Mass Spectrometer Instrument Research Articles

Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry

Genotoxicants originating from inflammation, diet, and environment can covalently modify DNA, possibly initiating the process of carcinogenesis. DNA adducts have been known for long, but the old methods allowed to target only a few known DNA adducts at a time, not providing a global picture of the “DNA adductome”. DNA adductomics is a new research field, aiming to screen for unknown DNA adducts by high resolution mass spectrometry (HRMS). However, DNA adductomics presents several analytical challenges such as the need for high sensitivity and for the development of effective screening approaches to identify novel DNA adducts. In this work, a sensitive untargeted DNA adductomics method was developed by using ultra-high performance liquid chromatography (UHPLC) coupled via an ESI source to a quadrupole-time of flight mass spectrometric instrumentation. Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, cone voltage, and detector voltage had most effect on the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. Hybrid surface-coated analytical columns were tested for reducing adsorption of the DNA adducts. The optimized method was applied to analyse DNA adducts in calf thymus, cat colon, and human colon DNA by performing a MSE acquisition (all-ion fragmentation acquisition) and screening for the loss of deoxyribose and the nucleobase fragment ions. Fifty-four DNA adducts were tentatively identified, hereof 38 never reported before. This is the first untargeted DNA adductomics study on human colon tissue, and one of the few untargeted DNA adductomics studies in the literature reporting the identification of such a high number of unknowns. This demonstrates promising results for the application of this sensitive method in future human studies for investigating novel potential cancer-causing factors.

Reanalysis of the Huygens GCMS dataset. I. High-resolution methane vertical profile in the atmosphere of Titan

More than 15 years after its landing on the surface of Titan, the data returned by the Huygens probe remain the only available in situ information on Titan’s lower atmosphere and its methane content. In this work, we present a reanalysis of the Huygens probe data obtained by the Gas Chromatograph Mass Spectrometer (GCMS) instrument on board Huygens. GCMS measured the atmospheric composition almost continuously during the Huygens probe descent by acquiring mass spectra between 145 km of altitude and Titan’s surface. We first focus on the recollection, reconstruction, and recalibration of the GCMS dataset to facilitate similar future work. We then reevaluate the methane vertical profile in Titan’s lower atmosphere by applying novel mass spectra data-treatment methods to this dataset. In addition to finding a slightly lower methane mixing ratio than those previously reported using GCMS measurements above the Huygens probe landing site, our work has revealed several kilometric to subkilometric-scale oscillations in the methane vertical profile below 30 km of altitude. We discuss several hypotheses that could explain these features, such as multiple layers of optically thin clouds or local convection cells, and strongly encourage the reanalysis of other Huygens datasets to further investigate these variations in the methane mixing ratio.

The Peregrine Ion Trap Mass Spectrometer (PITMS) Investigation Development and Preflight Planning

The Peregrine Ion Trap Mass Spectrometer (PITMS) is a mass spectrometer instrument that operated during the Astrobotic Peregrine Mission-1 as part of the NASA Commercial Lunar Payload Services initiative. This paper describes the instrument and investigation design, development, and planning conducted by the PITMS team, consisting of a successful partnership between NASA Goddard Space Flight Center (GSFC), The Open University, NASA, and ESA. PITMS was designed to measure the abundance and temporal variability of volatile species in the near-surface lunar exosphere from a landed platform on the lunar surface. The PITMS instrument consisted of a European Space Agency–provided Exospheric Mass Spectrometer (including sensor, electronics, controller, and power supply boards) and a GSFC wrapper that provided structural elements, thermal control, and a deployable dust cover. PITMS was designed to operate as a passive sampler, where ambient gases would enter PITMS through an aperture, diffuse around the mass analyzer cavity, become ionized by electron impact and trapped in an RF field, and then sequentially be released to a detector to build a mass spectrum. PITMS was capable of measuring species with a mass-to-charge ratio (m/z) from 10 to 150 Da, with a mass resolution of approximately 0.5 amu. The PITMS science investigation was planned to be operated by GSFC with an international team of scientists. Though the mission did not achieve its lunar landing, information about the PITMS instrument and planning is provided to be able to understand and effectively use data that will be forthcoming from the investigation.

