The Proteomics group is developing and utilising various MS-based platforms for the analysis of a wide range of biological samples, from single proteins to complete/in-depth proteomes of cells or tissues. We work together with researchers to provide a new level of understanding in tumour biology.
Our group has three LC-MS systems: the LTQ Orbitrap Velos, LTQ Orbitrap Elite and newest Q-Exactive HF that are coupled to Easy-nLC systems. We use a variety of methods for protein digestion, including in-gel, in-solution and filter-aided sample preparation (FASP). For in-depth proteomics and post-translational modifications analysis, we separate proteins and peptides using gel-based protein fractionation or peptide fractionation by high pH reverse phase and strong anion exchange chromatography. In addition, we provide label-free and SILAC-based approaches for state-of-the-art quantitative analysis of proteins and post-translational modifications.
We perform MS data analysis using two platforms: a MaxQuant software package for highly accurate quantitative analysis and a Mascot server for protein identification. Moreover, we use Progenesis and Skyline for the analysis of pRM data. Finally, we use Perseus and Scaffold for data compilation, analysis and dissemination.
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Hernandez-Fernaud JR, Ruengeler E, Casazza A, Neilson LJ, Pulleine E, Santi A, Ismail S, Lilla S, Dhayade S, MacPherson IR, McNeish I, Ennis D, Ali H, Kugeratski FG, Al Khamici H, van den Biggelaar M, van den Berghe PV, Cloix C, McDonald L, Millan D, Hoyle A, Kuchnio A, Carmeliet P, Valenzuela SM, Blyth K, Yin H, Mazzone M, Norman JC, Zanivan S. Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity. Nat Commun. 2017 Feb 15;8:14206
McGarry DJ, Shchepinova MM, Lilla S, Hartley RC, Olson MF. A Cell-Permeable Biscyclooctyne As a Novel Probe for the Identification of Protein Sulfenic Acids. ACS Chem Biol. 2016 Dec 16;11(12):3300-3304
Frej AD, Clark J, Le Roy CI, Lilla S, Thomason PA, Otto GP, Churchill G, Insall RH, Claus SP, Hawkins P, Stephens L, Williams RS. The Inositol-3-Phosphate Synthase Biosynthetic Enzyme Has Distinct Catalytic and Metabolic Roles. Mol Cell Biol. 2016 May 2;36(10):1464-79
Clarke CJ, Berg TJ, Birch J, Ennis D, Mitchell L, Cloix C, Campbell A, Sumpton D, Nixon C, Campbell K, Bridgeman VL, Vermeulen PB, Foo S, Kostaras E, Jones JL, Haywood L, Pulleine E, Yin H, Strathdee D, Sansom O, Blyth K, McNeish I, Zanivan S, Reynolds AR, Norman JC. The Initiator Methionine tRNA Drives Secretion of Type II Collagen from Stromal Fibroblasts to Promote Tumor Growth and Angiogenesis. Curr Biol. 2016 Mar 21;26(6):755-65
Cameron JM, Gabrielsen M, Chim YH, Munro J, McGhee EJ, Sumpton D, Eaton P, Anderson KI, Yin H, Olson MF. Polarized Cell Motility Induces Hydrogen Peroxide to Inhibit Cofilin via Cysteine Oxidation. Curr Biol 25: 1520-5, 2015
Deschoemaeker S, Di Conza G, Lilla S, Martín-Pérez R, Mennerich D, Boon L, Hendrikx S, Maddocks OD, Marx C, Radhakrishnan P, Prenen H, Schneider M, Myllyharju J, Kietzmann T, Vousden KH, Zanivan S, Mazzone M. PHD1 regulates p53-mediated colorectal cancer chemoresistance. EMBO Mol Med 7: 1350-65, 2015
Ducommun S, Deak M, Sumpton D, Ford RJ, Núñez Galindo A, Kussmann M, Viollet B, Steinberg GR, Foretz M, Dayon L, Morrice NA, Sakamoto K.. Motif affinity and mass spectrometry proteomic approach for the discovery of cellular AMPK targets: Identification of mitochondrial fission factor as a new AMPK substrate. Cellular Signalling 27: 978-88, 2015
Vijayakumar V, Monypenny J, Chen XJ, Machesky LM, Lilla S, Thrasher AJ, Anton IM, Calle Y, Jones GE. Tyrosine phosphorylation of WIP releases bound WASP and impairs podosome assembly in macrophages. J Cell Sci 128: 251-65, 2015
Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, Johnson TI, Gaude E, King A, Leach JD, Edrada-Ebel R, Hedley A, Morrice NA, Kalna G, Blyth K, Ruppin E, Frezza C, Gottlieb E. Fumarate induces redox-dependent senescence by modifying glutathione metabolism. Nat Commun 6: 6001, 2015
Giovanny Rodriguez Blanco