Ion Trap Mass Analyzer Research Articles

A simplified coaxial ion trap mass analyzer: Characterization of the simplified toroidal ion trap with a rectilinear ion guide

A new miniature coaxial ion trap mass analyzer with a rectilinear ion guide has been constructed using a combination of planar and cylindrical electrodes. The results reported here focus on characterizing the performance of the rectilinear ion guide and simplified toroidal ion trap components. The simplified toroidal ion trap was found to have an ion capacity in excess of 105 ions and mass spectral resolution of 0.5–0.6 when used as a mass analyzer. The ion storage efficiency within the toroidal trapping region was evaluated and found the stored ion population decreased exponentially with storage time. Ion losses depended slightly on the stored βz condition. Ion losses within the toroidal region are attributed primarily to field instabilities at the intersection point of the two components while charge exchange reactions were observed but considered a minor loss mechanism. The ability to mass selectively ejection ions of a specific mass from the toroidal trapping region was characterized and found to approach 100 % efficiency under appropriate ejection conditions.

Digital Ion Trap Isolation and Mass Analysis of Macromolecular Analytes with Multiply Charged Ion Attachment.

Multiply charged ions produced by electrospray ionization (ESI) of heterogeneous mixtures of macromolecular analytes under native conditions are typically confined to relatively narrow ranges of mass-to-charge (m/z) ratio, often with extensive overlap. This scenario makes charge and mass assignments extremely challenging, particularly when individual charge states are unresolved. An ion/ion reaction strategy involving multiply charged ion attachment (MIA) to the mixture components in a narrow range of m/z can facilitate charge and mass assignment. In MIA operation, multiply charged reagent ions are attached to the analyte ions of opposite polarity to provide large m/z displacements resulting from both large changes in mass and charge. However, charge reduction of the high m/z ions initially generated under native ESI conditions requires the ability to isolate high m/z ions and to analyze even higher m/z product ions. Digital ion trap (DIT) operation offers means for both high m/z ion isolation and high m/z mass analysis, in addition to providing conditions for the reaction of oppositely charged ions. The feasibility of conducting MIA experiments in a DIT that takes advantage of high m/z ion operation is demonstrated here using a tandem 2D-3D DIT instrument. Proof-of-concept MIA experiments with cations derived from β-galactosidase using the 20- charge state of human serum immunoglobulin G (IgG, ∼149 kDa) as the reagent anion are described. MIA experiments involving mixtures of ions derived from the E. coli. ribosome are also described. For example, three components in a mixture of 70S particles (>2.2 MDa) were resolved and assigned with masses and charges following an MIA experiment involving the 20- charge state of human serum IgG.

Fourier Transform Ion Trap Mass Analysis by Deciphering Ion Ejection Signals in the Frequency Domain.

Mass analysis in an ion trap is conventionally realized through time domain analysis of the ejected ion current collected from an electron multiplier (EM), in which the ion ejection time is found to have a correlation with the mass-to-charge (m/z) ratio of the ion. In this study, we investigated a new method for mass analysis by examining ion ejection signals in the frequency domain. Theoretical analysis and ion trajectory simulations show that ions of the same m/z ratio are ejected from an ion trap at regular intervals, producing a periodic pulsed signal on the EM. The period of this pulsed ejection signal is directly linked to the m/z values of the ions. To realize this method experimentally, a broadband preamplifier was built and integrated on a miniature ion trap mass spectrometer (the "Brick" series from Nier Inc.) to capture this pulsed ion ejection signal collected from the EM. Experimental results were in good agreement with theoretical and simulation analyses. This method has the potential to improve the mass resolution of an ion trap mass analyzer. As a proof-of-concept demonstration, a peak width of 0.1 Da at a m/z value of 281 was achieved in experiments.

Concept and simulation of a novel dual-layer linear ion trap mass analyzer for micro-electromechanical systems mass spectrometry.

