Gas-phase conformers of the [M + 2H](2+) ion of bradykinin investigated by combining high-field asymmetric waveform ion mobility spectrometry, hydrogen/deuterium exchange, and energy-loss measurements

Characterizing Multidevice Capillary Vibrating Sharp-Edge Spray Ionization for In-Droplet Hydrogen/Deuterium Exchange to Enhance Compound Identification

Multidevice capillary vibrating sharp-edge spray ionization (cVSSI) source parameters have been examined to determine their effects on conducting in-droplet hydrogen/deuterium exchange (HDX) experiments. Control experiments using select compounds indicate that the observed differences in mass spectral isotopic distributions obtained upon initiation of HDX result primarily from solution-phase reactions as opposed to gas-phase exchange. Preliminary studies have determined that robust HDX can only be achieved with the application of same-polarity voltage to both the analyte and the deuterium oxide reagent (D₂O) cVSSI devices. Additionally, a similar HDX reactivity dependence on the voltage applied to the D₂O device for various analytes is observed. Analyte and reagent flow experiments show that, for the multidevice cVSSI setup employed, there is a nonlinear dependence on the D₂O reagent flow rate; increasing the D₂O reagent flow by 100% results in only an ∼10-20% increase in deuterium incorporation for this setup. Instantaneous (subsecond) response times have been demonstrated in the initiation or termination of HDX, which is achieved by turning on or off the reagent cVSSI device piezoelectric transducer. The ability to distinguish isomeric species by in-droplet HDX is presented. Finally, a demonstration of a three-component cVSSI device setup to perform multiple (successive or in combination) in-droplet chemistries to enhance compound ionization and identification is presented and a hypothetical metabolomics workflow consisting of successive multidevice activation is briefly discussed.

Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces

Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.

Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry

High field asymmetric waveform ion mobility spectrometry (FAIMS) is well-established as a tool for separating peptide isomers (sequence inversions and post-translationally modified localization variants). Here, we demonstrate the FAIMS is able to differentiate cis and trans isomers of polyproline. Polyproline assumes an all-cis conformation-the PPI helix-in 1-propanol, and an all-trans conformation-the PPII helix-in aqueous solutions. Differentiation of these conformers may be achieved both through use of a cylindrical FAIMS device and a miniaturized ultrahigh field planar FAIMS device. Graphical Abstract ᅟ.

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.

Enhancement of mass spectrometry performance for proteomic analyses using high-field asymmetric waveform ion mobility spectrometry (FAIMS)

Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high-field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co-eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label-free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments.

Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS

We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.

Separation of a set of peptide sequence isomers using differential ion mobility spectrometry

Protein identification in bottom-up proteomics requires disentangling isomers of proteolytic peptides, a major class of which are sequence inversions. Their separation using ion mobility spectrometry (IMS) has been limited to isomeric pairs. Here we demonstrate baseline separation of all seven 8-mer tryptic peptide isomers using differential IMS. Evaluation of peak capacity implies that even larger libraries should be resolved for heavier peptides with higher charge states.

Miniaturized ultra high field asymmetric waveform ion mobility spectrometry combined with mass spectrometry for peptide analysis

Miniaturized ultra high field asymmetric waveform ion mobility spectrometry (ultra-FAIMS) combined with mass spectrometry (MS) has been applied to the analysis of standard and tryptic peptides, derived from α-1-acid glycoprotein, using electrospray and nanoelectrospray ion sources. Singly and multiply charged peptide ions were separated in the gas phase using ultra-FAIMS and detected by ion trap and time-of-flight MS. The small compensation voltage (CV) window for the transmission of singly charged ions demonstrates the ability of ultra-FAIMS-MS to generate pseudo-peptide mass fingerprints that may be used to simplify spectra and identify proteins by database searching. Multiply charged ions required a higher CV for transmission, and ions with different amino acid sequences may be separated on the basis of their differential ion mobility. A partial separation of conformers was also observed for the doubly charged ion of bradykinin. Selection on the basis of charge state and differential mobility prior to tandem mass spectrometry facilitates peptide and protein identification by allowing precursor ions to be identified with greater selectivity, thus reducing spectral complexity and enhancing MS detection.

