Tandem Mass Spectrometric Analysis of Metallocene Adducts with Short Oligonucleotides

Metallocene dichlorides constitute a remarkable class of antineoplastic agents that are highly effective against several cancer cell lines. They were shown to accumulate in the DNA-rich region, which suggests DNA as the primary target. These compounds exhibit two cyclopentadienyl ligands and two labile halide ligands, resulting in a bent sandwich structure. The cis-dihalide motif is structurally related to the cis-chloro configuration of cisplatin and similar modes of action can thus be assumed. Cisplatin binds to two neighboring guanine nucleobases in DNA and consequently, distorts the double-helix, thereby inhibiting DNA replication and transcription. Platinum is classified as a soft Lewis acid and binds preferentially to the nitrogen atoms within the nucleobases. The metallocene dichlorides investigated in this study comprise the metal centers Ti, V, Nb, Mo, Hf, and W, which are classified as hard or intermediate Lewis acids, and thus, favor binding to the phosphate oxygen. Although several studies reported adduct formation of metallocene dichlorides with nucleic acids, substantial information about the adduct composition, the binding pattern, and the nucleobase selectivity has not been provided yet. ESI-MS analyses gave evidence for the formation of metallocene adducts (M = Ti, V, Mo, and W) with single-stranded DNA homologues at pH 7. No adducts were formed with Nb and Hf at neutral pH, albeit adducts with Nb were observed at a low pH. MS2 data revealed considerable differences of the adduct compositions. The product ion spectra of DNA adducts with hard Lewis acids (Ti, V) gave evidence for the loss of metallocene ligands and only moderate backbone fragmentation was observed. By contrast, adducts with intermediate Lewis acids (Mo, W) retained the hydroxy ligands. Preliminary results are in good agreement with the Pearson concept and DFT calculations. Since the metallodrugs were not lost upon CID, the nucleobase selectivity, stoichiometry, and binding patterns can be elucidated by means of tandem mass spectrometry.

Heterogeneity of patients with intermediate (BCLC B) Hepatocellular Carcinoma: proposal for a subclassification to facilitate treatment decisions

The intermediate stage of hepatocellular carcinoma (HCC) comprises a highly heterogeneous patient population and therefore poses unique challenges for therapeutic management, different from the early and advanced stages. Patients classified as having intermediate HCC by the Barcelona Clinic Liver Cancer (BCLC) staging system present with varying tumor burden and liver function. Transarterial chemoembolization (TACE) is currently recommended as the standard of care in this setting, but there is considerable variation in the clinical benefit patients derive from this treatment.In April 2012, a panel of experts convened to discuss unresolved issues surrounding the application of current guidelines when managing patients with intermediate HCC. The meeting explored the applicability of a subclassification system for intermediate HCC patients to tailor therapeutic interventions based on the evidence available to date and expert opinion. The present report summarizes the proposal of the expert panel: four substages of intermediate HCC patients, B1 to B4.

Radiation metabolomics. 5. Identification of urinary biomarkers of ionizing radiation exposure in nonhuman primates by mass spectrometry-based metabolomics

Mass spectrometry-based metabolomics has previously demonstrated utility for identifying biomarkers of ionizing radiation exposure in cellular, mouse and rat in vivo radiation models. To provide a valuable link from small laboratory rodents to humans, γ-radiation-induced urinary biomarkers were investigated using a nonhuman primate total-body-irradiation model. Mass spectrometry-based metabolomics approaches were applied to determine whether biomarkers could be identified, as well as the previously discovered rodent biomarkers of γ radiation. Ultra-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry analysis was carried out on a time course of clean-catch urine samples collected from nonhuman primates (n = 6 per cohort) exposed to sham, 1.0, 3.5, 6.5 or 8.5 Gy doses of (60)Co γ ray (∼0.55 Gy/min) ionizing radiation. By multivariate data analysis, 13 biomarkers of radiation were discovered: N-acetyltaurine, isethionic acid, taurine, xanthine, hypoxanthine, uric acid, creatine, creatinine, tyrosol sulfate, 3-hydroxytyrosol sulfate, tyramine sulfate, N-acetylserotonin sulfate, and adipic acid. N-Acetyltaurine, isethionic acid, and taurine had previously been identified in rats, and taurine and xanthine in mice after ionizing radiation exposure. Mass spectrometry-based metabolomics has thus successfully revealed and verified urinary biomarkers of ionizing radiation exposure in the nonhuman primate for the first time, which indicates possible mechanisms for ionizing radiation injury.

Gasoline emissions dominate over diesel in formation of secondary organic aerosol mass

Although laboratory experiments have shown that organic compounds in both gasoline fuel and diesel engine exhaust can form secondary organic aerosol (SOA), the fractional contribution from gasoline and diesel exhaust emissions to ambient SOA in urban environments is poorly known. Here we use airborne and ground-based measurements of organic aerosol (OA) in the Los Angeles (LA) Basin, California made during May and June 2010 to assess the amount of SOA formed from diesel emissions. Diesel emissions in the LA Basin vary between weekdays and weekends, with 54% lower diesel emissions on weekends. Despite this difference in source contributions, in air masses with similar degrees of photochemical processing, formation of OA is the same on weekends and weekdays, within the measurement uncertainties. This result indicates that the contribution from diesel emissions to SOA formation is zero within our uncertainties. Therefore, substantial reductions of SOA mass on local to global scales will be achieved by reducing gasoline vehicle emissions.

A mass spectrometric multicenter study supports classification of preeclampsia as heterogeneous disorder

The diagnostic value of affinity-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis to distinguish preeclampsia (PE) from matched controls was tested in a multicenter setting.

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

On the interference of Kr during carbon isotope analysis of methane using continuous-flow combustion–isotope ratio mass spectrometry

Stable carbon isotope analysis of methane (delta C-13 of CH4) on atmospheric samples is one key method to constrain the current and past atmospheric CH4 budget. A frequently applied measurement technique is gas chromatography (GC) isotope ratio mass spectrometry (IRMS) coupled to a combustion-preconcentration unit. This report shows that the atmospheric trace gas krypton (Kr) can severely interfere during the mass spectrometric measurement, leading to significant biases in delta C-13 of CH4, if krypton is not sufficiently separated during the analysis. According to our experiments, the krypton interference is likely composed of two individual effects, with the lateral tailing of the doubly charged Kr-86 peak affecting the neighbouring m/z 44 and partially the m/z 45 Faraday cups. Additionally, a broad signal affecting m/z 45 and especially m/z 46 is assumed to result from scattered ions of singly charged krypton. The introduced bias in the measured isotope ratios is dependent on the chromatographic separation, the krypton-to-CH4 mixing ratio in the sample, the focusing of the mass spectrometer as well as the detector configuration and can amount to up to several per mil in delta C-13. Apart from technical solutions to avoid this interference, we present correction routines to a posteriori remove the bias.

Measurement of the Higgs boson mass from the H→γγ and H→ZZ ∗ →4ℓ collisions at center-of-mass energies of 7 and 8 TeV with the ATLAS detector

An improved measurement of the mass of the Higgs boson is derived from a combined fit to the reconstructed invariant mass spectra of the decay channels H→γγ and H→ZZ ∗ →4ℓ . The analysis uses the pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at center-of-mass energies of 7 TeV and 8 TeV, corresponding to an integrated luminosity of 25  fb −1 . The measured value of the Higgs boson mass is m H =125.36±0.37(stat)±0.18(syst)  GeV . This result is based on improved energy-scale calibrations for photons, electrons, and muons as well as other analysis improvements, and supersedes the previous result from ATLAS. Upper limits on the total width of the Higgs boson are derived from fits to the invariant mass spectra of the H→γγ and H→ZZ ∗ →4ℓ decay channels.

