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Sample records for accurate mass spectra

  1. An Accurate de novo Algorithm for Glycan Topology Determination from Mass Spectra.

    PubMed

    Dong, Liang; Shi, Bing; Tian, Guangdong; Li, YanBo; Wang, Bing; Zhou, MengChu

    2015-01-01

    Determining the glycan topology automatically from mass spectra represents a great challenge. Existing methods fall into approximate and exact ones. The former including greedy and heuristic ones can reduce the computational complexity, but suffer from information lost in the procedure of glycan interpretation. The latter including dynamic programming and exhaustive enumeration are much slower than the former. In the past years, nearly all emerging methods adopted a tree structure to represent a glycan. They share such problems as repetitive peak counting in reconstructing a candidate structure. Besides, tree-based glycan representation methods often have to give different computational formulas for binary and ternary glycans. We propose a new directed acyclic graph structure for glycan representation. Based on it, this work develops a de novo algorithm to accurately reconstruct the tree structure iteratively from mass spectra with logical constraints and some known biosynthesis rules, by a single computational formula. The experiments on multiple complex glycans extracted from human serum show that the proposed algorithm can achieve higher accuracy to determine a glycan topology than prior methods without increasing computational burden.

  2. Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra

    PubMed Central

    Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Tian, Zhixin

    2015-01-01

    It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available. PMID:26439836

  3. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

    NASA Astrophysics Data System (ADS)

    Novák, Jiří; Lemr, Karel; Schug, Kevin A.; Havlíček, Vladimír

    2015-07-01

    Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/, where the User's manual and video tutorials can be found.

  4. Faster and more accurate graphical model identification of tandem mass spectra using trellises

    PubMed Central

    Wang, Shengjie; Halloran, John T.; Bilmes, Jeff A.; Noble, William S.

    2016-01-01

    Tandem mass spectrometry (MS/MS) is the dominant high throughput technology for identifying and quantifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by an MS/MS experiment begins by assigning to each observed spectrum the peptide that is hypothesized to be responsible for generating the spectrum. This assignment is typically done by searching each spectrum against a database of peptides. To our knowledge, all existing MS/MS search engines compute scores individually between a given observed spectrum and each possible candidate peptide from the database. In this work, we use a trellis, a data structure capable of jointly representing a large set of candidate peptides, to avoid redundantly recomputing common sub-computations among different candidates. We show how trellises may be used to significantly speed up existing scoring algorithms, and we theoretically quantify the expected speedup afforded by trellises. Furthermore, we demonstrate that compact trellis representations of whole sets of peptides enables efficient discriminative learning of a dynamic Bayesian network for spectrum identification, leading to greatly improved spectrum identification accuracy. Contact: bilmes@uw.edu or william-noble@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307634

  5. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    PubMed

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-05

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit .

  6. Purification of pharmaceutical preparations using thin-layer chromatography to obtain mass spectra with Direct Analysis in Real Time and accurate mass spectrometry.

    PubMed

    Wood, Jessica L; Steiner, Robert R

    2011-06-01

    Forensic analysis of pharmaceutical preparations requires a comparative analysis with a standard of the suspected drug in order to identify the active ingredient. Purchasing analytical standards can be expensive or unattainable from the drug manufacturers. Direct Analysis in Real Time (DART™) is a novel, ambient ionization technique, typically coupled with a JEOL AccuTOF™ (accurate mass) mass spectrometer. While a fast and easy technique to perform, a drawback of using DART™ is the lack of component separation of mixtures prior to ionization. Various in-house pharmaceutical preparations were purified using thin-layer chromatography (TLC) and mass spectra were subsequently obtained using the AccuTOF™- DART™ technique. Utilizing TLC prior to sample introduction provides a simple, low-cost solution to acquiring mass spectra of the purified preparation. Each spectrum was compared against an in-house molecular formula list to confirm the accurate mass elemental compositions. Spectra of purified ingredients of known pharmaceuticals were added to an in-house library for use as comparators for casework samples. Resolving isomers from one another can be accomplished using collision-induced dissociation after ionization. Challenges arose when the pharmaceutical preparation required an optimized TLC solvent to achieve proper separation and purity of the standard. Purified spectra were obtained for 91 preparations and included in an in-house drug standard library. Primary standards would only need to be purchased when pharmaceutical preparations not previously encountered are submitted for comparative analysis. TLC prior to DART™ analysis demonstrates a time efficient and cost saving technique for the forensic drug analysis community. Copyright © 2011 John Wiley & Sons, Ltd.

  7. Fragmentation pathways of drugs of abuse and their metabolites based on QTOF MS/MS and MS(E) accurate-mass spectra.

    PubMed

    Bijlsma, Lubertus; Sancho, Juan V; Hernández, Félix; Niessen, Wilfried M A

    2011-09-01

    A study of the fragmentation pathways of several classes of drugs of abuse (cannabinoids, ketamine, amphetamine and amphetamine-type stimulants (ATS), cocaine and opiates) and their related substances has been made. The knowledge of the fragmentation is highly useful for specific fragment selection or for recognition of related compounds when developing MS-based analytical methods for the trace-level determination of these compounds in complex matrices. In this work, accurate-mass spectra of selected compounds were obtained using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry, performing both MS/MS and MS(E) experiments. As regards fragmentation behavior, the mass spectra of both approaches were quite similar and were useful to study the fragmentation of the drugs investigated. Accurate-mass spectra of 37 drugs of abuse and related compounds, including metabolites and deuterated analogues, were studied in this work, and structures of fragment ions were proposed. The accurate-mass data obtained allowed to confirm structures and fragmentation pathways previously proposed based on nominal mass measurements, although new insights and structure proposals were achieved in some particular cases, especially for amphetamine and ATS, 11-nor-9-carboxy-Δ(9)-tetrahydrocannabinol (THC-COOH) and opiates.

  8. New Photometry and Spectra of AB Doradus C: An Accurate Mass Determination of a Young Low-Mass Object with Theoretical Evolutionary Tracks

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Thatte, Niranjan; Nielsen, Eric L.; Abuter, Roberto; Clarke, Fraser; Tecza, Matthias

    2007-08-01

    We present new photometric and spectroscopic measurements for the unique, young, low-mass evolutionary track calibrator AB Dor C. While the new Ks photometry is similar to that we have previously published, the spectral type is found to be much earlier. Based on new H and K IFS spectra of AB Dor C from Thatte et al. (Paper I), we adopt a spectral type of M5.5+/-1.0 for AB Dor C. This is considerably earlier than the M8+/-1 previously estimated by Close et al. and Nielsen et al. yet is consistent with the M6+/-1 independently derived by Luhman & Potter. However, the spectrum presented in Paper I and analyzed here is a significant improvement over any previous spectrum of AB Dor C. We also present new astrometry for the system, which further supports a 0.090+/-0.005 Msolar mass for the system. Once armed with an accurate spectrum and Ks flux, we find L=0.0021+/-0.0005 Lsolar and Teff=2925+170-145 K for AB Dor C. These values are consistent with a ~75 Myr, 0.090+/-0.005 Msolar object like AB Dor C according to the DUSTY evolutionary tracks. Hence, masses can be estimated from the H-R diagram with the DUSTY tracks for young low-mass objects such as AB Dor C. However, we cautiously note that underestimates of the mass from the tracks can occur if one lacks a proper (continuum-preserved) spectrum or is relying on near-infrared fluxes alone. Based on observations made with ESO telescopes at the Paranal Observatories under program 276.C-5013.

  9. Accurate Anharmonic IR Spectra from Integrated Cc/dft Approach

    NASA Astrophysics Data System (ADS)

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Puzzarini, Cristina

    2014-06-01

    The recent implementation of the computation of infrared (IR) intensities beyond the double harmonic approximation [1] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Contrary to common beliefs, second-order perturbation theory is able to deliver results of high accuracy provided that anharmonic resonances are properly managed [1,2]. It has been already shown for several small closed- and open shell molecular systems that the differences between coupled cluster (CC) and DFT anharmonic wavenumbers are mainly due to the harmonic terms, paving the route to introduce effective yet accurate hybrid CC/DFT schemes [2]. In this work we present that hybrid CC/DFT models can be applied also to the IR intensities leading to the simulation of highly accurate fully anharmonic IR spectra for medium-size molecules, including ones of atmospheric interest, showing in all cases good agreement with experiment even in the spectral ranges where non-fundamental transitions are predominant[3]. [1] J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012) [2] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 16, 1759-1787 (2014) [3] I. Carnimeo, C. Puzzarini, N. Tasinato, P. Stoppa, A. P. Charmet, M. Biczysko, C. Cappelli and V. Barone, J. Chem. Phys., 139, 074310 (2013)

  10. Accurate Mass Assignment of Native Protein Complexes Detected by Electrospray Mass Spectrometry

    PubMed Central

    Liepold, Lars O.; Oltrogge, Luke M.; Suci, Peter; Douglas, Trevor; Young, Mark J.

    2009-01-01

    Correct charge state assignment is crucial to assigning an accurate mass to supramolecular complexes analyzed by electrospray mass spectrometry. Conventional charge state assignment techniques fall short of reliably and unambiguously predicting the correct charge state for many supramolecular complexes. We provide an explanation of the shortcomings of the conventional techniques and have developed a robust charge state assignment method that is applicable to all spectra. PMID:19103497

  11. Reanalysis of Tyrannosaurus rex Mass Spectra.

    PubMed

    Bern, Marshall; Phinney, Brett S; Goldberg, David

    2009-09-01

    Asara et al. reported the detection of collagen peptides in a 68-million-year-old Tyrannosaurus rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.

  12. Toward the Accurate Simulation of Two-Dimensional Electronic Spectra

    NASA Astrophysics Data System (ADS)

    Giussani, Angelo; Nenov, Artur; Segarra-Martí, Javier; Jaiswal, Vishal K.; Rivalta, Ivan; Dumont, Elise; Mukamel, Shaul; Garavelli, Marco

    2015-06-01

    Two-dimensional pump-probe electronic spectroscopy is a powerful technique able to provide both high spectral and temporal resolution, allowing the analysis of ultrafast complex reactions occurring via complementary pathways by the identification of decay-specific fingerprints. [1-2] The understanding of the origin of the experimentally recorded signals in a two-dimensional electronic spectrum requires the characterization of the electronic states involved in the electronic transitions photoinduced by the pump/probe pulses in the experiment. Such a goal constitutes a considerable computational challenge, since up to 100 states need to be described, for which state-of-the-art methods as RASSCF and RASPT2 have to be wisely employed. [3] With the present contribution, the main features and potentialities of two-dimensional electronic spectroscopy are presented, together with the machinery in continuous development in our groups in order to compute two-dimensional electronic spectra. The results obtained using different level of theory and simulations are shown, bringing as examples the computed two-dimensional electronic spectra for some specific cases studied. [2-4] [1] Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M, Int. J. Quantum Chem., 2014, 114, 85 [2] Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal V K, Altavilla S, Mukamel S, Garavelli M, Faraday Discuss. 2015, DOI: 10.1039/C4FD00175C [3] Nenov A, Giussani A, Segarra-Martí J, Jaiswal V K, Rivalta I, Cerullo G, Mukamel S, Garavelli M, J. Chem. Phys. submitted [4] Nenov A, Giussani A, Fingerhut B P, Rivalta I, Dumont E, Mukamel S, Garavelli M, Phys. Chem. Chem. Phys. Submitted [5] Krebs N, Pugliesi I, Hauer J, Riedle E, New J. Phys., 2013,15, 08501

  13. Odor Impression Prediction from Mass Spectra.

    PubMed

    Nozaki, Yuji; Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61).

  14. Odor Impression Prediction from Mass Spectra

    PubMed Central

    Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61). PMID:27326765

  15. USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER AND AN ION CORRELATION PROGRAM TO IDENTIFY COMPOUNDS

    EPA Science Inventory

    Most compounds are not found in mass spectral libraries and must be identified by other means. Often, compound identities can be deduced from the compositions of the ions in their mass spectra and review of the chemical literature. Confirmation is provided by mass spectra and r...

  16. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  17. Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra.

    PubMed

    Gay, Steven; Binz, Pierre-Alain; Hochstrasser, Denis F; Appel, Ron D

    2002-10-01

    Matrix-assisted laser desorption/ionization-time of flight mass spectrometry has become a valuable tool in proteomics. With the increasing acquisition rate of mass spectrometers, one of the major issues is the development of accurate, efficient and automatic peptide mass fingerprinting (PMF) identification tools. Current tools are mostly based on counting the number of experimental peptide masses matching with theoretical masses. Almost all of them use additional criteria such as isoelectric point, molecular weight, PTMs, taxonomy or enzymatic cleavage rules to enhance prediction performance. However, these identification tools seldom use peak intensities as parameter as there is currently no model predicting the intensities based on the physicochemical properties of peptides. In this work, we used standard datamining methods such as classification and regression methods to find correlations between peak intensities and the properties of the peptides composing a PMF spectrum. These methods were applied on a dataset comprising a series of PMF experiments involving 157 proteins. We found that the C4.5 method gave the more informative results for the classification task (prediction of the presence or absence of a peptide in a spectra) and M5' for the regression methods (prediction of the normalized intensity of a peptide peak). The C4.5 result correctly classified 88% of the theoretical peaks; whereas the M5' peak intensities had a correlation coefficient of 0.6743 with the experimental peak intensities. These methods enabled us to obtain decision and model trees that can be directly used for prediction and identification of PMF results. The work performed permitted to lay the foundations of a method to analyze factors influencing the peak intensity of PMF spectra. A simple extension of this analysis could lead to improve the accuracy of the results by using a larger dataset. Additional peptide characteristics or even PMF experimental parameters can also be taken into

  18. Game-theory-based search engine to automate the mass assignment in complex native electrospray mass spectra.

    PubMed

    Tseng, Yao-Hsin; Uetrecht, Charlotte; Yang, Shih-Chieh; Barendregt, Arjan; Heck, Albert J R; Peng, Wen-Ping

    2013-12-03

    Electrospray ionization coupled to native mass spectrometry (MS) has evolved into an important tool in structural biology to decipher the composition of protein complexes. However, the mass analysis of heterogeneous protein assemblies is hampered because of their overlapping charge state distributions, fine structure, and peak broadening. To facilitate the mass analysis, it is of importance to automate preprocessing raw mass spectra, assigning ion series to peaks and deciphering the subunit compositions. So far, the automation of preprocessing raw mass spectra has not been accomplished; Massign was introduced to simplify data analysis and decipher the subunit compositions. In this study, we develop a search engine, AutoMass, to automatically assign ion series to peaks without any additional user input, for example, limited ranges of charge states or ion mass. AutoMass includes an ion intensity-dependent method to check for Gaussian distributions of ion series and an ion intensity-independent method to address highly overlapping and non-Gaussian distributions. The minimax theorem from game theory is adopted to define the boundaries. With AutoMass, the boundaries of ion series in the well-resolved tandem mass spectra of the hepatitis B virus (HBV) capsids and those of the mass spectrum from CRISPR-related cascade protein complex are accurately assigned. Theoretical and experimental HBV ion masses are shown in agreement up to ~0.03%. The analysis is finished within a minute on a regular workstation. Moreover, less well-resolved mass spectra, for example, complicated multimer mass spectra and norovirus capsid mass spectra at different levels of desolvation, are analyzed. In sum, this first-ever fully automatic program reveals the boundaries of overlapping ion peak series and can further aid developing high-throughput native MS and top-down proteomics.

  19. Importance of accurate spectral simulations for the analysis of terahertz spectra: citric acid anhydrate and monohydrate.

    PubMed

    King, Matthew D; Davis, Eric A; Smith, Tiffany M; Korter, Timothy M

    2011-10-13

    The terahertz (THz) spectra of crystalline solids are typically uniquely sensitive to the molecular packing configurations, allowing for the detection of polymorphs and hydrates by THz spectroscopic techniques. It is possible, however, that coincident absorptions may be observed between related crystal forms, in which case careful assessment of the lattice vibrations of each system must be performed. Presented here is a THz spectroscopic investigation of citric acid in its anhydrous and monohydrate phases. Remarkably similar features were observed in the THz spectra of both systems, requiring the accurate calculation of the low-frequency vibrational modes by solid-state density functional theory to determine the origins of these spectral features. The results of the simulations demonstrate the necessity of reliable and rigorous methods for THz vibrational modes to ensure the proper evaluation of the THz spectra of molecular solids.

  20. Quantitative proteomic analysis by accurate mass retention time pairs.

    PubMed

    Silva, Jeffrey C; Denny, Richard; Dorschel, Craig A; Gorenstein, Marc; Kass, Ignatius J; Li, Guo-Zhong; McKenna, Therese; Nold, Michael J; Richardson, Keith; Young, Phillip; Geromanos, Scott

    2005-04-01

    Current methodologies for protein quantitation include 2-dimensional gel electrophoresis techniques, metabolic labeling, and stable isotope labeling methods to name only a few. The current literature illustrates both pros and cons for each of the previously mentioned methodologies. Keeping with the teachings of William of Ockham, "with all things being equal the simplest solution tends to be correct", a simple LC/MS based methodology is presented that allows relative changes in abundance of proteins in highly complex mixtures to be determined. Utilizing a reproducible chromatographic separations system along with the high mass resolution and mass accuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands of ions emanating from identically prepared control and experimental samples can be made. Using this configuration, we can determine the change in relative abundance of a small number of ions between the two conditions solely by accurate mass and retention time. Employing standard operating procedures for both sample preparation and ESI-mass spectrometry, one typically obtains under 5 ppm mass precision and quantitative variations between 10 and 15%. The principal focus of this paper will demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated, complementary qualitative capabilities.

  1. An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

    NASA Astrophysics Data System (ADS)

    Mead, A. J.; Peacock, J. A.; Heymans, C.; Joudaki, S.; Heavens, A. F.

    2015-12-01

    We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N-body simulations. For a variety of Λ cold dark matter (ΛCDM) and wCDM models, the halo-model power is accurate to ≃ 5 per cent for k ≤ 10h Mpc-1 and z ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from HALOFIT for a range of k-cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode.

  2. Accurate and efficient calculation of discrete correlation functions and power spectra

    NASA Astrophysics Data System (ADS)

    Xu, Y. F.; Liu, J. M.; Zhu, W. D.

    2015-07-01

    Operational modal analysis (OMA), or output-only modal analysis, has been widely conducted especially when excitation applied on a structure is unknown or difficult to measure. Discrete cross-correlation functions and cross-power spectra between a reference data series and measured response data series are bases for OMA to identify modal properties of a structure. Such functions and spectra can be efficiently transformed from each other using the discrete Fourier transform (DFT) and inverse DFT (IDFT) based on the cross-correlation theorem. However, a direct application of the theorem and transforms, including the DFT and IDFT, can yield physically erroneous results due to periodic extension of the DFT on a function of a finite length to be transformed, which is false most of the time. Padding zero series to ends of data series before applying the theorem and transforms can reduce the errors, but the results are still physically erroneous. A new methodology is developed in this work to calculate discrete cross-correlation functions of non-negative time delays and associated cross-power spectra, referred to as half spectra, for OMA. The methodology can be extended to cross-correlation functions of any time delays and associated cross-power spectra, referred to as full spectra. The new methodology is computationally efficient due to use of the transforms. Data series are properly processed to avoid the errors caused by the periodic extension, and the resulting cross-correlation functions and associated cross-power spectra perfectly comply with their definitions. A coherence function, a convergence function, and a convergence index are introduced to evaluate qualities of measured cross-correlation functions and associated cross-power spectra. The new methodology was numerically and experimentally applied to an ideal two-degree-of-freedom (2-DOF) mass-spring-damper system and a damaged aluminum beam, respectively, and OMA was conducted using half spectra to estimate

  3. High Resolution Mass Spectra Analysis with a Programmable Calculator.

    ERIC Educational Resources Information Center

    Holdsworth, David K.

    1980-01-01

    Highlighted are characteristics of programs written for a pocket-sized programmable calculator to analyze mass spectra data (such as displaying high resolution masses for formulas, predicting whether formulas are stable molecules or molecular ions, determining formulas by isotopic abundance measurement) in a laboratory or classroom. (CS)

  4. AUTOMATED DETERMINATION OF PRECURSOR ION, PRODUCT ION, AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF COMPOSITE MASS SPECTRA USING ION CORRELATION BASED ON EXACT MASSES AND RELATIVE ISOTOPIC ABUNDANCES

    EPA Science Inventory

    After a dispersive event, rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A Direct Analysis in Real Time (DART)® ion source interfaced to a JEOL AccuTOF® mass spectrometer provided exact masses accurate to ...

  5. Fast and accurate mock catalogue generation for low-mass galaxies

    NASA Astrophysics Data System (ADS)

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  6. Accurate halo-model matter power spectra with dark energy, massive neutrinos and modified gravitational forces

    NASA Astrophysics Data System (ADS)

    Mead, A. J.; Heymans, C.; Lombriser, L.; Peacock, J. A.; Steele, O. I.; Winther, H. A.

    2016-06-01

    We present an accurate non-linear matter power spectrum prediction scheme for a variety of extensions to the standard cosmological paradigm, which uses the tuned halo model previously developed in Mead et al. We consider dark energy models that are both minimally and non-minimally coupled, massive neutrinos and modified gravitational forces with chameleon and Vainshtein screening mechanisms. In all cases, we compare halo-model power spectra to measurements from high-resolution simulations. We show that the tuned halo-model method can predict the non-linear matter power spectrum measured from simulations of parametrized w(a) dark energy models at the few per cent level for k < 10 h Mpc-1, and we present theoretically motivated extensions to cover non-minimally coupled scalar fields, massive neutrinos and Vainshtein screened modified gravity models that result in few per cent accurate power spectra for k < 10 h Mpc-1. For chameleon screened models, we achieve only 10 per cent accuracy for the same range of scales. Finally, we use our halo model to investigate degeneracies between different extensions to the standard cosmological model, finding that the impact of baryonic feedback on the non-linear matter power spectrum can be considered independently of modified gravity or massive neutrino extensions. In contrast, considering the impact of modified gravity and massive neutrinos independently results in biased estimates of power at the level of 5 per cent at scales k > 0.5 h Mpc-1. An updated version of our publicly available HMCODE can be found at https://github.com/alexander-mead/hmcode.

  7. Is the Separable Propagator Perturbation Approach Accurate in Calculating Angle Resolved Photoelectron Diffraction Spectra?

    NASA Astrophysics Data System (ADS)

    Ng, C. N.; Chu, T. P.; Wu, Huasheng; Tong, S. Y.; Huang, Hong

    1997-03-01

    We compare multiple scattering results of angle-resolved photoelectron diffraction spectra between the exact slab method and the separable propagator perturbation method. In the slab method,footnote C.H. Li, A.R. Lubinsky and S.Y. Tong, Phys. Rev. B17, 3128 (1978). the source wave and multiple scattering within the strong scattering atomic layers are expanded in spherical waves while interlayer scattering is expressed in plane waves. The transformation between spherical waves and plane waves is done exactly. The plane waves are then matched across the solid-vacuum interface to a single outgoing plane wave in the detector's direction. The separable propagator perturbation approach uses two approximations: (i) A separable representation of the Green's function propagator and (ii) A perturbation expansion of multiple scattering terms. Results of c(2x2) S-Ni(001) show that this approximate method fails to converge due to the very slow convergence of the separable representation for scattering angles less than 90^circ. However, this method is accurate in the backscattering regime and may be applied to XAFS calculations.(J.J. Rehr and R.C. Albers, Phys. Rev. B41, 8139 (1990).) The use of this method for angle-resolved photoelectron diffraction spectra is substantially less reliable.

  8. Active and sterile neutrino mass effects on beta decay spectra

    SciTech Connect

    Boillos, Juan Manuel; Moya de Guerra, Elvira

    2013-06-10

    We study the spectra of the emitted charged leptons in charge current weak nuclear processes to analyze the effect of neutrino masses. Standard active neutrinos are studied here, with masses of the order of 1 eV or lower, as well as sterile neutrinos with masses of a few keV. The latter are warm dark matter (WDM) candidates hypothetically produced or captured as small mixtures with the active neutrinos. We compute differential decay or capture rates spectra in weak charged processes of different nuclei ({sup 3}H, {sup 187}Re, {sup 107}Pd, {sup 163}Ho, etc) using different masses of both active and sterile neutrinos and different values of the mixing parameter.

  9. Mass spectra and Regge trajectories of , , and baryons

    NASA Astrophysics Data System (ADS)

    Shah, Zalak; Thakkar, Kaushal; Rai, Ajay Kumar; Vinodkumar, P. C.

    2016-12-01

    We calculate the mass spectra of the singly charmed baryons (, , and ) using the hypercentral constituent quark model (hCQM). The hyper color Coulomb plus linear potential is used to calculate the masses of positive (up to ) and negative (up to ) parity excited states. The spin-spin, spin-orbital and tensor interaction terms are also incorporated for mass spectra. We have compared our results with other theoretical and lattice QCD predictions for each baryon. Moreover, the known experimental results are also reasonably close to our predicted masses. By using the radial and orbital excitation, we construct Regge trajectories for the baryons in the (n, M2) plane and find their slopes and intercepts. Other properties of these baryons, like magnetic moments, radiative transitions and radiative decay widths, are also calculated successfully. Supported in part (A. K. Rai) by DST, India (SERB Fast Track Scheme SR/FTP/PS-152/2012)

  10. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  11. Accurate mass - time tag library for LC/MS-based metabolite profiling of medicinal plants

    PubMed Central

    Cuthbertson, Daniel J.; Johnson, Sean R.; Piljac-Žegarac, Jasenka; Kappel, Julia; Schäfer, Sarah; Wüst, Matthias; Ketchum, Raymond E. B.; Croteau, Rodney B.; Marques, Joaquim V.; Davin, Laurence B.; Lewis, Norman G.; Rolf, Megan; Kutchan, Toni M.; Soejarto, D. Doel; Lange, B. Markus

    2013-01-01

    We report the development and testing of an accurate mass – time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents. PMID:23597491

  12. Mass spectra of 0+-, 1-+, and 2+- exotic glueballs

    NASA Astrophysics Data System (ADS)

    Tang, Liang; Qiao, Cong-Feng

    2016-03-01

    With appropriate interpolating currents the mass spectra of 0+-, 1-+, and 2+- oddballs are studied in the framework of QCD sum rules (QCDSR). We find there exits one stable 0+- oddball with mass of 4.57 ± 0.13GeV, and one stable 2+- oddball with mass of 6.06 ± 0.13GeV, whereas, no stable 1-+ oddball shows up. The possible production and decay modes of these glueballs with unconventional quantum numbers are analyzed, which are hopefully measurable in either BELLEII, PANDA, Super-B or LHCb experiments.

  13. The IAG solar flux atlas: Accurate wavelengths and absolute convective blueshift in standard solar spectra

    NASA Astrophysics Data System (ADS)

    Reiners, A.; Mrotzek, N.; Lemke, U.; Hinrichs, J.; Reinsch, K.

    2016-03-01

    We present a new solar flux atlas with the aim of understanding wavelength precision and accuracy in solar benchmark data. The atlas covers the wavelength range 405-2300 nm and was observed at the Institut für Astrophysik, Göttingen (IAG), with a Fourier transform spectrograph (FTS). In contrast to other FTS atlases, the entire visible wavelength range was observed simultaneously using only one spectrograph setting. We compare the wavelength solution of the new atlas to the Kitt Peak solar flux atlases and to the HARPS frequency-comb calibrated solar atlas. Comparison reveals systematics in the two Kitt Peak FTS atlases resulting from their wavelength scale construction, and shows consistency between the IAG and the HARPS atlas. We conclude that the IAG atlas is precise and accurate on the order of ± 10 m s-1 in the wavelength range 405-1065 nm, while the Kitt Peak atlases show deviations as large as several ten to 100 m s-1. We determine absolute convective blueshift across the spectrum from the IAG atlas and report slight differences relative to results from the Kitt Peak atlas that we attribute to the differences between wavelength scales. We conclude that benchmark solar data with accurate wavelength solution are crucial to better understand the effect of convection on stellar radial velocity measurements, which is one of the main limitations of Doppler spectroscopy at m s -1 precision. Data (FITS files of the spectra) and Table A.1 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/587/A65

  14. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  15. Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

    NASA Astrophysics Data System (ADS)

    Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

    2016-08-01

    The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

  16. Verification of automated peptide identifications from proteomic tandem mass spectra

    PubMed Central

    Tabb, David L; Friedman, David B; Ham, Amy-Joan L

    2010-01-01

    Shotgun proteomics yields tandem mass spectra of peptides that can be identified by database search algorithms. When only a few observed peptides suggest the presence of a protein, establishing the accuracy of the peptide identifications is necessary for accepting or rejecting the protein identification. In this protocol, we describe the properties of peptide identifications that can differentiate legitimately identified peptides from spurious ones. The chemistry of fragmentation, as embodied in the ‘mobile proton’ and ‘pathways in competition’ models, informs the process of confirming or rejecting each spectral match. Examples of ion-trap and tandem time-of-flight (TOF/TOF) mass spectra illustrate these principles of fragmentation. PMID:17406459

  17. Theory analysis of mass spectra of long-chain isocyanates.

    PubMed

    Liu, Dongliang; Hao, Ce; Zhang, Hua; Qiao, Weihong; Li, Zongshi; Yu, Guanghui; Yan, Kelu; Guo, Yuliang; Cheng, Lvbo

    2008-07-01

    Electron impact mass spectra of four long-chain isocyanates, lauryl isocyanate, tetradecyl isocyanate, hexadecyl isocyanate and octadecyl isocyanate, were obtained with a GCT high-resolution time-of-flight mass spectrometer. The four isocyanates studied gave a common base peak of m/z 99, which suggested the formation of a stable six-membered ring structure to decentralize the positive charge. Quantum-mechanical energy calculation justified that the six-membered ring base peak had the lowest energy. The positive charge assigned during the fragmentation of the radical cation, and the relative intensity of the fragment ion peaks, were explained by quantum-mechanical calculations as well.

  18. Cosmic ray mass and momentum spectra at mountain altitude

    NASA Technical Reports Server (NTRS)

    Barber, H. B.; Bowen, T.; Delise, D. A.; Jenkins, E. W.; Jones, J. J.; Kalbach, R. M.; Pifer, A. E.

    1975-01-01

    A cosmic ray mass spectrometer using a superconducting magnet, digitized wire spark chambers, and a scintillation counter time of flight system, has been operated at an altitude of 2750 meters. The apparatus is most sensitive to charged particles with momentum to mass ratios between 0.2 and 2.0. Results for the momentum spectra of protons and deuterons are presented, as well as upper limits for H-3 and He-3. The reaction nucleon + nucleon yields deuteron + pion accounts for part of the observed deuteron spectrum in the 0.9 to 3 GeV/c region.-

  19. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

    NASA Astrophysics Data System (ADS)

    Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

    2016-02-01

    Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

  20. ACCURATE LOW-MASS STELLAR MODELS OF KOI-126

    SciTech Connect

    Feiden, Gregory A.; Chaboyer, Brian; Dotter, Aaron

    2011-10-10

    The recent discovery of an eclipsing hierarchical triple system with two low-mass stars in a close orbit (KOI-126) by Carter et al. appeared to reinforce the evidence that theoretical stellar evolution models are not able to reproduce the observational mass-radius relation for low-mass stars. We present a set of stellar models for the three stars in the KOI-126 system that show excellent agreement with the observed radii. This agreement appears to be due to the equation of state implemented by our code. A significant dispersion in the observed mass-radius relation for fully convective stars is demonstrated; indicative of the influence of physics currently not incorporated in standard stellar evolution models. We also predict apsidal motion constants for the two M dwarf companions. These values should be observationally determined to within 1% by the end of the Kepler mission.

  1. Mono-isotope Prediction for Mass Spectra Using Bayes Network

    PubMed Central

    Li, Hui; Rwebangira, Mugizi Robert; Burge, Legand

    2015-01-01

    Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized naïve Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected from validated theoretical spectra were used as prior information in the Bayes method. Three main features extracted from the dataset were employed as independent variables in our model. The application of the proposed algorithm to publicMo dataset demonstrates that our naïve Bayes classifier is advantageous over existing methods in both accuracy and sensitivity. PMID:25620856

  2. MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

    PubMed Central

    2014-01-01

    Today’s highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda, is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform. PMID:24909410

  3. Quantitative proteomics using the high resolution accurate mass capabilities of the quadrupole-orbitrap mass spectrometer.

    PubMed

    Gallien, Sebastien; Domon, Bruno

    2014-08-01

    High resolution/accurate mass hybrid mass spectrometers have considerably advanced shotgun proteomics and the recent introduction of fast sequencing capabilities has expanded its use for targeted approaches. More specifically, the quadrupole-orbitrap instrument has a unique configuration and its new features enable a wide range of experiments. An overview of the analytical capabilities of this instrument is presented, with a focus on its application to quantitative analyses. The high resolution, the trapping capability and the versatility of the instrument have allowed quantitative proteomic workflows to be redefined and new data acquisition schemes to be developed. The initial proteomic applications have shown an improvement of the analytical performance. However, as quantification relies on ion trapping, instead of ion beam, further refinement of the technique can be expected.

  4. A highly accurate method for the determination of mass and center of mass of a spacecraft

    NASA Technical Reports Server (NTRS)

    Chow, E. Y.; Trubert, M. R.; Egwuatu, A.

    1978-01-01

    An extremely accurate method for the measurement of mass and the lateral center of mass of a spacecraft has been developed. The method was needed for the Voyager spacecraft mission requirement which limited the uncertainty in the knowledge of lateral center of mass of the spacecraft system weighing 750 kg to be less than 1.0 mm (0.04 in.). The method consists of using three load cells symmetrically located at 120 deg apart on a turntable with respect to the vertical axis of the spacecraft and making six measurements for each load cell. These six measurements are taken by cyclic rotations of the load cell turntable and of the spacecraft, about the vertical axis of the measurement fixture. This method eliminates all alignment, leveling, and load cell calibration errors for the lateral center of mass determination, and permits a statistical best fit of the measurement data. An associated data reduction computer program called MASCM has been written to implement this method and has been used for the Voyager spacecraft.

  5. Excited state mass spectra of doubly heavy Ξ baryons

    NASA Astrophysics Data System (ADS)

    Shah, Zalak; Rai, Ajay Kumar

    2017-02-01

    In this paper, the mass spectra are obtained for doubly heavy Ξ baryons, namely, Ξ _{cc}+, Ξ _{cc}^{++}, Ξ _{bb}-, Ξ _{bb}0, Ξ _{bc}0 and Ξ _{bc}+. These baryons consist of two heavy quarks ( cc, bb, and bc) with a light ( d or u) quark. The ground, radial, and orbital states are calculated in the framework of the hypercentral constituent quark model with Coulomb plus linear potential. Our results are also compared with other predictions, thus, the average possible range of excited states masses of these Ξ baryons can be determined. The study of the Regge trajectories is performed in ( n, M2) and ( J, M2) planes and their slopes and intercepts are also determined. Lastly, the ground state magnetic moments of these doubly heavy baryons are also calculated.

  6. Accurate, reliable control of process gases by mass flow controllers

    SciTech Connect

    Hardy, J.; McKnight, T.

    1997-02-01

    The thermal mass flow controller, or MFC, has become an instrument of choice for the monitoring and controlling of process gas flow throughout the materials processing industry. These MFCs are used on CVD processes, etching tools, and furnaces and, within the semiconductor industry, are used on 70% of the processing tools. Reliability and accuracy are major concerns for the users of the MFCs. Calibration and characterization technologies for the development and implementation of mass flow devices are described. A test facility is available to industry and universities to test and develop gas floe sensors and controllers and evaluate their performance related to environmental effects, reliability, reproducibility, and accuracy. Additional work has been conducted in the area of accuracy. A gravimetric calibrator was invented that allows flow sensors to be calibrated in corrosive, reactive gases to an accuracy of 0.3% of reading, at least an order of magnitude better than previously possible. Although MFCs are typically specified with accuracies of 1% of full scale, MFCs may often be implemented with unwarranted confidence due to the conventional use of surrogate gas factors. Surrogate gas factors are corrections applied to process flow indications when an MFC has been calibrated on a laboratory-safe surrogate gas, but is actually used on a toxic, or corrosive process gas. Previous studies have indicated that the use of these factors may cause process flow errors of typically 10%, but possibly as great as 40% of full scale. This paper will present possible sources of error in MFC process gas flow monitoring and control, and will present an overview of corrective measures which may be implemented with MFC use to significantly reduce these sources of error.

  7. Device for accurately measuring mass flow of gases

    DOEpatents

    Hylton, J.O.; Remenyik, C.J.

    1994-08-09

    A device for measuring mass flow of gases which utilizes a substantially buoyant pressure vessel suspended within a fluid/liquid in an enclosure is disclosed. The pressure vessel is connected to a weighing device for continuously determining weight change of the vessel as a function of the amount of gas within the pressure vessel. In the preferred embodiment, this pressure vessel is formed from inner and outer right circular cylindrical hulls, with a volume between the hulls being vented to the atmosphere external the enclosure. The fluid/liquid, normally in the form of water typically with an added detergent, is contained within an enclosure with the fluid/liquid being at a level such that the pressure vessel is suspended beneath this level but above a bottom of the enclosure. The buoyant pressure vessel can be interconnected with selected valves to an auxiliary pressure vessel so that initial flow can be established to or from the auxiliary pressure vessel prior to flow to or from the buoyant pressure vessel. 5 figs.

  8. Device for accurately measuring mass flow of gases

    DOEpatents

    Hylton, James O.; Remenyik, Carl J.

    1994-01-01

    A device for measuring mass flow of gases which utilizes a substantially buoyant pressure vessel suspended within a fluid/liquid in an enclosure. The pressure vessel is connected to a weighing device for continuously determining weight change of the vessel as a function of the amount of gas within the pressure vessel. In the preferred embodiment, this pressure vessel is formed from inner and outer right circular cylindrical hulls, with a volume between the hulls being vented to the atmosphere external the enclosure. The fluid/liquid, normally in the form of water typically with an added detergent, is contained within an enclosure with the fluid/liquid being at a level such that the pressure vessel is suspended beneath this level but above a bottom of the enclosure. The buoyant pressure vessel can be interconnected with selected valves to an auxiliary pressure vessel so that initial flow can be established to or from the auxiliary pressure vessel prior to flow to or from the buoyant pressure vessel.

  9. Mass measurement using energy spectra in three-body decays

    SciTech Connect

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin; Wardlow, Kyle

    2016-05-24

    In previous works we have demonstrated how the energy distribution of massless decay products in two body decays can be used to measure the mass of decaying particles. In this study, we show how such results can be generalized to the case of multi-body decays. The key ideas that allow us to deal with multi-body final states are an extension of our previous results to the case of massive decay products and the factorization of the multi-body phase space. The mass measurement strategy that we propose is distinct from alternative methods because it does not require an accurate reconstruction of the entire event, as it does not involve, for instance, the missing transverse momentum, but rather requires measuring only the visible decay products of the decay of interest. To demonstrate the general strategy, we study a supersymmetric model wherein pair-produced gluinos each decay to a stable neutralino and a bottom quark-antiquark pair via an off -shell bottom squark. The combinatorial background stemming from the indistinguishable visible final states on both decay sides can be treated by an “event mixing” technique, the performance of which is discussed in detail. In conclusion, taking into account dominant backgrounds, we are able to show that the mass of the gluino and, in favorable cases, that of the neutralino can be determined by this mass measurement strategy.

  10. Mass measurement using energy spectra in three-body decays

    DOE PAGES

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin; ...

    2016-05-24

    In previous works we have demonstrated how the energy distribution of massless decay products in two body decays can be used to measure the mass of decaying particles. In this study, we show how such results can be generalized to the case of multi-body decays. The key ideas that allow us to deal with multi-body final states are an extension of our previous results to the case of massive decay products and the factorization of the multi-body phase space. The mass measurement strategy that we propose is distinct from alternative methods because it does not require an accurate reconstruction ofmore » the entire event, as it does not involve, for instance, the missing transverse momentum, but rather requires measuring only the visible decay products of the decay of interest. To demonstrate the general strategy, we study a supersymmetric model wherein pair-produced gluinos each decay to a stable neutralino and a bottom quark-antiquark pair via an off -shell bottom squark. The combinatorial background stemming from the indistinguishable visible final states on both decay sides can be treated by an “event mixing” technique, the performance of which is discussed in detail. In conclusion, taking into account dominant backgrounds, we are able to show that the mass of the gluino and, in favorable cases, that of the neutralino can be determined by this mass measurement strategy.« less

  11. DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets

    SciTech Connect

    Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.; Polpitiya, Ashoka D.; Purvine, Samuel O.; Anderson, Gordon A.; Camp, David G.; Smith, Richard D.

    2009-12-16

    Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and MS/MS fragmentation have become widely available in recent years and have allowed for sig-nificantly better discrimination between true and false MS/MS pep-tide identifications by applying relatively narrow windows for maxi-mum allowable deviations for parent ion mass measurements. To fully gain the advantage of highly accurate parent ion mass meas-urements, it is important to limit systematic mass measurement errors. The DtaRefinery software tool can correct systematic errors in parent ion masses by reading a set of fragmentation spectra, searching for MS/MS peptide identifications, then fitting a model that can estimate systematic errors, and removing them. This results in a new fragmentation spectrum file with updated parent ion masses.

  12. Accurate vibrational spectra via molecular tailoring approach: a case study of water clusters at MP2 level.

    PubMed

    Sahu, Nityananda; Gadre, Shridhar R

    2015-01-07

    In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm(-1) with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

  13. An accurate retrieval of leaf water content from mid to thermal infrared spectra using continuous wavelet analysis.

    PubMed

    Ullah, Saleem; Skidmore, Andrew K; Naeem, Mohammad; Schlerf, Martin

    2012-10-15

    Leaf water content determines plant health, vitality, photosynthetic efficiency and is an important indicator of drought assessment. The retrieval of leaf water content from the visible to shortwave infrared spectra is well known. Here for the first time, we estimated leaf water content from the mid to thermal infrared (2.5-14.0 μm) spectra, based on continuous wavelet analysis. The dataset comprised 394 spectra from nine plant species, with different water contents achieved through progressive drying. To identify the spectral feature most sensitive to the variations in leaf water content, first the Directional Hemispherical Reflectance (DHR) spectra were transformed into a wavelet power scalogram, and then linear relations were established between the wavelet power scalogram and leaf water content. The six individual wavelet features identified in the mid infrared yielded high correlations with leaf water content (R(2)=0.86 maximum, 0.83 minimum), as well as low RMSE (minimum 8.56%, maximum 9.27%). The combination of four wavelet features produced the most accurate model (R(2)=0.88, RMSE=8.00%). The models were consistent in terms of accuracy estimation for both calibration and validation datasets, indicating that leaf water content can be accurately retrieved from the mid to thermal infrared domain of the electromagnetic radiation.

  14. Accurate vibrational spectra via molecular tailoring approach: A case study of water clusters at MP2 level

    NASA Astrophysics Data System (ADS)

    Sahu, Nityananda; Gadre, Shridhar R.

    2015-01-01

    In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm-1 with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

  15. Charmed-strange mesons revisited: Mass spectra and strong decays

    NASA Astrophysics Data System (ADS)

    Song, Qin-Tao; Chen, Dian-Yong; Liu, Xiang; Matsuki, Takayuki

    2015-03-01

    Inspired by the present experimental status of charmed-strange mesons, we perform a systematic study of the charmed-strange meson family in which we calculate the mass spectra of the charmed-strange meson family by taking a screening effect into account in the Godfrey-Isgur model and investigate the corresponding strong decays via the quark pair creation model. These phenomenological analyses of charmed-strange mesons not only shed light on the features of the observed charmed-strange states, but also provide important information on future experimental search for the missing higher radial and orbital excitations in the charmed-strange meson family, which will be a valuable task in LHCb, the forthcoming Belle II, and PANDA.

  16. Accurate modeling of fluorescence line narrowing difference spectra: Direct measurement of the single-site fluorescence spectrum

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Naibo, Virginia; Jankowiak, Ryszard

    2010-07-01

    Accurate lineshape functions for modeling fluorescence line narrowing (FLN) difference spectra (ΔFLN spectra) in the low-fluence limit are derived and examined in terms of the physical interpretation of various contributions, including photoproduct absorption and emission. While in agreement with the earlier results of Jaaniso [Proc. Est. Acad. Sci., Phys., Math. 34, 277 (1985)] and Fünfschilling et al. [J. Lumin. 36, 85 (1986)], the derived formulas differ substantially from functions used recently [e.g., M. Rätsep et al., Chem. Phys. Lett. 479, 140 (2009)] to model ΔFLN spectra. In contrast to traditional FLN spectra, it is demonstrated that for most physically reasonable parameters, the ΔFLN spectrum reduces simply to the single-site fluorescence lineshape function. These results imply that direct measurement of a bulk-averaged single-site fluorescence lineshape function can be accomplished with no complicated extraction process or knowledge of any additional parameters such as site distribution function shape and width. We argue that previous analysis of ΔFLN spectra obtained for many photosynthetic complexes led to strong artificial lowering of apparent electron-phonon coupling strength, especially on the high-energy side of the pigment site distribution function.

  17. Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra.

    PubMed

    Roussis, Stilianos G; Proulx, Richard

    2003-03-15

    A method has been developed for the reduction of the chemical formulas of compounds in complex mixtures from the isotopic peak distributions of high-resolution mass spectra. The method is based on the principle that the observed isotopic peak distribution of a mixture of compounds is a linear combination of the isotopic peak distributions of the individual compounds in the mixture. All possible chemical formulas that meet specific criteria (e.g., type and number of atoms in structure, limits of unsaturation, etc.) are enumerated, and theoretical isotopic peak distributions are generated for each formula. The relative amount of each formula is obtained from the accurately measured isotopic peak distribution and the calculated isotopic peak distributions of all candidate formulas. The formulas of compounds in simple spectra, where peak components are fully resolved, are rapidly determined by direct comparison of the calculated and experimental isotopic peak distributions. The singular value decomposition linear algebra method is used to determine the contributions of compounds in complex spectra containing unresolved peak components. The principles of the approach and typical application examples are presented. The method is most useful for the characterization of complex spectra containing partially resolved peaks and structures with multiisotopic elements.

  18. Accurate Simulation of Resonance-Raman Spectra of Flexible Molecules: An Internal Coordinates Approach.

    PubMed

    Baiardi, Alberto; Bloino, Julien; Barone, Vincenzo

    2015-07-14

    The interpretation and analysis of experimental resonance-Raman (RR) spectra can be significantly facilitated by vibronic computations based on reliable quantum-mechanical (QM) methods. With the aim of improving the description of large and flexible molecules, our recent time-dependent formulation to compute vibrationally resolved electronic spectra, based on Cartesian coordinates, has been extended to support internal coordinates. A set of nonredundant delocalized coordinates is automatically generated from the molecular connectivity thanks to a new general and robust procedure. In order to validate our implementation, a series of molecules has been used as test cases. Among them, rigid systems show that normal modes based on Cartesian and delocalized internal coordinates provide equivalent results, but the latter set is much more convenient and reliable for systems characterized by strong geometric deformations associated with the electronic transition. The so-called Z-matrix internal coordinates, which perform well for chain molecules, are also shown to be poorly suited in the presence of cycles or nonstandard structures.

  19. De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra

    SciTech Connect

    Vyatkina, Kira; Wu, Si; Dekker, Lennard J. M.; VanDuijn, Martijn M.; Liu, Xiaowen; Tolić, Nikola; Dvorkin, Mikhail; Alexandrova, Sonya; Luider, Theo M.; Paša-Tolić, Ljiljana; Pevzner, Pavel A.

    2015-11-06

    De novo sequencing of proteins and peptides is one of the most important problems in mass spectrometry-driven proteomics. A variety of methods have been developed to accomplish this task from a set of bottom-up tandem (MS/MS) mass spectra. However, a more recently emerged top-down technology, now gaining more and more popularity, opens new perspectives for protein analysis and characterization, implying a need in efficient algorithms for processing this kind of MS/MS data. Here we describe a method that allows to retrieve from a set of top-down MS/MS spectra long and accurate sequence fragments of the proteins contained in a sample. To this end, we outline a strategy for generating high-quality sequence tags from top-down spectra, and introduce the concept of a T-Bruijn graph by adapting to the case of tags the notion of an A-Bruijn graph widely used in genomics. The output of the proposed approach represents the set of amino acid strings spelled out by optimal paths in the connected components of a T-Bruijn graph. We illustrate its performance on top-down datasets acquired from carbonic anhydrase 2 (CAH2) and the Fab region of alemtuzumab.

  20. Accurate mass analysis of ethanesulfonic acid degradates of acetochlor and alachlor using high-performance liquid chromatography and time-of-flight mass spectrometry

    USGS Publications Warehouse

    Thurman, E.M.; Ferrer, Imma; Parry, R.

    2002-01-01

    Degradates of acetochlor and alachlor (ethanesulfonic acids, ESAs) were analyzed in both standards and in a groundwater sample using high-performance liquid chromatography-time-of-flight mass spectrometry with electrospray ionization. The negative pseudomolecular ion of the secondary amide of acetochlor ESA and alachlor ESA gave average masses of 256.0750+/-0.0049 amu and 270.0786+/-0.0064 amu respectively. Acetochlor and alachlor ESA gave similar masses of 314.1098+/-0.0061 amu and 314.1153+/-0.0048 amu; however, they could not be distinguished by accurate mass because they have the same empirical formula. On the other hand, they may be distinguished using positive-ion electrospray because of different fragmentation spectra, which did not occur using negative-ion electrospray.

  1. Accurate mass analysis of ethanesulfonic acid degradates of acetochlor and alachlor using high-performance liquid chromatography and time-of-flight mass spectrometry

    USGS Publications Warehouse

    Thurman, E.M.; Ferrer, I.; Parry, R.

    2002-01-01

    Degradates of acetochlor and alachlor (ethanesulfonic acids, ESAs) were analyzed in both standards and in a groundwater sample using high-performance liquid chromatography-time-of-flight mass spectrometry with electrospray ionization. The negative pseudomolecular ion of the secondary amide of acetochlor ESA and alachlor ESA gave average masses of 256.0750??0.0049 amu and 270.0786??0.0064 amu respectively. Acetochlor and alachlor ESA gave similar masses of 314.1098??0.0061 amu and 314.1153??0.0048 amu; however, they could not be distinguished by accurate mass because they have the same empirical formula. On the other hand, they may be distinguished using positive-ion electrospray because of different fragmentation spectra, which did not occur using negative-ion electrospray.