This paper proposed a dual-layer linear ion trap mass analyzer (dLIT) based on micro-electromechanical systems (MEMS) technology and stacked-layer structure for the development of MEMS mass spectrometry. Its basic performance and potential capabilities were explored by ion trajectory simulations. The theoretical formulas were modified by implementing multipole expansion. The simulation results were confirmed to be highly consistent with theoretical calculations in multiple aspects, including stability diagram, secular frequencies, and mass linearity, with only a deviation of 1-2%. In the boundary ejection mode, close to 100% ejection was achieved in a single dimension by applying extra quadrupole DC voltage. Preliminary simulation results showed that dLIT can achieve a peak width of ∼2 mass units (full width at half maximum, FWHM) for m/z 60 ions even at pressures as high as 50 Pa. Furthermore, the application of AC frequency scanning mode in dLIT was also evaluated, and preliminary simulation results yield a peak width of 0.3-0.4 mass units (FWHM). The dLIT offered several advantages, including high-precision fabrication at the sub-millimeter scale, excellent high-pressure performance, and a clear physical model. It preliminarily proved to be an ideal mass analyzer for MEMS mass spectrometry.

Research on double resonant excitation in a triangular electrode ion trap with asymmetric geometry.

The triangular electrode linear ion trap with asymmetric geometry has been reported to possess a high ion unidirectional ejection efficiency and a reasonable mass resolution. To further improve its performance, a double resonant excitation method involving a dipolar and a quadrupolar resonant excitation was applied here. The dipolar excitation method was carried out by applying a supplementary alternating voltage out of phase to one pair of the electrodes, whereas the quadrupolar excitation (QE) method was carried out by adding a supplementary alternating voltage in phase to another pair of electrodes. Numerical simulations were performed to explore the impact of the frequency difference between the alternating current (AC) and the QE voltage (∆ω), the frequency of the AC voltage (ωAC), and the QE voltage amplitude (VQE). The mass resolution could be improved to ~4700 , which was approximately twice compared to that with only dipolar resonant excitation, and the ion unidirectional ejection efficiency could be improved to 97%. Even with a high scan rate of 6000 Da/s, there was minimal loss of mass resolution caused by increased scan rate in double resonant excitation mode. By employing the double resonant excitation method, the mass resolution could be further increased while maintaining a considerably high ion unidirectional ejection efficiency, which might be a simple and practical approach for developing a high-performance miniature ion trap mass analyzer.

Development of a Modular, Open-Source, Reduced-Pressure, Drift Tube Ion Mobility Spectrometer.

Toward the goal of minimizing construction costs while maintaining high performance, a new, reduced-pressure, drift tube ion mobility system is coupled with an ion trap mass analyzer through a custom ion shuttle. The availability of reduced-pressure ion mobility systems remains limited due to comparatively expensive commercial options and limited shared design features in the open literature. This report details the complete design and benchmarking characteristics of a reduced-pressure ion mobility system. The system is constructed from FR4 PCB electrodes and encased in a PTFE vacuum enclosure with custom torque-tightened couplers to utilize standard KF40 bulkheads. The PTFE enclosure directly minimizes the overall system expenses, and the implementation of threaded brass inserts allows for facile attachments to the vacuum enclosure without damaging the thermoplastic housing. Front and rear ion funnels maximize ion transmission and help mitigate the effects of radial ion diffusion. A custom planar ion shuttle transports ions from the exit of the rear ion funnel into the ion optics of an ion trap mass analyzer. The planar ion shuttle can couple the IM system to any contemporary Thermo Scientific ion trap mass analyzer. Signal stability and ion intensity remain unchanging following the implementation of the planar ion shuttle when compared to the original stacked ring ion guide. The constructed IM system showed resolving powers up to 85 for various small molecules and proteins using the Fourier transform from a ∼1 m drift tube. Recorded mobilities derived from first principles agree with published literature results with an average error of 1.1% and an average error toward literature values using single field calibration of <1.3%.

