Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics

Anderson, James R ORCID: 0000-0003-0489-7997, Phelan, Marie M, Rubio-Martinez, Luis M, Fitzgerald, Matthew M, Jones, Simon W, Clegg, Peter D ORCID: 0000-0003-0632-0032 and Peffers, Mandy J ORCID: 0000-0001-6979-0440
(2020) Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics. Journal of Proteome Research, 19 (7). pp. 2585-2597.

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Synovial fluid (SF) is of great interest for the investigation of orthopaedic pathologies as it is in close proximity to various tissues which are primarily altered during these disease processes and can be collected using minimally invasive protocols. Multi 'omic' approaches are commonplace although little consideration is often given for multiple analysis techniques at sample collection. Nuclear magnetic resonance (NMR) metabolomics and liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics are two complementary techniques particularly suited to the study of SF. However, currently there are no agreed standard protocols which are published for SF collection and processing for use with NMR metabolomic analysis. Furthermore, the large protein concentration dynamic range present within SF can mask the detection of lower abundance proteins in proteomics. Whilst combinational ligand libraries (ProteoMinerTM columns) have been developed to reduce this dynamic range, their reproducibility when used in conjunction with SF, or on-bead protein digestion protocols, have yet to be investigated. Here we employ optimised protocols for the collection, processing and storage of SF for NMR metabolite analysis and LC-MS/MS proteome analysis, including a Lys-C endopeptidase digestion step prior to tryptic digestion which increased the number of protein identifications and improved reproducibility for on-bead ProteoMinerTM digestion.

Item Type: Article
Uncontrolled Keywords: Protein identification, Freezing, Peptides and proteins
Depositing User: Symplectic Admin
Date Deposited: 03 Apr 2020 10:33
Last Modified: 18 Jan 2023 23:56
DOI: 10.1021/acs.jproteome.0c00035
Open Access URL: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome...
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3081702