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.

2024

  • Bendzunas, G. N., D. P. Byrne, S. Shrestha, L. A. Daly, S. O. Oswald, S. Katiyar, A. Venkat, W. Yeung, C. E. Eyers, P. A. Eyers and N. Kannan (2024). "Redox Regulation of Brain Selective Kinases BRSK1/2: Implications for Dynamic Control of the Eukaryotic AMPK family through Cys-based mechanisms." bioRxiv DOI: 10.1101/2023.10.05.561145.
  • Eyers, C. E. and C. J. Clarke (2024). "Pyro(phospho)mania." Nat Chem Biol DOI: 10.1038/s41589-024-01606-4.
  • Georgana, I., M. Hosmillo, A. S. Jahun, E. Emmott, F. Sorgeloos, K. O. Cho and I. G. Goodfellow (2024). "Porcine Sapovirus Protease Controls the Innate Immune Response and Targets TBK1." Viruses 16(2) DOI: 10.3390/v16020247.
  • Georgana, I., S. R. Scutts, C. Gao, Y. Lu, A. A. Torres, H. Ren, E. Emmott, J. Men, K. Oei and G. L. Smith (2024). "Filamin B restricts vaccinia virus spread and is targeted by vaccinia virus protein C4." Journal of Virology 98(3): e0148523 DOI: 10.1128/jvi.01485-23.
  • Omar, M. H., D. P. Byrne, S. Shrestha, T. M. Lakey, K. S. Lee, S. M. Lauer, K. B. Collins, L. A. Daly, C. E. Eyers, G. S. Baird, S. E. Ong, N. Kannan, P. A. Eyers and J. D. Scott (2024). "Discovery of a Cushing's syndrome protein kinase A mutant that biases signaling through type I AKAPs." Sci Adv 10(8): eadl1258 DOI: 10.1126/sciadv.adl1258.

2023

  • Stewart, H., Y. Lu, S. O'Keefe, A. Valpadashi, L. D. Cruz-Zaragoza, H. A. Michel, S. K. Nguyen, G. W. Carnell, N. Lukhovitskaya, R. Milligan, Y. Adewusi, I. Jungreis, V. Lulla, D. A. Matthews, S. High, P. Rehling, E. Emmott, J. L. Heeney, A. D. Davidson, J. R. Edgar, G. L. Smith and A. E. Firth (2023). "The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity." iScience 26(11): 108080 DOI: 10.1016/j.isci.2023.108080.
  • Po, A. and C. E. Eyers (2023). "Top-Down Proteomics and the Challenges of True Proteoform Characterization." J Proteome Res 22(12): 3663-3675 DOI: 10.1021/acs.jproteome.3c00416.
  • Daly, L. A., D. P. Byrne, S. Perkins, P. J. Brownridge, E. McDonnell, A. R. Jones, P. A. Eyers and C. E. Eyers (2023). "Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides." J Proteome Res 22(12): 3754-3772 DOI: 10.1021/acs.jproteome.3c00425.
  • Daly, L. A., C. J. Clarke, A. Po, S. O. Oswald and C. E. Eyers (2023). "Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond." Chem Commun (Camb) 59(77): 11484-11499 DOI: 10.1039/d3cc02909c
  • Collings, K., C. Boisdon, T. T. Sham, K. Skinley, H. K. Oh, T. Prince, A. Ahmed, S. H. Pennington, P. J. Brownridge, T. Edwards, G. A. Biagini, C. E. Eyers, A. Lamb, P. Myers and S. Maher (2023). "Attaching protein-adsorbing silica particles to the surface of cotton substrates for bioaerosol capture including SARS-CoV-2." Nat Commun 14(1): 5033 DOI: 10.1038/s41467-023-40696-x.
  • Maher, R. E., P. J. Barry, E. Emmott, A. M. Jones, L. Lin, P. S. McNamara, J. A. Smith and R. W. Lord (2023). "Influence of highly effective modulator therapy on the sputum proteome in cystic fibrosis." J Cyst Fibros DOI: 10.1016/j.jcf.2023.10.019.
  • 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.

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