Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands - d(G(4)T(4)G(4)), d(G(3)T(4)G(4)), d(G(3)T(4)G(3)), and d(G(4)T(4)G(3)) - have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH4+ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G(3)T(4)G(3)) and d(G(4)T(4)G(3)) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH4+ in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G(4)T(4)G(3)), but not for the strand d(G(3)T(4)G(3)). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.

Studies on lignan constituents from Schisandra chinensis (Turcz.) Baill. fruits using high-performance liquid chromatography/electrospray ionization multiple-stage tandem mass spectrometry

A reversed-phase high-performance liquid chromatography-diode array detector-electrospray ionization multiple-stage tandem mass spectrometry (RP-HPLC-DAD-ESl-MSn) method has been developed for the detection and analysis of lignan constituents in the methanol extract from the fruits of Schisandra chinensis (Turcz.) Baill. RP-HPLC-DAD-ESI-MSn and electrospray ionization Fourier transform ion cyclotron resonance multiple-stage tandem mass spectrometry (ESI-FT-TCR-MSn) have been applied to investigate the characteristic product ions of four lignan reference compounds. Then, the logical fragmentation pathways of the lignans have been proposed. By comparing the retention time (t(R)) of HPLC, the ESI-MSn data and the structures of analyzed compounds with the data of reference compounds and in the literature, 11 peaks in HPLC have been unambiguously identified and another 5 peaks have been tentatively identified or deduced. Also, in the present paper, the extracted ion chromatograms (EIC) have been used to analyze the lignan isomers. The experimental results demonstrate that RP-HPLC-DAD-ESI-MSn is a specific and useful method for the identification of the lignan constituents and their isomers.

Investigation of heptakis(2,6-di-O-methyl)-beta-cyclodextrin inclusion complexes with flavonoid glycosides by electrospray ionization mass spectrometry

The non-covalent complexes between three flavonoid glycosides (quercitrin, hyperoside and rutin) and heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD) were investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The 1:1 complexation of each flavonoid glycoside (guest) to the DM-beta-CD (host) was monitored in the negative ion mode by mixing each guest with an up to 30-fold molar excess of the host. The binding constants for all complexes were calculated by a linear equation in the order: DM-beta-CD:quercitrin > DM-beta-CD:rutin > DM-beta-CD:hyperoside. A binding model for the complexes has also been proposed based on the binding constants and tandem mass spectrometric data of these complexes.

High resolution mass spectrometric alveolar proteomics: Identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients

In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micro preparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products.

Transition region, coronal heating and the fast solar wind

Li, Xing, 'Transition region, coronal heating and the fast solar wind', Astronomy and Astrophysics (2003) 406 pp.345-356 RAE2008

Contrasting the efficiency of radiation belt losses caused by ducted and nonducted whistler-mode waves from ground-based transmitters

It has long been recognized that whistler-mode waves can be trapped in plasmaspheric whistler ducts which guide the waves. For nonguided cases these waves are said to be "nonducted", which is dominant for L < 1.6. Wave-particle interactions are affected by the wave being ducted or nonducted. In the field-aligned ducted case, first-order cyclotron resonance is dominant, whereas nonducted interactions open up a much wider range of energies through equatorial and off-equatorial resonance. There is conflicting information as to whether the most significant particle loss processes are driven by ducted or nonducted waves. In this study we use loss cone observations from the DEMETER and POES low-altitude satellites to focus on electron losses driven by powerful VLF communications transmitters. Both satellites confirm that there are well-defined enhancements in the flux of electrons in the drift loss cone due to ducted transmissions from the powerful transmitter with call sign NWC. Typically, ∼80% of DEMETER nighttime orbits to the east of NWC show electron flux enhancements in the drift loss cone, spanning a L range consistent with first-order cyclotron theory, and inconsistent with nonducted resonances. In contrast, ∼1% or less of nonducted transmissions originate from NPM-generated electron flux enhancements. While the waves originating from these two transmitters have been predicted to lead to similar levels of pitch angle scattering, we find that the enhancements from NPM are at least 50 times smaller than those from NWC. This suggests that lower-latitude, nonducted VLF waves are much less effective in driving radiation belt pitch angle scattering. Copyright 2010 by the American Geophysical Union.