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.

Differential ion mobility separations of peptides with resolving power exceeding 50

Differential ion mobility spectrometry (IMS) or field asymmetric waveform IMS (FAIMS) separates gas-phase ions by mobility differences with respect to the electric field intensity. A major emerging FAIMS application is the fractionation of proteolytic digests. Using a planar FAIMS unit with helium/nitrogen mixtures, we have increased FAIMS resolving powers for peptide analyses from the prior maximum of approximately 20-30 to approximately 50-70. The resolution improved nearly 3-fold, allowing, in particular, separation of previously unresolved conformers.

Ultrafast differential ion mobility spectrometry at extreme electric fields coupled to mass spectrometry

Microchip-based field asymmetric waveform ion mobility spectrometry (FAIMS) analyzers featuring a grid of 35 mum-wide channels have allowed electric field intensity (E) over 60 kV/cm, or about twice that in previous devices with >0.5 mm gaps. Since the separation speed scales as E4 to E6, these chips filter ions in just approximately 20 micros (or approximately 100-10,000 times faster than "macroscopic" designs), although with reduced resolution. Here we report integration of these chips into electrospray ionization (ESI) mass spectrometry, with ESI coupled to FAIMS via a curtain plate/orifice interface with edgewise ion injection into the gap. Adjusting gas flows in the system permits control of ion residence time in FAIMS, which affects resolving power independently of ion desolvation after the ESI source. The results agree with a priori simulations and scaling rules. Applications illustrated include analyses of amino acids and peptides. Because of limited resolving power, the present FAIMS units are more suitable for distinguishing compound classes than individual species. In particular, peptides separate from many other classes, including PEGs that are commonly encountered in proteomic analyses. In practical analyses with realistic time constraints, the effective separation power of present FAIMS may approach that of "macroscopic" systems.

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics

Proteomics experiments on complex mixtures have benefited greatly from the advent of fast-scanning ion trap mass spectrometers. However, the complexity and dynamic range of mixtures analyzed using shotgun proteomics is still beyond what can be sampled by data-dependent acquisition. Furthermore, the total liquid chromatography-mass spectrometry (LC-MS) peak capacity is not sufficient to resolve the precursors within these mixtures, let alone acquire tandem mass spectra on all of them. Here we describe the application of a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device as an interface to an ion trap mass spectrometer. The dynamic range and peak capacity of the nanoflow LC-FAIMS-MS analysis was assessed using a complex tryptic digest of S. cerevisiae proteins. By adding this relatively simple device to the front of the mass spectrometer, we obtain an increase in peak capacity >8-fold and an increase in dynamic range of >5-fold, without increasing the length of the LC-MS analysis. Thus, the addition of FAIMS to the front of a table-top mass spectrometer can obtain the peak capacity of multidimensional protein identification technology (MudPIT) while increasing the throughput by a factor of 12.

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.

An IMS-IMS analogue of MS-MS

The development of a new ion mobility/mass spectrometry instrument that incorporates a multifield drift tube/ion funnel design is described. In this instrument, individual components from a mixture of ions can be resolved and selected on the basis of mobility differences prior to collisional activation inside the drift tube. The fragment ions that are produced can be dispersed again in a second ion mobility spectrometry (IMS) region prior to additional collisional activation and MS analysis. The result is an IMS-IMS analogue of MS-MS. Here, we describe the preliminary instrumental design and experimental approach. We illustrate the approach by examining the highly characterized bradykinin and ubiquitin systems. Mobility-resolved fragment ions of bradykinin show that b-type ions are readily discernible fragments, because they exist as two easily resolvable structural types. Current limitations and future directions are briefly discussed.

