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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane

  • Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similarMetaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.zeige mehrzeige weniger

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  • Schiebenhoefer et al. - 2020 - A complete and flexible workflow for metaproteomic.pdf
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Autor*innen:H. Schiebenhoefer, K. Schallert, B. Y. Renard, K. Trappe, E. Schmid, D. Benndorf, K. Riedel, Thilo MuthORCiD, S. Fuchs
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):Nature Protocols
Jahr der Erstveröffentlichung:2020
Organisationseinheit der BAM:VP Vizepräsident
VP Vizepräsident / VP.1 eScience
Verlag:Nature Publishing Group
Jahrgang/Band:15
Ausgabe/Heft:10
Erste Seite:3212
Letzte Seite:3239
DDC-Klassifikation:Naturwissenschaften und Mathematik / Chemie / Analytische Chemie
Freie Schlagwörter:Bioinformatics; Mass spectrometry; Metaproteomics; Microbial proteomics; Protocol; Software
Themenfelder/Aktivitätsfelder der BAM:Chemie und Prozesstechnik
DOI:10.1038/s41596-020-0368-7
ISSN:1750-2799
Verfügbarkeit des Dokuments:Datei im Netzwerk der BAM verfügbar ("Closed Access")
Datum der Freischaltung:30.09.2020
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:30.09.2020
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