Ion Trap Mass Spectrometer Research Articles

Toward the Rational Design of an OsM4 Center for Methane Activation: Gas-Phase Result-Derived Neural Network Model.

Gas-phase reactions of [OsBx]+ (x = 1-4) with methane at ambient temperature have been studied by using quadrupole-ion trap mass spectrometry combined with quantum chemical calculations. The [OsBx]+ (x = 1-4) cluster ions can undergo dehydrogenation reactions with methane. Comprehensive analysis of the [OsBx]+/CH4 (x = 1-4) system with Os-complexes ([OsCy]+ (y = 1-3) and [OsOz]+ (z = 1-3)) shows that the large polarity of the cluster and the high sum of the pair energies between Os and the ligand in the ETS-NOCV combine to promote the ability of the cluster to activate methane. Cluster polarity may induce heterolytic cleavage of the C-H bond, and the sum of the pair energies of the fragments may reduce the cluster orbital energy to match the methane orbital and improve the cluster stability. The synergistic interplay of these two factors may offer a viable approach for the activation of methane in the condensed phase, which involves modulating the coordination environment of the active sites to enhance the stability and facilitate C-H bond cleavage and the degree of matching with methane orbitals. A nonlinear function is used to extract second-order characteristic features that have a significant impact on the energy difference based on the limited energy difference data of the OsBmCnOlHk units. A neural network model is next designed to predict the reaction barrier for methane conversion by OsM4+ (M = C, N, O, Al, Si, or P) with high accuracy.

Hybrid Paul-optical trap with large optical access for levitated optomechanics

We present a hybrid trapping platform that allows us to levitate a charged nanoparticle in high vacuum using either optical fields, radio-frequency fields, or a combination thereof. Our hybrid approach combines an optical dipole trap with a linear Paul trap while maintaining a large numerical aperture (0.77 NA). We detail a controlled transfer procedure that allows us to use the Paul trap as a “safety net” to recover particles lost from the optical trap at high vacuum. The presented hybrid platform adds to the toolbox of levitodynamics and represents an important step towards fully controllable “dark” potentials, providing control in the absence of decoherence because of photon recoil. Published by the American Physical Society 2024

Simulation of Space Charge Effects in Fourier Transform Quadrupole Ion Traps (FT-QITs).

We present ion dynamics simulations regarding the effect of space charge on the performance of Fourier transform quadrupole ion traps (FT-QITs) with special attention to signal stability, mass resolving power, and sensitivity. Ion trajectory simulations within an idealized QIT geometry are performed by applying a dedicated application (QITSim) using an in-house developed open simulation framework (IDSimF). Image current detection transients are generated by the application and are subsequently transformed into frequency spectra of ion secular motion. Such frequency spectra are the basis for the calculation of mass spectra in FT-QIT instruments. The simulation results are used to assess the extent of space charge induced effects regarding the analytical performance of FT-QIT systems. The simulation results for two Cl+ and seven Xe+ isotope ions exhibit diverse space charge induced phenomena. Most prominently, complete isotope signal fusion, quantitative individual signal suppression, and severe signal distortions are observed even at low absolute numbers of trapped ions. Furthermore, significant shifts of the secular oscillation frequencies occur, even when the signal shape appears to be mostly unaffected and when the frequency separation for trapped ions with different masses is large. This significantly limits the applicability of FT-QIT systems for high resolution mass spectrometry. An increase of the RF amplitude of the trapping field as well as increasing the extent of ion excitation partly mitigate these adverse space charge effects; nevertheless, the usable operational range of the simulated FT-QIT system for analytical applications remains rather narrow.