High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers

Field asymmetric waveform ion mobility spectrometry (FAIMS) has emerged as a powerful tool of broad utility for separation and characterization of gas-phase ions, especially in conjunction with mass spectrometry (MS). In FAIMS, ions are filtered by the dependence of mobility on electric field while being carried by gas flow through the analytical gap between two electrodes of either planar (p-) or cylindrical (c-) geometry. Most FAIMS/MS systems employ c-FAIMS because of its ease of coupling to MS, yet the merits of the two geometries have not been compared in detail. Here, a priori simulations reveal that reducing the FAIMS curvature always improves resolution at equal sensitivity. In particular, the resolving power of p-FAIMS exceeds that of c-FAIMS, typically by a factor of 2-4 depending on the ion species and carrier gas. We have constructed a new planar FAIMS incorporating a curtain plate interface for effective operation with an ESI ion source and joined to an MS using an ion funnel interface with a novel slit aperture. The resolution increases up to 4-fold over existing c-FAIMS, even though the analysis is approximately 2 times faster. This allows separation of species not feasible in previous FAIMS studies, e.g., protonated leucine and isoleucine or new bradykinin isomers. The improvement for protein conformers (of ubiquitin) is less significant, possibly because of multiple unresolved geometries.

Analysis of pharmaceutical formulations using atmospheric pressure ion mobility spectrometry combined with liquid chromatography and nano-electrospray ionisation

The hyphenation of liquid chromatography with atmospheric pressure ion mobility spectrometry is reported using a custom-made dynamic nano-electrospray ionisation (nano-ESI) interface. The analysis of pharmaceutical actives is described, including beta blocker (timolol), antidepressant (paroxetine), analgesic (paracetamol) and opiate (codeine) preparations. On-line ultraviolet diode array (UV) spectroscopic detection was used prior to sample ionisation, to evaluate chromatographic and nano-ESI interface performance. Active drug responses were characterised by chromatographic retention time and electrophoretic ion mobility drift time, and selected ion mobility responses were used to evaluate method performance. Limits of detection for active drugs were in the low-nmol to pmol range. Quantitative responses were investigated using a series of standard solutions of caffeine, showing good linearity (R(2) = 0.9982, n = 6) and reproducibility (RSD = 2.3 %, n = 6). The analysis of an over the counter pharmaceutical formulation demonstrates the potential of ion mobility spectrometry combined with liquid chromatography and nano-electrospray ionisation for the rapid determination of active drugs, as a result of the electrophoretic separation and selectivity afforded by IMS.

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.

Rapid Separation and Quantitative Analysis of Peptides Using a New Nanoelectrospray- Differential Mobility Spectrometer−Mass Spectrometer System

Differential mobility spectrometry (DMS) (see Buryakov, I. A.; Krylov, E. V.; Nazarov, E. G.; Rasulev, U. Kh. Int. J. Mass Spectrom. Ion Processes 1993, 128, 143-148), also commonly referred to as high-field asymmetric waveform ion mobility spectrometry (FAIMS) (see Purves, R. W.; Guevremont, R.; Day, S.; Pipich, C. W.; Matyjaszcyk, M. S. Rev. Sci. Instrum. 1998, 69, 4094-4105), is a rapidly advancing technology for gas-phase ion separation. The interfacing of DMS with mass spectrometry (MS) offers potential advantages over the use of mass spectrometry alone. Such advantages include improvements to mass spectral signal-to-noise, orthogonal/complementary ion separation to mass spectrometry, enhanced ion and complexation structural analysis, and the potential for rapid analyte quantitation. In this report, we investigate the use of our nanoESI-DMS-MS system to demonstrate differential mobility separation of peptides. The formation of higher order peptide aggregate ions (ion complexes) via electrospray ionization and the negative impact this has on DMS peptide separation are examined. The successful use of differential mobility drift gas modifiers (dopants) to reduce aggregate ion size and improve DMS peptide ion separation is presented. Following optimization of DMS peptide separation conditions, we examined next the feasibility of a new analytical platform which uses direct sample infusion with nanoESI-DMS-MS for ultrarapid analyte quantitation. Quantitation of a selected peptide from a semicomplex peptide mixture is presented. Initial feasibility results with this new approach demonstrate good accuracy and reproducibility, as well as an absolute mass sensitivity of 6.8 amol and a minimum dynamic range of 2500 for the peptide of interest. This report offers a first look at utilizing nanoESI-DMS-MS to create an ultrarapid (under 5 s) quantitative analysis platform and its potential in the high-throughput arena. Each ion separation technique, DMS and MS, offers orthogonal ion separation to one another, enhancing the overall specificity for this quantitative approach.

