PXD017069 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-01-10 07:23:14 | ID requested | |
⏵ 1 | 2020-04-05 23:19:42 | announced | |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD017069
- Label: PRIDE project
- Name: Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics