A fifth opportunity lies in developing user-friendly, scalable workflows that are accessible to researchers without extensive computational expertise. These workflows should integrate advanced de novo sequencing tools with key post-processing steps such as FDR estimation, protein inference, taxonomic assignment, and functional annotation. As de novo sequencing improves, downstream analysis methods must also advance, particularly technologies that go beyond BLAST+ to handle large metaproteomic references. Hybrid approaches, like MetaNovo , which combine de novo sequencing with conventional database searches, offer great promise by incorporating probabilistic methods to refine protein and taxon inference. Streamlining these workflows will enable researchers to understand microbial community dynamics and discover novel proteins, taxa, and functions.