Scalable Multispecies Ion Transport in a Grid-Based Surface-Electrode Trap

Quantum processors based on linear arrays of trapped ions have achieved exceptional performance, but scaling to large qubit numbers requires realizing two-dimensional ion arrays as envisioned in the quantum charge-coupled device (QCCD) architecture. Here, we present a scalable method for the control of ion crystals in a grid-based surface-electrode Paul trap and characterize it in the context of transport operations that sort and reorder multispecies crystals. By combining cowiring of control electrodes at translationally symmetric locations in each grid site with the sitewise ability to exchange the voltages applied to two special electrodes gated by a binary input, site-dependent operations can be achieved using only a fixed number of analog voltage signals and a single digital input per site. In two separate experimental systems containing nominally identical grid traps, one using Yb+171−Ba+138 crystals and the other Ba+137−Sr+88, we demonstrate this method by characterizing the conditional intrasite crystal reorder and the conditional exchange of ions between adjacent sites on the grid. Averaged across a multisite region of interest, we measure subquanta motional excitation in the axial in-phase and out-of-phase modes of the crystals following these operations at exchange rates of 2.5 kHz. In this initial demonstration, the logic controlling the voltage exchange occurs in software, but the applied signals mimic a proposed hardware implementation using crossover switches. These techniques can be further extended to implement other conditional operations in the QCCD architecture such as gates, initialization, and measurement. Published by the American Physical Society 2024

Testing continuous spontaneous localization model with charged macromolecules

Abstract In the last decade, a growing interest has been devoted to models of spontaneous collapse of the wavefunction, known also as collapse models. They coherently solve the well-known quantum measurement problem by suitably modifying the Schrödinger evolution. Quantum experiments are now finally within the reach of testing such models (and thus testing the limits of quantum theory). Here, we propose a method based on a two-ions confined in a linear Paul trap to possibly enhance the testing capabilities of such experiments. The combination of an atomic and a macromolecular ion provide a good match for the cooling of the motional degrees of freedom and a non-negligible insight in the collapse mechanism, respectively.

Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.

Targeted mass spectrometry (MS) methods are powerful tools for the selective and sensitive analysis of peptides identified in global discovery experiments. Selected reaction monitoring (SRM) is the most widely accepted clinical MS method due to its reliability and performance. However, SRM and parallel reaction monitoring (PRM) are limited in throughput and are typically used for assays with around 100 targets or fewer. Here we introduce a new MS platform featuring a quadrupole mass filter, collision cell, and linear ion trap architecture, capable of targeting 5000-8000 peptides per hour. This high multiplexing capability is facilitated by acquisition rates of 70-100 Hz and real-time chromatogram alignment. We present a Skyline external software tool for building targeted methods based on data-independent acquisition chromatogram libraries or unscheduled analysis of heavy labeled standards. Our platform demonstrates ∼10× lower limits of quantitation (LOQs) than traditional SRM on a triple quadrupole instrument for highly multiplexed assays, due to parallel product ion accumulation. Finally, we explore how analytical figures of merit vary with method duration and the number of analytes, providing insights into optimizing assay performance.

Ion crystal size and structure in Paul traps.

This article presents a relationship between the size of an ion crystal in a Paul trap and the radio frequency potential applied on the central ring electrode. Using a simple and elegant derivation it has been shown that the distance of an ion in the crystal from the trap center is proportional to power of the applied radio frequency voltage. The validity of this power law has been demonstrated on ion crystals having up to 13 ions. A spring-mass model has been presented to predict structure of ion crystals in Paul traps operating in the Dehmelt regime. Structures are obtained by minimizing the total potential energy stored in an ion ensemble. The total potential energy is taken to be the sum of the electrostatic potential due to ion-ion interaction and the potential energy stored in the springs. Structures of crystals having up to 13 ions predicted by our model have been verified by comparing them with results obtained by direct numerical simulations.

Micro scale chromatography of human plasma proteins for nano LC-ESI-MS/MS

Organic precipitation of proteins with acetonitrile demonstrated complete protein recovery and improved chromatography of human plasma proteins. The separation of 25 μL of human plasma into 22 fractions on a QA SAX resin facilitated more effective protein discovery despite the limited sample size. Micro chromatography of plasma proteins over quaternary amine (QA) strong anion exchange (SAX) resins performed best, followed by diethylaminoethyl (DEAE), heparin (HEP), carboxymethyl cellulose (CMC), and propyl sulfate (PS) resins. Two independent statistical methods, Monte Carlo comparison with random MS/MS spectra and the rigorous X!TANDEM goodness of fit algorithm protein p-values corrected to false discovery rate q-values (q ≤ 0.01) agreed on at least 12,000 plasma proteins, each represented by at least three fully tryptic corrected peptide observations. There was qualitative agreement on 9393 protein/gene symbols between the linear quadrupole versus orbital ion trap but also quantitative agreement with a highly significant linear regression relationship between log observation frequency (F value 4,173, p-value 2.2e-16). The use of a QA resin showed nearly perfect replication of all the proteins that were also found using DEAE-, HEP-, CMC-, and PS-based chromatographic methods combined and together estimated the size of the size of the plasma proteome as ≥12,000 gene symbols.

