Protein Identification and Quantification

The Protein Identification and Quantification capability uses mass spectrometry to detect, identify and quantify protein biomarkers in complex biological samples, for example, to distinguish proteins on cancer cells from those on healthy cells. It also offers quality control services for recombinant proteins and peptides.

Mass spectrometry is used across a range of science disciplines to characterise proteins of interest from all organisms (e.g. viruses, bacteria, fungi, plants and animals), and as an analytical tool with many applications in pharmaceutical, biomedical, agricultural and environmental research, to name a few.


This capability is home to a range of instrumentation listed here

Thermo Scientific Orbitrap Eclipse™ Tribrid™ Mass Spectrometer (with ETD and FAIMS) - represents the latest ‘top of the line’ technology in liquid chromatography mass spectrometry. It features important advancements that offer unprecedented depth of analysis, especially for highly complex, low abundance, or difficult-to-analyse biological samples. It will enable identification and quantification of proteins in mixtures at much higher resolution than existing instrumentation in the facility, even enabling the characterisation of proteins within a single cell.

Thermo Scientific Q-Exactive HF with Ultimate 3000 RSLCnano - for protein, peptide and small molecule applications, it takes identification and quantitation to a new level with respect to speed, sensitivity and resolution.

Thermo Scientific LTQ Orbitrap Elite ETD Mass Spectrometer - provides excellent mass accuracy and resolution of proteins in high complexity samples (such as cell lysates, plasma and tissue homogenates) and the characterization of posttranslational modifications (such as phosphorylation and glycosylation).

Thermo Scientific TSQ Vantage Extended Mass Range Mass Spectrometer - enables accurate quantitative analysis of targeted peptides and small molecules from complex mixtures, such as serum, tissue homogenates, cell lysates and other biological fluids/preparations.

Bruker Daltonics Ultraflex III MALDI-TOF/TOF Mass Spectrometer - for quality control experiments to determine the mass of recombinant proteins, purified natural proteins, and commercially-prepared proteins and synthetic peptides.

Bruker Daltonics micrOTOF- Q Mass Spectrometer – used to determine accurate mass of proteins and small molecules in solution.

Dionex UltiMate 3000 Intelligent LC System - enables the separation of complex mixtures of proteins and biomolecules (such as cell lysates, plasma and tissue homogenates).

Proteineer Fc MALDI Spotting Robot - performs high throughput sample preparation for MALDI-TOF/TOF experiments by spotting samples with MALDI matrices to facilitate ionisation from solid to gas phase.

Agilent Technologies 3100 OFFGEL Fractionator – allows for the separation of proteins in complex mixtures based on isoelectric point for subsequent analysis by mass spectrometry.

Proteineer Gel Spot Picking Robot - enables the selection, excision and extraction of a gel band or spot of interest for subsequent mass spectrometry analysis.


There is a broad range of applications that this capability can assist you with including:

  • Accurate mass determination of purified proteins (e.g. over-expressed recombinant products)
  • Proteome profiling or protein parts list
  • Label-free quantification
  • Label-dependent quantification (e.g. SILAC)
  • Phosphoproteomics
  • Cross-linking mass spec

We provide advice on experimental design and methodology. Contact us to discuss your research applications.


There are a number of ways that you can access the services provided by this capability:

  1. Annual subscriptions for internal and external academic users:
    • Bronze (up to 50 samples per annum)
    • Silver (up to 100 samples per annum)
    • Gold (up to 230 samples per annum)
  2. Fee-for-service
  3. Research Contracts for bespoke projects

Contact Us

For more information and to discuss your requirements please email or contact a team member:

Dr Pierre Faou, Platform Service Manager

Dr Rohan Lowe, Senior Technical Officer

Dr Harinda Rajapaksha, Bioinformatician