Absolute single and multiple charge exchange cross sections for highly charged C, O, and Ne ions on H2O, CO, and CO2

Reported herein are measured absolute single, double, and triple charge exchange (CE) cross sections for the highly charged ions (HCIs) Cq+ (q=5,6), Oq+ (q=6,7,8), and Neq+ (q=7,8) colliding with the molecular species H2O, CO, and CO2. Present data can be applied to interpreting observations of x-ray emissions from comets as they interact with the solar wind. As such, the ion impact energies of 7.0q keV (1.62–3.06 keV/amu) are representative of the fast solar wind, and data at 1.5q keV for O6+ (0.56 keV/amu) on CO and CO2 and 3.5q keV for O5+ (1.09 keV/amu) on CO provide checks of the energy dependence of the cross sections at intermediate and typical slow solar wind velocities. The HCIs are generated within a 14 GHz electron cyclotron resonance ion source. Absolute CE measurements are made using a retarding potential energy analyzer, with measurement of the target gas cell pressure and incident and final ion currents. Trends in the cross sections are discussed in light of the classical overbarrier model (OBM), extended OBM, and with recent results of the classical trajectory Monte Carlo theory.

Absolute photoionization cross sections for Xe4+, Xe5+, and Xe6+ near 13.5 nm: Experiment and theory

Absolute photoionization cross-section measurements for a mixture of ground and metastable states of Xe4+, Xe5+, and Xe6+ are reported in the photon energy range of 4d -> nf transitions, which occur within or adjacent to the 13.5 nm window for extreme ultraviolet lithography light source development. The reported values allow the quantification of opacity effects in xenon plasmas due to these 4d -> nf autoionizing states. The oscillator strengths for the 4d -> 4f and 4d -> 5f transitions in Xeq+ (q=1-6) ions are calculated using nonrelativistic Hartree-Fock and random phase approximations. These are compared with published experimental values for Xe+ to Xe3+ and with the values obtained from the present experimental cross-section measurements for Xe4+ to Xe6+. The calculations assisted in the determination of the metastable content in the ion beams for Xe5+ and Xe6+. The experiments were performed by merging a synchrotron photon beam generated by an undulator beamline of the Advanced Light Source with an ion beam produced by an electron cyclotron resonance ion source.

Bridging the Gap between Ionic Liquids and Molten Salts: Group 1 Metal Salts of the Bistriflamide Anion in the Gas Phase

Fourier transform ion cyclotron resonance mass spectrometry experiments showed that liquid Group 1 metal salts of the bistriflamide anion undergoing reduced-pressure distillation exhibit a remarkable behavior that is in transition between that of the vapor-liquid equilibrium characteristics of aprotic ionic liquids and that of the Group 1 metal halides: the unperturbed vapors resemble those of aprotic ionic liquids, in the sense that they are essentially composed of discrete ion pairs. However, the formation of large aggregates through a succession of ion-molecule reactions is closer to what might be expected for Group I metal halides. Similar experiments were also carried out with bis{(trifluoromethyl)sulfonyl}amine to investigate the effect of H+, which despite being the smallest Group 1 cation, is generally regarded as a nonmetal species. In this case, instead of the complex ion-molecule reaction pattern found for the vapors of Group I metal salts, an equilibrium similar to those observed for aprotic ionic liquids was observed.

MEASUREMENT AND CALCULATION OF ABSOLUTE SINGLE AND MULTIPLE CHARGE EXCHANGE CROSS SECTIONS FOR Feq+ IONS IMPACTING H2O

Charge exchange (CE) plays a fundamental role in the collisions of solar- and stellar-wind ions with lunar and planetary exospheres, comets, and circumstellar clouds. Reported herein are absolute cross sections for single, double, triple, and quadruple CE of Feq+ (q = 5-13) ions with H2O at a collision energy of 7q keV. One measured value of the pentuple CE is also given for Fe9+ ions. An electron cyclotron resonance ion source is used to provide currents of the highly charged Fe ions. Absolute data are derived from knowledge of the target gas pressure, target path length, and incident and charge-exchanged ion currents. Experimental cross sections are compared with new results of the n-electron classical trajectory Monte Carlo approximation. The radiative and non-radiative cascades following electron transfers are approximated using scaled hydrogenic transition probabilities and scaled Auger rates. Also given are estimates of cross sections for single capture, and multiple capture followed by autoionization, as derived from the extended overbarrier model. These estimates are based on new theoretical calculations of the vertical ionization potentials of H2O up to H2O10+.

