A significant challenge in constructing metagenome databases for metaproteomics-particularly for cross-sample comparisons-is mapping genes and MAGs across different metagenomes or combined datasets. This task must accommodate the diversity of subspecies, mutations, and sequence variations while ensuring the database remains compact enough to support accurate FDR calculations. This issue is closely tied to proteogenomics, which combines genomic and proteomic data for deeper analysis . In the context of metaproteomics, proteogenomics has demonstrated that phages can employ alternative genetic coding strategies . Additionally, integrating a combined database or employing advanced tools enables a more detailed taxonomic and functional characterization of microbiomes from non-sequenced hosts .