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

Application of zero-phase digital filtering for effective denoising of field asymmetric waveform ion mobility spectrometry signal

RATIONALE

Field asymmetric waveform ion mobility spectrometry (FAIMS) has a great potential to become a portable technology for rapid detection of chemical and biological agents. However, the ion current signals, measured at the exit of the planar FAIMS directly, may contain different types of noises. The peak information in the FAIMS spectrum, such as the compensation voltage (CV) value at the maximum peak intensity (CV_P ) and the peak width at half maximum (W_h ), could not be accurately determined under the weak signal condition, which significantly limits the achievable instrument sensitivity, and there are no existing solutions to the problem.

METHODS

This study analyzed the noise type of FAIMS signal in detail, and three different signal processing algorithms, such as median filtering (MF), discrete wavelet transform (DWT), and zero-phase digital filtering (ZDF), were evaluated for their performance in denoising the FAIMS signal.

RESULTS

The results show that the standard deviation of CV_p obtained from the signal denoised using ZDF algorithm is at least 31.82% smaller as compared to using MF and DWT algorithms. The standard deviation of W_h is at least 45.45% smaller using ZDF algorithm. Moreover, only ZDF algorithm can keep the percentage error for the CV value of the denoised signal to be within 0.50 ± 0.47% of the true CV value, implying the effectiveness of ZDF algorithm in denoising while retaining the integrity of the signal.

CONCLUSIONS

The ZDF algorithm greatly reduces the analyte peak extraction error and improves the limit of detection in FAIMS measurements.

Separation of Structurally Similar Anabolic Steroids as Cation Adducts in FAIMS-MS

Novel synthetic anabolic androgenic steroids have been developed not only to dodge current antidoping tests at the professional sports level, but also for consumption by noncompetitive bodybuilders. These novel anabolic steroids are commonly referred to as "designer steroids" and pose a significant risk to users because of the lack of testing for toxicity and safety in animals or humans. Manufacturers of designer steroids dodge regulation by distributing them as nutritional or dietary supplements. Improving the throughput and accuracy of screening tests would help regulators to stay on top of illicit anabolic steroids. High-field asymmetric-waveform ion mobility spectrometry (FAIMS) utilizes an alternating asymmetric electric field to separate ions by their different mobilities at high- and low-fields as they travel through the separation space. When coupled to mass spectrometry (MS), FAIMS enhances the separation of analytes from other interfering compounds with little to no increase in analysis time. Here we investigate the effects of adding various cation species to sample solutions for the separation of structurally similar or isomeric anabolic androgenic steroids. FAIMS-MS spectra for these cation-modified samples show an increased number of compensation field (CF) peaks, some of which are confirmed to be unique for one steroid isomer over another. The CF peaks observed upon addition of cation species correspond to both monomer steroid-cation adduct ions and larger multimer ion complexes. Notably, the number of CF peaks and their CF shifts do not appear to have a straightforward relationship with cation size or electronegativity. Future directions aim at investigating the structures for these analyte-cation adduct ions for building a predictive model for their FAIMS separations.

Performance Enhancements in Differential Ion Mobility Spectrometry-Mass Spectrometry (DMS-MS) by Using a Modified CaptiveSpray Source

Differential ion mobility spectrometry (DMS) spatially separates ions in the gas phase using the mobility differences of the ions under applied low and high electric fields. The use of DMS as an ion filter (or ion selector) prior to mass spectrometry analysis has been compromised by the limited ion transmission efficiency. This paper reports enhancement of the DMS-MS sensitivity and signal stability using a modified CaptiveSpray™ source. In terms of the ion sampling and transmission efficiency, the modified CaptiveSpray source swept ~ 89% of the ions generated by the tapered capillary through the DMS device (compared to ~ 10% with a conventional microspray source). The signal fluctuation improved from 11.7% (relative standard deviation, RSD) with microspray DMS-MS to 3.6% using CaptiveSpray-DMS-MS. Coupling of LC to DMS-MS via the modified CaptiveSpray source was simple and robust. Using DMS as a noise-filtering device, LC-DMS-MS performed better than conventional LC-MS for analyzing a BSA digest standard. Although LC-DMS-MS had a lower sequence coverage (55%), a higher Mascot score (283) was obtained compared to those of LC-MS (sequence coverage 65%; Mascot score 192) under the same elution conditions. The improvement in the confidence of the search result was attributed to the preferential elimination of noise ions. Graphical Abstract ᅟ.