Design and development of a scanning magnet for high-resolution mass spectrometry

The magnets play a crucial role in sector mass spectrometers, directly influencing the resolution, sensitivity, and stability of these instruments. This study is based on the design requisites for high-resolution scanning magnet, alongside the optical layout schematics for mass spectrometer instrumentation. The analysis is conducted on the design parameters encompassing magnetic structure, field quality, and response dynamics. Utilizing Opera-3D simulation software, optimization designs are executed for the magnetic structure and performance, resulting in a magnet design exhibiting commendable attributes such as response time, magnetic field distortion characteristics, field range, linearity, and homogeneity. Following the completion of magnet fabrication and assembly, comprehensive evaluations of magnetic field performance and instrument testing are conducted. Results demonstrate good magnetic field linearity and minimal eddy current distortion, with a magnetic field homogeneity reaching up to ±0.05 % within the desired field region. The magnet exhibits versatility across a scan range spanning 7 to 238 u, with a scanning speed of 140 ms. Sensitivity and resolution tests, conducted using In-115, validated the magnet's compliance with the stringent design requirements of high-resolution mass spectrometry scanning magnets.

Stochastic dynamics mass spectrometric structural analysis of poly(methyl methacrylate)

Polymers such as poly(methyl methacrylate), comprising of all-carbon backbones are regarded as ubiquitous functional materials mainly due to their low cost, unique physical properties, and impressive robustness. The latter properties are results from relative chemical inertness of the polymer backbone carbon–carbon bonds. The highlighted stability crucially challenges not only innovations to plastic recycling polymer materials, but also developments of reliable analytical protocols for determining both quantitatively and structurally polymers. Despite, the fact that there are numerous applications of mass spectrometric methods to polymer science, the analysis involves chiefly annotation of monomers of polymers and additives, owing to the fact that the additives are low molecular weight analytes. The exact structural determining of end-chain groups, particularly highlighting chemically substituted end carbon–carbon bond represents significant challenge even utilizing the superior features of the analytical mass spectrometric instrumentation. This study, in the latter context, illustrates innovative stochastic dynamics approach and model equations capable of not only determining unambiguously substituted carbon–carbon end chain of the entitled polymer but also to predict mass spectra of its derivatives: thus, extending crucially the applicability of the method to many fields of the fundamental scientific and industrial research. The latter claim is argued still at the beginning of the study with the achieved method performances showing |r|=0.99998. The study utilizes experimental and theoretical mass spectrometric data on high resolution electrospray ionization mass spectrometry; high accuracy quantum chemical static methods, molecular dynamics; and chemometrics.

Advantages of the low-temperature secondary emission mass spectrometry in analysis of metal ions in water samples revisited

A problem of necessity of concentrating trace admixtures of metal ions required for ecological water analysis can be overcome by harnessing a physical phenomenon of phase separation in aqueous solutions during their freezing. It is shown that the accumulation of metal-containing solutes in the channels between ice crystallites in the frozen solids is sufficient for their successful detection by means of low-temperature secondary emission mass spectrometry. Sufficiency of microliters volumes of water is an advantage of such an approach. Observation of various types of metal ions in frozen water samples is demonstrated on the examples of tap water, sea water, snow and a medicinal preparation. Revisiting and summation of physical basics of mass spectrometric examining of frozen water-inorganic salt solutions and estimates of advancement of mass spectrometric instrumentation permit us to propose a workflow for accelerated and simplified mass spectrometric detection of metal pollutants in water.

Sex-Dependent Changes to the Intestinal and Hepatic Abundance of Drug Transporters and Metabolizing Enzymes in the SOD1G93A Mouse Model of Amyotrophic Lateral Sclerosis.

Amyotrophic lateral sclerosis (ALS) is characterized by death and dysfunction of motor neurons that result in a rapidly progressing loss of motor function. While there are some data on alterations at the blood-brain barrier (BBB) in ALS and their potential impact on CNS trafficking of drugs, little is reported on the impact of this disease on the expression of drug-handling proteins in the small intestine and liver. This may impact the dosing of the many medicines that individuals with ALS are prescribed. In the present study, a proteomic evaluation was performed on small intestine and liver samples from postnatal day 120 SOD1G93A mice (a model of familial ALS that harbors a human mutant form of superoxide dismutase 1) and wild-type (WT) littermates (n = 7/genotype/sex). Untargeted, quantitative proteomics was undertaken using either label-based [tandem mass tag (TMT)] or label-free [data-independent acquisition (DIA)] acquisition strategies on high-resolution mass spectrometric instrumentation. Copper chaperone for superoxide dismutase (CCS) was significantly higher in SOD1G93A samples compared to the WT samples for both sexes and tissues, therefore representing a potential biomarker for ALS in this mouse model. Relative to WT mice, male SOD1G93A mice had significantly different proteins (Padj < 0.05, |fold-change|>1.2) in the small intestine (male 22, female 1) and liver (male 140, female 3). This included an up-regulation of intestinal transporters for dietary glucose [solute carrier (SLC) SLC5A1] and cholesterol (Niemann-Pick c1-like 1), as well as for several drugs (e.g., SLC15A1), in the male SOD1G93A mice. There was both an up-regulation (e.g., SLCO2A1) and down-regulation (ammonium transporter rh type b) of transporters in the male SOD1G93A liver. In addition, there was both an up-regulation (e.g., phosphoenolpyruvate carboxykinase) and down-regulation (e.g., carboxylesterase 1) of metabolizing enzymes in the male SOD1G93A liver. This proteomic data set identified male-specific changes to key small intestinal and hepatic transporters and metabolizing enzymes that may have important implications for the bioavailability of nutrients and drugs in individuals with ALS.

Linear Ion Trap Mass Spectrometer (LITMS) Instrument Field and Laboratory Tests as Part of the ARADS Field Campaigns.

The highly compact Linear Ion Trap Mass Spectrometer (LITMS), developed at NASA Goddard Space Flight Center, combines Mars-ambient laser desorption-mass spectrometry (LD-MS) and pyrolysis-gas chromatography-mass spectrometry (GC-MS) through a single, miniaturized linear ion trap mass analyzer. The LITMS instrument is based on the Mars Organic Molecule Analyser (MOMA) investigation developed for the European Space Agency's ExoMars Rover Mission with further enhanced analytical features such as dual polarity ion detection and a dual frequency RF (radio frequency) power supply allowing for an increased mass range. The LITMS brassboard prototype underwent an extensive repackaging effort to produce a highly compact system for terrestrial field testing, allowing for molecular sample analysis in rugged planetary analog environments outside the laboratory. The LITMS instrument was successfully field tested in the Mars analog environment of the Atacama Desert in 2019 as part of the Atacama Rover Astrobiology Drilling Studies (ARADS) project, providing the first in situ planetary analog analysis for a high-fidelity, flight-like ion trap mass spectrometer. LITMS continued to serve as a laboratory tool for continued analysis of natural Atacama samples provided by the subsequent 2019 ARADS final field campaign.

Modeling Known Sources of Mass Calibration Deviations in High Resolution ToF MS.

Modern time-of-flight mass spectrometer instruments exhibit excellent mass accuracy in the parts per billion range. At this level, mass calibration methods should consider potential distortions in the basic calibration. Factors which can cause distortions are to be under control. We have analytically modeled and numerically verified the influence of the main causes of mass calibration distortions, including the uncompensated dependence of flight time on the starting position, spatial gradient of the accelerating field, and overshooting at the rising edge of the accelerating pulse. Additionally, the relativity correction has been taken into account.

