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  3. Proteomics
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  2. Core Facilities
  3. Proteomics

Expert services for protein identification, quantification and post–translational modification profiling using next–generation mass spectrometry platforms.

Our team works and collaborates with research groups providing access to specialist mass spectrometry and proteomic equipment and expertise that enables: protein identification characterisation and quantification, post-translational modification profiling, and targeted analyses using next-generation mass spectrometry platforms.

We can help design experimental strategies, 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. We strive to increase the scope, sensitivity, and throughput of proteomics technologies and their application to cancer-related questions. 

The Core focuses and specialises in using stable isotopic labelling  strategies (Tandem Mass Tags) as well as label free methods (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.

Dr Clive D’Santos

Head of Proteomics

Areas of interest

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Data dependant and independent protein profiling

Ultra-deep profiling of complex biological samples including tissue and cultured cell extracts and biofluids

We use several analytical strategies to generate ultra-deep proteomes, the choice is sample dependent.

  • Multidimensional protein/peptide fractionation by high pH capLC  
  • Protein profiling by nanoLC/MS 
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Targeted protein identification

Multiple/Parallel reaction monitoring (MRM/PRM analysis) 

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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) 
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Relative quantitation

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

Equipment and analysis

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    Orbitrap Mass Spectrometers

    We have three orbitrap mass spectrometers; a QExactive-HF (Thermo), Fusion Lumos Orbitrap (Thermo) and an Orbitrap Ascend, all of which are configured with either a Dionex Ultimate 3000 RSLC or Vanquish neo nano-HPLC systems.

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    Off-line separation platforms

    We have two off-line separation platforms to compliment the mass spectrometers. These systems (both Dionex Ultimate 3000 capHPLC systems) for multidimensional chromatography at the protein and peptide level

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    Data analysis

    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.

Team members

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    Clive D'Santos

    Core Facility Manager

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    Valar Franklin

    Senior Scientific Associate

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    Eva Papachristou

    Principle Scientific Associate

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