In the present paper, theoretical simulations and experimental observations are used to describe the ion dynamics in a trapped ion mobility spectrometer. In particular, the ion motion, ion transmission and mobility separation are discussed as a function of the bath gas velocity, radial confinement, analysis time and speed. Mobility analysis and calibration procedure are reported for the case of sphere-like molecules for positive and negative ion modes. Results showed that a maximal mobility resolution can be achieved by optimizing the gas velocity, radial confinement (RF amplitude) and ramp speed (voltage range and ramp time). The mobility resolution scales with the electric field and gas velocity and R = 100–250 can be routinely obtained at room temperature.

In the present work we describe the principles of operation, versatility and applicability of a trapped ion mobility spectrometer (TIMS) analyzer for fast, gas-phase separation of molecular ions based on their size-to-charge ratio. Mobility-based separation using a TIMS device is shown for a series for isobar pairs. In a TIMS device, mobility resolution depends on the bath gas velocity and analysis scan speed, with the particularity that the mobility separation can be easily tuned from low to high resolution (R>50) in accordance with the analytical challenge. In contrast to traditional drift tube IMS analyzer, a TIMS device can be easily integrated in a mass spectrometer without a noticeable loss in ion transmission or sensitivity, thus providing a powerful separation platform prior to mass analysis.

The integration of a trapped ion mobility spectrometer (TIMS) with a mass spectrometer (MS) for complementary fast, gas-phase mobility separation prior to mass analysis (TIMS-MS) is described. The ion transmission and mobility separation are discussed as a function of the ion source condition, bath gas velocity, analysis scan speed, RF ion confinement, and downstream ion optical conditions. TIMS mobility resolution depends on the analysis scan speed and the bath gas velocity, with the unique advantage that the IMS separation can be easily tuned from high speed (∼25 ms) for rapid analysis to slower scans for higher mobility resolution (R > 80). © 2011 American Institute of Physics. [doi:10.1063/1.3665933] Ion mobility spectrometry (IMS) coupling to mass spectrometry offers several advantages over traditional mass spectrometry (MS), including separation of ions from mixtures based on composition and charge state, the ability to separate geometric isomers, increased dynamic range, and discrimination against chemical noise. 1 Several research groups have focused on achieving high resolution IMS separation (R > 50) as this factor mainly limits the information that can be experimentally derived. In a different IMS approach, the use of a trapped ion mobility spectrometer (TIMS) device for fast, gas-phase separation of molecular isobar pairs has been recently described. 1 In the present note, we describe the TIMS-MS integration and its advantage over traditional drift tube based IMS-MS designs; discussion is also focused on the factors that influence TIMS-MS mobility separation, dynamic range, and versatility.In the example presented here, ions were generated by electrospray ionization (ESI) using an ESI ion source based on the Apollo II design (Bruker Daltonics Inc., MA). Accordingly, a quadrupolar funnel optic was used and the capillary coupling the ESI spray chamber to the first pumping stage was orthogonal to the axis of the TIMS analyzer. Each TIMS electrode is composed of four electrically isolated segments. In the entrance and exit funnel sections, a RF-induced pseudopotential keeps the ions away from the funnel walls (180 • out of phase between adjacent plates). However, in the analyzer section, the phase of the RF potential does not alternate between adjacent plates but only between adjacent segments. The RF field (typically 950 kHz and 200-400 Vpp) plays little or no direct role in the mobility analysis. The operating pressure difference (P1 = 2.6-3.4 and P2 = 2.6 mbars) produces a cylindrically symmetric gas flow of nitrogen at ∼300 K. After exiting the TIMS analyzer, ions are focused, using a series of lenses and a hexapole ion guide, through the main differential pumping region. In this transfer area, residual pressure drops from 2.6 mbars in the first funnel to 10 −4 mbars in the a) Author to whom correspondence should be addressed. Electronic mail: ffernandez@chem.tamu.edu.hexapole. After the transfer area, ions enter the quadrupole mass analyzer (Q), which can be operated in transmission or isolation...

Structural characterization of glycosaminoglycans (GAGs) has been a challenge in the field of mass spectrometry, and the application of electron detachment dissociation (EDD) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) has shown great promise to GAG oligosaccharide characterization in a single tandem mass spectrometry experiment. In this work, we apply the technique of negative electron transfer dissociation (NETD) to GAGs on a commercial ion trap mass spectrometer. NETD of GAGs, using fluoranthene or xenon as the reagent gas, produces fragmentation very similar to previously observed EDD fragmentation. Using fluoranthene or xenon, both glycosidic and cross-ring cleavages are observed, as well as even-and odd-electron products. The loss of SO 3 can be minimized and an increase in cross-ring cleavages is observed if a negativelycharged carboxylate is present during NETD, which can be controlled by the charge state or the addition of sodium. NETD effectively dissociates GAGs up to eight saccharides in length, but the low resolution of the ion trap makes assigning product ions difficult. Similar to EDD, NETD is also able to distinguish the epimers iduronic acid from glucuronic acid in heparan sulfate tetrasaccharides and suggests that a radical intermediate plays an important role in distinguishing these epimers. These results demonstrate that NETD is effective at characterizing GAG oligosaccharides in a single tandem mass spectrometry experiment on a widely available mass spectrometry platform.