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Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples

Bart Mesuere (UGent) , Bart Devreese (UGent) , Griet Debyser (UGent) , Maarten Aerts (UGent) , Peter Vandamme (UGent) and Peter Dawyndt (UGent)
(2012) JOURNAL OF PROTEOME RESEARCH. 11(12). p.5773-5780
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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.
Keywords
treemap visualization, biodiversity analysis, metaproteomics, tryptic peptides, INFORMATION, RESOURCE

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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.
@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},
}

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