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Ion signal detection at the true (unperturbed) cyclotron frequency instead of the conventional reduced cyclotron frequency has remained a formidable challenge since the inception of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Recently, routine FT-ICR MS at the true cyclotron frequency has become a reality with the implementation of ICR cells with narrow aperture detection electrodes (NADEL). Here, we describe the development and implementation of the next generation of these cells, namely, a 2xNADEL ICR cell, which comprises four flat detect and four ∼45° cylindrical excite electrodes, enabling independent ion excitation and quadrupolar ion detection. The performance of the 2xNADEL ICR cell was evaluated on two commercial FT-ICR MS platforms, 10 T LTQ FT from Thermo Scientific and 9.4 T SolariX XR from Bruker Daltonics. The cells provided accurate mass measurements in the analyses of singly and multiply charged peptides (root-mean-square, RMS, mass error Δm/m of 90 ppb), proteins (Δm/m = 200 ppb), and petroleum fractions (Δm/m < 200 ppb). Due to the reduced influence of measured frequency on the space charge and external (trapping) electric fields, the 2xNADEL ICR cells exhibited stable performance in a wide range of trapping potentials (1-20 V). Similarly, in a 13 h rat brain MALDI imaging experiment, the RMS mass error did not exceed 600 ppb even for low signal-to-noise ratio analyte peaks. Notably, the same set of calibration constants was applicable to Fourier spectra in all pixels, reducing the need for recalibration at the individual pixel level. Overall, these results support further experimental development and fundamentals investigation of this promising technology.

We consider the fluctuation-induced (Casimir) pressure in peptide films deposited on GaAs, Ge, and ZnS substrates which are either in dielectric or metallic state. Calculations of the Casimir pressure are performed in the framework of fundamental Lifshitz theory employing the frequency-dependent dielectric permittivities of all involved materials. The electric conductivity of semiconductor substrates is taken into account within the experimentally and thermodynamically consistent approach. According to our results, the Casimir pressure in peptide films deposited on dielectric-type semiconductor substrates vanishes for some definite film thickness, is repulsive for thinner and attractive for thicker films. The dependence of this effect on the fraction of water in the film and on the static dielectric permittivity of semiconductor substrate is determined. For the metallic-type semiconductor substrates, the Casimir pressure in peptide coatings is shown to be always repulsive. Possible applications of these results to the problem of stability of thin coatings in microdevices are discussed., Comment: 14 pages, 5 figures

Ion cyclotron resonance (ICR) cells provide stability and coherence of ion oscillations in crossed electric and magnetic fields over extended periods of time. Using the Fourier transform enables precise measurements of ion oscillation frequencies. These precisely measured frequencies are converted into highly accurate mass-to-charge ratios of the analyte ions by calibration procedures. In terms of resolution and mass accuracy, Fourier transform ICR mass spectrometry (FT-ICR MS) offers the highest performance of any MS technology. This is reflected in its wide range of applications. However, in the most challenging MS application, for example, imaging, enhancements in the mass accuracy of fluctuating ion fluxes are required to continue advancing the field. One approach is to shift the ion signal power into the peak corresponding to the true cyclotron frequency instead of the reduced cyclotron frequency peak. The benefits of measuring the true cyclotron frequency include increased tolerance to electric fields within the ICR cell, which enhances frequency measurement precision. As a result, many attempts to implement this mode of FT-ICR MS operation have occurred. Examples of true cyclotron frequency measurements include detection of magnetron inter-harmonics of the reduced cyclotron frequency (i.e., the sidebands), trapping field-free (i.e., screened) ICR cells, and hyperbolic ICR cells with quadrupolar ion detection. More recently, ICR cells with spatially distributed ion clouds have demonstrated attractive performance characteristics for true cyclotron frequency ion detection. Here, we review the corresponding developments in FT-ICR MS over the past 40 years.

