Feasibility of higher-order differential ion mobility separations using new asymmetric waveforms

Metal Polycation Adduction to Lipids Enables Superior Ion Mobility Separations with Ultrafast Ozone-Induced Dissociation

Specific lipid isomers are functionally critical, but their structural rigidity and usually minute geometry differences make separating them harder than other biomolecules. Such separations by ion mobility spectrometry (IMS) were recently enabled by new high-definition methods using dynamic electric fields, but major resolution gains are needed. Another problem of identifying many isomers with no unique fragments in ergodic collision-induced dissociation (CID) was partly addressed by the direct ozone-induced dissociation (OzID) that localizes the double bonds, but a low reaction efficiency has limited the sensitivity, dynamic range, throughput, and compatibility with other tools. Typically lipids are analyzed by MS as singly charged protonated, deprotonated, or ammoniated ions. Here, we explore the differential IMS (FAIMS) separations with OzID for exemplary lipids cationized by polyvalent metals. These multiply charged adducts have much greater FAIMS compensation voltages (UC) than the 1+ ions, with up to 10-fold resolution gain enabling baseline isomer separations even at a moderate resolving power of the SelexION stage. Concomitantly OzID speeds up by many orders of magnitude, producing a high yield of diagnostic fragments already in 1 ms. These capabilities can be ported to the superior high-definition FAIMS and high-pressure OzID systems to take lipidomic analyses to the next level.

Expanding Differential Ion Mobility Separations into the MegaDalton Range

Along with mass spectrometry (MS), ion mobility separations (IMS) are advancing to ever larger biomolecules. The emergence of electrospray ionization (ESI) and native MS enabled the IMS/MS analyses of proteins up to ∼100 kDa in the 1990s and whole protein complexes and viruses up to ∼10 MDa since the 2000s. Differential IMS (FAIMS) is substantially orthogonal to linear IMS based on absolute mobility K and offers exceptional resolution, unique selectivity, and steady filtering readily compatible with slower analytical methods such as electron capture or transfer dissociation (ECD/ETD). However, the associated MS stages had limited FAIMS to ions with m/z < 8000 and masses under ∼300 kDa. Here, we integrate high-definition FAIMS with the Q-Exactive Orbitrap UHMR mass spectrometer that can handle m/z up to 80,000 and MDa-size ions in the native ESI regime. In the initial evaluation, the oligomers of monoclonal antibody adalimumab (148 kDa) are size-selected up to at least the nonamers (1.34 MDa) with m/z values up to ∼17,000. This demonstrates the survival and efficient separation of noncovalent MDa assemblies in the FAIMS process, opening the door to novel analyses of the heaviest macromolecules.

Ion mobility calculations of flexible all-atom systems at arbitrary fields using two-temperature theory

Ion mobility spectrometry (IMS) separates and analyzes ions based on their mobility in a gas under an electric field. When the field is increased, the mobility varies in a complex way that depends on the relative velocity between gas and ion, their electrostatic potential interactions, and the effects from direct impingement. Recently, the two-temperature theory, primarily developed for monoatomic ions in monoatomic gases, has been extended to study mobilities at arbitrary fields using polyatomic ions in polyatomic gases, with some success. However, this extension poses challenges, such as inelastic collisions between gas and ion and structural modifications of ions as they heat up. These challenges become significant when working with diatomic gases and flexible molecules. In a previous study, experimental mobilities of tetraalkylammonium salts were obtained using a FAIMS instrument, showing satisfactory agreement with numerical two-temperature theory predictions. However, deviations occurred at fields greater than 100 Td. To address this issue, this paper introduces a modified high-field calculation method that accounts for the structural changes in ions due to field heating. The study focuses on tetraheptylammonium (THA+), tetradecylammonium (TDA+), and tetradodecylammonium (TDDA+) salts. Molecular structures were generated at various temperatures using MM2 forcefield. The mobility was calculated using IMoS 1.13 with two-temperature trajectory method calculations up to the fourth approximation. Multiple effective temperatures were considered, and a linear weighing system was used to create mobility vs. reduced field strength plots. The results suggest that the structural enlargement due to ion heating plays a significant role in mobility at high fields, aligning better with experimental data. FAIMS' dispersion plots also show improved agreement with experimental results. However, the contribution of inelastic collisions and energy transfer to rotational degrees of freedom in gas molecules remains a complex and challenging aspect.