  2. Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Can Accurately Differentiate between Mycobacterium masilliense (M. abscessus subspecies bolletti) and M. abscessus (Sensu Stricto)

    PubMed Central

    Teng, Shih-Hua; Chen, Chung-Ming; Lee, Meng-Rui; Lee, Tai-Fen; Chien, Kun-Yi; Teng, Lee-Jene

    2013-01-01

    Among 36 Mycobacterium masilliense and 22 M. abscessus isolates identified by erm(41) PCR and sequencing analysis of rpoB and 23S rRNA genes, the rate of accurate differentiation between these two subspecies was 100% by cluster analysis of spectra generated by Bruker Biotyper matrix-assisted laser desorption ionization–time of flight mass spectrometry. PMID:23824775

  3. Applicability of Density Functional Theory in Reproducing Accurate Vibrational Spectra of Surface Bound Species

    SciTech Connect

    Matanovic, Ivana; Atanassov, Plamen; Kiefer, Boris; Garzon, Fernando; Henson, Neil J.

    2014-10-05

    The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of 22.62 and 21.1% for the NAN stretching and RhAH stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the RhAH and NAN stretching modes from the bulk phonons and by solving one- and two-dimensional Schr€odinger equation associated with the RhAH, RhAN, and NAN potential energy we calculated the anharmonic correction for NAN and RhAH stretching modes as 231 cm21 and 277 cm21 at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.

  4. Accurate first-principles calculations for 12CH3D infrared spectra from isotopic and symmetry transformations

    NASA Astrophysics Data System (ADS)

    Rey, Michaël; Nikitin, Andrei V.; Tyuterev, Vladimir G.

    2014-07-01

    Accurate variational high-resolution spectra calculations in the range 0-8000 cm-1 are reported for the first time for the monodeutered methane (12CH3D). Global calculations were performed by using recent ab initio surfaces for line positions and line intensities derived from the main isotopologue 12CH4. Calculation of excited vibrational levels and high-J rovibrational states is described by using the normal mode Eckart-Watson Hamiltonian combined with irreducible tensor formalism and appropriate numerical procedures for solving the quantum nuclear motion problem. The isotopic H→D substitution is studied in details by means of symmetry and nonlinear normal mode coordinate transformations. Theoretical spectra predictions are given up to J = 25 and compared with the HITRAN 2012 database representing a compilation of line lists derived from analyses of experimental spectra. The results are in very good agreement with available empirical data suggesting that a large number of yet unassigned lines in observed spectra could be identified and modeled using the present approach.

  5. Accurate first-principles calculations for 12CH3D infrared spectra from isotopic and symmetry transformations.

    PubMed

    Rey, Michaël; Nikitin, Andrei V; Tyuterev, Vladimir G

    2014-07-28

    Accurate variational high-resolution spectra calculations in the range 0-8000 cm(-1) are reported for the first time for the monodeutered methane ((12)CH3D). Global calculations were performed by using recent ab initio surfaces for line positions and line intensities derived from the main isotopologue (12)CH4. Calculation of excited vibrational levels and high-J rovibrational states is described by using the normal mode Eckart-Watson Hamiltonian combined with irreducible tensor formalism and appropriate numerical procedures for solving the quantum nuclear motion problem. The isotopic H→D substitution is studied in details by means of symmetry and nonlinear normal mode coordinate transformations. Theoretical spectra predictions are given up to J = 25 and compared with the HITRAN 2012 database representing a compilation of line lists derived from analyses of experimental spectra. The results are in very good agreement with available empirical data suggesting that a large number of yet unassigned lines in observed spectra could be identified and modeled using the present approach.

  6. Accurate first-principles calculations for {sup 12}CH{sub 3}D infrared spectra from isotopic and symmetry transformations

    SciTech Connect

    Rey, Michaël Tyuterev, Vladimir G.; Nikitin, Andrei V.

    2014-07-28

    Accurate variational high-resolution spectra calculations in the range 0-8000 cm{sup −1} are reported for the first time for the monodeutered methane ({sup 12}CH{sub 3}D). Global calculations were performed by using recent ab initio surfaces for line positions and line intensities derived from the main isotopologue {sup 12}CH{sub 4}. Calculation of excited vibrational levels and high-J rovibrational states is described by using the normal mode Eckart-Watson Hamiltonian combined with irreducible tensor formalism and appropriate numerical procedures for solving the quantum nuclear motion problem. The isotopic H→D substitution is studied in details by means of symmetry and nonlinear normal mode coordinate transformations. Theoretical spectra predictions are given up to J = 25 and compared with the HITRAN 2012 database representing a compilation of line lists derived from analyses of experimental spectra. The results are in very good agreement with available empirical data suggesting that a large number of yet unassigned lines in observed spectra could be identified and modeled using the present approach.

  7. Reactions and mass spectra of complex particles using Aerosol CIMS

    NASA Astrophysics Data System (ADS)

    Hearn, John D.; Smith, Geoffrey D.

    2006-12-01

    Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

  8. Accurate wavelength calibration in the near-infrared for multielement analysis without the need for reference spectra

    SciTech Connect

    Asimellis, George; Giannoudakos, Aggelos; Kompitsas, Michael

    2006-12-10

    A new technique has been developed for an instant, precise, and accurate wavelength calibration over a wide pixel array for simultaneous, multielement spectral analysis based on an inverse numerical solution to the grating dispersion function.This technique is applicable to multielement analytical applications such as laser-induced breakdown spectroscopy (LIBS), particularly when using high-density gratings in the upper visible and in the near-infrared, where nonmetallic elements are detected.This application overcomes the need to use reference spectra for each window of observation and is tested on a commercially available LIBS instrument.

  9. MASS MEASUREMENTS BY AN ACCURATE AND SENSITIVE SELECTED ION RECORDING TECHNIQUE

    EPA Science Inventory

    Trace-level components of mixtures were successfully identified or confirmed by mass spectrometric accurate mass measurements, made at high resolution with selected ion recording, using GC and LC sample introduction. Measurements were made at 20 000 or 10 000 resolution, respecti...

  10. Accurate mass determination, quantification and determination of detection limits in liquid chromatography-high-resolution time-of-flight mass spectrometry: challenges and practical solutions.

    PubMed

    Vergeynst, Leendert; Van Langenhove, Herman; Joos, Pieter; Demeestere, Kristof

    2013-07-30

    Uniform guidelines for the data processing and validation of qualitative and quantitative multi-residue analysis using full-spectrum high-resolution mass spectrometry are scarce. Through systematic research, optimal mass accuracy and sensitivity are obtained after refining the post-processing of the HRMS data. For qualitative analysis, transforming the raw profile spectra to centroid spectra is recommended resulting in a 2.3 fold improved precision on the accurate mass determination of spectrum peaks. However, processing centroid data for quantitative purposes could lead to signal interruption when too narrow mass windows are applied for the construction of extracted ion chromatograms. Therefore, peak integration on the raw profile data is recommended. An optimal width of the mass window of 50 ppm, which is a trade-off between sensitivity and selectivity, was obtained for a TOF instrument providing a resolving power of 20,000 at full width at half maximum (FWHM). For the validation of HRMS analytical methods, widespread concepts such as the signal-to-noise ratios for the determination of decision limits and detection capabilities have shown to be not always applicable because in some cases almost no noise can be detected anymore. A statistical methodology providing a reliable alternative is extended and applied.

  11. An unsupervised machine learning method for assessing quality of tandem mass spectra

    PubMed Central

    2012-01-01

    Background In a single proteomic project, tandem mass spectrometers can produce hundreds of millions of tandem mass spectra. However, majority of tandem mass spectra are of poor quality, it wastes time to search them for peptides. Therefore, the quality assessment (before database search) is very useful in the pipeline of protein identification via tandem mass spectra, especially on the reduction of searching time and the decrease of false identifications. Most existing methods for quality assessment are supervised machine learning methods based on a number of features which describe the quality of tandem mass spectra. These methods need the training datasets with knowing the quality of all spectra, which are usually unavailable for the new datasets. Results This study proposes an unsupervised machine learning method for quality assessment of tandem mass spectra without any training dataset. This proposed method estimates the conditional probabilities of spectra being high quality from the quality assessments based on individual features. The probabilities are estimated through a constraint optimization problem. An efficient algorithm is developed to solve the constraint optimization problem and is proved to be convergent. Experimental results on two datasets illustrate that if we search only tandem spectra with the high quality determined by the proposed method, we can save about 56 % and 62% of database searching time while losing only a small amount of high-quality spectra. Conclusions Results indicate that the proposed method has a good performance for the quality assessment of tandem mass spectra and the way we estimate the conditional probabilities is effective. PMID:22759570

  12. Accurate Measurements of Multiple-Bond 13C- 1H Coupling Constants from Phase-Sensitive 2D INEPT Spectra

    NASA Astrophysics Data System (ADS)

    Ding, Keyang

    1999-10-01

    Measurements of multiple-bond 13C-1H coupling constants are of great interest for the assignment of nonprotonated 13C resonances and the elucidation of molecular conformation in solution. Usually, the heteronuclear multiple-bond coupling constants were measured either by the JCH splittings mostly in selective 2D spectra or in 3D spectra, which are time consuming, or by the cross peak intensity analysis in 2D quantitative heteronuclear J correlation spectra (1994, G. Zhu, A. Renwick, and A. Bax, J. Magn. Reson. A 110, 257; 1994, A. Bax, G. W. Vuister, S. Grzesiek, F. Delaglio, A. C. Wang, R. Tschudin, and G. Zhu, Methods Enzymol. 239, 79.), which suffer from the accuracy problem caused by the signal-to-noise ratio and the nonpure absorptive peak patterns. Concerted incrementation of the duration for developing proton antiphase magnetization with respect to carbon-13 and the evolution time for proton chemical shift in different steps in a modified INEPT pulse sequence provides a new method for accurate measurements of heteronuclear multiple-bond coupling constants in a single 2D experiment.

  13. 4-Neutrino mass schemes and the likelihood of (3+1)-mass spectra

    NASA Astrophysics Data System (ADS)

    Grimus, W.; Schwetz, T.

    2001-04-01

    We examine the (3+1)-class of 4-neutrino mass spectra within a rigorous statistical analysis based on the Bayesian approach to probability. The data of the Bugey, CDHS and KARMEN experiments are combined by using a likelihood function. Our statistical approach allows us to incorporate solar and atmospheric neutrino data and also the result of the CHOOZ experiment via inequalities which involve elements of the neutrino mixing matrix and are derived from these data. For any short-baseline Δ m^2 we calculate a bound on the LSND transition amplitude A_{μ;e} and find that, in the Δ m^2 A_{μ;e} plane, there is no overlap between the 99% CL region allowed by the latest LSND analysis and the region allowed by our bound on A_{μ;e} at 95% CL; there are some small overlap regions if we take the bound at 99% CL. Therefore, we conclude that, with the existing data, the (3+1)-neutrino mass spectra are not very likely. However, treating the (2+2)-spectra with our method, we find that they are well compatible with all data.

  14. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    SciTech Connect

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Anderson, Kevin K.; Daly, Don S.; Smith, Richard D.

    2005-08-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/- 5 ppm and 1 ppm) and NET value (no constraint, +/- 0.05 and 0.01 on a 0-1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LCMS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate easurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/- 1 ppm and elution time easurements within +/- 0.01 NET.

  15. Combinatorial Approach for Large-scale Identification of Linked Peptides from Tandem Mass Spectrometry Spectra*

    PubMed Central

    Wang, Jian; Anania, Veronica G.; Knott, Jeff; Rush, John; Lill, Jennie R.; Bourne, Philip E.; Bandeira, Nuno

    2014-01-01

    The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein–protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. PMID:24493012

  16. A Global Approach to Accurate and Automatic Quantitative Analysis of NMR Spectra by Complex Least-Squares Curve Fitting

    NASA Astrophysics Data System (ADS)

    Martin, Y. L.

    The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species

  17. Highly accurate isotope composition measurements by a miniature laser ablation mass spectrometer designed for in situ investigations on planetary surfaces

    NASA Astrophysics Data System (ADS)

    Riedo, A.; Meyer, S.; Heredia, B.; Neuland, M. B.; Bieler, A.; Tulej, M.; Leya, I.; Iakovleva, M.; Mezger, K.; Wurz, P.

    2013-10-01

    An experimental procedure for precise and accurate measurements of isotope abundances by a miniature laser ablation mass spectrometer for space research is described. The measurements were conducted on different untreated NIST standards and galena samples by applying pulsed UV laser radiation (266 nm, 3 ns and 20 Hz) for ablation, atomisation, and ionisation of the sample material. Mass spectra of released ions are measured by a reflectron-type time-of-flight mass analyser. A computer controlled performance optimiser was used to operate the system at maximum ion transmission and mass resolution. At optimal experimental conditions, the best relative accuracy and precision achieved for Pb isotope compositions are at the per mill level and were obtained in a range of applied laser irradiances and a defined number of accumulated spectra. A similar relative accuracy and precision was achieved in the study of Pb isotope compositions in terrestrial galena samples. The results for the galena samples are similar to those obtained with a thermal ionisation mass spectrometer (TIMS). The studies of the isotope composition of other elements yielded relative accuracy and precision at the per mill level too, with characteristic instrument parameters for each element. The relative accuracy and precision of the measurements is degrading with lower element/isotope concentration in a sample. For the elements with abundances below 100 ppm these values drop to the percent level. Depending on the isotopic abundances of Pb in minerals, 207Pb/206Pb ages with accuracy in the range of tens of millions of years can be achieved.

  18. Accurate mass measurements for peptide and protein mixtures by using matrix-assisted laser desorption/ionization Fourier transform mass spectrometry.

    PubMed

    Chan, T W D; Duan, L; Sze, T P E

    2002-10-15

    A new analytical scheme based on a combination of scanning FTMS, multiple-ion filling, and potential ramping methods has been developed for accurate molecular mass measurement of peptide and protein mixtures using broadband MALDI-FTMS. The scanning FTMS method alleviates the problems of time-of-flight effect for FTMS with an external MALDI ion source and provides a systematic means of sampling ions of different mass-to-charge ratios. The multiple-ion filling method is an effective way of trapping and retaining ions from successive ion generation/accumulation events. The potential ramping method allows the use of high trapping potentials for effective trapping of ions of high kinetic energies and the use of low trapping potentials for high-resolution detection of the trapped ions. With this analytical scheme, high-resolution broadband MALDI mass spectra covering a wide mass range of 1000-5700 Da were obtained. For peptide mixtures of mass range 1000-3500 Da, calibration errors of low part-per-millions were demonstrated using a parabolic calibration equation f2 = ML1/m2 + ML2/m + ML3, where f is the measured cyclotron frequency and ML1, ML2, and ML3 are calibration constants.

  19. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    PubMed Central

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Smith, Richard D.

    2007-01-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/− 5 ppm and 1 ppm) and NET value (no constraint, +/− 0.05 and 0.01 on a 0–1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LC-MS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate measurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/− 1 ppm and elution time measurements within +/− 0.01 NET. PMID:15979333

  20. Analysis of hydraulic fracturing flowback and produced waters using accurate mass: identification of ethoxylated surfactants.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Blotevogel, Jens; Borch, Thomas

    2014-10-07

    Two series of ethylene oxide (EO) surfactants, polyethylene glycols (PEGs from EO3 to EO33) and linear alkyl ethoxylates (LAEs C-9 to C-15 with EO3-EO28), were identified in hydraulic fracturing flowback and produced water using a new application of the Kendrick mass defect and liquid chromatography/quadrupole-time-of-flight mass spectrometry. The Kendrick mass defect differentiates the proton, ammonium, and sodium adducts in both singly and doubly charged forms. A structural model of adduct formation is presented, and binding constants are calculated, which is based on a spherical cagelike conformation, where the central cation (NH4(+) or Na(+)) is coordinated with ether oxygens. A major purpose of the study was the identification of the ethylene oxide (EO) surfactants and the construction of a database with accurate masses and retention times in order to unravel the mass spectral complexity of surfactant mixtures used in hydraulic fracturing fluids. For example, over 500 accurate mass assignments are made in a few seconds of computer time, which then is used as a fingerprint chromatogram of the water samples. This technique is applied to a series of flowback and produced water samples to illustrate the usefulness of ethoxylate "fingerprinting", in a first application to monitor water quality that results from fluids used in hydraulic fracturing.

  1. Excited State Mass Spectra of Ω0 c Baryon

    NASA Astrophysics Data System (ADS)

    Shah, Z.; Thakkar, K.; Rai, A. K.; Vinodkumar, P. C.

    2016-10-01

    We have calculated the radial and orbital excited states of singly charmed baryon Oc using the Hypercentral Constituent Quark Model (hCQM). The confinement potential is assumed as coulomb plus power potential (CPP V ). The ground state and excited state masses are determined with and with out first order correction to the potential. Furthermore, we plot graph between Mass(M) → Potential Index(v). Our calculated results are in good agreement with experimental and other theoretical predictions.

  2. Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers.

    PubMed

    Hopley, Chris; Bristow, Tony; Lubben, Anneke; Simpson, Alec; Bull, Elaine; Klagkou, Katerina; Herniman, Julie; Langley, John

    2008-06-01

    Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments - a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns. The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS. The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC

  3. Isotopic Ratio Outlier Analysis of the S. cerevisiae Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery.

    PubMed

    Qiu, Yunping; Moir, Robyn; Willis, Ian; Beecher, Chris; Tsai, Yu-Hsuan; Garrett, Timothy J; Yost, Richard A; Kurland, Irwin J

    2016-03-01

    Isotopic ratio outlier analysis (IROA) is a (13)C metabolomics profiling method that eliminates sample to sample variance, discriminates against noise and artifacts, and improves identification of compounds, previously done with accurate mass liquid chromatography/mass spectrometry (LC/MS). This is the first report using IROA technology in combination with accurate mass gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), here used to examine the S. cerevisiae metabolome. S. cerevisiae was grown in YNB media, containing randomized 95% (13)C, or 5%(13)C glucose as the single carbon source, in order that the isotopomer pattern of all metabolites would mirror the labeled glucose. When these IROA experiments are combined, the abundance of the heavy isotopologues in the 5%(13)C extracts, or light isotopologues in the 95%(13)C extracts, follows the binomial distribution, showing mirrored peak pairs for the molecular ion. The mass difference between the (12)C monoisotopic and the (13)C monoisotopic equals the number of carbons in the molecules. The IROA-GC/MS protocol developed, using both chemical and electron ionization, extends the information acquired from the isotopic peak patterns for formulas generation. The process that can be formulated as an algorithm, in which the number of carbons, as well as the number of methoximations and silylations are used as search constraints. In electron impact (EI/IROA) spectra, the artifactual peaks are identified and easily removed, which has the potential to generate "clean" EI libraries. The combination of chemical ionization (CI) IROA and EI/IROA affords a metabolite identification procedure that enables the identification of coeluting metabolites, and allowed us to characterize 126 metabolites in the current study.

  4. Application of the accurate mass and time tag approach in studies of the human blood lipidome

    PubMed Central

    Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. PMID:18502191

  5. Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When collision induced dissociation is used to fragment phosphorylated peptides during tandem mass spectrometry (MS2), an ion exhibiting the neutral loss of phosphoric acid can be the major product. The neutral loss ion can then be fragmented during MS3 for additional resolution of the peptide sequ...

  6. iPE-MMR: An integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

    PubMed Central

    Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won

    2010-01-01

    Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE-MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn; 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. By combining these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. PMID:20863060

  7. Search and decoy: the automatic identification of mass spectra.

    PubMed

    Eisenacher, Martin; Kohl, Michael; Turewicz, Michael; Koch, Markus-Hermann; Uszkoreit, Julian; Stephan, Christian

    2012-01-01

    In recent years, the generation and interpretation of MS/MS spectra for the identification of peptides and proteins has matured to a frequently used automatic workflow in Proteomics. Several software solutions for the automated analysis of MS/MS spectra allow for high-throughput/high-performance analyses of complex samples. Related to MS/MS searches, target-decoy approaches have gained more and more popularity: in a "decoy" part of the search database nonexistent sequences mimic real sequences (the "target" sequences). With their help, the number of falsely identified peptides/proteins can be estimated after a search and the resulting protein list can be cut at a specified false discovery rate (FDR). This is an essential prerequisite for all quantitative approaches, as they rely on correct identifications. Especially the label-free approach "spectral counting"-gaining more and more popularity due to low costs and simplicity-depends directly on the correctness of peptide-spectrum matches (PSMs). This work's aim is to describe five popular search engines-especially their general properties regarding protein identification, but also their quantification abilities, if those go beyond spectral counting. By doing so, Proteomics researchers are enabled to compare their features and to choose an appropriate solution for their specific question. Furthermore, the search engines are applied to a spectrum data set generated from a complex sample with a Thermo LTQ Velos OrbiTrap (Thermo Fisher Scientific, Waltham, MA, USA). The results of the search engines are compared, e.g., regarding time requirements, peptides and proteins found, and the search engines' behavior using the decoy approach.

  8. Accurate mass replacement method for the sediment concentration measurement with a constant volume container

    NASA Astrophysics Data System (ADS)

    Ban, Yunyun; Chen, Tianqin; Yan, Jun; Lei, Tingwu

    2017-04-01

    The measurement of sediment concentration in water is of great importance in soil erosion research and soil and water loss monitoring systems. The traditional weighing method has long been the foundation of all the other measuring methods and instrument calibration. The development of a new method to replace the traditional oven-drying method is of interest in research and practice for the quick and efficient measurement of sediment concentration, especially field measurements. A new method is advanced in this study for accurately measuring the sediment concentration based on the accurate measurement of the mass of the sediment-water mixture in the confined constant volume container (CVC). A sediment-laden water sample is put into the CVC to determine its mass before the CVC is filled with water and weighed again for the total mass of the water and sediments in the container. The known volume of the CVC, the mass of sediment-laden water, and sediment particle density are used to calculate the mass of water, which is replaced by sediments, therefore sediment concentration of the sample is calculated. The influence of water temperature was corrected by measuring water density to determine the temperature of water before measurements were conducted. The CVC was used to eliminate the surface tension effect so as to obtain the accurate volume of water and sediment mixture. Experimental results showed that the method was capable of measuring the sediment concentration from 0.5 up to 1200 kg m‑3. A good liner relationship existed between the designed and measured sediment concentrations with all the coefficients of determination greater than 0.999 and the averaged relative error less than 0.2%. All of these seem to indicate that the new method is capable of measuring a full range of sediment concentration above 0.5 kg m‑3 to replace the traditional oven-drying method as a standard method for evaluating and calibrating other methods.

  9. Determination of accurate protein monoisotopic mass with the most abundant mass measurable using high-resolution mass spectrometry.

    PubMed

    Chen, Ya-Fen; Chang, C Allen; Lin, Yu-Hsuan; Tsay, Yeou-Guang

    2013-09-01

    While recent developments in mass spectrometry enable direct evaluation of monoisotopic masses (M(mi)) of smaller compounds, protein M(mi) is mostly determined based on its relationship to average mass (Mav). Here, we propose an alternative approach to determining protein M(mi) based on its correlation with the most abundant mass (M(ma)) measurable using high-resolution mass spectrometry. To test this supposition, we first empirically calculated M(mi) and M(ma) of 6158 Escherichia coli proteins, which helped serendipitously uncover a linear correlation between these two protein masses. With the relationship characterized, liquid chromatography-mass spectrometry was employed to measure M(ma) of protein samples in its ion cluster with the highest signal in the mass spectrum. Generally, our method produces a short series of likely M(mi) in 1-Da steps, and the probability of each likely M(mi) is assigned statistically. It is remarkable that the mass error of this M(mi) is as miniscule as a few parts per million, indicating that our method is capable of determining protein M(mi) with high accuracy. Benefitting from the outstanding performance of modern mass spectrometry, our approach is a significant improvement over others and should be of great utility in the rapid assessment of protein primary structures.

  10. Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans.

    PubMed

    Dhieb, C; Normand, A C; L'Ollivier, C; Gautier, M; Vranckx, K; El Euch, D; Chaker, E; Hendrickx, M; Dalle, F; Sadfi, N; Piarroux, R; Ranque, S

    2015-02-01

    Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI-TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI-TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well-characterized collection strains, using a Microflex(TM) system and Biotyper(TM) software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI-TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra-clade spectra recognition were unsuccessful. In conclusion, MALDI-TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI-TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory.

  11. Mass spectra of heavy ions near comet Halley

    NASA Technical Reports Server (NTRS)

    Korth, A.; Richter, A. K.; Loidl, A.; Anderson, K. A.; Carlson, C. W.

    1986-01-01

    The heavy-ion analyzer, RPA2-PICCA, aboard the Giotto spacecraft, detected the first cometary ions at a distance of about 1.05 million km from the nucleus of comet Halley. In the inner coma the major ions identified are associated with the H2O, CO and CO2 groups. Ions of larger atomic mass unit are also present, corresponding possibly to various hydrocarbons, heavy metals of the iron-group or to sulphur compounds.

  12. Lateral Mixing DRI Analysis: Submesoscale Water-Mass Spectra

    DTIC Science & Technology

    2013-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Lateral Mixing DRI Analysis: Submesoscale Water-Mass... submesoscale on horizontal lengthscales of 0.1-10 km. These scales of the subinertial fields are not well understood dynamically for subinertial...program to determine submesoscale variability in the Sargasso Sea under weak-to-moderate mesoscale conditions. Two sites were examined, a quiet site

  13. Directed Sample Interrogation Utilizing an Accurate Mass Exclusion-Based Data-Dependent Acquisition Strategy (AMEx)

    PubMed Central

    Rudomin, Emily L.; Carr, Steven A.; Jaffe, Jacob D.

    2009-01-01

    The ability to perform thorough sampling is of critical importance when using mass spectrometry to characterize complex proteomic mixtures. A common approach is to re-interrogate a sample multiple times by LC-MS/MS. However, the conventional data-dependent acquisition methods that are typically used in proteomics studies will often redundantly sample high-intensity precursor ions while failing to sample low-intensity precursors entirely. We describe a method wherein the masses of successfully identified peptides are used to generate an accurate mass exclusion list such that those precursors are not selected for sequencing during subsequent analyses. We performed multiple concatenated analytical runs to sample a complex cell lysate, using either accurate mass exclusion-based data-dependent acquisition (AMEx) or standard data-dependent acquisition, and found that utilization of AMEx on an ESI-Orbitrap instrument significantly increases the total number of validated peptide identifications relative to a standard DDA approach. The additional identified peptides represent precursor ions that exhibit low signal intensity in the sample. Increasing the total number of peptide identifications augmented the number of proteins identified, as well as improved the sequence coverage of those proteins. Together, these data indicate that using AMEx is an effective strategy to improve the characterization of complex proteomic mixtures. PMID:19344186

  14. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).

    PubMed

    Rudomin, Emily L; Carr, Steven A; Jaffe, Jacob D

    2009-06-01

    The ability to perform thorough sampling is of critical importance when using mass spectrometry to characterize complex proteomic mixtures. A common approach is to reinterrogate a sample multiple times by LC-MS/MS. However, the conventional data-dependent acquisition methods that are typically used in proteomics studies will often redundantly sample high-intensity precursor ions while failing to sample low-intensity precursors entirely. We describe a method wherein the masses of successfully identified peptides are used to generate an accurate mass exclusion list such that those precursors are not selected for sequencing during subsequent analyses. We performed multiple concatenated analytical runs to sample a complex cell lysate, using either accurate mass exclusion-based data-dependent acquisition (AMEx) or standard data-dependent acquisition, and found that utilization of AMEx on an ESI-Orbitrap instrument significantly increases the total number of validated peptide identifications relative to a standard DDA approach. The additional identified peptides represent precursor ions that exhibit low signal intensity in the sample. Increasing the total number of peptide identifications augmented the number of proteins identified, as well as improved the sequence coverage of those proteins. Together, these data indicate that using AMEx is an effective strategy to improve the characterization of complex proteomic mixtures.

  15. Optical, mass, and auger spectra from e-bombarded KBr

    SciTech Connect

    Arakawa, E.T.; Kamada, M.

    1988-01-01

    We have measured the mass spectrum and optical emission lines of neutral potassium atoms ejected from KBr at T = 300/degree/K and 443/degree/K bombarded by 2-keV electrons. The room-temperature data may be complicated by the nonstoichiometry of the alkali-enriched sample surface and seem difficult to interpret. The high-temperature sample, which maintains the proper stoichiometry, produces data in support of gas-phase excitation of alkali atoms desorbed from the surface. 15 refs., 4 figs.

  16. Accurate Mass Determination of the Ancient White Dwarf ER 8 Through Astrometric Microlensing

    NASA Astrophysics Data System (ADS)

    Sahu, Kailash

    2005-07-01

    We propose to determine the mass of the very cool white dwarf ER 8 through astrometric microlensing. We have predicted that ER 8 will pass very close to a 15th-mag background star in January 2006, with an impact parameter of less than 0.05 arcsec. As it passes in front, it will cause a deflection of the background star's image by >8 milliarcsec, an amount easily detectable with HST/FGS. The gravitational deflection angle depends only on the distances and relative positions of the stars, and on the mass of the white dwarf. Since the distances and positions can be determined precisely before the event, the astrometric measurement offers a unique and direct method to measure the mass of the white dwarf to high accuracy {<5%}. Unlike all other stellar mass determinations, this technique works for single stars {but only if they are nearby and of sufficient mass}. The mass of ER 8 is of special interest because it is a member of the Galactic halo, and appears to be the oldest known field white dwarf. This object can thus set a lower limit on the age of the Galactic halo, but since white-dwarf cooling rates depend on their masses, the mass is a necessary ingredient in the age determination. As a byproduct, we will obtain an accurate parallax for ER 8, and thus its luminosity and {from its effective temperature} its radius. Such quantities are at present rather poorly known for the coolest white dwarfs, and will provide strong constraints on white-dwarf physics.

  17. Accurate Mass Determination of the Ancient White Dwarf ER 8 Through Astrometric Microlensing

    NASA Astrophysics Data System (ADS)

    Sahu, Kailash

    2004-07-01

    We propose to determine the mass of the very cool white dwarf ER 8 through astrometric microlensing. We have predicted that ER 8 will pass very close to a 15th-mag background star in January 2006, with an impact parameter of less than 0.05 arcsec. As it passes in front, it will cause a deflection of the background star's image by >8 milliarcsec, an amount easily detectable with HST/FGS. The gravitational deflection angle depends only on the distances and relative positions of the stars, and on the mass of the white dwarf. Since the distances and positions can be determined precisely before the event, the astrometric measurement offers a unique and direct method to measure the mass of the white dwarf to high accuracy {<5%}. Unlike all other stellar mass determinations, this technique works for single stars {but only if they are nearby and of sufficient mass}. The mass of ER 8 is of special interest because it is a member of the Galactic halo, and appears to be the oldest known field white dwarf. This object can thus set a lower limit on the age of the Galactic halo, but since white-dwarf cooling rates depend on their masses, the mass is a necessary ingredient in the age determination. As a byproduct, we will obtain an accurate parallax for ER 8, and thus its luminosity and {from its effective temperature} its radius. Such quantities are at present rather poorly known for the coolest white dwarfs, and will provide strong constraints on white-dwarf physics.

  18. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

    PubMed Central

    Lipton, Mary S.; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim; Hixson, Kim K.; Kostandarithes, Heather; Masselon, Christophe; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Stritmatter, Eric; Tolić, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical. PMID:12177431

  19. Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

    NASA Astrophysics Data System (ADS)

    Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  20. Identification of "known unknowns" utilizing accurate mass data and ChemSpider.

    PubMed

    Little, James L; Williams, Antony J; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  1. Cluster abundance in chameleon f(R) gravity I: toward an accurate halo mass function prediction

    NASA Astrophysics Data System (ADS)

    Cataneo, Matteo; Rapetti, David; Lombriser, Lucas; Li, Baojiu

    2016-12-01

    We refine the mass and environment dependent spherical collapse model of chameleon f(R) gravity by calibrating a phenomenological correction inspired by the parameterized post-Friedmann framework against high-resolution N-body simulations. We employ our method to predict the corresponding modified halo mass function, and provide fitting formulas to calculate the enhancement of the f(R) halo abundance with respect to that of General Relativity (GR) within a precision of lesssim 5% from the results obtained in the simulations. Similar accuracy can be achieved for the full f(R) mass function on the condition that the modeling of the reference GR abundance of halos is accurate at the percent level. We use our fits to forecast constraints on the additional scalar degree of freedom of the theory, finding that upper bounds competitive with current Solar System tests are within reach of cluster number count analyses from ongoing and upcoming surveys at much larger scales. Importantly, the flexibility of our method allows also for this to be applied to other scalar-tensor theories characterized by a mass and environment dependent spherical collapse.

  2. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments

    PubMed Central

    Eter, Wael A.; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin

    2016-01-01

    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, 111In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of 111In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers. PMID:27080529

  3. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments.

    PubMed

    Eter, Wael A; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin

    2016-04-15

    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, (111)In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of (111)In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers.

  4. SPARC: Mass Models for 175 Disk Galaxies with Spitzer Photometry and Accurate Rotation Curves

    NASA Astrophysics Data System (ADS)

    Lelli, Federico; McGaugh, Stacy S.; Schombert, James M.

    2016-12-01

    We introduce SPARC (Spitzer Photometry and Accurate Rotation Curves): a sample of 175 nearby galaxies with new surface photometry at 3.6 μm and high-quality rotation curves from previous H i/Hα studies. SPARC spans a broad range of morphologies (S0 to Irr), luminosities (∼5 dex), and surface brightnesses (∼4 dex). We derive [3.6] surface photometry and study structural relations of stellar and gas disks. We find that both the stellar mass–H i mass relation and the stellar radius–H i radius relation have significant intrinsic scatter, while the H i mass–radius relation is extremely tight. We build detailed mass models and quantify the ratio of baryonic to observed velocity (V bar/V obs) for different characteristic radii and values of the stellar mass-to-light ratio (ϒ⋆) at [3.6]. Assuming ϒ⋆ ≃ 0.5 M ⊙/L ⊙ (as suggested by stellar population models), we find that (i) the gas fraction linearly correlates with total luminosity (ii) the transition from star-dominated to gas-dominated galaxies roughly corresponds to the transition from spiral galaxies to dwarf irregulars, in line with density wave theory; and (iii) V bar/V obs varies with luminosity and surface brightness: high-mass, high-surface-brightness galaxies are nearly maximal, while low-mass, low-surface-brightness galaxies are submaximal. These basic properties are lost for low values of ϒ⋆ ≃ 0.2 M ⊙/L ⊙ as suggested by the DiskMass survey. The mean maximum-disk limit in bright galaxies is ϒ⋆ ≃ 0.7 M ⊙/L ⊙ at [3.6]. The SPARC data are publicly available and represent an ideal test bed for models of galaxy formation.

  5. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

    NASA Astrophysics Data System (ADS)

    Lu, Jonathan; Trnka, Michael J.; Roh, Soung-Hun; Robinson, Philip J. J.; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L.; Guan, Shenheng

    2015-12-01

    Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise.

  6. Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

    PubMed

    Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

    2016-08-17

    A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching.

  7. Quantitation of Insulin-Like Growth Factor 1 in Serum by Liquid Chromatography High Resolution Accurate-Mass Mass Spectrometry.

    PubMed

    Ketha, Hemamalini; Singh, Ravinder J

    2016-01-01

    Insulin-like growth factor 1 (IGF-1) is a 70 amino acid peptide hormone which acts as the principal mediator of the effects of growth hormone (GH). Due to a wide variability in circulating concentration of GH, IGF-1 quantitation is the first step in the diagnosis of GH excess or deficiency. Majority (>95 %) of IGF-1 circulates as a ternary complex along with its principle binding protein insulin-like growth factor 1 binding protein 3 (IGFBP-3) and acid labile subunit. The assay design approach for IGF-1 quantitation has to include a step to dissociate IGF-1 from its ternary complex. Several commercial assays employ a buffer containing acidified ethanol to achieve this. Despite several modifications, commercially available immunoassays have been shown to have challenges with interference from IGFBP-3. Additionally, inter-method comparison between IGF-1 immunoassays has been shown to be suboptimal. Mass spectrometry has been utilized for quantitation of IGF-1. In this chapter a liquid chromatography high resolution accurate-mass mass spectrometry (LC-HRAMS) based method for IGF-1 quantitation has been described.

  8. Assessing temporal flux of plant hormones in stored processing potatoes using high definition accurate mass spectrometry

    PubMed Central

    Ordaz-Ortiz, José Juan; Foukaraki, Sofia; Terry, Leon Alexander

    2015-01-01

    Plant hormones are important molecules which at low concentration can regulate various physiological processes. Mass spectrometry has become a powerful technique for the quantification of multiple classes of plant hormones because of its high sensitivity and selectivity. We developed a new ultrahigh pressure liquid chromatography–full-scan high-definition accurate mass spectrometry method, for simultaneous determination of abscisic acid and four metabolites phaseic acid, dihydrophaseic acid, 7′-hydroxy-abscisic acid and abscisic acid glucose ester, cytokinins zeatin, zeatin riboside, gibberellins (GA1, GA3, GA4 and GA7) and indole-3-acetyl-L-aspartic acid. We measured the amount of plant hormones in the flesh and skin of two processing potato cvs. Sylvana and Russet Burbank stored for up to 30 weeks at 6 °C under ambient air conditions. Herein, we report for the first time that abscisic acid glucose ester seems to accumulate in the skin of potato tubers throughout storage time. The method achieved a lowest limit of detection of 0.22 ng g−1 of dry weight and a limit of quantification of 0.74 ng g−1 dry weight (zeatin riboside), and was able to recover, detect and quantify a total of 12 plant hormones spiked on flesh and skin of potato tubers. In addition, the mass accuracy for all compounds (<5 ppm) was evaluated. PMID:26504563

  9. Assessing temporal flux of plant hormones in stored processing potatoes using high definition accurate mass spectrometry.

    PubMed

    Ordaz-Ortiz, José Juan; Foukaraki, Sofia; Terry, Leon Alexander

    2015-01-01

    Plant hormones are important molecules which at low concentration can regulate various physiological processes. Mass spectrometry has become a powerful technique for the quantification of multiple classes of plant hormones because of its high sensitivity and selectivity. We developed a new ultrahigh pressure liquid chromatography-full-scan high-definition accurate mass spectrometry method, for simultaneous determination of abscisic acid and four metabolites phaseic acid, dihydrophaseic acid, 7'-hydroxy-abscisic acid and abscisic acid glucose ester, cytokinins zeatin, zeatin riboside, gibberellins (GA1, GA3, GA4 and GA7) and indole-3-acetyl-L-aspartic acid. We measured the amount of plant hormones in the flesh and skin of two processing potato cvs. Sylvana and Russet Burbank stored for up to 30 weeks at 6 °C under ambient air conditions. Herein, we report for the first time that abscisic acid glucose ester seems to accumulate in the skin of potato tubers throughout storage time. The method achieved a lowest limit of detection of 0.22 ng g(-1) of dry weight and a limit of quantification of 0.74 ng g(-1) dry weight (zeatin riboside), and was able to recover, detect and quantify a total of 12 plant hormones spiked on flesh and skin of potato tubers. In addition, the mass accuracy for all compounds (<5 ppm) was evaluated.

  10. Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams.

    PubMed

    Shon, Hyun Kyong; Yoon, Sohee; Moon, Jeong Hee; Lee, Tae Geol

    2016-06-09

    The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

  11. Automatic Preocessing of Impact Ionization Mass Spectra Obtained by Cassini CDA

    NASA Astrophysics Data System (ADS)

    Villeneuve, M.

    2015-12-01

    Since Cassini's arrival at Saturn in 2004, the Comic Dust Analyzer (CDA) has recorded nearly 200,000 mass spectra of dust particles. A majority of this data has been collected in Saturn's diffuse E ring where sodium salts embedded in water ice particles indicate that many particles are in fact frozen droplets from Enceladus' subsurface ocean that have been expelled from cracks in the icy crust. So far only a small fraction of the obtained spectra have been processed because the steps in processing the spectra require human manipulation. We developed an automatic processing pipeline for CDA mass spectra which will consistently analyze this data. The preprocessing steps are to de-noise the spectra, determine and remove the baseline, calculate the correct stretch parameter, and finally to identify elements and compounds in the spectra. With the E ring constantly evolving due to embedded active moons, this data will provide valuable information about the source of the E ring, the subsurface of Saturn's ice moon Enceladus, as well as about the dynamics of the ring itself.

  12. In-Depth Glycoproteomic Characterization of γ-Conglutin by High-Resolution Accurate Mass Spectrometry

    PubMed Central

    Schiarea, Silvia; Arnoldi, Lolita; Fanelli, Roberto; De Combarieu, Eric; Chiabrando, Chiara

    2013-01-01

    The molecular characterization of bioactive food components is necessary for understanding the mechanisms of their beneficial or detrimental effects on human health. This study focused on γ-conglutin, a well-known lupin seed N-glycoprotein with health-promoting properties and controversial allergenic potential. Given the importance of N-glycosylation for the functional and structural characteristics of proteins, we studied the purified protein by a mass spectrometry-based glycoproteomic approach able to identify the structure, micro-heterogeneity and attachment site of the bound N-glycan(s), and to provide extensive coverage of the protein sequence. The peptide/N-glycopeptide mixtures generated by enzymatic digestion (with or without N-deglycosylation) were analyzed by high-resolution accurate mass liquid chromatography–multi-stage mass spectrometry. The four main micro-heterogeneous variants of the single N-glycan bound to γ-conglutin were identified as Man2(Xyl) (Fuc) GlcNAc2, Man3(Xyl) (Fuc) GlcNAc2, GlcNAcMan3(Xyl) (Fuc) GlcNAc2 and GlcNAc 2Man3(Xyl) (Fuc) GlcNAc2. These carry both core β1,2-xylose and core α1-3-fucose (well known Cross-Reactive Carbohydrate Determinants), but corresponding fucose-free variants were also identified as minor components. The N-glycan was proven to reside on Asn131, one of the two potential N-glycosylation sites. The extensive coverage of the γ-conglutin amino acid sequence suggested three alternative N-termini of the small subunit, that were later confirmed by direct-infusion Orbitrap mass spectrometry analysis of the intact subunit. PMID:24069245

  13. MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

    PubMed

    Tabb, David L; Thompson, Melissa R; Khalsa-Moyers, Gurusahai; VerBerkmoes, Nathan C; McDonald, W Hayes

    2005-08-01

    Shotgun proteomics experiments require the collection of thousands of tandem mass spectra; these sets of data will continue to grow as new instruments become available that can scan at even higher rates. Such data contain substantial amounts of redundancy with spectra from a particular peptide being acquired many times during a single LC-MS/MS experiment. In this article, we present MS2Grouper, an algorithm that detects spectral duplication, assesses groups of related spectra, and replaces these groups with synthetic representative spectra. Errors in detecting spectral similarity are corrected using a paraclique criterion-spectra are only assessed as groups if they are part of a clique of at least three completely interrelated spectra or are subsequently added to such cliques by being similar to all but one of the clique members. A greedy algorithm constructs a representative spectrum for each group by iteratively removing the tallest peaks from the spectral collection and matching to peaks in the other spectra. This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides.

  14. CAPILLARY ELECTROPHORESIS-ELECTROSPRAY MASS SPECTRA OF THE HERBICIDES PARAQUAT AND DIQUAT

    EPA Science Inventory

    The positive ion electrospray mass spectra of the quaternary ammonium salt herbicides paraquat and diquat are examined by on-line separation with capillary electrophoresis (CE) and by direct infusion of the analytes. The analytes are separated by CE in 7-10 min at pH 3.9 in 50% m...

  15. Localization and mass spectra of various matter fields on scalar-tensor brane

    SciTech Connect

    Xie, Qun-Ying; Zhao, Zhen-Hua; Zhong, Yi; Yang, Jie; Zhou, Xiang-Nan

    2015-03-10

    Recently, a new scalar-tensor braneworld model was presented in [http://dx.doi.org/10.1103/PhysRevD.86.127502]. It not only solves the gauge hierarchy problem but also reproduces a correct Friedmann-like equation on the brane. In this new model, there are two different brane solutions, for which the mass spectra of gravity on the brane are the same. In this paper, we investigate localization and mass spectra of various bulk matter fields (i.e., scalar, vector, Kalb-Ramond, and fermion fields) on the brane. It is shown that the zero modes of all the matter fields can be localized on the positive tension brane under some conditions, and the mass spectra of each kind of bulk matter field for the two brane solutions are different except for some special cases, which implies that the two brane solutions are not physically equivalent. When the coupling constants between the dilaton and bulk matter fields take special values, the mass spectra for both solutions are the same, and the scalar and vector zero modes are localized on the negative tension brane, while the KR zero mode is still localized on the positive tension brane.

  16. Fatty acids composition of Caenorhabditis elegans using accurate mass GCMS-QTOF.

    PubMed

    Henry, Parise; Owopetu, Olufunmilayo; Adisa, Demilade; Nguyen, Thao; Anthony, Kevin; Ijoni-Animadu, David; Jamadar, Sakha; Abdel-Rahman, Fawzia; Saleh, Mahmoud A

    2016-08-02

    The free living nematode Caenorhabditis elegans is a proven model organism for lipid metabolism research. Total lipids of C. elegans were extracted using chloroform and methanol in 2:1 ratio (v/v). Fatty acids composition of the extracted total lipids was converted to their corresponding fatty acids methyl esters (FAMEs) and analyzed by gas chromatography/accurate mass quadrupole time of flight mass spectrometry using both electron ionization and chemical ionization techniques. Twenty-eight fatty acids consisting of 12 to 22 carbon atoms were identified, 65% of them were unsaturated. Fatty acids containing 12 to17 carbons were mostly saturated with stearic acid (18:0) as the major constituent. Several branched-chain fatty acids were identified. Methyl-14-methylhexadecanoate (iso- 17:0) was the major identified branched fatty acid. This is the first report to detect the intact molecular parent ions of the identified fatty acids in C. elegans using chemical ionization compared to electron ionization which produced fragmentations of the FAMEs.

  17. Mass spectrometry in Earth sciences: the precise and accurate measurement of time.

    PubMed

    Schaltegger, Urs; Wotzlaw, Jörn-Frederik; Ovtcharova, Maria; Chiaradia, Massimo; Spikings, Richard

    2014-01-01

    Precise determinations of the isotopic compositions of a variety of elements is a widely applied tool in Earth sciences. Isotope ratios are used to quantify rates of geological processes that occurred during the previous 4.5 billion years, and also at the present time. An outstanding application is geochronology, which utilizes the production of radiogenic daughter isotopes by the radioactive decay of parent isotopes. Geochronological tools, involving isotopic analysis of selected elements from smallest volumes of minerals by thermal ionization mass spectrometry, provide precise and accurate measurements of time throughout the geological history of our planet over nine orders of magnitude, from the accretion of the proto-planetary disk, to the timing of the last glaciation. This article summarizes the recent efforts of the Isotope Geochemistry, Geochronology and Thermochronology research group at the University of Geneva to advance the U-Pb geochronological tool to achieve unprecedented precision and accuracy, and presents two examples of its application to two significant open questions in Earth sciences: what are the triggers and timescales of volcanic supereruptions, and what were the causes of mass extinctions in the geological past, driven by global climatic and environmental deterioration?

  18. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    PubMed

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data.

  19. ULTRAVIOLET EMISSION-LINE CORRELATIONS IN HST/COS SPECTRA OF ACTIVE GALACTIC NUCLEI: SINGLE-EPOCH BLACK HOLE MASSES

    SciTech Connect

    Tilton, Evan M.; Shull, J. Michael E-mail: michael.shull@colorado.edu

    2013-09-01

    Effective methods of measuring supermassive black hole masses in active galactic nuclei (AGNs) are of critical importance to studies of galaxy evolution. While there has been much success in obtaining masses through reverberation mapping, the extensive observing time required by this method has limited the practicality of applying it to large samples at a variety of redshifts. This limitation highlights the need to estimate these masses using single-epoch spectroscopy of ultraviolet (UV) emission lines. We use UV spectra of 44 AGNs from HST/COS, the International Ultraviolet Explorer, and the Far Ultraviolet Spectroscopic Explorer of the C IV {lambda}1549, O VI {lambda}1035, O III] {lambda}1664, He II {lambda}1640, C II {lambda}1335, and Mg II {lambda}2800 emission lines and explore their potential as tracers of the broad-line region and supermassive black hole mass. The higher signal-to-noise ratio and better spectral resolution of the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope (HST) resolve AGN intrinsic absorption and produce more accurate line widths. From these, we test the viability of mass-scaling relationships based on line widths and luminosities and carry out a principal component analysis based on line luminosities, widths, skewness, and kurtosis. At L{sub 1450} {<=} 10{sup 45} erg s{sup -1}, the UV line luminosities correlate well with H{beta}, as does the 1450 A continuum luminosity. We find that C IV, O VI, and Mg II can be used as reasonably accurate estimators of AGN black hole masses, while He II and C II are uncorrelated.

  20. lipID--a software tool for automated assignment of lipids in mass spectra.

    PubMed

    Hübner, Göran; Crone, Catharina; Lindner, Buko

    2009-12-01

    A new software tool called lipID is reported, which supports the identification of glycerophospholipids, glycosphingolipids, fatty acids and small oligosaccharides in mass spectra. The user-extendable software is a Microsoft (MS) Excel Add-In developed using Visual Basic for Applications and is compatible with all Versions of MS Excel since MS Excel 97. It processes singly given mass-to-charge values as well as mass lists considering a number of user-defined options. The software's mode of operation, usage and options are explained and the benefits and limitations of the tool are illustrated by means of three typical analytical examples of lipid analyses.

  1. Interpretation of collision-induced fragmentation tandem mass spectra of posttranslationally modified peptides.

    PubMed

    Bunkenborg, Jakob; Matthiesen, Rune

    2007-01-01

    Tandem collision-induced dissociation (CID) mass spectrometry (MS) provides a sensitive means of analyzing the amino acid sequence of peptides. Modern MS instrumentation is capable of rapidly generating many thousands of tandem mass spectra, and protein database search engines have been developed to cope with this avalanche of data. In most studies, there is a schism between discarding perfectly valid data and including nonsensical peptide identifications--this is currently a major bottleneck in data analysis and it calls for manual evaluation of the data. Especially for posttranslationally modified peptides, there is a need for manual validation of the data because search algorithms seldom have been optimized for the identification of modified peptides and because there are many pitfalls for the unwary. This chapter describes some of the issues that should be considered when interpreting and validating low-energy CID tandem mass spectra and gives some useful tables to aid this process.

  2. Importance of semicore states in GW calculations for simulating accurately the photoemission spectra of metal phthalocyanine molecules

    NASA Astrophysics Data System (ADS)

    Umari, P.; Fabris, S.

    2012-05-01

    The quasi-particle energy levels of the Zn-Phthalocyanine (ZnPc) molecule calculated with the GW approximation are shown to depend sensitively on the explicit description of the metal-center semicore states. We find that the calculated GW energy levels are in good agreement with the measured experimental photoemission spectra only when explicitly including the Zn 3s and 3p semicore states in the valence. The main origin of this effect is traced back to the exchange term in the self-energy GW approximation. Based on this finding, we propose a simplified approach for correcting GW calculations of metal phthalocyanine molecules that avoids the time-consuming explicit treatment of the metal semicore states. Our method allows for speeding up the calculations without compromising the accuracy of the computed spectra.

  3. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2014-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  4. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2015-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  5. Simulation of Accurate Vibrationally Resolved Electronic Spectra: the Integrated Time-Dependent and Time-Independent Framework

    NASA Astrophysics Data System (ADS)

    Baiardi, Alberto; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien

    2014-06-01

    Two parallel theories including Franck-Condon, Herzberg-Teller and Duschinsky (i.e., mode mixing) effects, allowing different approximations for the description of excited state PES have been developed in order to simulate realistic, asymmetric, electronic spectra line-shapes taking into account the vibrational structure: the so-called sum-over-states or time-independent (TI) method and the alternative time-dependent (TD) approach, which exploits the properties of the Fourier transform. The integrated TI-TD procedure included within a general purpose QM code [1,2], allows to compute one photon absorption, fluorescence, phosphorescence, electronic circular dichroism, circularly polarized luminescence and resonance Raman spectra. Combining both approaches, which use a single set of starting data, permits to profit from their respective advantages and minimize their respective limits: the time-dependent route automatically includes all vibrational states and, possibly, temperature effects, while the time-independent route allows to identify and assign single vibronic transitions. Interpretation, analysis and assignment of experimental spectra based on integrated TI-TD vibronic computations will be illustrated for challenging cases of medium-sized open-shell systems in the gas and condensed phases with inclusion of leading anharmonic effects. 1. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini Phys. Chem. Chem. Phys, 14, 12404, (2012) 2. A. Baiardi, V. Barone, J. Bloino J. Chem. Theory Comput., 9, 4097-4115 (2013)

  6. Accurate modeling of spectral fine-structure in Earth radiance spectra measured with the Global Ozone Monitoring Experiment.

    PubMed

    van Deelen, Rutger; Hasekamp, Otto P; Landgraf, Jochen

    2007-01-10

    We present what we believe to be a novel approach to simulating the spectral fine structure (<1 nm) in measurements of spectrometers such as the Global Ozone Monitoring Experiment (GOME). GOME measures the Earth's radiance spectra and daily solar irradiance spectra from which a reflectivity spectrum is commonly extracted. The high-frequency structures contained in such a spectrum are, apart from atmospheric absorption, caused by Raman scattering and by a shift between the solar irradiance and the Earth's radiance spectrum. Normally, an a priori high-resolution solar spectrum is used to simulate these structures. We present an alternative method in which all the required information on the solar spectrum is retrieved from the GOME measurements. We investigate two approaches for the spectral range of 390-400 nm. First, a solar spectrum is reconstructed on a fine spectral grid from the GOME solar measurement. This approach leads to undersampling errors of up to 0.5% in the modeling of the Earth's radiance spectra. Second, a combination of the solar measurement and one of the Earth's radiance measurement is used to retrieve a solar spectrum. This approach effectively removes the undersampling error and results in residuals close to the GOME measurement noise of 0.1%.

  7. Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

    PubMed

    Baran, Richard; Northen, Trent R

    2013-10-15

    Untargeted metabolite profiling using liquid chromatography and mass spectrometry coupled via electrospray ionization is a powerful tool for the discovery of novel natural products, metabolic capabilities, and biomarkers. However, the elucidation of the identities of uncharacterized metabolites from spectral features remains challenging. A critical step in the metabolite identification workflow is the assignment of redundant spectral features (adducts, fragments, multimers) and calculation of the underlying chemical formula. Inspection of the data by experts using computational tools solving partial problems (e.g., chemical formula calculation for individual ions) can be performed to disambiguate alternative solutions and provide reliable results. However, manual curation is tedious and not readily scalable or standardized. Here we describe an automated procedure for the robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming optimization (RAMSI). Chemical rules among related ions are expressed as linear constraints and both the spectra interpretation and chemical formula calculation are performed in a single optimization step. This approach is unbiased in that it does not require predefined sets of neutral losses and positive and negative polarity spectra can be combined in a single optimization. The procedure was evaluated with 30 experimental mass spectra and was found to effectively identify the protonated or deprotonated molecule ([M + H](+) or [M - H](-)) while being robust to the presence of background ions. RAMSI provides a much-needed standardized tool for interpreting ions for subsequent identification in untargeted metabolomics workflows.

  8. Galaxy And Mass Assembly: accurate panchromatic photometry from optical priors using LAMBDAR

    NASA Astrophysics Data System (ADS)

    Wright, A. H.; Robotham, A. S. G.; Bourne, N.; Driver, S. P.; Dunne, L.; Maddox, S. J.; Alpaslan, M.; Andrews, S. K.; Bauer, A. E.; Bland-Hawthorn, J.; Brough, S.; Brown, M. J. I.; Clarke, C.; Cluver, M.; Davies, L. J. M.; Grootes, M. W.; Holwerda, B. W.; Hopkins, A. M.; Jarrett, T. H.; Kafle, P. R.; Lange, R.; Liske, J.; Loveday, J.; Moffett, A. J.; Norberg, P.; Popescu, C. C.; Smith, M.; Taylor, E. N.; Tuffs, R. J.; Wang, L.; Wilkins, S. M.

    2016-07-01

    We present the Lambda Adaptive Multi-Band Deblending Algorithm in R (LAMBDAR), a novel code for calculating matched aperture photometry across images that are neither pixel- nor PSF-matched, using prior aperture definitions derived from high-resolution optical imaging. The development of this program is motivated by the desire for consistent photometry and uncertainties across large ranges of photometric imaging, for use in calculating spectral energy distributions. We describe the program, specifically key features required for robust determination of panchromatic photometry: propagation of apertures to images with arbitrary resolution, local background estimation, aperture normalization, uncertainty determination and propagation, and object deblending. Using simulated images, we demonstrate that the program is able to recover accurate photometric measurements in both high-resolution, low-confusion, and low-resolution, high-confusion, regimes. We apply the program to the 21-band photometric data set from the Galaxy And Mass Assembly (GAMA) Panchromatic Data Release (PDR; Driver et al. 2016), which contains imaging spanning the far-UV to the far-IR. We compare photometry derived from LAMBDAR with that presented in Driver et al. (2016), finding broad agreement between the data sets. None the less, we demonstrate that the photometry from LAMBDAR is superior to that from the GAMA PDR, as determined by a reduction in the outlier rate and intrinsic scatter of colours in the LAMBDAR data set. We similarly find a decrease in the outlier rate of stellar masses and star formation rates using LAMBDAR photometry. Finally, we note an exceptional increase in the number of UV and mid-IR sources able to be constrained, which is accompanied by a significant increase in the mid-IR colour-colour parameter-space able to be explored.

  9. A theoretical analysis on the vibronic spectra with mass analyzed threshold ionization spectroscopy

    NASA Astrophysics Data System (ADS)

    Chao, Sheng D.; Peng, Hsin Y.

    2008-01-01

    We have theoretically studied the absorption vibronic spectra with the resonance two-photon (R2P) and non-resonance two-photon (NR2P) mass analyzed threshold ionization (MATI) spectroscopy. The theory uses the inverse Born-Oppenheimer approximation (IBOA) to establish a proper basis set. To analyze the MATI vibronic spectra, we have calculated the Franck-Condon factors involved in the vibronic transitions. Several experimental spectra are analyzed using this theory with emphasis on the importance of the resonance intermediate states. The long vibrational progression in a MATI spectrum can be partly attributed to the result of including the anharmonic correction in the calculated Franck-Condon factors. The experimentally observed isotope effect is also analyzed.

  10. Toward Sensitive and Accurate Analysis of Antibody Biotherapeutics by Liquid Chromatography Coupled with Mass Spectrometry

    PubMed Central

    An, Bo; Zhang, Ming

    2014-01-01

    Remarkable methodological advances in the past decade have expanded the application of liquid chromatography coupled with mass spectrometry (LC/MS) analysis of biotherapeutics. Currently, LC/MS represents a promising alternative or supplement to the traditional ligand binding assay (LBA) in the pharmacokinetic, pharmacodynamic, and toxicokinetic studies of protein drugs, owing to the rapid and cost-effective method development, high specificity and reproducibility, low sample consumption, the capacity of analyzing multiple targets in one analysis, and the fact that a validated method can be readily adapted across various matrices and species. While promising, technical challenges associated with sensitivity, sample preparation, method development, and quantitative accuracy need to be addressed to enable full utilization of LC/MS. This article introduces the rationale and technical challenges of LC/MS techniques in biotherapeutics analysis and summarizes recently developed strategies to alleviate these challenges. Applications of LC/MS techniques on quantification and characterization of antibody biotherapeutics are also discussed. We speculate that despite the highly attractive features of LC/MS, it will not fully replace traditional assays such as LBA in the foreseeable future; instead, the forthcoming trend is likely the conjunction of biochemical techniques with versatile LC/MS approaches to achieve accurate, sensitive, and unbiased characterization of biotherapeutics in highly complex pharmaceutical/biologic matrices. Such combinations will constitute powerful tools to tackle the challenges posed by the rapidly growing needs for biotherapeutics development. PMID:25185260

  11. Identification of "Known Unknowns" Utilizing Accurate Mass Data and Chemical Abstracts Service Databases

    NASA Astrophysics Data System (ADS)

    Little, James L.; Cleven, Curtis D.; Brown, Stacy D.

    2011-02-01

    In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others.

  12. ClusterSculptor: Software for Expert-Steered Classification of Single Particle Mass Spectra

    SciTech Connect

    Zelenyuk, Alla; Imre, Dan G.; Nam, Eun Ju; Han, Yiping; Mueller, Klaus

    2008-08-01

    To take full advantage of the vast amount of highly detailed data acquired by single particle mass spectrometers requires that the data be organized according to some rules that have the potential to be insightful. Most commonly statistical tools are used to cluster the individual particle mass spectra on the basis of their similarity. Cluster analysis is a powerful strategy for the exploration of high-dimensional data in the absence of a-priori hypotheses or data classification models, and the results of cluster analysis can then be used to form such models. More often than not, when examining the data clustering results we find that many clusters contain particles of different types and that many particles of one type end up in a number of separate clusters. Our experience with cluster analysis shows that we have a vast amount of non-compiled knowledge and intuition that should be brought to bear in this effort. We will present new software we call ClusterSculptor that provides comprehensive and intuitive framework to aid scientists in data classification. ClusterSculptor uses k-means as the overall clustering engine, but allows tuning its parameters interactively, based on a non-distorted compact visual presentation of the inherent characteristics of the data in high-dimensional space. ClusterSculptor provides all the tools necessary for a high-dimensional activity we call cluster sculpting. ClusterSculptor is designed to be coupled to SpectraMiner, our data mining and visualization software package. The data are first visualized with SpectraMiner and identified problems are exported to ClusterSculptor, where the user steers the reclassification and recombination of clusters of tens of thousands particle mass spectra in real-time. The resulting sculpted clusters can be then imported back into SpectraMiner. Here we will greatly improved single particle chemical speciation in an example of application of this new tool to a number of particle types of atmospheric

  13. Assessment of quinoxyfen phototransformation pathways by liquid chromatography coupled to accurate mass spectrometry.

    PubMed

    Ferri, Priscila; Ramil, María; Rodríguez, Isaac; Bergamasco, Rosângela; Vieira, Angélica Marquetotti Salcedo; Cela, Rafael

    2017-04-01

    Quinoxyfen has been recently identified as a priority hazardous substance in the field of the European water policy. In this work, its fate in aqueous samples and solid supports under UV and solar radiation is investigated. Diverse degradation experiments were carried out, at lab scale, using spiked aliquots of different aqueous matrices (ultrapure, treated wastewater and river water) irradiated at different wavelengths (λ = 254 nm, λ = 365 nm and solar light). Half-lives of quinoxyfen (2-26 min) depended on the wavelength and the intensity of radiation whilst the nature of the aqueous matrix did not play an important role in degradation kinetics. Moreover, experiments under solar radiation of doped silicone tubes were performed to simulate degradation when quinoxyfen is adsorbed on plant leaves or soil. As the compound is not completely mineralized, the identification of quinoxyfen transformation products (TPs) was performed by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) injection of different irradiated time aliquots. The full-fragment ion spectra, at different collision energies, allowed the elucidation of the chemical structure of TPs formed by hydroxylation, cyclization or cleavage reactions. Five out of seven identified TPs have not been reported previously. The ecotoxicity simulation by software (TEST and ECOSAR) for TPs revealed that some of them could cause harmful effects to organisms such as Daphnia magna or Fathead minnow in a similar extent to the precursor; moreover, the time course profiles of major TPs (TP1 and TP2) revealed a much higher resistance to further photodegradation than quinoxyfen. Graphical abstract Quinoxyfen phototransformation pathways.

  14. Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides

    PubMed Central

    Toghi Eshghi, Shadi; Yang, Weiming; Hu, Yingwei; Shah, Punit; Sun, Shisheng; Li, Xingde; Zhang, Hui

    2016-01-01

    Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides. PMID:27869200

  15. Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides

    NASA Astrophysics Data System (ADS)

    Toghi Eshghi, Shadi; Yang, Weiming; Hu, Yingwei; Shah, Punit; Sun, Shisheng; Li, Xingde; Zhang, Hui

    2016-11-01

    Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides.

  16. Spectra and mass composition of ultrahigh-energy cosmic rays from point sources

    SciTech Connect

    Kalmykov, Nikolai N.

    2012-04-01

    We present spectra and mass composition of cosmic rays incoming to the Earth in the energy range (0.5−2)·10{sup 20} eV. As their sources we consider Seyfert galaxies located at distances ∼<40 Mpc, following an acceleration model for such moderate-power objects. Mass composition of the particles at sources is assumed to be mixed. Generation spectra are described by a function E{sup −γ{sub 0}}, where γ{sub 0} is an arbitrary parameter. It is shown that the assumptions adopted make it possible to describe experimental data provided by HiRes and Pierre Auger Observatory, using different values of γ{sub 0}.

  17. OMA and OPA--software-supported mass spectra analysis of native and modified nucleic acids.

    PubMed

    Nyakas, Adrien; Blum, Lorenz C; Stucki, Silvan R; Reymond, Jean-Louis; Schürch, Stefan

    2013-02-01

    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 double-stranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

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

    NASA Astrophysics Data System (ADS)

    Nyakas, Adrien; Blum, Lorenz C.; Stucki, Silvan R.; Reymond, Jean-Louis; Schürch, Stefan

    2013-02-01

    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 double-stranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

  19. Mass spectra of the particle-antiparticle system with a Dirac oscillator interaction

    NASA Technical Reports Server (NTRS)

    Moshinsky, M.; Loyola, G.

    1993-01-01

    The present view about the structure of mesons is that they are a quark-antiquark system. The mass spectrum corresponding to this system should, in principle, be given by chromodynamics, but this turns out to be a complex affair. Thus it is of some interest to consider relativistic systems of particle-antiparticle, with a simple type of interaction, which could give some insight on the spectra we can expect for mesons. This analysis is carried out when the interaction is of the Dirac oscillator type. It is shown that the Dirac equation of the antiparticle can be obtained from that of the particle by just changing the frequency omega into -omega. Following a procedure suggested by Barut, the equation for the particle-antiparticle system is derived and it is solved by a perturbation procedure. Thus, explicit expressions for the square of the mass spectra are obtained and its implications in the meson case is discussed.

  20. Identification of isobaric product ions in electrospray ionization mass spectra of fentanyl using multistage mass spectrometry and deuterium labeling.

    PubMed

    Wichitnithad, Wisut; McManus, Terence J; Callery, Patrick S

    2010-09-15

    Isobaric product ions cannot be differentiated by exact mass determinations, although in some cases deuterium labeling can provide useful structural information for identifying isobaric ions. Proposed fragmentation pathways of fentanyl were investigated by electrospray ionization ion trap mass spectrometry coupled with deuterium labeling experiments and spectra of regiospecific deuterium labeled analogs. The major product ion of fentanyl under tandem mass spectrometry (MS/MS) conditions (m/z 188) was accounted for by a neutral loss of N-phenylpropanamide. 1-(2-Phenylethyl)-1,2,3,6-tetrahydropyridine (1) was proposed as the structure of the product ion. However, further fragmentation (MS(3)) of the fentanyl m/z 188 ion gave product ions that were different from the product ion in the MS/MS fragmentation of synthesized 1, suggesting that the m/z 188 product ion from fentanyl includes an isobaric structure different from the structure of 1. MS/MS fragmentation of fentanyl in deuterium oxide moved one of the isobars to 1 Da higher mass, and left the other isobar unchanged in mass. Multistage mass spectral data from deuterium-labeled proposed isobaric structures provided support for two fragmentation pathways. The results illustrate the utility of multistage mass spectrometry and deuterium labeling in structural assignment of isobaric product ions.

  1. A pattern recognition system for prostate mass spectra discrimination based on the CUDA parallel programming model

    NASA Astrophysics Data System (ADS)

    Kostopoulos, Spiros; Glotsos, Dimitris; Sidiropoulos, Konstantinos; Asvestas, Pantelis; Cavouras, Dionisis; Kalatzis, Ioannis

    2014-03-01

    The aim of the present study was to implement a pattern recognition system for the discrimination of healthy from malignant prostate tumors from proteomic Mass Spectroscopy (MS) samples and to identify m/z intervals of potential biomarkers associated with prostate cancer. One hundred and six MS-spectra were studied in total. Sixty three spectra corresponded to healthy cases (PSA < 1) and forty three spectra were cancerous (PSA > 10). The MS-spectra are publicly available from the NCI Clinical Proteomics Database. The pre-processing comprised the steps: denoising, normalization, peak extraction and peak alignment. Due to the enormous number of features that rose from MS-spectra as informative peaks, and in order to secure optimum system design, the classification task was performed by programming in parallel the multiprocessors of an nVIDIA GPU card, using the CUDA framework. The proposed system achieved 98.1% accuracy. The identified m/z intervals displayed significant statistical differences between the two classes and were found to possess adequate discriminatory power in characterizing prostate samples, when employed in the design of the classification system. Those intervals should be further investigated since they might lead to the identification of potential new biomarkers for prostate cancer.

  2. Efficient Methods to Generate Reproducible Mass Spectra in Matrix-Assisted Laser Desorption Ionization of Peptides

    NASA Astrophysics Data System (ADS)

    Ahn, Sung Hee; Park, Kyung Man; Bae, Yong Jin; Kim, Myung Soo

    2013-06-01

    In our previous matrix-assisted laser desorption ionization (MALDI) studies of peptides, we found that their mass spectra were virtually determined by the effective temperature in the early matrix plume, Tearly, when samples were rather homogeneous. This empirical rule allowed acquisition of quantitatively reproducible spectra. A difficulty in utilizing this rule was the complicated spectral treatment needed to get Tearly. In this work, we found another empirical rule that the total number of particles hitting the detector, or TIC, was a good measure of the spectral temperature and, hence, selection of spectra with the same TIC resulted in reproducible spectra. We also succeeded in obtaining reproducible spectra throughout a measurement by controlling TIC near a preset value through feedback adjustment of laser pulse energy. Both TIC selection and TIC control substantially reduced the shot-to-shot spectral variation in a spot, spot-to-spot variation in a sample, and even sample-to-sample variation in MALDI using α-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid as matrix. Based on the utilization of acquired data, TIC control was more efficient than TIC selection by an order of magnitude. Both techniques produced calibration curves with excellent linearity, suggesting their utility in quantification of peptides.

  3. The Megamaser Cosmology Project. III. Accurate Masses of Seven Supermassive Black Holes in Active Galaxies with Circumnuclear Megamaser Disks

    NASA Astrophysics Data System (ADS)

    Kuo, C. Y.; Braatz, J. A.; Condon, J. J.; Impellizzeri, C. M. V.; Lo, K. Y.; Zaw, I.; Schenker, M.; Henkel, C.; Reid, M. J.; Greene, J. E.

    2011-01-01

    Observations of H2O masers from circumnuclear disks in active galaxies for the Megamaser Cosmology Project (MCP) allow accurate measurement of the mass of supermassive black holes (BH) in these galaxies. We present the Very Long Baseline Interferometry images and kinematics of water maser emission in six active galaxies: NGC 1194, NGC 2273, NGC 2960 (Mrk 1419), NGC 4388, NGC 6264 and NGC 6323. We use the Keplerian rotation curves of these six megamaser galaxies, plus a seventh previously published, to determine accurate enclosed masses within the central ~0.3 pc of these galaxies, smaller than the radius of the sphere of influence of the central mass in all cases. We also set lower limits to the central mass densities of between 0.12 × 1010 and 61 × 1010 M sun pc-3. For six of the seven disks, the high central densities rule out clusters of stars or stellar remnants as the central objects, and this result further supports our assumption that the enclosed mass can be attributed predominantly to a supermassive BH. The seven BHs have masses ranging between 0.75 × 107 and 6.5 × 107 M sun, with the mass errors dominated by the uncertainty of the Hubble constant. We compare the megamaser BH mass determination with BH mass measured from the virial estimation method. The virial estimation BH mass in four galaxies is consistent with the megamaser BH mass, but the virial mass uncertainty is much greater. Circumnuclear megamaser disks allow the best mass determination of the central BH mass in external galaxies and significantly improve the observational basis at the low-mass end of the M-σsstarf relation. The M-σsstarf relation may not be a single, low-scatter power law as originally proposed. MCP observations continue and we expect to obtain more maser BH masses in the future.

  4. Localization and mass spectra of fermions on symmetric and asymmetric thick branes

    SciTech Connect

    Liu Yuxiao; Fu, C.-E; Zhao Li; Duan Yishi

    2009-09-15

    A three-parameter (positive odd integer s, thickness factor {lambda}, and asymmetry factor a) family of asymmetric thick brane solutions in five dimensions were constructed from a two-parameter (s and {lambda}) family of symmetric ones in by R. Guerrero, R. O. Rodriguez, and R. Torrealba in [Phys. Rev. D 72, 124012 (2005).]. The values s=1 and s{>=}3 correspond to single branes and double branes, respectively. These branes have very rich inner structure. In this paper, by presenting the mass-independent potentials of Kaluza-Klein (KK) modes in the corresponding Schroedinger equations, we investigate the localization and mass spectra of fermions on the symmetric and asymmetric thick branes in an anti-de Sitter background. In order to analyze the effect of gravity-fermion interaction (i.e., the effect of the inner structure of the branes) and scalar-fermion interaction to the spectrum of fermion KK modes, we consider three kinds of typical kink-fermion couplings. The spectra of left chiral fermions for these couplings consist of a bound zero mode and a series of gapless continuous massive KK modes, some discrete bound KK modes including zero mode (exist mass gaps), and a series of continuous massive KK modes, infinite discrete bound KK modes, respectively. The structures of the spectra are investigated in detail.

  5. Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry.

    PubMed

    Angelakis, Emmanouil; Million, Matthieu; Henry, Mireille; Raoult, Didier

    2011-10-01

    Probiotic food is manufactured by adding probiotic strains simultaneously with starter cultures in fermentation tanks. Here, we investigate the accuracy and feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for bacterial identification at the species level in probiotic food and yoghurts. Probiotic food and yoghurts were cultured in Columbia and Lactobacillus specific agar and tested by quantitative real-time PCR (qPCR) for the detection and quantification of Lactobacillus sp. Bacterial identification was performed by MALDI-TOF analysis and by amplification and sequencing of tuf and 16S rDNA genes. We tested 13 probiotic food and yoghurts and we identified by qPCR that they presented 10(6) to 10(7) copies of Lactobacillus spp. DNA/g. All products contained very large numbers of living bacteria varying from 10(6) to 10(9) colony forming units/g. These bacteria were identified as Lactobacillus casei, Lactococcus lactis, Bifidobacterium animalis, Lactobacillus delbrueckii, and Streptococcus thermophilus. MALDI-TOF MS presented 92% specificity compared to the molecular assays. In one product we found L. lactis, instead of Bifidus spp. which was mentioned on the label and for another L. delbrueckii and S. thermophilus instead of Bifidus spp. MALDI-TOF MS allows a rapid and accurate bacterial identification at the species level in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified. Practical Application:  MALDI-TOF MS is rapid and specific for the identification of bacteria in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified.

  6. Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics

    PubMed Central

    Yang, Kui; Han, Xianlin

    2011-01-01

    Electrospray ionization mass spectrometry (ESI-MS) has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of lipidomics. Herein, we discuss the principles, advantages, and possible limitations of different mass spectrometry-based methodologies for lipid quantification, as well as a few practical issues important for accurate quantification of individual lipid species. Accordingly, accurate quantification of individual lipid species, one of the key challenges in lipidomics, can be practically met. PMID:22905337

  7. Evolution of organic aerosol mass spectra upon heating: implications for OA phase and partitioning behavior

    SciTech Connect

    UC Davis; Cappa, Christopher D.; Wilson, Kevin R.

    2010-10-28

    Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the alpha-pinene + O3 reaction (alphaP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the alphaP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the alphaP spectra suggest that the evaporation of alphaP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from the alphaP particles existing as in a glassy state instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.

  8. Towards automated discrimination of lipids versus peptides from full scan mass spectra

    PubMed Central

    Dittwald, Piotr; Nghia, Vu Trung; Harris, Glenn A.; Caprioli, Richard M.; Van de Plas, Raf; Laukens, Kris; Gambin, Anna; Valkenborg, Dirk

    2014-01-01

    Although physicochemical fractionation techniques play a crucial role in the analysis of complex mixtures, they are not necessarily the best solution to separate specific molecular classes, such as lipids and peptides. Any physical fractionation step such as, for example, those based on liquid chromatography, will introduce its own variation and noise. In this paper we investigate to what extent the high sensitivity and resolution of contemporary mass spectrometers offers viable opportunities for computational separation of signals in full scan spectra. We introduce an automatic method that can discriminate peptide from lipid peaks in full scan mass spectra, based on their isotopic properties. We systematically evaluate which features maximally contribute to a peptide versus lipid classification. The selected features are subsequently used to build a random forest classifier that enables almost perfect separation between lipid and peptide signals without requiring ion fragmentation and classical tandem MS-based identification approaches. The classifier is trained on in silico data, but is also capable of discriminating signals in real world experiments. We evaluate the influence of typical data inaccuracies of common classes of mass spectrometry instruments on the optimal set of discriminant features. Finally, the method is successfully extended towards the classification of individual lipid classes from full scan mass spectral features, based on input data defined by the Lipid Maps Consortium. PMID:25414814

  9. HST Spectra of White Dwarfs and the Mass-Radius Relation

    NASA Astrophysics Data System (ADS)

    Joyce, S. R. G.; Barstow, M. A.; Casewell, S. L.; Holberg, J. B.; Bond, H. E.

    2017-03-01

    We present HST spectra of the white dwarf HR1358b which is one of a number of white dwarfs we are studying in Sirius-like binaries. These binaries give us the best chance yet to test the mass-radius relation through observations of the Balmer lines of white dwarfs. These observations can be used to measure the white dwarf mass using both the spectroscopic method and the gravitational red-shift method. One of the major challenges for this type of observation is scattered light from the main sequence star contaminating the white dwarf spectrum. We will discuss methods that have been developed to correct for scattered light in the spectrum of HR1358b and the effect this correction can have on the mass-radius measurements.

  10. Recent advances in the practical and accurate calculation of core and valence XPS spectra of polymers: From interpretation to simulation?

    NASA Astrophysics Data System (ADS)

    Bureau, Christophe; Chong, Delano P.; Endo, Kazunaka; Delhalle, Joseph; Lecayon, Gérard; Le Moël, Alain

    1997-08-01

    Core and valence X-ray Photoelectron Spectroscopies (XPS) are routinely used to obtain information on the chemical composition, bonding and homogeneity of polymer surfaces. In spite of their apparent conceptual simplicity, Core and Valence Electron Binding Energies (CEBEs and VEBEs) a few electron-volts (eV) or fractions of an eV apart are difficult to interpret. We present some results obtained with various recent theoretical approaches. An emphasis is made on a procedure based on the Density Functional Theory (DFT) that enables the calculation of CEBEs and VEBEs which are in remarkable agreement with experiment. The method has been tested on numerous small (3-6 atoms) to fairly large (15-25 atoms) molecules, and shows an average absolute deviation with experiment of only 0.20 eV for CEBEs and 0.30 eV for VEBEs, i.e. compatible with the resolution of the best XPS experiments carried out at the moment. Besides the quality of its predictions, the procedure takes advantage of the speed and CPU time scaling of DFT as a function of system size: it is computationally tractable, even for surprisingly large systems such as polymers, and may be an interesting accurate alternative to interpret and simulate XPS-probing on real systems. We illustrate the usefullness and pitfalls of this approach in fundamental as well as applied fields such as in the study of Polyacrylonitrile (PAN), Polytetrafluoroethylene (PTFE), Polyvinyldifluoride (PVdF) and γ-Aminopropyltriethoxysilane (γ-APS, an adhesion promoter).

  11. The determination of phenolic profiles of Serbian unifloral honeys using ultra-high-performance liquid chromatography/high resolution accurate mass spectrometry.

    PubMed

    Kečkeš, Silvio; Gašić, Uroš; Veličković, Tanja Ćirković; Milojković-Opsenica, Dušanka; Natić, Maja; Tešić, Živoslav

    2013-05-01

    Polyphenolic profiles of 44 unifloral Serbian honeys were analyzed using ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid mass spectrometer which combines the Linear Trap Quadrupole (LTQ) and OrbiTrap mass analyzer. Rapid UHPLC method was developed in combination with a high sensitivity accurate mass scan and a simultaneous data dependent scan. The honey samples were of different botanical origin: acacia (Robinia pseudoacacia), sunflower (Helianthus annuus), linden (Tilia cordata), basil (Ocimum basilicum), buckwheat (Fagopyrum esculentum), oilseed rape (Brassica napus), and goldenrod (Solidago virgaurea). The presence of 43 compounds, mainly flavonoids, was proven in all honey samples by their characteristic mass spectra and fragmentation pattern. Relatively high amounts of chrysin, pinocembrin and galangin were identified in all honey extracts. p-Coumaric acid was not detected in basil, buckwheat and goldenrod honey extracts. A larger amount of gallic acid (max value 1.45 mg/kg) was found in the sunflower honey, while a larger amount of apigenin (0.97 mg/kg) was determined in the buckwheat honey in comparison with other honeys. The samples were classified according to the botanical origin using pattern recognition technique, Principal Component Analysis (PCA). The LTQ OrbiTrap technique was proven to be reliable for the unambiguous detection of phenolic acids, their derivatives, and flavonoid aglycones based on their molecular masses and fragmentation pattern.

  12. De novo analysis of peptide tandem mass spectra by spectral graph partitioning.

    PubMed

    Bern, Marshall; Goldberg, David

    2006-03-01

    We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as "likely b-ion" or "likely y-ion"). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all datasets, we outperform the other sequencers. Along with spectral graph theory techniques, the new de novo sequencer EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF dataset.

  13. Mass spectra in N=1 SQCD with additional colorless but flavored fields

    NASA Astrophysics Data System (ADS)

    Chernyak, Victor L.

    2017-01-01

    Considered is the N=1 supersymmetric QCD-like Φ -theory with SU(N_c) colors and 0< N_F<2N_c flavors of light quarks Q^i_a,{overline{Q}}^{ a}_j with equal small masses. In addition to quarks and gluons of the standard N=1 SQCD, it includes N^2_F colorless but flavored fields Φ ij, with the large mass parameter μ _{Φ } ≫ Λ _Q (Λ _Q is the scale factor of the gauge coupling), interacting with quarks through the Yukawa coupling in the superpotential. The mass spectra of this (direct) Φ -theory are first directly calculated in all vacua with the unbroken or spontaneously broken flavor symmetry U(N_F)→ U(n_1)× U(n_2) at 0mass spectra of both, this direct Φ -theory and its Seiberg's dual variant with SU(N_F-N_c) dual colors, the dΦ -theory, are calculated at 3N_c/2mass spectra of the direct Φ - and dual dΦ -theories are parametrically different, so that they are not equivalent. Besides it is shown in the direct Φ -theory that a qualitatively new phenomenon takes place: under appropriate conditions, the seemingly heavy and dynamically irrelevant fields Φ `turn back' and there appear two additional generations of light Φ -particles with small masses μ ^pole(Φ )≪ Λ _Q. Also considered is the X-theory which is the N=2 SQCD with SU(N_c) colors and 0< N_F<2N_c flavors of light quarks, broken down to N=1 by the large mass

  14. Ultrahigh mass resolution and accurate mass measurements as a tool to characterize oligomers in secondary organic aerosols.

    PubMed

    Reinhardt, Alain; Emmenegger, Christian; Gerrits, Bertran; Panse, Christian; Dommen, Josef; Baltensperger, Urs; Zenobi, Renato; Kalberer, Markus

    2007-06-01

    Organic aerosols are a major fraction, often more than 50%, of the total atmospheric aerosol mass. The chemical composition of the total organic aerosol mass is poorly understood, although hundreds of compounds have been identified in the literature. High molecular weight compounds have recently gained much attention because this class of compounds potentially represents a major fraction of the unexplained organic aerosol mass. Here we analyze secondary organic aerosols, generated in a smog chamber from alpha-pinene ozonolysis with ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). About 450 compounds are detected in the mass range of m/z 200-700. The mass spectrum is clearly divided into a low molecular weight range (monomer) and a high molecular weight range, where dimers and trimers are distinguishable. Using the Kendrick mass analysis, the elemental composition of about 60% of all peaks could be determined throughout the whole mass range. Most compounds have high O:C ratios between 0.4 and 0.6. Small compounds (i.e., monomers) have a higher maximum O:C ratio than dimers and trimers, suggesting that condensation reactions with, for example, the loss of water are important in the oligomer formation process. A program developed in-house was used to determine exact mass differences between peaks in the monomer, dimer, and trimer mass range to identify potential monomer building blocks, which form the co-oligomers observed in the mass spectrum. A majority of the peaks measured in the low mass region of the spectrum (m/z < 300) is also found in the calculated results. For the first time the elemental composition of the majority of peaks over a wide mass range was determined using advanced data analysis methods for the analysis of ultra-high-resolution MS data. Possible oligomer formation mechanisms in secondary organic aerosols were investigated.

  15. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra

    NASA Astrophysics Data System (ADS)

    Kose, Etem; Karabacak, Mehmet; Bardak, Fehmi; Atac, Ahmet

    2016-11-01

    One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The 1H and 13C NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm-1 (FT-IR) and 4000-10 cm-1 (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (1H and 13C) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of

  16. Mass spectra deconvolution of low, medium, and high volatility biogenic secondary organic aerosol.

    PubMed

    Kostenidou, Evangelia; Lee, Byong-Hyoek; Engelhart, Gabriella J; Pierce, Jeffrey R; Pandis, Spyros N

    2009-07-01

    Secondary organic aerosol (SOA) consists of compounds with a wide range of volatilities and its ambient concentration is sensitive to this volatility distribution. Recent field studies have shown that the typical mass spectrum of ambient oxygenated organic aerosol (OOA) as measured by the Aerodyne Aerosol Mass Spectrometer (AMS) is quite different from the SOA mass spectra reported in smog chamber experiments. Part of this discrepancy is due to the dependence of SOA composition on the organic aerosol concentration. High precursor concentrations lead to higher concentrations of the more volatile species in the produced SOA while at lower concentrations the less volatile compounds dominate the SOA composition. alpha-Pinene, beta-pinene, d-limonene, and beta-caryophyllene ozonolysis experiments were performed at moderate concentration levels. Using a thermodenuder the more volatile SOA species were removed achieving even lower SOA concentration. The less volatile fraction was then chemically characterized by an AMS. The signal fraction of m/z44, and thus the concentration of C02+, is significantly higher for the less volatile SOA. High NO(x) conditions result in less oxidized SOA than low NO(x) conditions, while increasing relative humidity levels results in more oxidized products for limonene but has little effect on alpha-and beta-pinene SOA. Combining a smog chamber with a thermodenuder model employing the volatility basis-set framework, the AMS SOA mass spectrum for each experiment and for each precursor is deconvoluted into low, medium, and high volatility component mass spectra. The spectrum of the surrogate component with the lower volatility is quite similar to that of ambient OOA.

  17. In vivo investigation of homocysteine metabolism to polyamines by high-resolution accurate mass spectrometry and stable isotope labeling.

    PubMed

    Ruseva, Silviya; Lozanov, Valentin; Markova, Petia; Girchev, Radoslav; Mitev, Vanio

    2014-07-15

    Polyamines are essential polycations, playing important roles in mammalian physiology. Theoretically, the involvement of homocysteine in polyamine synthesis via S-adenosylmethionine is possible; however, to our knowledge, it has not been established experimentally. Here, we propose an original approach for investigation of homocysteine metabolites in an animal model. The method is based on the combination of isotope-labeled homocysteine supplementation and high-resolution accurate mass spectrometry analysis. Structural identity of the isotope-labeled metabolites was confirmed by accurate mass measurements of molecular and fragment ions and comparison of the retention times and tandem mass spectrometry fragmentation patterns. Isotope-labeled methionine, spermidine, and spermine were detected in all investigated plasma and tissue samples. The induction of moderate hyperhomocysteinemia leads to an alteration in polyamine levels in a different manner. The involvement of homocysteine in polyamine synthesis and modulation of polyamine levels could contribute to a better understanding of the mechanisms connected with homocysteine toxicity.

  18. THE MEGAMASER COSMOLOGY PROJECT. III. ACCURATE MASSES OF SEVEN SUPERMASSIVE BLACK HOLES IN ACTIVE GALAXIES WITH CIRCUMNUCLEAR MEGAMASER DISKS

    SciTech Connect

    Kuo, C. Y.; Braatz, J. A.; Condon, J. J.; Impellizzeri, C. M. V.; Lo, K. Y.; Zaw, I.; Schenker, M.; Henkel, C.; Reid, M. J.; Greene, J. E.

    2011-01-20

    Observations of H{sub 2}O masers from circumnuclear disks in active galaxies for the Megamaser Cosmology Project (MCP) allow accurate measurement of the mass of supermassive black holes (BH) in these galaxies. We present the Very Long Baseline Interferometry images and kinematics of water maser emission in six active galaxies: NGC 1194, NGC 2273, NGC 2960 (Mrk 1419), NGC 4388, NGC 6264 and NGC 6323. We use the Keplerian rotation curves of these six megamaser galaxies, plus a seventh previously published, to determine accurate enclosed masses within the central {approx}0.3 pc of these galaxies, smaller than the radius of the sphere of influence of the central mass in all cases. We also set lower limits to the central mass densities of between 0.12 x 10{sup 10} and 61 x 10{sup 10} M{sub sun} pc{sup -3}. For six of the seven disks, the high central densities rule out clusters of stars or stellar remnants as the central objects, and this result further supports our assumption that the enclosed mass can be attributed predominantly to a supermassive BH. The seven BHs have masses ranging between 0.75 x 10{sup 7} and 6.5 x 10{sup 7} M{sub sun}, with the mass errors dominated by the uncertainty of the Hubble constant. We compare the megamaser BH mass determination with BH mass measured from the virial estimation method. The virial estimation BH mass in four galaxies is consistent with the megamaser BH mass, but the virial mass uncertainty is much greater. Circumnuclear megamaser disks allow the best mass determination of the central BH mass in external galaxies and significantly improve the observational basis at the low-mass end of the M-{sigma}{sub *} relation. The M-{sigma}{sub *} relation may not be a single, low-scatter power law as originally proposed. MCP observations continue and we expect to obtain more maser BH masses in the future.

  19. [Investigation of JinKui ShenQi pills by ultraviolet spectra and tandem mass spectrometry].

    PubMed

    Li, Wen-lan; Sun, Zhi; Cheng, Bin; Ji, Yu-bin; Bai, Jing

    2008-08-01

    On the base of establishing the fingerprint of JinKui ShenQi pills, the ultraviolet spectra-mass spectrometry/mass spectrometry, method was used to identify the fingerprint. Seperation was performed on the Symmetry Shield RP18 (5 microm, 4. 6 mm X 15 mm) analytical column with mobile phase consisting of 1% acetic acid and acetonitrile with gradient elute at the flow rate of 1.0 mL x min(-1), and the ultraviolet detection wavelength was set at 248 nm. Using the above-mentioned chromatographic condition, the fingerprint of different samples was established and the same fingerprint was defined. The fingerprints of different samples were compared with similarity evaluation software published by Pharmacopeia committee codex (2004A). The mass spectrograph with API-ESI ionization source was used, setting the flow rate at 0.5 mL x min(-1) after splitting stream. The pressure of atomization room was 50 Psi, the flow rate of dry gas was 9.0 L x min(-1), the capillary voltage was 4 kV, and the transmission voltage was 70 V. The negative scanner mode was chosen, scan scope was 100-2000, using ion trap to analyze quasimolecular ion peak and the selected fragment ion, and TIC chromatography and second order mass chromatogram were recorded. The major constituents among in JinKui ShenQi pills from different origins were separated well by HPLC. Although there was difference among different origins, they showed nineteen identical characteristic absorption bands. Three fingerprints chemical compositions such as loganin, cinnamal and paeonol were identified based on the retention time and ultraviolet spectra of standard preparation. According to their ultraviolet spectra, molecular weight and fragmentation information, ten peaks in the fingerprint were identified by ultraviolet spectroscopy-mass, spectrometry/massg spectrometry. They are 1,2,3-tri-O-galloyl-glucose, loganin, paeoniflorin, 1,2,3,6-tetro-O-galloyl-glucose, soya-cerebroside, cornuside, and PGG, benzoyl

  20. Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry.

    PubMed

    Santos, Hugo M; Reboiro-Jato, Miguel; Glez-Peña, Daniel; Nunes-Miranda, J D; Fdez-Riverola, Florentino; Carvallo, R; Capelo, J L

    2010-09-15

    The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase.

  1. Extracting temperature and transverse flow by fitting transverse mass spectra and HBT radii together

    NASA Astrophysics Data System (ADS)

    He, Ronghua; Qian, Jing; Chen, Jianyi; Wu, Qingxin; Huo, Lei

    2017-03-01

    Single particle transverse mass spectra and HBT radii of identical pion and identical kaon are analyzed with a blast-wave parametrization under the assumptions of local thermal equilibrium and transverse expansion. Under the assumptions, temperature parameter T and transverse expansion rapidity ρ are sensitive to the shapes of transverse mass mT spectrum and HBT radius Rs(KT). Negative and positive correlations between T and ρ are observed by fitting mT spectrum and HBT radius Rs(KT), respectively. For a Monte Carlo simulation using the blast-wave function, T and ρ are extracted by fitting mT spectra and HBT radii together utilizing a combined optimization function χ2. With this method, T and ρ of the Monte Carlo sources can be extracted. Using this method for A Multi-Phase Transport (AMPT) model at Relativistic Heavy Ion Collider (RHIC) energy, the differences of T and ρ between pion and kaon are observed obviously, and the tendencies of T and ρ versus collision energy sNN are similar with the results extracted directly from the AMPT model.

  2. Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra.

    PubMed

    Zhang, Jingfen; Gao, Wen; Cai, Jinjin; He, Simin; Zeng, Rong; Chen, Runsheng

    2005-01-01

    A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.

  3. Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra.

    PubMed

    Ledvina, A R; Savitski, M M; Zubarev, A R; Good, D M; Coon, J J; Zubarev, R A

    2011-10-15

    High-resolution and high-accuracy Fourier transform mass spectrometry (FTMS) is becoming increasingly attractive due to its specificity. However, the speed of tandem FTMS analysis severely limits the competitive advantage of this approach relative to faster low-resolution quadrupole ion trap MS/MS instruments. Here we demonstrate an entirely FTMS-based analysis method with a 2.5-3.0-fold greater throughput than a conventional FT MS/MS approach. The method consists of accumulating together the MS/MS fragments ions from multiple precursors, with subsequent high-resolution analysis of the mixture. Following acquisition, the multiplexed spectrum is deconvoluted into individual MS/MS spectra which are then combined into a single concatenated file and submitted for peptide identification to a search engine. The method is tested both in silico using a database of MS/MS spectra as well as in situ using a modified LTQ Orbitrap mass spectrometer. The performance of the method in the experiment was consistent with theoretical expectations.

  4. 4-Component correlated all-electron study on Eka-actinium Fluoride (E121F) including Gaunt interaction: Accurate analytical form, bonding and influence on rovibrational spectra

    NASA Astrophysics Data System (ADS)

    Amador, Davi H. T.; de Oliveira, Heibbe C. B.; Sambrano, Julio R.; Gargano, Ricardo; de Macedo, Luiz Guilherme M.

    2016-10-01

    A prolapse-free basis set for Eka-Actinium (E121, Z = 121), numerical atomic calculations on E121, spectroscopic constants and accurate analytical form for the potential energy curve of diatomic E121F obtained at 4-component all-electron CCSD(T) level including Gaunt interaction are presented. The results show a strong and polarized bond (≈181 kcal/mol in strength) between E121 and F, the outermost frontier molecular orbitals from E121F should be fairly similar to the ones from AcF and there is no evidence of break of periodic trends. Moreover, the Gaunt interaction, although small, is expected to influence considerably the overall rovibrational spectra.

  5. Accurate Empirical Radii and Masses of Planets and Their Host Stars with Gaia Parallaxes

    NASA Astrophysics Data System (ADS)

    Stassun, Keivan G.; Collins, Karen A.; Gaudi, B. Scott

    2017-03-01

    We present empirical measurements of the radii of 116 stars that host transiting planets. These radii are determined using only direct observables—the bolometric flux at Earth, the effective temperature, and the parallax provided by the Gaia first data release—and thus are virtually model independent, with extinction being the only free parameter. We also determine each star’s mass using our newly determined radius and the stellar density, a virtually model independent quantity itself from previously published transit analyses. These stellar radii and masses are in turn used to redetermine the transiting-planet radii and masses, again using only direct observables. The median uncertainties on the stellar radii and masses are 8% and 30%, respectively, and the resulting uncertainties on the planet radii and masses are 9% and 22%, respectively. These accuracies are generally larger than previously published model-dependent precisions of 5% and 6% on the planet radii and masses, respectively, but the newly determined values are purely empirical. We additionally report radii for 242 stars hosting radial-velocity (non-transiting) planets, with a median achieved accuracy of ≈2%. Using our empirical stellar masses we verify that the majority of putative “retired A stars” in the sample are indeed more massive than ∼1.2 {M}ȯ . Most importantly, the bolometric fluxes and angular radii reported here for a total of 498 planet host stars—with median accuracies of 1.7% and 1.8%, respectively—serve as a fundamental data set to permit the re-determination of transiting-planet radii and masses with the Gaia second data release to ≈3% and ≈5% accuracy, better than currently published precisions, and determined in an entirely empirical fashion.

  6. How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II.

    PubMed

    Beckwith, Martha A; Ames, William; Vila, Fernando D; Krewald, Vera; Pantazis, Dimitrios A; Mantel, Claire; Pécaut, Jacques; Gennari, Marcello; Duboc, Carole; Collomb, Marie-Noëlle; Yano, Junko; Rehr, John J; Neese, Frank; DeBeer, Serena

    2015-10-14

    First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.

  7. Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach

    PubMed Central

    Zimmer, Jennifer S.D.; Monroe, Matthew E.; Qian, Wei-Jun; Smith, Richard D.

    2007-01-01

    Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. PMID:16429408

  8. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida.

    PubMed

    Cameron, Simon J S; Bolt, Frances; Perdones-Montero, Alvaro; Rickards, Tony; Hardiman, Kate; Abdolrasouli, Alireza; Burke, Adam; Bodai, Zsolt; Karancsi, Tamas; Simon, Daniel; Schaffer, Richard; Rebec, Monica; Balog, Julia; Takáts, Zoltan

    2016-11-14

    Members of the genus Candida, such as C. albicans and C. parapsilosis, are important human pathogens. Other members of this genus, previously believed to carry minimal disease risk, are increasingly recognised as important human pathogens, particularly because of variations in susceptibilities to widely used anti-fungal agents. Thus, rapid and accurate identification of clinical Candida isolates is fundamental in ensuring timely and effective treatments are delivered. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has previously been shown to provide a high-throughput platform for the rapid and accurate identification of bacterial and fungal isolates. In comparison to commercially available matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF), REIMS based methods require no preparative steps nor time-consuming cell extractions. Here, we report on the ability of REIMS-based analysis to rapidly and accurately identify 153 clinical Candida isolates to species level. Both handheld bipolar REIMS and high-throughput REIMS platforms showed high levels of species classification accuracy, with 96% and 100% of isolates classified correctly to species level respectively. In addition, significantly different (FDR corrected P value < 0.05) lipids within the 600 to 1000 m/z mass range were identified, which could act as species-specific biomarkers in complex microbial communities.

  9. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida

    PubMed Central

    Cameron, Simon J. S.; Bolt, Frances; Perdones-Montero, Alvaro; Rickards, Tony; Hardiman, Kate; Abdolrasouli, Alireza; Burke, Adam; Bodai, Zsolt; Karancsi, Tamas; Simon, Daniel; Schaffer, Richard; Rebec, Monica; Balog, Julia; Takáts, Zoltan

    2016-01-01

    Members of the genus Candida, such as C. albicans and C. parapsilosis, are important human pathogens. Other members of this genus, previously believed to carry minimal disease risk, are increasingly recognised as important human pathogens, particularly because of variations in susceptibilities to widely used anti-fungal agents. Thus, rapid and accurate identification of clinical Candida isolates is fundamental in ensuring timely and effective treatments are delivered. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has previously been shown to provide a high-throughput platform for the rapid and accurate identification of bacterial and fungal isolates. In comparison to commercially available matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF), REIMS based methods require no preparative steps nor time-consuming cell extractions. Here, we report on the ability of REIMS-based analysis to rapidly and accurately identify 153 clinical Candida isolates to species level. Both handheld bipolar REIMS and high-throughput REIMS platforms showed high levels of species classification accuracy, with 96% and 100% of isolates classified correctly to species level respectively. In addition, significantly different (FDR corrected P value < 0.05) lipids within the 600 to 1000 m/z mass range were identified, which could act as species-specific biomarkers in complex microbial communities. PMID:27841356

  10. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. However, th...

  11. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  12. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. For phytochem...

  13. [Probabilistic calculations of biomolecule charge states that generate mass spectra of multiply charged ions].

    PubMed

    Raznikova, M O; Raznikov, V V

    2015-01-01

    In this work, information relating to charge states of biomolecule ions in solution obtained using the electrospray ionization mass spectrometry of different biopolymers is analyzed. The data analyses have mainly been carried out by solving an inverse problem of calculating the probabilities of retention of protons and other charge carriers by ionogenic groups of biomolecules with known primary structures. The approach is a new one and has no known to us analogues. A program titled "Decomposition" was developed and used to analyze the charge distribution of ions of native and denatured cytochrome c mass spectra. The possibility of splitting of the charge-state distribution of albumin into normal components, which likely corresponds to various conformational states of the biomolecule, has been demonstrated. The applicability criterion for using previously described method of decomposition of multidimensional charge-state distributions with two charge carriers, e.g., a proton and a sodium ion, to characterize the spatial structure of biopolymers in solution has been formulated. In contrast to known mass-spectrometric approaches, this method does not require the use of enzymatic hydrolysis or collision-induced dissociation of the biopolymers.