Electrochemical Oxidation of Resorcinol: An Integrated Experimental and Theoretical Study

Resorcinol polymerization is a quite important chemical reaction, also in connection with applicative aspects related to the production of industrial resins [1].In this work, we studied the electrochemical oxidation of resorcinol on platinum, palladium and glassy carbon (GC) electrodes. We propose an oxidation-polymerisation mechanism for the resorcinol molecule, which is based on the Kane-Maguire polymerization scheme. The results of an exhaustive electrochemical characterization are integrated with the outcome of complementary chromatographic analytical techniques: LC-DAD (high performance Liquid Chromatography, equipped with Diode Array Detector) and LC-MS (mass-spectroscopy by means of Ion Trap mass analyzer). We demonstrate that upon electrochemical oxidation, resorcinol polymerizes following an efficient and facile process and an organic film is obtained on the electrode surface.We used cyclic voltammetry (CV), and a three-electrode cell to perform electrochemical oxidation. Then we used LC-DAD and LC-MS to study the intermediates involved in the electro-polymerization of resorcinol. Electrochemical experiments were performed under different condition of pH and solvent. CVs in a 0.5M H2SO4 solution shows an irreversible oxidation peak at 1.0 V that is pH dependent, consistent with a one-proton, one electron oxidation reaction. Applying potentials higher than the oxidation potential we obtained an organic film adhering to the electrode surface [2]. The polymer film was characterized by atomic force microscopy (AFM) and Scanning Electron Microscopy combined with Energy-Dispersive X-ray spectroscopy (SEM-EDS).We also perform a theoretical study on the first steps of resorcinol electro oxidation using ab-initio quantum mechanical based methods and molecular dynamics analysis (DRC algorithm) at the B3LYP/6-31G(d) and B3LYP/cc-pVTZ level of theory [3]. The resorcinol polymerization is considered to proceed via the dissociation of one (or two) hydrogen atom to form C-C and C-O dimers.The proposed mechanism for the resorcinol electrochemical oxidation is fully consistent with experimental results. Moreover, the film obtained on the electrode surface could be a potential substrate for electrodepositions or electroless deposition of metals and could be a promising candidate for the development of new materials of technological and industrial interest.[1] Formaldehyde and Phenol-Resorcinol-Formaldehyde Condensation Reactions: A Theoretical Study. Polymers 2017, 9, 426, doi:10.3390/polym9090426.[2] Bonechi, M.; Giurlani, W.; Stefani, A.; Marchetti, A.; Innocenti, M.; Fontanesi, C. Resorcinol Electropolymerization Process Obtained via Electrochemical Oxidation. Electrochimica Acta 2022, 428, 140928, doi:10.1016/j.electacta.2022.140928.[3] Bonechi, M.; Innocenti, M.; Vanossi, D.; Fontanesi, C. The Fundamental and Underrated Role of the Base Electrolyte in the Polymerization Mechanism. The Resorcinol Case Study. J. Phys. Chem. A 2021, 125, 34–42, doi:10.1021/acs.jpca.0c07702.

Linear Ion Trap Mass Spectrometer (LITMS) Instrument Field and Laboratory Tests as Part of the ARADS Field Campaigns.

The highly compact Linear Ion Trap Mass Spectrometer (LITMS), developed at NASA Goddard Space Flight Center, combines Mars-ambient laser desorption-mass spectrometry (LD-MS) and pyrolysis-gas chromatography-mass spectrometry (GC-MS) through a single, miniaturized linear ion trap mass analyzer. The LITMS instrument is based on the Mars Organic Molecule Analyser (MOMA) investigation developed for the European Space Agency's ExoMars Rover Mission with further enhanced analytical features such as dual polarity ion detection and a dual frequency RF (radio frequency) power supply allowing for an increased mass range. The LITMS brassboard prototype underwent an extensive repackaging effort to produce a highly compact system for terrestrial field testing, allowing for molecular sample analysis in rugged planetary analog environments outside the laboratory. The LITMS instrument was successfully field tested in the Mars analog environment of the Atacama Desert in 2019 as part of the Atacama Rover Astrobiology Drilling Studies (ARADS) project, providing the first in situ planetary analog analysis for a high-fidelity, flight-like ion trap mass spectrometer. LITMS continued to serve as a laboratory tool for continued analysis of natural Atacama samples provided by the subsequent 2019 ARADS final field campaign.

