MetaproDB: A Flexible and Reproducible Framework for Biome-Informed Protein Sequence Database Construction for Metaproteomics
JOURNAL OF PROTEOME RESEARCH, 2026 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Tam Makale
- Basım Tarihi: 2026
- Doi Numarası: 10.1021/acs.jproteome.6c00326
- Dergi Adı: JOURNAL OF PROTEOME RESEARCH
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE
- İstanbul Üniversitesi Adresli: Evet
Özet
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 [].