  14. A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.

    PubMed

    Wenger, Craig D; Coon, Joshua J

    2013-03-01

    The acquisition of high-resolution tandem mass spectra (MS/MS) is becoming more prevalent in proteomics, but most researchers employ peptide identification algorithms that were designed prior to this development. Here, we demonstrate new software, Morpheus, designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a variety of organisms (E. coli, yeast, human) acquired on a variety of instruments (quadrupole-time-of-flight, ion trap-orbitrap, and quadrupole-orbitrap) in different laboratories, Morpheus gives more spectrum, peptide, and protein identifications at a 1% false discovery rate (FDR) than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest. Additionally, Morpheus is 1.5 to 4.6 times faster, depending on the data set, than the next fastest algorithm, OMSSA. Morpheus was developed in C# .NET and is available free and open source under a permissive license.

  15. Preliminary results of investigations into the use of artificial neural networks for discriminating gas chromatograph mass spectra of remote samples

    NASA Technical Reports Server (NTRS)

    Geller, Harold A.; Norris, Eugene; Warnock, Archibald, III

    1991-01-01

    Neural networks trained using mass spectra data from the National Institute of Standards and Technology (NIST) are studied. The investigations also included sample data from the gas chromatograph mass spectrometer (GCMS) instrument aboard the Viking Lander, obtained from the National Space Science Data Center. The work performed to data and the preliminary results from the training and testing of neural networks are described. These preliminary results are presented for the purpose of determining the viability of applying artificial neural networks in discriminating mass spectra samples from remote instrumentation such as the Mars Rover Sample Return Mission and the Cassini Probe.

  16. Discovery of protein acetylation patterns by deconvolution of peptide isomer mass spectra

    PubMed Central

    Abshiru, Nebiyu; Caron-Lizotte, Olivier; Rajan, Roshan Elizabeth; Jamai, Adil; Pomies, Christelle; Verreault, Alain; Thibault, Pierre

    2015-01-01

    Protein post-translational modifications (PTMs) play important roles in the control of various biological processes including protein–protein interactions, epigenetics and cell cycle regulation. Mass spectrometry-based proteomics approaches enable comprehensive identification and quantitation of numerous types of PTMs. However, the analysis of PTMs is complicated by the presence of indistinguishable co-eluting isomeric peptides that result in composite spectra with overlapping features that prevent the identification of individual components. In this study, we present Iso-PeptidAce, a novel software tool that enables deconvolution of composite MS/MS spectra of isomeric peptides based on features associated with their characteristic fragment ion patterns. We benchmark Iso-PeptidAce using dilution series prepared from mixtures of known amounts of synthetic acetylated isomers. We also demonstrate its applicability to different biological problems such as the identification of site-specific acetylation patterns in histones bound to chromatin assembly factor-1 and profiling of histone acetylation in cells treated with different classes of HDAC inhibitors. PMID:26468920

  17. Discovery of protein acetylation patterns by deconvolution of peptide isomer mass spectra.

    PubMed

    Abshiru, Nebiyu; Caron-Lizotte, Olivier; Rajan, Roshan Elizabeth; Jamai, Adil; Pomies, Christelle; Verreault, Alain; Thibault, Pierre

    2015-10-15

    Protein post-translational modifications (PTMs) play important roles in the control of various biological processes including protein-protein interactions, epigenetics and cell cycle regulation. Mass spectrometry-based proteomics approaches enable comprehensive identification and quantitation of numerous types of PTMs. However, the analysis of PTMs is complicated by the presence of indistinguishable co-eluting isomeric peptides that result in composite spectra with overlapping features that prevent the identification of individual components. In this study, we present Iso-PeptidAce, a novel software tool that enables deconvolution of composite MS/MS spectra of isomeric peptides based on features associated with their characteristic fragment ion patterns. We benchmark Iso-PeptidAce using dilution series prepared from mixtures of known amounts of synthetic acetylated isomers. We also demonstrate its applicability to different biological problems such as the identification of site-specific acetylation patterns in histones bound to chromatin assembly factor-1 and profiling of histone acetylation in cells treated with different classes of HDAC inhibitors.

  18. Theoretical spectra of nonmagnetized low-mass X-ray binaries

    NASA Technical Reports Server (NTRS)

    Czerny, Bozena; Czerny, Michal; Grindlay, Jonathan E.

    1986-01-01

    Theoretical X-ray spectra of low-mass X-ray binaries with negligible magnetic fields are presented. The geometry of the X-ray emitting region, the energetic efficiency of the accretion in the disk and in the boundary layer which leads to a relation between the disk and the boundary layer luminosities, and the irradiation of the disk by the boundary layer are studied. The model of the radiation spectrum emerging from the neutron star and the innermost part of the disk is presented. The relativistic and Doppler effects and their influence on the spectrum as a function of inclination angle are discussed. A simple method for comparing the spectrum model with observations by studying the hardness ratio is given, and the results for three X-ray sources in globular clusters observed by the Einstein satellite are presented. The range of applicability of the spectrum models is also discussed.

  19. How accurately do we know interannual variations of surface mass balance and firn volume in Antarctica?

    NASA Astrophysics Data System (ADS)

    Horwath, Martin; van den Broeke, Michiel R.; Lenaerts, Jan T. M.; Ligtenberg, Stefan R. M.; Legrésy, Benoît; Blarel, Fabien

    2013-04-01

    Knowing the interannual variations in the Antarctic ice sheet net snow accumulation, or surface mass balance (SMB), is essential for analyzing and interpreting present-day observations. For example, accumulation events like the one in East Antarctica in 2009 (Shepherd et al. 2012, Science, doi: 10.1126/science.1228102) challenge our ability to interpret observed decadal-scale trends in terms of long-term changes versus natural fluctuations. SMB variations cause changes in the firn density structure, which need to be accounted for when converting volume trends from satellite altimetry into mass trends. Recent assessments of SMB and firn volume variations mainly rely on atmospheric modeling and firn densification modeling (FDM). The modeling results need observational validation, which has been limited by now. Geodetic observations by satellite altimetry and satellite gravimetry reflect interannual firn volume and mass changes, among other signals like changes in ice flow dynamics. Therefore, these observations provide a means of validating modeling results over the observational period. We present comprehensive comparisons between interannual volume variations from ENVISAT radar altimetry (RA) and firn densification modeling (FDM), and between interannual mass variations from SMB modeling by the regional atmospheric climate model RACMO2 and GRACE satellite gravimetry. The comparisons are performed based on time series with approximately monthly sampling and with the overlapping period from 2002 to 2010. The RA-FDM comparison spans the spatial scales from 27 km to the continental scale. The mass comparison refers to the regional (drainage basin) and continental scale. Overall, we find good agreement between the interannual variations described by the models and by the geodetic observations. This agreement proves our ability to track and understand SMB-related ice sheet variations from year to year. The assessment of differences between modeling and observations

  20. Energy spectra of massive two-body decay products and mass measurement

    SciTech Connect

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; Kim, Doojin

    2016-04-26

    Here, we have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a massless product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, we utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.

  1. Energy spectra of massive two-body decay products and mass measurement

    DOE PAGES

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; ...

    2016-04-26

    Here, we have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a massless product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, wemore » utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.« less

  2. Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.

    PubMed

    Yu, Chuan-Yih; Mayampurath, Anoop; Zhu, Rui; Zacharias, Lauren; Song, Ehwang; Wang, Lei; Mechref, Yehia; Tang, Haixu

    2016-06-07

    Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/ .

  3. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

    PubMed Central

    Kind, Tobias; Fiehn, Oliver

    2007-01-01

    Background Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. Results An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. Conclusion The seven rules enable an

  4. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

    PubMed

    Turewicz, Michael; Deutsch, Eric W

    2011-01-01

    This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

  5. Increased Throughput of Proteomics Analysis by Multiplexing High-resolution Tandem Mass Spectra

    PubMed Central

    Ledvina, A. R.; Savitski, M. M.; Zubarev, A. R.; Good, D. M.; Coon, J. J.; Zubarev, R. A.

    2014-01-01

    High-resolution and accuracy Fourier-transform mass spectrometry (FTMS) is becoming increasingly attractive due to its specificity. However, the speed of tandem FTMS analysis severely limits the competitive advantage of this approach relative to faster low-resolution quadrupole ion trap MS/MS instruments. Here we demonstrate an entirely FTMS-based analysis method with a 2.5–3.0 fold greater throughput than a conventional FT MS/MS approach. The method consists of accumulating together the MS/MS fragments ions from multiple precursors, with subsequent high-resolution analysis of the mixture. Following acquisition, the multiplexed spectrum is deconvoluted into individual MS/MS datasets which are separately submitted for peptide identification to a search engine. The method is tested both in silico using a database of MS/MS spectra as well as in situ using a modified LTQ-Orbitrap mass spectrometer. The performance of the method in the experiment was consistent with theoretical expectations. PMID:21913643

  6. Accurate determination of silver nanoparticles in animal tissues by inductively coupled plasma mass spectrometry

    NASA Astrophysics Data System (ADS)

    Veverková, Lenka; Hradilová, Šárka; Milde, David; Panáček, Aleš; Skopalová, Jana; Kvítek, Libor; Petrželová, Kamila; Zbořil, Radek

    2014-12-01

    This study examined recoveries of silver determination in animal tissues after wet digestion by inductively coupled plasma mass spectrometry. The composition of the mineralization mixture for microwave assisted digestion was optimized and the best recoveries were obtained for mineralization with HNO3 and addition of HCl promptly after digestion. The optimization was performed on model samples of chicken meat spiked with silver nanoparticles and a solution of ionic silver. Basic calculations of theoretical distribution of Ag among various silver-containing species were implemented and the results showed that most of the silver is in the form of soluble complexes AgCl2- and AgCl32 - for the optimized composition of the mineralization mixture. Three animal tissue certified reference materials were then analyzed to verify the trueness and precision of the results.

  7. Accurate characterization of carcinogenic DNA adducts using MALDI tandem time-of-flight mass spectrometry

    NASA Astrophysics Data System (ADS)

    Barnes, Charles A.; Chiu, Norman H. L.

    2009-01-01

    Many chemical carcinogens and their in vivo activated metabolites react readily with genomic DNA, and form covalently bound carcinogen-DNA adducts. Clinically, carcinogen-DNA adducts have been linked to various cancer diseases. Among the current methods for DNA adduct analysis, mass spectroscopic method allows the direct measurement of unlabeled DNA adducts. The goal of this study is to explore the use of matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) to determine the identity of carcinogen-DNA adducts. Two of the known carcinogenic DNA adducts, namely N-(2'-deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenyl-imidazo [4,5-b] pyridine (dG-C8-PhIP) and N-(2'-deoxyguanosin-8yl)-4-aminobiphenyl (dG-C8-ABP), were selected as our models. In MALDI-TOF MS measurements, the small matrix ion and its cluster ions did not interfere with the measurements of both selected dG adducts. To achieve a higher accuracy for the characterization of selected dG adducts, 1 keV collision energy in MALDI-TOF/TOF MS/MS was used to measure the adducts. In comparison to other MS/MS techniques with lower collision energies, more extensive precursor ion dissociations were observed. The detection of the corresponding fragment ions allowed the identities of guanine, PhIP or ABP, and the position of adduction to be confirmed. Some of the fragment ions of dG-C8-PhIP have not been reported by other MS/MS techniques.

  8. Evaluation of accurate mass and relative isotopic abundance measurements in the LTQ-orbitrap mass spectrometer for further metabolomics database building.

    PubMed

    Xu, Ying; Heilier, Jean-François; Madalinski, Geoffrey; Genin, Eric; Ezan, Eric; Tabet, Jean-Claude; Junot, Christophe

    2010-07-01

    Recently, high-resolution mass spectrometry has been largely employed for compound identification, thanks to accurate mass measurements. As additional information, relative isotope abundance (RIA) is often needed to reduce the number of candidates prior to tandem MS(n). Here, we report on the evaluation of the LTQ-Orbitrap, in terms of accurate mass and RIA measurements for building further metabolomics spectral databases. Accurate mass measurements were achieved in the ppm range, using external calibration within 24 h, and remained at <5 ppm over a one-week period. The experimental relative abundances of (M+1) isotopic ions were evaluated in different data sets. First of all, 137 solutions of commercial compounds were analyzed by flow injection analysis in both the positive and negative ion modes. It was found that the ion abundance was the main factor impacting the accuracy of RIA measurements. It was possible to define some intensity thresholds above which errors were systematically <20% of their theoretical values. The same type of results were obtained with analyses from two biological media. Otherwise, no significant effect of ion transmission between the LTQ ion trap and the Orbitrap analyzer on RIA measurement errors was found, whereas the reliability of RIA measurements was dramatically improved by reducing the mass detection window. It was also observed that the signal integration method had a significant impact on RIA measurement errors, with the most-reliable results being obtained with peak height integrations. Finally, automatic integrations using the data preprocessing software XCMS and MZmine gave results similar to those obtained by manual integration, suggesting that it is relevant to use the RIA information in automatic elemental composition determination software from metabolomic peak tables.

  9. Neutral losses: a type of important variables in prediction of branching degree for acyclic alkenes from mass spectra.

    PubMed

    Zhang, Liangxiao; Fan, Wei; Cao, Dongsheng; Zeng, Maomao; Xiao, Hongbin; Liang, Yizeng

    2012-03-30

    Neutral losses are a type of important variables in mass spectral interpretation. Since it is hard to calculate or extract neutral losses from mass spectra, they are usually discarded. In this study, dissimilarity analysis was employed to extract mass spectral characteristics for predicting branching degree of acyclic alkenes. The relationships between branching degree and neutral loss were constructed under direction of experimental observation and mass spectral fragmentations. A branching degree predictor of acyclic alkenes was subsequently built based on the above relationships. After tested by the experimental data in previous studies, the predictor could correctly provide the branching degree from abundant ions of mass spectra. More importantly, this predictor was able to point out which acyclic alkenes could be predicted correctly or not.

  10. Identification of metallothionein subisoforms in HPLC using accurate mass and online sequencing by electrospray hybrid linear ion trap-orbital ion trap mass spectrometry.

    PubMed

    Mounicou, Sandra; Ouerdane, Laurent; L'Azou, Béatrice; Passagne, Isabelle; Ohayon-Courtès, Céline; Szpunar, Joanna; Lobinski, Ryszard

    2010-08-15

    A comprehensive approach to the characterization of metallothionein (MT) isoforms based on microbore HPLC with multimodal detection was developed. MTs were separated as Cd(7) complexes, detected by ICP MS and tentatively identified by molecular mass measured with 1-2 ppm accuracy using Orbital ion trap mass spectrometry. The identification was validated by accurate mass of the corresponding apo-MTs after postcolumn acidification and by their sequences acquired online by higher-energy collision dissociation MS/MS. The detection limits down to 10 fmol and 45 fmol could be obtained by ESI MS for apo- and Cd(7)-isoforms, respectively, and were lower than those obtained by ICP MS (100 fmol). The individual MT isoforms could be sequenced at levels as low as 200 fmol with the sequence coverage exceeding 90%. The approach was successfully applied to the identification of MT isoforms induced in a pig kidney cell line (LLC-PK(1)) exposed to CdS nanoparticles.

  11. The use of in vitro technologies coupled with high resolution accurate mass LC-MS for studying drug metabolism in equine drug surveillance.

    PubMed

    Scarth, James P; Spencer, Holly A; Timbers, Sarah E; Hudson, Simon C; Hillyer, Lynn L

    2010-01-01

    The detection of drug abuse in horseracing often requires knowledge of drug metabolism, especially if urine is the matrix of choice. In this study, equine liver/lung microsomes/S9 tissue fractions were used to study the phase I metabolism of eight drugs of relevance to equine drug surveillance (acepromazine, azaperone, celecoxib, fentanyl, fluphenazine, mepivacaine, methylphenidate and tripelennamine). In vitro samples were analyzed qualitatively alongside samples originating from in vivo administrations using LC-MS on a high resolution accurate mass Thermo Orbitrap Discovery instrument and by LC-MS/MS on an Applied Biosystems Sciex 5500 Q Trap.Using high resolution accurate mass full-scan analysis on the Orbitrap, the in vitro systems were found to generate at least the two most abundant phase I metabolites observed in vitro for all eight drugs studied. In the majority of cases, in vitro experiments were also able to generate the minor in vivo metabolites and sometimes metabolites that were only observed in vitro. More detailed analyses of fentanyl incubates using LC-MS/MS showed that it was possible to generate good quality spectra from the metabolites generated in vitro. These data support the suggestion of using in vitro incubates as metabolite reference material in place of in vivo post-administration samples in accordance with new qualitative identification guidelines in the 2009 International Laboratory Accreditation Cooperation-G7 (ILAC-G7) document.In summary, the in vitro and in vivo phase I metabolism results reported herein compare well and demonstrate the potential of in vitro studies to compliment, refine and reduce the existing equine in vivo paradigm.

  12. Accurate mass fragment library for rapid analysis of pesticides on produce using ambient pressure desorption ionization with high-resolution mass spectrometry.

    PubMed

    Kern, Sara E; Lin, Lora A; Fricke, Frederick L

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]⁺) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]⁺ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]⁺ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli

  13. Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The

  14. Accurate Spectral Fits of Jupiter's Great Red Spot: VIMS Visual Spectra Modelled with Chromophores Created by Photolyzed Ammonia Reacting with Acetyleneχ±

    NASA Astrophysics Data System (ADS)

    Baines, Kevin; Sromovsky, Lawrence A.; Fry, Patrick M.; Carlson, Robert W.; Momary, Thomas W.

    2016-10-01

    We report results incorporating the red-tinted photochemically-generated aerosols of Carlson et al (2016, Icarus 274, 106-115) in spectral models of Jupiter's Great Red Spot (GRS). Spectral models of the 0.35-1.0-micron spectrum show good agreement with Cassini/VIMS near-center-meridian and near-limb GRS spectra for model morphologies incorporating an optically-thin layer of Carlson (2016) aerosols at high altitudes, either at the top of the tropospheric GRS cloud, or in a distinct stratospheric haze layer. Specifically, a two-layer "crème brûlée" structure of the Mie-scattering Carlson et al (2016) chromophore attached to the top of a conservatively scattering (hereafter, "white") optically-thick cloud fits the spectra well. Currently, best agreement (reduced χ2 of 0.89 for the central-meridian spectrum) is found for a 0.195-0.217-bar, 0.19 ± 0.02 opacity layer of chromophores with mean particle radius of 0.14 ± 0.01 micron. As well, a structure with a detached stratospheric chromophore layer ~0.25 bar above a white tropospheric GRS cloud provides a good spectral match (reduced χ2 of 1.16). Alternatively, a cloud morphology with the chromophore coating white particles in a single optically- and physically-thick cloud (the "coated-shell model", initially explored by Carlson et al 2016) was found to give significantly inferior fits (best reduced χ2 of 2.9). Overall, we find that models accurately fit the GRS spectrum if (1) most of the optical depth of the chromophore is in a layer near the top of the main cloud or in a distinct separated layer above it, but is not uniformly distributed within the main cloud, (2) the chromophore consists of relatively small, 0.1-0.2-micron-radius particles, and (3) the chromophore layer optical depth is small, ~ 0.1-0.2. Thus, our analysis supports the exogenic origin of the red chromophore consistent with the Carlson et al (2016) photolytic production mechanism rather than an endogenic origin, such as upwelling of material

  15. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    PubMed

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-06-28

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  16. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    PubMed Central

    Ross, Charles W.; Simonsick, William J.; Bogusky, Michael J.; Celikay, Recep W.; Guare, James P.; Newton, Randall C.

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  17. Decay of COSAC and Ptolemy mass spectra at comet 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Krüger, Harald; Goesmann, Fred; Giri, Chaitanya; Wright, Ian; Morse, Andrew; Bredehöft, Jan Hendrik; Ulamec, Stephan; Cozzoni, Barbara; Ehrenfreund, Pascale; Gautier, Thomas; McKenna-Lawlor, Susan; Raulin, Francois; Steininger, Harald; Szopa, Cyril

    2017-03-01

    Context. The Rosetta lander Philae successfully landed on the nucleus of comet 67P/Churyumov-Gerasimenko on 12 November 2014. Philae is equipped with two gas analysers: The Cometary Sampling and Composition experiment (COSAC) and the gas chromatograph and mass spectrometer Ptolemy. Aims: COSAC is designed for in situ analysis of organic molecules on 67P while Ptolemy is optimised to measure ratios of stable isotopes. Methods: On 12 to 14 November 2014, both instruments measured the organic composition of the comet nucleus material through seven measurements in sniffing mode during Philae's hopping and at its final landing site Abydos. We compare the temporal evolution of intensities of several ion species identified by both mass spectrometers. For COSAC, this is the first analysis of the temporal behaviour of the measured ion species. Results: All ion species showed the highest intensities in the first spectra measured by both instruments approximately 20 to 30 min after Philae's first touchdown at Agilkia, and a decay during the six consecutive measurements at Abydos. Both instruments measured an almost identical decay of the water peak (m/z 18), and CO (m/z 28) behaved similarly. In the COSAC measurements, the peak at m/z 44 decays much slower than all the other ion species, including the water peak. In particular, the m/z 44 peak decays much slower in the COSAC measurements than in the Ptolemy data. This supports our earlier interpretation that COSAC analysed, for the first time, a regolith sample from a cometary nucleus in situ, while Ptolemy measured cometary gas from the ambient coma. The m/z 44 peak measured by COSAC was likely dominated by organic species, whereas the peak measured by Ptolemy was interpreted to be mostly due to CO2. Ion species heavier than m/z 30 tend to decay somewhat slower in the COSAC measurements than in the Ptolemy data, which may be related to differences in the exhaust designs between both instruments.

  18. A combined nuclear magnetic resonance and computational study of monohydroxyflavones applied to product ion mass spectra.

    PubMed

    Burns, Darcy C; Ellis, David A; Li, Hongxia; Lewars, Errol G; March, Raymond E

    2007-01-01

    A method is presented for the estimation of 13C-chemical shifts for carbon atoms in protonated and deprotonated molecules; in principle, this method can be applied to ions in general. Experimental 13C-chemical shifts were found to vary linearly with computed atomic charges using the PM3 method. Pseudo-13C-chemical shifts for atoms in protonated and deprotonated molecules can be estimated from computed atomic charges for such atoms using the above linear relationship. The pseudo-13C-chemical shifts obtained were applied to the rationalization of product ion mass spectra of protonated and deprotonated molecules of flavone and 3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavones, where product ion formation is due to either cross-ring cleavage of the C-ring (retro-Diels-Alder reaction) or to cleavage of a C-ring bond followed by loss of either a small neutral molecule or a radical. The total product ion abundance ratio of C-ring cross cleavage to C-ring bond cleavage, gamma, varied by a factor of 660 for deprotonated monohydroxyflavones, i.e., from 0.014:1 to 9.27:1. The magnitude of gamma, which is dependent on the relative bond orders within the C-ring of the protonated and deprotonated molecules of monohydroxyflavones, can be rationalized on the basis of the magnitudes of the 13C- and 1H-chemical shifts as determined by nuclear magnetic resonance spectroscopy.

  19. Measurement of branching fractions and mass spectra of B-->Kpipigamma.

    PubMed

    Aubert, B; Barate, R; Boutigny, D; Couderc, F; Karyotakis, Y; Lees, J P; Poireau, V; Tisserand, V; Zghiche, A; Grauges, E; Palano, A; Pappagallo, M; Pompili, A; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Ofte, I; Stugu, B; Abrams, G S; Battaglia, M; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Charles, E; Day, C T; Gill, M S; Gritsan, A V; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kolomensky, Yu G; Kukartsev, G; Lynch, G; Mir, L M; Oddone, P J; Orimoto, T J; Pripstein, M; Roe, N A; Ronan, M T; Wenzel, W A; Barrett, M; Ford, K E; Harrison, T J; Hart, A J; Hawkes, C M; Morgan, S E; Watson, A T; Fritsch, M; Goetzen, K; Held, T; Koch, H; Lewandowski, B; Pelizaeus, M; Peters, K; Schroeder, T; Steinke, M; Boyd, J T; Burke, J P; Chevalier, N; Cottingham, W N; Kelly, M P; Cuhadar-Donszelmann, T; Fulsom, B G; Hearty, C; Knecht, N S; Mattison, T S; McKenna, J A; Khan, A; Kyberd, P; Saleem, M; Teodorescu, L; Blinov, A E; Blinov, V E; Bukin, A D; Druzhinin, V P; Golubev, V B; Kravchenko, E A; Onuchin, A P; Serednyakov, S I; Skovpen, Yu I; Solodov, E P; Yushkov, A N; Best, D; Bondioli, M; Bruinsma, M; Chao, M; Eschrich, I; Kirkby, D; Lankford, A J; Mandelkern, M; Mommsen, R K; Roethel, W; Stoker, D P; Buchanan, C; Hartfiel, B L; Foulkes, S D; Gary, J W; Long, O; Shen, B C; Wang, K; Zhang, L; del Re, D; Hadavand, H K; Hill, E J; MacFarlane, D B; Paar, H P; Rahatlou, S; Sharma, V; Berryhill, J W; Campagnari, C; Cunha, A; Dahmes, B; Hong, T M; Mazur, M A; Richman, J D; Verkerke, W; Beck, T W; Eisner, A M; Flacco, C J; Heusch, C A; Kroseberg, J; Lockman, W S; Nesom, G; Schalk, T; Schumm, B A; Seiden, A; Spradlin, P; Williams, D C; Wilson, M G; Albert, J; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Narsky, I; Piatenko, T; Porter, F C; Ryd, A; Samuel, A; Andreassen, R; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Blanc, F; Bloom, P; Chen, S; Ford, W T; Nauenberg, U; Olivas, A; Rankin, P; Ruddick, W O; Smith, J G; Ulmer, K A; Wagner, S R; Zhang, J; Chen, A; Eckhart, E A; Soffer, A; Toki, W H; Wilson, R J; Zeng, Q; Altenburg, D; Feltresi, E; Hauke, A; Spaan, B; Brandt, T; Brose, J; Dickopp, M; Klose, V; Lacker, H M; Nogowski, R; Otto, S; Petzold, A; Schott, G; Schubert, J; Schubert, K R; Schwierz, R; Sundermann, J E; Bernard, D; Bonneaud, G R; Grenier, P; Schrenk, S; Thiebaux, Ch; Vasileiadis, G; Verderi, M; Bard, D J; Clark, P J; Gradl, W; Muheim, F; Playfer, S; Xie, Y; Andreotti, M; Azzolini, V; Bettoni, D; Bozzi, C; Calabrese, R; Cibinetto, G; Luppi, E; Negrini, M; Piemontese, L; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Zallo, A; Buzzo, A; Capra, R; Contri, R; Lo Vetere, M; Macri, M; Monge, M R; Passaggio, S; Patrignani, C; Robutti, E; Santroni, A; Tosi, S; Bailey, S; Brandenburg, G; Chaisanguanthum, K S; Morii, M; Won, E; Wu, J; Dubitzky, R S; Langenegger, U; Marks, J; Schenk, S; Uwer, U; Bhimji, W; Bowerman, D A; Dauncey, P D; Egede, U; Flack, R L; Gaillard, J R; Morton, G W; Nash, J A; Nikolich, M B; Taylor, G P; Vazquez, W P; Charles, M J; Mader, W F; Mallik, U; Mohapatra, A K; Cochran, J; Crawley, H B; Eyges, V; Meyer, W T; Prell, S; Rosenberg, E I; Rubin, A E; Yi, J; Arnaud, N; Davier, M; Giroux, X; Grosdidier, G; Höcker, A; Le Diberder, F; Lepeltier, V; Lutz, A M; Oyanguren, A; Petersen, T C; Pierini, M; Plaszczynski, S; Rodier, S; Roudeau, P; Schune, M H; Stocchi, A; Wormser, G; Cheng, C H; Lange, D J; Simani, M C; Wright, D M; Bevan, A J; Chavez, C A; Coleman, J P; Forster, I J; Fry, J R; Gabathuler, E; Gamet, R; George, K A; Hutchcroft, D E; Parry, R J; Payne, D J; Schofield, K C; Touramanis, C; Cormack, C M; Di Lodovico, F; Sacco, R; Brown, C L; Cowan, G; Flaecher, H U; Green, M G; Hopkins, D A; Jackson, P S; McMahon, T R; Ricciardi, S; Salvatore, F; Brown, D; Davis, C L; Allison, J; Barlow, N R; Barlow, R J; Hodgkinson, M C; Lafferty, G D; Naisbit, M T; Williams, J C; Chen, C; Farbin, A; Hulsbergen, W D; Jawahery, A; Kovalskyi, D; Lae, C K; Lillard, V; Roberts, D A; Simi, G; Blaylock, G; Dallapiccola, C; Hertzbach, S S; Kofler, R; Koptchev, V B; Li, X; Moore, T B; Saremi, S; Staengle, H; Willocq, S; Cowan, R; Koeneke, K; Sciolla, G; Sekula, S J; Spitznagel, M; Taylor, F; Yamamoto, R K; Kim, H; Patel, P M; Robertson, S H; Lazzaro, A; Lombardo, V; Palombo, F; Bauer, J M; Cremaldi, L; Eschenburg, V; Godang, R; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Zhao, H W; Brunet, S; Côté, D; Taras, P; Viaud, B; Nicholson, H; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Monorchio, D; Paolucci, P; Piccolo, D; Sciacca, C; Baak, M; Bulten, H; Raven, G; Snoek, H L; Wilden, L; Jessop, C P; LoSecco, J M; Allmendinger, T; Benelli, G; Gan, K K; Honscheid, K; Hufnagel, D; Jackson, P D; Kagan, H; Kass, R; Pulliam, T; Rahimi, A M; Ter-Antonyan, R; Wong, Q K; Brau, J; Frey, R; Igonkina, O; Lu, M; Potter, C T; Sinev, N B; Strom, D; Strube, J; Torrence, E; Dorigo, A; Galeazzi, F; Margoni, M; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; Del Buono, L; de la Vaissière, Ch; Hamon, O; John, M J J; Leruste, Ph; Malclès, J; Ocariz, J; Roos, L; Therin, G; Behera, P K; Gladney, L; Guo, Q H; Panetta, J; Biasini, M; Covarelli, R; Pacetti, S; Pioppi, M; Angelini, C; Batignani, G; Bettarini, S; Bucci, F; Calderini, G; Carpinelli, M; Cenci, R; Forti, F; Giorgi, M A; Lusiani, A; Marchiori, G; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Walsh, J; Haire, M; Judd, D; Wagoner, D E; Biesiada, J; Danielson, N; Elmer, P; Lau, Y P; Lu, C; Olsen, J; Smith, A J S; Telnov, A V; Bellini, F; Cavoto, G; D'Orazio, A; Di Marco, E; Faccini, R; Ferrarotto, F; Ferroni, F; Gaspero, M; Li Gioi, L; Mazzoni, M A; Morganti, S; Piredda, G; Polci, F; Safai Tehrani, F; Voena, C; Schröder, H; Wagner, G; Waldi, R; Adye, T; De Groot, N; Franek, B; Gopal, G P; Olaiya, E O; Wilson, F F; Aleksan, R; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P-F; Graziani, G; Hamel de Monchenault, G; Kozanecki, W; Legendre, M; London, G W; Mayer, B; Vasseur, G; Yèche, Ch; Zito, M; Purohit, M V; Weidemann, A W; Wilson, J R; Yumiceva, F X; Abe, T; Allen, M T; Aston, D; Bartoldus, R; Berger, N; Boyarski, A M; Buchmueller, O L; Claus, R; Convery, M R; Cristinziani, M; Dingfelder, J C; Dong, D; Dorfan, J; Dujmic, D; Dunwoodie, W; Fan, S; Field, R C; Glanzman, T; Gowdy, S J; Hadig, T; Halyo, V; Hast, C; Hryn'ova, T; Innes, W R; Kelsey, M H; Kim, P; Kocian, M L; Leith, D W G S; Libby, J; Luitz, S; Luth, V; Lynch, H L; Marsiske, H; Messner, R; Muller, D R; O'Grady, C P; Ozcan, V E; Perazzo, A; Perl, M; Ratcliff, B N; Roodman, A; Salnikov, A A; Schindler, R H; Schwiening, J; Snyder, A; Stelzer, J; Su, D; Sullivan, M K; Suzuki, K; Swain, S; Thompson, J M; Va'vra, J; Weaver, M; Weinstein, A J R; Wisniewski, W J; Wittgen, M; Wright, D H; Yarritu, A K; Yi, K; Young, C C; Burchat, P R; Edwards, A J; Majewski, S A; Petersen, B A; Roat, C; Ahmed, M; Ahmed, S; Alam, M S; Ernst, J A; Saeed, M A; Wappler, F R; Zain, S B; Bugg, W; Krishnamurthy, M; Spanier, S M; Eckmann, R; Ritchie, J L; Satpathy, A; Schwitters, R F; Izen, J M; Kitayama, I; Lou, X C; Ye, S; Bianchi, F; Bona, M; Gallo, F; Gamba, D; Bomben, M; Bosisio, L; Cartaro, C; Cossutti, F; Della Ricca, G; Dittongo, S; Grancagnolo, S; Lanceri, L; Vitale, L; Martinez-Vidal, F; Panvini, R S; Banerjee, Sw; Bhuyan, B; Brown, C M; Fortin, D; Hamano, K; Kowalewski, R; Roney, J M; Sobie, R J; Back, J J; Harrison, P F; Latham, T E; Mohanty, G B; Band, H R; Chen, X; Cheng, B; Dasu, S; Datta, M; Eichenbaum, A M; Flood, K T; Graham, M; Hollar, J J; Johnson, J R; Kutter, P E; Li, H; Liu, R; Mellado, B; Mihalyi, A; Pan, Y; Prepost, R; Tan, P; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Neal, H

    2007-05-25

    We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B-->Kpipigamma in the range m(Kpipi)<1.8 GeV/c(2). We reconstruct four final states: K(+)pi(-)pi(+)gamma, K(+)pi(-)pi(0)gamma, K(S)(0)pi(-)pi(+)gamma, and K(S)(0)pi(+)pi(0)gamma, where K(S)(0)-->pi(+)pi(-). Using 232 x 10(6) e(+)e(-)-->BB events recorded by the BABAR experiment at the SLAC PEP-II asymmetric-energy storage ring, we measure the branching fractions B(B(+)-->K(+)pi(-)pi(+)gamma)=[2.95+/-0.13(stat)+/-0.20(syst)] x 10(-5), B(B(0)-->K(+)pi(-)pi(0)gamma)=[4.07+/-0.22(stat)+/-0.31(syst)] x 10(-5), B(B(0)-->K(0)pi(+)pi(-)gamma)=[1.85+/-0.21(stat)+/-0.12(syst)] x 10(-5), and B(B(+)-->K(0)pi(+)pi(0)gamma)=[4.56+/-0.42(stat)+/-0.31(syst)] x 10(-5).

  20. FUV Spectra of Evolved Late-K and M Stars: Mass Loss Revisited and Stellar Activity

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2002-01-01

    This is the final report for the FUSE Cycle 1 program A100: FUV Spectra of Evolved Late-K and M Stars: Mass Loss revisited and Stellar Activity. Targets alpha TrA (K3 II) and gamma Cru (M3 III) were originally assigned 25 ksec each, to be observed in the medium aperture. Once the in-flight performance and telescope alignment problems were known, the observations were reprogrammed to optimized the scientific return of the program. Alpha TrA was scheduled for 25 ksec observations in both the medium and large apertures. The principle aim of this program was to measure the stellar FUV line and continuum emission, in order to estimate the photoionization radiation field and to determine the level of stellar activity through the fluxes in the collisionally excited high temperature diagnostics: C III 977Angstroms and O VI 1032,1038Angstrom doublet. The medium aperture observations were obtained successfully while the large aperture observations were thought by Johns Hopkins University (JHU)to be lost to satellite problems. There was insufficient signal-to- noise in the medium aperture short wavelength Sic channels to do quantitative science.

  1. Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography.

    PubMed

    Kolli, R Prakash

    2017-01-01

    Residual hydrogen (H2) gas in the analysis chamber of an atom probe instrument limits the ability to measure H concentration in metals and alloys. Measuring H concentration would permit quantification of important physical phenomena, such as hydrogen embrittlement, corrosion, hydrogen trapping, and grain boundary segregation. Increased insight into the behavior of residual H2 gas on the specimen tip surface in atom probe instruments could help reduce these limitations. The influence of user-selected experimental parameters on the field adsorption and desorption of residual H2 gas on nominally pure copper (Cu) was studied during ultraviolet pulsed laser atom probe tomography. The results indicate that the total residual hydrogen concentration, HTOT, in the mass spectra exhibits a generally decreasing trend with increasing laser pulse energy and increasing laser pulse frequency. Second-order interaction effects are also important. The pulse energy has the greatest influence on the quantity HTOT, which is consistently less than 0.1 at.% at a value of 80 pJ.

  2. Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline

    SciTech Connect

    Jaitly, Navdeep; Monroe, Matthew E.; Petyuk, Vladislav A.; Clauss, Therese RW; Adkins, Joshua N.; Smith, Richard D.

    2006-11-01

    Liquid chromatography coupled to mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS) has become a standard technique for analyzing complex peptide mixtures to determine composition and relative quantity. Several high-throughput proteomics techniques attempt to combine complementary results from multiple LC-MS and LC-MS/MS analyses to provide more comprehensive and accurate results. To effectively collate results from these techniques, variations in mass and elution time measurements between related analyses are corrected by using algorithms designed to align the various types of results: LC-MS/MS vs. LC-MS/MS, LC-MS vs. LC-MS/MS, and LC-MS vs. LC-MS. Described herein are new algorithms referred to collectively as Liquid Chromatography based Mass Spectrometric Warping and Alignment of Retention times of Peptides (LCMSWARP) which use a dynamic elution time warping approach similar to traditional algorithms that correct variation in elution time using piecewise linear functions. LCMSWARP is compared to a linear alignment algorithm that assumes a linear transformation of elution time between analyses. LCMSWARP also corrects for drift in mass measurement accuracies that are often seen in an LC-MS analysis due to factors such as analyzer drift. We also describe the alignment of LC-MS results and provide examples of alignment of analyses from different chromatographic systems to demonstrate more complex transformation functions.

  3. Accurate grading of brain gliomas by soft independent modeling of class analogy based on non-negative matrix factorization of proton magnetic resonance spectra.

    PubMed

    Ghasemi, K; Khanmohammadi, M; Saligheh Rad, H

    2016-02-01

    Hydrogen magnetic resonance spectroscopy ((1) H-MRS) is a non-invasive technique which provides a 'frequency-signal intensity' spectrum of biochemical compounds of tissues in the body. Although this method is currently used in human brain studies, accurate classification of in-vivo (1) H-MRS is a challenging task in the diagnosis of brain tumors. Problems such as overlapping metabolite peaks, incomplete information on background component and low signal-to-noise ratio disturb classification results of this spectroscopic method. This study presents an alternative approach to the soft independent modeling of class analogy (SIMCA) technique, using non-negative matrix factorization (NMF) for dimensionality reduction. In the adopted strategy, the performance of SIMCA was improved by application of a robust algorithm for classification in the presence of noisy measurements. Total of 219 spectra from two databases were taken by water-suppressed short echo-time (1) H-MRS, acquired from different subjects with different stages of glial brain tumors (Grade II (26 cases), grade III (24 cases), grade IV (41 cases), as well as 25 healthy cases). The SIMCA was performed using two approaches: (i) principal component analysis (PCA) and (ii) non-negative matrix factorization (NMF), as a modified approach. Square prediction error was considered to assess the class membership of the external validation set. Finally, several figures of merit such as the correct classification rate (CCR), sensitivity and specificity were calculated. Results of SIMCA based on NMF showed significant improvement in percentage of correctly classified samples, 91.4% versus 83.5% for PCA-based model in an independent test set.

  4. De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence

    PubMed Central

    Vyatkina, Kira

    2017-01-01

    De novo sequencing of tandem (MS/MS) mass spectra represents the only way to determine the sequence of proteins from organisms with unknown genomes, or the ones not directly inscribed in a genome—such as antibodies, or novel splice variants. Top-down mass spectrometry provides new opportunities for analyzing such proteins; however, retrieving a complete protein sequence from top-down MS/MS spectra still remains a distant goal. In this paper, we review the state-of-the-art on this subject, and enhance our previously developed Twister algorithm for de novo sequencing of peptides from top-down MS/MS spectra to derive longer sequence fragments of a target protein. PMID:28248257

  5. Ambient ionization-accurate mass spectrometry (AMI-AMS) for the identification of nonvisible set-off in food-contact materials.

    PubMed

    Bentayeb, Karim; Ackerman, Luke K; Begley, Timothy H

    2012-02-29

    Set-off is the unintentional transfer of substances used in printing from the external printed surface of food packaging to the inner, food-contact surface. Ambient ionization-accurate mass spectrometry (AMI-AMS) detected and identified compounds from print set-off not visible to the human eye. AMI mass spectra from inner and outer surfaces of printed and nonprinted food packaging were compared to detect and identify nonvisible set-off components. A protocol to identify unknowns was developed using a custom open-source database of printing inks and food-packaging compounds. The protocol matched print-related food-contact surface ions with the molecular formulas of common ions, isotopes, and fragments of compounds from the database. AMI-AMS was able to detect print set-off and identify seven different compounds. Set-off on the packaging samples was confirmed using gas chromatographic-mass spectrometric (GC-MS) analysis of single-sided solvent extracts. N-Ethyl-2(and 4)-methylbenzenesulfonamide, 2,4-diphenyl-4-methyl-1(and 2)-pentene, and 2,4,7,9-tetramethyl-5-decyne-4,7-diol were present on the food-contact layer at concentrations from 0.21 to 2.7 ± 1.6 μg dm⁻², corresponding to nearly milligram per kilogram concentrations in the packaged food. Other minor set-off compounds were detected only by AMI-AMS, a fast, simple, and thorough technique to detect and identify set-off in food packaging.

  6. Implications of (Less) Accurate Mass-Radius-Measurements for the Habitability of Extrasolar Terrestrial Planets: Why Do We Need PLATO?

    NASA Astrophysics Data System (ADS)

    Noack, L.; Wagner, F. W.; Plesa, A.-C.; Höning, D.; Sohl, F.; Breuer, D.; Rauer, H.

    2012-04-01

    Several space missions (CoRoT, Kepler and others) already provided promising candidates for terrestrial exoplanets (i.e. with masses less than about 10 Earth masses) and thereby triggered an exciting new research branch of planetary modelling to investigate the possible habitability of such planets. Earth analogues (low-mass planets with an Earth-like structure and composition) are likely to be found in the near future with new missions such as the proposed M3 mission PLATO. Planets may be more diverse in the universe than they are in the solar system. Our neighbouring planets in the habitable zone are all terrestrial by the means of being differentiated into an iron core, a silicate mantle and a crust. To reliably determine the interior structure of an exoplanet, measurements of mass and radius have to be sufficiently accurate (around +/-2% error allowed for the radius and +/-5% for the mass). An Earth-size planet with an Earth-like mass but an expected error of ~15% in mass for example may have either a Mercury-like, an Earth-like or a Moon-like (i.e. small iron core) structure [1,2]. Even though the atmospheric escape is not strongly influenced by the interior structure, the outgassing of volatiles and the likeliness of plate tectonics and an ongoing carbon-cycle may be very different. Our investigations show, that a planet with a small silicate mantle is less likely to shift into the plate-tectonics regime, cools faster (which may lead to the loss of a magnetic field after a short time) and outgasses less volatiles than a planet with the same mass but a large silicate mantle and small iron core. To be able to address the habitability of exoplanets, space missions such as PLATO, which can lead up to 2% accuracy in radius [3], are extremely important. Moreover, information about the occurrence of different planetary types helps us to better understand the formation of planetary systems and to further constrain the Drake's equation, which gives an estimate of the

  7. Accurate determination of peptide phosphorylation stoichiometry via automated diagonal capillary electrophoresis coupled with mass spectrometry: proof of principle.

    PubMed

    Mou, Si; Sun, Liangliang; Dovichi, Norman J

    2013-11-19

    While reversible protein phosphorylation plays an important role in many cellular processes, simple and reliable measurement of the stoichiometry of phosphorylation can be challenging. This measurement is confounded by differences in the ionization efficiency of phosphorylated and unphosphorylated sites during analysis by mass spectrometry. Here, we demonstrate diagonal capillary electrophoresis-mass spectrometry for the accurate determination of this stoichiometry. Diagonal capillary electrophoresis is a two-dimensional separation method that incorporates an immobilized alkaline phosphatase microreactor at the distal end of the first capillary and employs identical electrophoretic separation modes in both dimensions. The first dimension is used to separate a mixture of the phosphorylated and unphosphorylated forms of a peptide. Fractions are parked in the reactor where they undergo complete dephosphorylation. The products are then periodically transferred to the second capillary and analyzed by mass spectrometry (MS). Because the phosphorylated and unphosphorylated forms differ in charge, they are well resolved in the first dimension separation. Because the unphosphorylated and dephosphorylated peptides are identical, there is no bias in ionization efficiency, and phosphorylation stoichiometry can be determined by the ratio of the signal of the two forms. A calibration curve was generated from mixtures of a phosphorylated standard peptide and its unphosphorylated form, prepared in a bovine serum albumin tryptic digest. This proof of principle experiment demonstrated a linear response across nearly 2 orders of magnitude in stoichiometry.

  8. A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Cannon, William R.; Oehmen, Christopher S.; Shah, Anuj R.; Gurumoorthi, Vidhya; Lipton, Mary S.; Waters, Katrina M.

    2008-07-01

    Motivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares these profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (MS/MS) studies. It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic). Results: We present a Support Vector Machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity, and polarity for the quantitative prediction of proteotypic peptides. Using three independently derived AMT databases (Shewanella oneidensis, Salmonella typhimurium, Yersinia pestis) for training and validation within and across species, the SVM resulted in an average accuracy measure of ~0.8 with a standard deviation of less than 0.025. Furthermore, we demonstrate that these results are achievable with a small set of 12 variables and can achieve high proteome coverage. Availability: http://omics.pnl.gov/software/STEPP.php

  9. Typical ultraviolet spectra in combination with diagnostic mass fragmentation analysis for the rapid and comprehensive profiling of chlorogenic acids in the buds of Lonicera macranthoides.

    PubMed

    Zhang, Shui-Han; Hu, Xin; Shi, Shu-Yun; Huang, Lu-Qi; Chen, Wei; Chen, Lin; Cai, Ping

    2016-05-01

    A major challenge of profiling chlorogenic acids (CGA) in natural products is to effectively detect unknown or minor isomeric compounds. Here, we developed an effective strategy, typical ultraviolet (UV) spectra in combination with diagnostic mass fragmentation analysis based on HPLC-DAD-QTOF-MS/MS, to comprehensively profile CGA in the buds of Lonicera macranthoides. First, three CGA UV patterns were obtained by UV spectra screening. Second, 13 types of CGA classified by molecular weights were found by thorough analysis of CGA peaks using high-resolution MS. Third, selected ion monitoring (SIM) was carried out for each type of CGA to avoid overlooking of minor ones. Fourth, MS/MS spectra of each CGA were investigated. Then 70 CGA were identified by matching their UV spectra, accurate mass signals and fragmentation patterns with standards or previously reported compounds, including six caffeoylquinic acids (CQA), six diCQA, one triCQA, three caffeoylshikimic acids (CSA), six diCSA, one triCSA, three p-coumaroylquinic acids (pCoQA), four p-coumaroylcaffeoylquinic acids (pCoCQA), four feruloylquinic acids (FQA), five methyl caffeoylquinates (MCQ), three ethyl caffeoylquinates (ECQ), three dimethoxycinnamoylquinic acids (DQA), six caffeoylferuloylquinic acids (CFQA), six methyl dicaffeoylquinates (MdiCQ), four FQA glycosides (FQAG), six MCQ glycosides (MCQG), and three ethyl dicaffeoylquinates (EdiCQ). Forty-five of them were discovered from Lonicera species for the first time, and it is noted that CGA profiles were investigated for the first time in L. macranthoides. Results indicated that the developed method was a useful approach to explore unknown and minor isomeric compounds from complex natural products.

  10. AUTOMATED DECONVOLUTION OF COMPOSITE MASS SPECTRA OBTAINED WITH AN OPEN-AIR IONIZATIONS SOURCE BASED ON EXACT MASSES AND RELATIVE ISOTIPIC ABUNDANCES

    EPA Science Inventory

    Chemicals dispersed by accidental, deliberate, or weather-related events must be rapidly identified to assess health risks. Mass spectra from high levels of analytes obtained using rapid, open-air ionization by a Direct Analysis in Real Time (DART®) ion source often contain

  11. Identification of Novel Perfluoroalkyl Ether Carboxylic Acids (PFECAs) and Sulfonic Acids (PFESAs) in Natural Waters Using Accurate Mass Time-of-Flight Mass Spectrometry (TOFMS).

    PubMed

    Strynar, Mark; Dagnino, Sonia; McMahen, Rebecca; Liang, Shuang; Lindstrom, Andrew; Andersen, Erik; McMillan, Larry; Thurman, Michael; Ferrer, Imma; Ball, Carol

    2015-10-06

    Recent scientific scrutiny and concerns over exposure, toxicity, and risk have led to international regulatory efforts resulting in the reduction or elimination of certain perfluorinated compounds from various products and waste streams. Some manufacturers have started producing shorter chain per- and polyfluorinated compounds to try to reduce the potential for bioaccumulation in humans and wildlife. Some of these new compounds contain central ether oxygens or other minor modifications of traditional perfluorinated structures. At present, there has been very limited information published on these "replacement chemistries" in the peer-reviewed literature. In this study we used a time-of-flight mass spectrometry detector (LC-ESI-TOFMS) to identify fluorinated compounds in natural waters collected from locations with historical perfluorinated compound contamination. Our workflow for discovery of chemicals included sequential sampling of surface water for identification of potential sources, nontargeted TOFMS analysis, molecular feature extraction (MFE) of samples, and evaluation of features unique to the sample with source inputs. Specifically, compounds were tentatively identified by (1) accurate mass determination of parent and/or related adducts and fragments from in-source collision-induced dissociation (CID), (2) in-depth evaluation of in-source adducts formed during analysis, and (3) confirmation with authentic standards when available. We observed groups of compounds in homologous series that differed by multiples of CF2 (m/z 49.9968) or CF2O (m/z 65.9917). Compounds in each series were chromatographically separated and had comparable fragments and adducts produced during analysis. We detected 12 novel perfluoroalkyl ether carboxylic and sulfonic acids in surface water in North Carolina, USA using this approach. A key piece of evidence was the discovery of accurate mass in-source n-mer formation (H(+) and Na(+)) differing by m/z 21.9819, corresponding to the

  12. Masses of the components of SB2 binaries observed with Gaia - III. Accurate SB2 orbits for 10 binaries and masses of HIP 87895

    NASA Astrophysics Data System (ADS)

    Kiefer, F.; Halbwachs, J.-L.; Arenou, F.; Pourbaix, D.; Famaey, B.; Guillout, P.; Lebreton, Y.; Nebot Gómez-Morán, A.; Mazeh, T.; Salomon, J.-B.; Soubiran, C.; Tal-Or, L.