Simulation study of three new quadrupole ion funnels to improve low-mass ion transmission.

By applying radio frequency (RF) and direct current (DC) voltages to corresponding ring electrodes, ion funnel (IF) can efficiently focus and transmit ions. However, IF has an inherent mass discrimination problem that will greatly limit low mass-to-charge (m/z) ion focusing and transmission. To improve the transmission efficiency (TE) of the IF, this paper explores three new profile quadrupole ion funnels (QIF). Computer simulations of the potential field distributions of QIFs and conventional IFs were performed to assess their focusing characteristics. To compare the TE, ion optics simulation programs SIMION and AXSIM were used to perform a series of simulations. Three QIF types (toroidal, cylindrical, and hyperbolic configurations) were used to improve ion TE, and their transmission and focus performance were also compared with conventional IF. By simulating the trajectories of ions in the IF, the optimum electrical parameters for three new QIFs were obtained and compared with conventional IFs, with TE improvements recorded for m/z < 100 of 16%, 20%, and 13%. The results indicate that studying these three new IF configurations has great research significance for improving sensitivity to low m/z ions in mass spectrometer instruments.

Evaluation of the interference of Tenax®TA adsorbent with dimethylformamide dimethyl acetal reagent for gas chromatography-Dragonfly mass spectrometry and future gas chromatography-mass spectrometry in situ analysis

Among future space missions, national aeronautics and space administration (NASA) selected two of them to analyze the diversity in organic content within Martian and Titan soil samples using a gas chromatograph – mass spectrometer (GC–MS) instrument. The Dragonfly space mission is planned to be launched in 2027 to Titan's surface and explore the Shangri-La surface region for years. One of the main goals of this mission is to understand the past and actual abundant prebiotic chemistry on Titan, which is not well characterized yet. The ExoMars space mission is planned to be launched in 2028 to Mars’ surface and explore the Oxia Planum and Mawrth Vallis region for years. The main objectives focus on the exploration of the subsurface soil samples, potentially richer in organics, that might be relevant for the search of past life traces on Mars where irradiation does not impact the matrices and organics. One recently used sample pre-treatment for gas chromatography – mass spectrometry analysis is planned on both space missions to detect refractory organic molecules of interest for astrobiology. This pre-treatment is called derivatization and uses a chemical reagent – called dimethylformamide dimethyl acetal (DMF-DMA) – to sublimate organic compounds keeping them safe from thermal degradation and conserving the chirality of the molecules extracted from Titan or Mars’ matrices. Indeed, the detection of building blocks of life or enantiomeric excess of some organics (e.g. amino acids) after DMF-DMA pre-treatment and GC–MS analyses would be both bioindicators. The main results highlighted by our work on DMF-DMA and Tenax®TA interaction and efficiency to detect organic compounds at ppb levels in a fast and single preparation are first that Tenax®TA did not show the onset of degradation until after 150 experiments – a 120 h at 300 °C experiment – which greatly exceeds the experimental lifetimes for the DraMS and GC-space in situ investigations. Tenax®TA polymer and DMF-DMA produce many by-products (about 70 and 46, respectively, depending on the activation temperature). Further, the interaction between the two leads to the production of 22 additional by-products from DMF-DMA degradation, but these listed by-products do not prevent the detection of trace-level organic molecules after their efficient derivatization and volatilization by DMF-DMA in the oven ahead the GC–MS trap and column.

