Increasing capabilities for robust high-throughput clinical proteomics within the Centre for Proteome Research at the University of Liverpool

Lead Research Organisation: University of Liverpool
Department Name: Biochemistry & Systems Biology


Mass spectrometry (MS) is a core scientific technology used across all areas of biomedical research, as well as in clinical laboratories for patient sample analysis and biomarker-based screening prior to decision making in clinical trials, surgical procedures and stratification for treatment. It can very accurately determine the mass of molecules by measuring the mass-to-charge ratio (or m/z) of charged particles called ions. Such measurements allow scientists to characterise and quantify proteins (and other biological molecules), and to determine how they change in composition and/or amount under different conditions, including proteins that are associated with all the major diseases that affect humans. Mass spectrometry is exquisitely sensitive, and can 'fingerprint' both normal and disease-associated proteins and peptides that can both predict disease and measure response to treatment.
Through the acquisition of a state-of-the-art MS platform, our proposal seeks to replace aging instrumentation within the Centre for Proteome Research (CPR) at the University of Liverpool, an open-access facility managed through a transparent cost-recovery structure. The requested platform, which is designed for reproducible, robust, sensitive and high-throughput peptide quantification from complex biological samples such as blood, will significantly expand capability for clinical biomarker discovery. This MS system will also be used to explore mechanisms of drug resistance in infection and cancer alongside advanced screening for treatment stratification of patients, including those defined through genetic analysis. Using a well-established cost recovery model to ensure the longevity, value-for-money and maximal impact of the initial investment, we will work with (clinical) scientists both within and outside of Liverpool, providing the necessary expertise to generate quantitative proteomics data for projects across all the MRC strategic priority areas.
For example, by using this advanced technology to define protein level changes in well-defined model systems and carefully selected clinical cohorts, we will be able to speed up the time required to understand (amongst other things) mechanisms of drug resistance that occur after patient exposure to anti-microbials (AMR) and targeted cancer therapies, identify biomarkers/prognostic markers for stroke, long COVID and pancreatic cancer in newly diagnosed diabetics, and define factors that explain inter-individual response to prescribed anti-coagulants and anti-psychotics, which are taken by a significant percentage of the UK population at any one time.
Liverpool-shared research facilities (LIV-SRF), which underwrites the CPR SRF, where the equipment will be situated in our biosciences infrastructure, provides access to the very best UK research facilities for the maximal number of users, both inside and outside Liverpool, including financial support to maintain and develop 'open' and 'transparent' facilities such as ours. As well as facilitating access to cutting edge infrastructure (and the necessary expertise for optimal use), it also awards 'access grants', permitting academics, including Early Career Researchers (ECRs), to exploit these facilities to support new research ideas in advance of winning substantive peer-reviewed funding. Access to these research facilities enhances collaboration with external stakeholders such as the NHS and Industry, enabling them to outsource some of their analysis using professionally-managed technology in an academic setting. This model has helped drive the success of proteomics-based research at the University of Liverpool across the MRC remit, but which now needs to be bolstered by access to new equipment with state-of-the-art capabilities.

Technical Summary

We propose to install a ThermoFisher Scientific Orbitrap Exploris 480 mass spectrometer with high-field asymmetric waveform ion mobility spectrometry (FAIMS) and UHPLC for peptide separation prior to mass spectrometry (MS) analysis. This MS platform will be based in a purpose-built laboratory in the Centre for Proteome Research (CPR) at the University of Liverpool. The CPR is known internationally for developing MS-based strategies for protein quantification and post-translational modification (PTM) analysis, and their application to address diverse biological and biomedical questions. Through our shared research facility (SRF), we provide access to cutting-edge instrumentation and proteomics expertise to scientists outside of our immediate field (inside and outside of Liverpool) using an established fee-for-service model.
This MS system integrates features that minimise the need for instrument cleaning, maintenance and calibration, reducing 'down-time' and maximising output. Combined with the Vanquish Neo UHPLC and FAIMS Pro systems, the platform exhibits reduced sample-to-sample variability over hundreds of (clinical) samples, enabling peptide (protein) quantification across 8 orders of magnitude from biological samples such as serum; it is thus ideal for the analysis of large clinical cohorts for mechanistic investigation and biomarker discovery/validation, a highlight of our bid.
The system will be used to generate data for projects across the MRC remit. Outlined here are 12 exemplar projects addressing: i) prevention & early detection; ii) precision medicine; iii) multimorbidity; iv) mental health; v) anti-microbial resistance; vi) global health, for which ethics, funding and samples are already in place. Our collaborative proposal is also relevant to the MRC 'Foundations for Excellence', applying cutting-edge technology to transform the impact of biomedical research through discovery and applied investigation, and supporting staff at all career stages.


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