LC/MS/MS is becoming a very important tool for the on-line identification of natural products in crude plant extracts. For an efficient use of this technique in the dereplication of natural products, a careful study of the parameters used to generate informative MS/MS spectra is needed. In this paper the CID MS/MS spectra of ubiquitous flavonoids and related plant constituents have been systematically studied using hybrid quadrupole time of flight (Q-TOF) and ion trap (IT) mass analysers under various CID energy conditions. The results demonstrate that, if for hydroxylated flavonoids the CID MS/MS spectra generated on both instruments are similar, for partially methoxylated derivatives, important differences are observed hampering the creation of MS/MS databases exchangeable between instruments. Generally, fragments issued from C-ring cleavage, corresponding to those classically reported, were recorded but they were more easily observed on a Q-TOF instrument while losses of small molecules were favoured in IT-MS. MS/MS spectra recorded in the positive ion mode were more informative than those obtained from negative ions. For the assignment of flavonoids product ion spectra, on-line accurate mass measurement of all MS/MS fragments was obtained on the Q-TOF, while the multiple stage MSn capability of the ion trap was used to prove fragmentation pathways