Mass Spectrometric Study Research Articles

Isolation and Characterization of 1-Hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic Acid, a Metabolite in Bacterial Transformation of Abscisic Acid.

We report the discovery of a new abscisic acid (ABA) metabolite, found in the course of a mass spectrometric study of ABA metabolism by the rhizosphere bacterium Rhodococcus sp. P1Y. Analogue of (+)-ABA, enriched in tritium in the cyclohexene moiety, was fed in bacterial cells, and extracts containing radioactive metabolites were purified and analyzed to determine their structure. We obtained mass spectral fragmentation patterns and nuclear magnetic resonance spectra of a new metabolite of ABA identified as 1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic acid, which we named rhodococcal acid (RA) and characterized using several other techniques. This metabolite is the second bacterial ABA degradation product in addition to dehydrovomifoliol that we described earlier. Taken together, these data reveal an unknown ABA catabolic pathway that begins with side chain disassembly, as opposed to the conversion of the cyclohexene moiety in plants. The role of ABA-utilizing bacteria in interactions with other microorganisms and plants is also discussed.

Heat Shock-Induced Extracellular Vesicles Derived from Neural Stem Cells Confer Marked Neuroprotection Against Oxidative Stress and Amyloid-β-Caused Neurotoxicity.

Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and a leading cause of dementia. Although the amyloid-β (Aβ) peptide is deemed a crucial driver of AD, there are no effective therapeutics available to treat Aβ-caused neurotoxicity. Extracellular vesicles (EVs) are membrane-bound small particles mediating intercellular traffic of nucleic acids, lipids, proteins, and metabolites. Exosomes are a subtype of EVs with a size range of 30-150nm in diameter. Stem cell-derived EVs are a potential therapeutic for AD, while EVs isolated from normal stem cell cultures generally have a low yield. Here, we studied the EVs secreted by the rat neural stem cells in the presence of heat shock (HS) stimulus. Nanoparticle tracking analysis confirmed that HS-derived EVs exhibit significantly higher concentration and larger diameter in comparison to the non-heat shock (NHS)-derived EVs. Mass spectrometric studies of EV proteins revealed that HS-derived EVs contained fewer diverse proteins than NHS-derived exosomes. GO enrichment analysis of the proteins suggested that the top two biological functions of the proteins in HS-derived EVs are involved in the negative regulation of apoptotic process and positive modulation of DNA repair. Importantly, the therapeutic efficacy of the NHS- and HS-derived EVs were tested in a cell culture model of AD: HS-derived EVs exhibited greater neuroprotection against not only oxidative stress but also amyloid-β (Aβ) induced neurotoxicity compared to NHS-derived EVs. Moreover, HS-derived EVs were also able to dramatically attenuate Aβ-induced apoptosis and oxidative stress. These data indicate that in response to HS, neural stem cells increase EV production and alter EV morphology and cargo to confer better neuroprotection against oxidative stress and Aβ-caused neurotoxicity, suggesting that HS-induced EVs from neural stem cells can be a therapeutic agent for AD and possibly other neurological disorders.

Golden Details of a Funeral Wreath and Clothing from the Roman Time Bosporan Crypt: X-ray and Mass Spectrometric Studies

The results of a comprehensive study present the details of the funeral wreath and clothing from the crypt of the Roman period in the area of the modern Malyy Lane in the city of Kerch. A comparative analysis of the metal composition of similar items from synchronous sites of the Northern Black Sea region has been carried out. It has been established that the details of funeral wreaths and appliqués to them are made of a gold-silver alloy that can be easily worked, which was widely used in Roman times throughout the territory of the Bosporos. Items created in a local workshop for funeral vestments have traces of careless or not very skillful application of the image, and damage to the surface, as evidenced by X-ray tomography data.

Dinuclear Cobalt Complexes for Homogeneous Water Oxidation: Tuning Rate and Overpotential through the Non-Innocent Ligand.

