Construction of protein sequence databases for metaproteomics: a review of the current tools and databases

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dc.contributor.authorArıkan, Muzaffer
dc.contributor.authorAtabay, Başak
dc.date.accessioned2025-10-21T11:47:49Z
dc.date.available2025-10-21T11:47:49Z
dc.date.issued2024
dc.departmentİstanbul Medipol Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Biyomedikal Mühendisliği Bölümü
dc.description.abstractIn metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availability of well-curated reference databases and tools for custom database construction is essential to enhance the performance of metaproteomics analyses. In this review, we first provide an overview of metaproteomics by presenting a concise historical background, outlining a typical experimental and bioinformatics workflow, emphasizing the crucial step of constructing a protein sequence database for metaproteomics. We then delve into the current tools available for building such databases, highlighting their individual approaches, utility, and advantages and limitations. Next, we examine existing protein sequence databases, detailing their scope and relevance in metaproteomics research. Then, we provide practical recommendations for constructing protein sequence databases for metaproteomics, along with an overview of the current challenges in this area. We conclude with a discussion of anticipated advancements, emerging trends, and future directions in the construction of protein sequence databases for metaproteomics.
dc.identifier.citationArıkan, M. ve Atabay, B. (2024). Construction of protein sequence databases for metaproteomics: a review of the current tools and databases. Journal of Proteome Research, 23(12), 5250-5262. http://dx.doi.org/10.1021/acs.jproteome.4c00665
dc.identifier.doi10.1021/acs.jproteome.4c00665
dc.identifier.endpage5262
dc.identifier.issn1535-3893
dc.identifier.issn1535-3907
dc.identifier.issue12
dc.identifier.pmid39449618
dc.identifier.scopus2-s2.0-85207386002
dc.identifier.scopusqualityQ1
dc.identifier.startpage5250
dc.identifier.urihttp://dx.doi.org/10.1021/acs.jproteome.4c00665
dc.identifier.urihttps://hdl.handle.net/20.500.12511/13129
dc.identifier.volume23
dc.identifier.wosWOS:001343782200001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorAtabay, Başak
dc.institutionauthorid0009-0000-8811-6670
dc.language.isoen
dc.relation.ispartofJournal of Proteome Research
dc.relation.publicationcategoryDiğer
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectMetaproteogenomics
dc.subjectMetaproteomics
dc.subjectMicrobiome
dc.subjectProtein Sequence Database
dc.titleConstruction of protein sequence databases for metaproteomics: a review of the current tools and databases
dc.typeOther

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