Investigation of Zero-/High-Field Ion Mobility Orthogonal Separation Using a Hyphenated DMA-FAIMS System and Validation of the Two-Temperature Theory at Arbitrary Field for Tetraalkylammonium Salts in Nitrogen

Toward greater separation techniques for ions, a differential mobility analyzer (DMA) has been coupled with field asymmetric waveform ion mobility spectrometry (FAIMS) to take advantage of two mobility-related but different methods of separation. The filtering effect of the DMA allows ions to be selected individually based on low-field mobility and studied in FAIMS at variable electric field, yielding mobility separations in two dimensions. Because spectra fully describe ion mobility at variable field strength, results are then compared with a two-temperature theory-predicted mobility up to the fourth-order approximation. The comparison yields excellent results up to at least 100 Td, beyond which the theory deviates from experiments. This is attributed to two effects, the enlargement of the structure due to ion heating and the inelasticity of the collisions with the nitrogen bath gas. The corrected mobility can then be used to predict the dispersion plot through a newly developed implicit equation that circumvents the possible issues related to the more elaborate Buryakov equation. Our results simultaneously show that the DMA-FAIMS coupling yields complete information on ion mobility versus the field-strength to gas-density ratio and works toward predicting such spectra from ion structures and gas properties.

Disentangling Lipid Isomers by High-Resolution Differential Ion Mobility Spectrometry/Ozone-Induced Dissociation of Metalated Species

The preponderance and functional importance of isomeric biomolecules have become topical in biochemistry. Therefore, one must distinguish and identify all such forms across compound classes, over a wide dynamic range as minor species often have critical activities. With all the power of modern mass spectrometry for compositional assignments by accurate mass, the identical precursor and often fragment ion masses render this task a steep challenge. This is recognized in proteomics and epigenetics, where proteoforms are disentangled and characterized employing novel separations and non-ergodic dissociation mechanisms. This issue is equally pertinent to lipidomics, where the lack of isomeric depth has thwarted the deciphering of functional networks. Here we introduce a new platform, where the isomeric lipids separated by high-resolution differential ion mobility spectrometry (FAIMS) are identified using ozone-induced dissociation (OzID). Cationization by metals (here K⁺, Ag⁺, and especially Cu⁺) broadly improves the FAIMS resolution of isomers with alternative C═C double bond (DB) positions or stereochemistry, presumably via metal attaching to the DB and reshaping the ion around it. However, the OzID yield diminishes for Ag⁺ and vanishes for Cu⁺ adducts. Argentination still strikes the best compromise between efficient separation and diagnostic fragmentation for optimal FAIMS/OzID performance.

Ion Mobility Spectrometry of Superheated Macromolecules at Electric Fields up to 500 Td

Since its inception in 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) has been implemented at or near ambient gas pressure. We recently developed FAIMS at 15-30 Torr with mass spectrometry and utilized it to analyze amino acids, isomeric peptides, and protein conformers. The separations broadly mirrored those at atmospheric pressure, save for larger proteins that (as predicted) exhibited dipole alignment at ambient but not low pressure. Here we reduce the pressure down to 4.7 Torr, allowing normalized electric fields up to 543 Td-double the maximum in prior FAIMS or IMS studies of polyatomic ions. Despite the collisional heating to ∼1000 °C at the waveform peaks, the proteins of size from ubiquitin to albumin survived intact. The dissociation of macromolecules in FAIMS appears governed by the average ion temperature over the waveform cycle, unlike the isomerization controlled by the peak temperature. The global separation trends in this "superhot" regime extend those at moderately low pressures, with distinct conformers and no alignment as theorized. Although the scaling of the compensation voltage with the field fell below cubic at lower fields, the resolving power increased and the resolution of different proteins or charge states substantially improved.

Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms

Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility. We now use complete histone tails with diverse PTMs on alternative sites to demonstrate that high-resolution linear IMS, here trapped IMS (TIMS), broadly resolves the variants of ∼50 residues in full or into binary mixtures quantifiable by tandem MS, largely thanks to orthogonal separations across charge states. Separations using traveling-wave (TWIMS) and/or involving various time scales and electrospray ionization source conditions are similar (with lower resolution for TWIMS), showing the transferability of results across linear IMS instruments. The linear IMS and FAIMS dimensions are substantially orthogonal, suggesting FAIMS/IMS/MS as a powerful platform for proteoform analyses.

Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation

Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data. Graphical Abstract ᅟ.

Differential mobility spectrometry/mass spectrometry history, theory, design optimization, simulations, and applications

This review of differential mobility spectrometry focuses primarily on mass spectrometry coupling, starting with the history of the development of this technique in the Soviet Union. Fundamental principles of the separation process are covered, in addition to efforts related to design optimization and advancements in computer simulations. The flexibility of differential mobility spectrometry design features is explored in detail, particularly with regards to separation capability, speed, and ion transmission. 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:687-737, 2016.

Gridless overtone mobility spectrometry

A novel overtone mobility spectrometry (OMS) instrument utilizing a gridless elimination mechanism and cooperative radio frequency confinement is described. The gridless elimination region uses a set of mobility-discriminating radial electric fields that are designed so that the frequency of field application results in selective transmission and elimination of ions. To neutralize ions with mobilities that do not match the field application frequency, active elimination regions radially defocus ions toward the lens walls. Concomitantly, a lens-dependent radio frequency waveform is applied to the transmission regions of the drift tube resulting in radial confinement for mobility-matched ions. Compared with prior techniques, which use many grids for ion elimination, the new gridless configuration substantially reduces indiscriminate ion losses. A description of the apparatus and elimination process, including detailed simulations showing how ions are transmitted and eliminated is presented. A prototype 28 cm long OMS instrument is shown to have a resolving power of 20 and is capable of attomole detection limits of a model peptide (angiotensin I) spiked into a complex mixture (in this case peptides generated from digestion of β-casein with trypsin).

Separation of protein conformers by differential ion mobility in hydrogen-rich gases

Proteins in solution or the gas phase tend to exhibit multiple conformational families, each comprising distinct structures. Separation methods have generally failed to resolve these, with their convolution producing wide peaks. Here, we report full separation of >10 conformers for most ubiquitin charge states by the new approach of differential ion mobility spectrometry (field asymmetric waveform ion mobility spectrometry, FAIMS) employing H2/N2 gas mixtures with up to 85% H2. The resolving power (up to 400) is five times the highest previously achieved (using He/N2 buffers), greatly increasing the separation specificity. The peak widths match the narrowest obtained by FAIMS for any species under the same conditions and scale with the protein charge state (z) and ion residence time (t) as z(-1/2) and t(-1/2), as prescribed for instrumental (diffusional) broadening. This suggests resolution of specific geometries rather than broader ensembles.

Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS

Differential ion mobility spectrometry (FAIMS) separates ions in gases based on the difference between their mobilities in strong and weak electric fields, captured directly employing a periodic waveform with dissimilar profiles in opposite polarities. As that difference is not tightly correlated with the ion size or mass, FAIMS separations are generally quite orthogonal to both conventional IMS (based on the absolute ion mobility that reflects the physical ion size) and mass spectrometry (based on mass). Until a few years ago, that advantage was largely offset by poor FAIMS resolving power (∼10-20), an order of magnitude below that achieved with conventional (drift-tube) IMS. This article summarizes the major recent technical developments that have raised FAIMS resolving power up to ∼500. These include use of higher and more stable voltages provided by new waveform generators, novel buffer gas compositions comprising high helium or hydrogen fractions, and extended filtering times up to ∼1 s. These advances have enabled previously unthinkable analyses such as broad baseline separations of peptide sequence inversions, localization variants (post-translationally modified peptides with differing PTM attachment sites) even for the larger "middle-down" peptides and smallest PTMs, and lipid regioisomers.

