnson, J., Adair, K., Harman, V. M., Grant, C. M., Beynon, R. J. and Hubbard, S. J. (2023). "AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation." J Proteome Res 22(2): 594-604. DOI:  10.1021/acs.jproteome.2c00608.

2022

  • Maher, R. and Emmott, E. (2022). "Electrospray ionization: “We taught elephants to fly”." The Biochemist 44(5): 5-8. DOI:  10.1042/bio_2022_127.
  • Hunter, J. E., Campbell, A. E., Butterworth, J. A., Sellier, H., Hannaway, N. L., Luli, S., Floudas, A., Kenneth, N. S., Moore, A. J., Brownridge, P. J., Thomas, H. D., Coxhead, J., Taylor, L., Leary, P., Hasoon, M. S. R., Knight, A. M., Garrett, M. D., Collins, I., Eyers, C. E. and Perkins, N. D. (2022). "Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance." Biochemical Journal 479(19): 2087-2113. DOI:  10.1042/bcj20220089.
  • Hunter, J. E., Campbell, A. E., Hannaway, N. L., Kerridge, S., Luli, S., Butterworth, J. A., Sellier, H., Mukherjee, R., Dhillon, N., Sudhindar, P. D., Shukla, R., Brownridge, P. J., Bell, H. L., Coxhead, J., Taylor, L., Leary, P., Hasoon, M. S. R., Collins, I., Garrett, M. D., Eyers, C. E. and Perkins, N. D. (2022). "Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway." Biochemical Journal 479(19): 2063-2086. DOI:  10.1042/bcj20220102.
  • Hunter, J. E., Campbell, A. E., Kerridge, S., Fraser, C., Hannaway, N. L., Luli, S., Ivanova, I., Brownridge, P. J., Coxhead, J., Taylor, L., Leary, P., Hasoon, M. S. R., Eyers, C. E. and Perkins, N. D. (2022). "Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells." Biochemical Journal 479(19): 2131-2151. DOI:  10.1042/bcj20220103.
  • Maher, R. E., Barrett, E., Beynon, R. J., Harman, V. M., Jones, A. M., McNamara, P. S., Smith, J. A. and Lord, R. W. (2022). "The relationship between lung disease severity and the sputum proteome in cystic fibrosis." Respiratory Medicine: 107002. DOI: https://doi.org/10.1016/j.rmed.2022.107002.
  • Maher, R. E., Määttä, M., Beynon, R. J., Laurila, H. P., McNamara, P. S. and Rajamäki, M. M. (2022). "Quantitative proteomic analysis of bronchoalveolar lavage fluid in West Highland white terriers with canine idiopathic pulmonary fibrosis." BMC Vet Res 18(1): 121. DOI:  10.1186/s12917-022-03202-x.
  • Omar, M. H., Byrne, D. P., Jones, K. N., Lakey, T. M., Collins, K. B., Lee, K. S., Daly, L. A., Forbush, K. A., Lau, H. T., Golkowski, M., McKnight, G. S., Breault, D. T., Lefrancois-Martinez, A. M., Martinez, A., Eyers, C. E., Baird, G. S., Ong, S. E., Smith, F. D., Eyers, P. A. and Scott, J. D. (2022). "Mislocalization of protein kinase A drives pathology in Cushing's syndrome." Cell Rep 40(2): 111073. DOI:  10.1016/j.celrep.2022.111073.
  • Marr, L., Biswas, D., Daly, L. A., Browning, C., Vial, S. C. M., Maskell, D. P., Hudson, C., Bertrand, J. A., Pollard, J., Ranson, N. A., Khatter, H., Eyers, C. E., Sakamoto, K. and Zeqiraj, E. (2022). "Mechanism of glycogen synthase inactivation and interaction with glycogenin." Nature Communications 13(1): 3372. DOI:  10.1038/s41467-022-31109-6.
  • Huffman, R. G., Leduc, A., Wichmann, C., di Gioia, M., Borriello, F., Specht, H., Derks, J., Khan, S., Emmott, E., Petelski, A. A., Perlman, D. H., Cox, J., Zanoni, I. and Slavov, N. (2022). "Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages." bioRxiv: 2022.2003.2016.484655. DOI:  10.1101/2022.03.16.484655.
  • Kalyuzhnyy, A., Eyers, P. A., Eyers, C. E., Bowler-Barnett, E., Martin, M. J., Sun, Z., Deutsch, E. W. and Jones, A. R. (2022). "Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation." Journal of Proteome Research 21(6): 1510-1524. DOI:  10.1021/acs.jproteome.2c00131.
  • Wagner, I., Grigoraki, L., Enevoldson, P., Clarkson, M., Jones, S., Hurst, J. L., Beynon, R. J. and Ranson, H. (2022). "Rapid identification of mosquito species, sex and age by mass spectrometric analysis." bioRxiv: 2022.2003.2007.483241. DOI:  10.1101/2022.03.07.483241.
  • Davies, H. A., Caamano-Gutierrez, E., Sarsby, J., Chim, Y. H., Barrett, S., Nawaytou, O., Harky, A., Field, M., Akhtar, R. and Madine, J. (2022). "Rapid evaporative ionization mass spectrometry (intelligent knife) for point-of-care testing in acute aortic dissection surgery." Interactive CardioVascular and Thoracic Surgery 34(5): 833-840. DOI:  10.1093/icvts/ivac019.
  • Tomlinson, L. J., Batchelor, M., Sarsby, J., Byrne, D. P., Brownridge, P. J., Bayliss, R., Eyers, P. A. and Eyers, C. E. (2022). "Exploring the Conformational Landscape and Stability of Aurora A Using Ion-Mobility Mass Spectrometry and Molecular Modeling." Journal of the American Society for Mass Spectrometry 33(3): 420-435. DOI:  10.1021/jasms.1c00271.

