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PXD017069

PXD017069 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics
DescriptionSynovial 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.
HostingRepositoryPRIDE
AnnounceDate2020-04-06
AnnouncementXMLSubmission_2020-04-05_23:19:41.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD017069
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJames Anderson
SpeciesList scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationListOxidation; Carbamidomethyl; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-01-10 07:23:14ID requested
12020-04-05 23:19:42announced
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: Synovial Fluid, Metabolomics, Nuclear Magnetic Resonance, Proteomics, Mass Spectrometry, Lys-C Endopeptidase
Contact List
Professor Mandy Peffers
contact affiliationUniversity of Liverpool
contact emailpeffs@liverpool.ac.uk
lab head
James Anderson
contact affiliationUniversity of Liverpool
contact emailjanders@liverpool.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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