The Advanced Proteomics Facility provides access to the latest proteomics tools, specifically cutting edge mass spectrometry. It is available to researchers in the South Parks Road science area and to external commercial users.
We have experience in protein identification, quantitative mass spectrometry (SILAC, label-free, dimethyl labelling, TMT) and characterisation methods for a range of post-translational modifications.
The facility is equipped with a wide range of mass spectrometry instrumentation, sample preparation technologies and data analysis software.
Mass Spectrometers and Sample Preparation Equipment
- LTQ XL (tens of proteins identified per hour). Fixed setup for rapid analysis, most likely one sample every 35 to 45 minutes.
- Orbitrap Classic (hundreds of proteins identified per hour) is more than capable of protein identification and is ideal for IP experiments. Fixed setup for rapid analysis, most likely one sample every 30 to 60 minutes.
- Orbitrap Elite and a number of QExactives (thousands of proteins identified per hour). These instruments are optimised for state of the art analyses. Single analysis will be anything from 45 minutes to 4 hours.
- HPLC systems to allow fractionation of samples to allow comprehensive proteome coverage.
- Mascot Server (protein identification).
- CPFP Server (protein identification, label-free quantitation and post translational modifications).
- Proteome Discover 1.4/2.0 (protein identification and quantitation).
- PEAKS (de novo sequencing and post translational modifications).
- Skyline and Pinpoint (targeted quantitation).
- Progenesis label free quantitation software.
- MaxQuant protein identification and quantification software.
- A number of open source software packages.
Through our service provision and collaboration with researchers, we aim to continually develop and improve the advanced tools available for proteomics.
New Biochemistry building, rooms 30-014 and 00-073.
For further information regarding use of the facility, contact the facility director, Prof. Shabaz Mohammed (firstname.lastname@example.org or Svenja Hester (email@example.com) or by phone on 01865 613220.
Please always contact us prior to commencing a new project in order to discuss project aims and requirements.
The sample drop-off (appointment necessary) point is at the side door closest to South Parks Road.
We have a strong track record of working with biotechnology and pharmaceutical companies. If you are a commercial organisation and are interested in the services or expertise of the Advanced Proteomics Facility, we would encourage you to contact Sally Sheard (firstname.lastname@example.org) of Oxford University Consulting to discuss how we may be able to help you.
Mascot Server is a commercial search engine which uses mass spectrometry data to identify proteins from primary sequence databases. The facility shares access to a multi-node Mascot Server cluster hosted by the Computational Biology Research Group (CBRG).
The Central Proteomics Facilities Pipeline allows simultaneous searching and result combination from multiple search engines for statistical analysis of results. It includes tools for quantitative proteomics (LIBRA for iTRAQ/TMT, and ASAP ratio for SILAC) and semi-quantitative label-free analysis (SINQ).
Access to these resources requires a CBRG account. If you wish to access these resources, please contact the facility; you may then apply for a proteomics-sponsored CBRG account using the links at the bottom of this page (from within the Oxford University network).
de Graaf EL, Kaplon J, Mohammed S, Vereijken LA, Duarte DP, Redondo Gallego L, Heck AJ, Peeper DS, Altelaar AF.
J Proteome Res. 2015 Jul 2;14(7):2906-14.
Binai NA, Marino F, Soendergaard P, Bache N, Mohammed S, Heck AJ.
J Proteome Res. 2015 Feb 6;14(2):977-85.
Low TY, Peng M, Magliozzi R, Mohammed S, Guardavaccaro D, Heck AJ.
Sci Signal. 2014 Dec 16;7(356):rs8.
Akiyoshi B and Gull K.
Cell 2014 156: 1247-1258.
Howden AJ, Geoghegan V, Katsch K, Efstathiou G, Bhushan B, Boutureira O, Thomas B, Trudgian DC, Kessler BM, Dieterich DC, Davis BG, Acuto O.
Nat Methods. 2013 10: 343-346.
Low TY, van Heesch S, van den Toorn H, Giansanti P, Cristobal A, Toonen P, Schafer S, Hübner N, van Breukelen B, Mohammed S, Cuppen E, Heck AJ, Guryev V.
Cell Rep. 2013 Dec 12;5(5):1469-78
Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.
Nat Methods. 2013 Aug;10(8):730-6
Uhlmann T, Geoghegan V, Thomas B, Ridlova G, Trudgian DC, Acuto O.
Mol Cell Prot. 2013 11: 1489-1499