2021

  • Hammond, D. E., D. M. Simpson, C. Franco, M. W. Muelas, J. Waters, R. W. Ludwig, M. C. Prescott, J. L. Hurst, R. J. Beynon and E. Lau (2021). "Harmonizing labeling and analytical strategies to obtain protein turnover rates in intact adult animals." bioRxiv: 2021.2012.2013.472439. DOI:  10.1101/2021.12.13.472439.
  • Specht, H., E. Emmott, A. A. Petelski, R. G. Huffman, D. H. Perlman, M. Serra, P. Kharchenko, A. Koller and N. Slavov (2021). "Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2." Genome Biology 22(1). DOI: doi.org/10.1186/s13059-021-02267-5.
  • Campbell, A. E., C. F. Franco, L. I. Su, E. K. Corbin, S. Perkins, A. Kalyuzhnyy, A. R. Jones, P. J. Brownridge, N. D. Perkins and C. E. Eyers (2021). "Temporal modulation of the NF-kappa B ReIA network in response to different types of DNA damage." Biochemical Journal 478(3): 533-551. DOI: 10.1042/Bcj20200627
  • Daly, L. A., P. J. Brownridge, M. Batie, S. Rocha, V. See and C. E. Eyers (2021). "Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1 alpha/2 alpha." Science Signaling 14(692). DOI: ARTN eabf6685 10.1126/scisignal.abf6685
  • Davies, H. A., E. Caamano-Gutierrez, J. Sarsby, O. Nawaytou, A. Harky, R. Akhtar, M. Field and J. Madine (2021). "Exploring the potential of rapid evaporative ionization mass spectrometry (Intelligent Knife) for point-of-care testing in aortic surgery." European Journal of Cardio-Thoracic Surgery 60(3): 562-568. DOI: 10.1093/ejcts/ezab166
  • Foulkes, D. M., K. McLean, Y. Zheng, J. Sarsby, A. S. Haneef, D. G. Fernig, C. Winstanley, N. Berry and S. B. Kaye (2021). "A pipeline to evaluate inhibitors of the Pseudomonas aeruginosa exotoxin U." Biochemical Journal 478(3): 647-668. DOI: 10.1042/BCJ20200780
  • Huokko, T., T. Ni, G. F. Dykes, D. M. Simpson, P. Brownridge, F. D. Conradi, R. J. Beynon, P. J. Nixon, C. W. Mullineaux, P. Zhang and L. N. Liu (2021). "Probing the biogenesis pathway and dynamics of thylakoid membranes." Nature Communications 12(1): 3475. DOI: 10.1038/s41467-021-23680-1
  • Johnson, J., V. M. Harman, C. Franco, E. Emmott, N. Rockliffe, Y. Sun, L. N. Liu, A. Takemori, N. Takemori and R. J. Beynon (2021). "Construction of a la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins." BMC Biology 19(1): 195. DOI: 10.1186/s12915-021-01135-9
  • Oldstone, M. B. A., B. C. Ware, A. Davidson, M. C. Prescott, R. J. Beynon and J. L. Hurst (2021). "Lymphocytic Choriomeningitis Virus Alters the Expression of Male Mouse Scent Proteins." Viruses 13(6). DOI: 10.3390/v13061180
  • Petelski, A. A., E. Emmott, A. Leduc, R. G. Huffman, H. Specht, D. H. Perlman and N. Slavov (2021). "Multiplexed single-cell proteomics using SCoPE2." Nature Protocols DOI: 10.1038/s41596-021-00616-z
  • Sutherland, H., M. J. Conley, E. Emmott, J. Streetley, I. G. Goodfellow and D. Bhella (2021). "The Cryo-EM Structure of Vesivirus 2117 Highlights Functional Variations in Entry Pathways for Viruses in Different Clades of the Vesivirus Genus." Journal of Virology 95(13): e0028221. DOI: 10.1128/JVI.00282-21
  • Tse, K., E. Beamer, D. Simpson, R. J. Beynon, G. J. Sills and T. Thippeswamy (2021). "The Impacts of Surgery and Intracerebral Electrodes in C57BL/6J Mouse Kainate Model of Epileptogenesis: Seizure Threshold, Proteomics, and Cytokine Profiles." Frontiers in Neurology 12: 625017. DOI: 10.3389/fneur.2021.625017
  • Uenoyama, R., T. Miyazaki, J. L. Hurst, R. J. Beynon, M. Adachi, T. Murooka, I. Onoda, Y. Miyazawa, R. Katayama, T. Yamashita, S. Kaneko, T. Nishikawa and M. Miyazaki (2021). "The characteristic response of domestic cats to plant iridoids allows them to gain chemical defense against mosquitoes." Acience Advances 7(4). DOI: 10.1126/sciadv.abd9135.

