“Data intersections.” Inspired by Miró and Piet Mondrian, Courtesy of Luis Schachner

The Proteomics core facility is a high throughput protein analysis laboratory. We focus on protein identification and quantification, structural analysis (post-translational modifications) and protein-protein interactions. We strive to increase the scope, sensitivity and throughput of proteomics technologies and their application to cancer related questions.

The facility helps design experimental strategies.  We implement and validate previously developed proteomic workflows to profile proteins from diverse biological samples as well as developing entirely new, bespoke methods and assays when required.

Instrumentation includes three orbitrap mass spectrometers; a QExactive (Thermo), QExactive-HF (Thermo) and Fusion Lumos Orbitrap (Thermo) mass spectrometers all of which are configured with Dionex Ultimate 3000 RSLC nano-HPLC systems. Two off-line separation platforms complement these systems (both Dionex Ultimate 3000 capHPLC systems) for multidimensional chromatography at the protein and peptide level.   Data analysis is carried out by core facility staff and/or using statistical software packages supported by the Bioinformatics facility. In addition to proteomic applications we exploit the high resolution and mass accuracy of both Orbitraps to quantify known and discover novel modified nucleosides from genomic DNA.

The core focuses and specialises in using stable isotopic (Tandem Mass Tags) and label free strategies (LFQ & DIA) for the relative quantification of protein expression levels and enrichment within protein complexes; currently our multiplexing capacity extends to 18 samples per run. We also develop and run PRM (parallel reaction monitoring assays for targeted quantification of panels of proteins.

Specific methods and areas of interest:

Protein profiling of complex biological samples, e.g. tissue and cultured cell extracts

  • Protein Profiling by nanoLC/MS
  • Multidimensional protein/peptide fractionation by capLC and/or geLC

Targeted protein identification by nanoLC/MS/MS

  • Multiple/Parallel reaction monitoring (MRM/PRM analysis)

Protein-protein interactions

  • Identification of protein-protein interactions from X-linking mass spectrometry
  • RIME (rapid immunoprecipitation and mass spectrometry of endogenous protein complexes)
  • qPLEX RIME (TMT-based quantitation of RIME analyses)

Relative quantitation

  • SILAC – stable isotope labelling of amino acids in cell culture
  • Isobaric tagging: TMT (tandem mass tags) up to 18 samples
  • Label free quantification
  • Data Independent Acquisition (DIA)