Skip to main content Skip to navigation

Proteomics RTP Publications

Proteomics RTP Publications

2020

(1) Linley, A. J.; Karydis, L. I.; Mondru, A.; D’Avola, A.; Cicconi, S.; Griffin, R.; Forconi, F.; Pettitt, A. R.; Kalakonda, N.; Rawstron, A.; Hillmen, P.; Steele, A. J.; MacEwan, D. J.; Packham, G.; Prior, I. A.; Slupsky, J. R. Kinobead Profiling Reveals Reprogramming of B-Cell Receptor Signaling in Response to Therapy Within Primary Chronic Lymphocytic Leukemia Cells. bioRxiv 2020, 841312. https://doi.org/10.1101/841312.

(2) Jacomin, A.-C.; Petridi, S.; Di Monaco, M.; Bhujabal, Z.; Jain, A.; Mulakkal, N. C.; Palara, A.; Powell, E. L.; Chung, B.; Zampronio, C.; Jones, A.; Cameron, A.; Johansen, T.; Nezis, I. P. Regulation of Expression of Autophagy Genes by Atg8a-Interacting Partners Sequoia, YL-1, and Sir2 in Drosophila. Cell Reports 2020, 31 (8), 107695. https://doi.org/10.1016/j.celrep.2020.107695.

(3) Zeeshan, M.; Pandey, R.; Ferguson, D. J. P.; Tromer, E. C.; Markus, R.; Abel, S.; Brady, D.; Daniel, E.; Limenitakis, R.; Bottrill, A. R.; Le Roch, K. G.; Holder, A. A.; Waller, R. F.; Guttery, D. S.; Tewari, R. Real-Time Dynamics of Plasmodium NDC80 Reveals Unusual Modes of Chromosome Segregation during Parasite Proliferation. J. Cell. Sci. 2020. https://doi.org/10.1242/jcs.245753.

(4) Chhun, A.; Sousoni, D.; Aguiló-Ferretjans, M. del M.; Song, L.; Corre, C.; Christie-Oleza, J. A. Phytoplankton Trigger the Production of Cryptic Metabolites in the Marine Actinobacteria Salinispora Tropica. bioRxiv 2020, 2020.05.18.103358. https://doi.org/10.1101/2020.05.18.103358.

(5) Firczuk, H.; Teahan, J.; Mendes, P.; McCarthy, J. E. G. Multisite Rate Control Analysis Identifies Ribosomal Scanning as the Sole High-Capacity/Low-Flux-Control Step in MRNA Translation. FEBS J. 2020, 287 (5), 925–940. https://doi.org/10.1111/febs.15059.

(6) Pandey, R.; Abel, S.; Boucher, M.; Wall, R. J.; Zeeshan, M.; Rea, E.; Freville, A.; Lu, X. M.; Brady, D.; Daniel, E.; Stanway, R. R.; Wheatley, S.; Batugedara, G.; Hollin, T.; Bottrill, A. R.; Gupta, D.; Holder, A. A.; Le Roch, K. G.; Tewari, R. Plasmodium Condensin Core Subunits SMC2/SMC4 Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission. Cell Rep 2020, 30 (6), 1883-1897.e6. https://doi.org/10.1016/j.celrep.2020.01.033.

(7) Hatano, T.; Sivashanmugam, L.; Suchenko, A.; Hussain, H.; Balasubramanian, M. K. Pick-Ya Actin – a Method to Purify Actin Isoforms with Bespoke Key Post-Translational Modifications. J Cell Sci 2020, 133 (2). https://doi.org/10.1242/jcs.241406.

(8) L. Parker, H.; F. Tomás, R. M.; M. Furze, C.; S. Guy, C.; Fullam, E. Asymmetric Trehalose Analogues to Probe Disaccharide Processing Pathways in Mycobacteria. Organic & Biomolecular Chemistry 2020, 18 (18), 3607–3612. https://doi.org/10.1039/D0OB00253D.