In this study, dinuclear cobalt complexes (1 and 2) featuring bis(benzimidazole)pyrazolide-type ligands (H2 L and Me2 L) were prepared and evaluated as molecular electrocatalysts for water oxidation. Notably, 1 bearing a non-innocent ligand (H2 L) displayed faster catalytic turnover than 2 under alkaline conditions, and the base dependence of water oxidation and kinetic isotope effect analysis indicated that the reaction mediated by 1 proceeded by a different mechanism relative to 2. Spectroelectrochemical, cold-spray ionization mass spectrometric and computational studies found that double deprotonation of 1 under alkaline conditions cathodically shifted the catalysis-initiating potential and further altered the turnover-limiting step from nucleophilic water attack on (H2 L)CoIII 2 (superoxo) to deprotonation of (L)CoIII 2 (OH)2 . The rate-overpotential analysis and catalytic Tafel plots showed that 1 exhibited a significantly higher rate than previously reported Ru-based dinuclear electrocatalysts at similar overpotentials. These observations suggest that using non-innocent ligands is a valuable strategy for designing effective metal-based molecular water oxidation catalysts.

The molecular species in saturated and overheated vapors of Sc(acac)3: A first structural study of bis-acetylacetonate scandium Sc(acac)2 radical

Mass spectrometric and gas-phase electron diffraction (GED/MS) studies of overheated Sc(acac)3 vapor at temperature 812(5) K were performed. Experimental data indicate that overheated vapor contains, along with tris-form Sc(acac)3, bis-complex Sc(acac)2, which is the result of partial thermal dissociation of tris form. Testing of three models D2h(2Ag), D2h(2B3g) and D2d(2B1) of bis-complex geometric and electronic structure showed that the planar model D2h(2B3g) best fits GED/MS data. Reinterpretation of GED/MS data for saturated vapor of Sc(acac)3 at T = 428 K was carried out. Temperature dependence of rg(Sc-O) parameters of effective temperature-averaged geometric configuration Sc(acac)3 is noted.

Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes

Chemo- and regio-selective catalysis of the C(sp3)-H halogenation reaction is a formidable goal in chemical synthesis. 2-Oxoglutarate (2OG)-dependent non-heme iron halogenases catalyze selective chlorination/bromination of C–H bonds and exhibit high sequence and structural similarities with non-heme iron hydroxylases. How the secondary coordination sphere (SCS) of these two enzyme systems differentiate and determine their reactivity is not well understood. In this work, we show that specific positioning of redox-active tyrosine residues in the SCS of non-heme iron halogenases has a huge impact on their structure, function, and reactivity. We discover that a tyrosine residue (F121Y) rationally incorporated to hydrogen bond to iron’s chloride ligand in SyrB2 halogenase undergoes post-translational oxidation to dihydroxyphenylalanine (DOPA) physiologically. A combination of spectroscopic, mass-spectrometric, and biochemical studies demonstrate that DOPA modification in SyrB2 renders the enzyme non-functional. Bioinformatic analysis suggests that SyrB2-like halogenases, unlike hydroxylases, have a conserved placement of phenylalanine at position 121 to preclude such unproductive oxidation. Furthermore, molecular dynamics simulations in tandem with experimental demonstration of DOPA incorporation exclusively at position 121 enables us to uniquely identify that an axial-chloro haloferryl isomer is operant in SyrB2. We also identify conserved redox-inactive residues in the SCS of other 2OG-dependent non-heme iron halogenases to avoid DOPA-like unproductive oxidations. Overall, this study demonstrates the importance of the SCS in controlling the structure and enzymatic activity of non-heme iron halogenases and will have significant implications toward the design of small-molecule and protein-based halogenation catalysts.

High-temperature mass spectrometric study of thermodynamic properties in the TiO2 -Al2 O3 -SiO2 system and modeling.

