title: The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.
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 nonredundant 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, for example, 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.
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium. unipept@ugent.be.
authors.forename: Bart
authors.initials: B
authors.lastname: Mesuere
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Felix
authors.initials: F
authors.lastname: Van der Jeugt
authors.affiliation: Laboratory for Protein Biochemistry and Biomolecular Engineering, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Bart
authors.initials: B
authors.lastname: Devreese
authors.affiliation: Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Dawyndt
mesh_terms: D000818:Animals; D001419:Bacteria / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D020543:Proteome
keywords: Bioinformatics; Biomarkers; Data visualization; Software; Targeted metaproteomics; Tryptic peptides