A mobile instrumentation platform to distinguish airway disorders

Asthma and chronic obstructive pulmonary disease (COPD) are distinct but clinically overlapping airway disorders which often create diagnostic and therapeutic dilemmas. Current strategies to discriminate these diseases are limited by insensitivity and poor performance due to biologic variability. We tested the hypothesis that a gas chromatograph/differential mobility spectrometer (GC/DMS) sensor could distinguish between clinically well-defined groups with airway disorders based on the volatile organic compounds (VOCs) obtained from exhaled breath. After comparing VOC profiles obtained from 13 asthma, 5 COPD and 13 healthy control subjects, we found that VOC profiles distinguished asthma from healthy controls and also a subgroup of asthmatics taking the drug omalizumab from healthy controls. The VOC profiles could not distinguish between COPD and any of the other groups. Our results show a potential application of the GC/DMS for non-invasive and bedside diagnostics of asthma and asthma therapy monitoring. Future studies will focus on larger sample sizes and patient cohorts.

High-resolution differential ion mobility spectrometry of a protein

Use of elevated electric fields and helium-rich gases has recently enabled differential ion mobility spectrometry (IMS) with a resolving power up to R ∼ 300. Here we applied that technique to a protein (ubiquitin), achieving R up to ∼80 and separating previously unresolved conformers. While still limited by conformational multiplicity, this resolution is some 4 times greater than that previously reported using either conventional (drift-tube or traveling-wave) or differential IMS. The capability for fine resolution of protein conformers may open new avenues for proteoform separations in top-down and intact-protein proteomics.

Uniform moment theory for charged particle motion in gases

Moment equations for the motion of trace amounts of charged particles through dilute gases are developed from the Boltzmann equation. A new method for truncating the coupled moment equations is used to develop differential equations governing the moments in successive approximations. The first approximation equations are shown to agree completely with equations known to describe ion motion in drift-tube mass spectrometers, ion mobility spectrometers, ion traps, and collision-dominated ion cyclotron resonance experiments. Applications to differential mobility spectrometers and other devices are also described.

High-field asymmetric waveform ion mobility spectrometry with solvent vapor addition: a potential greener bioanalytical technique

Green chemistry is a way to avoid threats to human health and the environment in chemical processes, including analytical methodology. According to the 12 principles provided by ACS Green Chemistry Institute, first described by Anastas and Warner, prevention of waste generation should be first considered as an alternative to ways of treating waste. Therefore, analytical techniques that may reduce solvent waste are of great interest towards greener analysis. High-field asymmetric waveform ion mobility spectrometry (FAIMS) utilizes electrical fields to achieve separation, post an ionization source, and could provide an alternative method for separation and reduce solvent use in comparison with traditional HPLC methodologies. In this article, the operational principles and developments of FAIMS will be discussed, including the advantages of adding solvent vapor to the carrier gas. In addition, applications and challenges of implementing FAIMS technology will also be discussed.

Predicting compensation voltage for singly-charged ions in high-field asymmetric waveform ion mobility spectrometry (FAIMS)

Correlation between compensation voltage (CV) and the m/z ratio of singly-charged ions was elucidated. The experimental data for various alkylammonium homologues and various pharmaceutical compounds were used to construct empirical calibration curves that were fit using commercial regression analysis software packages. The best fit equations were applied to calculate the CV differences (ΔCV) in pure N(2) and N(2)/He 50/50 carrier gasses and CV values for a variety of compounds using only m/z values. The calculated values were in good agreement with experimental data and ΔCV values exhibited a very strong correlation with m/z. Application of these empirical calculations may provide a powerful CV prediction tool for researchers using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the value of FAIMS as an analytical method.

Ion mobility mass spectrometry for peptide analysis

The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.

Separation and classification of lipids using differential ion mobility spectrometry

Correlations between the dimensions of a 2-D separation create trend lines that depend on structural or chemical characteristics of the compound class and thus facilitate classification of unknowns. This broadly applies to conventional ion mobility spectrometry (IMS)/mass spectrometry (MS), where the major biomolecular classes (e.g., lipids, peptides, nucleotides) occupy different trend line domains. However, strong correlation between the IMS and MS separations for ions of same charge has impeded finer distinctions. Differential IMS (or FAIMS) is generally less correlated to MS and thus could separate those domains better. We report the first observation of chemical class separation by trend lines using FAIMS, here for lipids. For lipids, FAIMS is indeed more independent of MS than conventional IMS, and subclasses (such as phospho-, glycero-, or sphingolipids) form distinct, often non-overlapping domains. Even finer categories with different functional groups or degrees of unsaturation are often separated. As expected, resolution improves in He-rich gases: at 70% He, glycerolipid isomers with different fatty acid positions can be resolved. These results open the door for application of FAIMS to lipids, particularly in shotgun lipidomics and targeted analyses of bioactive lipids.