    2016-05-01

    In anticipation of the Gaia astrometric mission, a large sample of spectroscopic binaries has been observed since 2010 with the Spectrographe pour l'Observation des PHénomènes des Intérieurs Stellaires et des Exoplanètes spectrograph at the Haute-Provence Observatory. Our aim is to derive the orbital elements of double-lined spectroscopic binaries (SB2s) with an accuracy sufficient to finally obtain the masses of the components with relative errors as small as 1 per cent when the astrometric measurements of Gaia are taken into account. In this paper, we present the results from five years of observations of 10 SB2 systems with periods ranging from 37 to 881 d. Using the TODMOR algorithm, we computed radial velocities from the spectra, and then derived the orbital elements of these binary systems. The minimum masses of the components are then obtained with an accuracy better than 1.2 per cent for the 10 binaries. Combining the radial velocities with existing interferometric measurements, we derived the masses of the primary and secondary components of HIP 87895 with an accuracy of 0.98 and 1.2 per cent, respectively.

  13. Vacuum ultraviolet photoionization mass spectra and cross-sections for volatile organic compounds at 10.5 eV.

    PubMed

    Kanno, Nozomu; Tonokura, Kenichi

    2007-08-01

    Vacuum ultraviolet single-photon ionization time-of-flight mass spectrometry (VUV-SPI-TOFMS) has been applied to the detection of volatile organic compounds (VOCs), including aromatic, chlorinated, and oxygenated compounds. Photoionization mass spectra of 23 VOCs were measured using SPI-TOFMS at 10.5 eV (118 nm). The limits of detection of VOCs using SPI-TOFMS at 10.5 eV were estimated to be a few ppbv. The mass spectra of 20 VOCs exhibit only the parent ion and its isotopes' signals. The ionization processes of the VOCs were discussed on the basis of the reaction enthalpies predicted by the quantum chemical calculations. Absolute photoionization cross-sections for 23 VOCs, including 12 newly measured VOCs, at 10.5 eV were determined in comparison to the reported absolute photoionization cross-section of NO.

  14. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species.

    PubMed

    Alanio, A; Beretti, J-L; Dauphin, B; Mellado, E; Quesne, G; Lacroix, C; Amara, A; Berche, P; Nassif, X; Bougnoux, M-E

    2011-05-01

    New Aspergillus species have recently been described with the use of multilocus sequencing in refractory cases of invasive aspergillosis. The classical phenotypic identification methods routinely used in clinical laboratories failed to identify them adequately. Some of these Aspergillus species have specific patterns of susceptibility to antifungal agents, and misidentification may lead to inappropriate therapy. We developed a matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based strategy to adequately identify Aspergillus species to the species level. A database including the reference spectra of 28 clinically relevant species from seven Aspergillus sections (five common and 23 unusual species) was engineered. The profiles of young and mature colonies were analysed for each reference strain, and species-specific spectral fingerprints were identified. The performance of the database was then tested on 124 clinical and 16 environmental isolates previously characterized by partial sequencing of the β-tubulin and calmodulin genes. One hundred and thirty-eight isolates of 140 (98.6%) were correctly identified. Two atypical isolates could not be identified, but no isolate was misidentified (specificity: 100%). The database, including species-specific spectral fingerprints of young and mature colonies of the reference strains, allowed identification regardless of the maturity of the clinical isolate. These results indicate that MALDI-TOF MS is a powerful tool for rapid and accurate identification of both common and unusual species of Aspergillus. It can give better results than morphological identification in clinical laboratories.

  15. Measurement of Branching Fractions and Mass Spectra of B to K pi pi gamma

    SciTech Connect

    Aubert, B.; Barate, R.; Boutigny, D.; Couderc, F.; Karyotakis, Y.; Lees, J.P.; Poireau, V.; Tisserand, V.; Zghiche, A.; Grauges, E.; Palano, A.; Pappagallo, M.; Pompili, A.; Chen, J.C.; Qi, N.D.; Rong, G.; Wang, P.; Zhu, Y.S.; Eigen, G.; Ofte, I.; Stugu, B. /Bergen U. /LBL, Berkeley /UC, Berkeley /Birmingham U. /Ruhr U., Bochum /Bristol U. /British Columbia U. /Brunel U. /Novosibirsk, IYF /UC, Irvine /UCLA /UC, Riverside /UC, San Diego /UC, Santa Barbara /UC, Santa Cruz /Caltech /Cincinnati U. /Colorado U. /Colorado State U. /Dortmund U. /Dresden, Tech. U. /Ecole Polytechnique /Edinburgh U. /Ferrara U. /INFN, Ferrara /Frascati /Genoa U. /INFN, Genoa /Harvard U. /Heidelberg U. /Imperial Coll., London /Iowa U. /Iowa State U. /Orsay, LAL /LLNL, Livermore /Liverpool U. /Queen Mary, U. of London /Royal Holloway, U. of London /Louisville U. /Manchester U. /Maryland U. /Massachusetts U., Amherst /MIT, LNS /McGill U. /Milan U. /INFN, Milan /Mississippi U. /Montreal U. /Mt. Holyoke Coll. /Naples U. /INFN, Naples /NIKHEF, Amsterdam /Notre Dame U. /Ohio State U. /Oregon U. /INFN, Padua /Padua U. /Paris U., VI-VII /Pennsylvania U. /Perugia U. /INFN, Perugia /Pisa U. /Pisa, Scuola Normale Superiore /INFN, Pisa /Prairie View A-M /Princeton U. /Rome U. /INFN, Rome /Rostock U. /Rutherford /DAPNIA, Saclay /South Carolina U. /SLAC /Stanford U., Phys. Dept. /SUNY, Albany /Tennessee U. /Texas U. /Texas U., Dallas /Turin U. /INFN, Turin /Trieste U. /INFN, Trieste /Valencia U., IFIC /Vanderbilt U. /Victoria U. /Warwick U. /Wisconsin U., Madison /Yale U.

    2005-07-12

    The authors present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B {yields} K{pi}{pi}{gamma} in the range m{sub K{pi}{pi}} < 1.8 GeV/c{sup 2}. They reconstruct four final states: K{sup +}{pi}{sup -}{pi}{sup +}{gamma}, K{sup +}{pi}{sup -}{pi}{sup 0}{gamma}, K{sub S}{sup 0}{pi}{sup -}{pi}{sup +}{gamma}, and K{sub S}{sup 0}{pi}{sup +}{pi}{sup 0}{gamma}, where K{sub S}{sup 0} {yields} {pi}{sup +}{pi}{sup -}. Using 232 million e{sup +}e{sup -} {yields} B{bar B} events recorded by the BABAR experiment at the PEP-II asymmetric-energy storage ring, they measure the branching fractions {Beta}(B{sup +} {yields} K{sup +}{pi}{sup -}{pi}{sup +}{gamma}) = (2.95 {+-} 0.13(stat.) {+-} 0.20(syst)) x 10{sup -5}, {Beta}(B{sup 0} {yields} K{sup +}{pi}{sup -}{pi}{sup 0}{gamma}) = (4.07 {+-} 0.22(stat.) {+-} 0.31(syst.)) x 10{sup -5}, {Beta}(B{sup 0} {yields} K{sup 0}{pi}{sup +}{pi}{sup -}{gamma}) = (1.85 {+-} 0.21(stat.) {+-} 0.12(syst.)) x 10{sup -5}, and {Beta}(B{sup +} {yields} K{sup 0}{pi}{sup +}{pi}{sup 0}{gamma}) = (4.56 {+-} 0.42(stat.) {+-} 0.31(syst.)) x 10{sup -5}.

  16. Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate

    PubMed Central

    Steinmetz, Melissa; Czupryna, Anna; Bigambo, Machunde; Mzimbiri, Imam; Powell, George; Gwakisa, Paul

    2015-01-01

    In this study we show that incentives (dog collars and owner wristbands) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey) method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey). Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere. PMID:26633821

  17. Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate.

    PubMed

    Minyoo, Abel B; Steinmetz, Melissa; Czupryna, Anna; Bigambo, Machunde; Mzimbiri, Imam; Powell, George; Gwakisa, Paul; Lankester, Felix

    2015-12-01

    In this study we show that incentives (dog collars and owner wristbands) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey) method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey). Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere.

  18. Exact masses and chemical formulas of individual Suwannee River fulvic acids from ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectra.

    PubMed

    Stenson, Alexandra C; Marshall, Alan G; Cooper, William T

    2003-03-15

    Molecular formulas have been assigned for 4626 individual Suwannee River fulvic acids based on accurate mass measurements from ions generated by electrospray ionization and observed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Formula assignments were possible because of the mass accuracy of FTICR MS at high field (9.4 T) and the regular mass spacing patterns found in fulvic acid mixtures. Sorting the 4626 individually observed ions according to Kendrick mass defect and nominal mass series (z* score) revealed that all could be assigned to 1 of 266 distinct homologous series that differ in oxygen content and double bond equivalence. Tandem mass spectrometry based on infrared multiphoton dissociation identified labile fragments of fulvic acid molecules, whose chemical formulas led to plausible structures consistent with degraded lignin as a source of Suwannee River fulvic acids.

  19. The Effect of Starspots on Accurate Radius Determination of the Low-Mass Double-Lined Eclipsing Binary Gu Boo

    NASA Astrophysics Data System (ADS)

    Windmiller, G.; Orosz, J. A.; Etzel, P. B.

    2010-04-01

    GU Boo is one of only a relatively small number of well-studied double-lined eclipsing binaries that contain low-mass stars. López-Morales & Ribas present a comprehensive analysis of multi-color light and radial velocity curves for this system. The GU Boo light curves presented by López-Morales & Ribas had substantial asymmetries, which were attributed to large spots. In spite of the asymmetry, López-Morales & Ribas derived masses and radii accurate to sime2%. We obtained additional photometry of GU Boo using both a CCD and a single-channel photometer and modeled the light curves with the ELC software to determine if the large spots in the light curves give rise to systematic errors at the few percent level. We also modeled the original light curves from the work of López-Morales & Ribas using models with and without spots. We derived a radius of the primary of 0.6329 ± 0.0026 R sun, 0.6413 ± 0.0049 R sun, and 0.6373 ± 0.0029 R sun from the CCD, photoelectric, and López-Morales & Ribas data, respectively. Each of these measurements agrees with the value reported by López-Morales & Ribas (R 1 = 0.623 ± 0.016 R sun) at the level of ≈2%. In addition, the spread in these values is ≈1%-2% from the mean. For the secondary, we derive radii of 0.6074 ± 0.0035 R sun, 0.5944 ± 0.0069 R sun, and 0.5976 ± 0.0059 R sun from the three respective data sets. The López-Morales & Ribas value is R 2 = 0.620 ± 0.020 R sun, which is ≈2%-3% larger than each of the three values we found. The spread in these values is ≈2% from the mean. The systematic difference between our three determinations of the secondary radius and that of López-Morales & Ribas might be attributed to differences in the modeling process and codes used. Our own fits suggest that, for GU Boo at least, using accurate spot modeling of a single set of multi-color light curves results in radii determinations accurate at the ≈2% level.

  20. Highly sensitive and accurate screening of 40 dyes in soft drinks by liquid chromatography-electrospray tandem mass spectrometry.

    PubMed

    Feng, Feng; Zhao, Yansheng; Yong, Wei; Sun, Li; Jiang, Guibin; Chu, Xiaogang

    2011-06-15

    A method combining solid phase extraction with high performance liquid chromatography-electrospray ionization tandem mass spectrometry was developed for the highly sensitive and accurate screening of 40 dyes, most of which are banned in foods. Electrospray ionization tandem mass spectrometry was used to identify and quantify a large number of dyes for the first time, and demonstrated greater accuracy and sensitivity than the conventional liquid chromatography-ultraviolet/visible methods. The limits of detection at a signal-to-noise ratio of 3 for the dyes are 0.0001-0.01 mg/L except for Tartrazine, Amaranth, New Red and Ponceau 4R, with detection limits of 0.5, 0.25, 0.125 and 0.125 mg/L, respectively. When this method was applied to screening of dyes in soft drinks, the recoveries ranged from 91.1 to 105%. This method has been successfully applied to screening of illegal dyes in commercial soft drink samples, and it is valuable to ensure the safety of food.

  1. Determination of Peptide and Protein Ion Charge States by Fourier Transformation of Isotope-Resolved Mass Spectra

    SciTech Connect

    Tabb, Dave L; Shah, Manesh B; Strader, Michael B; Connelly, Heather M; Hettich, Robert {Bob} L; Hurst, Gregory {Greg} B

    2006-01-01

    We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from 'zoom scan' data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly-through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution.

  2. A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy

    SciTech Connect

    Adkins, Joshua N.; Monroe, Matthew E.; Auberry, Kenneth J.; Shen, Yufeng; Jacobs, Jon M.; Camp, David G.; Vitzthum, Frank; Rodland, Karin D.; Zangar, Richard C.; Smith, Richard D.; Pounds, Joel G.

    2005-08-01

    Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an Accurate Mass and Time (AMT) tag strategy with high-resolution mass accuracy capillary liquid chromatography Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (cLC-FTICR MS) to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published “shotgun” proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index (IPI) redundant proteins, or 377 protein families by ProteinProphet, were identified over the 6 individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/-23) as found in the serum samples (average 440+/-20). These proteins were identified by an average of 956+/-35 unique peptides in plasma and 930+/-11 unique peptides in serum. In addition to this high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput, and provided a basis for estimated quantitation.

  3. Characterization of signatures from organic compounds in CDA mass spectra of ice particles in Saturn's E-ring

    NASA Astrophysics Data System (ADS)

    Khawaja, Nozair; Postberg, Frank; Reviol, Rene; Srama, Ralf

    2015-04-01

    The major source of ice particles in Saturn's E-ring is Enceladus - a geological active moon of Saturn. Enceladus is emanating ice particles from its fractured south polar terrain (SPT), the so-called "Tiger Stripes". The source of Enceladus activity and many of the ice particles is a subsurface ocean. The Cosmic Dust Analyzer (CDA) onboard the Cassini spacecraft is sampling these icy particles and producing TOF mass spectra of cations of impinging particles [1]. Three compositional types of ice particles have been identified from CDA-mass spectra: (i) pure water ice (Type-1) (ii) organic rich (Type-2) (iii) salt rich (Type-3) [2][3]. These organic rich (Type-2) spectra are particularly abundant in the icy jets of Enceladus as we found out during the Cassini's Enceladus flybys (E17 and E18) in 2012 [4]. We present a compositional analysis of the CDA spectra of these organic rich icy grains sampled in the E ring. We have characterized hundreds of Type-2 spectra of impinging ice particles. These were recorded at different impact velocities causing different molecular fragmentation patterns observed in the mass spectra. We defined 3 typical impact speed intervals: (i) 4-7 km/s (ii) 8-11 km/s and (iii) 12-16km/s. Organic features best observed at slow (4-7 km/s) or at intermediate (8-11 km/s) impact velocity ranges. Several classes of organic rich spectra are identified. Classifying Type-2 spectra are according to their characteristic mass lines of possible organic species. We try to infer the composition of each class of organic rich spectra is inferred by using an experimental setup (IR-FL-MALDI) to simulate the CDA spectra of different compositional types. In the laboratory we have used infrared laser to disperse a micro-beam of a water solution [5]. The laser energy is adjusted to simulate different impact velocities of ice particles on the CDA. Four families of organic compounds including alcohols, fatty acids, amines and aromatic, with varying number of carbon

  4. SVM model for quality assessment of medium resolution mass spectra from 18O-water labeling experiments.

    PubMed

    Nefedov, Alexey V; Gilski, Miroslaw J; Sadygov, Rovshan G

    2011-04-01

    We describe a method for assessing the quality of mass spectra and improving reliability of relative ratio estimations from (18)O-water labeling experiments acquired from low resolution mass spectrometers. The mass profiles of heavy and light peptide pairs are often affected by artifacts, including coeluting contaminant species, noise signal, instrumental fluctuations in measuring ion position and abundance levels. Such artifacts distort the profiles, leading to erroneous ratio estimations, thus reducing the reliability of ratio estimations in high throughput quantification experiments. We used support vector machines (SVMs) to filter out mass spectra that deviated significantly from expected theoretical isotope distributions. We built an SVM classifier with a decision function that assigns a score to every mass profile based on such spectral features as mass accuracy, signal-to-noise ratio, and differences between experimental and theoretical isotopic distributions. The classifier was trained using a data set obtained from samples of mouse renal cortex. We then tested it on protein samples (bovine serum albumin) mixed in five different ratios of labeled and unlabeled species. We demonstrated that filtering the data using our SVM classifier results in as much as a 9-fold reduction in the coefficient of variance of peptide ratios, thus significantly improving the reliability of ratio estimations.

  5. ROSAT Energy Spectra of Low-Mass X-Ray Binaries

    NASA Astrophysics Data System (ADS)

    Schulz, N. S.

    1999-01-01

    The 0.1-2.4 keV bandpass of the ROSAT Position Sensitive Proportional Counter (PSPC) offers an opportunity to study the very soft X-ray continuum of bright low-mass X-ray binaries (LMXBs). In 46 pointed observations, 23 LMXBs were observed with count rates between 0.4 and 165.4 counts s-1. The survey identified a total of 29 different luminosity levels, which are compared with observations and identified spectral states from other missions. The atoll source 4U 1705-44 was observed near Eddington luminosities in an unusually high intensity state. Spectral analysis provided a measure of the interstellar column density for all 49 observations. The sensitivity of spectral fits depends strongly on column density. Fits to highly absorbed spectra are merely insensitive toward any particular spectral model. Sources with column densities well below 1022 cm-2 are best fitted by power laws, while the blackbody model gives clearly worse fits to the data. Most single-component fits from sources with low column densities, however, are not acceptable at all. The inclusion of a blackbody component in eight sources can improve the fits significantly. The obtained emission radii of less than 5 km suggest emission from the neutron star surface. In 10 sources acceptable fits can only be achieved by including soft-line components. With a spectral resolution of the PSPC of 320-450 eV, between 0.6 and 1.2 keV unresolved broad-line features were detected around 0.65, 0.85, and 1.0 keV. The line fluxes range within 10-11 and 10-12 ergs cm-2 s-1, with equivalent widths between 24 and 210 eV. In LMC X-2, 2S 0918-549, and 4U 1254-690, line emission is indicated for the first time. The soft emission observed in 4U 0614+091 compares with recent ASCA results, with a new feature indicated at 1.31 keV. The deduced line fluxes in 4U 1820-30 and Cyg X-2 showed variability of a factor of 2 within timescales of 1-2 days. Average fluxes of line components in 4U 1820-30 varied by the same factor over a

  6. Method for calibrating mass spectrometers

    DOEpatents

    Anderson, Gordon A [Benton City, WA; Brands, Michael D [Richland, WA; Bruce, James E [Schwenksville, PA; Pasa-Tolic, Ljiljana [Richland, WA; Smith, Richard D [Richland, WA

    2002-12-24

    A method whereby a mass spectra generated by a mass spectrometer is calibrated by shifting the parameters used by the spectrometer to assign masses to the spectra in a manner which reconciles the signal of ions within the spectra having equal mass but differing charge states, or by reconciling ions having known differences in mass to relative values consistent with those known differences. In this manner, the mass spectrometer is calibrated without the need for standards while allowing the generation of a highly accurate mass spectra by the instrument.

  7. PHYSICAL PROPERTIES OF YOUNG BROWN DWARFS AND VERY LOW MASS STARS INFERRED FROM HIGH-RESOLUTION MODEL SPECTRA

    SciTech Connect

    Rice, Emily L.; Mclean, Ian S.; Barman, T.; Prato, L.; Kirkpatrick, J. Davy

    2010-01-01

    By comparing near-infrared spectra with atmospheric models, we infer the effective temperature, surface gravity, projected rotational velocity, and radial velocity for 21 very low mass stars and brown dwarfs. The unique sample consists of two sequences in spectral type from M6-M9, one of 5-10 Myr objects and one of >1 Gyr field objects. A third sequence is comprised of only {approx}M6 objects with ages ranging from <1 Myr to >1 Gyr. Spectra were obtained in the J band at medium (R {approx} 2000) and high (R {approx} 20,000) resolutions with NIRSPEC on the Keck II telescope. Synthetic spectra were generated from atmospheric structures calculated with the PHOENIX model atmosphere code. Using multi-dimensional least-squares fitting and Monte Carlo routines we determine the best-fit model parameters for each observed spectrum and note which spectral regions provide consistent results. We identify successes in the reproduction of observed features by atmospheric models, including pressure-broadened K I lines, and investigate deficiencies in the models, particularly missing FeH opacity, that will need to be addressed in order to extend our analysis to cooler objects. The precision that can be obtained for each parameter using medium- and high-resolution near-infrared spectra is estimated and the implications for future studies of very low mass stars and brown dwarfs are discussed.

  8. Suzaku spectra of the neutron-star low-mass X-ray binary 4U 1608-52

    NASA Astrophysics Data System (ADS)

    Lei, Yajuan; Zhang, Haotong; zhang, Yanxia

    2015-08-01

    We present the spectral analysis of the neutron-star low-mass X-ray binary 4U 1608-52 using data from four Suzaku observations in 2010 March. 4U 1608-52 is a transient atoll source, and the analyzed observations contain the “island” and “banana” states, corresponding transitional, and soft states. The spectra are fitted with the hybrid model for the soft states, which consists of two thermal components (a multicolor accretion disk and a single-temperature blackbody) plus a broken power law. The fitting results show that the continuum spectra evolve during the different states. Fe emission line is often detected in low-mass X-ray binary, however, no obviously Fe line is detected in the four observations of 4U 1608-52.

  9. Highly sensitive capillary electrophoresis-mass spectrometry for rapid screening and accurate quantitation of drugs of abuse in urine.

    PubMed

    Kohler, Isabelle; Schappler, Julie; Rudaz, Serge

    2013-05-30

    The combination of capillary electrophoresis (CE) and mass spectrometry (MS) is particularly well adapted to bioanalysis due to its high separation efficiency, selectivity, and sensitivity; its short analytical time; and its low solvent and sample consumption. For clinical and forensic toxicology, a two-step analysis is usually performed: first, a screening step for compound identification, and second, confirmation and/or accurate quantitation in cases of presumed positive results. In this study, a fast and sensitive CE-MS workflow was developed for the screening and quantitation of drugs of abuse in urine samples. A CE with a time-of-flight MS (CE-TOF/MS) screening method was developed using a simple urine dilution and on-line sample preconcentration with pH-mediated stacking. The sample stacking allowed for a high loading capacity (20.5% of the capillary length), leading to limits of detection as low as 2 ng mL(-1) for drugs of abuse. Compound quantitation of positive samples was performed by CE-MS/MS with a triple quadrupole MS equipped with an adapted triple-tube sprayer and an electrospray ionization (ESI) source. The CE-ESI-MS/MS method was validated for two model compounds, cocaine (COC) and methadone (MTD), according to the Guidance of the Food and Drug Administration. The quantitative performance was evaluated for selectivity, response function, the lower limit of quantitation, trueness, precision, and accuracy. COC and MTD detection in urine samples was determined to be accurate over the range of 10-1000 ng mL(-1) and 21-1000 ng mL(-1), respectively.

  10. Retrospective screening of relevant pesticide metabolites in food using liquid chromatography high resolution mass spectrometry and accurate-mass databases of parent molecules and diagnostic fragment ions.

    PubMed

    Polgár, László; García-Reyes, Juan F; Fodor, Péter; Gyepes, Attila; Dernovics, Mihály; Abrankó, László; Gilbert-López, Bienvenida; Molina-Díaz, Antonio

    2012-08-03

    In recent years, the detection and characterization of relevant pesticide metabolites in food is an important task in order to evaluate their formation, kinetics, stability, and toxicity. In this article, a methodology for the systematic screening of pesticides and their main metabolites in fruit and vegetable samples is described, using LC-HRMS and accurate-mass database search of parent compounds and their diagnostic fragment ions. The approach is based on (i) search for parent pesticide molecules; (ii) search for their metabolites in the positive samples, assuming common fragmentation pathways between the metabolites and parent pesticide molecules; and (iii) search for pesticide conjugates using the data from both parent species and diagnostic fragment ions. An accurate-mass database was constructed consisting of 1396 compounds (850 parent compounds, 447 fragment ions and 99 metabolites). The screening process was performed by the software in an automated fashion. The proposed methodology was evaluated with 29 incurred samples and the output obtained was compared to standard pesticide testing methods (targeted LC-MS/MS). Examples on the application of the proposed approach are shown, including the detection of several pesticide glycosides derivatives, which were found with significantly relevant intensities. Glucose-conjugated forms of parent compounds (e.g., fenhexamid-O-glucoside) and those of metabolites (e.g., despropyl-iprodione-N-glycoside) were detected. Facing the lack of standards for glycosylated pesticides, the study was completed with the synthesis of fenhexamid-O-glucoside for quantification purposes. In some cases the pesticide derivatives were found in a relatively high ratio, drawing the attention to these kinds of metabolites and showing that they should not be neglected in multi-residue methods. The global coverage obtained on the 29 analyzed samples showed the usefulness and benefits of the proposed approach and highlights the practical

  11. Innovations in Mass Spectrometry for Precise and Accurate Isotope Ratio Determination from Very Small Analyte Quantities (Invited)

    NASA Astrophysics Data System (ADS)

    Lloyd, N. S.; Bouman, C.; Horstwood, M. S.; Parrish, R. R.; Schwieters, J. B.

    2010-12-01

    This presentation describes progress in mass spectrometry for analysing very small analyte quantities, illustrated by example applications from nuclear forensics. In this challenging application, precise and accurate (‰) uranium isotope ratios are required from 1 - 2 µm diameter uranium oxide particles, which comprise less than 40 pg of uranium. Traditionally these are analysed using thermal ionisation mass spectrometry (TIMS), and more recently using secondary ionisation mass spectrometry (SIMS). Multicollector inductively-coupled plasma mass spectrometry (MC-ICP-MS) can offer higher productivity compared to these techniques, but is traditionally limited by low efficiency of analyte utilisation (sample through to ion detection). Samples can either be introduced as a solution, or sampled directly from solid using laser ablation. Large multi-isotope ratio datasets can help identify provenance and intended use of anthropogenic uranium and other nuclear materials [1]. The Thermo Scientific NEPTUNE Plus (Bremen, Germany) with ‘Jet Interface’ option offers unparalleled MC-ICP-MS sensitivity. An analyte utilisation of c. 4% has previously been reported for uranium [2]. This high-sensitivity configuration utilises a dry high-capacity (100 m3/h) interface pump, special skimmer and sampler cones and a desolvating nebuliser system. Coupled with new acquisition methodologies, this sensitivity enhancement makes possible the analysis of micro-particles and small sample volumes at higher precision levels than previously achieved. New, high-performance, full-size and compact discrete dynode secondary electron multipliers (SEM) exhibit excellent stability and linearity over a large dynamic range and can be configured to simultaneously measure all of the uranium isotopes. Options for high abundance-sensitivity filters on two ion beams are also available, e.g. for 236U and 234U. Additionally, amplifiers with high ohm (1012 - 1013) feedback resistors have been developed to

  12. Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modelling of complete high time-resolution aerosol mass spectra

    NASA Astrophysics Data System (ADS)

    McGuire, M. L.; Chang, R. Y.-W.; Slowik, J. G.; Jeong, C.-H.; Healy, R. M.; Lu, G.; Mihele, C.; Abbatt, J. P. D.; Brook, J. R.; Evans, G. J.

    2014-02-01

    Receptor modelling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's CRUISER mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach was compared to the more common method of analysing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulphate and oxygenated organic aerosol containing factor (Sulphate-OA); an ammonium nitrate and oxygenated organic aerosol containing factor (Nitrate-OA); an ammonium chloride containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analysing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case, an Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this method would be even more useful for HR-ToF-AMS data, due to the ability

  13. Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modeling of complete high time-resolution aerosol mass spectra

    NASA Astrophysics Data System (ADS)

    McGuire, M. L.; Chang, R. Y.-W.; Slowik, J. G.; Jeong, C.-H.; Healy, R. M.; Lu, G.; Mihele, C.; Abbatt, J. P. D.; Brook, J. R.; Evans, G. J.

    2014-08-01

    Receptor modeling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's Canadian Regional and Urban Investigation System for Environmental Research (CRUISER) mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach compared to the more common method of analyzing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulfate- and oxygenated organic aerosol-containing factor (Sulfate-OA); an ammonium nitrate- and oxygenated organic aerosol-containing factor (Nitrate-OA); an ammonium chloride-containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analyzing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case the Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this

  14. Mass spectra of cyclic ethers formed in the low-temperature oxidation of a series of n-alkanes

    PubMed Central

    Herbinet, Olivier; Bax, Sarah; Glaude, Pierre-Alexandre; Carré, Vincent; Battin-Leclerc, Frédérique

    2013-01-01

    Cyclic ethers are important intermediate species formed during the low-temperature oxidation of hydrocarbons. Along with ketones and aldehydes, they could consequently represent a significant part of the heavy oxygenated pollutants observed in the exhaust gas of engines. Apart a few of them such as ethylene oxide and tetrahydrofuran, cyclic ethers have not been much studied and very few of them are available for calibration and identification. Electron impact mass spectra are available for very few of them, making their detection in the exhaust emissions of combustion processes very difficult. The main goal of this study was to complete the existing set of mass spectra for this class of molecules. Thus cyclic ethers have been analyzed in the exhaust gases of a jet-stirred reactor in which the low-temperature oxidation of a series of n-alkanes was taking place. Analyzes were performed by gas chromatography coupled to mass spectrometry and to MS/MS. The second goal of this study was to derive some rules for the fragmentation of cyclic ethers in electron impact mass spectrometry and allow the identification of these species when no mass spectrum is available. PMID:24092947

  15. Rapid automated screening, identification and quantification of organic micro-contaminants and their main transformation products in wastewater and river waters using liquid chromatography-quadrupole-time-of-flight mass spectrometry with an accurate-mass database.

    PubMed

    Gómez, M J; Gómez-Ramos, M M; Malato, O; Mezcua, M; Férnandez-Alba, A R

    2010-11-05

    In this study we have developed and evaluated an analytical method for a rapid automated screening and confirmation of a large number of organic micro-contaminants (almost 400) and also the quantification of the positive findings in water samples of different types (surface and wastewaters) using liquid chromatography-electrospray quadrupole-time-of-flight mass spectrometry (LC-QTOFMS) based on the use of an accurate-mass database. The created database includes data not only on the accurate masses of the target ions but also on the characteristic in-source fragment ions, isotopic pattern and retention time data. This customized database was linked to commercially available software which extracted all the potential compounds of interest from the LC-QTOFMS raw data of each sample and matched them against the database to search for targeted compounds in the sample. The detailed fragmentation information has also been used as a powerful tool for the automatic identification of unknown compounds and/or transformation products with similar structures to those of known organic contaminants included in the database. The database can be continually enlarged. To confirm identification of compounds which have no fragment ions (or fragments with low intensity/relative abundance) from in-source CID fragmentation or isomers which are not distinguished within full single mass spectra, a "Targeted MS/MS" method is developed. Thereafter, these compounds can be further analyzed using the collision energy (CE) in QTOF-MS/MS mode. Linearity and limits of detection were studied. Method detection limits (MDLs) in effluent wastewater and river waters were, in most cases, lowers or equal to 5 and 2 ng/L, respectively. Only 15 compounds had MDLs between 5 and 50 ng/L in effluent wastewater matrix. We obtained a linearity of the calibration curves over two orders of magnitude. The method has been applied to real samples and the results obtained reveal that most of the pharmaceutically

  16. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sidebottom, Ashley M.; Karty, Jonathan A.; Carlson, Erin E.

    2015-11-01

    Siderophores are bacterially secreted, small molecule iron chelators that facilitate the binding of insoluble iron (III) for reuptake and use in various biological processes. These compounds are classified by their iron (III) binding geometry, as dictated by subunit composition and include groups such as the trihydroxamates (hexadentate ligand) and catecholates (bidentate). Small modifications to the core structure such as acetylation, lipid tail addition, or cyclization, make facile characterization of new siderophores difficult by molecular ion detection alone (MS1). We have expanded upon previous fragmentation-directed studies using electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS/MS) and identified diagnostic MS3 features from the trihydroxamate siderophore class for ferrioxamine B and E1 by accurate mass. Diagnostic features for MS3 include C-C, C-N, amide, and oxime cleavage events with proposed losses of water and -CO from the iron (III) coordination sites. These insights will facilitate the discovery of novel trihydroxamate siderophores from complex sample matrices.

  17. Accurate quantification of creatinine in serum by coupling a measurement standard to extractive electrospray ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Huang, Keke; Li, Ming; Li, Hongmei; Li, Mengwan; Jiang, You; Fang, Xiang

    2016-01-01

    Ambient ionization (AI) techniques have been widely used in chemistry, medicine, material science, environmental science, forensic science. AI takes advantage of direct desorption/ionization of chemicals in raw samples under ambient environmental conditions with minimal or no sample preparation. However, its quantitative accuracy is restricted by matrix effects during the ionization process. To improve the quantitative accuracy of AI, a matrix reference material, which is a particular form of measurement standard, was coupled to an AI technique in this study. Consequently the analyte concentration in a complex matrix can be easily quantified with high accuracy. As a demonstration, this novel method was applied for the accurate quantification of creatinine in serum by using extractive electrospray ionization (EESI) mass spectrometry. Over the concentration range investigated (0.166 ~ 1.617 μg/mL), a calibration curve was obtained with a satisfactory linearity (R2 = 0.994), and acceptable relative standard deviations (RSD) of 4.6 ~ 8.0% (n = 6). Finally, the creatinine concentration value of a serum sample was determined to be 36.18 ± 1.08 μg/mL, which is in excellent agreement with the certified value of 35.16 ± 0.39 μg/mL.

  18. Determination of the presence or absence of sulfur materials in drywall using direct analysis in real time in conjunction with an accurate-mass time-of-flight mass spectrometer.

    PubMed

    Curtis, Matthew E; Jones, Patrick R; Sparkman, O David; Cody, Robert B

    2009-11-01

    Based on the concern about the presence of sulfur materials being in drywall (wallboard), a quick and reliable test to confirm the presence or absence of these materials using direct analysis in real time (DART) mass spectrometry in conjunction with an accurate-mass time-of-flight (TOF) mass spectrometer has been developed and is described here.

  19. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family

    PubMed Central

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A.

    2016-01-01

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF3) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  20. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family.

    PubMed

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A

    2015-12-02

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF₃) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  1. Splitting mass spectra and muon g - 2 in Higgs-anomaly mediation

    NASA Astrophysics Data System (ADS)

    Yin, Wen; Yokozaki, Norimi

    2016-11-01

    We propose a scenario where only the Higgs multiplets have direct couplings to a supersymmetry (SUSY) breaking sector. The standard model matter multiplets as well as the gauge multiples are sequestered from the SUSY breaking sector; therefore, their masses arise via anomaly mediation at the high energy scale with a gravitino mass of ∼ 100TeV. Due to renormalization group running effects from the Higgs soft masses, the masses of the third generation sfermions become O (10)TeV at the low energy scale, while the first and second generation sfermion masses are O (0.1- 1)TeV, avoiding the tachyonic slepton problem and flavor changing neutral current problem. With the splitting mass spectrum, the muon g - 2 anomaly is explained consistently with the observed Higgs boson mass of 125 GeV. Moreover, the third generation Yukawa couplings are expected to be unified in some regions.

  2. MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra.

    PubMed

    Kim, Sangtae; Na, Seungjin; Sim, Ji Woong; Park, Heejin; Jeong, Jaeho; Kim, Hokeun; Seo, Younghwan; Seo, Jawon; Lee, Kong-Joo; Paek, Eunok

    2006-07-01

    MOD(i) (http://modi.uos.ac.kr/modi/) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage (http://www.unimod.org) and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)'s output in a user-friendly manner and helps users understand MOD(i)'s output quickly. In addition, one can perform manual de novo sequencing using MassPective.

  3. Tooth enamel EPR dosimetry: optimization of EPR spectra recording parameters and effect of sample mass on spectral sensitivity.

    PubMed

    Zhumadilov, Kassym; Ivannikov, Alexander; Skvortsov, Valeriy; Stepanenko, Valeriy; Zhumadilov, Zhaxybay; Endo, Satoru; Tanaka, Kenichi; Hoshi, Masaharu

    2005-12-01

    In order to improve the accuracy of the tooth enamel EPR dosimetry method, EPR spectra recording conditions were optimized. The uncertainty of dose determination was obtained as the mean square deviation of doses, determined with the use of a spectra deconvolution program, from the nominal doses for ten enamel samples irradiated in the range from 0 to 500 mGy. The spectra were recorded at different microwave powers and accumulation times. It was shown that minimal uncertainty is achieved at the microwave power of about 2 mW for a used spectrometer JEOL JES-FA100. It was found that a limit of the accumulation time exists beyond which uncertainty reduction is ineffective. At an established total time of measurement, reduced uncertainty is obtained by averaging the experimental doses determined from recorded spectra following intermittent sample shaking and sample tube rotation, rather than from one spectrum recorded at longer accumulation time. The effect of sample mass on the spectrometer's sensitivity was investigated in order to find out how to make appropriate corrections.

  4. iMet: A Network-Based Computational Tool To Assist in the Annotation of Metabolites from Tandem Mass Spectra.

    PubMed

    Aguilar-Mogas, Antoni; Sales-Pardo, Marta; Navarro, Miriam; Guimerà, Roger; Yanes, Oscar

    2017-03-21

    Structural annotation of metabolites relies mainly on tandem mass spectrometry (MS/MS) analysis. However, approximately 90% of the known metabolites reported in metabolomic databases do not have annotated spectral data from standards. This situation has fostered the development of computational tools that predict fragmentation patterns in silico and compare these to experimental MS/MS spectra. However, because such methods require the molecular structure of the detected compound to be available for the algorithm, the identification of novel metabolites in organisms relevant for biotechnological and medical applications remains a challenge. Here, we present iMet, a computational tool that facilitates structural annotation of metabolites not described in databases. iMet uses MS/MS spectra and the exact mass of an unknown metabolite to identify metabolites in a reference database that are structurally similar to the unknown metabolite. The algorithm also suggests the chemical transformation that converts the known metabolites into the unknown one. As a proxy for the structural annotation of novel metabolites, we tested 148 metabolites following a leave-one-out cross-validation procedure or by using MS/MS spectra experimentally obtained in our laboratory. We show that for 89% of the 148 metabolites at least one of the top four matches identified by iMet enables the proper annotation of the unknown metabolites. To further validate iMet, we tested 31 metabolites proposed in the 2012-16 CASMI challenges. iMet is freely available at http://imet.seeslab.net .

  5. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    NASA Astrophysics Data System (ADS)

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae; Kwon, Chan Ho

    2014-11-01

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm-1 (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state (2A2), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C2v symmetry through the C-N axis.

  6. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    SciTech Connect

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho E-mail: hlkim@kangwon.ac.kr

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  7. Excited and exotic charmonium, D s and D meson spectra for two light quark masses from lattice QCD

    NASA Astrophysics Data System (ADS)

    Cheung, Gavin K. C.; O'Hara, Cian; Moir, Graham; Peardon, Michael; Ryan, Sinéad M.; Thomas, Christopher E.; Tims, David

    2016-12-01

    We present highly-excited charmonium, D s and D meson spectra from dynamical lattice QCD calculations with light quarks corresponding to M π ˜ 240 MeV and compare these to previous results with M π ˜ 400 MeV. Utilising the distillation framework, large bases of carefully constructed interpolating operators and a variational procedure, we extract and reliably identify the continuum spin of an extensive set of excited mesons. These include states with exotic quantum numbers which, along with a number with non-exotic quantum numbers, we identify as having excited gluonic degrees of freedom and interpret as hybrid mesons. Comparing the spectra at the two different M π , we find only a mild light-quark mass dependence and no change in the overall pattern of states.

  8. AUTOMATED ELEMENTAL COMPOSITION DETERMINATION AND CORRELATION OF PRECURSOR WITH PRODUCT IONS BASED ON ORTHOGONAL ACCELERATION, TIME-OF-FLIGHT MASS SPECTRA

    EPA Science Inventory

    For more than a decade in our laboratory, elemental compositions of ions in mass spectra havebeen routinely determined by measuring exact masses and relative isotopic abundances of ions in isotopicclusters using a GC coupled to a double focusing mass spectrometer.1 HPLC interfac...

  9. Evolved Late-Type Star FUV Spectra: Mass Loss and Fluorescence

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2005-01-01

    This proposal was for a detailed analysis of the far ultraviolet (FUV) photoionizing radiation that provides crucial input physics for mass loss studies, e.g., observations of the flux below 10448, allow us to constrain the Ca II/Ca III balance and make significant progress beyond previous optical studies on stellar mass loss and circumstellar photochemistry. Our targets selection provided good spectral-type coverage required to help unravel the Ca II/Ca III balance as the mass-loss rates increase by over three orders of magnitude from K5 III to M5 III. We also explored the relationship between the FUV radiation field and other UV diagnostics to allow us to empirically estimate the FUV radiation field for the vast majority of stars which are too faint to be observed with FUSE, and to improve upon their uncertain mass-loss rates.

  10. Accurate physical laws can permit new standard units: The two laws F→=ma→ and the proportionality of weight to mass

    NASA Astrophysics Data System (ADS)

    Saslow, Wayne M.

    2014-04-01

    Three common approaches to F→=ma→ are: (1) as an exactly true definition of force F→ in terms of measured inertial mass m and measured acceleration a→; (2) as an exactly true axiom relating measured values of a→, F→ and m; and (3) as an imperfect but accurately true physical law relating measured a→ to measured F→, with m an experimentally determined, matter-dependent constant, in the spirit of the resistance R in Ohm's law. In the third case, the natural units are those of a→ and F→, where a→ is normally specified using distance and time as standard units, and F→ from a spring scale as a standard unit; thus mass units are derived from force, distance, and time units such as newtons, meters, and seconds. The present work develops the third approach when one includes a second physical law (again, imperfect but accurate)—that balance-scale weight W is proportional to m—and the fact that balance-scale measurements of relative weight are more accurate than those of absolute force. When distance and time also are more accurately measurable than absolute force, this second physical law permits a shift to standards of mass, distance, and time units, such as kilograms, meters, and seconds, with the unit of force—the newton—a derived unit. However, were force and distance more accurately measurable than time (e.g., time measured with an hourglass), this second physical law would permit a shift to standards of force, mass, and distance units such as newtons, kilograms, and meters, with the unit of time—the second—a derived unit. Therefore, the choice of the most accurate standard units depends both on what is most accurately measurable and on the accuracy of physical law.

  11. Synthesis of nanoparticles in helium droplets—A characterization comparing mass-spectra and electron microscopy data

    SciTech Connect

    Thaler, Philipp; Volk, Alexander; Lackner, Florian; Steurer, Johannes; Schnedlitz, Martin; Ernst, Wolfgang E.; Knez, Daniel; Haberfehlner, Georg

    2015-10-07

    Micrometer sized helium droplets provide an extraordinary environment for the growth of nanoparticles. The method promises great potential for the preparation of core-shell particles as well as one-dimensional nanostructures, which agglomerate along quantum vortices, without involving solvents, ligands, or additives. Using a new apparatus, which enables us to record mass spectra of heavy dopant clusters (>10{sup 4} amu) and to produce samples for transmission electron microscopy simultaneously, we synthesize bare and bimetallic nanoparticles consisting of various materials (Au, Ni, Cr, and Ag). We present a systematical study of the growth process of clusters and nanoparticles inside the helium droplets, which can be described with a simple theoretical model.

  12. A responsivity-based criterion for accurate calibration of FTIR emission spectra: identification of in-band low-responsivity wavenumbers.

    PubMed

    Rowe, Penny M; Neshyba, Steven P; Cox, Christopher J; Walden, Von P

    2011-03-28

    Spectra measured by remote-sensing Fourier transform infrared spectrometers are often calibrated using two calibration sources. At wavenumbers where the absorption coefficient is large, air within the optical path of the instrument can absorb most calibration-source signal, resulting in extreme errors. In this paper, a criterion in terms of the instrument responsivity is used to identify such wavenumbers within the instrument bandwidth of two remote-sensing Fourier transform infrared spectrometers. Wavenumbers identified by the criterion are found to be correlated with strong absorption line-centers of water vapor. Advantages of using a responsivity-based criterion are demonstrated.

  13. Dielectron Mass Spectra in square root of sNN = 200 GeV Copper plus Copper Collisions at PHENIX

    NASA Astrophysics Data System (ADS)

    Campbell, Sarah Catherine

    The dielectron mass spectrum consists of light vector meson decays, correlated heavy quark contributions and decays from other hadronic and photonic sources. Thermal radiation and modifications to the light vector mesons may provide additional signals at low masses above known hadronic sources. The PHENIX sNN = 200 GeV Au+Au and Cu+Cu analyses have measured a centrality dependent excess in the the low mass region between 0.15 GeV/c 2 and 0.75 GeV/c2. Between the φ and the J/ψ, in the intermediate mass range, the correlated heavy quark decays are the primary dielectron source; direct photons may augment this region as well. The Cu+Cu system is sensitive to the onset of the dielectron excess. By studying the Cu+Cu mass spectra and yields as a function of pair pT and collision centrality we obtain further understanding of its behavior. Comparisons to the PHENIX Au+Au and p+p measurements an extrapolations from theory are presented.

  14. Virial Black Hole Mass Estimates for 280,000 AGNs from the SDSS Broadband Photometry and Single-epoch Spectra

    NASA Astrophysics Data System (ADS)

    Kozłowski, Szymon

    2017-01-01

    We use the Sloan Digital Sky Survey (SDSS) Quasar Data Release 12 (DR12Q), containing nearly 300,000 active galactic nuclei (AGNs), to calculate the monochromatic luminosities at 5100, 3000, and 1350 Å, derived from the broadband extinction-corrected SDSS magnitudes. After matching these sources to their counterparts from the SDSS Quasar Data Release 7 (DR7Q), we find very high correlations between our luminosities and DR7Q spectra-based luminosities with minute mean offsets (∼0.01 dex) and dispersions of differences of 0.11, 0.10, and 0.12 dex, respectively, across a luminosity range of 2.5 dex. We then estimate the black hole (BH) masses of the AGNs using the broad line region radius–disk luminosity relations and the FWHM of the Mg ii and C iv emission lines, to provide a catalog of 283,033 virial BH mass estimates (132,451 for Mg ii, 213,071 for C iv, and 62,489 for both) along with the estimates of the bolometric luminosity and Eddington ratio for 0.1 < z < 5.5 and for roughly a quarter of the sky covered by SDSS. The BH mass estimates from Mg ii turned out to be closely matched to the ones from DR7Q with a dispersion of differences of 0.34 dex across a BH mass range of ∼2 dex. We uncovered a bias in the derived C iv FWHMs from DR12Q as compared to DR7Q, which we correct empirically. The C iv BH mass estimates should be used with caution because the C iv line is known to cause problems in the estimation of BH mass from single-epoch spectra. Finally, after the FWHM correction, the AGN BH mass estimates from C iv closely match the DR7Q ones (with a dispersion of 0.28 dex), and more importantly the Mg ii and C iv BH masses agree internally with a mean offset of 0.07 dex and a dispersion of 0.39 dex.

  15. Randomness in the dark sector: Emergent mass spectra and Dynamical Dark Matter ensembles

    NASA Astrophysics Data System (ADS)

    Dienes, Keith R.; Fennick, Jacob; Kumar, Jason; Thomas, Brooks

    2016-04-01

    In general, nonminimal models of the dark sector such as Dynamical Dark Matter posit the existence of an ensemble of individual dark components with differing masses, cosmological abundances, and couplings to the Standard Model. Perhaps the most critical among these features is the spectrum of masses, as this goes a long way towards determining the cosmological abundances and lifetimes of the corresponding states. Many different underlying theoretical structures can be imagined for the dark sector, each giving rise to its own mass spectrum and corresponding density of states. In this paper, by contrast, we investigate the spectrum of masses that emerges statistically from underlying processes which are essentially random. We find a density of states n (m ) which decreases as a function of mass and actually has an upper limit mmax beyond which n (m )=0 . We also demonstrate that this "emergent" density of states is particularly auspicious from the perspective of the Dynamical Dark Matter framework, leading to cosmological abundances and decay widths that are suitably balanced against each other across the dark-matter ensemble. Thus randomness in the dark sector coexists quite naturally with Dynamical Dark Matter, and we examine the prospects for observing the signals of such scenarios in dark-matter indirect-detection experiments.

  16. BRIGHT RAY-LIKE FEATURES IN THE AFTERMATH OF CORONAL MASS EJECTIONS: WHITE LIGHT VERSUS ULTRAVIOLET SPECTRA

    SciTech Connect

    Ciaravella, A.; Webb, D. F.; Giordano, S.; Raymond, J. C.

    2013-03-20

    Current sheets (CSs) are important signatures of magnetic reconnection in the eruption of confined solar magnetic structures. Models of coronal mass ejections (CMEs) involve formation of a CS connecting the ejected flux rope with the post-eruption magnetic loops. CSs have been identified in white light (WL) images of CMEs as narrow rays trailing the outward moving CME core, and in ultraviolet spectra as narrow bright features emitting the [Fe XVIII] line. In this work, samples of rays detected in WL images or in ultraviolet spectra have been analyzed. Temperatures, widths, and line intensities of the rays have been measured, and their correlation to the CME properties has been studied. The samples show a wide range of temperatures with hot, coronal, and cool rays. In some cases, the UV spectra support the identification of rays as CSs, but they show that some WL rays are cool material from the CME core. In many cases, both hot and cool material are present, but offset from each other along the Ultraviolet Coronagraph Spectrometer slit. We find that about 18% of the WL rays show very hot gas consistent with the CS interpretation, while about 23% show cold gas that we attribute to cool prominence material draining back from the CME core. The remaining events have ordinary coronal temperatures, perhaps because they have relaxed back to a quiescent state.

