{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T13:53:28Z","timestamp":1790949208667,"version":"4.1.0"},"reference-count":43,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"Health Institutes of T?rkiye (TUSEB)","award":["41292"],"award-info":[{"award-number":["41292"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Metaproteomic analyses commonly rely on protein sequence databases, yet database construction remains one of the most variable steps in metaproteomic workflows. Here, I present MetaproDB, a flexible and reproducible framework for biome-informed protein-sequence-database construction in metaproteomics. MetaproDB integrates ecological taxon selection, build-plan generation, genome resource linkage, protein sequence assembly, exact-sequence deduplication, completeness assessment, and provenance tracking within a unified workflow. It supports both database generation from a curated reference panel of representative biomes and cohort-specific construction from user-provided microbiome profiles. I demonstrate the functionality of MetaproDB through three case studies that compare different database construction strategies. MetaproDB provides a practical framework for explicit and reproducible biome-informed database design in metaproteomics and is available at [https:\/\/github.com\/arikanlab\/MetaproDB].<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00326","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T16:02:30Z","timestamp":1789574550000},"page":"5305-5318","source":"Crossref","is-referenced-by-count":0,"title":["MetaproDB:\nA Flexible and Reproducible Framework for\nBiome-Informed Protein Sequence Database Construction for Metaproteomics"],"prefix":"10.1021","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5162-2000","authenticated-orcid":true,"given":"Muzaffer","family":"Ar\u0131kan","sequence":"first","affiliation":[{"name":"Istanbul University , , ,","place":["Istanbul, Tu\u0308rkiye, 34134"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"issue":"8","key":"2026100208422802800_cit1","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1039\/d3mo00089c","article-title":"Integrated Multi-Omics Analyses of Microbial Communities: A Review\nof the Current State and Future Directions","volume":"19","author":"Ar\u0131kan","year":"2023","journal-title":"Mol. 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Proteome Res."},{"issue":"11","key":"2026100208422802800_cit5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0027173","article-title":"Strategies for Metagenomic-Guided Whole-Community Proteomics\nof Complex Microbial Environments","volume":"6","author":"Cantarel","year":"2011","journal-title":"PLoS One"},{"issue":"5","key":"2026100208422802800_cit6","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1080\/14789450.2019.1609944","article-title":"Challenges and Promise at the Interface of Metaproteomics\nand Genomics: An Overview of Recent Progress in Metaproteogenomic\nData Analysis","volume":"16","author":"Schiebenhoefer","year":"2019","journal-title":"Expert Rev. 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