Fast identification of any microbial pathogens is of utmost interest in the CBRN-E and medical fields. For this, we developed a proteotyping method without any a priori named “Phylopeptidomics”. This approach is based on protein extraction from complex unknown samples, followed by their sequencing by high resolution tandem mass spectrometry. The recorded data are then interpreted by an in house developed software called “µOrg.ID”, which matches sequenced peptides to taxonomical information and deconvolutes the shared peptides to discriminate the different species and quantify them. This method has proved successful in identifying pathogens in complex biological matrices during several Biotox-Piratox French national exercises. The software has been deployed on a laptop in order to perform blind tests in other laboratories. We recently demonstrated the performances of the method at the Culture Collection of the University of Gothenburg in Sweden which is the largest European public strain collection of clinically-relevant microorganisms. A set of five samples prepared in our laboratory and five samples from the CCUG research laboratory were analyzed in Gothenburg by CCUG scientists. Identification of the exact species for the ten samples was straightforwardly achieved. In addition, the software established the potential antibiotic resistances associated with each of the identified species.