Chemical Fingerprinting of PM2.5 via Sequential Speciation Analysis Using Electrochemical Mass Spectrometry.

Chemical fingerprinting to characterize the occurrence state and abundance of organic and inorganic constituents within fine particulate matter (PM2.5) is useful in evaluating the associated health risks and tracing pollution sources. Herein, an analytical strategy for the rapid analysis of metal and organic constituents in PM2.5 was developed employing a combination of sequential chemical extraction coupled with mass spectrometry detection. H2O, CH3OH, EDTA-2Na, electrochemical oxidation, and electrochemical reduction were sequentially utilized to extract the chemical constituents in PM2.5 samples on a homemade device employing simultaneous online detection using two linear trap quadrupole mass spectrometers (LTQ-MS) with electrospray ionization (ESI) in positive and negative modes. After a single analytical procedure, dozens of metals (e.g., Pb, Cr, and Cu), organic compounds (e.g., amines, polycyclic aromatic hydrocarbons, and aliphatic acids), and negative ions (e.g., NO3-, NO2-, and Cl-) were comprehensively detected in the water-soluble, liposoluble, insoluble, oxidizable, and reducible fractions of PM2.5 samples, and their physical and chemical relationships were established.

A comprehensive study on a tapered Paul trap: from design to potential applications

Abstract We present a tapered Paul trap whose radio frequency electrodes are inclined to the symmetric axis of the endcap electrodes, resulting in a funnel-shaped trapping potential. With this configuration, a charged particle confined in this trap has its radial degrees of freedom coupled to that of the axial direction. The same design was successfully used to experimentally realize a single-atom heat engine, and with this setup amplification of zeptonewton forces was implemented. In this paper, we show the design, implementation, and characterization of such an ion trap in detail. This system offers a high level of control over the ion’s motion. Its novel features promise applications in the field of quantum thermodynamics, quantum sensing, and quantum information.

Single-Base Methylome Analysis of Sweet Cherry (Prunus avium L.) on Dwarfing Rootstocks Reveals Epigenomic Differences Associated with Scion Dwarfing Conferred by Grafting

Plant grafting using dwarfing rootstocks is one of the important cultivation measures in the sweet cherry (Prunus avium) industry. In this work, we aimed to explore the effects of the dwarfing rootstock “Pd1” (Prunus tomentosa) on sweet cherry ‘Shuguang2’ scions by performing morphological observations using the paraffin slice technique, detecting GA (gibberellin) and IAA (auxin) contents using UPLC-QTRAP-MS (ultra-performance liquid chromatography coupled with a hybrid triple quadrupole-linear ion trap mass spectrometer), and implementing integration analyses of the epigenome and transcriptome using whole-genome bisulfite sequencing and transcriptome sequencing. Anatomical analysis indicated that the cell division ability of the SAM (shoot apical meristem) in dwarfing plants was reduced. Pd1 rootstock significantly decreased the levels of GAs and IAA in sweet cherry scions. Methylome analysis showed that the sweet cherry genome presented 15.2~18.6%, 59.88~61.55%, 28.09~33.78%, and 2.99~5.28% methylation at total C, CG, CHG, and CHH sites, respectively. Shoot tips from dwarfing plants exhibited a hypermethylated pattern mostly due to increased CHH methylation, while leaves exhibited a hypomethylated pattern. According to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, DMGs (differentially methylated genes) and DEGs (differentially expressed genes) were enriched in hormone-related GO terms and KEGG pathways. Global correlation analysis between methylation and transcription revealed that mCpG in the gene body region enhanced gene expression and mCHH in the region near the TSS (transcription start site) was positively correlated with gene expression. Next, we found some hormone-related genes and TFs with significant changes in methylation and transcription, including SAURs, ARF, GA2ox, ABS1, bZIP, MYB, and NAC. This study presents a methylome map of the sweet cherry genome, revealed widespread DNA methylation alterations in scions caused by dwarfing rootstock, and obtained abundant genes with methylation and transcription alterations that are potentially involved in rootstock-induced growth changes in sweet cherry scions. Our findings can lay a good basis for further epigenetic studies on sweet cherry dwarfing and provide valuable new insight into understanding rootstock–scion interactions.