Incorporation of a flared inlet capillary tube on a fourier transform ion cyclotron resonance mass spectrometer

Flared inlet capillary tubes have been coupled with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer to help the ion transmission from the atmospheric pressure to the first vacuum region. We investigated different types of atmospheric pressure ionization methods using flared inlet tubes. For most of the ionization methods, such as ESI and DESI, increased ion current transmitted from the atmospheric pressure ion source to the first stage vacuum system was observed with the use of our enhanced ion inlet designs. The corresponding ion intensity detected on a FT-ICR mass spectrometer was also observed to increase two- to fivefold using ESI or DESI with the flared tube inlet. Moreover, increased spray tip positional tolerance was observed with implementation of the flared inlet tube. We also include our preliminary results obtained by coupling AP-MALDI with flared inlet tube in this paper. For AP-MALDI, the measured ion current transferred through the flared inlet tube was about 2 to 3 times larger than the ion current through the control non-flared inlet tube.

Enhanced mixture analysis of poly(ethylene glycol) using high-field asymmetric waveform ion mobility spectrometry combined with fourier transform ion cyclotron resonance mass spectrometry

The combination of high-field asymmetric waveform ion mobility spectrometry (FAIMS) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) makes possible lower detection limits, increased sensitivity, and increased dynamic range in the analysis of poly(ethylene glycol) (PEG) samples of low molecular weight. The signal gain obtained using FAIMS depends on ion identity, with a range between 1.8x and 14x obtained for various molecular ions of PEG 600. A 1.7-fold reduction in noise is obtained using FAIMS due to the elimination of chemical noise. The improved detection performance is predominantly due to a reduction in adverse Coulomb effects as a result of ions being selectively introduced into the mass spectrometer. The high ion transmission obtained using FAIMS combined with the high sensitivity of FTICR-MS detection make possible separation of multiple gas-phase conformers of PEG molecular cations that have low abundance (less than 0.2% relative abundance) and that have not been detected previously. Mixed dications of PEG that have the same nominal mass but differ by the number polymer subunits (m/Delta m up to 25,000) can be separately introduced into the mass spectrometer using FAIMS. Interactions of the carrier gas with the metal ions that are attached to the PEG molecules appear to be the most significant factor in these FAIMS separations.

Compensation voltage shifting in high-field asymmetric waveform ion mobility spectrometry-mass spectrometry

The separation and ion focusing properties of High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) depend on desolvated ions entering the device, leading to a compound-specific, reproducible compensation voltage (CV) for each ion. This study shows that the conditions identified for stable spray and satisfactory ion desolvation in normal electrospray ionization mass spectrometry (ESI-MS) operation might significantly differ from those required for FAIMS-MS. In a typical setup with high-flow electrospray conditions, ions could be incompletely desolvated, resulting in the formation of unidentified clusters with differing behavior in a FAIMS environment. This causes compound-specific shifts of as much as 10 V in CV values when the mobile phase composition and/or flow rate are varied. The shifts diminish and finally disappear when the flow rate of methanol, used as mobile phase, is reduced to 40 microL/min and that of acetonitrile to 20 microL/min. The reproducibility of the observed CV was determined by scanning the CV while infusing a five-component mixture into a 400 microL/min flow of methanol or 50:50 acetonitrile/water. The relative standard deviation (RSD) for these multiple scans ranged from 0.7% to 6%. Therefore, under a constant set of experimental parameters, the CV does not shift appreciably. These observations have an impact on method development strategies. High flow rates can be used with the FAIMS device, since the CV values are reproducible, but it is likely that clusters are forming. Therefore, CV scans should be performed under conditions which mimic the chromatographic elution or flow injection analysis conditions, including matrix composition, to minimize errors in CV determination. An alternative approach is to determine the liquid flow rate at which the CV becomes compound-specific and to split the mobile phase stream accordingly. These experimental results may be specific to the setup used for this study and may not be directly applicable to other instrument FAIMS devices.