The TiO2 -Al2 O3 -SiO2 system is the base for various glass-ceramic materials, which have great practical value for a large number of modern technologies. Many TiO2 -Al2 O3 -SiO2 materials are synthesized or applied at high temperatures, which justifies the relevance of the present study. The samples in the TiO2 -Al2 O3 -SiO2 system were synthesized using the method of induction melting in a cold crucible. The thermodynamic properties of the TiO2 -Al2 O3 -SiO2 system were studied using the Knudsen effusion mass spectrometric method. The derived thermodynamic functions were optimized within the generalized lattice theory of associated solutions (GLTAS) approach and compared with the results of calculation using the semiempirical Kohler, Muggianu, Toop, Redlich-Kister, and Wilson methods based on the corresponding data in the binary systems. The SiO2 selective vaporization from the samples under study was shown at temperatures above 1940 K. The thermodynamic properties in the TiO2 -Al2 O3 -SiO2 system, including the TiO2 -SiO2 system, were obtained in the temperature range 1965-2012 K and were optimized using GLTAS to obtain the consistent concentration dependences of the component activities and excess Gibbs energies. Positive deviations from the ideal behavior were observed in the TiO2 -Al2 O3 -SiO2 system at high temperatures. Comparison of these values with the results of the modeling based on the GLTAS approach allowed the recommendations regarding the optimal semiempirical methods for the excess Gibbs energy calculation in different concentration ranges to be made.

Elucidating the Oligomerization and Cellular Interactions of a Trimer Derived from Aβ through Fluorescence and Mass Spectrometric Studies.

Aβ oligomers play a central role in the neurodegeneration observed with Alzheimer’s disease. Our laboratory has developed covalently stabilized trimers derived from residues 17–36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells. 2AT-L and fluorescently labeled 2AT-L analogues assemble in the membrane-like environment of SDS-PAGE, showing diffuse bands of oligomers in equilibrium. Native ion mobility-mass spectrometry (native IM-MS) of 2AT-L allows for the identification of discrete oligomers in solution and shows similar patterns of oligomer formation between 2AT-L and fluorescently labeled analogues. Fluorescence microscopy with SH-SY5Y cells reveals that fluorescently labeled 2AT-L analogues colocalize within lysosomes. FLIM studies with phasor analysis further elucidate the assembly of 2AT-L within cells and establish the occurrence of FRET, indicating the presence of oligomers within cells. Collectively, these multiple complementary techniques help better understand the complex behavior of the 2AT-L model system.

Photoionization spectroscopy of the SiH free radical in the vacuum-ultraviolet range.

The first measurement of the photoelectron spectrum of the silylidyne free radical, SiH, is reported between 7 and 10.5eV. Two main photoionizing transitions involving the neutral ground state, X+1Σ+ ← X2Π and a+3Π ← X2Π, are assigned by using ab initio calculations. The corresponding adiabatic ionization energies are derived, IEad(X+1Σ+) = 7.934(5)eV and IEad(a+3Π) = 10.205(5)eV, in good agreement with our calculated values and the previous determination by Berkowitz et al. [J. Chem. Phys. 86, 1235 (1987)] from a photoionization mass spectrometric study. The photoion yield of SiH recorded in this work exhibits a dense autoionization landscape similar to that observed in the case of the CH free radical [Gans et al., J. Chem. Phys. 144, 204307 (2016)].

Mass Spectrometric Studies of Valine Molecules by Electron Shock in the Gas Phase

Relevance. Valine is one of the eight amino acids not synthesised by the human body, necessary for the synthesis and growth of body tissues, muscle coordination; regulation of nervous processes, nitrogen metabolism, and stabilisation of the hormonal background. Since α-amino acids contain an asymmetric carbon atom, they can exist as optical isomers (mirror antipodes) that play an essential role in protein biosynthesis. The structure of matter and the physical processes that occur in it are studied using the method of mass spectrometry and spectral analysis. This indicates the relevance of the problem that was studied in this paper. Purpose. Mass spectrometric studies of the formation of ionic products of single and dissociative ionisation of the valine molecule (C5 H11NO2) with electrons according to the method of beams intersecting within the energy range of bombarding electrons 6-70 eV. To consider the mechanisms of formation of the most intense ion fragments during dissociative ionisation by electron shock. Methods. The experiment was conducted on an installation with a monopole mass spectrometer of the MX-7304A type, which belongs to the class of dynamic mass analysers with electron shock ionisation in the range of mass numbers 0-120 Da. The mass spectra of molecules were investigated at different temperatures of the source of molecules in the range of 300-600 K. Results. The obtained results are compared with the mass spectra of the D-, L-, and DL-enantiomeric forms of the valine molecule with data from the NIST and SDBS databases. The features of the processes of formation of ion fragments of valine molecules by electronic shock are analysed in detail, and the dynamics of the yield of ion fragments in the range of evaporation temperatures of the initial substance of 300-440 K is also studied. The total relative ionisation cross-section of the molecule under study was measured according to mass spectrometric method with an ionising electron energy of 5-60 eV. Based on the results of experimental studies, a threshold section of the dependence of the total relative cross-section of valine ionisation is determined and given in this paper. Conclusions. A detailed analysis of the processes of formation of fragment ions in the mass spectra allows demonstrating the influence of the structural forms of valine enantiomers on the redistribution of relative intensities of product ions