Controlling Protein Orientation in Vacuum Using Electric Fields

Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas phase. One of the largest difficulties in realizing this goal is the unknown orientation of the individual sample molecules at the time of exposure. Preorientation of the molecules has been identified as a possible solution to this problem. Using molecular dynamics simulations, we identify a range of electric field strengths where proteins become oriented without losing their structure. For a number of experimentally relevant cases we show that structure determination is possible only when orientation information is included in the orientation-recovery process. We conclude that nondestructive field orientation of intact proteins is feasible and that it enables a range of new structural investigations with single-particle imaging.

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.

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.

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.

Analysis of Supramolecular Complexes of 3-Methylxanthine with Field Asymmetric Waveform Ion Mobility Spectrometry Combined with Mass Spectrometry

Miniaturised field asymmetric waveform ion mobility spectrometry (FAIMS), combined with mass spectrometry (MS), has been applied to the study of self-assembling, noncovalent supramolecular complexes of 3-methylxanthine (3-MX) in the gas phase. 3-MX forms stable tetrameric complexes around an alkali metal (Na(+), K(+)) or ammonium cation, to generate a diverse array of complexes with single and multiple charge states. Complexes of (3-MX)n observed include: singly charged complexes where n = 1-8 and 12 and doubly charged complexes where n = 12-24. The most intense ions are those associated with multiples of tetrameric units, where n = 4, 8, 12, 16, 20, 24. The effect of dispersion field on the ion intensities of the self-assembled complexes indicates some fragmentation of higher order complexes within the FAIMS electrodes (in-FAIMS dissociation), as well as in-source collision induced dissociation within the mass spectrometer. FAIMS-MS enables charge state separation of supramolecular complexes of 3-MX and is shown to be capable of separating species with overlapping mass-to-charge ratios. FAIMS selected transmission also results in an improvement in signal-to-noise ratio for low intensity complexes and enables the visualization of species undetectable without FAIMS.

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.

Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations

Multidimensional high throughput separations are ideal for analyzing distinct ion characteristics simultaneously in one analysis. We report on the first evaluation of a platform coupling a high speed field asymmetric ion mobility spectrometry microchip (μFAIMS) with drift tube ion mobility and mass spectrometry (IMS-MS). The μFAIMS/IMS-MS platform was used to analyze biological samples and simultaneously acquire multidimensional FAIMS compensation fields, IMS drift times, and accurate ion masses for the detected features. These separations thereby increased the overall measurement separation power, resulting in greater information content and more complete characterization of the complex samples. The separation conditions were optimized for sensitivity and resolving power by the selection of gas compositions and pressures in the FAIMS and IMS separation stages. The resulting performance provided three dimensional separations, benefitting both broad complex mixture studies and targeted analyses by improving isomeric separations and allowing detection of species obscured by interfering peaks.

Liquid extraction surface analysis field asymmetric waveform ion mobility spectrometry mass spectrometry for the analysis of dried blood spots

LESA mass spectrometry coupled with high field asymmetric waveform ion mobility spectrometry (FAIMS) for the analysis of dried blood spots.

Differential ion mobility separations in up to 100% helium using microchips

The performance of differential IMS (FAIMS) analyzers is much enhanced by gases comprising He, especially He/N2 mixtures. However, electrical breakdown has limited the He fraction to ~50%-75%, depending on the field strength. By the Paschen law, the threshold field for breakdown increases at shorter distances. This allows FAIMS using chips with microscopic channels to utilize much stronger field intensities (E) than "full-size" analyzers with wider gaps. Here we show that those chips can employ higher He fractions up to 100%. Use of He-rich gases improves the resolution and resolution/sensitivity balance substantially, although less than for full-size analyzers. The optimum He fraction is ~80%, in line with first-principles theory. Hence, one can now measure the dependences of ion mobility on E in pure He, where ion-molecule cross section calculations are much more tractable than in other gases that form deeper and more complex interaction potentials. This capability may facilitate quantitative modeling of high-field ion mobility behavior and, thus, FAIMS separation properties, which would enable a priori extraction of structural information about the ions.

Low-mobility-pass filter between atmospheric pressure chemical ionization and electrospray ionization sources and a single quadrupole mass spectrometer: computational models and measurements

RATIONALE

Mixtures of ions produced in sources at atmospheric pressure, including chemical ionization (APCI) and electrospray ionization (ESI) can be simplified at or near ambient pressure using ion mobility based filters.

METHODS

A low-mobility-pass filter (LMPF) based on a simple mechanical design and simple electronic control was designed, modeled and tested with vapors of 2-hexadecanone in an APCI source and with spray of peptide solutions in an ESI source. The LMPF geometry was planar and small (4 mm wide × 13 mm long) and electric control was through a symmetric waveform in low kHz with amplitude between 0 and 10 V.

RESULTS

Computational models established idealized performance for transmission efficiency of ions of several reduced mobility coefficients over the range of amplitudes and were matched by computed values from ion abundances in mass spectra. The filter exhibited a broad response function, equivalent to a Bode Plot in electronic filters, suggesting that ion filtering could be done in blocks ~50 m/z units wide.

CONCLUSIONS

The benefit of this concept is that discrimination against ions of high mobility is controlled by only a single parameter: waveform amplitude at fixed frequency. The effective removal of high mobility ions, those of low mass-to-charge, can be beneficial for applications with ion-trap-based mass spectrometers to remove excessive levels of solvent or matrix ions.

Resolution enhancement of field asymmetric waveform ion mobility spectrometry (FAIMS) by ion focusing

BACKGROUND

Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) is a material analysis technology which develops very fast in recent years. Resolution is an important factor used to estimate the performance of this technology. With greater resolution, it's always easier to separate complex mixtures.

RESULTS

A method to increase the resolution of FAIMS is put forward which focuses ions before they enter the drift tube. By adding several pairs of focus electrodes loaded with DC or RF voltage in front of the FAIMS drift tube, the height of the ion beam flowing into the drift tube is decreased, which improves the resolution of the FAIMS spectrum. The effectiveness of this method is verified through SIMION simulation and experiments. Both the DC focusing mode and the AC focusing mode can improve the resolution of the FAIMS system, with the biggest increase of 37%.

CONCLUSIONS

Compared with other methods of improving FAIMS resolution, this method needs neither additional special gases, nor additional auxiliary equipment. It is easy to miniaturize, and can work under atmospheric pressure.

High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that separates gas-phase ions by their behavior in strong and weak electric fields. FAIMS is easily interfaced with electrospray ionization and has been implemented as an additional separation mode between liquid chromatography (LC) and mass spectrometry (MS) in proteomic studies. FAIMS separation is orthogonal to both LC and MS and is used as a means of on-line fractionation to improve the detection of peptides in complex samples. FAIMS improves dynamic range and concomitantly the detection limits of ions by filtering out chemical noise. FAIMS can also be used to remove interfering ion species and to select peptide charge states optimal for identification by tandem MS. Here, the authors review recent developments in LC-FAIMS-MS and its application to MS-based proteomics.

Enhanced performance in the determination of ibuprofen 1-β-O-acyl glucuronide in urine by combining high field asymmetric waveform ion mobility spectrometry with liquid chromatography-time-of-flight mass spectrometry

The incorporation of a chip-based high field asymmetric waveform ion mobility spectrometry (FAIMS) separation in the ultra (high)-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) determination of the (R/S) ibuprofen 1-β-O-acyl glucuronide metabolite in urine is reported. UHPLC-FAIMS-HRMS reduced matrix chemical noise, improved the limit of quantitation approximately two-fold and increased the linear dynamic range compared to the determination of the metabolite without FAIMS separation. A quantitative evaluation of the prototype UHPLC-FAIMS-HRMS system showed better reproducibility for the drug metabolite (%RSD 2.7%) at biologically relevant concentrations in urine. In-source collision induced dissociation of the FAIMS-selected deprotonated metabolite was used to fragment the ion prior to mass analysis, enhancing selectivity by removing co-eluting species and aiding the qualitative identification of the metabolite by increasing the signal-to-noise ratio of the fragment ions.

Protein analyses using differential ion mobility microchips with mass spectrometry

Differential ion mobility spectrometry (FAIMS) integrated with mass spectrometry (MS) is a powerful new tool for biological and environmental analyses. Large proteins occupy regions of FAIMS spectra distinct from peptides, lipids, or other medium-size biomolecules, likely because strong electric fields align huge dipoles common to macroions. Here we confirm this phenomenon in separations of proteins at extreme fields using FAIMS chips coupled to MS and demonstrate their use to detect even minor amounts of large proteins in complex matrixes of smaller proteins and peptides.

Enhanced analyte detection using in-source fragmentation of field asymmetric waveform ion mobility spectrometry-selected ions in combination with time-of-flight mass spectrometry

Miniaturized ultra high field asymmetric waveform ion mobility spectrometry (FAIMS) is used for the selective transmission of differential mobility-selected ions prior to in-source collision-induced dissociation (CID) and time-of-flight mass spectrometry (TOFMS) analysis. The FAIMS-in-source collision induced dissociation-TOFMS (FISCID-MS) method requires only minor modification of the ion source region of the mass spectrometer and is shown to significantly enhance analyte detection in complex mixtures. Improved mass measurement accuracy and simplified product ion mass spectra were observed following FAIMS preselection and subsequent in-source CID of ions derived from pharmaceutical excipients, sufficiently close in m/z (17.7 ppm mass difference) that they could not be resolved by TOFMS alone. The FISCID-MS approach is also demonstrated for the qualitative and quantitative analysis of mixtures of peptides with FAIMS used to filter out unrelated precursor ions thereby simplifying the resulting product ion mass spectra. Liquid chromatography combined with FISCID-MS was applied to the analysis of coeluting model peptides and tryptic peptides derived from human plasma proteins, allowing precursor ion selection and CID to yield product ion data suitable for peptide identification via database searching. The potential of FISCID-MS for the quantitative determination of a model peptide spiked into human plasma in the range of 0.45-9.0 μg/mL is demonstrated, showing good reproducibility (%RSD < 14.6%) and linearity (R(2) > 0.99).

Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that can be used to reduce sample complexity and increase dynamic range in tandem mass spectrometry experiments. FAIMS fractionates ions in the gas-phase according to characteristic differences in mobilities in electric fields of different strengths. Undesired ion species such as solvated clusters and singly charged chemical background ions can be prevented from reaching the mass analyzer, thus decreasing chemical noise. To date, there has been limited success using the commercially available Thermo Fisher FAIMS device with both standard ESI and nanoLC-MS. We have modified a Thermo Fisher electrospray source to accommodate a fused silica pulled tip capillary column for nanospray ionization, which will enable standard laboratories access to FAIMS technology. Our modified source allows easily obtainable stable spray at flow rates of 300 nL/min when coupled with FAIMS. The modified electrospray source allows the use of sheath gas, which provides a fivefold increase in signal obtained when nanoLC is coupled to FAIMS. In this work, nanoLC-FAIMS-MS and nanoLC-MS were compared by analyzing a tryptic digest of a 1:1 mixture of SILAC-labeled haploid and diploid yeast to demonstrate the performance of nanoLC-FAIMS-MS, at different compensation voltages, for post-column fractionation of complex protein digests. The effective dynamic range more than doubled when FAIMS was used. In total, 10,377 unique stripped peptides and 1649 unique proteins with SILAC ratios were identified from the combined nanoLC-FAIMS-MS experiments, compared with 6908 unique stripped peptides and 1003 unique proteins with SILAC ratios identified from the combined nanoLC-MS experiments. This work demonstrates how a commercially available FAIMS device can be combined with nanoLC to improve proteome coverage in shotgun and targeted type proteomics experiments.

Elimination of the helium requirement in high-field asymmetric waveform ion mobility spectrometry (FAIMS): beneficial effects of decreasing the analyzer gap width on peptide analysis

Cylindrical geometry high-field asymmetric waveform ion mobility spectrometry (FAIMS) focuses and separates gas-phase ions at atmospheric pressure and room (or elevated) temperature. Addition of helium to a nitrogen-based separation medium offers significant advantages for FAIMS including improved resolution, selectivity and sensitivity. Aside from gas composition, ion transmission through FAIMS is governed by electric field strength (E/N) that is determined by the applied voltage, the analyzer gap width, atmospheric pressure and electrode temperature. In this study, the analyzer width of a cylindrical FAIMS device is varied from 2.5 to 1.25 mm to achieve average electric field strengths as high as 187.5 Townsend (Td). At these electric fields, the performance of FAIMS in an N(2) environment is dramatically improved over a commercial system that uses an analyzer width of 2.5 mm in 1:1 N(2) /He. At fields of 162 Td using electrodes at room temperature, the average effective temperature for the [M+2H](2+) ion of angiotensin II reaches 365 K. This has a dramatic impact on the curtain gas flow rate, resulting in lower optimum flows and reduced turbulence in the ion inlet. The use of narrow analyzer widths in a N(2) carrier gas offers previously unattainable baseline resolution of the [M+2H](2+) and [M+3H](3+) ions of angiotensin II. Comparisons of absolute ion current with FAIMS to conventional electrospray ionization (ESI) are as high as 77% with FAIMS versus standard ESI-MS.