This project or dataset comprises raw data of the proteome of different mutant strains of M. pneumoniae (∆mpn453; ∆mpn372; CV2 (∆mpn133∆mpn372); CV0 (WT_gp35) and ∆mpn133).The proteome of the strain was used to corroborate the genotype of the obtained mutants and to discard unspected changes in the protein expression profile.