Proteomics

Overview

The proteomics service was created in June 2015 to provide support, expertise and advice to the scientist of the Oxford Institute for Radiation Oncology and the Department of Oncology on how to use proteomics workflows to better understand and characterise their biological models.

The main focus of proteomics is to study proteins on a large scale. Proteins are vital to living organisms and their multi-functional characteristics act as potential targets for drug therapies. Therefore, proteomics can be used for biomarker and target discovery, drug profiling and target validation.

To identify and characterise proteins, proteomics relies mainly on liquid chromatography technology coupled to mass spectrometry (LC-MS/MS). We have access to state of the art mass spectrometers at the Discovery Proteomics Facility in the Target Discovery Institute (Oxford; headed by Roman Fischer and led by Professor Benedikt Kessler) which includes Ultimate 3000-Ultra High Performance Liquid Chromatography (UHPLC) systems connected to QExactive-classic, QExactive-HF and Orbitrap Fusion-Lumos tribid (ThermoFisher).

Applications

• Protein identification from gel-bands
• Global proteome profiling (bottom-up proteomics), deep proteome
• Protein interactions i.e. immunoprecipitation / pull downs for binding partners study; DNA protein crosslinks; proteins bound to nascent DNA - iPOND
• Post-translational modifications (PTM) i.e. phosphorylation, ubiquitination, acetylation, SUMOylation

Data Analysis

We have access to multiple data analysis packages: MASCOT, PEAKS, Andromeda for data search analysis and Progenesis QI, Proteome DiscovererTM, PEAKS, MaxQuant for generating quantitative datasets, label or label free.