2019

(9) Palani, S.; Köster, D. V.; Hatano, T.; Kamnev, A.; Kanamaru, T.; Brooker, H. R.; Hernandez-Fernaud, J. R.; Jones, A. M. E.; Millar, J. B. A.; Mulvihill, D. P.; Balasubramanian, M. K. Phosphoregulation of Tropomyosin Is Crucial for Actin Cable Turnover and Division Site Placement. J Cell Biol 2019, jcb.201809089. https://doi.org/10.1083/jcb.201809089.

(10) Fenn, J. S.; Nepravishta, R.; Guy, C. S.; Harrison, J.; Angulo, J.; Cameron, A. D.; Fullam, E. Structural Basis of Glycerophosphodiester Recognition by the Mycobacterium Tuberculosis Substrate-Binding Protein UgpB. ACS Chem. Biol. 2019, 14 (9), 1879–1887. https://doi.org/10.1021/acschembio.9b00204.

(11) Siddiqui, N.; Zwetsloot, A. J.; Bachmann, A.; Roth, D.; Hussain, H.; Brandt, J.; Kaverina, I.; Straube, A. PTPN21 and Hook3 Relieve KIF1C Autoinhibition and Activate Intracellular Transport. Nat Commun 2019, 10 (1), 1–16. https://doi.org/10.1038/s41467-019-10644-9.

(12) Pandey, R.; Abel, S.; Boucher, M.; Wall, R. J.; Zeeshan, M.; Rea, E.; Freville, A.; Lu, X. M.; Brady, D.; Daniel, E.; Stanway, R. R.; Wheatley, S.; Batugedara, G.; Hollin, T.; Bottrill, A. R.; Gupta, D.; Holder, A. A.; Roch, K. G. L.; Tewari, R. Plasmodium Condensin Core Subunits (SMC2/SMC4) Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission. bioRxiv 2019, 674028. https://doi.org/10.1101/674028.

(13) Guy, C. S.; Gibson, M. I.; Fullam, E. Targeting Extracellular Glycans: Tuning Multimeric Boronic Acids for Pathogen-Selective Killing of Mycobacterium Tuberculosis. Chem. Sci. 2019, 10 (23), 5935–5942. https://doi.org/10.1039/C9SC00415G.

(14) Jacomin, A.-C.; Petridi, S.; DiMonaco, M.; Jain, A.; Bhujabal, Z.; Mulakkal, N.; Palara, A.; Powell, E. L.; Chung, B.; Zampronio, C. G.; Jones, A.; Cameron, A.; Johansen, T.; Nezis, I. P. Atg8a Interacts with Transcription Factor Sequoia to Control the Expression of Autophagy Genes in Drosophila. bioRxiv 2019, 611731. https://doi.org/10.1101/611731.

(15) Tchoupa, A. K.; Jones, R. A.; Kuroki, A.; Alam, M. T.; Perrier, S.; Chen, Y.; Unnikrishnan, M. The Type VII Secretion System Protects Staphylococcus Aureus against Antimicrobial Host Fatty Acids. bioRxiv 2019, 572172. https://doi.org/10.1101/572172.

(16) Syed, J.; Palani, S.; Clarke, S. T.; Asad, Z.; Bottrill, A. R.; Jones, A. M. E.; Sampath, K.; Balasubramanian, M. K. Expanding the Zebrafish Genetic Code through Site-Specific Introduction of Azido-Lysine, Bicyclononyne-Lysine, and Diazirine-Lysine. International Journal of Molecular Sciences 2019, 20 (10), 2577. https://doi.org/10.3390/ijms20102577.

(17) Kröber, E.; Schäfer, H. Identification of Proteins and Genes Expressed by Methylophaga Thiooxydans During Growth on Dimethylsulfide and Their Presence in Other Members of the Genus. Front. Microbiol. 2019, 10. https://doi.org/10.3389/fmicb.2019.01132.

2018

(18) Siddiqui, N.; Bachmann, A.; Zwetsloot, A. J.; Hussain, H.; Roth, D.; Kaverina, I.; Straube, A. Activation of Intracellular Transport by Relieving KIF1C Autoinhibition. bioRxiv 2018, 488049. https://doi.org/10.1101/488049.