B-166 Differentiation of Aziridine Functionality from Related Functional Groups in Protonated Analytes by Using Selective Ion-Molecule Reactions

Abstract Background The development of better methods for the rapid and reliable identification of unknown compounds in mixtures is urgently needed in drug development. Aziridines, in particular, are used for drug synthesis but are potentially mutagenic and carcinogenic compounds. However, the detection and identification of these compounds pose challenges for many analytical methods, such as Nuclear Magnetic Resonance (NMR) spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), and X-ray crystallography. These techniques are time-consuming and often require large quantities of highly pure compounds. Methods Therefore, this study demonstrates that selective gas-phase ion-molecule reactions of protonated analytes with neutral tris(dimethylamino)borane (TDMAB), followed by diagnostic collision-activated dissociation (CAD), can be used to differentiate aziridines from structurally related compounds in a modified linear quadrupole ion trap (LQIT) mass spectrometer. The experiments were performed using an atmospheric pressure chemical ionization (APCI) source in positive ion detection mode. TDMAB was purchased from Sigma-Aldrich and used without purification. It was introduced into the ion trap (2 mtorr of helium buffer gas) via an external reagent mixing manifold through a syringe pump at a flow rate of 10 μL h-1 and diluted with helium before entering the ion trap through a variable leak valve. All analytes were prepared at a concentration of 1 mM in methanol. The protonated analytes were transferred into the ion trap, isolated, and allowed to react with TDMAB (MS2 experiments). Results Product ions formed upon reactions of the analyte ions with TDMAB were subjected to a collision-activated dissociation (CAD) experiment (MS3 experiments). CAD on product ions produced diagnostic fragment ions with 25- and 43 m/z-units lower m/z values than the adduct - DMA product ions. Quantum chemical calculations were employed using the Gaussian 16 program calculated at the M06-2X/6-311++G(d,p) level of theory to provide theoretical foundation and to explore the underlying mechanisms of the observed gas-phase reactions. None of the tested structurally related analytes produced a similar fragmentation pattern Conclusions The innovative approach presented in this study offers a promising avenue for enhancing efficiency and accuracy in drug development. The successful differentiation of aziridine is an alternative method in overcoming the limitation of traditional techniques. The findings from the research contributes to the advancement of analytical techniques, addressing critical issues in identifying impurities in drug products. The versatility of the methods extends beyond drug developments, making it applicable in various other fields such as in molecular diagnostics, metabolism and laboratory medicines.

Characterization of a levitated sub-milligram ferromagnetic cube in a planar alternating-current magnetic Paul trap

Microscopic levitated objects are a promising platform for inertial sensing, testing gravity at small scales, optomechanics in the quantum regime, and large-mass superpositions. However, existing levitation techniques harnessing optical and electrical fields suffer from noise induced by elevated internal temperatures and charge noise, respectively. Meissner-based magnetic levitation circumvents both sources of decoherence but requires cryogenic environments. Here, we characterize a sub-milligram ferromagnetic cube levitated in an alternating-current planar magnetic Paul trap at room temperature. We show behavior in line with the Mathieu equations and quality factors of up to 2500 for the librational modes. Besides technological sensing applications, this technique sets out a path for megahertz librational modes in the micrometer-sized particle limit and can be extended by implementing superconducting traps in cryogenic environments, allowing for magnetic coupling to superconducting circuits and spin-based quantum systems.

