Proteomics core facility

The Proteomics core facility focuses on the systematic study of proteins, particularly their structures, interactions and expression levels. The facility is equipped with state-of-the-art instrumentation for CRI researchers requiring access to proteomics technology and expertise.

Proteomics applications can help obtain a better understanding of the processes that contribute to the development of cancer. The facility has been designed to apply the latest proteomic methods to key areas of cancer research: the definition and comparison of protein profiles in normal and pathological samples, the identification of disease mechanisms at a molecular (protein) level, the identification of temporal patterns of expression, and to help define the function of uncharacterised proteins.

The Proteomics core facility provides help in designing experimental strategies and implements and validates previously developed proteomic workflows to profile proteins from diverse biological samples. We also aim to modify or develop entirely new methods and assays when warranted. In addition, we have bioinformatics support for data management and analysis as well as software development.

The facility has already been well equipped with state-of-the-art analytical instrumentation for proteomic studies, including the latest orbitrap mass spectrometer, the LTQ Velos Orbitrap (Thermo), which has been configured to a Dionex Ultimate 3000 RSLC nanoHPLC system (Figure 1). In addition an Agilent 6520 QToF with ChIP cube technology was installed in 2010. The mass spectrometers are supported by off-line chromatography platforms: two Dionex Ultimate 3000 capHPLC systems for multidimensional chromatography at the protein and peptide level. These are supported by 1D and 2D gel electrophoresis systems as well as a GE Healthcare Typhoon Trio+ imager available in the equipment park run by Jane Gray. Data analysis is supported by an array of bioinformatics and statistical analysis tools.

Dionex Ultimate 3000 RSLC nanoHPLC system (Proteomics core facility report 2010; figure 1)
Figure 1
Dionex Ultimate 3000 RSLC nanoHPLC system.

Specific methods and areas of interest include:

  • Protein profiling of complex biological samples, e.g. serum, tissue, cell extracts:
    • Profiling by nanoLC/MS;
    • Multidimensional protein/peptide fractionation by capLC and/or geLC.
  • Targeted protein identification by nanoLC/MS/MS:
    • Coomassie and silver stained gel bands of purified proteins
    • In solution digestion of purified proteins.
  • Identification of protein and peptide modifications:
    • Phosphorylation sites;
    • Protein modifications such as acetylation and methylation;
    • Coomassie stain only, purified proteins.
  • Relative quantitation by nanoLC/MS/MS:
    • SILAC - stable isotope labeling of amino acids in cell culture;
    • ITRAQ - an isobaric peptide tagging system.

Facility manager
Clive D'Santos is the head of the Proteomics core facility.