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD(3)OD

Doubly-protonated bradykinin (RPPGFSPFR) and an angiotensin III analogue (RVYIFPF) were subjected to hydrogen/deuterium (H/D) exchange with CD(3)OD in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. A bimodal distribution of deuterium incorporation was present for bradykinin after H/D exchange for 90 s at a CD(3)OD pressure of 4 x 10(-7) Torr, indicating the existence of at least two distinct populations. Bradykinin ion populations corresponding to 0-2 and 5-11 deuteriums (i.e., D(0), D(1), D(2), D(5), D(6), D(7), D(8), D(9), D(10), and D(11)) were each monoisotopically selected and fragmented via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID). The D(0)-D(2) ion populations, which correspond to the slower exchanging population, consistently require lower SORI amplitude to achieve a similar precursor ion survival yield as the faster-reacting (D(5)-D(11)) populations. These results demonstrate that conformation/protonation motif has an effect on fragmentation efficiency for bradykinin. Also, the partitioning of the deuterium atoms into fragment ions suggests that the C-terminal arginine residue exchanges more rapidly than the N-terminal arginine. Total deuterium incorporation in the b(1)/y(8) and b(2)/y(7) ion pairs matches very closely the theoretical values for all ion populations studied, indicating that the ions of a complementary pair are likely formed during the same fragmentation event, or that no scrambling occurs upon SORI. Deuterium incorporation into the y(1)/a(8) pseudo-ion pair does not closely match the expected theoretical values. The other peptide, doubly-protonated RVYIFPF, has a trimodal distribution of deuterium incorporation upon H/D exchange with CD(3)OD at a pressure of 1 x 10(-7) Torr for 600 s, indicating at least three distinct ion populations. After 90 s of H/D exchange where at least two distinct populations are detected, the D(0)-D(7) ion populations were monoisotopically selected and fragmented via SORI-CID over a range of SORI amplitudes. The precursor ion survival yield as a function of SORI amplitude falls into two distinct behaviors corresponding to slower- and faster-reacting ion populations. The slower-reacting population requires larger SORI amplitudes to achieve the same precursor ion survival yield as the faster exchanging population. Total deuterium incorporation into the y(2)/b(5) ion pairs matches closely the theoretical values over all ion populations and SORI amplitudes studied. This result indicates the y(2) and b(5) ions are likely formed by the same mechanism over the SORI amplitudes studied.

Combining H–D exchange and ESI-FAIMS-MS for detecting gas-phase conformers of equine cytochrome c

Conformers of equine cytochrome c were investigated in the gas phase using a combination of high-field asymmetric waveform ion mobility spectrometry (FAIMS) and hydrogen–deuterium (H–D) exchange. Electrospray generated ions of equine cytochrome c were exposed to a low concentration of D2O vapour while being transported by a flow of nitrogen through a FAIMS device. During this transport period of about 250 ms in the FAIMS analyzer, the various conformers of multiply charged ions of cytochrome c were simultaneously undergoing H–D exchange and being separated from each other. The extent of H–D exchange was calculated from the observed m/z of conformers after exposure to D2O vapour in FAIMS. The complementary nature of these two methods resulted in observations supporting a greater number of conformers (e.g., at least 11 conformers were identified for the +16 charge state) than would be expected by analyzing the FAIMS data and the H–D exchange data independently.Key words: FAIMS, H–D exchange, mass spectrometry, protein conformations, electrospray ionization.

Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures

Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight (TOF) MS. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions and, hence, the benefit of FAIMS filtering prior to IMS/MS. The effective peak capacities in analyses of tryptic peptides are approximately 500 for FAIMS/IMS separations and approximately 10(6) for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures.

