  Metaproteomics has become a crucial omics technology for studying
microbiomes. In this area, the Unipept ecosystem, accessible at
https://unipept.ugent.be, has emerged as an invaluable resource for analyzing
metaproteomic data. It offers in-depth insights into both taxonomic
distributions and functional characteristics of complex ecosystems. This
tutorial explains essential concepts like Lowest Common Ancestor (LCA)
determination and the handling of peptides with missed cleavages. It also
provides a detailed, step-by-step guide on using the Unipept Web application
and Unipept Desktop for thorough metaproteomics analyses. By integrating
theoretical principles with practical methodologies, this tutorial empowers
researchers with the essential knowledge and tools needed to fully utilize
metaproteomics in their microbiome studies.
