Visualizing biological material helps to map the distribution of cells and organelles to better understand the principles of life. Most methods to date rely on microscopy and different labeling techniques. However, imaged elements are observed indirectly and lack molecular specificity. Mass spectrometry imaging (MSI) directly provides information related to the mass of the compound and possibly structural data taken from collision-induced-dissociation (CID) mass spectra. Distribution maps of secondary metabolites, obtained by MSI, already answered pending questions in chemical ecology.