Measurement of dijet cross sections in pp collisions at 7 TeV centre-of-mass energy using the ATLAS detector

Double-differential dijet cross-sections measured in pp collisions at the LHC with a 7TeV centre-of-mass energy are presented as functions of dijet mass and half the rapidity separation of the two highest-pT jets. These measurements are obtained using data corresponding to an integrated luminosity of 4.5 fb−1, recorded by the ATLAS detector in 2011. The data are corrected for detector effects so that cross-sections are presented at the particle level. Cross-sections are measured up to 5TeV dijet mass using jets reconstructed with the anti-kt algorithm for values of the jet radius parameter of 0.4 and 0.6. The cross-sections are compared with next-to-leading-order perturbative QCD calculations by NLOJet++ corrected to account for non-perturbative effects. Comparisons with POWHEG predictions, using a next-to-leading-order matrix element calculation interfaced to a partonshower Monte Carlo simulation, are also shown. Electroweak effects are accounted for in both cases. The quantitative comparison of data and theoretical predictions obtained using various parameterizations of the parton distribution functions is performed using a frequentist method. In general, good agreement with data is observed for the NLOJet++ theoretical predictions when using the CT10, NNPDF2.1 and MSTW 2008 PDF sets. Disagreement is observed when using the ABM11 and HERAPDF1.5 PDF sets for some ranges of dijet mass and half the rapidity separation. An example setting a lower limit on the compositeness scale for a model of contact interactions is presented, showing that the unfolded results can be used to constrain contributions to dijet production beyond that predicted by the Standard Model.

Modeling the formation and aging of secondary organic aerosols during CalNex 2010

Four different literature parameterizations for the formation and evolution of urban secondary organic aerosol (SOA) frequently used in 3-D models are evaluated using a 0-D box model representing the Los Angeles metropolitan region during the California Research at the Nexus of Air Quality and Climate Change (CalNex) 2010 campaign. We constrain the model predictions with measurements from several platforms and compare predictions with particle- and gas-phase observations from the CalNex Pasadena ground site. That site provides a unique opportunity to study aerosol formation close to anthropogenic emission sources with limited recirculation. The model SOA that formed only from the oxidation of VOCs (V-SOA) is insufficient to explain the observed SOA concentrations, even when using SOA parameterizations with multi-generation oxidation that produce much higher yields than have been observed in chamber experiments, or when increasing yields to their upper limit estimates accounting for recently reported losses of vapors to chamber walls. The Community Multiscale Air Quality (WRF-CMAQ) model (version 5.0.1) provides excellent predictions of secondary inorganic particle species but underestimates the observed SOA mass by a factor of 25 when an older VOC-only parameterization is used, which is consistent with many previous model–measurement comparisons for pre-2007 anthropogenic SOA modules in urban areas. Including SOA from primary semi-volatile and intermediate-volatility organic compounds (P-S/IVOCs) following the parameterizations of Robinson et al. (2007), Grieshop et al. (2009), or Pye and Seinfeld (2010) improves model–measurement agreement for mass concentration. The results from the three parameterizations show large differences (e.g., a factor of 3 in SOA mass) and are not well constrained, underscoring the current uncertainties in this area. Our results strongly suggest that other precursors besides VOCs, such as P-S/IVOCs, are needed to explain the observed SOA concentrations in Pasadena. All the recent parameterizations overpredict urban SOA formation at long photochemical ages (3 days) compared to observations from multiple sites, which can lead to problems in regional and especially global modeling. However, reducing IVOC emissions by one-half in the model to better match recent IVOC measurements improves SOA predictions at these long photochemical ages. Among the explicitly modeled VOCs, the precursor compounds that contribute the greatest SOA mass are methylbenzenes. Measured polycyclic aromatic hydrocarbons (naphthalenes) contribute 0.7% of the modeled SOA mass. The amounts of SOA mass from diesel vehicles, gasoline vehicles, and cooking emissions are estimated to be 16–27, 35–61, and 19–35 %, respectively, depending on the parameterization used, which is consistent with the observed fossil fraction of urban SOA, 71(+-3) %. The relative contribution of each source is uncertain by almost a factor of 2 depending on the parameterization used. In-basin biogenic VOCs are predicted to contribute only a few percent to SOA. A regional SOA background of approximately 2.1 μgm-3 is also present due to the long-distance transport of highly aged OA, likely with a substantial contribution from regional biogenic SOA. The percentage of SOA from diesel vehicle emissions is the same, within the estimated uncertainty, as reported in previous work that analyzed the weekly cycles in OA concentrations (Bahreini et al., 2012; Hayes et al., 2013). However, the modeling work presented here suggests a strong anthropogenic source of modern carbon in SOA, due to cooking emissions, which was not accounted for in those previous studies and which is higher on weekends. Lastly, this work adapts a simple two-parameter model to predict SOA concentration and O/C from urban emissions. This model successfully predicts SOA concentration, and the optimal parameter combination is very similar to that found for Mexico City. This approach provides a computationally inexpensive method for predicting urban SOA in global and climate models. We estimate pollution SOA to account for 26 Tg yr-1 of SOA globally, or 17% of global SOA, one third of which is likely to be non-fossil.

