This experiment looked at the fragmentation of isoflavones and its derivatives using APCI-MS/MS. This yielded results such as the loss of common moieties CO, OH and methyl radical. The possible fragment ions detected on the spectra were also identified through a proposed fragmentation pathway. The collision energy (CE) at 50% survival yield was determined and the fragmentation stability of the analysed samples were also calculated based on CE at 50%. The technique used was valuable in identifying the possible product ions of the ionized samples and rank them based on their fragmentation stabilities.