Forced degradation studies on axitinib and characterization of its degradation products by liquid chromatography‐high resolution mass spectrometry and nuclear magnetic resonance spectroscopy along with its insilico toxicity assessment

AbstractThe prime focus of the present study includes forced degradation studies on axitinib and the characterization of novel degradation products formed. As per International Council for Harmonisation guidelines, axitinib was exposed to harsher conditions such as acidic, alkali, oxidative, photolytic, and thermal conditions. Axitinib was found unstable upon exposure to oxidative and photolytic conditions, generating a total of four degradation products. Out of four degradation products, three are novel and were not reported in the literature. The degradation products formed were well separated by high‐performance liquid chromatography and characterized by liquid chromatography‐high resolution mass spectrometric studies. Further, their structures were confirmed by nuclear magnetic resonance spectroscopic studies. The possible degradation products were characterized as sulfoxide, sulfone, isomeric and dimer impurities. A detailed mechanistic explanation for the formation of degradation products along with its insilico toxicity prediction was laid out.

Mass Spectrometric Study on Ions and Radicals in Tetramethylsilane Plasma for Si-containing Diamond-Like Carbon Coating

Mass Spectrometric Study on Ions and Radicals in Tetramethylsilane Plasma for Si-containing Diamond-Like Carbon Coating

Mass Spectrometric Study of the Reaction of a Fluorine Atom and Monocloroacetic Acid

Mass Spectrometric Study of the Reaction of a Fluorine Atom and Monocloroacetic Acid

Mass spectrometric study of the laser-produced carbon vapor up to 4500 K

The mass spectrometric measurements of the molecular composition in a carbon vapor produced by the laser-induced sublimation of pyrolitic graphite have been carried out up to 4500 K, temperature that stands very close to the carbon's triple point. The measurements of the relative partial pressure of the dominant С3 molecule up to the maximum temperature achieved did not deliver any unanticipated results, which could be attributed to any kind of the phase transitions. This has therefore indirectly confirmed that the temperature of the carbon triple point cannot be below 4500 К. The widely known problem of a significant deviation of evaporation coefficients of carbon molecules from unity has been largely addressed by a comparative analysis of the evaporation of two planes of pyrolitic graphite. The technical means that allowed for the mass spectrometric study of the carbon sublimation at extreme temperatures are further discussed in detail.

HDL, heart disease, and the lung

HDL, heart disease, and the lung

THE EFFECT OF SULFUR – CONTAINING COMPOUNDS ON THE STABILITY OF DIESEL FUELS

A high-resolution low-voltage mass spectrometric study has been carried out on the sulfur-containing fractions of fresh diesel fuel and on samples aged at 43°C in borosilicate bootles (ASTM D 4625 test) for periods of 6.5, 13, 19,5 and 26 weeks, and at 80°C for periods of 0.5, 1, 1.5, 2, 3, and 4 weeks. Homologous series of benze-and di benzothiophenes are the principal sulphur-containing compounds were detected. The concentrations of all species present with aging were monitored and the role of each compound in the gum-forming process assessed.

