PXD000194

PXD000194 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis of human pericardial fluid
Description	Pericardial fluid (PF) is considered as biochemical window of heart. Knowledge of the entire protein content, the proteome of human PF, would give insights into heart and cardiovascular diseases. To date, there have been limited attempt to perform an in-depth analysis of the PF proteome. In this study, a SDS-PAGE-LC-MS/MS platform was utilized to explore abundant protein-depleted PF samples and showed great coverage of low-abundance proteins. In total, 1,007 non-redundant proteins were identified with at least two peptides, generating the first human PF proteome. Data processing: The mass spectra were searched using MaxQuant (v1.2.2.5) against the human subset of the Uniprot database (2012/05/16), which contains 87,187 entries. The search parameters were set as follows: peptide (parent ion) tolerance of 20 ppm, fragment ion tolerance of 0.5 Da, two missed cleavages were allowed, fixed modification of carbamidomethylation on Cys (+57 Da), and a differential modification of oxidation on Met (+16 Da). The false discovery rates (FDR) for both peptides and proteins were evaluated by searching against the combined database with the reversed amino acid sequence, and calculated by MaxQuant. To get high-confidence peptide and protein identifications, the cutoffs used were 1% for peptides and 1% for proteins. Absolute protein amounts were calculated as the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (intensity based absolute quantification, or iBAQ).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:19:14.510.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	fei xiang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	mono N-acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-25 07:41:27	ID requested
1	2013-07-09 07:08:00	announced
1	2014-07-24 03:49:53	announced
2	2013-07-09 07:11:09	announced	Add reference
⏵ 3	2024-10-22 04:19:15	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201200317;

Xiang F, Guo X, Chen W, Wang J, Zhou T, Huang F, Cao C, Chen X, Proteomics analysis of human pericardial fluid. Proteomics, 13(17):2692-5(2013) [pubmed]

curator keyword: Cardiovascular

submitter keyword: Pericardial fluid, Heart, Proteomics, Cardiovascular diseases, Biomarkers

fei xiang
contact affiliation	Lab of Reproductive Medicine
contact email	jackie-xf@163.com
lab head
fei xiang
contact affiliation	Lab of Reproductive Medicine
contact email	jackie-xf@163.com
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/2013/07/PXD000194

PRIDE project URI

• PRIDE
  1. PXD000194
     1. Label: PRIDE project
     2. Name: Proteomics analysis of human pericardial fluid