Multidimensional separations of ubiquitin conformers in the gas phase: relating ion cross sections to H/D exchange measurements

Investigating gas-phase structures of protein ions can lead to an improved understanding of intramolecular forces that play an important role in protein folding. Both hydrogen/deuterium (H/D) exchange and ion mobility spectrometry provide insight into the structures and stabilities of different gas-phase conformers, but how best to relate the results from these two methods has been hotly debated. Here, high-field asymmetric waveform ion mobility spectrometry (FAIMS) is combined with Fourier-transform ion cyclotron resonance mass spectrometry (FT/ICR MS) and is used to directly relate ubiquitin ion cross sections and H/D exchange extents. Multiple conformers can be identified using both methods. For the 9+ charge state of ubiquitin, two conformers (or unresolved populations of conformers) that have cross sections differing by 10% are resolved by FAIMS, but only one conformer is apparent using H/D exchange at short times. For the 12+ charge state, two conformers (or conformer populations) have cross sections differing by <1%, yet H/D exchange of these conformers differ significantly (6 versus 25 exchanges). These and other results show that ubiquitin ion collisional cross sections and H/D exchange distributions are not strongly correlated and that factors other than surface accessibility appear to play a significant role in determining rates and extents of H/D exchange. Conformers that are not resolved by one method could be resolved by the other, indicating that these two methods are highly complementary and that more conformations can be resolved with this combination of methods than by either method alone.

Compensation voltage (CV) peak shapes using a domed FAIMS with the inner electrode translated to various longitudinal positions

High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates ions at atmospheric pressure based on the difference in the mobility of an ion in a strong electric field and in a weak electric field. This field-dependent mobility of an ion is reflected in the compensation voltage (CV) at which the ion is transmitted through FAIMS at an applied asymmetric waveform dispersion voltage (DV). In this report, we show that experimental CV peak shapes using dome tipped inner electrode FAIMS prototypes with inner/outer electrode radii of: (1) 0.2/0.4 cm and (2) 0.4/0.6 cm are a function of the longitudinal position of the inner electrode. Varying the longitudinal position of the inner electrode modifies the electric fields between the surfaces of the hemispherical shaped inner electrode and the outer electrode in the vicinity of the ion outlet. In this region the position-dependent electric field strength (E/N) effectively forms a second tandem FAIMS analyzer region having differing ion separation properties. The final tandem FAIMS separation is the intersection of the CV windows of these two differing FAIMS separations and, therefore, the peak width in the CV scan is dependent on the longitudinal tip displacement (LTD) of the inner electrode. CV scans are shown for a LTD range of 0.14 to 0.4 cm. These scans illustrate that it is possible to control the FAIMS resolution (CV/peak width) from about 1 for the 0.2/0.4 cm electrode set at intermediate longitudinal position to over 10 at the narrowest distance between the inner electrode and the ion outlet.

Comparison of experimental and calculated peak shapes for three cylindrical geometry FAIMS prototypes of differing electrode diameters

High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates ions at atmospheric pressure and room temperature based on the difference of the mobility of ions in strong electric fields and weak electric fields. This field-dependent mobility of an ion is reflected in the compensation voltage (CV) at which the ion is transmitted through FAIMS, at a given asymmetric waveform dispersion voltage (DV). Experimental CV, relative peak ion intensity, and peak width data were compared for three FAIMS prototypes with concentric cylindrical electrodes having inner/outer electrode radii of: (1) 0.4/0.6 cm, (2) 0.8/1.0 cm, and (3) 1.2/1.4 cm. The annular analyzer space was 0.2 cm wide in each case. A finite-difference numerical computation method is described for evaluation of peak shapes and widths in a CV spectrum collected using cylindrical geometry FAIMS devices. Simulation of the radial distribution of the ion density in the FAIMS analyzer is based upon calculation of diffusion, electric fields, and the electric fields introduced by coulombic ion-ion repulsion. Excellent agreement between experimental and calculated peak shapes were obtained for electrodes of wide diameter and for ions transmitted at low CV.