Gas Chromatography-Mass Spectroscopy(GC-MS) of Chloroform Extract of Ficus exasperata Vahl

Gas Chromatography-Mass Spectrometry (GCMS) analysis of chloroform leaves extract of Ficus exasperate Vahl was performed to identify the composition and percentage abundance of the various phytochemical constituents of Ficus exasperate Vahl. The extract was obtained by fractionating methanol crude leave extract of Ficus exasperate Vahl with in order of increasing polarity, n-Hexane then chloroform. GC-MS analysis was carried out on a GC system comprising a Gas Chromatograph interfaced to a Mass Spectrometer (GC-MS) instrument. The components were compared with the database of spectrum of known components stored in the gas chromatography-mass spectrometry library. Gas Chromatography-Mass Spectrometry analysis of the chloroform leave extract of Ficus exasperate revealed the presence of acyclic olefin which is used for tanning oils and in synthetic fatty acids, Isopryl myristate used in cosmetics, Dibutyl phthalate which is used in cosmetics, textile, safety glass additive, oleic acid used in pharmaceuticals, Cyclopropanecarboxylic acid, 3-(2,2-dichlor used in agrochemicals and pharmaceuticals. The presence of these compounds justifies the use of some parts of the plant for various elements in folklore and can be advised as a plant of phytopharmaceutical and industrial importance.

Evolution of organic carbon in the laboratory oxidation of biomass-burning emissions

Abstract. Biomass burning (BB) is a major source of reactive organic carbon into the atmosphere. Once in the atmosphere, these organic BB emissions, in both the gas and particle phases, are subject to atmospheric oxidation, though the nature and impact of the chemical transformations are not currently well constrained. Here we describe experiments carried out as part of the FIREX FireLab campaign, in which smoke from the combustion of fuels typical of the western United States was sampled into an environmental chamber and exposed to high concentrations of OH, to simulate the equivalent of up to 2 d of atmospheric oxidation. The evolution of the organic mixture was monitored using three real-time time-of-flight mass spectrometric instruments (a proton transfer reaction mass spectrometer, an iodide chemical ionization mass spectrometer, and an aerosol mass spectrometer), providing measurements of both individual species and ensemble properties of the mixture. The combined measurements from these instruments achieve a reasonable degree of carbon closure (within 15 %–35 %), indicating that most of the reactive organic carbon is measured by these instruments. Consistent with our previous studies of the oxidation of individual organic species, atmospheric oxidation of the complex organic mixture leads to the formation of species that on average are smaller and more oxidized than those in the unoxidized emissions. In addition, the comparison of mass spectra from the different fuels indicates that the oxidative evolution of BB emissions proceeds largely independent of fuel type, with different fresh smoke mixtures ultimately converging into a common, aged distribution of gas-phase compounds. This distribution is characterized by high concentrations of several small, volatile oxygenates, formed from fragmentation reactions, as well as a complex pool of many minor oxidized species and secondary organic aerosol, likely formed via functionalization processes.

The behavior of heteroatom compounds during the pyrolysis of waste composite plastics

Multilayer composite packaging plastic is commonly used in daily life. Due to the complex structures and the existence of heteroatoms, such as nitrogen and oxygen, the recycling of this kind of plastic is challenging. Recycling through the pyrolysis method may provide an efficient option with respect to the mechanical and solvent methods. An understanding of the behaviour of heteroatoms during pyrolysis is significant to optimize the operating conditions. In this work, two composite packaging plastics of PET/LDPE (Polyethylene Terephthalate/Low Density Polyethylene) and PA/LDPE (Polyamide//Low Density Polyethylene) were pyrolysed at various temperatures between 400 and 500 °C in a fixed bed reactor. Heteroatom balance and composition analysis were conducted. Especially, the composition of O- and N-containing compounds in oils was fully understood by using GC-MS (Gas Chromatograph - Mass Spectrometer) and APPI FT-ICR MS (Atmospheric Pressure Photoionization Fourier Transform-Ion Cyclotron Resonance Mass Spectrometer) instruments. At 400 °C, only 2.2 wt% oxygen was left in 53.9 wt% solid residues for PET/LDPE and 3.6 wt% nitrogen was retained in 61.0 wt% solid residues for PA6/LDPE, whereas nearly no oxygen was retained in solid residues for PA6/LDPE. So the PET/PA6 can be degraded in a much lower temperature range than LDPE indicating the possibility of separating heteroatoms by step-wise pyrolysis. A large amount of O-containing compounds were observed in oils from PET/LDPE pyrolysis, while O, N-containing compounds existed in oils from PA6/LDPE. The APPI FT-ICR MS analysis revealed that parts of O-containing compounds were generated through the interaction between O-containing functional groups and aliphatics during the PET/LDPE pyrolysis. For PA6/LDPE, the deoxygenation reaction was easier to occur than the denitrification reaction.

