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We report the effect of N2 gas‐mixing in the xenon electron cyclotron resonance (ECR) plasma, and abundance‐dependent novel, exciting and unusual trends of the isotope anomaly. The xenon plasma was produced using a 10 GHz all‐permanent‐magnet NANOGAN ECR ion source, and the charge state distributions of naturally abundant six stable xenon isotopes with and without N2 gas‐mixing (at 25%, 50%, and 75%) were recorded. The intensity ratio of the heavier to lighter isotope, where the heavier isotope is less abundant, showed a clear signature of the isotope anomaly as explained by the linear Landau wave damping theory. Contrary to the theoretical prediction that the isotope anomaly should vanish with a relatively large fraction of the heavier isotope in mixed plasmas, the trends of intensity ratios observed in such cases are very unusual and have almost the mirror‐symmetrical shapes of those trends recorded with less abundant heavier isotope. Further, the effect of relative mass difference on the isotope anomaly was also evidenced. The N2 gas‐mixing of the xenon plasma at 25% and 50% shifted the entire charge state distribution toward the higher intensity side owing to the supply of additional electrons that caused high ionization efficiency. However, a prominent gas‐mixing effect was observed at 75% of N2 mixing in the xenon plasma beyond the +7 charge state. The abundance‐dependent unusual trends in isotope anomaly have been explained by considering different ionic temperatures, ion heating by the wave damping, and Coulomb scattering in the core of the plasma. [ABSTRACT FROM AUTHOR]

The xcalib toolkit has been developed to calibrate the beam profile of an X‐ray free‐electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence‐dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core‐hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region. [ABSTRACT FROM AUTHOR]

We report the charge state distributions of the pure, 25% and 50% oxygen mixed krypton plasma to shed more light on the understanding of the gas mixing and the isotope anomaly [A. G. Drentje, Rev. Sci. Instrum. 63 (1992) 2875 and Y Kawai, D Meyer, A Nadzeyka, U Wolters and K Wiesemann, Plasma Sources Sci. Technol. 10 (2001) 451] in the electron cyclotron resonance (ECR) plasmas. The krypton plasma was produced using a 10 GHz all-permanent-magnet ECR ion source. The intensities of the highly abundant four isotopes, viz. 82Kr (~11.58%), 83Kr (~11.49%), 84Kr (~57%) and 86Kr (17.3%) up to ~ +14 charge state have been measured by extracting the ions from the plasma and analysing them in the mass and the energy using a large acceptance analyzer-cum-switching dipole magnet. The influence of the oxygen gas mixing on the isotopic krypton ion intensities is clearly evidenced beyond +9 charge state. With and without oxygen mixing, the charge state distribution of the krypton ECR plasma shows the isotope anomaly with unusual trends. The anomaly in the intensities of the isotopes having quite closer natural abundance, viz. 82Kr, 86Kr and 83Kr, 86Kr is prominent, whereas the intensity ratio of 86Kr to 84Kr shows a weak signature of it. The isotope anomaly tends to disappear with increasing oxygen mixing in the plasma. The observed trends in the intensities of the krypton isotopes do not follow the prediction of linear Landau wave damping in the plasma. [ABSTRACT FROM AUTHOR]

