MetaproDB: A Flexible and Reproducible Framework for Biome-Informed Protein Sequence Database Construction for Metaproteomics

Abstract 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].