Mass spectrometric study of variation in kinin peptide profiles in nasal fluids and plasma of adult healthy individuals

BackgroundThe kallikrein-kinin system is assumed to have a multifunctional role in health and disease, but its in vivo role in humans currently remains unclear owing to the divergence of plasma kinin level data published ranging from the low picomolar to high nanomolar range, even in healthy volunteers. Moreover, existing data are often restricted on reporting levels of single kinins, thus neglecting the distinct effects of active kinins on bradykinin (BK) receptors considering diverse metabolic pathways. A well-characterized and comprehensively evaluated healthy cohort is imperative for a better understanding of the biological variability of kinin profiles to enable reliable differentiation concerning disease-specific kinin profiles.MethodsTo study biological levels and variability of kinin profiles comprehensively, 28 healthy adult volunteers were enrolled. Nasal lavage fluid and plasma were sampled in customized protease inhibitor prespiked tubes using standardized protocols, proven to limit inter-day and interindividual variability significantly. Nine kinins were quantitatively assessed using validated LC–MS/MS platforms: kallidin (KD), Hyp4-KD, KD1-9, BK, Hyp3-BK, BK1-8, BK1-7, BK1-5, and BK2-9. Kinin concentrations in nasal epithelial lining fluid were estimated by correlation using urea.ResultsCirculating plasma kinin levels were confirmed in the very low picomolar range with levels below 4.2 pM for BK and even lower levels for the other kinins. Endogenous kinin levels in nasal epithelial lining fluids were substantially higher, including median levels of 80.0 pM for KD and 139.1 pM for BK. Hydroxylated BK levels were higher than mean BK concentrations (Hyp3-BK/BK = 1.6), but hydroxylated KD levels were substantially lower than KD (Hyp4-KD/KD = 0.37). No gender-specific differences on endogenous kinin levels were found.ConclusionsThis well-characterized healthy cohort enables investigation of the potential of kinins as biomarkers and would provide a valid control group to study alterations of kinin profiles in diseases, such as angioedema, sepsis, stroke, Alzheimer’s disease, and COVID-19.

Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer's disease.

This review covers the results of the application of mass spectrometric (MS) techniques to study the diversity of beta-amyloid (Aβ) peptides in human samples. Since Aβ is an important hallmark of Alzheimer's disease (AD), which is a socially significant neurodegenerative disorder of the elderly worldwide, analysis of its endogenous variations is of particular importance for elucidating the pathogenesis of AD, predicting increased risks of the disease onset, and developing effective therapy. MS approaches have no alternative for the study of complex samples, including a wide variety of Aβ proteoforms, differing in length and modifications. Approaches based on matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography with electrospray ionization tandem MS are most common in Aβ studies. However, Aβ forms with isomerized and/or racemized Asp and Ser residues require the use of special methods for separation and extra sensitive and selective methods for detection. Overall, this review summarizes current knowledge of Aβ species found in human brain, cerebrospinal fluid, and blood plasma; focuses on application of different MS approaches for Aβ studies; and considers the potential of MS techniques for further studies of Aβ-peptides.

Optimizing Coaxial Sonic Spray Geometry for Generating Water Microdroplets.

Sonic spray creates a stream of neutral and charged microdroplets without application of voltage, heating, laser irradiation, or corona discharge. The solvent of interest flows through an inner capillary (usually constructed of fused silica) that is surrounded by an outer stainless-steel tube through which a nebulizing gas flows under pressure. This technique has been widely used as the interface in mass spectrometric studies for chemical analysis and for understanding microdroplet chemistry. We have used light scattering to characterize the size distribution and density for water microdroplets as a function of several parameters, such as water quality, water flow rate, nebulizing gas pressure, and sonic sprayer geometry. We find that the size distribution of the microdroplets, which is critical to many applications, depends most sensitively on the distance between the inner and outer capillary outlets and the gas flow pressure. The best performance as measured by the smallness of the microdroplet diameters is obtained when the gas flow pressure is the highest and there is no separation distance, d, between the two capillary outlets. In addition, at d = 0 mm, the microdroplet diameter distribution is nearly independent of the water flow rate, indicating that studies under these conditions can be scaled up.

Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework.

BackgroundData-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging owing to the high complexity and large data and sample size, which require specialized software and vast computing infrastructures. Most available open-source DIA software necessitates basic programming skills and covers only a fraction of a complete DIA data analysis. In consequence, DIA data analysis often requires usage of multiple software tools and compatibility thereof, severely limiting the usability and reproducibility.FindingsTo overcome this hurdle, we have integrated a suite of open-source DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef, and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their use on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate the usability of an all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided to further increase access for the proteomics community.ConclusionThe integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework in combination with extensive training material empowers a broad community of researches to perform reproducible and transparent DIA data analysis.