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PXD053450

PXD053450 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA carrier-based quantitative proteomics method applied to biomarker discovery in pericardial fluid
DescriptionData-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS) is challenged by the large concentration range of proteins in plasma and related fluids. We adapted the SCoPE method from single-cell proteomics to pericardial fluid, where a myocardial tissue carrier was used to aid protein quantification. The carrier proteome and patient samples were labeled with distinct isobaric labels, which allowed separate quantification. Undepleted pericardial fluid from patients with type 2 diabetes mellitus and/or heart failure undergoing heart surgery was analyzed with either a traditional LC-MS/MS method or with the carrier proteome. In total, 1398 proteins were quantified with a carrier, compared to 265 without, and a higher proportion of these proteins were of myocardial origin. The number of differentially expressed proteins also increased nearly four-fold. For patients with both heart failure and type 2 diabetes mellitus, pathway analysis of upregulated proteins demonstrated enrichment of immune activation, blood coagulation, and stress pathways. Overall, our work demonstrates the applicability of a carrier for enhanced protein quantification in challenging biological matrices such as pericardial fluid, with potential applications for biomarker discovery.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:51:59.707.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAmanda Jessica Campbell
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; carbamoylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-06-26 22:37:56ID requested
12024-07-31 05:13:11announced
22024-10-22 06:52:00announced2024-10-22: Updated project metadata.
Publication List
10.1016/j.mcpro.2024.100812;
Campbell AJ, Cakar S, Palstr, ΓΈ, m NB, Riber LP, Rasmussen LM, Beck HC, A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid. Mol Cell Proteomics, 23(8):100812(2024) [pubmed]
Keyword List
submitter keyword: carrier proteome,single-cell proteomics, biomarker discovery
Contact List
Hans Christian Beck
contact affiliationAssociate Professor, Department of Clinical Biochemistry, Odense University Hospital and Department of Clinical Research, University of Southern Denmark
contact emailhans.christian.beck@rsyd.dk
lab head
Amanda Jessica Campbell
contact affiliationOdense University Hospital
contact emailamanda.jessica.campbell@rsyd.dk
dataset submitter
Full Dataset Link List
Dataset FTP location
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