Bioactive components in ethanol extract of Citrullus lanatus rind using Gas Chromatography- Mass Spectroscopy.

The knowledge of bioactive compounds present in a plant can be helpful in utilizing it for a medicinal purpose in life. The Gas Chromatography-Mass Spectrometry (GCMS) analysis of ethanol extract of Citrullus lanatus rind (CLR) was done to identify bioactive compounds and selectivity or abundance percentage in ethanol extract of CLR. The extract was obtained by fractionating crude ethanol CLR extract in order of increasing polarity, n-Hexane, chloroform, ethylacetate and ethanol. The GC-MS analysis was carried out on GC system comprising Gas Chromatograph interfaced to Mass Spectrometer (GC-MS) instrument. The bioactive compounds obtained were compared with database of spectrum of known components stored in the gas chromatography-mass spectrometry library. The GC-MS analysis of ethanol extract of CLR revealed the presence of androst-4-en-9-thiocyanomethyl-11-ol-3,17-dione a steroid which is a precusor for androgen and estrogen production. As well as cyclooctasiloxane hexadecamethyl and octasiloxane hexadecamethyl in which both of them contain silicon an essential trace element for collagen and bone formation .The presence of these compounds validates the use of ethanol extract of CLR as a good antioxidants, antibacterial agents and stimulant in precursor of male reproductive hormone production. The ethanol extract of CLR can be of great value in ethno-veterinary practice.

Sensitive and accurate determination of nitrogen in simulated Martian soil and environment with LIBS spectrum fusion and regression based on neural network

Nitrogen is a key element necessary for the emergence and development of life. It is one of the elements targeted by the landed missions on Mars in accordance with their scientific goal of investigation of habitability and search for traces of life. A gas chromatography mass spectrometer (GCMS) instrument on board the Mars Science Laboratory Curiosity rover has revealed the existence of oxidized nitrogen-bearing compounds on Martian surface with an equivalent nitrogen concentration up to 0.01 wt%. Although the detection with laser-induced breakdown spectroscopy (LIBS) also on board the Curiosity rover is desirable, the current performance of LIBS for nitrogen analysis does not show the capacity in terms of limit of detection (LOD) and accuracy. Research on a suitable method should therefore be first engaged in laboratory in order to guide further improvements of LIBS instrument on board Mars rover, as well as the data treatment method. Beyond the sensitivity issue, matrix effect also affects LIBS determination of nitrogen, especially due to its various chemical speciation in geological materials. Method research should answer thus double requirements of improving the sensitivity and reinforcing the robustness with respect to different nitrogen-bearing compounds. An experimental configuration of double detections with a narrow bandwidth Czerny-Tuner (CT) spectrometer and a broad bandwidth Echelle spectrometer, was implemented in this work, in such way that the first ensured a sensitive detection of emission lines from nitrogen and the second complemented with those from major elements in the sample. The fusion of the simultaneously acquired spectra took into account the emission characteristics of the both two types of elements, necessary for an effective and robust multivariate regression based on a neural network. In addition, for a better treatment of different chemical speciation of nitrogen in samples, generalized spectrum was used for training of regression models, after an unsupervised clustering having assigned a type label to each training spectrum. The trained model was tested by collections of independent test samples, resulting in a limit of detection (LOD) of 0.18 wt%, and a root mean square error of prediction (RMSEP) of 0.041 wt%, representing a step forward to nitrogen detection using LIBS on Mars.