Liquid chromatography–mass spectrometry profiling of propolis and royal jelly and their ameliorative effects on cadmium-instigated pathological consequences in ovarian tissues of rats

This study was undertaken to identify the bioactive components of propolis (PRO) and royal jelly (ROJ) and their therapeutic influence on attenuating cadmium chloride (CdCl2)-induced ovarian toxicity and dysfunction in rats. The composition of PRO or ROJ was ascertained employing the liquid chromatography–linear ion trap quadrupole–mass spectrometry (LC–LTQ–MS–MS) method. To further evaluate the anti-infertility properties of PRO and ROJ instigated by cadmium (Cd) in vivo, thirty female mature rats (183.3 ± 12.5 g) were randomly assigned into six groups (n = 5 per group). The established animal groups included (I) control, (II) Cd, (III) PRO, (IV) ROJ, (VI) PRO + Cd, and (VII) ROJ + Cd groups. Cadmium exposure disrupted ovarian tissue functions, demonstrating remarkable disorders in progesterone and estrogen. Furthermore, the comet assay exhibited a marked rise in DNA impairment in Cd-exposed rats, implying genotoxicity. Conversely, PRO or ROJ significantly counteracted the Cd-instigated pathophysiological consequences, ameliorating hormonal levels and lessening DNA damage. Critically, histological analysis revealed several anomalies in the ovarian tissues of the Cd-administered group. Interestingly, PRO or ROJ preserved the typical structure of ovarian tissues. Our findings indicate that both PRO and ROJ could be utilized to attenuate the pernicious influences incited by Cd due to their anti-androgenic attributes.

Trypsin Digestion Conditions of Human Plasma for Observation of Peptides and Proteins from Tandem Mass Spectrometry.

Previous meta-analysis indicated that plasma or serum proteome groups using various experimental conditions detected different peptides from the same plasma proteins, which is strong evidence for the veracity of blood fluid LC-ESI-MS/MS but also evidences that the trypsin digestion step is a key source of variation in plasma proteomics. Agreement between different digestion conditions and MS/MS algorithms may serve as an independent confirmation of the validity of the LC-ESI-MS/MS analysis of plasma peptides. Plasma contains a high percentage of albumin held together by multiple disulfide bonds; hence, reduction and/or alkylation may greatly enhance the digestion efficiency of albumin. Plasma proteins were precipitated in 90% acetonitrile, collected over quaternary amine resin, and eluted in NaCl prior to digestion treatments. To determine the effect of trypsin digestion methods, the plasma proteins were digested in 600 mM urea and 5% acetonitrile with trypsin alone, or reduced with 2 mM DTT followed by trypsin, or DTT followed by 15 mM iodoacetamide and then trypsin. The resulting peptides were analyzed by LC-ESI-MS/MS with a linear quadrupole ion trap (LIT). The MS/MS spectra were directly fit to peptides by the X!TANDEM and SEQUEST algorithms. Blank noise injections served as the analytical control, and 30 million random MS/MS served as the statistical control. Digesting human plasma with DTT reduction, or reduction and alkylation, resulted in a dramatic increase in the number and observation frequency of albumin peptides. In contrast, digestion with trypsin alone suppressed the observation of albumin, and instead, many low abundance plasma and cellular proteins showed higher observation frequency. Digestion with trypsin alone increased the observation frequency of APOC1, ACAN, ATRN, CPB2, GP2, GPX3, HBA1, PAPD5, PKD1, and many cellular proteins. After correction against noise and random controls, SEQUEST showed good agreement with the true positive plasma proteins identified by X!TANDEM and resulted in an R-squared of 0.5238 with an F-statistic of 10,930 on 9,935 protein gene symbols with a p-value < 2.2e-16. Digestion of plasma with trypsin alone avoids the complete digestion of albumin and permits the enhanced detection of some other cellular proteins from plasma. Different digestion approaches were complimentary and together resulted in a more comprehensive plasma proteome. The protein FDR q-values, the modest effect of background and Monte Carlo correction, and the significant STRING analysis were all consistent with the high fidelity of the rigorous X!TANDEM algorithm. In contrast, SEQUEST required significant correction against noise and statistical controls and selection of high cross correlation (XCorr) scores to show good agreement with X!TANDEM. There was qualitative and quantitative agreement between plasma proteins digested without alkylation from the orbital ion trap (OIT) versus the LIT instrument that showed highly significant regression against the X!TANDEM OIT monoisotopic results, those from heavy isotopes and other masses from X!TANDEM, and with those from MaxQuant. There was significant qualitative and quantitative agreement between the complementary digestion conditions consistent with the good fidelity of plasma analysis by LC-ESI-MS/MS with a sensitive linear ion trap.

