Das Suchergebnis hat sich seit Ihrer Suchanfrage verändert. Eventuell werden Dokumente in anderer Reihenfolge angezeigt.
  • Treffer 39 von 50
Zurück zur Trefferliste
Zitieren Sie bitte immer diesen URN: urn:nbn:de:kobv:b43-516358

Survey of metaproteomics software tools for functional microbiome analysis

  • To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics,To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.zeige mehrzeige weniger

Volltext Dateien herunterladen

Metadaten exportieren

Weitere Dienste

Teilen auf Twitter Suche bei Google Scholar Anzahl der Zugriffe auf dieses Dokument
Metadaten
Autor*innen:R. Sajulga, C. Easterly, M. Riffle, B. Mesuere, Thilo MuthORCiD, S. Mehta, P. Kumar, J. Johnson, B. Gruening, H. Schiebenhoefer, C. Kolmeder, S. Fuchs, B. Nunn, J. Rudney, T. Griffin, P. Jagtap
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):PLoS ONE
Jahr der Erstveröffentlichung:2020
Organisationseinheit der BAM:VP Vizepräsident
VP Vizepräsident / VP.1 eScience
Veröffentlichende Institution:Bundesanstalt für Materialforschung und -prüfung (BAM)
Erste Seite:e0241503
DDC-Klassifikation:Naturwissenschaften und Mathematik / Chemie / Analytische Chemie
Freie Schlagwörter:Bioinformatics; Mass spectrometry; Metaproteomics
Themenfelder/Aktivitätsfelder der BAM:Chemie und Prozesstechnik
DOI:10.1371/journal.pone.0241503
URN:urn:nbn:de:kobv:b43-516358
Verfügbarkeit des Dokuments:Datei für die Öffentlichkeit verfügbar ("Open Access")
Lizenz (Deutsch):License LogoCreative Commons - CC0 1.0 - Universell - Public Domain Dedication
Datum der Freischaltung:25.11.2020
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:25.11.2020
Schriftenreihen ohne Nummerierung:Wissenschaftliche Artikel der BAM
Einverstanden
Diese Webseite verwendet technisch erforderliche Session-Cookies. Durch die weitere Nutzung der Webseite stimmen Sie diesem zu. Unsere Datenschutzerklärung finden Sie hier.