(19) Goodman, J. K.; Zampronio, C. G.; Jones, A. M. E.; Hernandez-Fernaud, J. R. Updates of the In-Gel Digestion Method for Protein Analysis by Mass Spectrometry. Proteomics 2018, 18 (23), e1800236. https://doi.org/10.1002/pmic.201800236.

(20) Apta-Smith, M. J.; Hernandez-Fernaud, J. R.; Bowman, A. J. Evidence for the Nuclear Import of Histones H3.1 and H4 as Monomers. EMBO J. 2018, 37 (19). https://doi.org/10.15252/embj.201798714.

(21) Pilkington, E. H.; Gustafsson, O. J. R.; Xing, Y.; Hernandez-Fernaud, J.; Zampronio, C.; Kakinen, A.; Faridi, A.; Ding, F.; Wilson, P.; Ke, P. C.; Davis, T. P. Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide. ACS Nano 2018, 12 (6), 6066–6078. https://doi.org/10.1021/acsnano.8b02346.

(22) Lin, M.; Egertová, M.; Zampronio, C. G.; Jones, A. M.; Elphick, M. R. Functional Characterization of a Second Pedal Peptide/Orcokinin-Type Neuropeptide Signaling System in the Starfish Asterias Rubens. J. Comp. Neurol. 2018, 526 (5), 858–876. https://doi.org/10.1002/cne.24371.

(23) Hatano, T.; Alioto, S.; Roscioli, E.; Palani, S.; Clarke, S. T.; Kamnev, A.; Hernandez-Fernaud, J. R.; Sivashanmugam, L.; Chapa-Y-Lazo, B.; Jones, A. M. E.; Robinson, R. C.; Sampath, K.; Mishima, M.; McAinsh, A. D.; Goode, B. L.; Balasubramanian, M. K. Rapid Production of Pure Recombinant Actin Isoforms in Pichia Pastoris. J. Cell. Sci. 2018, 131 (8). https://doi.org/10.1242/jcs.213827.

(24) Kaur, A.; Hernandez-Fernaud, J. R.; Aguilo-Ferretjans, M. D. M.; Wellington, E. M.; Christie-Oleza, J. A. 100 Days of Marine Synechococcus-Ruegeria Pomeroyi Interaction: A Detailed Analysis of the Exoproteome. Environ. Microbiol. 2018, 20 (2), 785–799. https://doi.org/10.1111/1462-2920.14012.

(25) Cai, W.; Kim, C.-H.; Go, H.-J.; Egertová, M.; Zampronio, C. G.; Jones, A. M.; Park, N. G.; Elphick, M. R. Biochemical, Anatomical, and Pharmacological Characterization of Calcitonin-Type Neuropeptides in Starfish: Discovery of an Ancient Role as Muscle Relaxants. Front Neurosci 2018, 12, 382. https://doi.org/10.3389/fnins.2018.00382.

2017

(26) Lin, M.; Egertová, M.; Zampronio, C. G.; Jones, A. M.; Elphick, M. R. Pedal Peptide/Orcokinin-Type Neuropeptide Signaling in a Deuterostome: The Anatomy and Pharmacology of Starfish Myorelaxant Peptide in Asterias Rubens. J. Comp. Neurol. 2017, 525 (18), 3890–3917. https://doi.org/10.1002/cne.24309.

(27) Tyrakis, P. A.; Yurkovich, M. E.; Sciacovelli, M.; Papachristou, E. K.; Bridges, H. R.; Gaude, E.; Schreiner, A.; D’Santos, C.; Hirst, J.; Hernandez-Fernaud, J.; Springett, R.; Griffiths, J. R.; Frezza, C. Fumarate Hydratase Loss Causes Combined Respiratory Chain Defects. Cell Rep 2017, 21 (4), 1036–1047. https://doi.org/10.1016/j.celrep.2017.09.092.