Detection time comparison of non-hydrolysed sulphated metabolites of metenolone, mesterolone and 17α-methyltestosterone analysed by four different mass spectrometric techniques.

The frequent detection of anabolic androgenic steroids (AAS) indicates their popularity among rule-breaking athletes. The so called long-term metabolites play a crucial role in their detection, and non-hydrolysed sulphated metabolites have gained renewed interest, as research has demonstrated their extended detection time compared to the more conventional markers (e.g., for metenolone and mesterolone). Their potential has been investigated using liquid and gas chromatography-mass spectrometry (LC- and GC-MS). However, due to their complementary nature, chances are that the most promising metabolite on one technique does not necessarily exhibit the same behaviour on the other and vice versa. Therefore, a comparison was carried out where as a trial model, metenolone, mesterolone and 17α-methyltestosterone were selected and the most likely long-term sulphated metabolites identified on four mass spectrometric instruments. Additionally, using a modified sample preparation procedure, comparison between conventional and non-hydrolysed sulphated metabolites between different GC-MS instruments was also included. When focusing on each individual marker, no cases were observed where a single metabolite provided a superior detection time on all instruments. Furthermore, for each AAS, there were incidences where a metabolite provided the best detection time on one instrument but could only be detected for a shorter period or not at all on other instruments. This demonstrates that metabolite detection windows and hence their added-value as target substance are unique and dependent on the analytical technique and not only on their pharmacokinetic behaviour. Consequently, in each case, a metabolite versus instrument evaluation is needed to maximise the probabilities of detecting doping offences.

Comparison of isoprene chemical mechanisms under atmospheric night-time conditions in chamber experiments: evidence of hydroperoxy aldehydes and epoxy products from NO3 oxidation

Abstract. The gas-phase reaction of isoprene with the nitrate radical (NO3) was investigated in experiments in the outdoor SAPHIR chamber under atmospherically relevant conditions specifically with respect to the chemical lifetime and fate of nitrato-organic peroxy radicals (RO2). Observations of organic products were compared to concentrations expected from different chemical mechanisms: (1) the Master Chemical Mechanism, which simplifies the NO3 isoprene chemistry by only considering one RO2 isomer; (2) the chemical mechanism derived from experiments in the Caltech chamber, which considers different RO2 isomers; and (3) the FZJ-NO3 isoprene mechanism derived from quantum chemical calculations, which in addition to the Caltech mechanism includes equilibrium reactions of RO2 isomers, unimolecular reactions of nitrate RO2 radicals and epoxidation reactions of nitrate alkoxy radicals. Measurements using mass spectrometer instruments give evidence that the new reactions pathways predicted by quantum chemical calculations play a role in the NO3 oxidation of isoprene. Hydroperoxy aldehyde (HPALD) species, which are specific to unimolecular reactions of nitrate RO2, were detected even in the presence of an OH scavenger, excluding the possibility that concurrent oxidation by hydroxyl radicals (OH) is responsible for their formation. In addition, ion signals at masses that can be attributed to epoxy compounds, which are specific to the epoxidation reaction of nitrate alkoxy radicals, were detected. Measurements of methyl vinyl ketone (MVK) and methacrolein (MACR) concentrations confirm that the decomposition of nitrate alkoxy radicals implemented in the Caltech mechanism cannot compete with the ring-closure reactions predicted by quantum chemical calculations. The validity of the FZJ-NO3 isoprene mechanism is further supported by a good agreement between measured and simulated hydroxyl radical (OH) reactivity. Nevertheless, the FZJ-NO3 isoprene mechanism needs further investigations with respect to the absolute importance of unimolecular reactions of nitrate RO2 and epoxidation reactions of nitrate alkoxy radicals. Absolute concentrations of specific organic nitrates such as nitrate hydroperoxides would be required to experimentally determine product yields and branching ratios of reactions but could not be measured in the chamber experiments due to the lack of calibration standards for these compounds. The temporal evolution of mass traces attributed to product species such as nitrate hydroperoxides, nitrate carbonyl and nitrate alcohols as well as hydroperoxy aldehydes observed by the mass spectrometer instruments demonstrates that further oxidation by the nitrate radical and ozone at atmospheric concentrations is small on the timescale of one night (12 h) for typical oxidant concentrations. However, oxidation by hydroxyl radicals present at night and potentially also produced from the decomposition of nitrate alkoxy radicals can contribute to their nocturnal chemical loss.