Analytic validation of a gas chromatography-mass spectrometry method for quantification of six amino acids in canine serum samples.

OBJECTIVE To analytically validate a gas concentration of chromatography-mass spectrometry (GC-MS) method for measurement of 6 amino acids in canine serum samples and to assess the stability of each amino acid after sample storage. SAMPLES Surplus serum from 80 canine samples submitted to the Gastrointestinal Laboratory at Texas A&M University and serum samples from 12 healthy dogs. PROCEDURES GC-MS was validated to determine precision, reproducibility, limit of detection, and percentage recovery of known added concentrations of 6 amino acids in surplus serum samples. Amino acid concentrations in serum samples from healthy dogs were measured before (baseline) and after storage in various conditions. RESULTS Intra- and interassay coefficients of variation (10 replicates involving 12 pooled serum samples) were 13.4% and 16.6% for glycine, 9.3% and 12.4% for glutamic acid, 5.1% and 6.3% for methionine, 14.0% and 15.1% for tryptophan, 6.2% and 11.0% for tyrosine, and 7.4% and 12.4% for lysine, respectively. Observed-to-expected concentration ratios in dilutional parallelism tests (6 replicates involving 6 pooled serum samples) were 79.5% to 111.5% for glycine, 80.9% to 123.0% for glutamic acid, 77.8% to 111.0% for methionine, 85.2% to 98.0% for tryptophan, 79.4% to 115.0% for tyrosine, and 79.4% to 110.0% for lysine. No amino acid concentration changed significantly from baseline after serum sample storage at -80°C for ≤ 7 days. CONCLUSIONS AND CLINICAL RELEVANCE GC-MS measurement of concentration of 6 amino acids in canine serum samples yielded precise, accurate, and reproducible results. Sample storage at -80°C for 1 week had no effect on GC-MS results.

Comparing the performance of hyperbolic and circular rod quadrupole mass spectrometers with applied higher order auxiliary excitation

This work applies higher order auxiliary excitation techniques to two types of quadrupole mass spectrometers (QMSs): commercial systems and spaceborne instruments. The operational settings of a circular rod geometry commercial system and an engineering test-bed for a hyperbolic rod geometry spaceborne instrument were matched, with the relative performance of each sensor characterized with and without applied excitation using isotopic measurements of Kr+. Each instrument was operated at the limit of the test electronics to determine the effect of auxiliary excitation on extending instrument capabilities. For the circular rod sensor, with applied excitation, a doubling of the mass resolution at 1% of peak transmission resulted from the elimination of the low-mass side peak tail typical of such rod geometries. The mass peak stability and ion rejection efficiency were also increased by factors of 2 and 10, respectively, with voltage scan lines passing through the center of stability islands formed from auxiliary excitation. Auxiliary excitation also resulted in factors of 6 and 2 in peak stability and ion rejection efficiency, respectively, for the hyperbolic rod sensor. These results not only have significant implications for the use of circular rod quadrupoles with applied excitation as a suitable replacement for traditional hyperbolic rod sensors, but also for extending the capabilities of existing hyperbolic rod QMSs for the next generation of spaceborne instruments and low-mass commercial systems.