  17. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

    PubMed Central

    Allen, Felicity; Pon, Allison; Wilson, Michael; Greiner, Russ; Wishart, David

    2014-01-01

    CFM-ID is a web server supporting three tasks associated with the interpretation of tandem mass spectra (MS/MS) for the purpose of automated metabolite identification: annotation of the peaks in a spectrum for a known chemical structure; prediction of spectra for a given chemical structure and putative metabolite identification—a predicted ranking of possible candidate structures for a target spectrum. The algorithms used for these tasks are based on Competitive Fragmentation Modeling (CFM), a recently introduced probabilistic generative model for the MS/MS fragmentation process that uses machine learning techniques to learn its parameters from data. These algorithms have been extensively tested on multiple datasets and have been shown to out-perform existing methods such as MetFrag and FingerId. This web server provides a simple interface for using these algorithms and a graphical display of the resulting annotations, spectra and structures. CFM-ID is made freely available at http://cfmid.wishartlab.com. PMID:24895432

  18. Mass Ordering of Spectra from Fragmentation of Saturated Gluon States in High-Multiplicity Proton-Proton Collisions

    NASA Astrophysics Data System (ADS)

    Schenke, Björn; Schlichting, Sören; Tribedy, Prithwish; Venugopalan, Raju

    2016-10-01

    The mass ordering of mean transverse momentum ⟨pT⟩ and of the Fourier harmonic coefficient v2(pT) of azimuthally anisotropic particle distributions in high energy hadron collisions is often interpreted as evidence for the hydrodynamic flow of the matter produced. We investigate an alternative initial state interpretation of this pattern in high-multiplicity proton-proton collisions at the LHC. The QCD Yang-Mills equations describing the dynamics of saturated gluons are solved numerically with initial conditions obtained from the color-glass-condensate-based impact-parameter-dependent glasma model. The gluons are subsequently fragmented into various hadron species employing the well established Lund string fragmentation algorithm of the pythia event generator. We find that this initial state approach reproduces characteristic features of bulk spectra, in particular, the particle mass dependence of ⟨pT⟩ and v2(pT).

  19. Accurate mass analysis of N-acyl-homoserine-lactones and cognate lactone-opened compounds in bacterial isolates of Pseudomonas aeruginosa PAO1 by LC-ESI-LTQ-FTICR-MS.

    PubMed

    Cataldi, Tommaso R I; Bianco, Giuliana; Abate, Salvatore

    2009-02-01

    N-acyl-homoserine-lactones (AHSLs) are widely conserved signal molecules present in quorum sensing systems of Gram-negative bacteria such as Pseudomonas aeruginosa. We present here the results obtained with a hybrid linear trap/Fourier transform ion cyclotron resonance (LTQ-FTICR) mass spectrometer used to investigate the occurrence of AHSLs and cognate N-acyl-homoserines (AHSs) in bacterial isolates of P. aeruginosa (strain PAO1). Two hydrolysed AHSs were found in significant amounts, most likely formed through the lactone opening of N-3-oxo-decanoyl-L-homoserine-lactone (3OC10-HSL) and N-3-oxo-dodecanoyl-L-homoserine-lactone (3OC12-HSL). Structure elucidation of these ring-opened molecules, i.e. N-3-oxo-decanoyl-L-homoserine (3OC10-HS), and N-3-oxo-dodecanoyl-L-homoserine (3OC12-HS), which are not detected by bacterial biosensors, was performed by high-resolution and accurate mass measurements upon liquid chromatography (LC) and confirmed by tandem MS in the LTQ analyser. Assignment of chemical formula, with mass spectra in the form of [M+H]+, was significantly expedited by extracted ion chromatograms (XICs) because the number of potentially plausible formulae for each protonated signalling molecule was considerably reduced a priori by the LC behaviour, the high mass measurement accuracy available in FTICR mass spectra and the isotopic patterns. At least two concentration levels were observed in spent culture supernatants of P. aeruginosa: compounds at a relatively high content (5-15 microM) that is C4-HSL, 3OC10-HS, and 3OC12-HS and those occurring at a lower content (<0.2 microM) that is C6-HSL and C8-HSL. The implications of this work extend to a great variety of Gram-negative bacteria.

  20. Identification of protein O-glycosylation site and corresponding glycans using liquid chromatography-tandem mass spectrometry via mapping accurate mass and retention time shift.

    PubMed

    Huang, Li-Juan; Lin, Jen-Hui; Tsai, Jung-Heng; Chu, Yen-Yin; Chen, Yen-Wen; Chen, Shun-Li; Chen, Shu-Hui

    2014-12-05

    We reported an improved combinatorial approach for identifying site-specific O-glycosylation using both glycan cleaved and non-cleaved methods. In this approach, a non-reducing β-elimination kit coupled with non-specific enzymes performed efficient digestion, O-glycan cleavage, and partial dephosphorylation without significant side reactions, thus enabling an automatic database search for the cleaved O-glycosylation or serine/threonine (S/T) phosphorylation sites. From the same sample concurrently prepared without β-elimination, the corresponding intact O-glycopeptides were mapped by accurate precursor ion mass using an in-house glycan database majorly composed of GalNAc (mucin-type) core and the retention-time shift (ΔRt). Each glycopeptide assignment was verified by the detection of glycan-specific fragments using collision-induced dissociation (CID) to estimate False Discovery Rate (FDR). Using fetuin as a model, all identified S/T elimination sites were matched to multiple intact glycopeptides with a 31% FDR. This considerably reduced to 0% FDR by ΔRt filtering. This approach was then applied to a protein mixture composed of therapeutic Factor IX and Enbrel(®) mixed with fetuin and kappa-casein. A total of 26 glycosylation sites each of which corresponds to 1-4 glycans were positively mapped and confirmed. The FDR decreased from 33% to 3.3% by ΔRt filtering and exclusion of repeated peptide tags that covered the same glycosylation sites. Moreover, the phosphorylation and O-glycosylation on the same site such as T159 of Factor IX and T170 of kappa-casein were able to be unambiguously differentiated. Thus, our approach is useful for in-depth characterization of site-specific O-glycosylation of a simple mixture such as protein-based therapeutics.

  1. Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

    PubMed

    Tessier, Dominique; Lollier, Virginie; Larré, Colette; Rogniaux, Hélène

    2016-10-07

    Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.

  2. Mass spectra of neutral particles released during electrical breakdown of thin polymer films

    NASA Technical Reports Server (NTRS)

    Kendall, B. R. F.

    1985-01-01

    A special type of time-of-flight mass spectrometer triggered from the breakdown event was developed to study the composition of the neutral particle flux released during the electrical breakdown of polymer films problem. Charge is fed onto a metal-backed polymer surface by a movable smooth platinum contact. A slowly increasing potential from a high-impedance source is applied to the contact until breakdown occurs. The breakdown characteristics is made similar to those produced by an electron beam charging system operating at similar potentials. The apparatus showed that intense instantaneous fluxes of neutral particles are released from the sites of breakdown events. For Teflon FEP films of 50 and 75 microns thickness the material released consists almost entirely of fluorocarbon fragments, some of them having masses greater than 350 atomic mass units amu, while the material released from a 50 micron Kapton film consists mainly of light hydrocarbons with masses at or below 44 amu, with additional carbon monoxide and carbon dioxide. The apparatus is modified to allow electron beam charging of the samples.

  3. Accurate wavelength measurements and modeling of FeXV to FeXIX spectra recorded in high density plasmas between 13.5 to 17 A.

    SciTech Connect

    May, M; Beiersdorfer, P; Dunn, J; Jordan, N; Osterheld, A; Faenov, A; Pikuz, T; Skobelev, I; Fora, F; Bollanti, S; Lazzaro, P D; Murra, D; Reale, A; Reale, L; Tomassetti, G; Ritucci, A; Francucci, M; Martellucci, S; Petrocelli, G

    2004-09-28

    Iron spectra have been recorded from plasmas created at three different laser plasma facilities, the Tor Vergata University laser in Rome (Italy), the Hercules laser at ENEA in Frascati (Italy), and the Compact Multipulse Terawatt (COMET) laser at LLNL in California (USA). The measurements provide a means of identifying dielectronic satellite lines from FeXVI and FeXV in the vicinity of the strong 2p {yields} 3d transitions of FeXVII. About 80 {Delta}n {ge} 1 lines of FeXV (Mg-like) to FeXIX (O-like) were recorded between 13.8 to 17.1 {angstrom} with a high spectral resolution ({lambda}/{Delta}{lambda} {approx} 4000), about thirty of these lines are from FeXVI and FeXV. The laser produced plasmas had electron temperatures between 100 to 500 eV and electron densities between 10{sup 20} to 10{sup 22} cm{sup -3}. The Hebrew University Lawrence Livermore Atomic Code (HULLAC) was used to calculate the atomic structure and atomic rates for FeXV to FeXIX. HULLAC was used to calculate synthetic line intensities at T{sub e} = 200 eV and n{sub e} = 10{sup 21}cm{sup -3} for three different conditions to illustrate the role of opacity: optically thin plasmas with no excitation-autoionization/dielectronic recombination (EA/DR) contributions to the line intensities, optically thin plasmas that included EA/DR contributions to the line intensities, and optically thick plasmas (optical depth {approx} 200 {micro}m) that included EA/DR contributions to the line intensities. The optically thick simulation best reproduced the recorded spectrum from the Hercules laser. However some discrepancies between the modeling and the recorded spectra remain.

  4. Precursor charge state prediction for electron transfer dissociation tandem mass spectra.

    PubMed

    Sharma, Vagisha; Eng, Jimmy K; Feldman, Sergey; von Haller, Priska D; MacCoss, Michael J; Noble, William S

    2010-10-01

    Electron-transfer dissociation (ETD) induces fragmentation along the peptide backbone by transferring an electron from a radical anion to a protonated peptide. In contrast with collision-induced dissociation, side chains and modifications such as phosphorylation are left intact through the ETD process. Because the precursor charge state is an important input to MS/MS sequence database search tools, the ability to accurately determine the precursor charge is helpful for the identification process. Furthermore, because ETD can be applied to large, highly charged peptides, the need for accurate precursor charge state determination is magnified. Otherwise, each spectrum must be searched repeatedly using a large range of possible precursor charge states. To address this problem, we have developed an ETD charge state prediction tool based on support vector machine classifiers that is demonstrated to exhibit superior classification accuracy while minimizing the overall number of predicted charge states. The tool is freely available, open source, cross platform compatible, and demonstrated to perform well when compared with an existing charge state prediction tool. The program is available from http://code.google.com/p/etdz/.

  5. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF).

  6. Instrumental improvements and sample preparations that enable reproducible, reliable acquisition of mass spectra from whole bacterial cells

    PubMed Central

    Alusta, Pierre; Buzatu, Dan; Williams, Anna; Cooper, Willie-Mae; Tarasenko, Olga; Dorey, R Cameron; Hall, Reggie; Parker, W Ryan; Wilkes, Jon G

    2015-01-01

    Rationale Rapid sub-species characterization of pathogens is required for timely responses in outbreak situations. Pyrolysis mass spectrometry (PyMS) has the potential to be used for this purpose. Methods However, in order to make PyMS practical for traceback applications, certain improvements related to spectrum reproducibility and data acquisition speed were required. The main objectives of this study were to facilitate fast detection (<30 min to analyze 6 samples, including preparation) and sub-species-level bacterial characterization based on pattern recognition of mass spectral fingerprints acquired from whole cells volatilized and ionized at atmospheric pressure. An AccuTOF DART mass spectrometer was re-engineered to permit ionization of low-volatility bacteria by means of Plasma Jet Ionization (PJI), in which an electric discharge, and, by extension, a plasma beam, impinges on sample cells. Results Instrumental improvements and spectral acquisition methodology are described. Performance of the re-engineered system was assessed using a small challenge set comprised of assorted bacterial isolates differing in identity by varying amounts. In general, the spectral patterns obtained allowed differentiation of all samples tested, including those of the same genus and species but different serotypes. Conclusions Fluctuations of ±15% in bacterial cell concentrations did not substantially compromise replicate spectra reproducibility. © 2015 National Center for Toxicological Research. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26443394

  7. Fitting of Hadron Mass Spectra and Contributions to Perturbation Theory of Conformal Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Luna Acosta, German Aurelio

    The masses of observed hadrons are fitted according to the kinematic predictions of Conformal Relativity. The hypothesis gives a remarkably good fit. The isospin SU(2) gauge invariant Lagrangian L(,(pi)NN)(x,(lamda)) is used in the calculation of d(sigma)/d(OMEGA) to 2nd-order Feynman graphs for simplified models of (pi)N(--->)(pi)N. The resulting infinite mass sums over the nucleon (Conformal) families are done via the Generalized-Sommerfeld-Watson Transform Theorem. Even though the models are too simple to be realistic, they indicate that if (DELTA)-internal lines were to be included, 2nd-order Feynman graphs may reproduce the experimental data qualitatively. The energy -dependence of the propagator and couplings in Conformal QFT is different from that of ordinary QFT. Suggestions for further work are made in the areas of ultra-violet divergences and OPEC calculations.

  8. Reduction of metal adducts in oligonucleotide mass spectra in ion‐pair reversed‐phase chromatography/mass spectrometry analysis

    PubMed Central

    Gilar, Martin; Shion, Henry; Yu, Ying Qing; Chen, Weibin

    2016-01-01

    Rationale Electrospray ionization mass spectrometry (ESI‐MS)‐based techniques commonly used in oligonucleotide analyses are known to be sensitive to alkali metal adduct formation. Adducts directly impact the sensitivity of MS‐based analyses as the available charge is distributed across the parent peak and adduct(s). The current study systematically evaluated common liquid chromatography (LC) components in LC/ESI‐MS configurations used in oligonucleotide analysis to identify metal adduct contributions from LC instrumentation. Methods A UPLC liquid chromatography system was configured with a single quadrupole MS detector (ACQUITY QDa, Waters Corp.) to monitor adduct formation in oligonucleotide separations. An ion‐pairing mobile phase comprised of 15 mM triethylamine and 400 mM hexafluoro‐2‐propanol was used in conjunction with an oligonucleotide separation column (Waters OST BEH C18, 2.1 mm × 50 mm) for all separations. A 10‐min method was used to provide statistical figures of merit and evaluate adduct formation over time. Results Trace alkali metal salts in the mobile phase and reagents were determined to be the main source of metal salt adducts in LC/ESI‐MS‐based configurations. Non‐specific adsorption sites located throughout the fluidic path contribute to adduct formation in oligonucleotide analyses. Ion‐pairing mobile phases prepared at neutral or slightly basic pH result in up to a 57% loss of spectral abundance to adduct formation in the current study. Conclusions Implementation of a short low pH reconditioning step was observed to effectively displace trace metal salts non‐specifically adsorbed to surfaces in the fluidic path and was able to maintain an average MS spectral abundance ≥94% with a high degree of repeatability (relative standard deviation (R.S.D.) 0.8%) over an extended time study. The proposed method offers the ability to rapidly regenerate adsorption sites with minimal impact on productivity while retaining

  9. Thermospray liquid-chromatography mass spectrometry of thiol radioprotective agents: Characteristics spectra. Scientific report

    SciTech Connect

    Walden, T.L.; Buchner, J.; Pizzitola, V.; Blakeley, W.F.

    1988-01-01

    Ethiofos (S-2(3-aminopropylamino)ethylphosphorothioic acid or WR-2721) is currently being evaluated in clinical radiotherapy trials (Kligerman et al., 1980) because of its potential for enhancing the efficacy of radiotherapy (Kligerman et al., 1980; Yuhas and Storer, 1969). For proper drug usage and pharmacological studies, it is necessary to assess the stability of the aminothiol and the presence of impurities or decomposition products. In addition, monitoring the plasma levels of WR-2721 and its metabolites should improve the therapeutic usefulness of WR-2721. Several high-performance liquid chromatography (HPLC) methodologies have been developed that are applicable for routine analysis of aminothiols and endogeneous cellular thiols (Newton et al., 1981; Swynnerton et al., 1984). One of these methodologies, electrochemical detection, permits the simultaneous detection of the free thiol and the disulfides (Swynnerton et al. 1984). Mass spectrometry (MS) is a sensitive technique that can confirm purity and provide useful structural information. Using a thermospray interface, samples can be introduced into the mass spectrometer from a liquid chromatograph (LC) (Vestal, 1984). The interface thermally nebulizes the eluant into a high-pressure region of the mass spectrometer where a variety of soft-ionization techniques may be used to ionize the analyte molecules. The feasibility of LC coupled to MS-detection was studied for the analysis of thiol-containing radioprotective agents, including glutathione, WR-2721, and WR-1065, the dephosphorylated sulfhydryl form of WR-2721, which has been shown to be its active radioprotective metabolite (Calabro-Jones et al., 1983).

  10. Cycloquest: Identification of cyclopeptides via database search of their mass spectra against genome databases

    PubMed Central

    Mohimani, Hosein; Liu, Wei-Ting; Mylne, Joshua S.; Poth, Aaron G.; Colgrave, Michelle L.; Tran, Dat; Selsted, Michael E.; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2011-01-01

    Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computational techniques for cyclopeptide identification are still in their infancy, with many such peptides remaining uncharacterized. Tandem mass spectrometry has occupied a niche role in cyclopeptide identification, taking over from traditional techniques such as nuclear magnetic resonance spectroscopy (NMR). MS/MS studies require only picogram quantities of peptide (compared to milligrams for NMR studies) and are applicable to complex samples, abolishing the requirement for time-consuming chromatographic purification. While database search tools such as Sequest and Mascot have become standard tools for the MS/MS identification of linear peptides, they are not applicable to cyclopeptides, due to the parent mass shift resulting from cyclization, and different fragmentation pattern of cyclic peptides. In this paper, we describe the development of a novel database search methodology to aid in the identification of cyclopeptides by mass spectrometry, and evaluate its utility in identifying two peptide rings from Helianthus annuus, a bacterial cannibalism factor from Bacillus subtilis, and a θ-defensin from Rhesus macaque. PMID:21851130

  11. Solid CO2 in low-mass young stellar objects. Comparison between Spitzer and laboratory spectra

    NASA Astrophysics Data System (ADS)

    Ioppolo, S.; Sangiorgio, I.; Baratta, G. A.; Palumbo, M. E.

    2013-06-01

    Context. Solid interstellar CO2 is an abundant component of ice dust mantles. Its ubiquity towards quiescent molecular clouds, as well as protostellar envelopes, has recently been confirmed by the IRS (InfraRed Spectrograph) aboard the Spitzer Space Telescope. Although it has been shown that CO2 cannot be efficiently formed in the gas phase, the CO2 surface formation pathway is still unclear. To date several CO2 surface formation mechanisms induced by energetic (e.g., UV photolysis and cosmic ray irradiation) and non-energetic (e.g., cold atom addition) input have been proposed. Aims: Our aim is to investigate the contribution of cosmic ray irradiation to the formation of CO2 in different regions of the interstellar medium (ISM). To achieve this goal we compared quantitatively laboratory data with the CO2 bending mode band profile observed towards several young stellar objects (YSOs) and a field star by the Spitzer Space Telescope. Methods: All the experiments presented here were performed at the Laboratory for Experimental Astrophysics in Catania (Italy). The interstellar relevant samples were all irradiated with fast ions (30-200 keV) and subsequently annealed in a stainless steel high vacuum chamber (P < 10-7 mbar). Chemical and structural modifications of the ice samples were monitored by means of infrared spectroscopy. Laboratory spectra were then used to fit some thirty observational spectra. Results: A qualitative analysis shows that a good fit can be obtained with a minimum of two components. The choice of the laboratory components is based on the chemical-physical condition of each source. A quantitative analysis of the sources with known visual extinction (AV) and methanol abundances highlights that the solid carbon dioxide can be efficiently and abundantly formed after ion irradiation of interstellar ices in all the selected YSOs in a time compatible with cloud lifetimes (3 × 107 years). Only in the case of field stars can the expected CO2 column

  12. CLARREO Cornerstone of the Earth Observing System: Measuring Decadal Change Through Accurate Emitted Infrared and Reflected Solar Spectra and Radio Occultation

    NASA Technical Reports Server (NTRS)

    Sandford, Stephen P.

    2010-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is one of four Tier 1 missions recommended by the recent NRC Decadal Survey report on Earth Science and Applications from Space (NRC, 2007). The CLARREO mission addresses the need to provide accurate, broadly acknowledged climate records that are used to enable validated long-term climate projections that become the foundation for informed decisions on mitigation and adaptation policies that address the effects of climate change on society. The CLARREO mission accomplishes this critical objective through rigorous SI traceable decadal change observations that are sensitive to many of the key uncertainties in climate radiative forcings, responses, and feedbacks that in turn drive uncertainty in current climate model projections. These same uncertainties also lead to uncertainty in attribution of climate change to anthropogenic forcing. For the first time CLARREO will make highly accurate, global, SI-traceable decadal change observations sensitive to the most critical, but least understood, climate forcings, responses, and feedbacks. The CLARREO breakthrough is to achieve the required levels of accuracy and traceability to SI standards for a set of observations sensitive to a wide range of key decadal change variables. The required accuracy levels are determined so that climate trend signals can be detected against a background of naturally occurring variability. Climate system natural variability therefore determines what level of accuracy is overkill, and what level is critical to obtain. In this sense, the CLARREO mission requirements are considered optimal from a science value perspective. The accuracy for decadal change traceability to SI standards includes uncertainties associated with instrument calibration, satellite orbit sampling, and analysis methods. Unlike most space missions, the CLARREO requirements are driven not by the instantaneous accuracy of the measurements, but by accuracy in

  13. Wide-Scope Screening of Illegal Adulterants in Dietary and Herbal Supplements via Rapid Polarity-Switching and Multistage Accurate Mass Confirmation Using an LC-IT/TOF Hybrid Instrument.

    PubMed

    Guo, Bin; Wang, Meiling; Liu, Yanyan; Zhou, Jing; Dai, Hua; Huang, Zhiqiang; Shen, Lingling; Zhang, Qingsheng; Chen, Bo

    2015-08-12

    A new analytical strategy was developed that integrates a generic sample preparation into a liquid chromatography-multistage ion trap/time-of-flight mass spectrometry (LC-IT(MS(n))/TOF), allowing for large-scale screening and qualitative confirmation of wide-scope illegal adulterants in different food matrices. Samples were pretreated by a fast single-tube multifunction extraction for accurate multistage mass measurement on the hybrid LC-IT/TOF system. A qualitative validation performed for over 500 analyte-matrix pairs showed the method can reduce most of the matrix effects and achieve a lower limit of confirmation at 0.1 mg/kg for 73% of the target compounds. A unique combination of dual-polarity detection, retention time, isotopic profile, and accurate MS(n) spectra enables more comprehensive and precise confirmation, based on the multiparameter matching by automated library searching against the user-created database. Finally, the applicability of this LC-IT(MS(n))/TOF-based screening procedure for discriminating coeluting isobars, identifying nontarget adulterants, and even tentatively elucidating unexpected species in real samples is demonstrated.

  14. Constraining black hole masses in low-accreting active galactic nuclei using X-ray spectra

    NASA Astrophysics Data System (ADS)

    Jang, I.; Gliozzi, M.; Hughes, C.; Titarchuk, L.

    2014-09-01

    In a recent work we demonstrated that a novel X-ray scaling method, originally introduced for Galactic black holes (BHs), can be reliably extended to estimate the mass of supermassive BHs accreting at a moderate to high level. Here we investigate the limits of applicability of this method to low-accreting active galactic nuclei (AGN), using a control sample with good-quality X-ray data and dynamically measured mass. For low-accreting AGN (LX/LEdd ≤ 10-4), because the basic assumption that the photon index positively correlates with the accretion rate no longer holds the X-ray scaling method cannot be used. Nevertheless, the inverse correlation in the Γ-LX/LEdd diagram, found in several low-accreting BHs and confirmed by this sample, can be used to constrain MBH within a factor of ˜10 from the dynamically determined values. We provide a simple recipe to determine MBH using solely X-ray spectral data, which can be used as a sanity check for MBH determination based on indirect optical methods.

  15. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

    2017-02-14

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of (16)O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm(-1) is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  16. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands

    NASA Astrophysics Data System (ADS)

    Tyuterev, Vladimir G.; Kochanov, Roman V.; Tashkun, Sergey A.

    2017-02-01

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to Δ V = 6. A particular challenge was a correct description of the B-type bands (even Δ V3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μ m range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm-1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  17. Accurate sky Subtraction of Long-Slit Spectra: Velocity Dispersions at Sigma(v) = 24.0 Mag/arcsec^2

    NASA Astrophysics Data System (ADS)

    Sembach, Kenneth R.; Tonry, Joh L.

    1996-08-01

    We describe an observing strategy for obtaining accurate sky subtraction when observing with a long-slit spectrograph. The technique is a chopping procedure in which the telescope is sequentially moved from object to sky on short time scales (~300 s), but instead of reading out the CCD detector with each exposure, we repeatedly clock the charge on the chip in the parallel direction in a manner that produces two complete exposures (one object+sky, one sky) on each CCD frame. The background subtraction proceeds naturally by differencing these two exposures. We show that this method provides superior results to more traditional sky- subtraction methods that rely on measuring the sky brightness at the ends of the slit. We find that we can reach a V-band surface brightness of 24 mag arcsec^2^ in about 8 hours of observing time on the 2.4-meter Hiltner telescope at the Michigan-Dartmouth-MIT Observatory. We present some preliminary results obtained with this method for the stellar dynamics in the outer envelopes of three elliptical galaxies (M87, NGC 5846, and IC 1101). We use cross-correlation and Fourier quotient techniques to derive radial velocity and velocity dispersion profiles. We confirm that the velocity dispersion in the outer envelope of IC 1101 (the central galaxy in Abell 2029) rises with distance from the center of the galaxy, as noted by Dressler [APJ. 23,659 (1979)].

  18. Simultaneous factor analysis of organic particle and gas mass spectra: AMS and PTR-MS measurements at an urban site

    NASA Astrophysics Data System (ADS)

    Slowik, J. G.; Vlasenko, A.; McGuire, M.; Evans, G. J.; Abbatt, J. P. D.

    2009-03-01

    During the winter component of the SPORT (Seasonal Particle Observations in the Region of Toronto) field campaign, particulate non-refractory chemical composition and concentration of selected volatile organic compounds (VOCs) were measured by an Aerodyne time-of-flight aerosol mass spectrometer (AMS) and a proton transfer reaction-mass spectrometer (PTR-MS), respectively. Sampling was performed in downtown Toronto ~15 m from a major road. The mass spectra from the AMS and PTR-MS were combined into a unified dataset, which was analyzed using positive matrix factorization (PMF). The two instruments were given equal weight in the PMF analysis by application of a scaling factor to the uncertainties of each instrument. A residual based metric, Δesc, was used to evaluate the relative weight. The PMF analysis yielded a 5-factor solution that included factors characteristic of regional transport, local traffic emissions, charbroiling, and oxidative processing. The unified dataset provides information on particle and VOC sources and atmospheric processing that cannot be obtained from the datasets of the individual instruments, such as apportionment of oxygenated VOCs to direct emission sources vs. secondary reaction products, improved correlation of oxygenated aerosol factors with photochemical age, and increased detail regarding the composition of oxygenated organic aerosol factors. This analysis represents the first application of PMF to a unified AMS/PTR-MS dataset.

  19. Simultaneous factor analysis of organic particle and gas mass spectra: AMS and PTR-MS measurements at an urban site

    NASA Astrophysics Data System (ADS)

    Slowik, J. G.; Vlasenko, A.; McGuire, M.; Evans, G. J.; Abbatt, J. P. D.

    2010-02-01

    During the winter component of the SPORT (Seasonal Particle Observations in the Region of Toronto) field campaign, particulate non-refractory chemical composition and concentration of selected volatile organic compounds (VOCs) were measured by an Aerodyne time-of-flight aerosol mass spectrometer (AMS) and a proton transfer reaction-mass spectrometer (PTR-MS), respectively. Sampling was performed in downtown Toronto ~15 m from a major road. The mass spectra from the AMS and PTR-MS were combined into a unified dataset, which was analysed using positive matrix factorization (PMF). The two instruments were given balanced weight in the PMF analysis by the application of a scaling factor to the uncertainties of each instrument. A residual based metric, Δesc, was used to evaluate the instrument relative weight within each solution. The PMF analysis yielded a 6-factor solution that included factors characteristic of regional transport, local traffic emissions, charbroiling and oxidative processing. The unified dataset provides information on emission sources (particle and VOC) and atmospheric processing that cannot be obtained from the datasets of the individual instruments: (1) apportionment of oxygenated VOCs to either direct emission sources or secondary reaction products; (2) improved correlation of oxygenated aerosol factors with photochemical age; and (3) increased detail regarding the composition of oxygenated organic aerosol factors. This analysis represents the first application of PMF to a unified AMS/PTR-MS dataset.

  20. An application of artificial intelligence to the interpretation of mass spectra.

    NASA Technical Reports Server (NTRS)

    Buchanan, B. G.; Duffield, A. M.; Robertson, A. V.

    1971-01-01

    Description of the DENDRAL (Dendritic Algorithm) project, the objectives of which were to base the computer program on an alogorithm that generates an exhaustive, nonredundant list of all the structural isomers of a given chemical composition, and to devise a computer program that would perform an organic structure determination, given a molecular formula and a mass spectrum. This program is called 'Heuristic DENDRAL' and it operates by using the known structure/spectrum correlations to constrain the DENDRAL isomer generator to produce a single isomer for that composition. The collaboration of chemists and computer scientists has produced a tool of some practical utility from the chemical viewpoint, and an interesting program from the viewpoint of artificial intelligence.

  1. Rest-frame Optical Spectra and Black Hole Masses of 3 < z < 6 Quasars

    NASA Astrophysics Data System (ADS)

    Jun, Hyunsung David; Im, Myungshin; Lee, Hyung Mok; Ohyama, Youichi; Woo, Jong-Hak; Fan, Xiaohui; Goto, Tomotsugu; Kim, Dohyeong; Kim, Ji Hoon; Kim, Minjin; Lee, Myung Gyoon; Nakagawa, Takao; Pearson, Chris; Serjeant, Stephen

    2015-06-01

    We present the rest-frame optical spectral properties of 155 luminous quasars at 3.3 < z < 6.4 taken with the AKARI space telescope, including the first detection of the Hα emission line as far out as z ∼ 6. We extend the scaling relation between the rest-frame optical continuum and the line luminosity of active galactic nuclei (AGNs) to the high-luminosity, high-redshift regime that has rarely been probed before. Remarkably, we find that a single log-linear relation can be applied to the 5100 Å and Hα AGN luminosities over a wide range of luminosity (1042 < L5100 < 1047 ergs s-1) or redshift (0 < z < 6), suggesting that the physical mechanism governing this relation is unchanged from z = 0 to 6, over five decades in luminosity. Similar scaling relations are found between the optical and the UV continuum luminosities or line widths. Applying the scaling relations to the Hβ black hole (BH) mass (MBH) estimator of local AGNs, we derive the MBH estimators based on the Hα, Mg ii, and C iv lines, finding that the UV-line-based masses are overall consistent with the Balmer-line-based, but with a large intrinsic scatter of 0.40 dex for the C iv estimates. Our 43 MBH estimates from Hα confirm the existence of BHs as massive as ∼ 1010 M⊙ out to z ∼ 5 and provide a secure footing for previous results from Mg ii-line-based studies that a rapid MBH growth has occurred in the early universe.

  2. The mass spectra, hierarchy and cosmology of B-L MSSM heterotic compactifications

    SciTech Connect

    Ambroso, Michael; Ovrut, Burt A.

    2011-04-10

    The matter spectrum of the MSSM, including three right-handed neutrino supermultiplets and one pair of Higgs-Higgs conjugate superfields, can be obtained by compactifying the E₈ x E₈ heterotic string and M-theory on Calabi-Yau manifolds with specific SU(4) vector bundles. These theories have the standard model gauge group augmented by an additional gauged U(1)B-L. Their minimal content requires that the B-L gauge symmetry be spontaneously broken by a vacuum expectation value of at least one right-handed neutrino. In previous papers, we presented the results of a quasi-analytic renormalization group analysis showing that B-L gauge symmetry is indeed radiatively broken with an appropriate B-L/electroweak hierarchy. In this paper, we extend these results by 1) enlarging the initial parameter space and 2) explicitly calculating all renormalization group equations numerically. The regions of the initial parameter space leading to realistic vacua are presented and the B-L/electroweak hierarchy computed over these regimes. At representative points, the mass spectrum for all particles and Higgs fields is calculated and shown to be consistent with present experimental bounds. Some fundamental phenomenological signatures of a non-zero right-handed neutrino expectation value are discussed, particularly the cosmology and proton lifetime arising from induced lepton and baryon number violating interactions.

  3. The mass spectra, hierarchy and cosmology of B-L MSSM heterotic compactifications

    DOE PAGES

    Ambroso, Michael; Ovrut, Burt A.

    2011-04-10

    The matter spectrum of the MSSM, including three right-handed neutrino supermultiplets and one pair of Higgs-Higgs conjugate superfields, can be obtained by compactifying the E₈ x E₈ heterotic string and M-theory on Calabi-Yau manifolds with specific SU(4) vector bundles. These theories have the standard model gauge group augmented by an additional gauged U(1)B-L. Their minimal content requires that the B-L gauge symmetry be spontaneously broken by a vacuum expectation value of at least one right-handed neutrino. In previous papers, we presented the results of a quasi-analytic renormalization group analysis showing that B-L gauge symmetry is indeed radiatively broken with anmore » appropriate B-L/electroweak hierarchy. In this paper, we extend these results by 1) enlarging the initial parameter space and 2) explicitly calculating all renormalization group equations numerically. The regions of the initial parameter space leading to realistic vacua are presented and the B-L/electroweak hierarchy computed over these regimes. At representative points, the mass spectrum for all particles and Higgs fields is calculated and shown to be consistent with present experimental bounds. Some fundamental phenomenological signatures of a non-zero right-handed neutrino expectation value are discussed, particularly the cosmology and proton lifetime arising from induced lepton and baryon number violating interactions.« less

  4. Mass spectra of four-quark states in the hidden charm sector

    NASA Astrophysics Data System (ADS)

    Patel, Smruti; Shah, Manan; Vinodkumar, P. C.

    2014-08-01

    Masses of the low-lying four-quark states in the hidden charm sector ( are calculated within the framework of a non-relativistic quark model. The four-body system is considered as two two-body systems such as diquark-antidiquark ( - and quark-antiquark-quark-antiquark ( - q molecular-like four-quark states. Here, the Cornell-type potential has been used for describing the two-body interactions among Q - q , - , Q - , Qq - and Q - q , with appropriate string tensions. Our present analysis suggests the following exotic states: X(3823) , Z c(3900) , X(3915) , Z c(4025) , (4040) , Z 1(4050) and X(4160) as Q - q molecular-like four-quark states, while Z c(3885) , X(3940) and Y(4140) as the diquark-antidiquark four-quark states. We have been able to assign the JPC values for many of the recently observed exotic states according to their structure. Apart from this, we have identified the charged state Z(4430) recently confirmed by LHCb as the first radial excitation of Zc(3885) with G = + 1 and Y(4360) state as the first radial excitation of Y(4008) with G = - 1 and the state as the first radial excitation of the state.

  5. Mass spectrometry of analytical derivatives. 2. "Ortho" and "Para" effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids.

    PubMed

    Todua, Nino G; Mikaia, Anzor I

    2016-01-01

    Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS(1) spectra of unlabeled compounds to their (2)H and (13)C labeled analogs, and analysis of collision-induced dissociation data from MS(2) spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested.

  6. Matching unknown empirical formulas to chemical structure using LC/MS TOF accurate mass and database searching: example of unknown pesticides on tomato skins.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Fernández-Alba, Amadeo Rodriguez

    2005-03-04

    Traditionally, the screening of unknown pesticides in food has been accomplished by GC/MS methods using conventional library searching routines. However, many of the new polar and thermally labile pesticides and their degradates are more readily and easily analyzed by LC/MS methods and no searchable libraries currently exist (with the exception of some user libraries, which are limited). Therefore, there is a need for LC/MS approaches to detect unknown non-target pesticides in food. This report develops an identification scheme using a combination of LC/MS time-of-flight (accurate mass) and LC/MS ion trap MS (MS/MS) with searching of empirical formulas generated through accurate mass and a ChemIndex database or Merck Index database. The approach is different than conventional library searching of fragment ions. The concept here consists of four parts. First is the initial detection of a possible unknown pesticide in actual market-place vegetable extracts (tomato skins) using accurate mass and generating empirical formulas. Second is searching either the Merck Index database on CD (10,000 compounds) or the ChemIndex (77,000 compounds) for possible structures. Third is MS/MS of the unknown pesticide in the tomato-skin extract followed by fragment ion identification using chemical drawing software and comparison with accurate-mass ion fragments. Fourth is the verification with authentic standards, if available. Three examples of unknown, non-target pesticides are shown using a tomato-skin extract from an actual market place sample. Limitations of the approach are discussed including the use of A + 2 isotope signatures, extended databases, lack of authentic standards, and natural product unknowns in food extracts.

  7. Accurate determination of ultra-trace impurities, including europium, in ultra-pure barium carbonate materials through inductively coupled plasma-tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Wu, Shuchao; Zeng, Xiangcheng; Dai, Xuefeng; Hu, Yongping; Li, Gang; Zheng, Cunjiang

    2016-09-01

    Impurities, especially ultra-trace europium (Eu), in ultra-pure barium carbonate materials were accurately determined through inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS). Two reaction modes, namely, mass shift (with O2 as reaction gas) and on-mass modes(with NH3/He and He as reaction gases), were extensively investigated using Eu+ as target analyte. The use of Eu+ → EuO2+, instead of Eu+ → EuO+, as ion pairs in mass shift mode eliminated polyatomic interferences based on Ba matrix ions (135Ba16O2+ on 151Eu16O+ and 137Ba16O2+ on 153Eu16O+). This procedure exhibited enhanced sensitivity and selectivity. When the ICP-MS/MS was operated in NH3 on-mass mode, Eu+ can be determined in its original mass in interference-free conditions because NH3 did not react with Eu+ but with BaO+ to form a neutral product (BaO). The two reaction modes, especially NH3 on mass mode, were validated to be accurate because their resultant isotope ratios of 153Eu/151Eu matched well with that of the natural abundance ratio. The proposed ICP-MS/MS method is a sensitive technique with a limit of detection as low as 2.0 ng L- 1 for 153Eu+. Compared with conventional single-quadrupole (SQ) ICP-MS, both NH3 on-mass mode and O2 mass shift mode in ICP-MS/MS can be used to accurately determine Eu+ in ultra-pure BaCO3 materials. The detected concentration of Eu+ was 4.0 ng L- 1 to 15 ng L- 1, with spiked recoveries ranging from 100%-110%. ICP-MS/MS was also used to eliminate polyatomic interferences, particularly Ba-based interferences, prior to measurement of Gd and Sm. Impurities, including Na, Mg, Al, K, Mn, Fe, Cr, Sr, and Cs, in ultra-pure BaCO3 materials were also determined using ICP-MS/MS in conventional SQ mode.

  8. Accurate mass measurements for the confirmation of Sudan azo-dyes in hot chilli products by capillary liquid chromatography-electrospray tandem quadrupole orthogonal-acceleration time of flight mass spectrometry.

    PubMed

    Calbiani, F; Careri, M; Elviri, L; Mangia, A; Zagnoni, I

    2004-11-26

    The potential of capillary liquid chromatography (microLC)-quadrupole/time-of-flight mass spectrometry (Q-TOF MS) for the confirmation of Sudan I, II, III and IV azo-dyes as contaminants in hot-chilli food products was demonstrated. Using the microLC-electrospray ionization (ESI)-Q-TOF MS technique, accurate mass measurements of Sudan dyes were performed both on standard solutions and on matrices. Precision of exact mass measurements was calculated taking into account the ion statistics according to the number of ion sampled in the measurement. Accurate mass measurements by MS/MS experiments were performed to elucidate azo-dye fragmentation patterns. Selectivity of the microLC-Q-TOF MS method was assessed by evaluating matrix suppression effects by pre-column injection of blank hot chilli tomato sauce matrices. The results were compared with those obtained on a LC-triple quadrupole-MS system. Confirmation of Sudan I present in hot chill tomato sauce samples was obtained by accurate mass measurements. In real samples trueness of exact mass measurements was estimated to be 1.6 and 4.4 ppm when calculated for hot chilli tomato sauce and hot chilli tomato with cheese sauce samples, respectively; precision was calculated around 9.5 ppm.

  9. Statistical analysis of fragmentation patterns of electron ionization mass spectra of enolized-trimethylsilylated anabolic androgenic steroids

    NASA Astrophysics Data System (ADS)

    Fragkaki, A. G.; Angelis, Y. S.; Tsantili-Kakoulidou, A.; Koupparis, M.; Georgakopoulos, C.

    2009-08-01

    Anabolic androgenic steroids (AAS) are included in the List of prohibited substances of the World Anti-Doping Agency (WADA) as substances abused to enhance athletic performance. Gas chromatography coupled to mass spectrometry (GC-MS) plays an important role in doping control analyses identifying AAS as their enolized-trimethylsilyl (TMS)-derivatives using the electron ionization (EI) mode. This paper explores the suitability of complementary GC-MS mass spectra and statistical analysis (principal component analysis, PCA and partial least squares-discriminant analysis, PLS-DA) to differentiate AAS as a function of their structural and conformational features expressed by their fragment ions. The results obtained showed that the application of PCA yielded a classification among the AAS molecules which became more apparent after applying PLS-DA to the dataset. The application of PLS-DA yielded a clear separation among the AAS molecules which were, thus, classified as: 1-ene-3-keto, 3-hydroxyl with saturated A-ring, 1-ene-3-hydroxyl, 4-ene-3-keto, 1,4-diene-3-keto and 3-keto with saturated A-ring anabolic steroids. The study of this paper also presents structurally diagnostic fragment ions and dissociation routes providing evidence for the presence of unknown AAS or chemically modified molecules known as designer steroids.

  10. A versatile detector system to measure the change states, mass compositions and energy spectra of interplanetary and magnetosphere ions

    NASA Technical Reports Server (NTRS)

    Gloeckler, G.

    1977-01-01

    An instrument is described for measuring the mass and charge state composition as well as the energy spectra and angular distributions of 0.5 to 350 kev/charge ions in interplanetary space and in magnetospheres of planets such as Jupiter and earth. Electrostatic deflection combined with a time-of-flight and energy measurement allows three-parameter analysis of output signals from which the mass, charge states, and energy are determined. Post-acceleration by 30 kV extends the energy range of the detector system into the solar wind and magnetosphere plasma regime. Isotopes of H and He are easily resolved as are individual elements up to Ne and the dominant elements up to and including Fe. This instrument has an extremely large dynamic range in intensity and is sensitive to rare elements even in the presence of high intensity radiation, and is adapted for interplanetary, deep-space, and out-of-the-ecliptic missions, as well as for flights on spacecraft orbiting Jupiter and earth.

  11. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

    PubMed Central

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  12. CLASH-VLT: Constraints on the Dark Matter Equation of State from Accurate Measurements of Galaxy Cluster Mass Profiles

    NASA Astrophysics Data System (ADS)

    Sartoris, Barbara; Biviano, Andrea; Rosati, Piero; Borgani, Stefano; Umetsu, Keiichi; Bartelmann, Matthias; Girardi, Marisa; Grillo, Claudio; Lemze, Doron; Zitrin, Adi; Balestra, Italo; Mercurio, Amata; Nonino, Mario; Postman, Marc; Czakon, Nicole; Bradley, Larry; Broadhurst, Tom; Coe, Dan; Medezinski, Elinor; Melchior, Peter; Meneghetti, Massimo; Merten, Julian; Annunziatella, Marianna; Benitez, Narciso; Czoske, Oliver; Donahue, Megan; Ettori, Stefano; Ford, Holland; Fritz, Alexander; Kelson, Dan; Koekemoer, Anton; Kuchner, Ulrike; Lombardi, Marco; Maier, Christian; Moustakas, Leonidas A.; Munari, Emiliano; Presotto, Valentina; Scodeggio, Marco; Seitz, Stella; Tozzi, Paolo; Zheng, Wei; Ziegler, Bodo

    2014-03-01

    A pressureless scenario for the dark matter (DM) fluid is a widely adopted hypothesis, despite the absence of direct observational evidence. According to general relativity, the total mass-energy content of a system shapes the gravitational potential well, but different test particles perceive this potential in different ways depending on their properties. Cluster galaxy velocities, being Ltc, depend solely on the gravitational potential, whereas photon trajectories reflect the contributions from the gravitational potential plus a relativistic-pressure term that depends on the cluster mass. We exploit this phenomenon to constrain the equation of state (EoS) parameter of the fluid, primarily DM, contained in galaxy clusters. We use complementary information provided by the kinematic and lensing mass profiles of the galaxy cluster MACS 1206.2-0847 at z = 0.44, as obtained in an extensive imaging and spectroscopic campaign within the Cluster Lensing And Supernova survey with Hubble. The unprecedented high quality of our data set and the properties of this cluster are well suited to determine the EoS parameter of the cluster fluid. Since baryons contribute at most 15% to the total mass in clusters and their pressure is negligible, the EoS parameter we derive describes the behavior of the DM fluid. We obtain the most stringent constraint on the DM EoS parameter to date, w = (pr + 2 pt )/(3 c 2ρ) = 0.00 ± 0.15 (stat) ± 0.08 (syst), averaged over the radial range 0.5 Mpc <= r <= r 200, where pr and pt are the radial and tangential pressure, and ρ is the density. We plan to further improve our constraint by applying the same procedure to all clusters from the ongoing Cluster Lensing And Supernova Survey with Hubble-Very Large Telescope program.

  13. Retrieval of Precise Radial Velocities from Near-infrared High-resolution Spectra of Low-mass Stars

    NASA Astrophysics Data System (ADS)

    Gao, Peter; Plavchan, P.; Gagné, J.; Furlan, E.; Bottom, M.; Anglada-Escudé, G.; White, R.; Davison, C. L.; Beichman, C.; Brinkworth, C.; Johnson, J.; Ciardi, D.; Wallace, K.; Mennesson, B.; von Braun, K.; Vasisht, G.; Prato, L.; Kane, S. R.; Tanner, A.; Crawford, T. J.; Latham, D.; Rougeot, R.; Geneser, C. S.; Catanzarite, J.

    2016-10-01

    Given that low-mass stars have intrinsically low luminosities at optical wavelengths and a propensity for stellar activity, it is advantageous for radial velocity (RV) surveys of these objects to use near-infrared (NIR) wavelengths. In this work, we describe and test a novel RV extraction pipeline dedicated to retrieving RVs from low-mass stars using NIR spectra taken by the CSHELL spectrograph at the NASA Infrared Telescope Facility, where a methane isotopologue gas cell is used for wavelength calibration. The pipeline minimizes the residuals between the observations and a spectral model composed of templates for the target star, the gas cell, and atmospheric telluric absorption; models of the line-spread function, continuum curvature, and sinusoidal fringing; and a parameterization of the wavelength solution. The stellar template is derived iteratively from the science observations themselves without a need for separate observations dedicated to retrieving it. Despite limitations from CSHELL’s narrow wavelength range and instrumental systematics, we are able to (1) obtain an RV precision of 35 m s-1 for the RV standard star GJ 15 A over a time baseline of 817 days, reaching the photon noise limit for our attained signal-to-noise ratio; (2) achieve ˜3 m s-1 RV precision for the M giant SV Peg over a baseline of several days and confirm its long-term RV trend due to stellar pulsations, as well as obtain nightly noise floors of ˜2-6 m s-1 and (3) show that our data are consistent with the known masses, periods, and orbital eccentricities of the two most massive planets orbiting GJ 876. Future applications of our pipeline to RV surveys using the next generation of NIR spectrographs, such as iSHELL, will enable the potential detection of super-Earths and mini-Neptunes in the habitable zones of M dwarfs.

  14. Accurate determination of ⁴¹Ca concentrations in spent resins from the nuclear industry by accelerator mass spectrometry.

    PubMed

    Nottoli, Emmanuelle; Bourlès, Didier; Bienvenu, Philippe; Labet, Alexandre; Arnold, Maurice; Bertaux, Maité

    2013-12-01

    The radiological characterisation of nuclear waste is essential for managing storage sites. Determining the concentration of Long-Lived RadioNuclides (LLRN) is fundamental for their long-term management. This paper focuses on the measurement of low (41)Ca concentrations in ions exchange resins used for primary fluid purification in Pressurised Water Reactors (PWR). (41)Ca concentrations were successfully measured by Accelerator Mass Spectrometry (AMS) after the acid digestion of resin samples, followed by radioactive decontamination and isobaric suppression through successive hydroxide, carbonate, nitrate and final CaF2 precipitations. Measured (41)Ca concentrations ranged from 0.02 to 0.03 ng/g, i.e. from 0.06 to 0.09 Bq/g. The (41)Ca/(60)Co activity ratios obtained were remarkably reproducible and in good agreement with the current ratio used for resins management.

  15. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

  16. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    PubMed Central

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2016-01-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

  17. Massive processing of pyro-chromatogram mass spectra (py-GCMS) of soil samples using the PARAFAC2 algorithm

    NASA Astrophysics Data System (ADS)

    Cécillon, Lauric; Quénéa, Katell; Anquetil, Christelle; Barré, Pierre

    2015-04-01

    Due to its large heterogeneity at all scales (from soil core to the globe), several measurements are often mandatory to get a meaningful value of a measured soil property. A large number of measurements can therefore be needed to study a soil property whatever the scale of the study. Moreover, several soil investigation techniques produce large and complex datasets, such as pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) which produces complex 3-way data. In this context, straightforward methods designed to speed up data treatments are needed to deal with large datasets. GC-MS pyrolysis (py-GCMS) is a powerful and frequently used tool to characterize soil organic matter (SOM). However, the treatment of the results of a py-GCMS analysis of soil sample is time consuming (number of peaks, co-elution, etc.) and the treatment of large data set of py-GCMS results is rather laborious. Moreover, peak position shifts and baseline drifts between analyses make the automation of GCMS programs data treatment difficult. These problems can be fixed using the Parallel Factor Analysis 2 (PARAFAC 2, Kiers et al., 1999; Bro et al., 1999). This algorithm has been applied frequently on chromatography data but has never been applied to analyses of SOM. We developed a Matlab routine based on existing Matlab packages dedicated to the simultaneous treatment of dozens of pyro-chromatograms mass spectra. We applied this routine on 40 soil samples. The benefits and expected improvements of our method will be discussed in our poster. References Kiers et al. (1999) PARAFAC2 - PartI. A direct fitting algorithm for the PARAFAC2 model. Journal of Chemometrics, 13: 275-294. Bro et al. (1999) PARAFAC2 - PartII. Modeling chromatographic data with retention time shifts. Journal of Chemometrics, 13: 295-309.

  18. Accurate determination of ochratoxin A in Korean fermented soybean paste by isotope dilution-liquid chromatography tandem mass spectrometry.