Gravity wave driven variability in the Mars ionosphere-thermosphere system

Gravity waves (GWs) have been persistently observed in neutral species in the Martian thermosphere. In this paper, we study characteristics of GWs in O2+ and O+ ions in the Mars ionosphere (∼160–200 km) and examine their relation to GWs in the thermosphere. For this purpose, we use O2+, O+, and Ar densities measured by the Neutral Gas and Ion Mass spectrometer (NGIMS) instrument aboard the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission. The amplitudes and (horizontal) wavelengths of the GWs are extracted from the density profiles. The results of the present study show that GWs are ubiquitous in the Martian ionosphere-thermosphere system. We found that the amplitudes of GWs in ions are ∼2 times larger than those in neutrals. While the amplitudes in ions reach as high as 70% of the background densities, the most probable amplitude 5%. The amplitudes of the GWs in ions are more on the nightside than on the dayside; more during the 2018 global dust storm period than during nominal dust conditions; and increase with decreasing in solar activity. All these results are qualitatively similar to those observed in neutrals. In addition, amplitudes of the GWs in ions show moderate correlation with those neutrals while the wavelengths show good correlation. The amplitudes of GWs in ions and neutrals show moderate negative correlation with thermospheric temperatures. All these results strongly suggest that the GWs in ions are due to those in neutrals and ion-neutral coupling may be strong in the altitude range of interest. The correlation between the amplitudes of GWs in ions and neutral, however, is local time dependent with weak correlation on the nightside. Other factors such as recombination or particle precipitation may be playing an important role in distorting the wavy nature in ions leading to weaker correlation with neutral waves on the night side. Furthermore, the correlation between GW amplitudes in ions and neutrals is weaker in strong crustal magnetic field regions. This implies that the magnetic fields control the motion of the ions leading to distorting in wavy nature in ions.

Tuzaklamalı İyon Hareketliliği-Kütle Spektrometrisi Tekniği Kullanılarak İnsülinin Bakır ve Alkali Metal Komplekslerinin Konformasyonel Farklılıklarının Analizi

Molecular recognition, protein folding, and formation of supramolecular structures that occur at the molecular level of biological processes are based on noncovalent interactions. Interactions between metal atoms and proteins are based on noncovalent interactions that underlie the mechanisms involved in many cellular processes. The activities of enzymes are highly dependent on the interactions of such protein groups with cofactors, substrates, metal ions, and other proteins. The compositions and binding stoichiometry of protein-metal complexes can be determined with high accuracy performing mass spectrometry (MS) analysis. The conformational features of protein-metal complexes can be studied additionally using a mass spectrometer with ion mobility spectrometry (IMS) capability. This study focuses the monitoring the differences in the conformational changes of insulin protein during the formation of its complex with copper and alkali metals using trapped ion mobility spectrometry – time-of-flight (TIMS–TOF) mass spectrometer instrument. The compaction of the insulin structure by the formation of the insulin-copper complexes in the gas phase was determined with TIMS-TOF-MS analyses. However, no change was observed in the insulin structure with the addition of H, Na, and K atoms as adducts at the same analysis conditions.