This work is based on the fragmentation of flavonoid derivatives under atmospheric pressure chemical ionization conditions (APCI) using mass spectrometry. For all the analyzed samples, the survival yield decreased as the collision energy increased. Based on the fragmentation pattern some samples were observed to follow similar fragmentation pathways. The modified characteristic collision energy revealed the relative fragmentation stability for each sample. Based on the results it can be concluded that the APCI ion source was found to be an appropriate method to measure the flavonoids derivatives and to study their fragmentation processes.