Trapped ion mobility spectrometry (TIMS) is a relatively new gas-phase separation method that has been coupled to quadrupole orthogonal acceleration time-of-flight mass spectrometry. The TIMS analyzer is a segmented rf ion guide wherein ions are mobility-analyzed using an electric field that holds ions stationary against a moving gas, unlike conventional drift tube ion mobility spectrometry where the gas is stationary. Ions are initially trapped, and subsequently eluted from the TIMS analyzer over time according to their mobility (K). Though TIMS has achieved a high level of performance (R > 250) in a small device (<5 cm) using modest operating potentials (<300 V), a proper theory has yet to be produced. Here, we develop a quantitative theory for TIMS via mathematical derivation and simulations. A one-dimensional analytical model, used to predict the transit time and theoretical resolving power, is described. Theoretical trends are in agreement with experimental measurements performed as a function of K, pressure, and the axial electric field scan rate. The linear dependence of the transit time with 1/K provides a fundamental basis for determination of reduced mobility or collision cross section values by calibration. The quantitative description of TIMS provides an operational understanding of the analyzer, outlines the current performance capabilities, and provides insight into future avenues for improvement.

Past experimental results and molecular dynamics simulations provide evidence that, under some conditions, electrospray ionization (ESI) of biomolecules produces ions that retain elements of solution phase structures. However, there is a dearth of information regarding the question raised by Breuker and McLafferty, "for how long, under what conditions, and to what extent, can solution structure be retained without solvent?" (Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18145). Here, we use cryogenic ion mobility-mass spectrometry to experimentally probe the structural evolution of the undecapeptide substance P (SP) during the final stages of ESI. The results reveal that anhydrous SP conformers originate from evaporation of cluster ions, specifically, [SP + 2H](2+) (H2O)n (n = 0 to ∼50) and [SP + 3H](3+) (H2O)n (n = 0 to ∼30), and that major structural changes do not occur during the evaporative process. In the case of [SP + 3H](3+), the results demonstrate that a compact dehydrated conformer population can be kinetically trapped on the time scale of several milliseconds, even when an extended gas phase conformation is energetically favorable.

In the present work, we employ trapped ion mobility spectrometry (TIMS) for conformational analysis of several model peptides. The TIMS distributions are extensively compared to recent ion mobility spectrometry (IMS) studies reported in the literature. At a resolving power (R) exceeding 250, many new features, otherwise hidden by lower resolution IMS analyzers, are revealed. Though still principally limited by the plurality of conformational states, at present, TIMS offers R up to ∼3 to 8 times greater than modern drift tube or traveling wave IMS techniques, respectively. Unlike differential IMS, TIMS not only is able to resolve congested conformational features but also can be used to determine information about their relative size, via the ion-neutral collision cross section, offering a powerful new platform to probe the structure and dynamics of biochemical systems in the gas phase.

The present work employs trapped ion mobility spectrometry (TIMS) for the analysis of ubiquitin ions known to display a multitude of previously unresolved interchangeable conformations upon electrospray ionization. The conformational distributions of ubiquitin [M + 6H](6+) through [M + 13H](13+) ions observed by TIMS are nearly identical to numerous drift tube ion mobility spectrometry studies reported in the literature. At an experimental resolving power up to ∼300, many of the congested conformations within the well-known compact, partially folded, and elongated [M + 7H](7+) states are separated. Minimizing the voltages (RF and DC) in the entrance funnel results in exclusive observation of compact [M + 7H](7+) conformers. However, under these conditions, the mobility-dependent pseudopotential coefficient may discriminate against ions having larger collision cross sections-a universal effect for all RF ion guides, funnels, and traps operating in the presence of a gas. The data presented underscore the complications associated with direct comparison of collision cross section values that represent an ensemble average of multiple underlying conformations. As illustrated herein, the microheterogeneity within a particular conformational family and the relative state-to-state abundance can be altered by solvent memory, energetic, and kinetic effects.

Evaporation of water from extensively hydrated protons and peptides formed by electrospray ionization (ESI) has been examined for the first time by cryogenic ion mobility-mass spectrometry (IM-MS). The extent of hydration was controlled using a heated capillary inlet operated between 340 and 391 K. Cold cluster ions formed in the source region were transported into a low temperature (∼80 K) IM drift tube using an electrostatic ion guide where they were separated on the basis of size-to-charge via low-energy collisions with helium gas. The eluting IM profile was subsequently pulsed into an orthogonal time-of-flight (TOF) mass spectrometer for mass-to-charge (m/z) identification of the cluster ion species. Key parameters that influence the cluster distributions were critically examined including the inlet temperature, drift tube temperature, and IM field strength. In agreement with previous studies, our findings indicate that water evaporation is largely dependent upon the particular charge-carrying species within the cluster. IM-MS results for protonated water clusters suggest that the special stability of H(+)(H(2)O)(n) (n = 21) is attributed to the presence of a compact isomer (assigned to a clathrate cage) that falls below the trendline produced by adjacent clusters in the n = 15 to 35 size range. Peptide studies are also presented in which specific and nonspecific solvation is observed for gramicidin S [GS + 2H](2+)(H(2)O)(n) (n = 0 to ∼26) and bradykinin [BK + 2H](2+)(H(2)O)(n) (n = 0 to ∼73), respectively.