Small Molecule Structural Elucidation by TAP Fragmentation using a Hybrid Quadrupole/Travelling Wave Ion Mobility/oa-TOF Mass Spectrometer

John Shockcor, Jose Castro-Perez and Kate Yu

Waters Corporation, 34 Maple Street, Milford, MA, USA

Ion mobility mass spectrometry (IMS) allows separation of ionic species as they drift through a gas phase under the influence of an electric field. The rate of an ion drift depends on the mass of the ion, its particular charge state and the average cross-section of the ion. It is possible to separate ions with the same nominal mass if they have different charge states or different interaction cross-sections.

In the hybrid quadrupole/Travelling Wave IM/oa-TOF instrument, the instrument was configured with three T-wave devices in sequence. The second T-wave functions as an ion mobility drift tube, the pre-IMS T-wave traps ions, and the post-IMS T-wave transfers the ions after they are separated from drift tube. An interesting consequence of this configuration is that the pre-IMS T-wave and post-IMS T-wave can function as two separate collision cells and produce fragment ions independently. The fragment ions produced in the trap T-wave (pre-IMS) can be separated basis on their charge states and their size as they move through the IMS. These ions separated by their different drift times can then be further fragmented in the transfer T-wave (post-IMS). As a result, the fragment ions generated in transfer T-wave are drift time aligned with their respective precursor ions resulting in Time Aligned Parallel fragmentation (TAP) pattern. If a single precursor ion is selected in the quadrupole stage prior to the Tri-Wave , this TAP fragmentation pattern is in effect offering some very selective MS3 information for the compound of interest. When these fragmentation results are combined with a structure elucidation software tools such as MassFragment™, structure confirmations for small molecule unknowns or hits from a database are greatly simplified.

In this work, we have chosen some small molecules to evaluate the applicability of the TAP fragmentation. Molecules from different chemical classes were used so that the TAP fragmentation could be generated and evaluated in ESI+ mode and in ESI- modes. Examples chosen include natural product extracts such as Ginsenosides; and several phospholipids. The TAP fragmentation patterns of these compounds were analyzed with the Mass Fragment™ software tool providing a rapid confirmation of the proposed structures. In addition, the reproducibility of the drift times of the compounds were studied during the course of the experiments.