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Proteomics

CIMR proteomics facility

The CIMR Proteomics Facility (CIPF) was established to allow researchers access to cutting-edge proteomics technologies. The facility focuses on peptide analysis by LC–MSMS and we have a number of instruments capable of supporting a variety of different experiments. We routinely perform work ranging from SDS-PAGE band analysis to quantitative proteomics but we would encourage researchers to contact us about any projects they are considering and we are happy to discuss collaborating on the application or development of new methods.

CIPF is overseen by a steering committee comprising researchers from CIMR and IMS. Members of the committee include Paul Lehner (chair), Robin Antrobus, Pawan Gulati, Richard Kay, Margaret Robinson, David Rubinsztein, David Ron, Michael Weekes, David Cheesman and Yagnesh Umrania.

The CIPF is situated on level 5 of CIMR.

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Instruments

CIPF has three Orbitrap mass spectrometers with nanoflow ultra-high pressure LCs configured for peptide and protein analysis. They have been optimised for certain applications but we will endeavour to accommodate most requests wherever possible.

Thermo Orbitrap Fusion Lumos with ETD and Dionex RSLC 3000 nano UPLC. The unique geometry of this instrument means it can generate data from TMT labelled samples without suffering ratio compression. The high sensitivity and range of fragmentation methods, including ETD, make it ideal for PTM analysis.

Thermo Orbitrap Q Exactive Plus with EASY-spray source and Dionex RSLC 3000 nano UPLC. This instrument is awaiting installation and will be principally used for medium to high complexity peptide samples but because the instrument is equipped with protein and high resolution mode it can be used for analysing intact proteins.

Thermo Orbitrap Q Exactive with EASY-spray source and Dionex RSLC 3000 nano UPLC. This instrument is used to identify proteins in low to medium complexity samples. The EASY-spray source accommodates a range of columns up to 50cm in length which support long gradients without an appreciable loss in chromatographic resolution

Off-line Dionex RS 3000 UHPLC. This is used to pre-fractionate complex samples and is currently configured to run high-pH reverse phase.

Bioinformatics

The facility has a dedicated bioinformatician who can advise on all aspects of data processing and analysis and help with tasks such as submitting data to public repositories.

Recent papers:

TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway. Neerincx A, Hermann C, Antrobus R, van Hateren A, Cao H, Trautwein N, Stevanović S, Elliott T, Deane JE, Boyle LH. Elife. 2017 Apr 20;6. pii: e23049. doi: 10.7554/eLife.23049. PMID:28425917

VAMP3/Syb and YKT6 are required for the fusion of constitutive secretory carriers with the plasma membrane. Gordon DE, Chia J, Jayawardena K, Antrobus R, Bard F, Peden AA. PLoS Genet. 2017 Apr 12;13(4):e1006698. doi: 10.1371/journal.pgen.1006698. eCollection 2017 Apr. PMID:28403141

Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity. Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG. J Exp Med. 2017 Apr 3;214(4):1111-1128. doi: 10.1084/jem.20161382. Epub 2017 Mar 28. PMID:28351984

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease. Connor TM, Hoer S, Mallett A, Gale DP, Gomez-Duran A, Posse V, Antrobus R, Moreno P, Sciacovelli M, Frezza C, Duff J, Sheerin NS, Sayer JA, Ashcroft M, Wiesener MS, Hudson G, Gustafsson CM, Chinnery PF, Maxwell PH. PLoS Genet. 2017 Mar 7;13(3):e1006620. doi: 10.1371/journal.pgen.1006620. eCollection 2017 Mar. PMID:28267784

Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW. Elife. 2017 Feb 10;6. pii: e22206. doi: 10.7554/eLife.22206. PMID:28186488

Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants. Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ. Elife. 2016 Sep 30;5. pii: e18296. doi: 10.7554/eLife.18296. PMID:27690223

ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex. Timms RT, Tchasovnikarova IA, Antrobus R, Dougan G, Lehner PJ. Cell Rep. 2016 Oct 11;17(3):653-659. doi: 10.1016/j.celrep.2016.09.050. PMID:27732843

 

Staff

Robin Antrobus

Dr Robin Antrobus

CIMR Level 5.9 lab

contact: pra29@cam.ac.uk

01223 763361

 

Dr Kamburpola Jayawardena (Jay)

CIMR Level 5.9 lab

contact: kgij2@cam.ac.uk

01223 763361

 

Dr Yagnesh Umrania

CIMR Level 5.9 lab

contact: yu206@cam.ac.uk

01223 763361