Understanding and designing field asymmetric waveform ion mobility spectrometry separations in gas mixtures

Field asymmetric waveform ion mobility spectrometry (FAIMS) has significant potential for post-ionization separations in conjunction with MS analyses. FAIMS fractionates ion mixtures by exploiting the fact that ion mobilities in gases depend on the electric field in a manner specific to each ion. Nearly all previous work has used pure gases, for which FAIMS fundamentals are understood reasonably well; however, unexpected phenomena observed in some gas mixtures (e.g., N(2)/CO(2)) but not in others (N(2)/O(2)) remain unexplained. Here, we introduce and experimentally test a universal model for FAIMS separations in mixtures, derived from formalisms that determine high-field mobilities in heteromolecular gases. Overall, the theoretical findings are consistent with data for N(2)/CO(2) (although quantitative discrepancies remain), while results for N(2)/O(2) fit Blanc's law, in agreement with measurements. Calculations for He/N(2) and He/CO(2) are also consistent with observations and suggest why adding He to the working gas generally enhances FAIMS performance. As predicted, mixtures of gases with extremely disparate molecular masses and collision cross sections, such as He/SF(6), exhibit spectacular non-Blanc effects, which greatly improve the resolution and peak capacity of technique. Understanding FAIMS operation in gas mixtures is expected to enable the rational design of media for both targeted and global analyses.

Optimization of the design and operation of FAIMS analyzers

Field asymmetric waveform ion mobility spectrometry (FAIMS) holds significant promise for post-ionization separations in conjunction with mass-spectrometric analyses. However, a limited understanding of fundamentals of FAIMS analyzers has made their design and operation largely an empirical exercise. Recently, we developed an a priori simulation of FAIMS that accounts for both ion diffusion (including anisotropic components) and Coulomb repulsion, and validated it by extensive comparisons with FAIMS/MS data. Here it is corroborated further by FAIMS-only measurements, and applied to explore how key instrumental parameters (analytical gap width and length, waveform frequency and profile, the identity and flow speed of buffer gas) affect FAIMS response. We find that the trade-off between resolution and sensitivity can be managed by varying gap width, RF frequency, and (in certain cases) buffer gas, with equivalent outcome. In particular, the resolving power can be approximately doubled compared to "typical" conditions. Throughput may be increased by either accelerating the gas flow (preferable) or shortening the device, but below certain minimum residence times performance deteriorates. Bisinusoidal and clipped-sinusoidal waveforms have comparable merit, but switching to rectangular waveforms would improve resolution and/or sensitivity. For any waveform profile, the ratio of two between voltages in high and low portions of the cycle produces the best performance.

Modeling the resolution and sensitivity of FAIMS analyses

Field asymmetric waveform ion mobility spectrometry (FAIMS) is rapidly gaining acceptance as a robust, versatile tool for post-ionization separations prior to mass-spectrometric analyses. The separation is based on differences between ion mobilities at high and low electric fields, and proceeds at atmospheric pressure. Two major advantages of FAIMS over condensed-phase separations are its high speed and an ion focusing effect that often improves sensitivity. While selected aspects of FAIMS performance are understood empirically, no physical model rationalizing the resolving power and sensitivity of the method and revealing their dependence on instrumental variables has existed. Here we present a first-principles computational treatment capable of simulating the FAIMS analyzer for virtually any geometry (including the known cylindrical and planar designs) and arbitrary operational parameters. The approach involves propagating an ensemble of ion trajectories through the device in real time under the influence of applied asymmetric potential, diffusional motion incorporating the high-field and anisotropic phenomena, and mutual Coulomb repulsion of ionic charges. Calculations for both resolution and sensitivity are validated by excellent agreement with measurements in different FAIMS modes for ions representing diverse types and analyte classes.

H/D exchange of gas phase bradykinin ions in a linear quadrupole ion trap

The gas phase H/D exchange reaction of bradykinin ions, as well as fragment ions of bradykinin generated through collisions in an orifice skimmer region, have been studied with a linear quadrupole ion trap (LIT) reflectron time-of-flight (rTOF) mass spectrometer system. The reaction in the trap takes only tens of seconds at a pressure of few mTorr of D2O or CD3OD. The exchange rate and hydrogen exchange level are not sensitive to the trapping q value over a broad range, provided q is not close to the stability boundary (q = 0.908). The relative rates and hydrogen exchange levels of protonated and sodiated +1 and +2 ions are similar to those observed previously by others with a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer system. The doubly and triply protonated ions show multimodal isotopic distributions, suggesting the presence of several different conformations. The y fragment ions show greater exchange rates and levels than a or b ions, and when water or ammonia is lost from the fragment ions, no exchange is observed.