Ultrahigh-resolution differential ion mobility spectrometry using extended separation times

Ion mobility spectrometry (IMS), and particularly differential IMS or field asymmetric waveform IMS (FAIMS), is emerging as a versatile tool for separation and identification of gas-phase ions, especially in conjunction with mass spectrometry. For over two decades since its inception, the utility of FAIMS was constrained by resolving power (R) of less than ∼20. Stronger electric fields and optimized gas mixtures have recently raised achievable R to ∼200, but further progress with such approaches is impeded by electrical breakdown. However, the resolving power of planar FAIMS devices using any gas and field intensity scales as the square root of separation time (t). Here, we extended t from the previous maximum of 0.2 s up to 4-fold by reducing the carrier gas flow and increased the resolving power by up to 2-fold as predicted, to >300 for multiply charged peptides. The resulting resolution gain has enabled separation of previously "co-eluting" peptide isomers, including folding conformers and localization variants of modified peptides. More broadly, a peak capacity of ∼200 has been reached in tryptic digest separations.

Separation of peptide isomers with variant modified sites by high-resolution differential ion mobility spectrometry

Many proteins and proteolytic peptides incorporate the same post-translational modification (PTM) at different sites, creating multiple localization variants with different functions or activities that may coexist in cells. Current analytical methods based on liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS) are challenged by such isomers that often coelute in LC and/or produce nonunique fragment ions. The application of ion mobility spectrometry (IMS) was explored, but success has been limited by insufficient resolution. We show that high-resolution differential ion mobility spectrometry (FAIMS) employing helium-rich gases can readily separate phosphopeptides with variant modification sites. Use of He/N(2) mixtures containing up to 74% He has allowed separating to >95% three monophosphorylated peptides of identical sequence. Similar separation was achieved at 50% He, using an elevated electric field. Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate FAIMS capabilities for such separations to extend to other PTMs.

High-resolution differential ion mobility separations using planar analyzers at elevated dispersion fields

The ion mobility spectrometry (IMS) methods are grouped into conventional IMS, based on the absolute ion mobility, and differential or field asymmetric waveform IMS (FAIMS), based on mobility differences between strong and weak electric fields. A key attraction of FAIMS is substantial orthogonality to mass spectrometry (MS). Although several FAIMS/MS platforms were commercialized, their utility was limited by FAIMS resolving power, typically ∼10-20. Recently, gas mixtures comprising up to 75% He have enabled resolving power >100 that permits separation of numerous heretofore "coeluting" isomers. This performance opens major new proteomic and other biological applications. Here, we show that raising the separation field by ∼35% over the previous 21 kV/cm provides similar or better resolution (with resolving powers of >200 for multiply charged peptides) using only 50% He, which avoids problems due to elevated pressure and He content in the mass spectrometer. The heating of ions by the separation field in this regime exceeds that at higher He content but weaker field, inducing greater isomerization of labile species.

A high voltage asymmetric waveform generator for FAIMS

High field asymmetric waveform ion mobility spectrometry (FAIMS) has been used increasingly in recent years as an additional method of ion separation and selection before mass spectrometry. The FAIMS electrodes are relatively simple to design and fabricate for laboratories wishing to implement their own FAIMS designs. However, construction of the electronics apparatus needed to produce the required high magnitude asymmetric electric field oscillating at a frequency of several hundred kilohertz is not trivial. Here we present an entirely custom-built electronics setup capable of supplying the required waveforms and voltages. The apparatus is relatively simple and inexpensive to implement. We also present data acquired on this system demonstrating the use of FAIMS as a gas-phase ion filter interface to an ion trap mass spectrometer.

