Project PXD000072

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Summary

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.

Sample Processing Protocol

See details in reference(s) : 23640497

Data Processing Protocol

See details in reference(s) : 23640497

Contact

Patrick Wijten, Faculty of Science

Submission Date

20/11/2012

Publication Date

03/02/2014

Publication

    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. 2013 Jul;33(7):1635-8 PubMed: 23640497

Assay

Showing 1 - 9 of 9 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 27928 Biological replicate 1-ETD-FT 51 149 72 5591 135
2 27929 Biological replicate 1-ETD-IT 3145 29206 7202 110002 19588
3 27930 Biological replicate 1 � HCD 2039 26535 5735 122699 18335
4 27931 Biological replicate 2 - ETD_FT 212 517 273 11339 467
5 27932 Biological replicate 2 - ETD_IT 4482 47339 12158 124287 34405
6 27933 Biological replicate 2 - HCD 3369 56538 12306 199533 37692
7 27934 Biological replicate 3 � ETD-FT 61 174 82 5596 150
8 27935 Biological replicate 3 � ETD-IT 3629 36549 9481 107771 26046
9 27936 Biological replicate 3 � HCD 2858 44443 9450 156879 30249