    PubMed

    Ahn, Seonghee; Lee, Suyoung; Lee, Joonhee; Kim, Byungjoo

    2016-01-01

    Ochratoxin A (OTA), a naturally occurring mycotoxin, has been frequently detected in doenjang, a traditional fermented soybean paste, when it is fermented under improper conditions. Reliable screening of OTA in traditional fermented soybean paste (doenjang) is a special food-safety issue in Korea. Our laboratory, the National Metrology Institute of Korea, established an isotope dilution-liquid chromatography tandem mass spectrometry (ID-LC/MS/MS) method as a higher-order reference method to be used for SI-traceable value-assignment of OTA in certified reference materials (CRMs). (13)C20-OTA was used as an internal standard. Sample preparation conditions and LC/MS measurement parameters were optimised for this purpose. The analytical method was validated by measuring samples fortified with OTA at various levels. Repeatability and reproducibility studies showed that the ID-LC/MS/MS method is reliable and reproducible within 2% relative standard deviation. The analytical method was applied to determine OTA in various commercial doenjang products and home-made doenjang products.

  19. CLASH-VLT: Insights on the Mass Substructures in the Frontier Fields Cluster MACS J0416.1-2403 through Accurate Strong Lens Modeling

    NASA Astrophysics Data System (ADS)

    Grillo, C.; Suyu, S. H.; Rosati, P.; Mercurio, A.; Balestra, I.; Munari, E.; Nonino, M.; Caminha, G. B.; Lombardi, M.; De Lucia, G.; Borgani, S.; Gobat, R.; Biviano, A.; Girardi, M.; Umetsu, K.; Coe, D.; Koekemoer, A. M.; Postman, M.; Zitrin, A.; Halkola, A.; Broadhurst, T.; Sartoris, B.; Presotto, V.; Annunziatella, M.; Maier, C.; Fritz, A.; Vanzella, E.; Frye, B.

    2015-02-01

    We present a detailed mass reconstruction and a novel study on the substructure properties in the core of the Cluster Lensing And Supernova survey with Hubble (CLASH) and Frontier Fields galaxy cluster MACS J0416.1-2403. We show and employ our extensive spectroscopic data set taken with the VIsible Multi-Object Spectrograph instrument as part of our CLASH-VLT program, to confirm spectroscopically 10 strong lensing systems and to select a sample of 175 plausible cluster members to a limiting stellar mass of log (M */M ⊙) ~= 8.6. We reproduce the measured positions of a set of 30 multiple images with a remarkable median offset of only 0.''3 by means of a comprehensive strong lensing model comprised of two cluster dark-matter halos, represented by cored elliptical pseudo-isothermal mass distributions, and the cluster member components, parameterized with dual pseudo-isothermal total mass profiles. The latter have total mass-to-light ratios increasing with the galaxy HST/WFC3 near-IR (F160W) luminosities. The measurement of the total enclosed mass within the Einstein radius is accurate to ~5%, including the systematic uncertainties estimated from six distinct mass models. We emphasize that the use of multiple-image systems with spectroscopic redshifts and knowledge of cluster membership based on extensive spectroscopic information is key to constructing robust high-resolution mass maps. We also produce magnification maps over the central area that is covered with HST observations. We investigate the galaxy contribution, both in terms of total and stellar mass, to the total mass budget of the cluster. When compared with the outcomes of cosmological N-body simulations, our results point to a lack of massive subhalos in the inner regions of simulated clusters with total masses similar to that of MACS J0416.1-2403. Our findings of the location and shape of the cluster dark-matter halo density profiles and on the cluster substructures provide intriguing tests of the

  20. CLASH-VLT: INSIGHTS ON THE MASS SUBSTRUCTURES IN THE FRONTIER FIELDS CLUSTER MACS J0416.1–2403 THROUGH ACCURATE STRONG LENS MODELING

    SciTech Connect

    Grillo, C.; Suyu, S. H.; Umetsu, K.; Rosati, P.; Caminha, G. B.; Mercurio, A.; Balestra, I.; Munari, E.; Nonino, M.; De Lucia, G.; Borgani, S.; Biviano, A.; Girardi, M.; Lombardi, M.; Gobat, R.; Zitrin, A.; Halkola, A. and others

    2015-02-10

    We present a detailed mass reconstruction and a novel study on the substructure properties in the core of the Cluster Lensing And Supernova survey with Hubble (CLASH) and Frontier Fields galaxy cluster MACS J0416.1–2403. We show and employ our extensive spectroscopic data set taken with the VIsible Multi-Object Spectrograph instrument as part of our CLASH-VLT program, to confirm spectroscopically 10 strong lensing systems and to select a sample of 175 plausible cluster members to a limiting stellar mass of log (M {sub *}/M {sub ☉}) ≅ 8.6. We reproduce the measured positions of a set of 30 multiple images with a remarkable median offset of only 0.''3 by means of a comprehensive strong lensing model comprised of two cluster dark-matter halos, represented by cored elliptical pseudo-isothermal mass distributions, and the cluster member components, parameterized with dual pseudo-isothermal total mass profiles. The latter have total mass-to-light ratios increasing with the galaxy HST/WFC3 near-IR (F160W) luminosities. The measurement of the total enclosed mass within the Einstein radius is accurate to ∼5%, including the systematic uncertainties estimated from six distinct mass models. We emphasize that the use of multiple-image systems with spectroscopic redshifts and knowledge of cluster membership based on extensive spectroscopic information is key to constructing robust high-resolution mass maps. We also produce magnification maps over the central area that is covered with HST observations. We investigate the galaxy contribution, both in terms of total and stellar mass, to the total mass budget of the cluster. When compared with the outcomes of cosmological N-body simulations, our results point to a lack of massive subhalos in the inner regions of simulated clusters with total masses similar to that of MACS J0416.1–2403. Our findings of the location and shape of the cluster dark-matter halo density profiles and on the cluster substructures provide intriguing

  1. Multivariate analysis of electron detachment dissociation and infrared multiphoton dissociation mass spectra of heparan sulfate tetrasaccharides differing only in hexuronic acid stereochemistry.

    PubMed

    Oh, Han Bin; Leach, Franklin E; Arungundram, Sailaja; Al-Mafraji, Kanar; Venot, Andre; Boons, Geert-Jan; Amster, I Jonathan

    2011-03-01

    The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture.

  2. Rapid, Automated Determination of Elemental Compositions of Ions in Mass Spectra Obtained with an Open-Air Ion Source (2 of 2)

    EPA Science Inventory

    An inexpensive autosampler for a DART/TOFMS provides mass spectra from analytes absorbed on 76 cotton swab, wipe samples in 7.5 min. A field sample carrier simplifies sample collection and provides swabs nearly ready for analysis to the lab. Applications of the high throughput pr...

  3. Correlating mass physical properties with ALOS reflectance spectra for intertidal sediments from the Ba Lat Estuary (northern Vietnam): an exploratory laboratory study

    NASA Astrophysics Data System (ADS)

    Ngoc, Nguyen Thi; Koike, Katsuaki; Tue, Nguyen Tai

    2013-08-01

    Characterization of the sediment composition of tidal flats and monitoring of their spatiotemporal changes has become an important part of the sustainable management of coastal environments. To accurately classify sediments through remote sensing, a comprehensive understanding of sediment reflectance spectra is indispensable. The present laboratory-based study explores the performance of the high spatial resolution (10 × 10 m) Advanced Land Observing Satellite (ALOS) launched in 2006. Relationships between reflectance spectra (bands 1 to 4) and four typical mass physical properties were investigated under wet and dry experimental conditions for intertidal sediments sampled near the Ba Lat Estuary in northern Vietnam. Reflectance in the near-infrared region corresponding to ALOS band 4 (0.76-0.89 μm) was found (1) to have a strong negative correlation with sand content (dry wt%) under both wet and dry conditions (linear correlation coefficient r = -0.7859 and -0.8094, respectively), (2) to increase with decreasing relative water content (%) in a given sediment type (r = -0.7748 to -0.9367 for mud, sandy mud, muddy sand, and sand), (3) to have a positive correlation with organic matter content (r = 0.7610 and 0.6460 under wet and dry conditions for contents >0.20 dry wt%), and (4) to be insignificantly correlated with mineral composition assessed in terms of contents (wt%) of quartz, clay minerals, and mica group minerals. Positive relationships between reflectance and water content for the pooled data of all sediment types (r = 0.6395) or organic matter content contrast with previous findings, and can be attributed to close interrelationships between these properties and the predominance of sand content as controlling factor of reflectance. This study clarifies that ALOS band 4 provides the most useful imagery for intertidal monitoring because its reflectance, as simulated using the laboratory data, shows the strongest correlation with sand content. In a next step

  4. c2d Spitzer IRS spectra of embedded low-mass young stars: gas-phase emission lines

    NASA Astrophysics Data System (ADS)

    Lahuis, F.; van Dishoeck, E. F.; Jørgensen, J. K.; Blake, G. A.; Evans, N. J.

    2010-09-01

    Context. A survey of mid-infrared gas-phase emission lines of H2, H2O and various atoms toward a sample of 43 embedded low-mass young stars in nearby star-forming regions is presented. The sources are selected from the Spitzer “Cores to Disks” (c2d) legacy program. Aims: The environment of embedded protostars is complex both in its physical structure (envelopes, outflows, jets, protostellar disks) and the physical processes (accretion, irradiation by UV and/or X-rays, excitation through slow and fast shocks) which take place. The mid-IR spectral range hosts a suite of diagnostic lines which can distinguish them. A key point is to spatially resolve the emission in the Spitzer-IRS spectra to separate extended PDR and shock emission from compact source emission associated with the circumstellar disk and jets. Methods: An optimal extraction method is used to separate both spatially unresolved (compact, up to a few hundred AU) and spatially resolved (extended, thousand AU or more) emission from the IRS spectra. The results are compared with the c2d disk sample and literature PDR and shock models to address the physical nature of the sources. Results: Both compact and extended emission features are observed. Warm (T_ex few hundred K) H2, observed through the pure rotational H2 S(0), S(1) and S(2) lines, and [S i] 25 μm emission is observed primarily in the extended component. [S i] is observed uniquely toward truly embedded sources and not toward disks. On the other hand hot (T_ex ⪆ 700 K) H2, observed primarily through the S(4) line, and [Ne ii] emission is seen mostly in the spatially unresolved component. [Fe ii] and [Si ii] lines are observed in both spatial components. Hot H2O emission is found in the spatially unresolved component of some sources. Conclusions: The observed emission on ≥1000 AU scales is characteristic of PDR emission and likely originates in the outflow cavities in the remnant envelope created by the stellar wind and jets from the embedded

  5. Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?

    PubMed Central

    Balthasart, Françoise; Plavec, Janez; Gabelica, Valérie

    2013-01-01

    G-quadruplex nucleic acids can bind ammonium ions in solution and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG4T4G4)2, (dG4T3G4)2 and (dG3T4G4)2, and the intramolecular G-quadruplexes dG4(T4G4)3 and dG2T2G2TGTG2T2G2 (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure travelling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments therefore help assigning the number of inner ammonium ions in the solution phase structure. PMID:23132414

  6. An accurate method for microanalysis of carbon monoxide in putrid postmortem blood by head-space gas chromatography-mass spectrometry (HS/GC/MS).

    PubMed

    Hao, Hongxia; Zhou, Hong; Liu, Xiaopei; Zhang, Zhong; Yu, Zhongshan

    2013-06-10

    Carbon monoxide (CO) may be the cause of more than half the fatal poisonings reported in many countries, with some of these cases under-reported or misdiagnosed by medical professionals. Therefore, an accurate and reliable analytical method to measure blood carboxyhemoglobin level (COHb%), in the 1% to lethal range, is essential for correct diagnosis. Herein a method was established, i.e. head-space gas chromatography-mass spectrometry (HS/GC/MS) that has numerous advantages over other techniques, such as UV spectrometry, for determination of COHb%. There was a linear relationship (R(2)=0. 9995) between the peak area for CO and the COHb% in blood. Using a molecular sieve-packed column, CO levels in the air down to 0.01% and COHb% levels in small blood samples down to 0.2% could be quantitated rapidly and accurately. Furthermore, this method showed good reproducibility with a relative standard deviation for COHb% of <1%. Therefore, this technique provides an accurate and reliable method for determining CO and COHb% levels and may prove useful for investigation of deaths potentially related to CO exposure.

  7. Multi-residue screening of veterinary drugs in egg, fish and meat using high-resolution liquid chromatography accurate mass time-of-flight mass spectrometry.

    PubMed

    Peters, R J B; Bolck, Y J C; Rutgers, P; Stolker, A A M; Nielen, M W F

    2009-11-13

    The last 2 years multi-compound methods are gaining ground as screening methods. In this study a high-resolution liquid chromatography combined with time-of-flight mass spectrometry (HRLC-ToF-MS) is tested for the screening of about 100 veterinary drugs in three matrices, meat, fish and egg. While the results are satisfactory for 70-90% of the veterinary drugs, a more efficient sample preparation or extract purification is required for quantitative analysis of all analytes in more difficult matrices like egg. The average mass measurement error of the ToF-MS for the veterinary drugs spiked at concentrations ranging from 4 to 400 microg/kg, is 3.0 ppm (median 2.5 ppm) with little difference between the three matrices, but slightly decreases with increasing concentration. The SigmaFit value, a new feature for isotope pattern matching, also decreases with increasing concentration and, in addition, shows an increase with increasing matrix complexity. While the average SigmaFit value is 0.04, the median is 0.01 indicating some high individual deviations. As with the mass measurement error, the highest deviations are found in those regions of the chromatogram where most compounds elute from the column, be it analytes or matrix compounds. The median repeatability of the method ranges from 8% to 15%, decreasing with increasing concentration, while the median reproducibility ranges from 15% to 20% with little difference between matrices and concentrations. The median accuracy is in between 70% and 100% with a few compounds showing higher values due to matrix interference. The squared regression coefficient is >0.99 for 92% of the compounds showing a good overall linearity for most compounds. The detection capability, CCbeta, is within 2 times the associated validation level for >90% of the compounds studied. By changing a few conditions in the analyses protocol and analysing a number of blank samples, it was determined that the method is robust as well as specific. Finally

  8. Combining Fits of The Optical Photometry and X-ray Spectra of the Low Mass X-ray Binary V1408 Aquilae.

    NASA Astrophysics Data System (ADS)

    Gomez, Sebastian; Mason, Paul A.; Robinson, Edward L.

    2015-01-01

    V1408 Aquilae is a binary system with a black hole primary accreting matter from a low mass secondary. We observed the system at the McDonald Observatory and collected 126 hours of high speed optical photometry on the source. We modeled the optical light curve using the XRbinary light curve synthesis software. The best fits to the optical light curve seem to suggest that the primary is a low mass black hole, however we cannot exclude some high mass solutions. Our models slightly favor a 3 solar mass primary at an inclination of about 13 degrees. In order to further constrain these parameters, and verify their validity we compared the fits of the optical light curve to fits to the X-ray spectra of the source. Using data from the Chandra Transmission Grating Catalog and Archive and the ISIS software analysis package we modeled the spectra of the source with a multi-temperature blackbody for a relativistic accretion disk around a spinning black hole and an additional photon power law component. The fits to the optical lightcurve and X-ray spectra are in agreement, from this we conclude that the case for V1408 Aql to be at a low inclination and harbor a low mass black hole is plausible.

  9. Quantum synchrotron spectra from semirelativistic electrons in teragauss magnetic fields

    NASA Technical Reports Server (NTRS)

    Brainerd, J. J.

    1987-01-01

    Synchrotron spectra are calculated from quantum electrodynamic transition rates for thermal and power-law electron distributions. It is shown that quantum effects appear in thermal spectra when the photon energy is greater than the electron temperature, and in power-law spectra when the electron energy in units of the electron rest mass times the magnetic field strength in units of the critical field strength is of order unity. These spectra are compared with spectra calculated from the ultrarelativistic approximation for synchrotron emission. It is found that the approximation for the power-law spectra is good, and the approximation for thermal spectra produces the shape of the spectrum accurately but fails to give the correct normalization. Single photon pair creation masks the quantum effects for power-law distributions, so only modifications to thermal spectra are important for gamma-ray bursts.

  10. A mass spectrometric system for analyzing thermal desorption spectra of ion-implanted argon and cesium in tungsten. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Wood, G. M., Jr.

    1974-01-01

    A mass spectrometric system for determining the characteristics of materials used in instrumental development and aerospace applications was developed. The desorption spectra of cesium that was ion-implanted into polycrystalline tungsten and the effects on the spectra of bombardment of the tungsten by low energy (70 eV) electrons were investigated. Work function changes were measured by the retarding potential diode method. Flash desorption characteristics were observed and gas-reaction mechanisms of the surface of heated metal filaments were studied. Desorption spectra were measured by linearly increasing the sample temperature at a selected rate, the temperature cycling being generated from a ramp-driven dc power supply, with the mass spectrometer tuned to a mass number of interest. Results of the study indicate an anomolous desorption mechanism following an electron bombardment of the sample surface. The enhanced spectra are a function of the post-bombardment time and energy and are suggestive of an increased concentration of cesium atoms, up to 10 or more angstroms below the surface.

  11. Non-targeted screening for contaminants in paper and board food-contact materials using effect-directed analysis and accurate mass spectrometry.

    PubMed

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia; Jensen, Lisbeth Krüger; Granby, Kit; Vinggaard, Anne Marie; Driffield, Malcolm; Højslev Petersen, Jens

    2016-06-01

    Due to large knowledge gaps in chemical composition and toxicological data for substances involved, paper and board food-contact materials (P&B FCM) have been emerging as a FCM type of particular concern for consumer safety. This study describes the development of a step-by-step strategy, including extraction, high-performance liquid chromatography (HPLC) fractionation, tentative identification of relevant substances and in vitro testing of selected tentatively identified substances. As a case study, we used two fractions from a recycled pizza box sample which exhibited aryl hydrocarbon receptor (AhR) activity. These fractions were analysed by gas chromatography (GC) and ultra-HPLC (UHPLC) coupled to quadrupole time-of-flight mass spectrometers (QTOF MS) in order tentatively to identify substances. The elemental composition was determined for peaks above a threshold, and compared with entries in a commercial mass spectral library for GC-MS (GC-EI-QTOF MS) analysis and an in-house built library of accurate masses for substances known to be used in P&B packaging for UHPLC-QTOF analysis. Of 75 tentatively identified substances, 15 were initially selected for further testing in vitro; however, only seven were commercially available and subsequently tested in vitro and quantified. Of these seven, the identities of three pigments found in printing inks were confirmed by UHPLC tandem mass spectrometry (QqQ MS/MS). Two pigments had entries in the database, meaning that a material relevant accurate mass database can provide a fast tentative identification. Pure standards of the seven tentatively identified substances were tested in vitro but could not explain a significant proportion of the AhR-response in the extract. Targeted analyses of dioxins and PCBs, both well-known AhR agonists, was performed. However, the dioxins could explain approximately 3% of the activity observed in the pizza box extract indicating that some very AhR active substance(s) still remain to be

  12. Absorption-mode Fourier transform mass spectrometry: the effects of apodization and phasing on modified protein spectra.

    PubMed

    Qi, Yulin; Li, Huilin; Wills, Rebecca H; Perez-Hurtado, Pilar; Yu, Xiang; Kilgour, David P A; Barrow, Mark P; Lin, Cheng; O'Connor, Peter B

    2013-06-01

    The method of phasing broadband Fourier transform ion cyclotron resonance (FT-ICR) spectra allows plotting the spectra in the absorption-mode; this new approach significantly improves the quality of the data at no extra cost. Herein, an internal calibration method for calculating the phase function has been developed and successfully applied to the top-down spectra of modified proteins, where the peak intensities vary by 100×. The result shows that the use of absorption-mode spectra allows more peaks to be discerned within the recorded data, and this can reveal much greater information about the protein and modifications under investigation. In addition, noise and harmonic peaks can be assigned immediately in the absorption-mode.

  13. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples

    NASA Astrophysics Data System (ADS)

    Harvey, David J.; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H.

    2015-07-01

    Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.

  14. Collective-coupling analysis of spectra of mass-7 isobars: {sup 7}He, {sup 7}Li, {sup 7}Be, and {sup 7}B

    SciTech Connect

    Canton, L.; Pisent, G.; Amos, K.; Karataglidis, S.; Svenne, J. P.; Knijff, D. van der

    2006-12-15

    A nucleon-nucleus interaction model has been applied to ascertain the underlying character of the negative-parity spectra of four isobars of mass-7, from neutron- to proton-emitter drip lines. With a single nuclear potential defined by a simple coupled-channel model, a multichannel algebraic scattering approach (MCAS) has been used to determine the bound and resonant spectra of the four nuclides, of which {sup 7}He and {sup 7}B are particle unstable. Incorporation of Pauli blocking into the model enables a description of all known spin-parity states of the mass-7 isobars. We have also obtained spectra of similar quality by using a large space no-core shell model. Additionally, we have studied {sup 7}Li and {sup 7}Be using a dicluster model. We have found a dicluster-model potential that can reproduce the lowest four states of the two nuclei, as well as the relevant low-energy elastic scattering cross sections. But, with this model, the rest of the energy spectra cannot be obtained.

  15. Investigation of mass dependence effects for the accurate determination of molybdenum isotope amount ratios by MC-ICP-MS using synthetic isotope mixtures.

    PubMed

    Malinovsky, Dmitry; Dunn, Philip J H; Petrov, Panayot; Goenaga-Infante, Heidi

    2015-01-01

    Methodology for absolute Mo isotope amount ratio measurements by multicollector inductively coupled plasma-mass spectrometry (MC-ICP-MS) using calibration with synthetic isotope mixtures (SIMs) is presented. For the first time, synthetic isotope mixtures prepared from seven commercially available isotopically enriched molybdenum metal powders ((92)Mo, (94)Mo, (95)Mo, (96)Mo, (97)Mo, (98)Mo, and (100)Mo) are used to investigate whether instrumental mass discrimination of Mo isotopes in MC-ICP-MS is consistent with mass-dependent isotope distribution. The parent materials were dissolved and mixed as solutions to obtain mixtures with accurately known isotope amount ratios. The level of elemental impurities in the isotopically enriched molybdenum metal powders was quantified by ICP-MS by using both high-resolution and reaction cell instruments to completely resolve spectral interferences. The Mo isotope amount ratio values with expanded uncertainty (k = 2), determined by MC-ICP-MS for a high-purity Mo rod from Johnson Matthey, were as follows: (92)Mo/(95)Mo = 0.9235(9), (94)Mo/(95)Mo = 0.5785(8), (96)Mo/(95)Mo = 1.0503(9), (97)Mo/(95)Mo = 0.6033(6), (98)Mo/(95)Mo = 1.5291(20), and (100)Mo/(95)Mo = 0.6130(7). A full uncertainty budget for the measurements is presented which shows that the largest contribution to the uncertainty budget comes from correction for elemental impurities (∼51%), followed by the contribution from weighing operations (∼26 %). The atomic weight of molybdenum was calculated to be 95.947(2); the uncertainty in parentheses is expanded uncertainty with the coverage factor of 2. A particular advantage of the developed method is that calibration factors for all six Mo isotope amount ratios, involving the (95)Mo isotope, were experimentally determined. This allows avoiding any assumption on mass-dependent isotope fractions in MC-ICP-MS, inherent to the method of double spike previously used for Mo isotope amount ratio

  16. Measurement of Dielectron Invariant Mass Spectra in Au + Au Collisions at p sNN = 200GeV with HBD in PHENIX

    NASA Astrophysics Data System (ADS)

    Sun, Jiayin

    Dileptons are emitted throughout the entire space-time evolution of heavy ion collisions. Being colorless, these electromagnetic probes do not participate in the final-state strong interactions during the passage through the hot medium, and retain the information on the conditions of their creation. This characteristic renders them valuable tools for studying the properties of the Quark Gluon Plasma created during ultra-relativistic heavy ion collisions. The invariant mass spectra of dileptons contain a wealth of information on every stage of the evolution of heavy ion collisions. At low mass, dilepton spectra consist mainly of light meson decays. The medium modification of the light vector mesons gives insight on the chiral symmetry restoration in heavy ion collisions. At intermediate and high mass, there are significant contributions from charm and bottom, with a minor contribution from QGP thermal radiation. The region was utilized to measure cross sections of open charm and open bottom, as well as quarkonium suppression as demonstrated by PHENIX. An earlier PHENIX measurement of dielectron spectra in heavy ion collisions, using data taken in 2004, shows significant deviations from the hadronic decay expectations. The measurement, however, suffered from an unfavorable signal to background ratio. Random combination of electron-positron pairs from unrelated sources, mostly Dalitz decay of pi0 and external conversion of decay photon to electrons, is the main contributor to the background. Mis-identified hadrons are another major background source. To improve the situation, the Hadron Blind Detector (HBD), a windowless proximity focusing Cerenkov detector, is designed to reduce this background by identifying electron tracks from photon conversions and pi. 0 Dalitzdecays. The detector has been installed and operated in PHENIX in 2009 and 2010, where reference p+p and Au+Au data sets were successfully taken. We will present the dielectron results from the analysis of

  17. Extensive Peptide Fractionation and y1 Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry.

    PubMed

    Niu, Mingming; Cho, Ji-Hoon; Kodali, Kiran; Pagala, Vishwajeeth; High, Anthony A; Wang, Hong; Wu, Zhiping; Li, Yuxin; Bi, Wenjian; Zhang, Hui; Wang, Xusheng; Zou, Wei; Peng, Junmin

    2017-02-22

    Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS. Systematic investigation shows that quantitative interference was impacted by LC fractionation depth, MS isolation window, and peptide loading amount. Exhaustive fractionation (320 × 4 h) can nearly eliminate the interference and achieve results comparable to the MS3-based method. Importantly, the interference in MS2 scans can be estimated by the intensity of contaminated y1 product ions, and we thus developed an algorithm to correct reporter ion ratios of tryptic peptides. Our data indicate that intermediate fractionation (40 × 2 h) and y1 ion-based correction allow accurate and deep TMT profiling of more than 10 000 proteins, which represents a straightforward and affordable strategy in isobaric labeling proteomics.

  18. Screening and characterization of reactive compounds with in vitro peptide-trapping and liquid chromatography/high-resolution accurate mass spectrometry.

    PubMed

    Wei, Cong; Chupak, Louis S; Philip, Thomas; Johnson, Benjamin M; Gentles, Robert; Drexler, Dieter M

    2014-02-01

    The present study describes a novel methodology for the detection of reactive compounds using in vitro peptide-trapping and liquid chromatography-high-resolution accurate mass spectrometry (LC-HRMS). Compounds that contain electrophilic groups can covalently bind to nucleophilic moieties in proteins and form adducts. Such adducts are thought to be associated with drug-mediated toxicity and therefore represent potential liabilities in drug discovery programs. In addition, reactive compounds identified in biological screening can be associated with data that can be misinterpreted if the reactive nature of the compound is not appreciated. In this work, to facilitate the triage of hits from high-throughput screening (HTS), a novel assay was developed to monitor the formation of covalent peptide adducts by compounds suspected to be chemically reactive. The assay consists of in vitro incubations of test compounds (under conditions of physiological pH) with synthetically prepared peptides presenting a variety of nucleophilic moieties such as cysteine, lysine, histidine, arginine, serine, and tyrosine. Reaction mixtures were analyzed using full-scan LC-HRMS, the data were interrogated using postacquisition data mining, and modified amino acids were identified by subsequent LC-HRMS/mass spectrometry. The study demonstrated that in vitro nucleophilic peptide trapping followed by LC-HRMS analysis is a useful approach for screening of intrinsically reactive compounds identified from HTS exercises, which are then removed from follow-up processes, thus obviating the generation of data from biochemical activity assays.

  19. Hybrid quadrupole-orbitrap mass spectrometry analysis with accurate-mass database and parallel reaction monitoring for high-throughput screening and quantification of multi-xenobiotics in honey.

    PubMed

    Li, Yi; Zhang, Jinzhen; Jin, Yue; Wang, Lin; Zhao, Wen; Zhang, Wenwen; Zhai, Lifei; Zhang, Yaping; Zhang, Yongxin; Zhou, Jinhui

    2016-01-15

    This study reports a rapid, automated screening and quantification method for the determination of multi-xenobiotic residues in honey using ultra-high performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-Q-Orbitrap) with a user-built accurate-mass database plus parallel reaction monitoring (PRM). The database contains multi-xenobiotic information including formulas, adduct types, theoretical exact mass and retention time, characteristic fragment ions, ion ratios, and mass accuracies. A simple sample preparation method was developed to reduce xenobiotic loss in the honey samples. The screening method was validated based on retention time deviation, mass accuracy via full scan-data-dependent MS/MS (full scan-ddMS2), multi-isotope ratio, characteristic ion ratio, sensitivity, and positive/negative switching performance between the spiked sample and corresponding standard solution. The quantification method based on the PRM mode is a promising new quantitative tool which we validated in terms of selectivity, linearity, recovery (accuracy), repeatability (precision), decision limit (CCα), detection capability (CCβ), matrix effects, and carry-over. The optimized methods proposed in this study enable the automated screening and quantification of 157 compounds in less than 15 min in honey. The results of this study, as they represent a convenient protocol for large-scale screening and quantification, also provide a research approach for analysis of various contaminants in other matrices.

  20. Computer programs for the interpretation of low resolution mass spectra: Program for calculation of molecular isotopic distribution and program for assignment of molecular formulas

    NASA Technical Reports Server (NTRS)

    Miller, R. A.; Kohl, F. J.

    1977-01-01

    Two FORTRAN computer programs for the interpretation of low resolution mass spectra were prepared and tested. One is for the calculation of the molecular isotopic distribution of any species from stored elemental distributions. The program requires only the input of the molecular formula and was designed for compatability with any computer system. The other program is for the determination of all possible combinations of atoms (and radicals) which may form an ion having a particular integer mass. It also uses a simplified input scheme and was designed for compatability with any system.

  1. Eclipsing Binaries as Astrophysical Laboratories: CM Draconis - Accurate Absolute Physical Properties of Low Mass Stars and an Independent Estimate of the Primordial Helium Abundance

    NASA Astrophysics Data System (ADS)

    McCook, G. P.; Guinan, E. F.; Saumon, D.; Kang, Y. W.

    1997-05-01

    CM Draconis (Gl 630.1; Vmax = +12.93) is an important eclipsing binary consisting of two dM4.5e stars with an orbital period of 1.2684 days. This binary is a high velocity star (s= 164 km/s) and the brighter member of a common proper motion pair with a cool faint white dwarf companion (LP 101-16). CM Dra and its white dwarf companion were once considered by Zwicky to belong to a class of "pygmy stars", but they turned out to be ordinary old, cool white dwarfs or faint red dwarfs. Lacy (ApJ 218,444L) determined the first orbital and physical properties of CM Dra from the analysis of his light and radial velocity curves. In addition to providing directly measured masses, radii, and luminosities for low mass stars, CM Dra was also recognized by Lacy and later by Paczynski and Sienkiewicz (ApJ 286,332) as an important laboratory for cosmology, as a possible old Pop II object where it may be possible to determine the primordial helium abundance. Recently, Metcalfe et al.(ApJ 456,356) obtained accurate RV measures for CM Dra and recomputed refined elements along with its helium abundance. Starting in 1995, we have been carrying out intensive RI photoelectric photometry of CM Dra to obtain well defined, accurate light curves so that its fundamental properties can be improved, and at the same time, to search for evidence of planets around the binary from planetary transit eclipses. During 1996 and 1997 well defined light curves were secured and these were combined with the RV measures of Metcalfe et al. (1996) to determine the orbital and physical parameters of the system, including a refined orbital period. A recent version of the Wilson-Devinney program was used to analyze the data. New radii, masses, mean densities, Teff, and luminosities were found as well as a re-determination of the helium abundance (Y). The results of the recent analyses of the light and RV curves will be presented and modelling results discussed. This research is supported by NSF grants AST-9315365

  2. Ultra-high-performance liquid chromatography electrospray ionization tandem mass spectrometry for accurate analysis of glycerophospholipids and sphingolipids in drug resistance tumor cells.

    PubMed

    Li, Lin; Wang, Linlin; Shangguan, Dihua; Wei, Yanbo; Han, Juanjuan; Xiong, Shaoxiang; Zhao, Zhenwen

    2015-02-13

    Glycerophospholipids and sphingolipids are important signaling molecules which are involved in many physiological and pathological processes. Here we reported an effective method for accurate analysis of these lipids by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The methanol method was adopted for extraction of lipids due to its simplicity and high efficiency. It was found that two subclasses of sphingolipids, sulfatide (ST) and cerebroside (CB), were heat labile, so a decreased temperature in the ion source of MS might be necessary for these compounds analysis. In addition, it was found that the isobaric interferences were commonly existent, for example, the m/z of 16:0/18:1 PC containing two (13)C isotope being identical to that of 16:0/18:0 PC determined by a unit mass resolution mass spectrometer; therefore, a baseline separation of interferential species was required to maintain selectivity and accuracy of analysis. In this work, an ultra-high-performance liquid chromatography (UHPLC)-based method was developed for separation of interferential species. Moreover, in order to deal with the characteristics of different polarity and wide dynamic range of glycerophospholipids and sphingolipids in biological systems, three detecting conditions were combined together for comprehensive and rational analysis of glycerophospholipids and sphingolipids. The method was utilized to profile glycerophospholipids and sphingolipids in drug resistant tumor cells. Our results showed that many lipids were significantly changed in drug resistant tumor cells compared to paired drug sensitive tumor cells. This is a systematic report about the isobaric interferences and heat labile compounds interferences when analyzing glycerophospholipids and sphingolipids by ESI-MS/MS, which aids in ruling out one potential source of systematic error to ensure the accuracy of analysis.

  3. Probing shock geometry via the charge to mass ratio dependence of heavy ion spectra from multiple spacecraft observations of the 2013 November 4 event

    NASA Astrophysics Data System (ADS)

    Zhao, Lulu; Li, Gang; Mason, Glenn M.; Cohen, Christina; Mewaldt, Richard; Desai, Mihir; Ebert, Rob; Al-Dayeh, Maher

    2016-12-01

    In large Solar Energetic Particle (SEP) events, ions can be accelerated at coronal mass ejection (CME)-driven shocks to very high energies. The spectra of heavy ions in many large SEP events show features such as roll-overs or spectral breaks. In some events when the spectra are plotted in terms of energy/nucleon, they can be shifted relative to each other to make the spectral breaks align. The amount of shift is charge to mass ratio (Q/A) dependent and varies from event to event. This can be understood if the spectra of heavy ions are organized by the diffusion coefficients (Cohen et al. 2005). In the work of Li et al. (2009), the Q/A dependence of the scaling is related to shock geometry when the CME-driven shock is close to the Sun. For events where multiple in-situ spacecraft observations exist, one may expect that different spacecraft are connected to different portions of the CME-driven shock that have different shock geometries, therefore yielding different Q/A dependence. In this work, we examine one SEP event which occurred on 2013 November 4. We study the Q/A dependence of the energy scaling for heavy ion spectra using helium, oxygen and iron ions. Observations from STEREO-A, STEREO-B and ACE are examined. We find that the scalings are different for different spacecraft. We suggest that this is because ACE, STEREO-A and STEREO-B are connected to different parts of the shock that have different shock geometries. Our analysis indicates that studying the Q/A scaling of in-situ particle spectra can serve as a powerful tool to remotely examine the shock geometry for large SEP events.

  4. Simple and accurate measurement of carbamazepine in surface water by use of porous membrane-protected micro-solid-phase extraction coupled with isotope dilution mass spectrometry.

    PubMed

    Teo, Hui Ling; Wong, Lingkai; Liu, Qinde; Teo, Tang Lin; Lee, Tong Kooi; Lee, Hian Kee

    2016-03-17

    To achieve fast and accurate analysis of carbamazepine in surface water, we developed a novel porous membrane-protected micro-solid-phase extraction (μ-SPE) method, followed by liquid chromatography-isotope dilution tandem mass spectrometry (LC-IDMS/MS) analysis. The μ-SPE device (∼0.8 × 1 cm) was fabricated by heat-sealing edges of a polypropylene membrane sheet to devise a bag enclosing the sorbent. The analytes (both carbamazepine and isotope-labelled carbamazepine) were first extracted by μ-SPE device in the sample (10 mL) via agitation, then desorbed in an organic solvent (1 mL) via ultrasonication. Several parameters such as organic solvent for pre-conditioning of μ-SPE device, amount of sorbent, adsorption time, and desorption solvent and time were investigated to optimize the μ-SPE efficiency. The optimized method has limits of detection and quantitation estimated to be 0.5 ng L(-1) and 1.6 ng L(-1), respectively. Surface water samples spiked with different amounts of carbamazepine (close to 20, 500, and 1600 ng L(-1), respectively) were analysed for the validation of method precision and accuracy. Good precision was obtained as demonstrated by relative standard deviations of 0.7% for the samples with concentrations of 500 and 1600 ng kg(-1), and 5.8% for the sample with concentration of 20 ng kg(-1). Good accuracy was also demonstrated by the relative recoveries in the range of 96.7%-103.5% for all samples with uncertainties of 1.1%-5.4%. Owing to the same chemical properties of carbamazepine and isotope-labelled carbamazepine, the isotope ratio in the μ-SPE procedure was accurately controlled. The use of μ-SPE coupled with IDMS analysis significantly facilitated the fast and accurate measurement of carbamazepine in surface water.

  5. Detection and quantitation of trace phenolphthalein (in pharmaceutical preparations and in forensic exhibits) by liquid chromatography-tandem mass spectrometry, a sensitive and accurate method.

    PubMed

    Sharma, Kakali; Sharma, Shiba P; Lahiri, Sujit C

    2013-01-01

    Phenolphthalein, an acid-base indicator and laxative, is important as a constituent of widely used weight-reducing multicomponent food formulations. Phenolphthalein is an useful reagent in forensic science for the identification of blood stains of suspected victims and for apprehending erring officials accepting bribes in graft or trap cases. The pink-colored alkaline hand washes originating from the phenolphthalein-smeared notes can easily be determined spectrophotometrically. But in many cases, colored solution turns colorless with time, which renders the genuineness of bribe cases doubtful to the judiciary. No method is known till now for the detection and identification of phenolphthalein in colorless forensic exhibits with positive proof. Liquid chromatography-tandem mass spectrometry had been found to be most sensitive, accurate method capable of detection and quantitation of trace phenolphthalein in commercial formulations and colorless forensic exhibits with positive proof. The detection limit of phenolphthalein was found to be 1.66 pg/L or ng/mL, and the calibration curve shows good linearity (r(2) = 0.9974).

  6. Accurate determination of Curium and Californium isotopic ratios by inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) in 248Cm samples for transmutation studies

    SciTech Connect

    Gourgiotis, A.; Isnard, H.; Aubert, M.; Dupont, E.; AlMahamid, I.; Cassette, P.; Panebianco, S.; Letourneau, A.; Chartier, F.; Tian, G.; Rao, L.; Lukens, W.

    2011-02-01

    The French Atomic Energy Commission has carried out several experiments including the mini-INCA (INcineration of Actinides) project for the study of minor-actinide transmutation processes in high intensity thermal neutron fluxes, in view of proposing solutions to reduce the radiotoxicity of long-lived nuclear wastes. In this context, a Cm sample enriched in {sup 248}Cm ({approx}97 %) was irradiated in thermal neutron flux at the High Flux Reactor (HFR) of the Laue-Langevin Institute (ILL). This work describes a quadrupole ICP-MS (ICP-QMS) analytical procedure for precise and accurate isotopic composition determination of Cm before sample irradiation and of Cm and Cf after sample irradiation. The factors that affect the accuracy and reproducibility of isotopic ratio measurements by ICP-QMS, such as peak centre correction, detector dead time, mass bias, abundance sensitivity and hydrides formation, instrumental background, and memory blank were carefully evaluated and corrected. Uncertainties of the isotopic ratios, taking into account internal precision of isotope ratio measurements, peak tailing, and hydrides formations ranged from 0.3% to 1.3%. This uncertainties range is quite acceptable for the nuclear data to be used in transmutation studies.

  7. Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra.

    PubMed

    Hansen, Thomas A; Kryuchkov, Fedor; Kjeldsen, Frank

    2012-08-07

    With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.

  8. Multiple hydrogen bonds. Mass spectra of hydrogen bonded heterodimers. A comparison of ESI- and REMPI-ReTOF-MS.

    PubMed

    Taubitz, Jörg; Lüning, Ulrich; Grotemeyer, Jürgen

    2004-11-07

    Resonance enhanced multi-photon ionization-reflectron time of flight mass spectrometry is the analytical method of choice to observe hydrogen bonded supramolecules in the gas phase when protonation of basic centers competes with cluster formation.

  9. Non-targeted analysis of electronics waste by comprehensive two-dimensional gas chromatography combined with high-resolution mass spectrometry: Using accurate mass information and mass defect analysis to explore the data.

    PubMed

    Ubukata, Masaaki; Jobst, Karl J; Reiner, Eric J; Reichenbach, Stephen E; Tao, Qingping; Hang, Jiliang; Wu, Zhanpin; Dane, A John; Cody, Robert B

    2015-05-22

    Comprehensive two-dimensional gas chromatography (GC×GC) and high-resolution mass spectrometry (HRMS) offer the best possible separation of their respective techniques. Recent commercialization of combined GC×GC-HRMS systems offers new possibilities for the analysis of complex mixtures. However, such experiments yield enormous data sets that require new informatics tools to facilitate the interpretation of the rich information content. This study reports on the analysis of dust obtained from an electronics recycling facility by using GC×GC in combination with a new high-resolution time-of-flight (TOF) mass spectrometer. New software tools for (non-traditional) Kendrick mass defect analysis were developed in this research and greatly aided in the identification of compounds containing chlorine and bromine, elements that feature in most persistent organic pollutants (POPs). In essence, the mass defect plot serves as a visual aid from which halogenated compounds are recognizable on the basis of their mass defect and isotope patterns. Mass chromatograms were generated based on specific ions identified in the plots as well as region of the plot predominantly occupied by halogenated contaminants. Tentative identification was aided by database searches, complementary electron-capture negative ionization experiments and elemental composition determinations from the exact mass data. These included known and emerging flame retardants, such as polybrominated diphenyl ethers (PBDEs), hexabromobenzene, tetrabromo bisphenol A and tris (1-chloro-2-propyl) phosphate (TCPP), as well as other legacy contaminants such as polychlorinated biphenyls (PCBs) and polychlorinated terphenyls (PCTs).

  10. Emissions and ambient distributions of Biogenic Volatile Organic Compounds (BVOC) in a ponderosa pine ecosystem: interpretation of PTR-MS mass spectra

    NASA Astrophysics Data System (ADS)

    Kim, S.; Karl, T.; Guenther, A.; Tyndall, G.; Orlando, J.; Harley, P.; Rasmussen, R.; Apel, E.

    2010-02-01

    Two proton-transfer-reaction mass spectrometry systems were deployed at the Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen-Southern Rocky Mountain 2008 field campaign (BEACHON-SRM08; July to September, 2008) at the Manitou Forest Observatory in a ponderosa pine woodland near Woodland Park, Colorado USA. The two PTR-MS systems simultaneously measured BVOC emissions and ambient distributions of their oxidation products. Here, we present mass spectral analysis in a wide range of masses (m/z 40+ to 210+) to assess our understanding of BVOC emissions and their photochemical processing inside of the forest canopy. The biogenic terpenoids, 2-methyl-3-butene-2-ol (MBO, 50.2%) and several monoterpenes (MT, 33.5%) were identified as the dominant BVOC emissions from a transmission corrected mass spectrum (PTR-MS), averaged over the daytime (11 a.m. to 3 p.m., local time) of three days. To assess contributions of oxidation products of local BVOC, we calculate an oxidation product spectrum with the OH- and ozone-initiated oxidation product distribution mass spectra of two major BVOC emissions at the ecosystem (MBO and β-pinene) that were observed from laboratory oxidation experiments. The majority (~76%) of the total signal in the transmission corrected PTR-MS spectra could be explained by identified compounds. The remainder are attributed to oxidation products of BVOC emitted from nearby ecosystems and transported to the site, and oxidation products of unidentified BVOC emitted from the ponderosa pine ecosystem.

  11. Modelling the high-mass accretion rate spectra of GX 339-4: black hole spin from reflection?

    NASA Astrophysics Data System (ADS)

    Kolehmainen, Mari; Done, Chris; Díaz Trigo, María

    2011-09-01

    We extract all the XMM-Newton European Photon Imaging Camera (EPIC) pn burst mode spectra of GX 339-4, together with simultaneous/contemporaneous RXTE data. These include three disc-dominated and two soft intermediate spectra, and the combination of broad bandpass/moderate spectral resolution gives some of the best data on these bright soft states in black hole binaries. The disc-dominated spectra span a factor of 3 in luminosity, and all show that the disc emission is broader than the simplest multicolour disc model. This is consistent with the expected relativistic smearing and changing colour temperature correction produced by atomic features in the newest disc models. However, these models do not match the data at the 5 per cent level as the predicted atomic features are not present in the data, perhaps indicating that irradiation is important even when the high-energy tail is weak. Whatever the reason, this means that the data have smaller errors than the best physical disc models, forcing use of more phenomenological models for the disc emission. We use these for the soft intermediate state data, where previous analysis using a simple disc continuum found an extremely broad residual, identified as the red wing of the iron line from reflection around a highly spinning black hole. However, the iron line energy is close to where the disc and tail have equal fluxes, so using a broader disc continuum changes the residual 'iron line' profile dramatically. With a broader disc continuum model, the inferred line is formed outside of 30Rg, so it cannot constrain black hole spin. We caution that a robust determination of black hole spin from the iron line profile is very difficult where the disc makes a significant contribution at the iron line energy, i.e. in most bright black hole states.

  12. Extreme ultraviolet ionization of pure He nanodroplets: Mass-correlated photoelectron imaging, Penning ionization, and electron energy-loss spectra

    SciTech Connect

    Buchta, D.; Stienkemeier, F.; Mudrich, M.; Krishnan, S. R.; Moshammer, R.; Brauer, N. B.; Drabbels, M.; O’Keeffe, P.; Coreno, M.; Devetta, M.; Di Fraia, M.; Callegari, C.; Richter, R.; Prince, K. C.; Ullrich, J.

    2013-08-28

    The ionization dynamics of pure He nanodroplets irradiated by Extreme ultraviolet radiation is studied using Velocity-Map Imaging PhotoElectron-PhotoIon COincidence spectroscopy. We present photoelectron energy spectra and angular distributions measured in coincidence with the most abundant ions He{sup +}, He{sub 2}{sup +}, and He{sub 3}{sup +}. Surprisingly, below the autoionization threshold of He droplets, we find indications for multiple excitation and subsequent ionization of the droplets by a Penning-like process. At high photon energies we observe inelastic collisions of photoelectrons with the surrounding He atoms in the droplets.

  13. Emissions and ambient distributions of Biogenic Volatile Organic Compounds (BVOC) in a Ponderosa pine ecosystem: interpretation of PTR-MS mass spectra

    NASA Astrophysics Data System (ADS)

    Kim, S.; Karl, T.; Guenther, A.; Tyndall, G.; Orlando, J.; Harley, P.; Rasmussen, R.; Apel, E.

    2009-10-01

    Two proton-transfer-reaction mass spectrometry systems were deployed at the Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen-Southern Rocky Mountain 2008 field campaign (BEACHON-SRM08; July to September 2008) at the Manitou Forest observatory in a Ponderosa pine woodland near Woodland Park, Colorado USA to simultaneously measure BVOC emissions and ambient distributions of their oxidation products. Here, we present mass spectral analysis in a wide range of masses (m/z=40+ to 210+) to assess our understanding of BVOC emissions and their photochemical process inside of the forest canopy. The biogenic terpenoids, 2-methyl-3-butene-2-ol (MBO, 50.2%) and several monoterpenes (MT, 33.5%) were identified as the dominant BVOC emissions from a transmission corrected mass spectrum, averaged over the daytime (11 am to 3 p.m., local time) of three days. To assess contributions of oxidation products of local BVOC, we calculate a oxidation product spectrum with the OH- and ozone-initiated oxidation product distribution mass spectra of two major BVOC at the ecosystem (MBO and β-pinene) that were observed from laboratory oxidation experiments. A majority (~73%) of the total signal could be explained by known compounds. The remainder are attributed to oxidation products of BVOC, emitted from nearby ecosystems and transported to the site, and oxidation products of unidentified BVOC emitted from the Ponderosa pine ecosystem.

  14. A High Resolution/Accurate Mass (HRAM) Data-Dependent MS3 Neutral Loss Screening, Classification, and Relative Quantitation Methodology for Carbonyl Compounds in Saliva

    NASA Astrophysics Data System (ADS)

    Dator, Romel; Carrà, Andrea; Maertens, Laura; Guidolin, Valeria; Villalta, Peter W.; Balbo, Silvia

    2016-10-01

    Reactive carbonyl compounds (RCCs) are ubiquitous in the environment and are generated endogenously as a result of various physiological and pathological processes. These compounds can react with biological molecules inducing deleterious processes believed to be at the basis of their toxic effects. Several of these compounds are implicated in neurotoxic processes, aging disorders, and cancer. Therefore, a method characterizing exposures to these chemicals will provide insights into how they may influence overall health and contribute to disease pathogenesis. Here, we have developed a high resolution accurate mass (HRAM) screening strategy allowing simultaneous identification and relative quantitation of DNPH-derivatized carbonyls in human biological fluids. The screening strategy involves the diagnostic neutral loss of hydroxyl radical triggering MS3 fragmentation, which is only observed in positive ionization mode of DNPH-derivatized carbonyls. Unique fragmentation pathways were used to develop a classification scheme for characterizing known and unanticipated/unknown carbonyl compounds present in saliva. Furthermore, a relative quantitation strategy was implemented to assess variations in the levels of carbonyl compounds before and after exposure using deuterated d 3 -DNPH. This relative quantitation method was tested on human samples before and after exposure to specific amounts of alcohol. The nano-electrospray ionization (nano-ESI) in positive mode afforded excellent sensitivity with detection limits on-column in the high-attomole levels. To the best of our knowledge, this is the first report of a method using HRAM neutral loss screening of carbonyl compounds. In addition, the method allows simultaneous characterization and relative quantitation of DNPH-derivatized compounds using nano-ESI in positive mode.

  15. Cosmological constraints from the CFHTLenS shear measurements using a new, accurate, and flexible way of predicting non-linear mass clustering

    NASA Astrophysics Data System (ADS)

    Angulo, Raul E.; Hilbert, Stefan

    2015-03-01

    We explore the cosmological constraints from cosmic shear using a new way of modelling the non-linear matter correlation functions. The new formalism extends the method of Angulo & White, which manipulates outputs of N-body simulations to represent the 3D non-linear mass distribution in different cosmological scenarios. We show that predictions from our approach for shear two-point correlations at 1-300 arcmin separations are accurate at the ˜10 per cent level, even for extreme changes in cosmology. For moderate changes, with target cosmologies similar to that preferred by analyses of recent Planck data, the accuracy is close to ˜5 per cent. We combine this approach with a Monte Carlo Markov chain sampler to explore constraints on a Λ cold dark matter model from the shear correlation functions measured in the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS). We obtain constraints on the parameter combination σ8(Ωm/0.27)0.6 = 0.801 ± 0.028. Combined with results from cosmic microwave background data, we obtain marginalized constraints on σ8 = 0.81 ± 0.01 and Ωm = 0.29 ± 0.01. These results are statistically compatible with previous analyses, which supports the validity of our approach. We discuss the advantages of our method and the potential it offers, including a path to model in detail (i) the effects of baryons, (ii) high-order shear correlation functions, and (iii) galaxy-galaxy lensing, among others, in future high-precision cosmological analyses.

