An electrospray ionization-dual gate-ion mobility-quadrupole ion trap mass spectrometer was used to evaluate the separation characteristics of isomeric flavonoid diglycosides adducted with sodium, potassium, and silver. This instrumental configuration allows ions to be selectively accumulated within the ion trap on the basis of their gas phase conformation prior to mass analysis. For the metal cations examined, silver produced the most compact adducts with flavonoid diglycosides. Listed in order of increasing size, the trend of flavonoid diglycoside ion-neutral cross sections adducted with Na+, K+, and Ag+ was narirutin < naringin < hesperidin < neohesperidin < rutin. To examine the separation contribution of the carbohydrate group, hesperetin, the aglycone of hesperidin, and neohesperin were compared to quercetin, the aglycone of rutin. Separation of the flavonoid diglycosides indicated that quercetin-derived diglycosides drifted longer than their hesperetin-derived isomers. Combined with the observed collision assisted dissociation (CAD) data, these findings suggest that carbohydrate moiety plays a significant role in both the separation and metal chelating characteristics of flavonoid diglycosides. Copyright (c) 2006 John Wiley & Sons, Ltd.