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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. All proteomics techniques are routine and are offered to both internal and external users.

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.

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

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

The Central Proteomics Facility and staff should be acknowledged in publications where data produced by the facility is included in a publication. Acknowldedgements are important to the continued funding and development of the facility. Where substantial experimental design, training or data interpretation expertise has been provided by the staff of the CPF co-authorship may be warranted. Staff can provide information on how to acknowledge the facility

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

This provides open access to the Central Proteomics Facility Pipeline (CPFP) to any users. The CPFP is hosted on an Amazon Cloud in this case and doesn't require a user account to access. CPFP accepts .mgf, .mzML and .mzXML file formats, uses multiple search engines to increase the number of protein identifications, calculates user defined False Discovery Rates (FDR) and supports labelled and label free quantitation strategies.

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.

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