Another major challenge in metaproteomics lies both in identifying non-tryptic peptides and in inferring homologous proteins across the vast diversity of microbial species. Due to the vast diversity in microbial genomes and, thus, proteomes, traditional database-driven approaches often need help with incomplete or mismatched databases. Many proteins, especially those involved in resistance mechanisms, are poorly represented in existing databases. This challenge makes homologous protein identification a significant bottleneck, as the inability to match proteins accurately leads to gaps in understanding how microbial species express resistance.