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

doi:10.1021/pr900885k

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 journal › Article › peer-review

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 language	English (US)
Pages (from-to)	990-996
Number of pages	7
Journal	Journal of Proteome Research
Volume	9
Issue number	2
DOIs	https://doi.org/10.1021/pr900885k
State	Published - Feb 5 2010

Keywords

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

ASJC Scopus subject areas

Biochemistry
Chemistry(all)

Access to Document

10.1021/pr900885k

Fingerprint Dive into the research topics of 'A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome'. Together they form a unique fingerprint.

Cite this

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 journal › Article › peer-review

@article{0f257bde66864451ba120048b4de7fd8,

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.",

keywords = "De novo sequencing, Genome-wide database search, Indexed genome, Neuropeptide, Peptidomics, Sea urchin",

author = "Gerben Menschaert and Vandekerckhove, {Tom T.M.} and Geert Baggerman and Bart Landuyt and Sweedler, {Jonathan V.} and Liliane Schoofs and Walter Luyten and {Van Criekinge}, Wim",

year = "2010",

month = feb,

day = "5",

doi = "10.1021/pr900885k",

language = "English (US)",

volume = "9",

pages = "990--996",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "American Chemical Society",

number = "2",

}

TY - JOUR

T1 - A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome

AU - Menschaert, Gerben

AU - Vandekerckhove, Tom T.M.

AU - Baggerman, Geert

AU - Landuyt, Bart

AU - Sweedler, Jonathan V.

AU - Schoofs, Liliane

AU - Luyten, Walter

AU - Van Criekinge, Wim

PY - 2010/2/5

Y1 - 2010/2/5

N2 - 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.

AB - 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.

KW - De novo sequencing

KW - Genome-wide database search

KW - Indexed genome

KW - Neuropeptide

KW - Peptidomics

KW - Sea urchin

UR - http://www.scopus.com/inward/record.url?scp=76149127020&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=76149127020&partnerID=8YFLogxK

U2 - 10.1021/pr900885k

DO - 10.1021/pr900885k

M3 - Article

C2 - 20000637

AN - SCOPUS:76149127020

VL - 9

SP - 990

EP - 996

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 2

ER -