A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome
- Author
- Gerben Menschaert (UGent) , Tom Vandekerckhove (UGent) , Geert Baggerman, Bart Landuyt, Jonathan V Sweedler, Liliane Schoofs, Walter Luyten and Wim Van Criekinge (UGent)
- Organization
- 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, sea urchin, peptidomics, PEPTIDE SEQUENCE TAGS, TANDEM MASS-SPECTROMETRY, SECRETORY PATHWAY, IDENTIFICATION, TOOL, THROUGHPUT, PROTEOMICS, SOFTWARE, BROWSER, Neuropeptide, MODEL, indexed genome
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-822528
- MLA
- Menschaert, Gerben, et al. “A Hybrid, de Novo Based, Genome-Wide Database Search Approach Applied to the Sea Urchin Neuropeptidome.” JOURNAL OF PROTEOME RESEARCH, vol. 9, no. 2, 2010, pp. 990–96, doi:10.1021/pr900885k.
- APA
- Menschaert, G., Vandekerckhove, T., 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
- Chicago author-date
- Menschaert, Gerben, Tom Vandekerckhove, Geert Baggerman, Bart Landuyt, Jonathan V Sweedler, Liliane Schoofs, Walter Luyten, and Wim Van Criekinge. 2010. “A Hybrid, de Novo Based, Genome-Wide Database Search Approach Applied to the Sea Urchin Neuropeptidome.” JOURNAL OF PROTEOME RESEARCH 9 (2): 990–96. https://doi.org/10.1021/pr900885k.
- Chicago author-date (all authors)
- Menschaert, Gerben, Tom Vandekerckhove, Geert Baggerman, Bart Landuyt, Jonathan V Sweedler, Liliane Schoofs, Walter Luyten, and Wim Van Criekinge. 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. doi:10.1021/pr900885k.
- Vancouver
- 1.Menschaert G, Vandekerckhove T, Baggerman G, Landuyt B, Sweedler JV, Schoofs L, et al. A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. JOURNAL OF PROTEOME RESEARCH. 2010;9(2):990–6.
- IEEE
- [1]G. Menschaert et al., “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, 2010.
@article{822528,
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.}},
author = {{Menschaert, Gerben and Vandekerckhove, Tom and Baggerman, Geert and Landuyt, Bart and Sweedler, Jonathan V and Schoofs, Liliane and Luyten, Walter and Van Criekinge, Wim}},
issn = {{1535-3893}},
journal = {{JOURNAL OF PROTEOME RESEARCH}},
keywords = {{de novo sequencing,genome-wide database search,sea urchin,peptidomics,PEPTIDE SEQUENCE TAGS,TANDEM MASS-SPECTROMETRY,SECRETORY PATHWAY,IDENTIFICATION,TOOL,THROUGHPUT,PROTEOMICS,SOFTWARE,BROWSER,Neuropeptide,MODEL,indexed genome}},
language = {{eng}},
number = {{2}},
pages = {{990--996}},
title = {{A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome}},
url = {{http://doi.org/10.1021/pr900885k}},
volume = {{9}},
year = {{2010}},
}
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