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The unique peptidome : taxon-specific tryptic peptides as biomarkers for targeted metaproteomics

Bart Mesuere (UGent) , Felix Van der Jeugt (UGent) , Bart Devreese (UGent) , Peter Vandamme (UGent) and Peter Dawyndt (UGent)
(2016) PROTEOMICS. 16(17). p.2313-2318
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Abstract
The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and non-redundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, e.g. in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the Lowest Common Ancestor algorithm implemented in Unipept and modern web technologies that facilitate in-browser data storage and parallel processing.
Keywords
biomarkers, data visualization, software, targeted metaproteomics, tryptic peptides, ACINETOBACTER-BAUMANNII, PROTEOMICS, INFORMATION, PREDICTION, GENOMICS, DATABASE

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Chicago
Mesuere, Bart, Felix Van der Jeugt, Bart Devreese, Peter Vandamme, and Peter Dawyndt. 2016. “The Unique Peptidome : Taxon-specific Tryptic Peptides as Biomarkers for Targeted Metaproteomics.” Proteomics 16 (17): 2313–2318.
APA
Mesuere, B., Van der Jeugt, F., Devreese, B., Vandamme, P., & Dawyndt, P. (2016). The unique peptidome : taxon-specific tryptic peptides as biomarkers for targeted metaproteomics. PROTEOMICS, 16(17), 2313–2318.
Vancouver
1.
Mesuere B, Van der Jeugt F, Devreese B, Vandamme P, Dawyndt P. The unique peptidome : taxon-specific tryptic peptides as biomarkers for targeted metaproteomics. PROTEOMICS. 2016;16(17):2313–8.
MLA
Mesuere, Bart, Felix Van der Jeugt, Bart Devreese, et al. “The Unique Peptidome : Taxon-specific Tryptic Peptides as Biomarkers for Targeted Metaproteomics.” PROTEOMICS 16.17 (2016): 2313–2318. Print.
@article{8507600,
  abstract     = {The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and non-redundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, e.g. in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the Lowest Common Ancestor algorithm implemented in Unipept and modern web technologies that facilitate in-browser data storage and parallel processing.},
  author       = {Mesuere, Bart and Van der Jeugt, Felix and Devreese, Bart and Vandamme, Peter and Dawyndt, Peter},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {biomarkers,data visualization,software,targeted metaproteomics,tryptic peptides,ACINETOBACTER-BAUMANNII,PROTEOMICS,INFORMATION,PREDICTION,GENOMICS,DATABASE},
  language     = {eng},
  number       = {17},
  pages        = {2313--2318},
  title        = {The unique peptidome : taxon-specific tryptic peptides as biomarkers for targeted metaproteomics},
  url          = {http://dx.doi.org/10.1002/pmic.201600023},
  volume       = {16},
  year         = {2016},
}

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