Proteomics

Introduction

Head: Sara Zanivan

Zanivan Sara 032

The Advanced Technology Proteomic Facility develops MS-based platforms and works together with researchers to provide a new level of understanding in tumour biology. We have developed pipelines for the analysis of a wide range of biological samples, from single proteins to the complete proteome of cells, organoids and tissues.

Our group has recently developed new methods to study cysteine oxidation (van der Reest, Lilla et al. Nature Communications 2018), cell secretomes (Hernandez-Fernaud, Ruengeler et al. Nature Communications 2017) and transmembrane receptor trafficking (Diaz-Vera et al. Journal Cell Science 2017).

We have three MS instruments, each coupled to an Easy-nLC system:

  • Orbitrap Fusion Lumos
  • Q-Exactive HF
  • LTQ Orbitrap Elite

We use a variety of methods for protein digestion:

  • filter-aided sample preparation (FASP)
  • in-gel
  • in-solution

for proteome and post-translational modifications analysis:

  • high-pH reversed-phase chromatography peptide fractionation
  • gel-based protein fractionation

to accurately measure proteins and peptides:

  • Label-free
  • TMT
  • SILAC
  • Dimethyl
  • Isotope-labelled IAA (for cysteine oxidation)

We analyse our MS data with

  • MaxQuant computational platform
  • Progenesis and Skyline for the analysis of pRM data
  • Mascot for single protein identification
  • Perseus and Scaffold for data compilation, analysis and dissemination.

Link to Sara Zanivan's research page

Recent Publications

2018

Dandoulaki M, Petsalaki E, Sumpton D, Zanivan S, Zachos G. Src activation by Chk1 promotes actin patch formation and prevents chromatin bridge breakage in cytokinesis. J Cell Biol 2018. doi: 10.1083/jcb.201802102

Fort L, Batista JM, Thomason PA, Spence HJ, Whitelaw JA, Tweedy L, Greaves J, Martin KJ, Anderson KI, Brown P, Lilla S, Neilson MP, Tafelmeyer P, Zanivan S, Ismail S, Bryant DM, Tomkinson NCO, Chamberlain LH, Mastick GS, Insall RH, Machesky LM. Fam49/CYRI interacts with Rac1 and locally suppresses protrusions. Nat Cell Biol. 2018 Oct; 20(10): 1159-71. doi: 10.1038/s41556-018-0198-9

Port J, Muthalagu N, Raja M, Ceteci F, Monteverde T, Kruspig B, Hedley A, Kalna G, Lilla S, Neilson L, Brucoli M, Gyuraszova K, Tait-Mulder J, Mezna M, Svambaryte S, Bryson A, Sumpton D, McVie A, Nixon C, Drysdale M, Esumi H, Murray GI, Sansom OJ, Zanivan SR, Murphy DJ. Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress. Cancer Discov. 2018 May; 8(5): 632-47. doi: 10.1158/2159-8290.CD-17-0533

Unbekandt M, Belshaw S, Bower J, Clarke M, Cordes J, Crighton D, Croft DR, Drysdale MJ, Garnett MJ, Gill K, Gray C, Greenhalgh DA, Hall JA, Konczal J, Lilla S, McArthur D, McConnell P, McDonald L, McGarry L, McKinnon H. Discovery of potent and selective MRCK inhibitors with therapeutic effect on skin cancer. Cancer Res. 2018 Jan 30. pii: canres.2870.2017. doi: 10.1158/0008-5472.CAN-17-2870 [Epub ahead of print]

van der Reest J, Lilla S, Zheng L, Zanivan S, Gottlieb E. Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress. Nat Commun. 2018 Apr 20;9(1):1581. doi: 10.1038/s41467-018-04003-3

2017

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

2016

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

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

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

2015

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

Group Members

Proteomics lab Y70 Sept 2018

Head

Sara Zanivan

Senior Scientific Officers

Kelly Hodge
Sergio Lilla

Bioinformatician

Grigorios Koulouras

 

Research

At the bench 3 160

Read more about the Research Groups working at the Beatson Institute.

More

Seminars

Running a gel 154

Find out more about our seminars including our Distinguished Seminar Programme.

More