CIMR–Institute of Metabolic Science proteomics facility
The CIMR–IMS Proteomics Facility (CIPF) was established to allow researchers at both institutes 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, 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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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.
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.
NOTCH1 mediates a switch between two distinct secretomes during senescence. Hoare M, Ito Y, Kang TW, Weekes MP, Matheson NJ, Patten DA, Shetty S, Parry AJ, Menon S, Salama R, Antrobus R, Tomimatsu K, Howat W, Lehner PJ, Zender L, Narita M. Nat Cell Biol. 2016 Aug. PMID:27525720
Plasma Membrane Profiling Reveals Upregulation of ABCA1 by Infected Macrophages Leading to Restriction of Mycobacterial Growth. Long J, Basu Roy R, Zhang YJ, Antrobus R, Du Y, Smith DL, Weekes MP, Javid B. Front Microbiol. 2016 Jul. PMID: 27462310
SQSTM1/p62 mediates crosstalk between autophagy and the UPS in DNA repair. Hewitt G, Carroll B, Sarallah R, Correia-Melo C, Ogrodnik M, Nelson G, Otten EG, Manni D, Antrobus R, Morgan BA, von Zglinicki T, Jurk D, Seluanov A, Gorbunova V, Johansen T, Passos JF, Korolchuk VI. Autophagy. 2016 Jul. PMID: 27391408
Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens. Timms RT, Menzies SA, Tchasovnikarova IA, Christensen LC, Williamson JC, Antrobus R, Dougan G, Ellgaard L, Lehner PJ. Nat Commun. 2016 Jun. PMID: 27283361
Human Cytomegalovirus Infection Upregulates the Mitochondrial Transcription and Translation Machineries. Karniely S, Weekes MP, Antrobus R, Rorbach J, van Haute L, Umrania Y, Smith DL, Stanton RJ, Minczuk M, Lehner PJ, Sinclair JH. MBio. 2016 Mar. PMID: 27025248
AMPylation matches BiP activity to client protein load in the endoplasmic reticulum. Preissler S, Rato C, Chen R, Antrobus R, Ding S, Fearnley IM, Ron D. Elife. 2015 Dec. PMID: 26673894
Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Matheson NJ, Sumner J, Wals K, Rapiteanu R, Weekes MP, Vigan R, Weinelt J, Schindler M, Antrobus R, Costa AS, Frezza C, Clish CB, Neil SJ, Lehner PJ. Cell Host Microbe. 2015 Oct. PMID: 26439863