Ultrasensitive identification of localization variants of modified peptides using ion mobility spectrometry

Localization of the modification sites on peptides is challenging, particularly when multiple modifications or mixtures of localization isomers (variants) are involved. Such variants commonly coelute in liquid chromatography and may be undistinguishable in tandem mass spectrometry (MS/MS) for lack of unique fragments. Here, we have resolved the variants of singly and doubly phosphorylated peptides employing drift tube ion mobility spectrometry (IMS) coupled to time-of-flight mass spectrometry. Even with a moderate IMS resolving power of ～80-100, substantial separation was achieved for both 2+ and 3+ ions normally generated by electrospray ionization, including for the variants indistinguishable by MS/MS. Variants often exhibit a distribution of 3-D conformers, which can be adjusted for optimum IMS separation by prior field heating of ions in a funnel trap. The peak assignments were confirmed using MS/MS after IMS separation, but known species could be identified using just the ion mobility "tag". Avoiding the MS/MS step lowers the detection limit of localization variants to <100 amol, an order of magnitude better than that provided by electron transfer dissociation in an Orbitrap MS.     

Effect of thermal pretreatment on porous structure of asphalt-based carbon

The effect of thermal pretreatment on the porous structure and adsorption properties of asphalt-based carbons activated with potassium hydroxide was investigated by FTIR, Raman spectroscopy, TEM, N₂ and CO₂ adsorption. Two series of the activated carbons were prepared by a one-stage method using KOH as the activating agent and a two-stage method including pretreatment of asphalt at 450 °C. A cross-effect of the KOH/asphalt ratio and pretreatment conditions on the characteristics of the porous structure of the activated carbons was revealed. The pretreatment of asphalt before activation is demonstrated to be a necessary stage for the effective control of the carbon porous structure by variation the KOH/asphalt ratio from 2 to 4. The porous carbon derived from petroleum asphalt exhibited the high CO₂ adsorption capacity of 3.8 mmol/g at 25 °C and 1 atm and good selectivity for CO₂ over N₂, indicating possible applications in CO₂ capture technology.

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Evaluation of data analysis strategies for improved mass spectrometry-based phosphoproteomics

Here we describe a set of enhanced data processing and filtering methods to improve significance and coverage of phosphopeptide identifications by mass spectrometry. We demonstrate that for samples of limited complexity, spectra-based estimation of false discovery rates will lead to overprediction of confidently identified phosphorylated peptides due to a bias caused by multiple fragmentation of highly abundant peptide species. We further provide evidence that fragmentation of abundant peptides at the tails of their chromatographic peaks is a major source for false positive peptide matches and that overall confidence in phosphopeptide identifications can be improved by a chromatographic peak-based aggregation scheme, intensity rank-based neutral loss and optimized mass error filters. When replicate runs of a standard sample were performed using different fragmentation techniques on an Orbitrap mass spectrometer we observed improvements of 7-31% in phosphopeptide coverage depending on the fragmentation method and the desired false discovery rate.     

Comparative crystal field calculations of the Cr<Superscript>3+</Superscript> energy level schemes in ZnAl<Subscript>2</Subscript>S<Subscript>4</Subscript> and ZnGa<Subscript>2</Subscript>O<Subscript>4</Subscript>

The exchange charge model of crystal field (which includes the covalent effects) is used to analyze the energy level schemes of Cr³⁺ ion in ZnAl₂S₄ and ZnGa₂O₄ crystals with spinel structure. Calculations of the overlap integrals and crystal field parameters were performed before getting the Cr³⁺ energy levels. The calculated energy level schemes are compared with available experimental data; a new interpretation of the absorption peaks is suggested.     

On the effect of water and oxygen in chemical vapor deposition of boron nitride

Growth studies of sp²-hybridized boron nitride (BN) phases by thermal chemical vapor deposition (CVD) are presented; of particular interest is the presence of oxygen and water during growth. While Fourier transform infrared spectroscopy reveals the presence of BN bonds and elemental analysis by elastic recoil detection analysis shows that the films are close to stoichiometric, although containing a few atomic percent oxygen and hydrogen, X-ray diffraction measurements show no indications for nucleation of any crystalline BN phases, despite change in N/B-ratio and/or process temperature. Thermodynamic modeling suggests that this is due to formation of strong BO bonds already in the gas phase in the presence of water or oxygen during growth. This growth behavior is believed to be caused by an uncontrolled release of water and/or oxygen in the deposition chamber and highlights the sensitivity of the BN CVD process towards oxygen and water.     

