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The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile

Lennart Martens UGent, Petra Van Damme UGent, Jozef Van Damme UGent, An Staes UGent, Evy Timmerman UGent, Bart Ghesquière UGent, Grégoire R Thomas, Joël Vandekerckhove and Kris Gevaert UGent (2005) PROTEOMICS. 5(12). p.3193-3204
abstract
Several studies have been published in which holistic approaches were used to characterise the proteome and transcriptome of human platelets. The key intent being that a deeper understanding of the normal and aberrant physiological functions of platelets can only be achieved if most biomolecular building blocks are mapped. Here we present the application of recently developed novel technologies that overcome some of the shortcomings of gel-based proteomics. Central in our approach is the so-called combined fractional diagonal chromatography (COFRADIC)-technology in which sets of representative peptides are sorted in a diagonal RP chromatographic system through a specific modification of their side chain. In this study we combined three different COFRADIC sorting techniques to analyse the proteome of human platelets. Methionyl, cysteinyl and amino terminal peptides were isolated and analysed by MS/MS. Merging the peptide identifications obtained after database searching resulted in a core set of 641 platelet proteins, which comprises the largest set identified today. in comparison to previously published platelet proteomes, we identified 404 novel platelet proteins containing a high number of hydrophobic membrane proteins and hypothetical proteins. Furthermore we discuss the observed characteristics and potential benefits of each of the different COFRADIC technologies for proteome analysis and highlight important issues that need to be considered when searching sequence databases using data obtained in peptide-centric, non-gel proteomics studies.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
bioinformatics, 2-DIMENSIONAL GEL-ELECTROPHORESIS, TANDEM MASS-SPECTROMETRY, CHROMATOGRAPHIC ISOLATION, PHOSPHORYLATED PROTEINS, ESCHERICHIA-COLI, IDENTIFICATION, SOLUBILIZATION, PURIFICATION, METHIONINE, COMPLEX, non-gel proteomics, combined fractional diagonal chromatography, human platelets
journal title
PROTEOMICS
Proteomics
volume
5
issue
12
issue title
Proteomics for health SPS : proceedings 4th annual congress, Bern, Switzerland, 6-8 December 2004
pages
3193 - 3204
Web of Science type
Article
Web of Science id
000231315900024
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
6.088 (2005)
JCR rank
5/51 (2005)
JCR quartile
1 (2005)
ISSN
1615-9853
DOI
10.1002/pmic.200401142
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
339288
handle
http://hdl.handle.net/1854/LU-339288
date created
2006-06-09 16:07:00
date last changed
2016-12-19 15:44:22
@article{339288,
  abstract     = {Several studies have been published in which holistic approaches were used to characterise the proteome and transcriptome of human platelets. The key intent being that a deeper understanding of the normal and aberrant physiological functions of platelets can only be achieved if most biomolecular building blocks are mapped. Here we present the application of recently developed novel technologies that overcome some of the shortcomings of gel-based proteomics. Central in our approach is the so-called combined fractional diagonal chromatography (COFRADIC)-technology in which sets of representative peptides are sorted in a diagonal RP chromatographic system through a specific modification of their side chain. In this study we combined three different COFRADIC sorting techniques to analyse the proteome of human platelets. Methionyl, cysteinyl and amino terminal peptides were isolated and analysed by MS/MS. Merging the peptide identifications obtained after database searching resulted in a core set of 641 platelet proteins, which comprises the largest set identified today. in comparison to previously published platelet proteomes, we identified 404 novel platelet proteins containing a high number of hydrophobic membrane proteins and hypothetical proteins. Furthermore we discuss the observed characteristics and potential benefits of each of the different COFRADIC technologies for proteome analysis and highlight important issues that need to be considered when searching sequence databases using data obtained in peptide-centric, non-gel proteomics studies.},
  author       = {Martens, Lennart and Van Damme, Petra and Van Damme, Jozef and Staes, An and Timmerman, Evy and Ghesqui{\`e}re, Bart and Thomas, Gr{\'e}goire R and Vandekerckhove, Jo{\"e}l and Gevaert, Kris},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {bioinformatics,2-DIMENSIONAL GEL-ELECTROPHORESIS,TANDEM MASS-SPECTROMETRY,CHROMATOGRAPHIC ISOLATION,PHOSPHORYLATED PROTEINS,ESCHERICHIA-COLI,IDENTIFICATION,SOLUBILIZATION,PURIFICATION,METHIONINE,COMPLEX,non-gel proteomics,combined fractional diagonal chromatography,human platelets},
  language     = {eng},
  number       = {12},
  pages        = {3193--3204},
  title        = {The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile},
  url          = {http://dx.doi.org/10.1002/pmic.200401142},
  volume       = {5},
  year         = {2005},
}

Chicago
Martens, Lennart, Petra Van Damme, Jozef Van Damme, An Staes, Evy Timmerman, Bart Ghesquière, Grégoire R Thomas, Joël Vandekerckhove, and Kris Gevaert. 2005. “The Human Platelet Proteome Mapped by Peptide-centric Proteomics: a Functional Protein Profile.” Proteomics 5 (12): 3193–3204.
APA
Martens, Lennart, Van Damme, P., Van Damme, J., Staes, A., Timmerman, E., Ghesquière, B., Thomas, G. R., et al. (2005). The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile. PROTEOMICS, 5(12), 3193–3204.
Vancouver
1.
Martens L, Van Damme P, Van Damme J, Staes A, Timmerman E, Ghesquière B, et al. The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile. PROTEOMICS. 2005;5(12):3193–204.
MLA
Martens, Lennart, Petra Van Damme, Jozef Van Damme, et al. “The Human Platelet Proteome Mapped by Peptide-centric Proteomics: a Functional Protein Profile.” PROTEOMICS 5.12 (2005): 3193–3204. Print.