Rapid and reliable detection, identification, and typing of bacterial species are necessary in response to natural or terrorist-caused outbreaks of infectious diseases and play crucial roles in diagnosis and efficient treatment. We report here two proteomic approaches with a high potential in the detection and identification of Coxiella burnetii, the causative agent of Q fever. The first of them starts with the acetonitrile (ACN) and trichloroacetic acid extractions of inactivated C. burnetii cells followed by the detection of extracted molecules and ions derived from the inactivated cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In the second approach, identification of the proteins extracted by ACN is accomplished after enzymatic digestion by electrospray tandem mass spectrometry coupled to a nanoscale ultraperformance liquid chromatography (LC-MS/MS). In order to observe morphological differences on the surface structures upon extraction, the inactivated and treated cells of the bacterium were examined by electron microscopy. The LC-MS/MS approach has allowed identification of 20 proteins in the ACN extracts of C. burnetii strain RSA 493 that were observed in more than 3 out of 10 experiments.