Dataset Information

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

ABSTRACT: 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. Therefore, SF has substantial potential for improved understanding of underlying disease pathogenesis and biomarker discovery. Nuclear magnetic resonance (NMR) metabolomics is a rapidly expanding field, providing comprehensive metabolite profiling of complex biological samples with high levels of technical reproducibility. However, currently there are no agreed standard protocols which are published for SF collection and processing for use with NMR metabolomic analysis. The development of liquid chromatography tandem mass spectrometry (LC-MS/MS) has provided a fast and sensitive methodology to identify and quantify proteins within complex biological samples. However, the large protein concentration dynamic range present within SF can mask the detection of lower abundance proteins. Combinational ligand libraries (ProteoMinerTM columns) have been developed to reduce this dynamic range, achieving peptide-based depletion, whilst allowing preservation of the whole proteome. However, the reproducibility of ProteoMinerTM columns when used in conjunction with SF or on-bead protein digestion protocol reproducibility have yet to be investigated. During this study, protocols have been optimised for the collection, processing and storage of SF for NMR metabolite analysis. We have also optimised protocols for analysis of the SF proteome using LC-MS/MS.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Equus Caballus (horse)

TISSUE(S): Synovial Tissue

SUBMITTER: James Anderson

LAB HEAD: Professor Mandy Peffers

PROVIDER: PXD017069 | Pride | 2020-04-06

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Digest_Methods_Native_Trypsin_Only_Protocol_16hr.mgf	Mgf
	Digest_Methods_Native_Trypsin_Only_Protocol_16hr.mzid.gz	Mzid
	Digest_Methods_Native_Trypsin_Only_Protocol_16hr.pride.mgf.gz	Mgf
	Digest_Methods_Native_Trypsin_Only_Protocol_16hr.pride.mztab.gz	Mztab
	Digest_Methods_Native_Trypsin_Only_Protocol_16hr.raw	Raw

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Publications

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

Anderson James R JR Phelan Marie M MM Rubio-Martinez Luis M LM Fitzgerald Matthew M MM Jones Simon W SW Clegg Peter D PD Peffers Mandy J MJ

Journal of proteome research 20200407 7

Synovial fluid (SF) is of great interest for the investigation of orthopedic pathologies, as it is in close proximity to various tissues that 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) ...[more]

PMID: 32227958

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