Nucleon and pion structure with lattice QCD simulations at physical value of the pion mass

We present results on the nucleon scalar, axial, and tensor charges as well as on the momentum fraction, and the helicity and transversity moments. The pion momentum fraction is also presented. The computation of these key observables is carried out using lattice QCD simulations at a physical value of the pion mass. The evaluation is based on gauge configurations generated with two degenerate sea quarks of twisted mass fermions with a clover term. We investigate excited states contributions with the nucleon quantum numbers by analyzing three sink-source time separations. We find that, for the scalar charge, excited states contribute significantly and to a less degree to the nucleon momentum fraction and helicity moment. Our result for the nucleon axial charge agrees with the experimental value. Furthermore, we predict a value of 1.027(62) in the MS¯¯¯¯¯ scheme at 2 GeV for the isovector nucleon tensor charge directly at the physical point. The pion momentum fraction is found to be ⟨x⟩π±u−d=0.214(15)(+12−9) in the MS¯¯¯¯¯ at 2 GeV.

Chemical Composition of Micrometer-Sized Filaments in an Aragonite Host by a Miniature Laser Ablation/Ionization Mass Spectrometer

Detection of extraterrestrial life is an ongoing goal in space exploration, and there is a need for advanced instruments and methods for the detection of signatures of life based on chemical and isotopic composition. Here, we present the first investigation of chemical composition of putative microfossils in natural samples using a miniature laser ablation/ionization time-of-flight mass spectrometer (LMS). The studies were conducted with high lateral (similar to 15 mu m) and vertical (similar to 20-200 nm) resolution. The primary aim of the study was to investigate the instrument performance on micrometer-sized samples both in terms of isotope abundance and element composition. The following objectives had to be achieved: (1) Consider the detection and calculation of single stable isotope ratios in natural rock samples with techniques compatible with their employment of space instrumentation for biomarker detection in future planetary missions. (2) Achieve a highly accurate chemical compositional map of rock samples with embedded structures at the micrometer scale in which the rock matrix is easily distinguished from the micrometer structures. Our results indicate that chemical mapping of strongly heterogeneous rock samples can be obtained with a high accuracy, whereas the requirements for isotope ratios need to be improved to reach sufficiently large signal-to-noise ratio (SNR). Key Words: Biogenicity-Biomarkers-Biosignatures-Filaments-Fossilization. Astrobiology 15, 669-682.

Prototype of the gas chromatograph-mass spectrometer to investigate volatile species in the lunar soil for the Luna-Resurs mission

In preparation for the Russian Luna-Resurs mission we combined our compact time-of-flight mass spectrometer (TOF-MS) with a chemical pre-separation of the species by gas chromatography (GC). Coupled measurements with both instruments were successfully performed with the prototype of the mass spectrometer and a flight-like gas chromatograph. The system was tested with two test gas mixtures, a mixture of hydrocarbons and a mixture of noble gases. Due to its capability to record mass spectra over the full mass range at once with high sensitivity and a dynamic range of up to 10(6) within 1 s, the TOF-MS system is a valuable extension of the GC analytical system. Based on the measurements with calibration gases performed with the combined GC-MS prototype and under assumption of mean characteristics for the Moon's regolith, the detection limit for volatile species in a soil sample is estimated to 2.10(-10) by mass for hydrocarbons and 2.10(-9) by mass for noble gases. (C) 2015 Elsevier Ltd. All rights reserved.