High-resolution differential ion mobility separations using helium-rich gases

Analyses of complex mixtures and characterization of ions increasingly involve gas-phase separations by ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) based on the difference of ion mobility in strong and weak electric fields. The key advantage of FAIMS is substantial orthogonality to mass spectrometry (MS), which makes FAIMS/MS hybrid a powerful analytical platform of broad utility. However, the potential of FAIMS has been constrained by limited resolution. Here, we report that the use of gas mixtures comprising up to 75% He dramatically increases the FAIMS separation capability, with the resolving power for peptides and peak capacity for protein digests reaching and exceeding 100. The resolution gains extend to small molecules, where previously unresolved isomers can now be separated. These performance levels open major new applications of FAIMS in proteomic and other biomolecular analyses.

Ultrafast differential ion mobility spectrometry at extreme electric fields in multichannel microchips

The maximum electric field intensity (E) in field asymmetric waveform ion mobility spectrometry (FAIMS) analyses was doubled to E > 60 kV/cm. In earlier devices with >0.5 mm gaps, such strong fields cause electrical breakdown for nearly all gases at ambient pressure. As the Paschen curves are sublinear, thinner gaps permit higher E: here, we established 61 kV/cm in N(2) using microchips with 35 microm gaps. As FAIMS efficiency is exceptionally sensitive to E, such values can in theory accelerate analyses at equal resolution by over an order of magnitude. Here we demonstrate FAIMS filtering in approximately 20 micros or approximately 1% of the previously needed time, with a resolving power of about half that for "macroscopic" units but sufficing for many applications. Microscopic gaps enable concurrent ion processing in multiple (here, 47) channels, which greatly relaxes the charge capacity constraints of planar FAIMS designs. These chips were integrated with a beta-radiation ion source and charge detector. The separation performance is in line with first-principles modeling that accounts for high-field and anisotropic ion diffusion. By extending FAIMS operation into the previously inaccessible field range, the present instrument advances the capabilities for research into ion transport and expands options for separation of hard-to-resolve species.

Overtone mobility spectrometry: part 1. Experimental observations

A new method that allows a linear drift tube to be operated as a continuous ion mobility filter is described. Unlike conventional ion mobility instruments that use an electrostatic gate to introduce a packet of ions into a drift region, the present approach uses multiple segmented drift regions with modulated drift fields to produce conditions that allow only ions with appropriate mobilities to pass through the instrument. In this way, the instrument acts as a mobility filter for continuous ion sources. By changing the frequency of the applied drift fields it is possible to tune this instrument to transmit ions having different mobilities. A scan over a wide range of drift field frequencies for a single ion species shows a peak corresponding to the expected resonance time of the ions in one drift region segment and a series of peaks at higher frequencies that are overtones of the resonant frequency. The measured resolving power increases for higher overtones, making it possible to resolve structures that were unresolved in the region of the fundamental frequency. We demonstrate the approach by examining oligosaccharide isomers, raffinose and melezitose as well as a mixture of peptides obtained from enzymatic digestion of myoglobin.

Two-dimensional ion mobility analyses of proteins and peptides

Ion mobility separations have emerged as a major tool for mass spectrometry of proteins and peptides. The high speed of ion mobility spectrometry (IMS) compared with chromatography enables accelerating proteomic analyses at same separation power or raising the peak capacity at equal throughput. Of interest to structural biology, tractable physics of ion transport in gases permits characterizing the structure of macromolecules by matching measured mobilities to values calculated for candidate geometries. The two known experimental methods are drift-tube IMS based on absolute mobility and field asymmetric waveform IMS (FAIMS) based on differential mobility as a function of electric field. Here, we describe combining them into 2D separations coupled to time-of-flight MS, a development made practical by electrodynamic ion funnel interfaces that effectively convey ions in and out of IMS, including "hourglass" funnels to accumulate ions filtered by FAIMS between pulsed injections into IMS. For peptide separations, the peak capacity of FAIMS/IMS is ~500 and potentially higher, a metric close to that of top capillary LC systems. In structural investigations, FAIMS/IMS allows more protein conformers to be distinguished than either stage alone, and extends the dynamic range of detection by an order of magnitude over 1D IMS. A controlled heating of ions by rf field over a variable time in the funnel trap between FAIMS and IMS stages allows following the evolution of selected isomers in both thermodynamic and kinetic aspects, which opens a new approach to mapping the pathways and energy surfaces of protein folding.

Optimum waveforms for differential ion mobility spectrometry (FAIMS)

Differential mobility spectrometry or field asymmetric waveform ion mobility spectrometry (FAIMS) is a new tool for separation and identification of gas-phase ions, particularly in conjunction with mass spectrometry. In FAIMS, ions are filtered by the difference between mobilities in gases (K) at high and low electric field intensity (E) using asymmetric waveforms. An infinite number of possible waveform profiles make maximizing the performance within engineering constraints a major issue for FAIMS technology refinement. Earlier optimizations assumed the non-constant component of mobility to scale as E(2), producing the same result for all ions. Here we show that the optimum profiles are defined by the full series expansion of K(E) that includes terms beyond the first that is proportional to E(2). For many ion/gas pairs, the first two terms have different signs, and the optimum profiles at sufficiently high E in FAIMS may differ substantially from those previously reported, improving the resolving power by up to 2.2 times. This situation arises for some ions in all FAIMS systems, but becomes more common in recent miniaturized devices that employ higher E. With realistic K(E) dependences, the maximum waveform amplitude is not necessarily optimum, and reducing it by up to approximately 20% to 30% is beneficial in some cases. The present findings are particularly relevant to targeted analyses where separation depends on the difference between K(E) functions for specific ions.

Differential mobility separation of ions using a rectangular asymmetric waveform

The performance of a planar differential mobility spectrometer (DMS) is investigated when operated in air at ambient pressure and driven by a rectangular asymmetric waveform, limited to frequencies of <1.2 MHz and voltage pulse amplitudes of <1 kV with steep rise times of the order of approximately 15 ns. Independent control of frequency, voltage pulse amplitude, and duty cycle allow for characterizing the DMS in terms of transmission, resolution and separation. The tradeoff between sensitivity and resolution and the effect of duty cycle on instrument performance are demonstrated experimentally. The dependence of ion mobility on the magnitude of the electric field determines the displacement of ions measured by the DC compensation voltage as a function of the duty cycle. Optimum values for the duty cycle exist for the separation of A- and C-type ions, while, B-type ions exhibit a more complex behavior. An analytical expression for describing the effect of duty cycle on the separation of the ions, determined by variations in the compensation voltage, is developed and compared to experimental results obtained in air below 75 Td using estimated alpha parameters for a set of ketones. In this context, errors associated with the calculation of alpha parameters using polynomials of even powers are highlighted.

Biomolecule analysis by ion mobility spectrometry

Although nonnative protein conformations, including intermediates along the folding pathway and kinetically trapped misfolded species that disfavor the native state, are rarely isolated in the solution phase, they are often stable in the gas phase, where macromolecular ions from electrospray ionization can exist in varying charge states. Differences in the structures of nonnative conformations in the gas phase are often large enough to allow different shapes and charge states to be separated because of differences in their mobilities through a gas. Moreover, gentle collisional activation can be used to induce structural transformations. These new structures often have different mobilities. Thus, there is the possibility of developing a multidimensional separation that takes advantage of structural differences of multiple stable states. This review discusses how nonnative states differ in the gas phase compared with solution and presents an overview of early attempts to utilize and manipulate structures in order to develop ion mobility spectrometry as a rapid and sensitive technique for separating complex mixtures of biomolecules prior to mass spectrometry.

Scaling of the resolving power and sensitivity for planar FAIMS and mobility-based discrimination in flow- and field-driven analyzers

Continuing development of the technology and applications of field asymmetric waveform ion mobility spectrometry (FAIMS) calls for better understanding of its limitations and factors that govern them. While key performance metrics such as resolution and ion transmission have been calculated for specific cases employing numerical simulations, the underlying physical trends remained obscure. Here we determine that the resolving power of planar FAIMS scales as the square root of separation time and sensitivity drops exponentially at the rate controlled by absolute ion mobility and several instrument parameters. A strong dependence of ion transmission on mobility severely discriminates against species with higher mobility, presenting particular problems for analyses of complex mixtures. While the time evolution of resolution and sensitivity is virtually identical in existing FAIMS systems using gas flow and proposed devices driven by electric field, the distributions of separation times are not. The inverse correlation between mobility (and thus diffusion speed) and residence time for ions in field-driven FAIMS greatly reduces the mobility-based discrimination and provides much more uniform separations. Under typical operating conditions, the spread of elimination rates for commonly analyzed ions is reduced from >5 times in flow-driven to 1.6 times in field-driven FAIMS while the difference in resolving power decreases from approximately 60% to approximately 15%.