In this study, alleviation of ion suppression effect in sonic spray ionization mass spectrometry (SSI-MS) was investigated. Ion suppression effect was firstly compared between electrospray ionization (ESI) and conventional SSI, and more severe ion suppression effect was observed with SSI. Ion suppression effect of SSI was also found difficult to be alleviated by simply optimizing major parameters. Alternatively, we found that with the assistance of an alternating current (AC) voltage with low amplitude, the ion suppression effect was greatly alleviated (comparable with conventional ESI). That AC voltage was applied outside the SSI spray tip, and no direct contact between the electrode and spray solution was necessary. Besides the alleviation of the ion suppression effect, this newly-developed method, termed as induced electrosonic spray ionization (IESSI), appeared to preserve similar charge state distribution with SSI for protonated cytochrome c, hemoglobin, and bradykinin. IESSI could also obtain significantly improved ion intensities (~1000-fold over conventional SSI). In addition, tolerance of concentrated salts for IESSI-MS was investigated through the analysis of cytochrome c in the presence of concentrated sodium chloride (NaCl) or ammonium acetate (NH4OAc). Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The exposure of electrospray droplets to vapors of deuterating reagents during droplet desolvation in the interface of a mass spectrometer results in hydrogen/deuterium exchange (HDX) on the sub-millisecond time scale. Deuterated water is used to label ubiquitin and cytochrome c with minimal effect on the observed charge state distribution (CSD), suggesting that the protein conformation is not being altered. However, the introduction of deuterated versions of various acids (e.g., CD3COOD and DCl) and bases (ND3) induces unfolding or refolding of the protein while also labeling these newly formed conformations. The extent of HDX within a protein CSD associated with a particular conformation is essentially constant, whereas the extent of HDX can differ significantly for CSDs associated with different conformations from the same protein. In some cases, multiple HDX distributions can be observed within a given charge state (as is demonstrated with cytochrome c) suggesting that the extent of HDX and CSDs share a degree of complementarity in their sensitivities for protein conformation. The CSD is established late in the evolution of ions in electrospray whereas the HDX process presumably takes place in the bulk of the droplet throughout the electrospray process. Back exchange is also performed in which proteins are prepared in deuterated solvents prior to ionization and exposed to undeuterated vapors to exchange deuteriums for hydrogens. The degree of deuterium uptake is easily controlled by varying the identity and partial pressure of the reagent introduced into the interface. Since the exchange occurs on the sub-millisecond time scale, the use of deuterated acids or bases allows for transient species to be generated and labeled for subsequent mass analysis. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The fundamental aspects of charging in electrospray ionization (ESI) are hotly debated. In the present study, ESI charging of DNA oligonucleotides was explored in both positive (ESI+) and negative (ESI−) polarity using mass spectrometry detection. Single-stranded 12-mer CCCCAATTCCCC in buffer solution (aqueous NH4Ac, 100 mM) produced similar charge state distribution (CSD) in either ESI+ or ESI−. Similarity of CSD in ESI+ and ESI− was also observed for the double-stranded 12-mer CGCGAATTCGCG. By adding typical low-vapor reagents (e.g. m-nitro benzyl alcohol, m-NBA; sulfolane) into the same buffer solution (<0.5% w/v), both CCCCAATTCCCC and CGCGAATTCGCG revealed strong supercharging (SC) effect in ESI−, while very little or no SC effect was observed in ESI+. With either sulfolane or m-NBA, the CGCGAATTCGCG duplex dissociated into single strands in ESI−. No SC was observed in both ESI+ and ESI− for thermally denatured CGCGAATTCGCG duplex in NH4Ac buffer without the reagents. These findings are difficult to reconcile with the earlier model, which attributes SC in aqueous buffer solution to the conformational changes of analytes. Our observations suggest that the ionic strength of ESI droplets strongly affects the CSD of biopolymers such as DNA oligonucleotides and that SC effect is related to the depletion of ionic strength during the ESI process. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Bacteriophage λ integrase (λ-Int) is the prototypical member of a large family of enzymes that catalyze site-specific DNA recombination via single-strand cleavage and the formation of a Holliday junction intermediate. Crystallographic and biochemical evidence indicate that substantial conformational change (i.e., folding) in the catalytic domain of the protein is required for substrate recognition and catalysis. We have examined the solution conformation of the catalytic domain (C170) in the absence and presence of a cognate 'half-site' DNA oligonucleotide by electrospray ionization mass spectrometry, and circular dichroism and fluorescence spectroscopy. The distribution of ions in the positive ion electrospray mass spectrum of the free protein reveals the presence of three distinct species in solution, one corresponding to the folded protein, one to the unfolded protein, and one to a dimer. In the presence of DNA, ions are observed only for the protein-DNA complex and the folded form of the free protein. We therefore conclude that DNA binding stabilizes the global fold of the protein in a manner that is consistent with folding-coupled target recognition as a mechanism to control site-specific recombination. Furthermore, we find that inspection of the charge state distribution of ions in electrospray mass spectra provides a quick and effective means to identify conformational heterogeneity of proteins in solution and to investigate dynamic protein-nucleic acid interactions. [ABSTRACT FROM AUTHOR]