2020

  • Bayram, H. L., C. Franco, P. Brownridge, A. J. Claydon, N. Koch, J. L. Hurst, R. J. Beynon and P. Stockley (2020). "Social status and ejaculate composition in the house mouse." Philosophical Transactions of the Royal Society B: Biological Sciences 375(1813): 20200083. DOI: 10.1098/rstb.2020.0083
  • Byrne, D. P., C. J. Clarke, P. J. Brownridge, A. Kalyuzhnyy, S. Perkins, A. Campbell, D. Mason, A. R. Jones, P. A. Eyers and C. E. Eyers (2020). "Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics." Biochemical Journal 477(13): 2451-2475. DOI: 10.1042/Bcj20200309
  • Byrne, D. P., S. Shrestha, M. Galler, M. Cao, L. A. Daly, A. E. Campbell, C. E. Eyers, E. A. Veal, N. Kannan and P. A. Eyers (2020). "Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity." Science Signaling 13(639). DOI: ARTN eaax2713 10.1126/scisignal.aax2713
  • Choi, H., D. Simpson, D. Wang, M. Prescott, A. A. Pitsillides, J. Dudhia, P. D. Clegg, P. Ping and C. T. Thorpe (2020). "Heterogeneity of proteome dynamics between connective tissue phases of adult tendon." eLife 9. DOI: 10.7554/eLife.55262
  • Demir, E., K. Li, N. Bobrowski-Khoury, J. I. Sanders, R. J. Beynon, J. L. Hurst, A. Kepecs and R. Axel (2020). "The pheromone darcin drives a circuit for innate and reinforced behaviours." Nature 578(7793): 137-141. DOI: 10.1038/s41586-020-1967-8
  • Eyers, C. E. (2020). Histidine Phosphorylation Methods and Protocols Preface. Histidine Phosphorylation. 2077: V-V. Book-DOI: 10.1007/978-1-4939-9884-5
  • Garcia-Albornoz, M., S. W. Holman, T. Antonisse, P. Daran-Lapujade, B. Teusink, R. J. Beynon and S. J. Hubbard (2020). "A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae." Molecular Omics 16(1): 59-72. DOI: 10.1039/c9mo00136k
  • Goodhead, I., F. Blow, P. Brownridge, M. Hughes, J. Kenny, R. Krishna, L. McLean, P. Pongchaikul, R. Beynon and A. C. Darby (2020). "Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont." Microbial Genomics 6(1). DOI: 10.1099/mgen.0.000285
  • Hardman, G. and C. E. Eyers (2020). "High-Throughput Characterization of Histidine Phosphorylation Sites Using UPAX and Tandem Mass Spectrometry." Methods in Molecular Biology 2077: 225-235. DOI: 10.1007/978-1-4939-9884-5_15
  • Loxley, G. M., D. O. Hooks, A. Antonopoulos, A. Dell, S. M. Haslam, W. L. Linklater, J. L. Hurst and R. J. Beynon (2020). "Vulpeculin: a novel and abundant lipocalin in the urine of the common brushtail possum, Trichosurus vulpecula." Open Biology 10(10): 200218. DOI: 10.1098/rsob.200218
  • Neves, L. X., R. A. Wilson, P. Brownridge, V. M. Harman, S. W. Holman, R. J. Beynon, C. E. Eyers, R. DeMarco and W. Castro-Borges (2020). "Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni Pinpoints Secreted Proteins for Vaccine Development." Journal of Proteome Research 19(1): 314-326. DOI: 10.1021/acs.jproteome.9b00531
  • Soh, T. K., C. T. R. Davies, J. Muenzner, L. M. Hunter, H. G. Barrow, V. Connor, C. R. Bouton, C. Smith, E. Emmott, R. Antrobus, S. C. Graham, M. P. Weekes and C. M. Crump (2020). "Temporal Proteomic Analysis of Herpes Simplex Virus 1 Infection Reveals Cell-Surface Remodeling via pUL56-Mediated GOPC Degradation." Cell Reports 33(1). DOI: ARTN 108235 10.1016/j.celrep.2020.108235
