Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase

At present, the secondary structure of oligonucleotide ions in a gas phase is almost not understood. One of the main points is the retention of a hairpin secondary structure during ionization. In this work, we used a deuterium–hydrogen exchange reaction in a gas phase at atmospheric pressure for studying the conformational dynamics of oligonucleotide ions formed as a result of electrospray ionization. The exchange reactions of two oligonucleotides, which consisted of the identical sets of nucleotides but differed in their sequence, have been studied. One of these oligonucleotides formed a hairpin secondary structure, but the other did not. It has been found that both of the oligonucleotides demonstrate similar reaction dynamics of deuterium/hydrogen exchange in the gas phase; thereby indicating that the secondary structure has been completely destroyed during ionization.     

Analysis of the diamagnetic effect in multipole Galatea traps

The toroidal current emerging after the injection of a plasmoid through the magnetic shell of the Trimyx-3M (microwave) multipole trap is measured using the Rogowski loop. This current is due to diamagnetism of the plasma. The relation between the diamagnetic current and the maximal plasma pressure produced at the magnetic field separatrix is obtained. It is shown hence that magnetic measurements in a multi-pole trap for a known concentration make it possible to determine the plasma temperature in the trap and the energy confinement time.     

Plasma parameters in the upgraded Trimyx-M Galathea

Results are presented from measurements of the plasma parameters in the upgraded Trimyx-M Galathea. After the barrier magnetic field and the energy of the injected hydrogen plasma bunch were increased to B _bar ∼ 0.1 T and W ₀ ≈ 200 J, respectively, the following plasma parameters were achieved: the density n ∼ 5 × 10¹³ cm⁻³, the plasma confinement time τ* = 800–900 μs, the elergy of the confined plasma W ₁ ∼ 100 J, the ratio of the plasma pressure to the barrier magnetic pressure β ₀ ∼ 0.2, the electron temperature T _e ∼ 20 eV, and the ion temperature T _i ∼ 2T _e . The maximum time during which the plasma density decreased e-fold, τ _p , was found to be 300 μs at B _bar = 0.1 T, which agrees with the classical transport model.     

Probe measurements in the channel of a magnetic annular arc

The profiles of the electron temperature and density in the channel of a magnetic annular arc have been measured with the help of an electrical circuit developed for large probe currents.Translated from Zhurnal Prikladnoi Mekhaniki i Tekhnicheskoi Fiziki, No. 5, pp. 158–160, September–October, 1973.     

Probabilistic model applied to ion abundances in product-ion spectra: quantitative analysis of aspartic acid isomerization in peptides

Evaluation of post-translational modifications of protein molecules is important for both basic and applied biomedical research. Mass spectrometric quantitative studies of modifications, which do not change the mass of the protein, such as isomerization of aspartic acid, do not necessarily require the use of isotope-labelled standards. However, the accurate solution of this problem requires a deep understanding of the relationship between the mole fractions of the isomers and the peak intensities in the mass spectra. In previous studies on the isomerization of aspartic acid in short beta-amyloid fragments, it has been shown that calibration curves used for such quantitative studies often have a non-linear form. The reason for the deviation in the shape of the calibration curves from linearity has not yet been established. Here, we propose an explanation for this phenomenon based on a probabilistic model of the fragmentation process and present a general approach for the selection of fragments that can be used for quantitative studies of the degree of isomerization.

Graphical Abstract

     

Label‐free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

Cervicovaginal fluid (CVF) is a valuable source of clinical information about the female reproductive tract in both nonpregnant and pregnant women. The aim of this study is to specify the CVF proteome at different stages of cervix neoplastic transformation by label‐free quantitation approach based on liquid chromatography tandem mass spectrometry (LC‐MS/MS) method. The proteome composition of CVF from 40 women of reproductive age with human papillomavirus (HPV)‐associated cervix neoplastic transformation (low‐grade squamous intraepithelial lesion [LSIL], high‐grade squamous intraepithelial lesion [HSIL], and CANCER) was investigated. Hierarchical clustering and principal component analysis (PCA) of the proteomic data obtained by a label‐free quantitation approach show the distribution of the sample set between four major clusters (no intraepithelial lesion or malignancy [NILM], LSIL, HSIL and CANCER) depending on the form of cervical lesion. Multisample ANOVA with subsequent Welch's t test resulted in 117 that changed significantly across the four clinical stages, including 27 proteins significantly changed in cervical cancer. Some of them were indicated as promising biomarkers previously (ACTN4, VTN, ANXA1, CAP1, ANXA2, and MUC5B). CVF proteomic data from the discovery stage were analyzed by the partial least squares‐discriminant analysis (PLS‐DA) method to build a statistical model, allowing to differentiate severe dysplasia (HSIL and CANCER) from the mild/normal stage (NILM and LSIL), and receiver operating characteristic (ROC) area under the curve (AUC) were obtained on an independent set of 33 samples. The sensitivity of the model was 77%, and the specificity was 94%; AUC was equal to 0.87. CVF proteome proved to be reflect the stage of cervical epithelium neoplastic process.     

On levitation of diamagnetic bodies in a magnetic field

Various methods for calculating the force characteristics of a suspension ensuring levitation of diamagnetic bodies of various origin and shape are considered. The method of calculation is based on the computation of the energy of interaction of a body upon its displacement from the center of suspension for an arbitrary configuration of the suspending field. The method of quasi-homogeneous approximation is considered and compared with the method for calculating the force characteristics based on the general formula for the magnetic energy. The necessary and sufficient conditions for conservative stability of the equilibrium state are formulated, and the stability domain is determined. It is shown that the stability domain depends on the size of the body. Calculations of force characteristics are performed specifically for the suspension of a diamagnetic sphere. The dependences of forces and stiffnesses on the magnetic field strength are obtained, which makes it possible to analyze the stability of confinement of the diamagnetic sphere in the field of the system of circular currents.     

Rapid Automatic Determination of Four Cardiomarkers in the Blood Plasma of Patients with Cardiopathologies

Journal of Analytical Chemistry - We proposed a method for the simultaneous rapid determination of four protein cardiomarkers (C?reactive protein, cystatin C, myoglobin, and D-dimer) in the...