Advanced Proteomics Facility

 

The APF team have expertise in sample preparation, protein chemistry, mass spectrometry and bioinformatics.  The facility is equipped with a wide range of mass spectrometry instrumentation, HPLC fractionation systems, sample preparation technologies and data analysis software. We provide protein, protein complex, proteome identification as routine services. Often once identified the questions switch to how much is there and how is it regulated? So, we also have extensive experience in quantitative mass spectrometry and characterisation methods for a range of post-translational modifications, which aid regulation, such as phosphorylation, methylation and ubiquitylation.  The facility is also carrying out research and is constantly evolving introducing new technologies and services.

We can handle all the steps in an experiment from protein extraction out of a cell pellet/tissue biopsy to data analysis. However, we do encourage all to perform their own experiments and offer training courses that cover most aspects of a proteomics experiment. The facility is open to all Oxford researchers as well as external academic and commercial users.

Find out more at: http://www.proteomics.ox.ac.uk/ 

 

Please contact the new facility manager Marjorie Fournier marjorie.fournier@bioch.ox.ac.uk for any enquiries regarding usage of the facility and discussion of proteomics projects

 

Details of equipment used by the proteomics facility

 

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 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 for comprehensive proteome coverage.

Bioinformatics Software

  • Mascot Server (protein identification).
  • 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.

 

Contact and Sample Submission

Please see: https://intranet.bioch.ox.ac.uk/aspsite/services/proteomics - please note that this link will require an Oxford SSO login.

External Work

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 Ms Emma Packard (emma.packard@innovation.ox.ac.uk) of Oxford University Innovation to discuss how we may be able to help you.

 

Acknowledging the Facility in Publications tab text