Proteomics

Dataset Information

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High precision platelet releasate definition by quantitative reversed protein profiling


ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Platelet

SUBMITTER: Patrick Wijten  

LAB HEAD: Patrick Wijten

PROVIDER: PXD000072 | Pride | 2014-02-03

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
OR5_111110_MD_LLW2_F13.raw Raw
OR5_111110_MD_LLW2_F14.raw Raw
OR5_111110_MD_LLW2_F15.raw Raw
OR5_111110_MD_LLW2_F16.raw Raw
OR5_111110_MD_LLW2_F17.raw Raw
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Publications

High precision platelet releasate definition by quantitative reversed protein profiling--brief report.

Wijten Patrick P   van Holten Thijs T   Woo Liy Liy LL   Bleijerveld Onno B OB   Roest Mark M   Heck Albert J R AJ   Scholten Arjen A  

Arteriosclerosis, thrombosis, and vascular biology 20130502 7


<h4>Objective</h4>Platelet activation and subsequent protein release play an important role in healthy hemostasis and inflammatory responses, yet the identity and quantity of proteins in the platelet releasate are still debated. Here, we present a reversed releasate proteomics approach to determine unambiguously and quantitatively proteins released from activated platelets.<h4>Approach and results</h4>Isolated platelets were mock and fully stimulated after which the released proteins in the supe  ...[more]

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