An open source ion gate pulser for ion mobility spectrometry

Excluding the ion source, an ion mobility spectrometer is fundamentally comprised of drift chamber, ion gate, pulsing electronics, and a mechanism for amplifying and recording ion signals. Historically, the solutions to each of these challenges have been custom and rarely replicated exactly. For the IMS research community few detailed resources exist that explicitly detail the construction and operation of ion mobility systems. In an effort to address this knowledge gap we outline a solution to one of the key aspects of a drift tube ion mobility system, the ion gate pulser. Bradbury-Nielsen or Tyndall ion gates are found in nearly every research-grade and commercial IMS system. While conceptually simple, these gate structures often require custom, high-voltage, floating electronics. In this report we detail the operation and performance characteristics of a wifi-enabled, MOSFET-based pulser design that uses a lithium-polymer battery and does not require high voltage isolation transformers. Currently, each output of this circuit follows a TTL signal with ~20 ns rise and fall times, pulses up to +/? 200 V, and is entirely isolated using fiber optics. Detailed schematics and source code are provided to enable continued use of robust pulsing electronics that ease experimental efforts for future comparison.     

TOF MS Investigation of Nickel Oxide CVD

NiO layers were deposited by metal-organic chemical vapor deposition using bis-(ethylcyclopentadienyl) nickel (EtCp)₂Ni and oxygen or ozone. As a continuation of kinetic study of NiO MOCVD the gas-phase, transformations of (EtCp)₂Ni were studied in the temperature range of 380–830 K. Time of reactions corresponding to the residence time of the gas stream in hot zone of the reactor was about 0.1 s under conditions studied. The interaction of (EtCp)₂Ni with oxygen started at 450 K and its conversion rate reached the maximum at 700 K. The interaction of (EtCp)₂Ni with ozone started at 400 K and its conversion rate reached the maximum at 600 K. Transformations of the gas phase with the temperature in the reaction zone were studied, the model reaction schemes illustrating (EtCp)₂Ni transformations in the reaction systems containing oxygen and ozone have developed. In the reaction system (EtCp)₂Ni–O₂–Ar the main gas-phase products at 380–500 K were CO, CO₂, HCO, C₂H₅OH, CpCOOH, and CpO. Formation of the C₂H₂O, C₃H₄O, and C₅H₈O was found at 630–830 K. The same gas-phase species, (C₄H₃O)₂Ni and dialdehydes was formed in the reaction system (EtCp)₂Ni–O₃–O₂–Ar.

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Dual-Polarity Ion Trap Mass Spectrometry: Dynamic Monitoring and Controlling Gas-phase Ion–Ion Reactions

A dual-polarity linear ion trap (LIT) mass spectrometer was developed in this study, and the method for simultaneously controlling and detecting cations and anions was proposed and realized in the LIT. With the application of an additional dipolar DC field on the ejection electrodes of an LIT, dual-polarity mass spectra could be obtained, which include both the mass-to-charge (m/z) ratio and charge polarity information of an ion. Compared with conventional method, the ion ejection and detection efficiency could also be improved by about one-fold. Furthermore, ion–ion reactions within the LIT could be dynamically controlled and monitored by manipulating the distributions of ions with opposite charge polarities. This method was then used to control and study the reaction kinetics of ion–ion reactions, including electron transfer dissociation (ETD) and charge inversion reactions. A dual-polarity collision-induced dissociation (CID) experiment was proposed and performed to enhance the sequence coverage of a peptide ion. Ion trajectory simulations were also carried out for concept validation and system optimization.

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Detailed Structural Characterization of Sphingolipids via 193 nm Ultraviolet Photodissociation and Ultra High Resolution Tandem Mass Spectrometry

Sphingolipids serve not only as components of cellular membranes but also as bioactive mediators of numerous cellular functions. As the biological activities of these lipids are dependent on their structures, and due to the limitations of conventional ion activation methods employed during tandem mass spectrometry (MS/MS), there is a recognized need for the development of improved structure-specific methods for their comprehensive identification and characterization. Here, positive-ionization mode 193 nm ultraviolet photodissociation (UVPD)-MS/MS has been implemented for the detailed structural characterization of lipid species from a range of sphingolipid classes introduced to the mass spectrometer via electrospray ionization as their lithiated or protonated adducts. These include sphingosine d18:1(4E), dihydrosphingosine (sphinganine) d18:0, sphingadiene d18:2(4E,11Z), the isomeric sphingolipids ceramide d18:1(4E)/18:0 and dihydroceramide d18:0/18:1(9Z), ceramide-1-phosphate d18:1(4Z)/16:0, sphingomyelin d18:1(4E)/18:1(9Z) the glycosphingolipids galactosyl ceramide d18:1(4E)/24:1(15Z) and lactosyl ceramide d18:1(4E)/24:0, and several endogenous lipids present within a porcine brain total lipid extract. In addition to the product ions formed by higher energy collision dissociation (HCD), UVPD is shown to yield a series of novel structurally diagnostic product ions resulting from cleavage of both sphingosine carbon–carbon and acyl chain carbon–carbon double bonds for direct localization of site(s) of unsaturation, as well as via diagnostic cleavages of the sphingosine backbone and N–C amide bond linkages. With activation timescales and dissociation efficiencies similar to those found in conventional MS/MS strategies, this approach is therefore a promising new tool in the arsenal of ion activation techniques toward providing complete structural elucidation in automated, high-throughput lipid analysis workflows.

