Proteomics

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

Our team collaborates with research groups to provide access to specialist mass spectrometry and proteomics equipment and expertise. We support protein identification, characterisation and quantification, post-translational modification profiling, and targeted analyses using state-of-the-art 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 develop 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 (DDA and DIA) for the relative quantification of protein expression levels and enrichment within protein complexes. We also develop and run PRM (parallel reaction monitoring) assays for targeted quantification of defined panels of proteins.

Dr Clive D’Santos

Head of Proteomics

Proteomics help

We are open to collaborations with researchers from outside of the Institute, and would welcome the opportunity to discuss your project.

Please get in touch via our contact form on the Working with the Core Facilities page to explore the support we can provide.

Areas of interest

Full proteome profiling

We offer comprehensive full-proteome profiling to quantify thousands of proteins in a single experiment, providing an unbiased overview of global protein expression changes.

For examples of this technique in application, see:

Post-translational modifications (PTMs)

We provide comprehensive post-translational modification (PTM) analysis, including identification of phosphorylation, ubiquitination, and acetylation, with additional modifications available upon discussion.

For examples of these techniques in application, see:

Interaction proteomics

Our interaction proteomics services enable the study of protein–protein, DNA–protein, and RNA–protein interactions, providing insights into complex molecular networks. We offer specialist expertise in RIME (Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins).

For examples of RIME in application, see:

Cross-linking mass spectrometry (XL-MS)

Our crosslinking mass spectrometry (XL-MS) services enable the identification of direct protein–protein interactions within complexes, providing valuable insights into structural details that are difficult to capture by other methods.

Plasma/Seer platform

Specialised proteomic analysis of biofluids, including plasma, is supported by our in-house Seer platform for enhanced depth and sensitivity.

Targeted proteomics – PRM

Targeted proteomics using PRM (Parallel Reaction Monitoring) for quantification of selected proteins, enables robust, sensitive and reproducible measurements.

For an example of this technique in action, see:

Assessment of early response to neoadjuvant chemotherapy in multi-site high-grade serous ovarian cancer using hyperpolarized-13C MRI (EJNMMI Research, 2025)

Secretome analysis

We are currently developing secretome analysis capabilities. Please get in touch if you are interested in collaborating or learning more.

Equipment and analysis

Orbitrap Mass Spectrometers

We have three state-of-the-art mass spectrometers: Astral-Zoom, Ascend and Fusion Lumos, all of which are configured with a Vanquish Neo nano-HPLC system.
Off-line Separation Platforms

We operate two offline Dionex Ultimate 3000 capHPLC systems to provide multidimensional protein- and peptide-level separation, complementing our mass spectrometry workflows.
Relative quantification

Our quantification services include label-free methods (DDA and DIA), label-based approaches (SILAC and TMT), and targeted proteomics using PRM.
Data analysis

Data analysis is performed by Core Facility staff using the latest software, including DIANN, Proteome Discoverer, and Skyline. Additional statistical analysis can be provided by the Bioinformatics Core Facility upon request.