Transition metal catalysts in pharmaceutical processes is widely used, but health care agencies such as the Food and Drug Administration and the European Medicines Agency highly regulate the residual level of elemental impurities in the final drug substance and drug product to avoid any adverse effect on patients. Controlling these elemental impurities requires a thorough understanding of the catalytic mechanism and the fate of each elemental impurity. Only with this knowledge in hand can a process be developed to sufficiently remove residual elemental impurities to acceptable levels. Recently, there has been tremendous progress in metal speciation directly assisted by HPLC-ICP-MS. To investigate the removal of elemental impurities from reaction process, we have utilized metal speciation data to provide critical information on the fate of each elemental impurity and a deeper understanding of the catalytic mechanism. Herein we present our recent analytical showcases on (i) how we successfully implemented analytical methods such as HPLC-ICP-MS and HPLC-ESI-TOF-MS to understand and quantify metal species in process development, (ii) how such analytical tools provided a guidance to control residual palladium down to less than 1 ppm level in drug substance, and (iii) how uncontrolled metallic impurities can cause analytical challenges including on-column degradation.