In-space plasma propulsion is today a necessity for the economic competitiveness of commercial satellites. In plasma thrusters the impulse is imparted by a mesothermal plasma jet where ions drift a supersonic velocities. Compact multi-electrode systems for ion acceleration are studied by a combination of analytical calculations and computer simulations. The results show exahust speeds of 140 km/s can be reached with specific impulses higher than unsual plasma thrusters. Additionally, the ion velocity distribution functions of the plasma jet exhasut obtained with retarded field energy analyzers that can be used to cross validate the results of numerical simulations.

The advances made in telecommunication technologies imply that new functional materials are developed for the components used in advanced electronics. Creating biomolecular films with certain impedance characteristics for telecommunication devices is an urgent task. This paper presents the results of experiments on preparing thin films by dehydration of water-salt solutions of albumin protein on a dielectric substrate. Periodic cellular structures forming in the films during the phase transition were studied. The values of the parameters and the results of the experiments were refined by computer simulation. We reached a conclusion about the significant value of the electric micro-potential, electrical conductivity and the flow of local currents in such processes. Depending on the conditions of formation, various spatial, frequency and energy characteristics of the transmission of electrical signals through self-assembled biomolecular films can be achieved, making it possible to use these films to create devices and elements of advanced electronics and telecommunications.

Instantaneous dipole moments of polyalanine peptides in vacuum and in the aqueous medium have been calculated on the picosecond time scale in order to evaluate the external influence of temperature, of the electrostatic field's amplitude and direction. Computer simulation was performed using the molecular dynamics method. The dynamic scenarios induced by the external electrostatic field above 100 MV/m were obtained for polyalanine molecules of different lengths (from 2 to 24 groups) placed in vacuum and in aqueous medium, the time step of 1 fs and the simulation time up to 100 ns being taken. The simulated scenarios can be used for a further analysis and a generalized description of structural properties and conformational dynamics of molecules. The mastered software packages are appropriate for computing the representational scenarios of biomolecular behavior under various conditions.

The ionized states of molecular analytes located on solid surfaces require profound investigation and better understanding for applications in the basic sciences in general, and in the design of nanobiosensors, in particular. Such ionized states are induced by the interactions of molecules between them in the analyzed substance and with the target surface. Here, computer simulations using COMSOL Multiphysics software show the effect of surface charge density and distribution on the output generation in a dynamic PIN diode with gate control. This device, having built-in potential barriers, has a unique internal integration of output signal generation. The identified interactions showed the possibility of a new design for implementing a nanobiosensor based on a dynamic PIN diode in a mode with surface charge control.

In this paper, we study the processes related to a semiconductor sensor detection of electromagnetic wave irradiation. The distribution of the electric potential and the motion of the charge carriers in the semiconductor sensor with embedded gate-control potential barriers are under investigation using the computer simulation software Comsol Multiphysics. For the first time, the dependence on the accumulated dynamic charge concentration of the potential barriers height as a value used in analytical models was obtained. The appropriate mechanism of potential barriers and charge carrier dynamics and some possible applications were revealed and estimated.

Photodiodes detect the separation of charge carriers in a semiconductor upon irradiation with photons. Recently, new high sensitivity low noise photodetector-integrator based on a PIN diode with embedded gate-control potential barrier was developed. In the study of its characteristics, were observed effects of external particles on the surface of the substrate. In this paper, we studied the effect of surface charges on the potential distribution and charge carriers motion in such PIN diode by means computer simulation using the software Comsol Multiphysics. The appropriate mechanism of surface charge operation was revealed and estimated. The obtained results broaden the possibilities of using this PIN diode as a radiation detector, a particle detector, a biochemical sensor, etc.

Molecular communication systems became a promising paradigm of modern nanonetworks. Quantum carrier transfer creates communication channels between parts of a molecule and/or connects a few domains inside a molecular metamaterial network. This manuscript presents our studies of such channels activated by means of modulated laser beam irradiation resulting in molecular fluorescence, probably at a shifted frequency. The acquisition system for the electromagnetic field generated by a molecule based on the novel dynamic pin-photo diode is characterized by a high sensitivity and a low noise level due to the signal amplitude-time function integration.