Multiplexing Quadrupole and Ion Trap Operation Modes on a "Brick" Miniature Mass Spectrometer.

Although a quadruple mass analyzer and an ion trap mass analyzer have complementary analytical features, they usually have different geometries, operational modes, and electronic control systems. As a continuous effort to extend its coverage, both quadrupole and ion trap operation modes were realized on a "brick" miniature mass spectrometer with a single mass analyzer. In the quadrupole operation mode, low-mass ions ranging from 31 to 502 Th can be analyzed. On the other hand, the ion trap mode can be utilized to cover ions with higher mass to charge ratios (up to 922 Th), as well as performing tandem mass spectrometry. To realize the multiplexing of both operation modes, a printed circuit board (PCB)-based multi-electrode quadrupole-ion trap mass analyzer was designed and integrated in the system. To cover both volatile and non-volatile molecules, two ionization sources were also implemented, including a nano electrospray ionization source and an in-vacuum plasma ionization source. Performances of the instrument operated in these two modes were characterized, such as mass resolution, sensitivity, and mass range. Results demonstrate that the combination of the quadrupole and ion trap operation modes can provide new capabilities when solving analytical problems.

Simulation of double resonant excitation of ions in an asymmetric linear ion trap mass analyzer.

Improving the analytical performance of linear ion traps (LITs) is crucial for the advancement of high-performance LIT mass spectrometers. In this study, a double resonant excitation method was employed in an asymmetric LIT to achieve high ion unidirectional ejection efficiency and enhanced mass resolution. The asymmetric trapping field was generated by stretching one x electrode with a distance α. The double resonant excitation was achieved by applying an alternating voltage out of phase and a supplementary alternating voltage in phase to the x and y electrode pairs of the LIT, respectively. Numerical simulations of ion trajectories were performed to validate the effectiveness of this method. The mass resolution of the asymmetric LIT with double resonant excitation could be improved to ~3800, which was over two times compared to that with only dipolar resonant excitation, while both reached ~90% in ion unidirectional ejection efficiency. By employing the double resonant excitation method, the mass resolution could be improved significantly in the asymmetric LIT, while maintaining a considerably high ion unidirectional ejection efficiency. This method might provide a general solution for enhancing ion detection efficiency and mass resolution of LIT mass spectrometers.

Isomers Recognition in HPLC-MS/MS Analysis of Human Plasma Samples by Using an Ion Trap Supported by a Linear Equations-Based Algorithm.

The tandem mass spectrometry (MS/MS) approach employing an ion trap mass analyzer (IT) was evaluated in isomers recognition. The proposed approach consists of sole, simple, and rapid liquid chromatographic separation (HPLC) without requiring resolution between the analytes. Then, the MS/MS properties were optimized to solve the signal assignment using post-processing data elaboration (LEDA). The IT-MS/MS experiment uses the same site, helium as collision gas, and different time steps to modify the applied conditions on the studied ions. Nevertheless, helium cannot ensure the quick energization of the precursor ion due to its small cross-section. Then, different combinations between excitation amplitude (ExA) and excitation time (ExT) were tested to achieve the activation of the fragmentation channels and the formation of the MS/MS spectrum. Usually, the IT-MS/MS acquisition cycle is longer for other multistage instruments, decreasing the frequency of sample data collection and influencing the chromatographic profile. To solve these problems, two time segments were set up, and the elution conditions were optimized with a compromise between peaks distinction and run time reduction. The developed HPLC-MS/MS method was checked and applied to analyze a series of human plasma samples spiked with an equimolar mixture of pair of isomers.

PE, or not PE, that is the question: The case of overlooked lyso-N-acylphosphatidylethanolamines.

