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

  • Kukkola, A., A. J. Chetwynd, S. Krause and I. Lynch (2024). "Beyond microbeads: Examining the role of cosmetics in microplastic pollution and spotlighting unanswered questions." J Hazard Mater 476: 135053 DOI: 10.1016/j.jhazmat.2024.135053.
  • Zhang, P., M. Cao, A. J. Chetwynd, K. Faserl, F. Abdolahpur Monikh, W. Zhang, R. Ramautar, L. A. Ellis, H. H. Davoudi, K. Reilly, R. Cai, K. E. Wheeler, D. S. T. Martinez, Z. Guo, C. Chen and I. Lynch (2024). "Analysis of nanomaterial biocoronas in biological and environmental surroundings." Nat Protoc DOI: 10.1038/s41596-024-01009-8.
  • Chetwynd, A. J., M. V. Louyer, F. Mercier, V. Bessonneau and A. David (2024). "Polar organic pollutants, micro-nano plastics and nanomaterials: Analytical techniques to reveal the still invisible human physico-chemical exposome." Trac-Trends in Analytical Chemistry 177 DOI:10.1016/j.trac.2024.117816.
  • 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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