Photoionization cross section calculations for the halogen-like ions Kr + and Xe +

Photoionization cross section calculations on the halogen-like ions; Kr + and Xe + have been performed for a photon energy range from each ion threshold to 15 eV, using large-scale close-coupling calculations within the Dirac--Coulomb R -matrix approximation. The results from our theoretical work are compared with recent measurements made at the ASTRID merged-beam set-up at the University of Aarhus in Denmark and from the Fourier transform ion cyclotron resonance trap method at the SOLEIL synchrotron radiation facility in Saint-Aubin, France Bizau et al (2011 J. Phys. B: At. Mol. Opt. Phys. 44 055205) and the advanced light source M{ü}ller (2012 private communication), Aguliar et al (2012 J. Phys.: Conf. Ser . at press). For each of these complex ions our theoretical cross section results over the photon energy range investigated are seen to be in excellent agreement with experiment. Resonance energy positions and quantum defects of the prominent Rydberg resonances series identified in the spectra are compared with experiment for these complex halogen-like ions.

Multiplexed quantitative proteomics using differential metabolic 15N-labeling

There are several advantages of using metabolic labeling in quantitative proteomics. The early pooling of samples compared to post-labeling methods eliminates errors from different sample processing, protein extraction and enzymatic digestion. Metabolic labeling is also highly efficient and relatively inexpensive compared to commercial labeling reagents. However, methods for multiplexed quantitation in the MS-domain (or ‘non-isobaric’ methods), suffer from signal dilution at higher degrees of multiplexing, as the MS/MS signal for peptide identification is lower given the same amount of peptide loaded onto the column or injected into the mass spectrometer. This may partly be overcome by mixing the samples at non-uniform ratios, for instance by increasing the fraction of unlabeled proteins. We have developed an algorithm for arbitrary degrees of nonisobaric multiplexing for relative protein abundance measurements. We have used metabolic labeling with different levels of 15N, but the algorithm is in principle applicable to any isotope or combination of isotopes. Ion trap mass spectrometers are fast and suitable for LC-MS/MS and peptide identification. However, they cannot resolve overlapping isotopic envelopes from different peptides, which makes them less suitable for MS-based quantitation. Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry is less suitable for LC-MS/MS, but provides the resolving power required to resolve overlapping isotopic envelopes. We therefore combined ion trap LC-MS/MS for peptide identification with FTICR LC-MS for quantitation using chromatographic alignment. We applied the method in a heat shock study in a plant model system (A. thaliana) and compared the results with gene expression data from similar experiments in literature.

Comparison of bottom-up protein identification methods

With the rapid development of proteomics, a number of different methods appeared for the basic task of protein identification. We made a simple comparison between a common liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow using an ion trap mass spectrometer and a combined LC-MS and LC-MS/MS method using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and accurate peptide masses. To compare the two methods for protein identification, we grew and extracted proteins from E. coli using established protocols. Cystines were reduced and alkylated, and proteins digested by trypsin. The resulting peptide mixtures were separated by reversed-phase liquid chromatography using a 4 h gradient from 0 to 50% acetonitrile over a C18 reversed-phase column. The LC separation was coupled on-line to either a Bruker Esquire HCT ion trap or a Bruker 7 tesla APEX-Qe Qh-FTICR hybrid mass spectrometer. Data-dependent Qh-FTICR-MS/MS spectra were acquired using the quadrupole mass filter and collisionally induced dissociation into the external hexapole trap. Proteins were in both schemes identified by Mascot MS/MS ion searches and the peptides identified from these proteins in the FTICR MS/MS data were used for automatic internal calibration of the FTICR-MS data, together with ambient polydimethylcyclosiloxane ions.

Identification of geodesic chirping Alfven modes and q-factor estimation in hot core tokamak plasmas in ASDEX Upgrade

Alfven eigenmodes (AE) driven by ion cyclotron resonance heating are usually registered by different diagnostic channels in the hot core plasmas of large tokamaks like JET and ASDEX Upgrade. These AE appear very near to the extremum points of Alfven wave continuum, which is modified by the geodesic effect due to poloidal mode coupling. It is shown that the AE spectrum may be explored as the magnetic spectroscopy (like Alfven cascades by Sharapov et al 2001 Phys. Lett. A 289 127) to determine the q-factor minimum and geodesic frequency at the magnetic axis in standard sawtoothed discharges without reversed shear.

Energy States of Phosphorous Donor in Silicon in Fields up to 18 T

The evolution of the energy states of the phosphorous donor in silicon with magnetic field has been the subject of previous experimental and theoretical studies to fields of 10 T. We now present experimental optical absorption data to 18 T in combination with theoretical data to the same field. We observe features that are not revealed in the earlier work, including additional interactions and anti-crossings between the different final states. For example, according to the theory, for the ""1s -> 2p (+)"" transition, there are anti-crossings at about 5, 10, 14, 16, and 18 T. In the experiments, we resolve at least the 5, 10, and 14 T anti-crossings, and our data at 16 and 18 T are consistent with the calculations.