Isoflavonoids were rich in natural source and gained great attention due to their
diverse activities such as antioxidant, estrogenic, radical scavenging and prevention of
cardiovascular and coronary heart diseases. Numerous isoflavonoids, usually present as
isomers, were found in traditional medicines and dietary supplements. For better
understanding of the unknown components, thorough investigation on the known analogue compounds was
essential and helpful. In the present study, a new developed fourier transform mass spectrometry (FTMS),
named Orbitrap, which applied as a hybrid instrument with one type of linear ion trap (LTQ), was used.
Collision induced dissociation (CID) and higher collision energy dissociation (HCD) were applied in both
negative and positive ion modes. Association between fragmentation patterns and different substitution modes
were clarified. In most cases, the key differences just lie in distinct abundance of the fragment ions.
Therefore, comparative studies on series of spectra profiles were more useful than simple consideration of the
fragmentation pathways sometimes. General fragmentation rules of isoflavonoinds and distinctive
characteristic of some isomers were summarized by combined use of CID and HCD methods. The obtained
results would be valuable for structural characterization of analogues in isoflavone rich traditional medicines
and dietary supplements.