title: 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.
authors.affiliation: Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B-9000 Ghent, Belgium. Gerben.Menschaert@ugent.be
authors.forename: Gerben
authors.initials: G
authors.lastname: Menschaert
authors.forename: Tom T M
authors.initials: TT
authors.lastname: Vandekerckhove
authors.forename: Geert
authors.initials: G
authors.lastname: Baggerman
authors.forename: Bart
authors.initials: B
authors.lastname: Landuyt
authors.forename: Jonathan V
authors.initials: JV
authors.lastname: Sweedler
authors.forename: Liliane
authors.initials: L
authors.lastname: Schoofs
authors.forename: Walter
authors.initials: W
authors.lastname: Luyten
authors.forename: Wim
authors.initials: W
authors.lastname: Van Criekinge
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002851:Chromatography, High Pressure Liquid; D030562:Databases, Protein; D016678:Genome; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism*; D020543:Proteome; D012617:Sea Urchins; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D009419:Nerve Tissue Proteins; D020543:Proteome