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Within the genus <i>Corynebacterium</i>, six species are potential carriers of the <i>tox</i> gene, which encodes the highly potent diphtheria exotoxin: <i>Corynebacterium diphtheriae</i>, <i>Corynebacterium belfantii</i>, <i>Corynebacterium rouxii</i>, <i>Corynebacterium ulcerans</i>, <i>Corynebacterium pseudotuberculosis</i> and <i>Corynebacterium silvaticum.</i> Based on their potential to infect different host species and cause either human infections, zoonotic diseases or infections of economically important animals, these bacteria are of high scientific and economic interest and different research groups have carried out proteome analyses. These showed that especially the combination of MS-based proteomics with bioinformatic tools helped significantly to elucidate the functional aspects of corynebacterial genomes and to handle the genome and proteome complexity. The combination of proteomic and bioinformatic approaches was also used to discover new vaccine and drug targets. In addition, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been established as a fast and precise tool for the identification of these bacteria.