PXD000072

PXD000072 is an original dataset announced via ProteomeXchange.

Title	High precision platelet releasate definition by quantitative reversed protein profiling
Description	The platelet releasate defined by quantitative reversed protein profiling. Dimethyl labeled proteins of platelets in resting (light label) and activated state (collagen and thrombin activation, intermediate label) from three healthy volunteers fractionated by SCX, analyzed on a LTQ Obitrap Velos using a data dependent decision tree method (HCD/ETD).Peak lists were generated from the raw data files using the Proteome Discoverer software package version 1.3.339. Peptide identification was performed by searching the individual peak lists (HCD, ETD-IT and ETD-FT) against a concatenated target-decoy database containing the human sequences in the Uniprot database (release 2012_06) supplemented with a common contaminants database using the Mascot search engine version 2.3 (Matrix Science, London, United Kingdom) via the Proteome Discoverer interface (version 1.3). The search parameters included the use of semitrypsin as proteolytic enzyme allowing up to a maximum of 2 missed cleavages. Carbamidomethylation of cysteines was set as a fixed modification whereas oxidation of methionines and the dimethyl light and intermediate labels on N-termini and lysine residues were set as variable modifications. Precursor mass tolerance was initially set at 50 ppm, while fragment mass tolerance was set at 0.6 Da for ETD-IT fragmentation and 0.05 Da for HCD and ETD-FT fragmentation. Subsequently, the peptide identifications were filtered for true mass accuracy <4 ppm and an ion score of 40 until an FDR <1% at peptide level was achieved.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_08:45:01.930.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000072
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Patrick Wijten
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	dihydroxylated residue; monohydroxylated residue; formylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2012-11-20 05:42:46	ID requested
1	2014-02-03 05:12:35	announced
2	2014-07-25 08:04:41	announced	Updated project metadata.
3	2014-07-28 00:37:15	announced	Updated project metadata.
⏵ 4	2024-10-07 08:45:03	announced	2024-10-07: Updated project metadata.

10.6019/PXD000072;

10.1161/ATVBAHA.113.301147;

Wijten P, van Holten T, Woo LL, Bleijerveld OB, Roest M, Heck AJ, Scholten A, High precision platelet releasate definition by quantitative reversed protein profiling--brief report. Arterioscler Thromb Vasc Biol, 33(7):1635-8(2013) [pubmed]

submitter keyword: Human, LC-MSMS, Releasate, Blood, LTQ Orbitrap Velos, Isotope labeling, Platelets, Alpha granules

Patrick Wijten
contact affiliation	Faculty of Science
contact email	P.wijten@uu.nl
lab head
Patrick Wijten
contact affiliation	Faculty of Science
contact email	P.wijten@uu.nl
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/2014/02/PXD000072

PRIDE project URI

• PRIDE
  1. PXD000072
     1. Label: PRIDE project
     2. Name: High precision platelet releasate definition by quantitative reversed protein profiling