Lyso derivatives of N-acyl-1,2-diacylglycero-3-phosphoethanolamines (L-NAPEs) are a lipid class mostly expressed in vegetables during stress and tissue damage that is involved in the synthesis of the lipid mediator N-acylethanolamines. L-NAPEs can be challenging to distinguish from isomeric phosphatidylethanolamines (PEs), especially in extracted complex samples where they could be confused with abundant PEs. In this study, hydrophilic interaction liquid chromatography with electrospray ionization hyphenated with (tandem) mass spectrometry (MS) was proposed to distinguish L-NAPEs and PEs as deprotonated molecules, [M - H]─ , using both high-resolution/accuracy Fourier transform MS and low-resolution linear ion trap (LIT) mass analyzers. MS3 experiments of [M - H - KE]─ as precursor ions (KE, ketene loss) using the LIT instrument allowed us to distinguish between isomeric L-NAPE and PE species. Regiochemical rules were proposed working on enzymatically synthesized L-NAPEs. A few key differences in MS/MS spectra, including abnormal intensity of acyl chain losses as fatty acids, the presence of N-acylphosphoethanolamine ions, and diagnostic ions of the polar head, were disclosed. Additionally, MS3 spectra of [M - H - KE]─ as precursor ions allowed us to confirm the identification of L-NAPE species. The proposed rules were applied to samples extracted from tomato by-products including stems and leaves. Overall, our methodology is demonstrated as a robust approach to recognizing L-NAPEs in complex samples. L-NAPEs 18:2-N-18:2, 18:2-N-18:3, 18:3-N-18:2, and 18:2-N-18:1 were the prevailing compounds in the analyzed tomato samples, accounting for more than 90%. In summary, a reliable method for identifying L-NAPEs in complex samples is described. The proposed method could prevent overlooking L-NAPEs and overestimating isomeric PE species in future lipid analyses.

Development of a linear ion trap mass spectrometer capable of analyzing megadalton MALDI ions

Detecting megadalton matrix-assisted laser desorption/ionization (MALDI) ions in an ion trap mass spectrometer is a technical challenge. In this study, megadalton protein and polymer ions were successfully measured by MALDI linear ion trap mass spectrometer (LIT-MS) for the first time. The LIT-MS is comprised of a Thermo linear ion trap mass analyzer and a highly sensitive charge-sensing particle detector (CSPD). A newly designed radio frequency (rf) scan mode with dipolar resonance ejection techniques is proposed to extend the mass range of LIT-MS up to one million Thomson (Th). We analyze high mass ions with mass-to charge (m/z) ratios ranging from 100 kTh to 1 MTh, including thyroglobulin, alpha-2-macroglobulin, immunoglobulins (e.g., IgG and IgM), and polymer (∼ 940 kTh) ions. Besides, it is also very challenging for ion trap mass spectrometry to detect megadalton ions at low concentrations. By adopting high affinity carboxylated/oxidized detonation nanodiamonds (oxDNDs) to enrich IgM molecules and form antibody-nanodiamond conjugates, we have successfully reached ∼ 5 nM (5 μg/mL) concentration which is better than that by the other techniques.

Differential Urinary Proteomic Analysis of High-Risk Cervical Intraepithelial Neoplasia.

Human papillomavirus (HPV)-associated lesions and malignancies exhibit alterations in the composition and functionality of the extracellular matrix (ECM) that represent the complex molecular pathways present between infection and disease. A total of 20 urine samples were used, including from 10 patients with cervical intraepithelial neoplasia grade 3 (CIN3) and 10 healthy controls to perform the label-free quantitative analysis using the nano-HPLC and ESI-MS ion trap mass analyzer and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) fast screening. Among 476 identified/quantified proteins, 48 were significantly changed (log2-fold change ≥1.0 or ≤-1.0, -log10 (bbinominal, p-value ≥ 1.3), of which were 40 proteins (down-regulated) and 8 proteins (up-regulated) in CIN3, in comparison to healthy controls. The biological function and key pathway enrichment of the gene set using gen set enrichment analysis (GSEA) were analyzed. The ECM-receptor interaction pathway (NES = -1.64, p = 0.026) was down-regulated by 13 proteins (HSPG2, COL6A1, COL6A3, SPP1, THBS1, TNC, DAG1, FN1, COMP, GP6, VTN, SDC1, and CD44; log2 FC range from -0.03 to -1.48) for the CIN3 group in the KEGG database. The MALDI-TOF/MS screening showed the difference of protein profiles between the control and CIN3 groups, i.e., using the scatter plot with a well-separated shape, as well as effectively distinguishing both groups (control and CIN3) using genetic algorithms (GA) with cross-validation (51.56%) and recognition capability (95.0%). Decreased levels of ECM-receptor interaction proteins may cause disturbances in the interactions of cells with the ECM and play an important role in the development and progression of cervical cancer.

