A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome

Gerben Menschaert, Tom T.M. Vandekerckhove, Geert Baggerman, Bart Landuyt, Jonathan V. Sweedler, Liliane Schoofs, Walter Luyten, Wim Van Criekinge

Research output: Contribution to journalArticle

Abstract

Peptidomics is the identification and study of the in vivo biologically active peptide profile. A combination of high performance liquid chromatography, mass spectrometry, and bioinformatics tools such as database search engines are commonly used to perform the analysis. We report a methodology based on a database system holding the completed translated genome, whereby de novo sequencing and genome-wide database searching are combined. The methodology was applied to the sea urchin neuropeptidome resulting in a 30% increase in identification rate.

Original languageEnglish (US)
Pages (from-to)990-996
Number of pages7
JournalJournal of Proteome Research
Volume9
Issue number2
DOIs
StatePublished - Feb 5 2010

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Sea Urchins
Genes
Genome
Databases
Search Engine
High performance liquid chromatography
Bioinformatics
Search engines
Computational Biology
Mass spectrometry
Mass Spectrometry
High Pressure Liquid Chromatography
Peptides

Keywords

  • De novo sequencing
  • Genome-wide database search
  • Indexed genome
  • Neuropeptide
  • Peptidomics
  • Sea urchin

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Menschaert, G., Vandekerckhove, T. T. M., Baggerman, G., Landuyt, B., Sweedler, J. V., Schoofs, L., ... Van Criekinge, W. (2010). A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. Journal of Proteome Research, 9(2), 990-996. https://doi.org/10.1021/pr900885k

A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. / Menschaert, Gerben; Vandekerckhove, Tom T.M.; Baggerman, Geert; Landuyt, Bart; Sweedler, Jonathan V.; Schoofs, Liliane; Luyten, Walter; Van Criekinge, Wim.

In: Journal of Proteome Research, Vol. 9, No. 2, 05.02.2010, p. 990-996.

Research output: Contribution to journalArticle

Menschaert, G, Vandekerckhove, TTM, Baggerman, G, Landuyt, B, Sweedler, JV, Schoofs, L, Luyten, W & Van Criekinge, W 2010, 'A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome', Journal of Proteome Research, vol. 9, no. 2, pp. 990-996. https://doi.org/10.1021/pr900885k
Menschaert, Gerben ; Vandekerckhove, Tom T.M. ; Baggerman, Geert ; Landuyt, Bart ; Sweedler, Jonathan V. ; Schoofs, Liliane ; Luyten, Walter ; Van Criekinge, Wim. / A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. In: Journal of Proteome Research. 2010 ; Vol. 9, No. 2. pp. 990-996.
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