(28) Narvaez, A. J.; Ber, S.; Crooks, A.; Emery, A.; Hardwick, B.; Guarino Almeida, E.; Huggins, D. J.; Perera, D.; Roberts-Thomson, M.; Azzarelli, R.; Hood, F. E.; Prior, I. A.; Walker, D. W.; Boyce, R.; Boyle, R. G.; Barker, S. P.; Torrance, C. J.; McKenzie, G. J.; Venkitaraman, A. R. Modulating Protein-Protein Interactions of the Mitotic Polo-like Kinases to Target Mutant KRAS. Cell Chem Biol 2017, 24 (8), 1017-1028.e7. https://doi.org/10.1016/j.chembiol.2017.07.009.

(29) Christie-Oleza, J. A.; Sousoni, D.; Lloyd, M.; Armengaud, J.; Scanlan, D. J. Nutrient Recycling Facilitates Long-Term Stability of Marine Microbial Phototroph-Heterotroph Interactions. Nat Microbiol 2017, 2, 17100. https://doi.org/10.1038/nmicrobiol.2017.100.

(30) Lin, M.; Mita, M.; Egertová, M.; Zampronio, C. G.; Jones, A. M.; Elphick, M. R. Cellular Localization of Relaxin-like Gonad-Stimulating Peptide Expression in Asterias Rubens: New Insights into Neurohormonal Control of Spawning in Starfish. J. Comp. Neurol. 2017, 525 (7), 1599–1617. https://doi.org/10.1002/cne.24141.

(31) Lidbury, I. D. E. A.; Fraser, T.; Murphy, A. R. J.; Scanlan, D. J.; Bending, G. D.; Jones, A. M. E.; Moore, J. D.; Goodall, A.; Tibbett, M.; Hammond, J. P.; Wellington, E. M. H. The “known” Genetic Potential for Microbial Communities to Degrade Organic Phosphorus Is Reduced in Low-PH Soils. Microbiologyopen 2017, 6 (4). https://doi.org/10.1002/mbo3.474.

(32) Lidbury, I. D. E. A.; Murphy, A. R. J.; Fraser, T. D.; Bending, G. D.; Jones, A. M. E.; Moore, J. D.; Goodall, A.; Tibbett, M.; Hammond, J. P.; Scanlan, D. J.; Wellington, E. M. H. Identification of Extracellular Glycerophosphodiesterases in Pseudomonas and Their Role in Soil Organic Phosphorus Remineralisation. Sci Rep 2017, 7 (1), 2179. https://doi.org/10.1038/s41598-017-02327-6.

2016

(33) Üstün, S.; Sheikh, A.; Gimenez-Ibanez, S.; Jones, A.; Ntoukakis, V.; Börnke, F. The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors. Plant Physiol. 2016, 172 (3), 1941–1958. https://doi.org/10.1104/pp.16.00808.

(34) Lidbury, I. D. E. A.; Murphy, A. R. J.; Scanlan, D. J.; Bending, G. D.; Jones, A. M. E.; Moore, J. D.; Goodall, A.; Hammond, J. P.; Wellington, E. M. H. Comparative Genomic, Proteomic and Exoproteomic Analyses of Three Pseudomonas Strains Reveals Novel Insights into the Phosphorus Scavenging Capabilities of Soil Bacteria. Environ. Microbiol. 2016, 18 (10), 3535–3549. https://doi.org/10.1111/1462-2920.13390.

Contact us

Lab C115,
School of Life Sciences,
Gibbet Hill Road,
University of Warwick,
CV4 7AL

Tel: 024 7615 0439
proteomics@warwick.ac.uk


People

Alex Jones (Director)

Andrew Bottrill (Manager)

Cleidi Zampronio (Senior Technician)


Learn More

(PDF Document) What we do (Flyer)

(PDF Document) What we do (Poster)

(PDF Document) Proteomics Concepts Poster


Training

University of Warwick users can learn more about the service, and undertake training modules via the Proteomics Moodle


"How to?" Video Guides

Video Introduction to the lab

Video protocol: Gel Digest

Video protocol: In Solution Digest

Video protocol: Stage Tip


Reading Resources

Essential background reading for those wanting a deeper understanding of Proteomics and Mass Spectrometry (library subscriptions required):

Proteomics: Methods and Protocols

Mass Spectrometry Data Analysis in Proteomics

Introduction to Proteomics: Principles and Applications

Mass Spectrometry: a Text Book