Computer simulation of instantaneous time-dependent dipole moment and related nano-electromagnetic field of peptide network, or cluster, in vacuum and aquatic environment, reveal possibilities of molecular system control by means of external electric field. Protein water solution electrical conductivity measurements show some frequency resonances. Probably, revealed effects could be used in nano communication systems in RF-Microwave-THz frequency range.

Recent experimental and theoretical findings suggest that the concept of time-dependent instantaneous frequency(IF) is required to comprehensively describe ion motion and mass spectra generation in Fourier transform mass spectrometry (FTMS). Here, we derive a set of differential equations describing ion motion in ion cyclotron resonance (ICR) and Orbitrap FTMS mass analyzers from the IF standpoint. A moving ion is represented by two 2D oscillators: first with oscillations coupled in the radius-azimuth, (r, phi), and second in the radius-z axis, (r, z), coordinate planes. The presented description is thus fundamentally different from a standard representation of ion motion in FT-ICR MS in a form of a superposition of cyclotron and magnetron radii. Analysis of ion motion with the developed theory validates the hypothesis that time-dependent IF is the most probable characteristic condition of ion motion in FTMS mass analyzers. Application of IF theory improves understanding of FTMS fundamentals and should advance FTMS implementation and practice. For instance, the obtained relations between an ion's IF values and mass-to-charge ratios may be used to refine calibration and frequency shift equations. Other envisioned benefits are improved descriptions of ion RF excitation and transient generation processes, as well as of an influence of a space-charge and of an image charge fields. (C) 2014 Elsevier B.V. All rights reserved.

Nano-devices with embedded molecular films appear as promising nano communications tools. In general, processing in such hybrid nano-device consists of initial energy of both activated electronic and atomic subsystems of an embedded molecular species, followed by intra- and inter-molecular nanoscale signals generation and reception of the transmitted signal at remote site. Actually, electromagnetic radiation can establish wireless nano communication in Visible, Infrared, and Microwave frequency ranges. In this manuscript, we estimate some properties of a microelectronics receiver in such systems, presented by novel dynamic operation pin photodetector, possesses signal integration, and required for receiving and demodulation of an electromagnetic wave. Revealed both theoretical and experimental characteristics of a photodetector have allowed designing dynamic process scenarios, as well as its possible applications inside a nano network.

Successful electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) applications to peptide and protein structural analysis have been enabled by constant progress in implementation of improved electron injection techniques. The rate of ECD product ion formation has been increased to match the liquid chromatography and capillary electrophoresis timescales, and ECD has been combined with infrared multiphoton dissociation in a single experimental configuration to provide simultaneous irradiation, fast switching between the two techniques, and good spatial overlap between ion, photon, and electron beams. Here we begin by describing advantages and disadvantages of the various existing electron injection techniques for ECD in FT-ICR MS. We next compare multiple-pass and single-pass ECD to provide better understanding of ECD efficiency at low and high negative cathode potentials. We introduce compressed hollow electron beam injection to optimize the overlap of ion, photon, and electron beams in the ICR ion trap. Finally, to overcome significant outgassing during operation of a powerful thermal cathode, we introduce nonthermal electron emitter-based electron injection. We describe the first results obtained with cold cathode ECD, and demonstrate a general way to obtain low-energy electrons in FT-ICR MS by use of multiple-pass ECD.

