Evidence of isomerization during ion isolation in the quadrupole ion trap.

Evidence of ion isomerization during isolation in an ion trap mass spectrometer is presented. An ion-molecule reaction that is specific for the tolyl cation was used to monitor the relative abundance of this species. In particular, it has been observed that ion isolation in the ion trap can impart sufficient energy to the tolyl cation to cause it to isomerize to a form (presumably either the benzyl or the tropylium ion) that is not reactive with the neutral reagent. These results are important to consider in ion trap applications involving ion species having activation barriers for isomerization lower than the activation barriers for dissociation.