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Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples

Bart Mesuere UGent, Bart Devreese UGent, Griet Debyser, Maarten Aerts UGent, Peter Vandamme UGent and Peter Dawyndt UGent (2012) JOURNAL OF PROTEOME RESEARCH. 11(12). p.5773-5780
abstract
The Unipept web application (http://unipept.ugent.be) supports biodiversity analysis of large and complex metaproteome samples using tryptic peptide information obtained from shotgun MS/MS experiments. Its underlying index structure is designed to quickly retrieve all occurrences of a tryptic peptide in UniProtKB records. Taxon-specificity of the tryptic peptide is successively derived from these occurrences using a novel lowest common ancestor approach that is robust against taxonomic misarrangements, misidentifications, and inaccuracies. Not taking into account this identification noise would otherwise result in drastic loss of information. Dynamic treemaps visualize the biodiversity of metaproteome samples, which eases the exploration of samples with highly complex compositions. The potential of Unipept to gain novel insights into the biodiversity of a sample is evaluated by reanalyzing publicly available metaproteome data sets taken from the bacterial phyllosphere and the human gut.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
treemap visualization, biodiversity analysis, metaproteomics, tryptic peptides, INFORMATION, RESOURCE
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
11
issue
12
pages
5773 - 5780
Web of Science type
Article
Web of Science id
000311925900018
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.056 (2012)
JCR rank
10/74 (2012)
JCR quartile
1 (2012)
ISSN
1535-3893
DOI
10.1021/pr300576s
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
3070064
handle
http://hdl.handle.net/1854/LU-3070064
date created
2012-12-12 11:48:40
date last changed
2016-12-19 15:46:48
@article{3070064,
  abstract     = {The Unipept web application (http://unipept.ugent.be) supports biodiversity analysis of large and complex metaproteome samples using tryptic peptide information obtained from shotgun MS/MS experiments. Its underlying index structure is designed to quickly retrieve all occurrences of a tryptic peptide in UniProtKB records. Taxon-specificity of the tryptic peptide is successively derived from these occurrences using a novel lowest common ancestor approach that is robust against taxonomic misarrangements, misidentifications, and inaccuracies. Not taking into account this identification noise would otherwise result in drastic loss of information. Dynamic treemaps visualize the biodiversity of metaproteome samples, which eases the exploration of samples with highly complex compositions. The potential of Unipept to gain novel insights into the biodiversity of a sample is evaluated by reanalyzing publicly available metaproteome data sets taken from the bacterial phyllosphere and the human gut.},
  author       = {Mesuere, Bart and Devreese, Bart and Debyser, Griet and Aerts, Maarten and Vandamme, Peter and Dawyndt, Peter},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {treemap visualization,biodiversity analysis,metaproteomics,tryptic peptides,INFORMATION,RESOURCE},
  language     = {eng},
  number       = {12},
  pages        = {5773--5780},
  title        = {Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples},
  url          = {http://dx.doi.org/10.1021/pr300576s},
  volume       = {11},
  year         = {2012},
}

Chicago
Mesuere, Bart, Bart Devreese, Griet Debyser, Maarten Aerts, Peter Vandamme, and Peter Dawyndt. 2012. “Unipept: Tryptic Peptide-based Biodiversity Analysis of Metaproteome Samples.” Journal of Proteome Research 11 (12): 5773–5780.
APA
Mesuere, B., Devreese, B., Debyser, G., Aerts, M., Vandamme, P., & Dawyndt, P. (2012). Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples. JOURNAL OF PROTEOME RESEARCH, 11(12), 5773–5780.
Vancouver
1.
Mesuere B, Devreese B, Debyser G, Aerts M, Vandamme P, Dawyndt P. Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples. JOURNAL OF PROTEOME RESEARCH. 2012;11(12):5773–80.
MLA
Mesuere, Bart, Bart Devreese, Griet Debyser, et al. “Unipept: Tryptic Peptide-based Biodiversity Analysis of Metaproteome Samples.” JOURNAL OF PROTEOME RESEARCH 11.12 (2012): 5773–5780. Print.