Metaproteomics allows identification and characterization of functional pathways and interactions between microorganisms. This approach combines high-throughput tandem mass spectrometry of proteins, metagenomics data, giant databases and advanced bioinformatics. This approach is also a useful tool to quickly establish an inventory of organisms present in a sample by proteotyping. We have developed a new proteotyping concept, named phylopeptidomics, for a fast identification of organisms, without any a priori, and quantitation of their respective biomasses. We have shown its application for quick surveys of pathogens and determine their antibiotic resistances, and deciphering complex microbiota.