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

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.

SUBMITTER: Menschaert G

PROVIDER: S-EPMC2845465 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

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

Menschaert Gerben G Vandekerckhove Tom T M TT Baggerman Geert G Landuyt Bart B Sweedler Jonathan V JV Schoofs Liliane L Luyten Walter W Van Criekinge Wim W

Journal of proteome research 20100201 2

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 ...[more]

PMID: 20000637

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