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Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses.
Verschaffelt, Pieter; Tanca, Alessandro; Abbondio, Marcello; Van Den Bossche, Tim; Moortele, Tibo Vande; Dawyndt, Peter; Martens, Lennart; Mesuere, Bart.
Afiliación
  • Verschaffelt P; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.
  • Tanca A; VIB - UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
  • Abbondio M; Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.
  • Van Den Bossche T; Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.
  • Moortele TV; VIB - UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
  • Dawyndt P; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.
  • Martens L; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.
  • Mesuere B; VIB - UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
J Proteome Res ; 22(8): 2620-2628, 2023 08 04.
Article en En | MEDLINE | ID: mdl-37459443
Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference databases that only contain proteins (originating from the UniProtKB resource) associated with a predetermined list of taxa. This improves both the taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By limiting the proteins present in a reference database, it is also possible to perform (meta)proteogenomics analyses. Since the protein reference database resides on the user's local machine, they have complete control over the database used during an analysis. Data no longer need to be transmitted over the Internet, decreasing the time required for an analysis and better safeguarding privacy-sensitive data. As a proof of concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using different targeted databases based on matched 16S rRNA gene sequencing data.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteínas / Metagenómica Límite: Humans Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Bélgica Pais de publicación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteínas / Metagenómica Límite: Humans Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Bélgica Pais de publicación: Estados Unidos