Microorganisms play a major role in human, animal and vegetal health, as well as in key terrestrial geochemical processes. To understand how microbial communities function, how they interact with the host and the risks of dysbiosis, we need to identify the diversity of microorganisms present and quantify the numerous molecular players at work, especially proteins which are the workhorses of biological systems. Metaproteomics is a key technology for such functional studies, as it can provide important answers for these highly complex samples: 1) identification of the taxa present, 2) quantification of the biomass of these organisms, 3) identification of the proteins of these taxa and their function, 4) identification of host biomarkers explaining their global response, and 5) overall functional representation of the biological system. The first important key step in metaproteomics is the selection of the database best suited to the specificities of the sample. Proteotyping of organisms enables us to establish the identity of microorganisms and their corresponding biomass. Several examples will be presented to demonstrate the power of proteotyping. The challenges of metaproteomics in terms of mass spectrometry, interpretation and exploitation of results will be discussed addressed. Moreover, results from recent technologies such as the Astral tandem mass spectrometer will be presented to demonstrate the new power of next-generation metaproteomics for deep functional analysis of microbiomes.