PXD053450

PXD053450 is an original dataset announced via ProteomeXchange.

Title	A carrier-based quantitative proteomics method applied to biomarker discovery in pericardial fluid
Description	Data-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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:51:59.707.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amanda Jessica Campbell
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; carbamoylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-26 22:37:56	ID requested
1	2024-07-31 05:13:11	announced
⏵ 2	2024-10-22 06:52:00	announced	2024-10-22: Updated project metadata.

10.1016/j.mcpro.2024.100812;

Campbell AJ, Cakar S, Palstr, ø, 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]

submitter keyword: carrier proteome,single-cell proteomics, biomarker discovery

Hans Christian Beck
contact affiliation	Associate Professor, Department of Clinical Biochemistry, Odense University Hospital and Department of Clinical Research, University of Southern Denmark
contact email	hans.christian.beck@rsyd.dk
lab head
Amanda Jessica Campbell
contact affiliation	Odense University Hospital
contact email	amanda.jessica.campbell@rsyd.dk
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/2024/07/PXD053450

PRIDE project URI

• PRIDE
  1. PXD053450
     1. Label: PRIDE project
     2. Name: A carrier-based quantitative proteomics method applied to biomarker discovery in pericardial fluid