A high resolution Fourier transform ion trap enabled by image current splicing: a theoretical study.

The relatively high work pressure within an ion trap has limited the implementation of the Fourier transform technique for high resolution mass analysis. The main reason is that high buffer gas pressure will cause the rapid decay of ion oscillations. In this study, an image current splicing method based on the filter diagonalization method (FDM) and the Hilbert transform was developed to increase the resolving power of nondestructive mass analysis in a linear ion trap. First, multiple repeated experiments (or ion trajectory simulations) were performed to collect multiple sets of data. Using the FDM, the frequency component distribution was extracted from short image current transients collected from each experiment. The Hilbert transform was then applied to calculate and normalize the decay envelope of each transient. The relative abundance was calculated by counting the envelopes. Finally, image current transients collected from these multiple experiments were spliced and merged into a whole signal with much longer duration and continuous phase. This splicing method could effectively increase the duration of the image current, and thus improve the mass resolution of the ion trap mass analyzer. The mass resolution (m/Δm) was improved from 183.5 to 5.8 × 103, and the average relative difference was 2.8%. The proposed method resolved 3 adjacent peaks which originally could not be resolved from the raw signal by the fast Fourier transform (FFT). Besides simulated data, this method was also applied to the experimental data collected from a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The influence of electronic noise on the proposed method was also discussed in this study.

LC-MS-based metabolite profiling of aqueous extract of Pergularia tomentosa L. and its anti-hyperglycemic effect.

In this study, to find scientific evidence for the traditional use of Pergularia tomentosa as an anti-diabetic remedy, the effects of its aqueous extract on streptozotocin-induced diabetes mellitus in rats were evaluated. Wistar rats were fasted overnight and diabetes mellitus was induced using streptozotocin (50 mg/kg body weight). The rats were randomly and equally divided into four groups (n=5): group I (normoglycaemic control), group II (diabetic rats), group III (diabetic rats treated with 200 mg/kg BW of an aqueous extract of P. tomentosa), group IV (normoglycemic rats treated with 200 mg/kg BW of an aqueous extract of P. tomentosa). Chemical profiling of the aqueous extract was carried out using liquid chromatography coupled with electrospray ionization and multiple-stage linear ion-trap and orbitrap high-resolution mass spectrometry (LC-ESI/LTQOrbitrap/MS/MS). In addition, the quantitative determination of the main cardenolides in the extract was carried out by an analytical approach based on LC coupled to tandem mass spectrometry with ESI source and hybrid triple quadrupole-linear ion trap mass analyzer (LC-ESI/QTrap/MS/MS). Aqueous extract of P. tomentosa showed a reasonable reduction in blood glucose level. Probably, the P. tomentosa effect on hyperglycemic and hyperlipidemic diabetic animals was associated with antioxidant properties, triglyceride levels, as well as liver enzymes. Meanwhile, LC-ESI/LTQOrbitrap/MS/MS analysis led to identification of double-linked cardenolides along with cardenolides and flavone glycosides as the main bioactive compounds. The extract decreased the glucose level and induced a beneficial effect on the lipid profile, probably due to the presence of cardenolide glycosides.

Off-Line SPE LC-LRMS Polyphenolic Fingerprinting and Chemometrics to Classify and Authenticate Spanish Honey.

