The analysis of nucleic acids by mass spectrometry (MS) has evolved to a user friendly technology for characterising DNA, and RNA in clinical research and molecular medicine. Recently, the technology has become a versatile tool for microbial identification utilising comparative sequence analysis as shown for 16S based typing of mycobacteria [1]. Here, we present examples for the development of MS specific assays for molecular typing of the M. tuberculosis Complex including spoligotyping and antibiotic resistance identification, which is essential for epidemiological analysis. One technology, the MassARRAY® platform can be used with different assay formats and typing schemes to obtain results from species to strain identification in an automated fashion