The communication among molecular networks may be specifically realized by nanomechanical, acoustic, and electromagnetic fields and molecular transport. Here, experimental and theoretical studies of peptide and protein films and single molecules in static and radiofrequency electromagnetic fields are reported. Impedance (dielectric) electrochemical spectroscopy revealed nonlinear properties of glycine, alanine and albumen films in the external electromagnetic field in frequency range 0.5–100 MHz. Computer “all atom” simulation allows one to calculate the nanoelectromagnetic field of molecular systems and to evaluate the self-assembled supramolecular architectures. Theoretical studies revealed the dipole moment dynamics of polyalanine peptides. Further, we combine both approaches, thus providing a prediction model of nanoelectromagnetic field generation, and molecular transportation/communication.

The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90A degrees wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90A degrees excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS-increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.

Non-Fourier transformation algorithm and computer program for efficient analysis of short broadband signals for the mass-spectrometry data transmission via wireless networks to remote data users have been developed and tested. It has been shown that even in the case no preliminary data on the signal phase parameters are available, short broad-band multicomponent transients can be transformed into high-resolution signals with high signal-to-noise ratios. Such signals are suitable for high-speed transmission via wireless networks.

Sidebands in mass spectra are an intrinsic feature of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Appearance of the sidebands there is detrimental for the analytical performance, especially in case of complex mixtures analyzed at high resolution. Yet, the sidebands have a practical potential as well. Specifically, they can be applied for fine tuning of ICR cells and were previously employed to improve mass measurement accuracy for small molecules and atoms in fundamental physics experiments. Moreover, experimental characteristics of sidebands allow evaluating the theory of the ICR signal, which provides the metrological basis in FT-ICR MS. Here, we revisit the sidebands phenomenon in the conventional FT-ICR MS, specifically applied to macromolecules. We extend the previous reports on sidebands by examining the appearance of sidebands as functions of ICR cell trapping potentials, resolution, and number of charges for the first three harmonics of the reduced cyclotron frequency. Next, we develop an analytical model of sidebands that contributes to the existing theory of the ICR signal by showing the origin of sidebands to be the result of the broadband amplitude-phase modulation occurring in the ICR signal. Finally, we evaluate the theory of the ICR signal on the basis of the obtained experimental sidebands. Further progress in the theory of the ICR signal shall outline the way for further improvements in FT-ICR MS performance. (C) 2012 Elsevier B.V. All rights reserved.

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, contrary to preferential channels of fragmentation in slow heating-based tandem mass spectrometry. Here we demonstrate that for amphipathic peptides and proteins, modulation of ECD product ion abundance (PIA) along the sequence is pronounced. Moreover, because of the specific primary (and presumably secondary) structure of amphipathic peptides, PIA in ECD demonstrates a clear and reproducible periodic sequence distribution. On the one hand, the period of ECD PIA corresponds to periodic distribution of spatially separated hydrophobic and hydrophilic domains within the peptide primary sequence. On the other hand, the same period correlates with secondary structure units, such as a-helical turns, known for solution-phase structure. Based on a number of examples, we formulate a set of characteristic features for ECD of amphipathic peptides and proteins: (1) periodic distribution of PIA is observed and is reproducible in a wide range of ECD parameters and on different experimental platforms; (2) local maxima of PIA are not necessarily located near the charged site; (3) ion activation before ECD not only extends product ion sequence coverage but also preserves ion yield modulation; (4) the most efficient cleavage (e.g. global maximum of ECD PIA distribution) can be remote from the charged site; (5) the number and location of PIA maxima correlate with amino acid hydrophobicity maxima generally to within a single amino acid displacement; and (6) preferential cleavage sites follow a selected hydrogen spine in an a-helical peptide segment. Presently proposed novel insights into ECD behavior are important for advancing understanding of the ECD mechanism, particularly the role of peptide sequence on PIA. An improved ECD model could facilitate protein sequencing and improve identification of unknown proteins in proteomics technologies. In structural biology, the periodic/preferential product ion yield in ECD of a-helical structures potentially opens the way toward de novo site-specific secondary structure determination of peptides and proteins in the gas phase and its correlation with solution-phase structure. (J Am Soc Mass Spectrom 2009, 20, 1182-1192) (C) 2009 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry