PXD008620

PXD008620 is an original dataset announced via ProteomeXchange.

Title	Characterization of pericardial fluid proteome through fractionation with magnetic nanoparticles (NPs@EDTA)
Description	Despite the invasive nature of its collection, being in close contact to the heart, the pericardial fluid (PF) proteome reflects the pathophysiological status of this organ. Therefore, whenever it is available, e.g. on occasion of open-heart surgery, PF proteomic analysis can give important clues of the molecular mechanisms underlying heart disease and it may help uncover new diagnostic/prognostic markers as well as new therapeutic targets. Still, the characterization of its protein fraction is challenged by large amounts of albumin, that can be relatively higher than in plasma/serum. To help expand the PF catalogued to date and to validate the technique for future applications, we have fractionated and characterized the pericardial fluid, using N-(trimethoxysilylpropyl)ethylenediamine triacetic acid (EDTA)-functionalized magnetic nanoparticles (NPs@EDTA) followed by a GeLC-MS/MS approach. As compared to a traditional albumin and IgG-depletion kit, we found this method to be as efficient in removing albumin, with similar inter-individual proteome variability. Furthermore, the NPs@EDTA-based fractionation approach could expand the protein dynamic range and displayed good proteome reproducibility. Overall, 565 proteins were identified, with more than half being new assignments to PF proteome.
HostingRepository	PRIDE
AnnounceDate	2018-01-10
AnnouncementXML	Submission_2018-01-10_00:30:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fábio Trindade
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine
Instrument	LTQ Orbitrap Velos; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-09 01:38:51	ID requested
1	2018-01-09 04:02:37	announced
⏵ 2	2018-01-10 00:30:29	announced	Updated project metadata.

Trindade F, Bastos P, Leite-Moreira A, Manadas B, Ferreira R, Soares SF, Daniel-da-Silva AL, Falc, ã, o-Pires I, Vitorino R, A fractionation approach applying chelating magnetic nanoparticles to characterize pericardial fluid's proteome. Arch Biochem Biophys, 634():1-10(2017) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: Human, Pericardial Fluid, Fractionation, Magnetic Nanoparticles

Rui Miguel Pinheiro Vitorino
contact affiliation	iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; UnIC - Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
contact email	rvitorino@ua.pt
lab head
Fábio Trindade
contact affiliation	iBiMED, University of Aveiro; UnIC, Faculty of Medicine, University of Porto
contact email	fabiotrindade@ua.pt
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/2018/01/PXD008620

PRIDE project URI

• PRIDE
  1. PXD008620
     1. Label: PRIDE project
     2. Name: Characterization of pericardial fluid proteome through fractionation with magnetic nanoparticles (NPs@EDTA)