PXD017069

PXD017069 is an original dataset announced via ProteomeXchange.

Title	Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics
Description	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.
HostingRepository	PRIDE
AnnounceDate	2020-04-06
AnnouncementXML	Submission_2020-04-05_23:19:41.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD017069
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	James Anderson
SpeciesList	scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	Oxidation; Carbamidomethyl; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-10 07:23:14	ID requested
⏵ 1	2020-04-05 23:19:42	announced

Anderson JR, Phelan MM, Rubio-Martinez LM, Fitzgerald MM, Jones SW, Clegg PD, Peffers MJ, Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics. J Proteome Res, 19(7):2585-2597(2020) [pubmed]

curator keyword: Technical

submitter keyword: Synovial Fluid, Metabolomics, Nuclear Magnetic Resonance, Proteomics, Mass Spectrometry, Lys-C Endopeptidase

Professor Mandy Peffers
contact affiliation	University of Liverpool
contact email	peffs@liverpool.ac.uk
lab head
James Anderson
contact affiliation	University of Liverpool
contact email	janders@liverpool.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD017069

PRIDE project URI

• PRIDE
  1. PXD017069
     1. Label: PRIDE project
     2. Name: Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics