High-field Asymmetric Ion Mobility Spectrometry Research Articles

Application and performance enhancement of FAIMS spectral data for deep learning analysis using generative adversarial network reinforcement

When using High-field asymmetric ion mobility spectrometry (FAIMS) to process complex mixtures for deep learning analysis, there is a problem of poor recognition performance due to the lack of high-quality data and low sample diversity. In this paper, a Generative Adversarial Network (GAN) method is introduced to simulate and generate highly realistic and diverse spectral for expanding the dataset using real mixture spectral data of 15 classes collected by FAIMS. The mixed datasets were put into VGG and ResNeXt for testing respectively, and the experimental results proved that the best recognition effect was achieved when the ratio of real data to generated data was 1:4: where accuracy improved by 24.19 % and 6.43 %; precision improved by 23.71 % and 6.97 %; recall improved by 21.08 % and 7.09 %; and F1-score improved by 24.50 % and 8.23 %. The above results strongly demonstrate that GAN can effectively expand the data volume and increase the sample diversity without increasing the additional experimental cost, which significantly enhances the experimental effect of FAIMS spectral for the analysis of complex mixtures.

Theoretical and experimental study on the effect of scanning speed on FAIMS peaks

High-Field Asymmetric Ion Mobility Spectrometry (FAIMS) is a technique for ion separation and detection based on ion mobility variation under high electronic field. While compensation voltage scanning speed is a fundamental parameter in FAIMS, its impact on spectra remains unclear. In this work, a function referred to as F-EMG is introduced to describe the impact of compensation voltage scanning speed on FAIMS spectra, and the properties of the function are studied. Theoretical analysis emphasizes the impact of the scanning speed on peak height, position, and symmetry, as well as the capability of the F-EMG function to progressively approach Gaussian function at lower scanning speeds. Furthermore, the function indicates that spectra obtained in positive and negative scanning modes exhibits symmetry. An experimental validation, conducted with a custom FAIMS setup and analyzing hydrogen sulfide, ethylbenzene, toluene, styrene, benzene and ammonia, confirms the model's influence on peak features, fitting accuracy, and exhibits a closer alignment with the Gaussian function at lower scanning speeds. Additionally, the experimental data indicate that the spectra show symmetry in positive and negative scanning models. This work not only improves understanding of FAIMS spectral analysis but also introduces a robust method for enhancing data accuracy across varying scanning speeds.

A broad-spectrum peptide screening method using an optimized solid-phase extraction and liquid chromatography-high-field asymmetric ion mobility spectrometry-mass spectrometry for doping control in equine urine.

The abuse of prohibited peptide-based drugs with a broad spectrum of chemical characteristics poses a significant concern for the horseracing industry. Recently, there has been a notable increase in positive cases of small-peptide drugs reported in equine and canine sports. In addition to small peptides, large peptides (over 2 kDa) with structural diversity have also entered the market in increasing numbers as drugs for humans and livestock. However, the simultaneous analysis of both small- and large-peptide-based drugs is still challenging. In this study, a screening method was developed to cover 74 analytes, including peptides, their catabolites, and/or their mimetics, with molecular weights ranging from 0.3 kDa to greater than 5 kDa. The simultaneous extraction of both small and large peptides was achieved using a weak cation-exchange solid-phase extraction cartridge with a mixture of different pore sizes (suitable for large peptides), followed by analysis using liquid chromatography high-field asymmetric ion mobility spectrometry tandem mass spectrometry (LC-FAIMS-MS/MS). For method validation, the limits of detection (LoDs), reproducibility, recovery, matrix effect, selectivity, and carryover were evaluated. Remarkably, the LoDs of ∼80% of the analytes were less than or equal to 50 pg ml-1, with the lowest LoD (1 pg ml-1) being observed for selected peptides in horse urine. These results indicate a substantial advancement in achieving comprehensive coverage for both small and large peptides with high sensitivity for the purpose of doping control in horseracing and equestrian sports.

Rapid method for accurate peak position extraction in high-field asymmetric ion mobility spectrometry

Rapid method for accurate peak position extraction in high-field asymmetric ion mobility spectrometry

Advanced mass spectrometry workflows for accurate quantification of trace-level host cell proteins in drug products: Benefits of FAIMS separation and gas-phase fractionation DIA.

Therapeutic monoclonal antibodies (mAb) production relies on multiple purification steps before release as a drug product (DP). A few host cell proteins (HCPs) may co-purify with the mAb. Their monitoring is crucial due to the considerable risk they represent for mAb stability, integrity, and efficacy and their potential immunogenicity. Enzyme-linked immunosorbent assays (ELISA) commonly used for global HCP monitoring present limitations in terms of identification and quantification of individual HCPs. Therefore, liquid chromatography tandem mass spectrometry (LC-MS/MS) has emerged as a promising alternative. Challenging DP samples show an extreme dynamic range requiring high performing methods to detect and reliably quantify trace-level HCPs. Here, we investigated the benefits of adding high-field asymmetric ion mobility spectrometry (FAIMS) separation and gas phase fractionation (GPF) prior to data independent acquisition (DIA). FAIMS LC-MS/MS analysis allowed the identification of 221 HCPs among which 158 were reliably quantified for a global amount of 880ng/mg of NIST mAb Reference Material. Our methods have also been successfully applied to two FDA/EMA approved DPs and allowed digging deeper into the HCP landscape with the identification and quantification of a few tens of HCPs with sensitivity down to the sub-ng/mg of mAb level.

High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing.

Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.

Identification of proteoforms by top-down proteomics using two-dimensional low/low pH reversed-phase liquid chromatography-mass spectrometry.

In top-down (TD) proteomics, efficient proteoform separation is crucial to reduce the sample complexity and increase the depth of the analysis. Here, we developed a two-dimensional low pH/low pH reversed-phase liquid chromatography separation scheme for TD proteomics. The first dimension for offline fractionation was performed using a polymeric reversed-phase (PLRP-S) column with trifluoroacetic acid as ion-pairing reagent. The second dimension, a C4 nanocolumn with formic acid as ion-pairing reagent, was coupled online with a high-field asymmetric ion mobility spectrometry (FAIMS) Orbitrap Tribrid mass spectrometer. For both dimensions several parameters were optimized, such as the adaption of the LC gradients in the second dimension according to the elution time (i.e., fraction number) in the first dimension. Avoidance of elevated temperatures and prolonged exposure to acidic conditions minimized cleavage of acid labile aspartate-proline peptide bonds. Furthermore, a concatenation strategy was developed to reduce the total measurement time. We compared our low/low pH with a previously published high pH (C4, ammonium formate)/low pH strategy and found that both separation strategies led to complementary proteoform identifications, mainly below 20kDa, with a higher number of proteoforms identified by the low/low pH separation. With the optimized separation scheme, more than 4900 proteoforms from 1250 protein groups were identified in Caco-2 cells.

Atmospheric pressure photoionization – High-field asymmetric ion mobility spectrometry (APPI-FAIMS) studies for on-site monitoring of aromatic volatile organic compounds (VOCs) in groundwater

A continuously operating system for monitoring groundwater contamination by aromatic VOCs has been developed. For this purpose, a novel gas-water separation unit was to be used in combination with APPI-FAIMS. The gas-water separation unit successfully reduced the humidity in the sample flow to ≤1.6 ppmv prior to analyte ionization. Initially, toluene was selected as a model aromatic VOC. The quantitative response of toluene, as a single VOC in water (LOD <1 mg L−1), was used to investigate the feasibility of the monitoring system and the effect of humidity on the signal produced by the APPI-FAIMS. With humidity increase (up to 400 ppmv) an increase of the toluene signal for about 30% was observed, including the possible formation and detection of water clusters and toluene-water clusters. Similar effects were noted in the case of benzene. However, for the detection of single contaminants such as indane and trimethylbenzenes (TMBs) this was not observed even at relative high humidity (500 ppmv). Additionally, on-site, continuous, groundwater monitoring of the aromatic VOCs contamination was carried out successfully with the gas-water separation APPI-FAIMS at low humidity (0.3–1.6 ppmv) allowing simplified monitoring of a specific, total aromatic VOCs signal in groundwater.

FAIMS Enhances the Detection of PTM Crosstalk Sites.

Protein post-translational modifications (PTMs) enable cells to rapidly change in response to biological stimuli. With hundreds of different PTMs, understanding these control mechanisms is complex. To date, efforts have focused on investigating the effect of a single PTM on protein function. Yet, many proteins contain multiple PTMs. Moreover, one PTM can alter the prevalence of another, a phenomenon termed PTM crosstalk. Understanding PTM crosstalk is critical; however, its detection is challenging since PTMs occur substoichiometrically. Here, we develop an enrichment-free, label-free proteomics method that utilizes high-field asymmetric ion mobility spectrometry (FAIMS) to enhance the detection of PTM crosstalk. We show that by searching for multiple combinations of dynamic PTMs on peptide sequences, a 6-fold increase in candidate PTM crosstalk sites is identified compared with that of standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflows. Additionally, by cycling through FAIMS compensation voltages within a single LC-FAIMS-MS/MS run, we show that our LC-FAIMS-MS/MS workflow can increase multi-PTM-containing peptide identifications without additional increases in run times. With 159 novel candidate crosstalk sites identified, we envisage LC-FAIMS-MS/MS to play an important role in expanding the repertoire of multi-PTM identifications. Moreover, it is only by detecting PTM crosstalk that we can “see” the full picture of how proteins are regulated.

Identification of Specific Substances in the FAIMS Spectra of Complex Mixtures Using Deep Learning.

High-field asymmetric ion mobility spectrometry (FAIMS) spectra of single chemicals are easy to interpret but identifying specific chemicals within complex mixtures is difficult. This paper demonstrates that the FAIMS system can detect specific chemicals in complex mixtures. A homemade FAIMS system is used to analyze pure ethanol, ethyl acetate, acetone, 4-methyl-2-pentanone, butanone, and their mixtures in order to create datasets. An EfficientNetV2 discriminant model was constructed, and a blind test set was used to verify whether the deep-learning model is capable of the required task. The results show that the pre-trained EfficientNetV2 model completed convergence at a learning rate of 0.1 as well as 200 iterations. Specific substances in complex mixtures can be effectively identified using the trained model and the homemade FAIMS system. Accuracies of 100%, 96.7%, and 86.7% are obtained for ethanol, ethyl acetate, and acetone in the blind test set, which are much higher than conventional methods. The deep learning network provides higher accuracy than traditional FAIMS spectral analysis methods. This simplifies the FAIMS spectral analysis process and contributes to further development of FAIMS systems.

Helium-assisted enhanced discharge in a hollow needle for high-field asymmetric ion mobility spectrometry (FAIMS).

A carrier gas mixture of nitrogen and helium has been employed to improve the resolving power at the expense of sensitivity for planar high-field asymmetric ion mobility spectrometry (FAIMS) in previous work. In this paper, a new hollow needle-to-ring ion source was developed, where the helium and nitrogen enter from the hollow needle and ring, respectively. It was found that the signal strengths of acetone, ethanol, and ethyl acetate increased by 8.5, 2.0, and 3.3 times for helium ratios of 20%, 20%, and 10%, respectively. At the same time, the absolute value of compensation voltage and the number of ion peaks increases. It shows that adding an appropriate helium ratio to nitrogen simultaneously improved the sensitivity and resolving power of planar FAIMS, which is reported for the first time.

Remodeling nanoDESI Platform with Ion Mobility Spectrometry to Expand Protein Coverage in Cancerous Tissue.

Nanospray desorption electrospray ionization mass spectrometry is an ambient ionization technique that is capable of mapping proteins in tissue sections. However, high-abundant molecules or isobaric interference in biological samples hampers its broad applications in probing low-abundant proteins. To address this challenge, herein we demonstrated an integrated module that coupled pneumatic-assisted nanospray desorption electrospray ionization mass spectrometry with high-field asymmetric ion mobility spectrometry. Using this module to analyze mouse brain sections, the protein coverage was significantly increased. This improvement allowed the mapping of low-abundant proteins in tissue sections with a 5 μm spatial resolution enabled by computationally assisted fusion with optical microscopic images. Moreover, the module was successfully applied to characterize melanoma in skin tissues based on the enhanced protein profiles. The results suggested that this integrating module will be potentially applied to discover novel proteins in cancers.

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable. Though tolerances are used to ensure such transferred identifications are reasonably located and meet certain quality thresholds, little work has been done to evaluate the statistical confidence of MBR. Here, we present a mixture model-based approach to estimate the false discovery rate (FDR) of peptide and protein identification transfer, which we implement in the label-free quantification tool IonQuant. Using several benchmarking datasets generated on both Orbitrap and timsTOF mass spectrometers, we demonstrate superior performance of IonQuant with FDR-controlled MBR compared with MaxQuant (19–38 times faster; 6–18% more proteins quantified and with comparable or better accuracy). We further illustrate the performance of IonQuant and highlight the need for FDR-controlled MBR, in two single-cell proteomics experiments, including one acquired with the help of high-field asymmetric ion mobility spectrometry separation. Fully integrated in the FragPipe computational environment, IonQuant with FDR-controlled MBR enables fast and accurate peptide and protein quantification in label-free proteomics experiments.

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell.

We report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.

Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching.

A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. A mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth is used. To this end, this strategy leverages TMTpro16-based sample multiplexing, high-field asymmetric ion mobility spectrometry, and real-time database searching. The data show that the differences in the relative protein abundance profiles reflect cell line diversity. The authors also determine several hundred proteins to be highly enriched for a given cell line, and perform gene ontology and pathway analysis on these cell line-enriched proteins. An R Shiny application is designed to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection for addressing a given scientific inquiry or for improving an experimental design.

Printed Circuit Board (PCB) Brazing and Ion Source Integration of a High-Field Asymmetric Ion Mobility Spectrometry (FAIMS) Chip

A high-field asymmetric ion mobility spectrometry (FAIMS) chip based on printed circuit board (PCB) brazing has been fabricated. A needle-to-ring structure was used as the ion source. The ring electrode was formed by punching a 3 mm hole on the PCB and covering it with copper. The FAIMS chip was composed of two PCB boards connected by brazing. The peak value of a FAIMS spectrum was increased by reducing the ballast resistance and increasing the discharge voltage and gas velocity. When ethanol was used as the analyte, the limit of detection (LOD) is approximately 0.06 mg/L.

Design, Fabrication and Mass-spectrometric Studies of a Micro Ion Source for High-Field Asymmetric Waveform Ion Mobility Spectrometry.

A needle-to-cylinder electrode, adopted as an ion source for high-field asymmetric ion mobility spectrometry (FAIMS), is designed and fabricated by lithographie, galvanoformung and abformung (LIGA) technology. The needle, with a tip diameter of 20 μm and thickness of 20 μm, and a cylinder, with a diameter of 400 μm, were connected to the negative high voltage and ground, respectively. A negative corona and glow discharge were realized. For acetone with a density of 99.7 ppm, ethanol with a density of 300 ppm, and acetic ether with a density of 99.3 ppm, the sample gas was ionized by the needle-to-cylinder chip and the ions were detected by an LTQ XL™ (Thermo Scientific Corp.) mass spectrometer. The mass spectra show that the ions are mainly the protonated monomer, the proton bound dimer, and an ion-H2O molecule cluster. In tandem with a FAIMS system, the FAIMS spectra show that the resolving power increases with an increase in the RF voltage. The obtained experimental results showed that the micro needle-to-cylinder chip may serve as a miniature, low cost and non-radioactive ion source for FAIMS.

Measuring the Integrity of Gas-Phase Conformers of Sodiated 25-Hydroxyvitamin D3 by Drift Tube, Traveling Wave, Trapped, and High-Field Asymmetric Ion Mobility.

Quantitation of the serum concentration of 25-hydroxyvitamin D is a high-demand assay that suffers from long chromatography time to separate 25-hydroxyvitamin D from its inactive epimer; however, ion mobility spectrometry can distinguish the epimer pair in under 30 ms due to the presence of a unique extended or "open" gas-phase sodiated conformer, not shared with the epimer, reducing the need for chromatographic separation. Five ion mobility mass spectrometers utilizing commercially available IMS technologies, including drift tube, traveling wave, trapped, and high-field asymmetric ion mobility spectrometry, are evaluated for their ability to resolve the unique open conformer. Additionally, settings for each instrument are evaluated to understand their influence on ion heating, which can drive the open conformer into a compact or "closed" conformer shared with the epimer. The four low-field instruments successfully resolved the open conformer from the closed conformer at baseline or near-baseline resolution at typical operating parameters. High-field asymmetric ion mobility was unable to resolve a unique peak but detected two peaks for the epimer, in contrast to the low-field methods that detected one conformer. This study seeks to expand the instrument space by highlighting the potential of each platform for the separation of 25-hydroxyvitamin D epimers.

Integration of paper spray ionization high-field asymmetric waveform ion mobility spectrometry for forensic applications.

Paper spray ionization (PSI) is an attractive ambient ionization source for mass spectrometry (MS) since it allows the combination of surface sampling and ionization. The minimal sample preparation inherent in this approach greatly reduces the time needed for analysis. However, the ions generated from interfering compounds in the sample and the paper substrate may interfere with the analyte ions. Therefore, the integration of PSI with high-field asymmetric ion mobility spectrometry (FAIMS) is of significant interest since it should reduce the background ions entering the mass analyzer without complicating the analysis or increasing analysis time. Here we demonstrate the integration of PSI with FAIMS/MS and its potential for analysis of samples of forensic interest. In this work, the parameters that can influence the integration, including sampling and ionization by paper spray, the FAIMS separation of analytes from each other and background interferences, and the length of time that a usable signal can be observed for explosives on paper, were evaluated with the integrated system. In the negative ion analysis of 2,4,6-trinitrotoluene (TNT), pentaerythritol tetranitrate (PETN), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), and 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), amounts as low as 1ng on paper were readily observed. The successful positive ion separation of a set of illicit drugs including heroin, methamphetamine, and cocaine was also achieved. In addition, the positive ion analysis of the chemical warfare agent simulants dimethyl methylphosphonate (DMMP) and diisopropyl methylphosphonate (DIMP) was evaluated. The integration of PSI-FAIMS/MS was demonstrated for the analyses of explosives in negative ion mode and for illicit drugs and CW simulants in positive mode. Paper background ions that could interfere with these analyses were separated by FAIMS. The compensation voltage of an ion obtained by FAIMS provided an additional identification parameter to be combined with the mass spectrum for each analyte.

Effects of the Discharge Parameters on the Efficiency and Stability of Ambient Metastable-Induced Desorption Ionization**supported by National Natural Science Foundation of China (No. 61374016), the Changzhou Science and Technology Support Program, China (No. CE20120081) and the External Cooperation Program of Chinese Academy of Sciences (No. GJHZ1218)

Ionization efficiency is an important factor for ion sources in mass spectrometry and ion mobility spectrometry. Using helium as the discharge gas, acetone as the sample, and high-field asymmetric ion mobility spectrometry (FAIMS) as the ion detection method, this work investigates in detail the effects of discharge parameters on the efficiency of ambient metastable-induced desorption ionization (AMDI) at atmospheric pressure. The results indicate that the discharge power and gas flow rate are both significantly correlated with the ionization efficiency. Specifically, an increase in the applied discharge power leads to a rapid increase in the ionization efficiency, which gradually reaches equilibrium due to ion saturation. Moreover, when the discharge voltage is fixed at 2.1 kV, a maximum efficiency can be achieved at the flow rate of 9.0 m/s. This study provides a foundation for the design and application of AMDI for on-line detection with mass spectrometry and ion mobility spectrometry.