Collision-induced fragmentation of biomolecules inside an ion funnel

Ion funnels are radiofrequency (RF) devices used for the transmission of ions through a relatively high-pressure vacuum interface (typically 0.01 mbar - 10 mbar) [1]. They are made of ring electrodes with RF voltages of opposite polarity applied on successive electrodes for confining the ions radially, and a DC gradient for guiding the ions along the length of the device. The ring electrodes have reducing inner diameters toward the exit of the ion funnel so that the ions are effectively focused from the entrance to the exit of the device. They are routinely employed as a vacuum interface for electrospray ionization sources. It is known that the ion funnels could induce fragmentation of biomolecular ions generated in an electrospray ion source [2]. However, no systematic characterization of this process is not available in the literature. In this work, we study systematically the collision-induced fragmentation [3] of one of the building blocks of DNA while passing through an ion funnel. We show that the ion funnel parameters can be optimized to reduce the fragmentation process without sacrificing the total number of ions transmitted through the device.

References:

[1] S. A. Shaffer, et al., Rapid Commun. Mass Spectrom. 11, 1813 (1997).

[2] R. T. Kelly, et al., Mass Spectrom. Rev. 29, 294 (2010).

[3] Y. Ho and P. Kebarle, Int. J. Mass Spectrom. Ion Process. 165, 433 (1997).