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Assessing the molecular component of biological samples in situ by mass spectrometry (molecular histology) is a rapidly developing technique. Much of the recent improvement has been due to the synergistic benefits and complementary nature of DESI (Desorption Electrospray) and MALDI (Matrix Assisted Laser Desorption) ionization coupled with high resolution mass spectrometry and ion mobility separation. Types of experiments that benefit from this technique are drug distribution and metabolism, lipid profiling, and biomarker identification, each of which are performed directly from sectioned biological and tissue samples. This discussion will highlight examples of these analyses as well as developments in sampling technology and data management that make real results readily available.