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Insight into Signal Response of Protein Ions in Native ESI-MS from the Analysis of Model Mixtures of Covalently Linked Protein Oligomers

Native ESI-MS is increasingly used for quantitative analysis of biomolecular interactions. In such analyses, peak intensity ratios measured in mass spectra are treated as abundance ratios of the respective molecules in solution. While signal intensities of similar-size analytes, such as a protein and its complex with a small molecule, can be directly compared, significant distortions of the peak ratio due to unequal signal response of analytes impede the application of this approach for large oligomeric biomolecular complexes. We use a model system based on concatenated maltose binding protein units (MBPn, n = 1, 2, 3) to systematically study the behavior of protein mixtures in ESI-MS. The MBP concatamers differ from each other only by their mass while the chemical composition and other properties remain identical. We used native ESI-MS to analyze model mixtures of MBP oligomers, including equimolar mixtures of two proteins, as well as binary mixtures containing different fractions of the individual components. Pronounced deviation from a linear dependence of the signal intensity with concentration was observed for all binary mixtures investigated. While equimolar mixtures showed linear signal dependence at low concentrations, distinct ion suppression was observed above 20 μM. We systematically studied factors that are most often used in the literature to explain the origin of suppression effects. Implications of this effect for quantifying protein–protein binding affinity by native ESI-MS are discussed in general and demonstrated for an example of an anti-MBP antibody with its ligand, MBP.

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Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH₄OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin–TBA complex and 1 M NH₄OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin–TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein–DNA complexes.

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Magnetically nano core–shell Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>@Cu(OH)<Subscript>x</Subscript>: a highly efficient and reusable catalyst for rapid and green reduction of nitro compounds

Magnetically separable nano core–shell Fe₃O₄@Cu(OH)_x with 22 % Cu content was prepared by the addition of sodium hydroxide to a mixture of CuCl₂·2H₂O and nano Fe₃O₄ in water. Characterization of the impregnated copper hydroxide was carried out by X-ray fluorescence (XRF), X-ray diffraction (XRD) atomic absorption spectroscopy (AAS), scanning electron microscopy (SEM), value stream mapping (VSM) and Brunauer–Emmett–Teller (BET) analysis. The core–shell nanocatalyst exhibited the excellent catalytic activity toward reduction of various nitro compounds to the corresponding amines with NaBH₄. All reactions were carried out in H₂O (55–60 °C) within 3–15 min to afford amines in high to excellent yields. Reusability of core–shell Cu(OH)_x catalyst was examined 9 times without significant loss of its catalytic activity.     

Inhibitory effect of safranal and crocin,two principle compounds of <Emphasis Type="Italic">Crocus sativus</Emphasis>, on fibrillation of lysozyme

A key feature in more than twenty amyloid-related diseases is the aggregation of intra-and/or extracellular misfolded proteins as amyloid fibrils. Therefore, preventing or reversing amyloid aggregation by using of small molecules is considered as useful approaches to the treatment of these diseases. We have evaluated the ability of safranal and crocin, to inhibit amyloid self-assembly of hen egg white lysozyme (HEWL), as an in vitro model system. Structural properties of HEWL in the presence of these compounds were investigated individually using thioflavin T, anilinonaphthalene-8-sulfonic acid fluorescence assays, far-UV circular dichroism and scanning electron microscopy as well as docking method. Our results showed that incubation of HEWL with either crocin or safranal at various concentrations leads a significant inhibition in the rate of amyloid formation. Docking analysis revealed crocin and safranal interact with the central hydrophobic region of lysozyme through van der Waals interaction. Hydroxyl group in crocin through hydrogen bonds connected to the several hydrophilic amino acids of lysozyme, while in safranal there are just one aldehyde group that through hydrogen bonds connected to aspartic acid in lysozyme. It can be concluded that both hydrophobic and hydrophilic groups contribute to lower lysozyme fibril accumulation.     

Determination of trace amounts of nystatin in water and vaccine samples using sodium dodecyl sulfate-coated iron oxide magnetic nanoparticles followed by high-performance liquid chromatography–ultraviolet detection

In this work, magnetic solid-phase extraction based on sodium dodecyl sulfate-coated Fe₃O₄ nanoparticles has been successfully applied for extraction and preconcentration of trace amounts of nystatin from water and vaccine samples prior to high-performance liquid chromatography–ultraviolet detection. Various experimental parameters affecting extraction and recovery of the analyte, such as the amount of sodium dodecyl sulfate, pH of the sample solution, salt concentration, extraction time, sample volume and desorption conditions, were systematically studied and optimized. Under optimized conditions, nystatin was quantitatively extracted. Proper linear range with good coefficient of determination, (R ² > 0.99) and limit of detection and quantification (based on signal-to-noise ratios of 3 and 10) of 2.0 and 5.0 µg L^?1, over the investigated concentration range (5–700 µg L^?1), were obtained, respectively. The intra-day and inter-day relative standard deviations at 50 µg L^?1 level of NYS were 1.4 and 4.5% based on six replicate determinations. The accuracy of the method was evaluated by recovery measurements on spiked samples. Suitable recoveries of 96–102 and 26–44% were achieved (at spiked levels of 50, 300 and 500 µg L^?1) for water and vaccine samples, respectively.     

Boron nitride nanotube (BNNT) as a sensor of hydroperoxyl radical (HO<Subscript>2</Subscript>): A DFT study

In this present study, the adsorption behavior of HO₂ radical on the exterior surface of (5, 0) zigzag boron nitride nanotube (BNNT) has been investigated. The electronic structures and geometries of studied complexes were calculated at B3LYP-D3/6-31++G (d, p) computational level. The value of adsorption energy for the most stable configuration (A) is obtained ?0.68 eV, indicating physisorption process. Meaningful change of HOMO–LUMO gap after adsorption confirming BNNT can be introduced as a promising sensor for sensing of HO₂ radical.