Advanced multi-omics technologies provide revolutionary strategies to study complex biological processes, e.g. to systematically decipher biosynthetic pathways to mechanistically challenging, structurally complex, widely used plant medicinals that cannot be economically synthesized. A multi-omics strategy is proposed to deduce biosynthetic pathway to rohitukine, a chromone alkaloid, widely used in cancer treatment. Distinct cell types involved in plantawill be identified using mass spectrometry based metabolite imaging in situand laser microscope dissection. Knowledge gained can be applied to developing synthetic biology approaches in order to obtain new sources of these compounds in other host systems.