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SILAC & quantitative proteomics
Absolute Quantitation

Dunn School | CPF (Headington) | CBRG | University of Oxford

Dunn School of Pathology

Central Proteomics Facility

Introduction - Oxford University Central Proteomics Service provides mass spectrometry and proteomics services to UK and international academic labs and biotech/pharma clients. One proteomics facility is located in the Sir William Dunn Pathology School where the antibiotic age was ushered in, while the other proteomics facility is located at the Welcome Trust Centre for Human Genetics in east Oxford.

Mass Spectrometry and Proteomics Services - The proteomics facility can provide access to advanced mass spectrometry and proteomics technologies enabling protein identification and quantitation using LCMSMS Orbitrap mass spectrometry in conjuction with techniques such as SILAC, iTRAQ, heavy-dimethyl labelling and label-free quantitation approaches.

Please email CPF - Pathology. We're happy to be contacted for advice and can offer help on proteomic based experimental design, training, data interpretation and grant writing.

New research projects involving the generation of proteomics data must be discussed with the Facility Director prior to commencement of the project. Note this also applies to existing users of the facility starting new projects. New users of the facility are requested to read the New User FAQ first.

post the gel band/s in microcentrifuge tubes at room temperature for proteomic mass spectrometry analysis and a hardcopy of the Sample Submission form to:
Dr. B Thomas
Central Proteomics Facility
Sir William Dunn Pathology School
Oxford University

Tel: +44(0)1865 275 557

Email: benjamin.thomas@path.ox.ac.uk

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 Central Proteomics Facility, we would encourage you to contact Dr Josef Walker of Oxford University Consulting to discuss how we may be able to help you.

Email: josef.walker@isis.ox.ac.uk

Telephone: +44 1865 280901

Publication Acknowledgements and Co-authorship

It is a condition of service that the Central Proteomics Facility and its staff be acknowledged in publications. Acknowldedgements are important to the continued funding and development of the facility. Where the contribution is significant (for example contributed to experimental design, conducted data analysis or provided training) please include the team member(s) that aided the research as named author(s).

As a general rule, routine protein gel band identification with a Mascot database search, where you interpret the data, does not require co-authorship. More advanced workflows, such as label-free quantitation (SINQ, MaxQuant, Progenesis LCMS), labelled quantitation (SILAC, iTRAQ/TMT, Dimethyl), post-translational modification identification with site localization require co-authorship. Please contact facility staff for more information.

We would appreciate any reference that is published to be emailed to proteomics@path.ox.ac.uk so that we can maintain an up to date list of publications which CPF have contributed towards.

Data Analysis and Software

Proteomics Facility Pipeline (CPFP) is now operational and available for proteomics data analysis. The pipeline can be accessed using your CBRG login. The CPFP provides multiple search engines for data analysis, statistical analysis of proteomics data (False Discovery Rates) and tools for quantitative proteomics (LIBRA for iTRAQ/TMT, and ASAP ratio for SILAC). The proteomics pipeline also includes tools for comparing protein abundance in samples using label free quantitation. Please contact the facility if you wish to use this computational proteomics resource.

Database search engine for identifying proteins.

Highly automated data analysis pipeline using multiple search engines (Mascot, OMSSA, x!tandem) with labelled and label free quantitation capabilities. Learn more

Software tool for providing biological insight and comparing, clustering, annotating and filtering complex proteomics datasets using Gene Ontology (GO) terms. learn more

basic proteomic protein identification workflow

proteomic protein quantitation workflow using Stable isotope Labelling be Amino Acids in Cell Cultyre (SILAC)

proteomics label free protein Quantitation workflows: Progenesis LCMS, MaxQuant label free and SINQ></td>

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Announcements -

  • December 2012: 2 new Thermo Q Exactive Orbitrap mass spectrometers are installed in the Central Proteomics Facility. The new instruments will rapidly identify and quantify thousands of proteins present in whole cell lysates and usher in an age where global protein expression profiling becomes fast, reliable and cheap.

What Proteomics Can Tell You - If you're working with proteins, proteomics can help you characterise them.

  • It can identify a single protein to several thousand proteins.

  • It can tell you which proteins are in a complex with your protein of interest.

  • It can identify and quantify posttranslational modifications.

  • It can quantify the difference in protein expression between two or more states.

  • It can check the molecular weight of your protein.

mass spectrometry, proteomics


Please contact us to see if we can help.

© Copyright 2007. All rights reserved. | Contact: CPF - Pathology