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Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

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dc.contributor.author Tanca, Alessandro
dc.contributor.author Palomba, Antonio
dc.contributor.author Deligios, Massimo
dc.contributor.author Cubeddu, Tiziana
dc.contributor.author Fraumene, Cristina
dc.contributor.author Biosa, Grazia
dc.contributor.author Pagnozzi, Daniela
dc.contributor.author Addis, Maria Filippa
dc.contributor.author Uzzau, Sergio
dc.date.accessioned 2014-12-17T10:01:13Z
dc.date.available 2014-12-17T10:01:13Z
dc.date.issued 2013-12-09
dc.identifier.citation Tanca A, Palomba A, Deligios M, Cubeddu T, Fraumene C, et al. (2013) Evaluating the Impact of Different Sequence ?Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture. PLoS ONE 8(12): e82981 IT
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/11050/1140
dc.description.abstract Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data. IT
dc.language.iso en IT
dc.publisher Public Library of Science IT
dc.relation.ispartof PLoS ONE IT
dc.relation.ispartofseries 8;12
dc.rights Attribuzione - Non commerciale - Non opere derivate 3.0 Italia *
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/it/ *
dc.subject microbial mixture IT
dc.subject protein databases (DBs) IT
dc.subject metaproteomics IT
dc.title Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture IT
dc.type Articolo IT
dc.description.status Pubblicato IT
dc.identifier.doi 10.1371/journal.pone.0082981 IT
dc.subject.een-cordis EEN CORDIS::SCIENZE BIOLOGICHE ::Ricerca sul genoma ::Espressione genica, ricerca proteomica IT
dc.subject.een-cordis EEN CORDIS::SCIENZE BIOLOGICHE ::Biologia / biotecnologia ::Microbiologia IT
dc.identifier.eissn 1932-6203


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Attribuzione - Non commerciale - Non opere derivate 3.0 Italia Attribuzione - Non commerciale - Non opere derivate 3.0 Italia