Review of applications of high-field asymmetric waveform ion mobility spectrometry (FAIMS) and differential mobility spectrometry (DMS)

High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) and Differential Mobility Spectrometry (DMS) harness differences in ion mobility in low and high electric fields to achieve a gas-phase separation of ions at atmospheric pressure. This separation is orthogonal to either chromatographic or mass spectrometric separation, thereby increasing the selectivity and specificity of analysis. The orthogonality of separation, which in some cases may obviate chromatographic separation, can be used to differentiate isomers, to reduce background, to resolve isobaric species, and to improve signal-to-noise ratios by selective ion transmission. This review will focus on the applications of these techniques to the separation of various classes of analytes, including chemical weapons, explosives, biologically active molecules, pharmaceuticals and pollutants. These papers cover the period up to January 2007.

Distortion of ion structures by field asymmetric waveform ion mobility spectrometry

Field asymmetric waveform ion mobility spectrometry (FAIMS) is emerging as a major analytical tool, especially in conjunction with mass spectrometry (MS), conventional ion mobility spectrometry (IMS), or both. In particular, FAIMS is used to separate protein or peptide conformers prior to characterization by IMS, MS/MS, or H/D exchange. High electric fields in FAIMS induce ion heating, previously estimated at <10 degrees C on average and believed too weak to affect ion geometries. Here we use a FAIMS/IMS/MS system to compare the IMS spectra for ESI-generated ubiquitin ions that have and have not passed FAIMS and find that some unfolding occurs for most charge states. These data and their comparison with the reported protein unfolding in a Paul trap imply that at least some structural transitions observed in FAIMS, or previously in an ion trap, are not spontaneous. The observed unfolding is similar to that produced by heating of approximately 50 degrees C above room temperature, consistent with the calculated heating of ions at FAIMS waveform peaks. Hence, the ion isomerization in FAIMS likely proceeds in steps during the "hot" periods, especially right after entering the device. The process distorts ion geometries and causes ion losses by a "self-cleaning" mechanism and thus should be suppressed as much as possible. We propose achieving that via cooling FAIMS by the amount of ion heating; in most cases, cooling by approximately 75 degrees C should suffice.

Field Asymmetric Waveform Ion Mobility Spectrometry Studies of Proteins: Dipole Alignment in Ion Mobility Spectrometry?

Approaches to separation and characterization of ions based on their mobilities in gases date back to the 1960s. Conventional ion mobility spectrometry (IMS) measures the absolute mobility, and field asymmetric waveform IMS (FAIMS) exploits the difference between mobilities at high and low electric fields. However, in all previous IMS and FAIMS experiments ions experienced an essentially free rotation; thus the separation was based on the orientationally averaged cross-sections Omega(avg) between ions and buffer gas molecules. Virtually all large ions are permanent electric dipoles that will be oriented by a sufficiently strong electric field. Under typical FAIMS conditions this will occur for dipole moments >400 D, found for many macroions including most proteins above approximately 30 kDa. Mobilities of aligned dipoles depend on directional cross-sections Omega(dir) (rather than Omega(avg)), which should have a major effect on FAIMS separation parameters. Here we report the FAIMS behavior of electrospray-ionization-generated ions for 10 proteins up to approximately 70 kDa. Those above 29 kDa exhibit a strong increase of mobility at high field, which is consistent with predicted ion dipole alignment. This effect expands the useful FAIMS separation power by an order of magnitude, allowing separation of up to approximately 10(2) distinct protein conformers and potentially revealing information about Omega(dir) and ion dipole moment that is of utility for structural characterization. Possible approaches to extending dipole alignment to smaller ions are discussed.