  • Stockley, P., C. Franco, A. J. Claydon, A. Davidson, D. E. Hammond, P. J. Brownridge, J. L. Hurst and R. J. Beynon (2020). "Revealing mechanisms of mating plug function under sexual selection." Proceedings of the National Academy of Sciences of the United States of America 117(44): 27465-27473. DOI: 10.1073/pnas.1920526117
  • Struwe, W., E. Emmott, M. Bailey, M. Sharon, A. Sinz, F. J. Corrales, K. Thalassinos, J. Braybrook, C. Mills, P. Barran and C. M. Coalition (2020). "The COVID-19 MS Coalition-accelerating diagnostics, prognostics, and treatment." Lancet 395(10239): 1761-1762. DOI: 10.1016/S0140-6736(20)31211-3.
  • Takemori, A., D. S. Butcher, V. M. Harman, P. Brownridge, K. Shima, D. Higo, J. Ishizaki, H. Hasegawa, J. Suzuki, M. Yamashita, J. A. Loo, R. R. O. Loo, R. J. Beynon, L. C. Anderson and N. Takemori (2020). "PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry." Journal of Proteome Research 19(9): 3779-3791. DOI: 10.1021/acs.jproteome.0c00303.
  • Tomlinson, L. J., A. K. M. C. Coldron, P. A. Eyers and C. E. Eyers (2020). "Determination of Phosphohistidine Stoichiometry in Histidine Kinases by Intact Mass Spectrometry." Methods in Molecular Biology 2077: 83-91. DOI: 10.1007/978-1-4939-9884-5_6.
  • Tomlinson, L. J. and C. E. Eyers (2020). "Ion Mobility-Mass Spectrometry to Evaluate the Effects of Protein Modification or Small Molecule Binding on Protein Dynamics." Ion Mobility-Mass Spectrometry: Methods and Protocols 2084: 179-190. DOI: 10.1007/978-1-0716-0030-6_11.
  • Tsuchiya, Y., D. P. Byrne, S. G. Burgess, J. Bormann, J. Bakovic, Y. Y. Huang, A. Zhyvoloup, B. Y. K. Yu, S. Peak-Chew, T. Tran, F. Bellany, A. B. Tabor, A. W. E. Chang, L. Guruprasad, O. Garifulin, V. Filonenko, M. Vonderach, S. Ferries, C. E. Eyers, J. Carroll, M. Skehel, R. Bayliss, P. A. Eyers and I. Gout (2020). "Covalent Aurora A regulation by the metabolic integrator coenzyme A." Redox Biology 28. DOI: ARTN 101318 10.1016/j.redox.2019.101318.
  • Wagner, I., N. I. Koch, J. Sarsby, N. White, T. A. R. Price, S. Jones, J. L. Hurst and R. J. Beynon (2020). "The application of rapid evaporative ionization mass spectrometry in the analysis of Drosophila species-a potential new tool in entomology." Open Biology 10(11): 200196. DOI: 10.1098/rsob.200196.
  • Wall, E. C., P. Brownridge, G. Laing, V. S. Terra, V. Mlozowa, B. Denis, M. Nyirenda, T. Allain, E. Ramos-Sevillano, E. Carrol, A. Collins, S. B. Gordon, D. G. Lalloo, B. Wren, R. Beynon, R. S. Heyderman and J. S. Brown (2020). "CSF Levels of Elongation Factor Tu Is Associated With Increased Mortality in Malawian Adults With Streptococcus pneumoniae Meningitis." Frontiers in Cellular and Infection Microbiology 10: 603623. DOI: 10.3389/fcimb.2020.603623
  • Yang, M., D. M. Simpson, N. Wenner, P. Brownridge, V. M. Harman, J. C. D. Hinton, R. J. Beynon and L. N. Liu (2020). "Decoding the stoichiometric composition and organisation of bacterial metabolosomes." Nature Communications 11(1): 1976. DOI: 10.1038/s41467-020-15888-4.

Back to: Centre for Proteome Research (CPR)