Adaptive wavefront control with asynchronous stochastic parallel gradient descent clusters

A scalable adaptive optics (AO) control system architecture composed of asynchronous control clusters based on the stochastic parallel gradient descent (SPGD) optimization technique is discussed. It is shown that subdivision of the control channels into asynchronous SPGD clusters improves the AO system performance by better utilizing individual and/or group characteristics of adaptive system components. Results of numerical simulations are presented for two different adaptive receiver systems based on asynchronous SPGD clusters-one with a single deformable mirror with Zernike response functions and a second with tip-tilt and segmented wavefront correctors. We also discuss adaptive wavefront control based on asynchronous parallel optimization of several local performance metrics-a control architecture referred to as distributed adaptive optics (DAO). Analysis of the DAO system architecture demonstrated the potential for significant increase of the adaptation process convergence rate that occurs due to partial decoupling of the system control clusters optimizing individual performance metrics.     

Porous low dielectric constant materials for microelectronics

Materials with a low dielectric constant are required as interlayer dielectrics for the on-chip interconnection of ultra-large-scale integration devices to provide high speed, low dynamic power dissipation and low cross-talk noise. The selection of chemical compounds with low polarizability and the introduction of porosity result in a reduced dielectric constant. Integration of such materials into microelectronic circuits, however, poses a number of challenges, as the materials must meet strict requirements in terms of properties and reliability. These issues are the subject of the present paper.     

Label-free detection of DNA hybridization at a liquid|liquid interface

A novel electrochemical approach for label-free detection of DNA primary sequence has been proposed. The flow of nonelectroactive ions across a liquid|liquid interface was used as an electrochemical probe for detection of DNA hybridization. Disposable graphite screen-printed electrodes shielded with a thin layer of inert polymer plasticized with water-immiscible polar organic solvent were modified by probe oligonucleotide and used as a DNA sensor. The specific DNA coupling has been detected with impedance spectroscopy by decrease of ion-transfer resistance. The detection limit was of 10-8 M of target oligonucleotide. The reported sensor was suitable for discrimination of a single mismatch oligonucleotide from the full complementary one. The reported DNA sensor was advantageous over known physicochemical approaches, providing the most significant changes in the measured parameters.     

Simultaneous tomographic reconstruction and segmentation with class priors

We consider tomographic imaging problems where the goal is to obtain both a reconstructed image and a corresponding segmentation. A classical approach is to first reconstruct and then segment the image; more recent approaches use a discrete tomography approach where reconstruction and segmentation are combined to produce a reconstruction that is identical to the segmentation. We consider instead a hybrid approach that simultaneously produces both a reconstructed image and segmentation. We incorporate priors about the desired classes of the segmentation through a Hidden Markov Measure Field Model, and we impose a regularization term for the spatial variation of the classes across neighbouring pixels. We also present an efficient implementation of our algorithm based on state-of-the-art numerical optimization algorithms. Simulation experiments with artificial and real data demonstrate that our combined approach can produce better results than the classical two-step approach.     

Magnetic Domains and Twin Boundary Movement of NiMnGa Magnetic Shape Memory Crystals

Time‐resolved metallographic optical microscopy techniques are used together with magnetic domain imaging to clarify the interaction between magnetic domains and twin boundary (TB) motion in magnetic shape memory NiMnGa single crystals. The magnetic field and stress induced magnetic domain formation is imaged by a magneto‐optical indicator film technique. Reversible TB motion is visualized up to high actuation speeds. From domain observation at adjacent crystal surfaces the fundamental volume magnetic processes during strain and field induced TB motions are derived. For magnetic field induced structural reorientations a concurrent absence of magnetic domain wall motion is found. In contrast, for strain induced reorientations processes, a complete rearrangement of the magnetic domain structure by the moving TB is observed. Dynamic actuation experiments on TB motion reveal non‐linear time effects on TB mobility. In addition to training effects, the maximum field induced strain increases with actuation speed. Both effects can be interpreted as the interaction of moving twin boundaries with local non‐fixed defects. The summarized results provide key information for the understanding of the connection of magnetic and crystallographic domains in magnetic shape memory alloys and for the optimization of devices for future technical applications.