The feasibility of non-targeted off-line SPE LC-LRMS polyphenolic fingerprints to address the classification and authentication of Spanish honey samples based on both botanical origin (blossom and honeydew honeys) and geographical production region was evaluated. With this aim, 136 honey samples belonging to different botanical varieties (multifloral and monofloral) obtained from different Spanish geographical regions with specific climatic conditions were analyzed. Polyphenolic compounds were extracted by off-line solid-phase extraction (SPE) using HLB (3 mL, 60 mg) cartridges. The obtained extracts were then analyzed by C18 reversed-phase LC coupled to low-resolution mass spectrometry in a hybrid quadrupole-linear ion trap mass analyzer and using electrospray in negative ionization mode. Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were employed to assess the pattern recognition capabilities of the obtained fingerprints to address honey classification and authentication. In general, a good sample discrimination was accomplished by PLS-DA, being able to differentiate both blossom-honey and honeydew-honey samples according to botanical varieties. Multiclass predictions by cross-validation for the set of blossom-honey samples showed sensitivity, specificity, and classification ratios higher than 60%, 85%, and 87%, respectively. Better results were obtained for the set of honeydew-honey samples, exhibiting 100% sensitivity, specificity, and classification ratio values. The proposed fingerprints also demonstrated that they were good honey chemical descriptors to deal with climatic and geographical issues. Characteristic polyphenols of each botanical variety were tentatively identified by LC-MS/MS in multiple-reaction monitoring mode to propose possible honey markers for future experiments (i.e., naringin for orange/lemon blossom honeys, syringic acid in thyme honeys, or galangin in rosemary honeys).

High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps.

In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations.

Simulation of a Miniature Linear Ion Trap with Half-Round Rod Electrodes.

The miniaturization of ion trap mass analyzers is an important direction in the development of mass spectrometers. In this work, we proposed two models of miniaturized HreLIT with a field radius of about 2 mm based on the existing research on conventional HreLIT and other ion traps, one with ions ejection slits on one pair of electrodes only (2-slit model) and the other with the same slits on all electrodes (4-slit model). The relationship of mass resolution with r/rx and the “stretch” distance of electrodes in the ejection direction is investigated by theoretical simulations. Trends of electric fields inside the ion traps were discussed as well. The comparable maximum resolution is observed at r/rx = 2/1.4 in both models, but stretching simulations revealed that the peak resolution of the 2-slit model was higher than that of the other model by about 8%. The highest value of 517 was obtained when stretching 1.1 mm. Furthermore, the resolution of ions with m/z = 119 could exceed 1000 when the scan rate was reduced to 800 Th/s. The mass spectrometry capability of miniature HreLIT has been confirmed theoretically, and it laid the foundation for the subsequent fabrication with MEMS technology.

Trident Nano-Indexing the Proteomics Table: Next-Version Clustering of Iron Carbide NPs and Protein Corona.

Protein corona composition and precise physiological understanding of differentially expressed proteins are key for identifying disease biomarkers. In this report, we presented a distinctive quantitative proteomics table of molecular cell signaling differentially expressed proteins of corona that formed on iron carbide nanoparticles (NPs). High-performance liquid chromatography/electrospray ionization coupled with ion trap mass analyzer (HPLC/ESI-Orbitrap) and MASCOT helped quantify 142 differentially expressed proteins. Among these proteins, 104 proteins showed upregulated behavior and 38 proteins were downregulated with respect to the control, whereas 48, 32 and 24 proteins were upregulated and 8, 9 and 21 were downregulated CW (control with unmodified NPs), CY (control with modified NPs) and WY (modified and unmodified NPs), respectively. These proteins were further categorized on behalf of their regularity, locality, molecular functionality and molecular masses using gene ontology (GO). A STRING analysis was used to target the specific range of proteins involved in metabolic pathways and molecular processing in different kinds of binding functionalities, such as RNA, DNA, ATP, ADP, GTP, GDP and calcium ion bindings. Thus, this study will help develop efficient protocols for the identification of latent biomarkers in early disease detection using protein fingerprints.