Solutions of the Mathieu–Hill Equation for a Trapped-Ion Harmonic Oscillator—A Qualitative Discussion

We investigate solutions of the classical Mathieu–Hill (MH) equation that characterizes the dynamics of trapped ions. The analytical model we introduce demonstrates the equations of motion are equivalent to those of a harmonic oscillator (HO). Two independent approaches are used, based on two classes of complex solutions of the MH equation. This paper addresses both a damped HO and parametric oscillator (PO) for an ion confined in an electrodynamic (Paul) trap, along with stability and instability regions for the associated periodic orbits.

IR and UV Spectroscopy of Gas-Phase Monohydrated Protonated Guanine.

We use UV and infrared photodissociation spectroscopy to study monohydrated protonated guanine in a dual cryogenic ion trap spectrometer. The monohydrated complexes are formed through helium-mediated collisions between bare electrosprayed protonated guanine and low-pressure water vapor in a clustering trap maintained at 180 K, before being transferred to a quadrupole ion trap at 10 K. The spectrum of the monohydrated complex exhibits sharp vibronic transitions at the band origin and becomes broader and higher in intensity further in blue, which is very similar to protonated guanine but with a notable blue shift of ∼1850 cm-1 (∼0.23 eV). The UV hole-burning experiments showed that the vibronic bands recorded in the region of the band origin belong to a single conformer under our experimental conditions. The IR photodissociation spectrum in the 3000-3600 cm-1 range, with the aid of theoretical calculations (SCS-CC2/aug-cc-pVDZ), allowed us to assign the structure to the lowest energy N7-O conformer.

Characterization and comparison of metabolites in colostrum from yaks, buffaloes, and cows based on UPLC-QTRAP-MS metabolomics

Colostrum from yaks and buffaloes possesses substantial nutritional value, yet the complete array of metabolites within remains insufficiently elucidated. This study scrutinizes the metabolite profiles of yak, buffalo, and cow colostrum utilizing targeted metabolomics paired with ultra-performance liquid chromatography-tandem triple quadrupole linear ion trap mass spectrometry (UPLC-QTRAP-MS). The analysis detected 362 metabolites across all samples. Furthermore, 63, 77, and 46 differential metabolites were selected between yak and buffalo colostrum, yak and cow colostrum, and buffalo and cow colostrum, respectively. Yak colostrum notably contained higher concentrations of inositol, glycine, and carnitine, whereas buffalo colostrum was distinguished by a substantial presence of primary bile acids, which facilitate fat digestion. These findings offer profound insights into yak and buffalo colostrum, providing critical data to propel advancements in the dairy industry.

Zeeman decoherence effect of trapped 199Hg+ ion Ramsey spectra

Abstract In the 199Hg+ ion microwave clock, the Zeeman decoherence effect caused by the overlapping of Zeeman sidebands and the radial secular motion sidebands will decrease the contrast of the Ramsey fringe, thus reducing the signal-to-noise ratio of the spectra. In this paper, the Zeeman decoherence effect is analyzed theoretically and investigated experimentally. A simplified model is built to describe the Ramsey spectral probability, in which the transverse relaxation time T 2 is introduced to characterize the influence of the Zeeman decoherence effect phenomenologically. The experiments were carried out on a linear quadrupole trap 199Hg+ ion clock. The results show that the probability model matches well with the experimental data, and the magnetic field value should be more than 150 mGs (1 Gs = 10−4 T) to avoid the Zeeman decoherence effect.

Evaluation of MagneTOF detector signals for the determination of many-ion bunches

In preparation of space-change studies a MagneTOF detector is evaluated for bunches with a wide range of ion numbers. The detector is calibrated based on the comparison between single-ion counting and ion-bunch-signal integration. This allows to determine up to several ten thousands of ions in a bunch with a FWHM of about 700ns, the integrated signal of which increases linearly with the ion number. Furthermore, this detector limit can be circumvented using transmission-limiting elements in front of the detector. Based on this, ion bunches are investigated up to several million ions, which are prepared with a linear Paul trap. Thus, in addition to the MagneTOF detector this trap is characterized with respect to its space-charge limits at low potential-well depth.