A versatile mass spectrometry platform for quantitative proteomics underpinning biomedical research at The University of Sheffield.

Proteins and metabolites best represent the state of a cell or organism at a given moment in time. The total collection of these proteins and metabolites (proteomes and metabolomes) is, therefore, a very informative readout of biology or an individual's health.

Analysing proteins and metabolites is challenging due to the many different types and diverse characteristics. However, an analytical approach called mass spectrometry is well suited to both the identification and, importantly, quantification of a vast range of these biological molecules.

We propose installing a versatile mass spectrometry platform in our mass spectrometry research facility to provide state-of-the-art proteome and metabolome analysis for researchers across the university. This instrument will allow us to increase the number of samples we can analyse and compare, perform a more detailed analysis of samples that are challenging with existing technology and permit precise measurement of specific sets of proteins and metabolites in a range of samples.

Researchers at The University of Sheffield will use this technology to understand the molecular processes underlying antimicrobial resistance, neurodegeneration and cancer and to identify molecular changes in patient samples to develop and test novel drugs to treat a range of diseases.

We propose to install an Orbitrap Exploris 240 (OE 240) system in the Faculty of Science Mass Spectrometry Centre at the University of Sheffield. This instrument is a state-of-the-art platform for the quantitative analysis of a wide range of molecules in complex mixtures. It offers several new capabilities for proteomics due to the ability to perform fundamentally different types of quantification that we can not currently perform efficiently with existing instrumentation. The OE 240 is a recently developed compact hybrid Quadrupole-Orbitrap mass spectrometer that offers high resolution, high sensitivity, and relatively fast (up to 20 Hertz) data acquisition. The narrow isolation widths afforded by the quadrupole mass filter and high-resolution analysis using a high-field orbitrap analyser makes this instrument well suited for highly multiplex MS2-level reporter ion quantification. This instrument permits different types of label-free quantification, including DIA, which can deliver excellent coverage and low missing values in library or library-free data analysis strategies. Targeted analysis of sets of peptides or metabolites can be performed using PRM with excellent precision (5 orders of dynamic range, CV <10 % for > 80% of peptides). In addition to sensitivity and speed gains compared to our existing instrumentation, the OE 240 will provide an outstanding capability for quantitative proteomics from analyses of samples from multiple conditions that require multiplexing, clinical studies that are challenging due to dynamic range and targeted studies that require precise measurement of pre-determined sets of biomolecules in a range of samples.