  16. Studies on anabolic steroids. The mass spectra of 17 alpha-methyl-17 beta-hydroxy-1,4-androstadien-3-one (Dianabol) and its metabolites.

    PubMed

    Dürbeck, H W; Büker, I

    1980-10-01

    The metabolism of 17 alpha-methyl-17 beta-hydroxy-1,4-androstadien-3-one (dianabol) in human adults has been studied in detail by computer aided capillary gas chromatography mass spectrometry. After oral administration to man six metabolites were determined in the free fraction of the urine samples, the structures of which have been identified as 17-epidianabol, three isomers of 6-hydroxydianabol, 17 alpha-methyl-17 beta-hydroxy-1,4,6-androstatrien-3-one (delta 6-dianabol) and 18-nor-17,17-dimethyl-1,4,13(14)-androstatrien-3-one, respectively. In agreement with previous observations no measurable amounts of the administered drug itself could be detected in any of the urine samples investigated. The mass spectra of all metabolites and the main fragmentation processes are discussed in detail.

  17. Matrix-assisted ultraviolet laser desorption/ionization time-of-flight (UV-MALDI-TOF) mass spectra of N-acylated and N,O-acylated glycosylamines.

    PubMed

    Sato, Yasuto; Fukuyama, Yuko; Nonami, Hiroshi; Erra-Balsells, Rosa; Stortz, Carlos A; Cerezo, Alberto S; Matulewicz, María C

    2007-12-10

    Matrix-assisted ultraviolet laser desorption/ionization time-of-flight mass spectrometry (UV-MALDI-TOF-MS) has shown to be a very useful technique for the study of the non-volatile and thermally non-stable N-acylated glycopyranosyl- and glycofuranosyl-amines. Of the several matrices tested, 2,5-dihydroxybenzoic acid (DHB) was the most effective giving good spectra in the positive-ion mode. In the linear and reflectron modes, the [M+Na](+) ions appeared with high intensity. Their fragmentation patterns were investigated by post-source decay (PSD) UV-MALDI-TOF-MS showing mainly cross-ring cleavages. In addition, N,O-acylated glycopyranosyl- and glycofuranosyl-amines were also analyzed by this technique. PSD UV-MALDI-TOF-MS gave significant signals for several primary fragment ions, which were proposed but not detected, or observed with very low abundance, in electron ionization mass spectrometry (EI-MS) experiments.

  18. Search for narrow resonances in dilepton mass spectra in pp collisions at √{ s} = 7TeV

    NASA Astrophysics Data System (ADS)

    Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hammer, J.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Liko, D.; Mikulec, I.; Pernicka, M.; Rahbaran, B.; Rohringer, C.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Wagner, P.; Waltenberger, W.; Walzel, G.; Widl, E.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Luyckx, S.; Maes, T.; Mucibello, L.; Ochesanu, S.; Roland, B.; Rougny, R.; Selvaggi, M.; Staykova, Z.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Gonzalez Suarez, R.; Kalogeropoulos, A.; Maes, M.; Olbrechts, A.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Charaf, O.; Clerbaux, B.; De Lentdecker, G.; Dero, V.; Gay, A. P. R.; Hreus, T.; Léonard, A.; Marage, P. E.; Reis, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Adler, V.; Beernaert, K.; Cimmino, A.; Costantini, S.; Garcia, G.; Grunewald, M.; Klein, B.; Lellouch, J.; Marinov, A.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Vanelderen, L.; Verwilligen, P.; Walsh, S.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Lemaitre, V.; Liao, J.; Militaru, O.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Schul, N.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Alves, G. A.; Correa Martins Junior, M.; De Jesus Damiao, D.; Martins, T.; Pol, M. E.; Souza, M. H. G.; Aldá Júnior, W. L.; Carvalho, W.; Custódio, A.; Da Costa, E. M.; De Oliveira Martins, C.; Fonseca De Souza, S.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Oguri, V.; Prado Da Silva, W. L.; Santoro, A.; Silva Do Amaral, S. M.; Soares Jorge, L.; Sznajder, A.; Bernardes, C. A.; Dias, F. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Lagana, C.; Marinho, F.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Genchev, V.; Iaydjiev, P.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Tcholakov, V.; Trayanov, R.; Vutova, M.; Dimitrov, A.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Jiang, C. H.; Liang, D.; Liang, S.; Meng, X.; Tao, J.; Wang, J.; Wang, X.; Wang, Z.; Xiao, H.; Xu, M.; Zang, J.; Zhang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Guo, S.; Guo, Y.; Li, W.; Liu, S.; Mao, Y.; Qian, S. J.; Teng, H.; Wang, S.; Zhu, B.; Zou, W.; Avila, C.; Gomez Moreno, B.; Osorio Oliveros, A. F.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Plestina, R.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Duric, S.; Kadija, K.; Luetic, J.; Morovic, S.; Attikis, A.; Galanti, M.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Finger, M.; Finger, M.; Assran, Y.; Elgammal, S.; Ellithi Kamel, A.; Khalil, S.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Müntel, M.; Raidal, M.; Rebane, L.; Tiko, A.; Azzolini, V.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Heikkinen, A.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Ungaro, D.; Wendland, L.; Banzuzi, K.; Korpela, A.; Tuuva, T.; Besancon, M.; Choudhury, S.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Millischer, L.; Nayak, A.; Rander, J.; Rosowsky, A.; Shreyber, I.; Titov, M.; Baffioni, S.; Beaudette, F.; Benhabib, L.; Bianchini, L.; Bluj, M.; Broutin, C.; Busson, P.; Charlot, C.; Daci, N.; Dahms, T.; Dobrzynski, L.; Granier de Cassagnac, R.; Haguenauer, M.; Miné, P.; Mironov, C.; Ochando, C.; Paganini, P.; Sabes, D.; Salerno, R.; Sirois, Y.; Veelken, C.; Zabi, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Bodin, D.; Brom, J.-M.; Cardaci, M.; Chabert, E. C.; Collard, C.; Conte, E.; Drouhin, F.; Ferro, C.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Juillot, P.; Karim, M.; Le Bihan, A.-C.; Van Hove, P.; Fassi, F.; Mercier, D.; Beauceron, S.; Beaupere, N.; Bondu, O.; Boudoul, G.; Brun, H.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Sordini, V.; Tosi, S.; Tschudi, Y.; Verdier, P.; Viret, S.; Tsamalaidze, Z.; Anagnostou, G.; Beranek, S.; Edelhoff, M.; Feld, L.; Heracleous, N.; Hindrichs, O.; Jussen, R.; Klein, K.; Merz, J.

    2012-08-01

    A search for narrow, high-mass resonances decaying to electron or muon pairs has been performed using pp collision data collected at √{ s} = 7TeV by the CMS experiment in 2011. The data sample corresponds to an integrated luminosity of approximately 5 fb-1. The event yields observed in the signal regions are consistent with predictions of the standard model backgrounds, and upper limits on the cross section times branching fraction for a resonance decaying to dileptons are extracted from a shape analysis of the dilepton invariant mass distribution. The resulting mass limits at 95% confidence level are 2330 GeV for the Z‧ in the Sequential Standard Model, 2000 GeV for the superstring-inspired Zψ‧ resonance, 890 (540) GeV for the Stueckelberg extension ZSt‧ with the mass parameter ɛ = 0.06 (0.04), and 2140 (1810) GeV for Kaluza-Klein gravitons with the coupling parameter k /MbarPl of 0.10 (0.05). These limits are the most stringent to date.

  19. Effect of Vaporizer Temperature on Ambient Non-Refractory Submicron Aerosol Composition and Mass Spectra Measured by the Aerosol Mass Spectrometer

    EPA Science Inventory

    Aerodyne Aerosol Mass Spectrometers (AMS) are routinely operated with a constant vaporizer temperature (Tvap) of 600oC in order to facilitate quantitative detection of non-refractory submicron (NR-PM1) species. By analogy with other thermal desorption instrument...

  20. AN ION CORRELATION PROGRAM FOR DECONVOLUTING COMPOSITE MASS SPECTRA ACQUIRED USING A DIRECT SURFACE IONIZATION SOURCE INTERFACED TO A TIME-OF-FLIGHT MASS SPECTROMETER

    EPA Science Inventory

    The rapid sampling provided by the DART in ambient air will allow rapid delineation of areas of dispersed chemicals after natural or man-made disasters. Exact masses and RIAs of dimer, precursor, and product ions measured by the oa-TOFMS entered dinto the Ion Correlation Program...

  1. VizieR Online Data Catalog: Spectra of low-mass stars in Upper Sco (Lodieu+, 2011)

    NASA Astrophysics Data System (ADS)

    Lodieu, N.; Dobbie, P. D.; Hambly, N. C.

    2010-11-01

    Coordinates (J2000), ZYJHK photometry from the UKIDSS Galactic Clusters Survey, and proper motions derived from the UKIDSS/2MASS cross-match (in arcsec/yr) of stars in the AAOmega field-of-view ordered by increasing Z magnitude. The last column provides a tentative estimate of the spectral type. Data obtained with the AAOmega spectrograph on the Anglo-Australian telescope in May 2007. (4 data files).

  2. Structural Characterization of Methylenedianiline Regioisomers by Ion Mobility-Mass Spectrometry, Tandem Mass Spectrometry, and Computational Strategies: I. Electrospray Spectra of 2-Ring Isomers

    PubMed Central

    2015-01-01

    Purified methylenedianiline (MDA) regioisomers were structurally characterized and differentiated using tandem mass spectrometry (MS/MS), ion mobility-mass spectrometry (IM-MS), and IM-MS/MS in conjunction with computational methods. It was determined that protonation sites on the isomers can vary depending on the position of amino groups, and the resulting protonation sites play a role in the gas-phase stability of the isomer. We also observed differences in the relative distributions of protonated conformations depending on experimental conditions and instrumentation, which is consistent with previous studies on aniline in the gas phase. This work demonstrates the utility of a multifaceted approach for the study of isobaric species and elucidates why previous MDA studies may have been unable to detect and/or differentiate certain isomers. Such analysis may prove useful in the characterization of larger MDA multimeric species, industrial MDA mixtures, and methylene diphenyl diisocyanate (MDI) mixtures used in polyurethane synthesis. PMID:24678803

  3. Accurate Fission Data for Nuclear Safety

    NASA Astrophysics Data System (ADS)

    Solders, A.; Gorelov, D.; Jokinen, A.; Kolhinen, V. S.; Lantz, M.; Mattera, A.; Penttilä, H.; Pomp, S.; Rakopoulos, V.; Rinta-Antila, S.

    2014-05-01

    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyväskylä. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (1012 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons for benchmarking and to study the energy dependence of fission yields. The scientific program is extensive and is planed to start in 2013 with a measurement of isomeric yield ratios of proton induced fission in uranium. This will be followed by studies of independent yields of thermal and fast neutron induced fission of various actinides.

  4. Oil spill source identification by principal component analysis of electrospray ionization Fourier transform ion cyclotron resonance mass spectra.

    PubMed

    Corilo, Yuri E; Podgorski, David C; McKenna, Amy M; Lemkau, Karin L; Reddy, Christopher M; Marshall, Alan G; Rodgers, Ryan P

    2013-10-01

    One fundamental challenge with either acute or chronic oil spills is to identify the source, especially in highly polluted areas, near natural oil seeps, when the source contains more than one petroleum product or when extensive weathering has occurred. Here we focus on heavy fuel oil that spilled (~200,000 L) from two suspected fuel tanks that were ruptured on the motor vessel (M/V) Cosco Busan when it struck the San Francisco-Oakland Bay Bridge in November 2007. We highlight the utility of principal component analysis (PCA) of elemental composition data obtained by high resolution FT-ICR mass spectrometry to correctly identify the source of environmental contamination caused by the unintended release of heavy fuel oil (HFO). Using ultrahigh resolution electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry, we uniquely assigned thousands of elemental compositions of heteroatom-containing species in neat samples from both tanks and then applied principal component analysis. The components were based on double bond equivalents for constituents of elemental composition, CcHhN1S1. To determine if the fidelity of our source identification was affected by weathering, field samples were collected at various intervals up to two years after the spill. We are able to identify a suite of polar petroleum markers that are environmentally persistent, enabling us to confidently identify that only one tank was the source of the spilled oil: in fact, a single principal component could account for 98% of the variance. Although identification is unaffected by the presence of higher polarity, petrogenic oxidation (weathering) products, future studies may require removal of such species by anion exchange chromatography prior to mass spectral analysis due to their preferential ionization by ESI.

  5. Approach toward minimizing chemical interference in FAB mass spectra: the development and application of thermally - assisted FAB

    SciTech Connect

    Ackermann, B.L.

    1987-01-01

    Interferences with fast atom bombardment (FAB) mass spectrometry can be classified into two major categories. The first includes impurities which remain after analyte isolation/purification, and is especially problematic in samples of biological origin. The second type of chemical interference originates from the matrix used for FAB. An example of the first type, also known as sample-related interference, is presented in the context of the analysis of the urinary metabolites of the analgesic acetaminophen by means of the off-line combination of reverse phase HPLC and FAB. Recommendations are made for efficient use of these two methods with specific regard to minimizing chemical interferences. In addition, a method for calculating analyte signal to background (S/B) values is introduced as a means of evaluating the quality of the FAB mass spectrum. A method known as thermally-assisted FAB (TA-FAB) is introduced as a means of minimizing matrix-related background. Success to date has been achieved using aqueous saccharide solutions as TA-FAB matrices. Several important improvements to FAB result from thermal control of the matrix including a selection against matrix background, and the possibility of valid background subtraction. The development of TA-FAB is described in the context of applications of the technique to the analysis of several representative nonvolatile biomolecules including a series of cyclic tetrapeptide mycotoxins. In the final section, the hypothesis of ternary perculation (TP) is submitted to account for behavior observed during TA-FAB.

  6. Low-Energy Collision-Induced Dissociation Mass Spectra of Protonated p-Toluenesulfonamides Derived from Aliphatic Amines

    NASA Astrophysics Data System (ADS)

    Bialecki, Jason B.; Weisbecker, Carl S.; Attygalle, Athula B.

    2014-06-01

    Collision-induced fragmentation of protonated N-alkyl- p-toluenesulfonamides primarily undergo either an elimination of the amine to form CH3-(C6H4)-SO2 + cation ( m/z 155) or an alkene to form a cation for the protonated p-toluenesulfonamide ( m/z 172). To comprehend the fragmentation pathways, several deuterated analogs of N-decyl- p-toluenesulfonamides were prepared and evaluated. Hypothetically, two mechanisms, both of which involve ion-neutral complexes, can be envisaged. In one mechanism, the S-N bond fragments to produce an intermediate [sulfonyl cation/amine] complex, which dissociates to afford the m/z 155 cation (Pathway A). In the other mechanism, the C-N bond dissociates to produce a different intermediate complex. The fragmentation of this [ p-toluenesulfonamide/carbocation] complex eliminates p-toluenesulfonamide and releases the carbocation (Pathway B). Computations carried out by the Hartree-Fock method suggested that the Pathway B is more favorable. However, a peak for the carbocation is observed only when the carbocation formed is relatively stable. For example, the spectrum of N-phenylethyl- p-toluenesulfonamide is dominated by the peak at m/z 105 for the incipient phenylethyl cation, which rapidly isomerizes to the remarkably stable methylbenzyl cation. The peaks for the carbocations are weak or absent in the spectra of most of N-alkyl- p-toluenesulfonamides because alkyl carbocations, such as the decyl cation, rearrange to more stable secondary cations by 1,2-hydride and alkyl shifts. The energy freed is not dissipated, but gets internalized, causing the carbocation to dissociate either by transferring a proton to the sulfonamide or by releasing smaller alkenes to form smaller carbocations. The loss of the positional integrity in this way was proven by deuterium labeling experiments.

  7. Evaluation of comprehensive two-dimensional gas chromatography with accurate mass time-of-flight mass spectrometry for the metabolic profiling of plant-fungus interaction in Aquilaria malaccensis.

    PubMed

    Wong, Yong Foo; Chin, Sung-Tong; Perlmutter, Patrick; Marriott, Philip J

    2015-03-27

    To explore the possible obligate interactions between the phytopathogenic fungus and Aquilaria malaccensis which result in generation of a complex array of secondary metabolites, we describe a comprehensive two-dimensional gas chromatography (GC × GC) method, coupled to accurate mass time-of-flight mass spectrometry (TOFMS) for the untargeted and comprehensive metabolic profiling of essential oils from naturally infected A. malaccensis trees. A polar/non-polar column configuration was employed, offering an improved separation pattern of components when compared to other column sets. Four different grades of the oils displayed quite different metabolic patterns, suggesting the evolution of a signalling relationship between the host tree (emergence of various phytoalexins) and fungi (activation of biotransformation). In total, ca. 550 peaks/metabolites were detected, of which tentative identification of 155 of these compounds was reported, representing between 20.1% and 53.0% of the total ion count. These are distributed over the chemical families of monoterpenic and sesquiterpenic hydrocarbons, oxygenated monoterpenes and sesquiterpenes (comprised of ketone, aldehyde, oxide, alcohol, lactone, keto-alcohol and diol), norterpenoids, diterpenoids, short chain glycols, carboxylic acids and others. The large number of metabolites detected, combined with the ease with which they are located in the 2D separation space, emphasises the importance of a comprehensive analytical approach for the phytochemical analysis of plant metabolomes. Furthermore, the potential of this methodology in grading agarwood oils by comparing the obtained metabolic profiles (pattern recognition for unique metabolite chemical families) is discussed. The phytocomplexity of the agarwood oils signified the production of a multitude of plant-fungus mediated secondary metabolites as chemical signals for natural ecological communication. To the best of our knowledge, this is the most complete

  8. Estimation of Mass-Loss Rates from Emission Line Profiles in the UV Spectra of Cool Stars

    NASA Technical Reports Server (NTRS)

    Carpenter, K. G.; Robinson, R. D.; Harper, G. M.

    1999-01-01

    The photon-scattering winds of cool, low-gravity stars (K-M giants and supergiants) produce absorption features in the strong chromospheric emission lines. This provides us with an opportunity to assess important parameters of the wind, including flow and turbulent velocities, the optical depth of the wind above the region of photon creation, and the star's mass-loss rate. We have used the Lamers et al. Sobolev with Exact Integration (SEI) radiative transfer code along with simple models of the outer atmospheric structure to compute synthetic line profiles for comparison with the observed line profiles. The SEI code has the advantage of being computationally fast and allows a great number of possible wind models to be examined. We therefore use it here to obtain initial first-order estimates of the wind parameters. More sophisticated, but more time-consuming and resource intensive calculations will be performed at a later date, using the SEI-deduced wind parameters as a starting point. A comparison of the profiles over a range of wind velocity laws, turbulence values, and line opacities allows us to constrain the wind parameters, and to estimate the mass-loss rates. We have applied this analysis technique (using lines of Mg II, 0 I, and Fe II) so far to four stars: the normal K5-giant alpha Tau, the hybrid K-giant gamma Dra, the K5 supergiant lambda Vel, and the M-giant gamma Cru. We present in this paper a description of the technique, including the assumptions which go into its use, an assessment of its robustness, and the results of our analysis.

  9. The Visible Photodissociation Spectra of the Molecular Ions of Negative Carbonate, Negative Ozone, and Positive Ozone by Triple Quadrupole Mass Spectrometry.

    NASA Astrophysics Data System (ADS)

    Hiller, Joseph Francis, Jr.

    A modified version of the triple quadrupole photodissociation mass spectrometer utilizing a chemical ionization ion source and a nitrogen pumped tunable dye laser is described. The visible photodissociation spectra are reported for the processes. CO(,3)('-) + h(nu) (--->) O('-) + CO(,2). O(,3)('-) + h(nu) (--->) O('-) + O(,2). (--->) O(,2)('-) + O. O(,3)('+) + h(nu) (--->) O('+) + O(,2). (--->) O(,2)('+) + O. as absolute cross sections as functions of photon energy. Sequential two photon processes and excited state ion/neutral. reactions are observed directly for the visible excitation of CO(,3)('-). Rate constants and absolute cross sections are presented for these. reactions, and for the inferred fluorescent and relaxation processes. as well. Thresholds are located for three of these dissociations as. D(CO(,2)-O('-)) 2.258 (+OR-) 0.008 eV. D(O-O(,2)('-)) 2.410 (+OR-) 0.010 eV. D(O(,2)-O('+)) 1.860 (+OR-) 0.005 eV. Excited states of O(,3)('-) are identified, and vibrational analyses are included for the O(,3)('-) and O(,3)('+) spectra.

  10. Differentiation of microbial species and strains in coculture biofilms by multivariate analysis of laser desorption postionization mass spectra.

    PubMed

    Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C; Carlson, Ross P; Ahmed, Musahid; Hanley, Luke

    2013-11-21

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups, two "pure" groups, and a mixed region. Furthermore, the "pure" regions of the E. coli cocultures showed greater variance by PCA at 7.87 eV photon energies compared to 10.5 eV radiation. This is consistent with the expectation that the 7.87 eV photoionization selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

  11. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    SciTech Connect

    University of Illinois at Chicago; Montana State University; Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-04-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups two ?pure? groups and a mixed region. Furthermore, the ?pure? regions of the E. coli cocultures showed greater variance by PCA when analyzed by 7.87 eV photon energies than by 10.5 eV radiation. Comparison of the 7.87 and 10.5 eV data is consistent with the expectation that the lower photon energy selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

  12. Evaluation of the occurrence and biodegradation of parabens and halogenated by-products in wastewater by accurate-mass liquid chromatography-quadrupole-time-of-flight-mass spectrometry (LC-QTOF-MS).

    PubMed

    González-Mariño, Iria; Quintana, José Benito; Rodríguez, Isaac; Cela, Rafael

    2011-12-15

    An assessment of the sewage occurrence and biodegradability of seven parabens and three halogenated derivatives of methyl paraben (MeP) is presented. Several wastewater samples were collected at three different wastewater treatment plants (WWTPs) during April and May 2010, concentrated by solid-phase extraction (SPE) and analysed by liquid chromatography-electrospray-quadrupole-time-of-flight mass spectrometry (LC-QTOF-MS). The performance of the QTOF system proved to be comparable to triple-quadrupole instruments in terms of quantitative capabilities, with good linearity (R(2) > 0.99 in the 5-500 ng mL(-1) range), repeatability (RSD < 5.6%) and LODs (0.3-4.0 ng L(-1) after SPE). MeP and n-propyl paraben (n-PrP) were the most frequently detected and the most abundant analytes in raw wastewater (0.3-10 μg L(-1)), in accordance with the data displayed in the bibliography and reflecting their wider use in cosmetic formulations. Samples were also evaluated in search for potential halogenated by-products of parabens, formed as a result of their reaction with residual chlorine contained in tap water. Monochloro- and dichloro-methyl paraben (ClMeP and Cl(2)MeP) were found and quantified in raw wastewater at levels between 0.01 and 0.1 μg L(-1). Halogenated derivatives of n-PrP could not be quantified due to the lack of standards; nevertheless, the monochlorinated species (ClPrP) was identified in several samples from its accurate precursor and product ions mass/charge ratios (m/z). Removal efficiencies of parabens and MeP chlorinated by-products in WWTPs exceeded 90%, with the lowest percentages corresponding to the latter species. This trend was confirmed by an activated sludge biodegradation batch test, where non-halogenated parabens had half-lives lower than 4 days, whereas halogenated derivatives of MeP turned out to be more persistent, with up to 10 days of half-life in the case of dihalogenated derivatives. A further stability test performed with raw wastewater

  13. Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions.

    PubMed

    Solano, Eduardo A; Mohamed, Sabria; Mayer, Paul M

    2016-10-28

    The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions pME,Tchar. The mean vibrational energy excess of the ions was characterized by the parameter Tchar ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below Tchar = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of Tchar as a function of Ecom (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dEvib/dEcom) changes with Ecom according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.

  14. Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions

    NASA Astrophysics Data System (ADS)

    Solano, Eduardo A.; Mohamed, Sabria; Mayer, Paul M.

    2016-10-01

    The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions p M (" separators=" E , T char ) . The mean vibrational energy excess of the ions was characterized by the parameter Tchar ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below Tchar = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of Tchar as a function of Ecom (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dEvib/dEcom) changes with Ecom according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.

  15. A combined strategy of mass fragmentation, post-column cobalt complexation and shift in ultraviolet absorption spectra to determine the uridine 5'-diphospho-glucuronosyltransferase metabolism profiling of flavones after oral administration of a flavone mixture in rats.

    PubMed

    Li, Qiang; Wang, Liping; Dai, Peimin; Zeng, Xuejun; Qi, Xiaoxiao; Zhu, Lijun; Yan, Tongmeng; Wang, Ying; Lu, Linlin; Hu, Ming; Wang, Xinchun; Liu, Zhongqiu

    2015-05-22

    The use of dietary flavones is becoming increasingly popular for their prevention of cancers, cardiovascular diseases, and other diseases. Despite many pharmacokinetic studies on flavone mixtures, the position(s) of glucuronidation sites on the flavone skeleton in vivo remain(s) uncertain because of the lack of a convenient method to differentiate the isomers in biological samples. Accordingly, this study aimed to develop a new strategy to identify the position of the mono-O-glucuronide of flavones in vivo and to simultaneously determine the parent agent and its major metabolites responsible for complex pharmacokinetic characteristics. The novel strategy involves accurate mass measurements of flavone glucuronides, their [Co(II) (flavone glucuronide-H) (4,7-diphenyl-1,10-phenanthroline)2](+) complexes generated via the post-column addition of CoBr2 and 4,7-diphenyl-1,10-phenanthroline, and their mass spectrometric fragmentation by UPLC-DAD-Q-TOF and the comparison of retention times with biosynthesized standards of different isomers that were identified by analyzing the shift in UV spectra compared with the spectra of their respective aglycones. We successfully generated a metabolite profiling of flavones in rat plasma after oral administration of a flavone mixture from Dracocephalum moldavica L., which was used here as the model to demonstrate the strategy. Twelve flavone glucuronides, which were glucuronidated derivatives of acacetin, apigenin, luteolin, diosmetin, chrysoeriol and cirsimaritin, were detected and identified. Glucuronidation of the flavone skeleton at the 3'-/7-position was more prevalent, however, luteolin 4'-glucuronide levels exceeded luteolin 7-glucuronide levels. Based on the UDP-glucuronosyltransferase (UGT) metabolism profiling of flavones in rat plasma, six main compounds (tilianin, acacetin 7-glucuronide, apigenin 7-glucuronide, luteolin 3'-glucuronide, acacetin, and apigenin) were selected as pharmacokinetic markers. Pharmacokinetic

  16. Accurate and reliable quantification of 25-hydroxy-vitamin D species by liquid chromatography high-resolution tandem mass spectrometry[S

    PubMed Central

    Liebisch, Gerhard; Matysik, Silke

    2015-01-01

    In general, mass spectrometric quantification of small molecules in routine laboratory testing utilizes liquid chromatography coupled to low mass resolution triple-quadrupole mass spectrometers (QQQs). Here we introduce high-resolution tandem mass spectrometry (quadrupole-Orbitrap) for the quantification of 25-hydroxy-vitamin D [25(OH)D], a marker of the vitamin D status, because the specificity of 25(OH)D immunoassays is still questionable and mass spectrometric quantification is becoming increasingly important. Liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/HR-MS) was used to quantify 25-hydroxy-cholecalciferol [25(OH)D3], 25-hydroxy-ergocalciferol [25(OH)D2], and their C3-epimers 3-epi-25(OH)D3 and 3-epi-25(OH)D2. The method has a run time of 5 min and was validated according to the US Food and Drug Administration and the European Medicines Agency guidelines. High mass resolution was advantageously applied to separate a quasi-isobaric interference of the internal standard D6-25(OH)D2 with 3-epi-25(OH)D3. All analytes showed an imprecision of below 10% coefficient of variation (CV), trueness between 90% and 110%, and limits of quantification below 10 nM. Concentrations measured by LC-MS/HR-MS are in good agreement with those of the National Institute of Standards and Technology reference methods using LC-MS/MS (QQQ). In conclusion, quantification of 25(OH)D by LC-MS/HR-MS is applicable for routine testing and also holds promise for highly specific quantification of other small molecules. PMID:25833687

  17. X-Ray Spectra of the High-mass X-Ray Binary 4U 1700-37 Using BeppoSAX, Suzaku, and RXTE Observations

    NASA Astrophysics Data System (ADS)

    Seifina, Elena; Titarchuk, Lev; Shaposhnikov, Nikolai

    2016-04-01

    We present an X-ray spectral analysis of the high-mass binary 4U 1700-37 during its hard-soft state evolution. We use BeppoSAX, Suzaku, and Rossi X-ray Timing Explorer observations for this investigation. We argue that the X-ray broadband spectra during all of the spectral states can be adequately reproduced by a model consisting of a low-temperature blackbody component, two Comptonized components which are both due to the presence of a Compton cloud (CC) that up-scatters seed photons of Ts1 ≲ 1.4 keV and Ts2 < 1 keV, and an iron-line component. Using this model, we find that the photon power-law index is almost constant, Γ1 ∼ 2 for all spectral states. However, Γ2 shows behavior that is dependent on the spectral state. Namely, Γ2 is quasi-constant at the level of Γ2 ∼ 2 while the CC plasma temperature {{kT}}e(2) is less than 40 keV; on the other hand, Γ2 is in the range of 1.3 < Γ2 < 2 when {{kT}}e(2) is greater than 40 keV. We explain this quasi-stability of Γ during most of the hard-soft transitions of 4U 1700-37 in the framework of a model in which the resulting spectrum is described by two Comptonized components. We find that these Comptonized spectral components of the high-mass X-ray binaries 4U 1700-37 are similar to those previously found in neutron star (NS) sources. This index dependence versus both the mass accretion rate and kTe revealed in 4U 1700-37 is universal observational evidence for the presence of an NS in 4U 1700-37.

  18. The use of IR, magnetism, reflectance, and mass spectra together with thermal analyses in structure investigation of codeine phosphate complexes of d-block elements

    NASA Astrophysics Data System (ADS)

    Zayed, M. A.; El-shahat, M. F.; Abdullah, S. M.

    2005-06-01

    Codeine is an analgesic with uses similar to morphines, but it is of much less effect, i.e., it had a mild sedative effect; codeine is usually used as the phosphate form (Cod.P) and is often administrated by mouth with aspirin of paracetamol. Due to its serious use, if it is in large dose, attention is paid in this research to the synthesis and stereochemistry of new iron, cobalt, nickel, copper, and zinc complexes of this drug in both solution and the solid states. The spectra of these complexes in solution and the study of their stoichiometry refer to the formation of 1:1 ratio of metal (M) to ligand (L). The steriochemical structures of the solid complexes were studied on the basis of their analytical, spectroscopic, magnetic, and thermal data. Infrared spectra proved the presence of M sbnd O bonds. Magnetic susceptibility and solid reflectance spectral measurements were used to infer the structures. The prepared complexes were found to have the general formulae [ML(OH) x(H 2O) y](H 2O) zH 3PO 4, M: Co(II), Ni(II), and Cu(II), x = 1, y = 0, z = 0; M: Fe(II), x = 1, y = 2, z = 1; Fe(III), x = 2, y = 1, z = 0; Co(III), x = 0, y = 2, z = 1; Zn(II), x = 1, y = 0, z = 3; and L: (Cod.P) of the general formula C 18H 24NO 7P (anhydrate). Octahedral, tetrahedral, and square planer structures were proposed for these complexes depending upon the magnetic and reflectance data and were confirmed by detailed mass and thermal analyses comparative studies.

  19. Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach

    SciTech Connect

    Fang, Ruihua; Elias, Dwayne A.; Monroe, Matthew E.; Shen, Yufeng; McIntosh, Martin; Wang, Pei; Goddard, Carrie D.; Callister, Stephen J.; Moore, Ronald J.; Gorby, Yuri A.; Adkins, Joshua N.; Fredrickson, Jim K.; Lipton, Mary S.; Smith, Richard D.

    2006-04-01

    We describe the application of liquid chromatography coupled to mass spectrometry (LC/MS) without the use of stable isotope labeling for differential quantitative proteomics analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and sub-oxic conditions. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used to initially identify peptide sequences, and LC coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) was used to confirm these identifications, as well as measure relative peptide abundances. 2343 peptides, covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as SAM, while another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis is transitioned from aerobic to sub-oxic conditions.

  20. A Comprehensive Review of School-Based Body Mass Index Screening Programs and Their Implications for School Health: Do the Controversies Accurately Reflect the Research?

    ERIC Educational Resources Information Center

    Ruggieri, Dominique G.; Bass, Sarah B.

    2015-01-01

    Background: Whereas legislation for body mass index (BMI) surveillance and screening programs has passed in 25 states, the programs are often subject to ethical debates about confidentiality and privacy, school-to-parent communication, and safety and self-esteem issues for students. Despite this debate, no comprehensive analysis has been completed…

  1. Background correction in separation techniques hyphenated to high-resolution mass spectrometry - Thorough correction with MS scans recorded as profile spectra.

    PubMed

    Erny, Guillaume L; Acunha, Tanize; Simó, Carolina; Cifuentes, Alejandro; Alves, Arminda

    2017-03-01

    Separation techniques hyphenated with high-resolution mass spectrometry have been a true revolution in analytical separation techniques. Such instruments not only provide unmatched resolution, but they also allow measuring the peaks accurate masses that permit identifying monoisotopic formulae. However, data files can be large, with a major contribution from background noise and background ions. Such unnecessary contribution to the overall signal can hide important features as well as decrease the accuracy of the centroid determination, especially with minor features. Thus, noise and baseline correction can be a valuable pre-processing step. The methodology that is described here, unlike any other approach, is used to correct the original dataset with the MS scans recorded as profiles spectrum. Using urine metabolic studies as examples, we demonstrate that this thorough correction reduces the data complexity by more than 90%. Such correction not only permits an improved visualisation of secondary peaks in the chromatographic domain, but it also facilitates the complete assignment of each MS scan which is invaluable to detect possible comigration/coeluting species.

  2. Mass

    SciTech Connect

    Quigg, Chris

    2007-12-05

    In the classical physics we inherited from Isaac Newton, mass does not arise, it simply is. The mass of a classical object is the sum of the masses of its parts. Albert Einstein showed that the mass of a body is a measure of its energy content, inviting us to consider the origins of mass. The protons we accelerate at Fermilab are prime examples of Einsteinian matter: nearly all of their mass arises from stored energy. Missing mass led to the discovery of the noble gases, and a new form of missing mass leads us to the notion of dark matter. Starting with a brief guided tour of the meanings of mass, the colloquium will explore the multiple origins of mass. We will see how far we have come toward understanding mass, and survey the issues that guide our research today.

  3. Rapid and accurate liquid chromatography and tandem mass spectrometry method for the simultaneous quantification of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes.

    PubMed

    Shi, Rong; Ma, Bingliang; Wu, Jiasheng; Wang, Tianming; Ma, Yueming

    2015-10-01

    The hepatic cytochrome P450 enzymes play a central role in the biotransformation of endogenous and exogenous substances. A sensitive high-throughput liquid chromatography with tandem mass spectrometry assay was developed and validated for the simultaneous quantification of the products of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes. After the substrates were incubated separately, the samples were pooled and analyzed by liquid chromatography with tandem mass spectrometry using an electrospray ionization source in the positive and negative ion modes. The method exhibited linearity over a broad concentration range, insensitivity to matrix effects, and high accuracy, precision, and stability. The novel method was successfully applied to study the kinetics of phenacetin-O deethylation, coumarin-7 hydroxylation, bupropion hydroxylation, taxol-6 hydroxylation, omeprazole-5 hydroxylation, dextromethorphan-O demethylation, tolbutamide-4 hydroxylation, chlorzoxazone-6 hydroxylation, testosterone-6β hydroxylation, and midazolam-1 hydroxylation in rat liver microsomes.

  4. Accurate prediction of H3O+ and D3O+ sensitivity coefficients to probe a variable proton-to-electron mass ratio

    NASA Astrophysics Data System (ADS)

    Owens, A.; Yurchenko, S. N.; Polyansky, O. L.; Ovsyannikov, R. I.; Thiel, W.; Špirko, V.

    2015-12-01

    The mass sensitivity of the vibration-rotation-inversion transitions of H316O+, H318O+, and D316O+ is investigated variationally using the nuclear motion program TROVE (Yurchenko, Thiel & Jensen). The calculations utilize new high-level ab initio potential energy and dipole moment surfaces. Along with the mass dependence, frequency data and Einstein A coefficients are computed for all transitions probed. Particular attention is paid to the Δ|k| = 3 and Δ|k - l| = 3 transitions comprising the accidentally coinciding |J, K = 0, v2 = 0+> and |J, K = 3, v2 = 0-> rotation-inversion energy levels. The newly computed probes exhibit sensitivities comparable to their ammonia and methanol counterparts, thus demonstrating their potential for testing the cosmological stability of the proton-to-electron mass ratio. The theoretical TROVE results are in close agreement with sensitivities obtained using the non-rigid and rigid inverter approximate models, confirming that the ab initio theory used in the present study is adequate.

  5. Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

    SciTech Connect

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C. -E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D’Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Dos Reis Martins, T.; Mora Herrera, C.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zou, W.; Avila, C.; Chaparro Sierra, L. 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L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J. -L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J. -M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J. -C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A. -C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Pook, T.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Heister, A.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garay Garcia, J.; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I. -A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Roland, B.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Poehlsen, J.; Poehlsen, T.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Markou, C.; Psallidas, A.; Topsis-Giotis, I.; Agapitos, A.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Stiliaris, E.; Aslanoglou, X.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Swain, S. K.; Beri, S. B.; Bhatnagar, V.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, M.; Kumar, R.; Mittal, M.; Nishu, N.; Singh, J. B.; Kumar, Ashok; Kumar, Arun; Ahuja, S.; Bhardwaj, A.; Choudhary, B. 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S.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D’Alessandro, R.; Focardi, E.; Gallo, E.; Gonzi, S.; Gori, V.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Ferretti, R.; Ferro, F.; Lo Vetere, M.; Robutti, E.; Tosi, S.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Gerosa, R.; Ghezzi, A.; Govoni, P.; Lucchini, M. T.; Malvezzi, S.; Manzoni, R. A.; Martelli, A.; Marzocchi, B.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Ragazzi, S.; Redaelli, N.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Azzi, P.; Bacchetta, N.; Bisello, D.; Branca, A.; Carlin, R.; Checchia, P.; Dall’Osso, M.; Dorigo, T.; Dosselli, U.; Galanti, M.; Gasparini, F.; Gasparini, U.; Giubilato, P.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Tosi, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Gabusi, M.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vitulo, P.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell’Orso, R.; Donato, S.; Fiori, F.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Moon, C. S.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Vernieri, C.; Barone, L.; Cavallari, F.; D’imperio, G.; Del Re, D.; Diemoz, M.; Grassi, M.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Nourbakhsh, S.; Organtini, G.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Ortona, G.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Potenza, A.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Belforte, S.; Candelise, V.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; La Licata, C.; Marone, M.; Schizzi, A.; Umer, T.; Zanetti, A.; Chang, S.; Kropivnitskaya, A.; Nam, S. K.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Kong, D. J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Kim, J. Y.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Yoo, H. D.; Choi, M.; Kim, J. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Seo, H.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Ali, M. A. B. Md; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khalid, S.; Khan, W. A.; Khurshid, T.; Shah, M. A.; Shoaib, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Brona, G.; Bunkowski, K.; Cwiok, M.; Dominik, W.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Wolszczak, W.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Lloret Iglesias, L.; Nguyen, F.; Rodrigues Antunes, J.; Seixas, J.; Varela, J.; Vischia, P.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Konoplyanikov, V.; Kozlov, G.; Lanev, A.; Malakhov, A.; Matveev, V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Savina, M.; Shmatov, S.; Shulha, S.; Skatchkov, N.; Smirnov, V.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, An.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Spiridonov, A.; Stolin, V.; Vlasov, E.; Zhokin, A.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Mesyats, G.; Rusakov, S. V.; Vinogradov, A.; Belyaev, A.; Boos, E.; Bunichev, V.; Dubinin, M.; Dudko, L.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Obraztsov, S.; Perfilov, M.; Savrin, V.; Snigirev, A.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Ekmedzic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Battilana, C.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Domínguez Vázquez, D.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; Albajar, C.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. F.; Bernet, C.; Bloch, P.; Bocci, A.; Bonato, A.; Bondu, O.; Botta, C.; Breuker, H.; Camporesi, T.; Cerminara, G.; Colafranceschi, S.; D’Alfonso, M.; d’Enterria, D.; Dabrowski, A.; David, A.; De Guio, F.; De Roeck, A.; De Visscher, S.; Di Marco, E.; Dobson, M.; Dordevic, M.; Dorney, B.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Eugster, J.; Franzoni, G.; Funk, W.; Gigi, D.; Gill, K.; Giordano, D.; Girone, M.; Glege, F.; Guida, R.; Gundacker, S.; Guthoff, M.; Hammer, J.; Hansen, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kousouris, K.; Krajczar, K.; Lecoq, P.; Lourenço, C.; Magini, N.; Malgeri, L.; Mannelli, M.; Marrouche, J.; Masetti, L.; Meijers, F.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Musella, P.; Orsini, L.; Pape, L.; Perez, E.; Perrozzi, L.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Plagge, M.; Racz, A.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Sharma, A.; Siegrist, P.; Silva, P.; Simon, M.; Sphicas, P.; Spiga, D.; Steggemann, J.; Stieger, B.; Stoye, M.; Takahashi, Y.; Treille, D.; Tsirou, A.; Veres, G. I.; Wardle, N.; Wöhri, H. K.; Wollny, H.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Renker, D.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Buchmann, M. A.; Casal, B.; Chanon, N.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dünser, M.; Eller, P.; Grab, C.; Hits, D.; Hoss, J.; Lustermann, W.; Mangano, B.; Marini, A. C.; Martinez Ruiz del Arbol, P.; Masciovecchio, M.; Meister, D.; Mohr, N.; Nägeli, C.; Nessi-Tedaldi, F.; Pandolfi, F.; Pauss, F.; Peruzzi, M.; Quittnat, M.; Rebane, L.; Rossini, M.; Starodumov, A.; Takahashi, M.; Theofilatos, K.; Wallny, R.; Weber, H. A.; Amsler, C.; Canelli, M. F.; Chiochia, V.; De Cosa, A.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Lange, C.; Millan Mejias, B.; Ngadiuba, J.; Robmann, P.; Ronga, F. J.; Taroni, S.; Verzetti, M.; Yang, Y.; Cardaci, M.; Chen, K. H.; Ferro, C.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Volpe, R.; Yu, S. S.; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Grundler, U.; Hou, W. -S.; Kao, K. Y.; Lei, Y. J.; Liu, Y. F.; Lu, R. -S.; Majumder, D.; Petrakou, E.; Tzeng, Y. M.; Wilken, R.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Dozen, C.; Dumanoglu, I.; Eskut, E.; Girgis, S.; Gokbulut, G.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Kayis Topaksu, A.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Vergili, M.; Akin, I. V.; Bilin, B.; Bilmis, S.; Gamsizkan, H.; Karapinar, G.; Ocalan, K.; Sekmen, S.; Surat, U. E.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Isildak, B.; Kaya, M.; Kaya, O.; Cankocak, K.; Vardarlı, F. I.; Levchuk, L.; Sorokin, P.; Brooke, J. J.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Meng, Z.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Senkin, S.; Smith, V. J.; Williams, T.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Womersley, W. J.; Worm, S. D.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Burton, D.; Colling, D.; Cripps, N.; Cutajar, M.; Dauncey, P.; Davies, G.; Della Negra, M.; Dunne, P.; Ferguson, W.; Fulcher, J.; Futyan, D.; Gilbert, A.; Hall, G.; Iles, G.; Jarvis, M.; Karapostoli, G.; Kenzie, M.; Lane, R.; Lucas, R.; Lyons, L.; Magnan, A. -M.; Malik, S.; Mathias, B.; Nash, J.; Nikitenko, A.; Pela, J.; Pesaresi, M.; Petridis, K.; Raymond, D. M.; Rogerson, S.; Rose, A.; Seez, C.; Sharp, P.; Tapper, A.; Vazquez Acosta, M.; Virdee, T.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leggat, D.; Leslie, D.; Martin, W.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Scarborough, T.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Lawson, P.; Richardson, C.; Rohlf, J.; John, J. St.; Sulak, L.; Alimena, J.; Berry, E.; Bhattacharya, S.; Christopher, G.; Cutts, D.; Demiragli, Z.; Dhingra, N.; Ferapontov, A.; Garabedian, A.; Heintz, U.; Kukartsev, G.; Laird, E.; Landsberg, G.; Luk, M.; Narain, M.; Segala, M.; Sinthuprasith, T.; Speer, T.; Swanson, J.; Breedon, R.; Breto, G.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Miceli, T.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Searle, M.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Rakness, G.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova Rikova, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Luthra, A.; Malberti, M.; Nguyen, H.; Olmedo Negrete, M.; Shrinivas, A.; Sumowidagdo, S.; Wimpenny, S.; Andrews, W.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D’Agnolo, R. T.; Evans, D.; Holzner, A.; Kelley, R.; Klein, D.; Lebourgeois, M.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Palmer, C.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Sudano, E.; Tadel, M.; Tu, Y.; Vartak, A.; Welke, C.; Würthwein, F.; Yagil, A.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Danielson, T.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Incandela, J.; Justus, C.; Mccoll, N.; Richman, J.; Stuart, D.; To, W.; West, C.; Yoo, J.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Rogan, C.; Spiropulu, M.; Timciuc, V.; Vlimant, J. R.; Wilkinson, R.; Xie, S.; Zhu, R. Y.; Azzolini, V.; Calamba, A.; Carlson, B.; Ferguson, T.; Iiyama, Y.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Ryd, A.; Salvati, E.; Skinnari, L.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Kaadze, K.; Klima, B.; Kreis, B.; Kwan, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mishra, K.; Mrenna, S.; Musienko, Y.; Nahn, S.; Newman-Holmes, C.; O’Dell, V.; Prokofyev, O.; Sexton-Kennedy, E.; Sharma, S.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitbeck, A.; Whitmore, J.; Yang, F.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Carver, M.; Cheng, T.; Curry, D.; Das, S.; De Gruttola, M.; Di Giovanni, G. P.; Field, R. D.; Fisher, M.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Kypreos, T.; Low, J. F.; Matchev, K.; Milenovic, P.; Mitselmakher, G.; Muniz, L.; Rinkevicius, A.; Shchutska, L.; Snowball, M.; Sperka, D.; Yelton, J.; Zakaria, M.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Baarmand, M. M.; Hohlmann, M.; Kalakhety, H.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Bazterra, V. E.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Khalatyan, S.; Kurt, P.; Moon, D. H.; O’Brien, C.; Silkworth, C.; Turner, P.; Varelas, N.; Albayrak, E. A.; Bilki, B.; Clarida, W.; Dilsiz, K.; Duru, F.; Haytmyradov, M.; Merlo, J. -P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Rahmat, R.; Sen, S.; Tan, P.; Tiras, E.; Wetzel, J.; Yetkin, T.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Shrestha, S.; Skhirtladze, N.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y. -J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Zvada, M.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R. -J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; De Mattia, M.; Gutay, L.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Kaplan, S.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Taylor, D.; Verwilligen, P.; Vuosalo, C.; Woods, N.

    2015-04-07

    Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb–1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter than 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.

  6. Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

    DOE PAGES

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

    2015-04-07

    Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb–1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter than 2.57more » TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.« less

  7. Comparing Multiple Reaction Monitoring and Sequential Window Acquisition of All Theoretical Mass Spectra for the Relative Quantification of Barley Gluten in Selectively Bred Barley Lines.

    PubMed

    Colgrave, Michelle L; Byrne, Keren; Blundell, Malcolm; Heidelberger, Sibylle; Lane, Catherine S; Tanner, Gregory J; Howitt, Crispin A

    2016-09-20

    Celiac disease (CD) is a disease of the small intestine that occurs in genetically susceptible subjects triggered by the ingestion of cereal gluten proteins for which the only treatment is strict adherence to a life-long gluten-free diet. Barley contains four gluten protein families, and the existence of barley genotypes that do not accumulate the B-, C-, and D-hordeins paved the way for the development of an ultralow gluten phenotype. Using conventional breeding strategies, three null mutations behaving as recessive alleles were combined to create a hordein triple-null barley variety. Proteomics has become an invaluable tool for characterization and quantification of the protein complement of cereal grains. In this study multiple reaction monitoring (MRM) mass spectrometry, viewed as the gold standard for peptide quantification, was compared to the data-independent acquisition strategy known as SWATH-MS (sequential window acquisition of all theoretical mass spectra). SWATH-MS was comparable (p < 0.001) to MRM-MS for 32/33 peptides assessed across the four families of hordeins (gluten) in eight barley lines. The results of SWATH-MS analysis further confirmed the absence of the B-, C-, and D-hordeins in the triple-null barley line and showed significantly reduced levels ranging from <1% to 16% relative to wild-type (WT) cv Sloop for the minor γ-hordein class. SWATH-MS represents a valuable tool for quantitative proteomics based on its ability to generate reproducible data comparable with MRM-MS, but has the added benefits of allowing reinterrogation of data to improve analytical performance, ask new questions, and in this case perform quantification of trypsin-resistant proteins (C-hordeins) through analysis of their semi- or nontryptic fragments.

  8. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectra of poly(butylene adipate).

    PubMed

    Rizzarelli, Paola; Puglisi, Concetto; Montaudo, Giorgio

    2006-01-01

    Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze four poly(butylene adipate) (PBAd) oligomers and to investigate their fragmentation pathways as a continuation of our work on the MALDI-TOF/TOF-MS/MS study of synthetic polymers. MALDI-TOF/TOF-MS/MS analysis was performed on oligomers terminated by carboxyl and hydroxyl groups, methyl adipate and hydroxyl groups, dihydroxyl groups, and dicarboxyl groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated polyester oligomers and similar series of product ions were observed in all the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified in the present work, three fragmentation pathways have been proposed to occur most frequently in PBAd: beta-hydrogen-transfer rearrangement, leading to the selective cleavage of the --O--CH(2)-- bonds; --CH(2)--CH(2)-- (beta--beta) bond cleavage in the adipate moiety; and ester bond scission.

  9. A Simple Approach for Obtaining High Resolution, High Sensitivity ¹H NMR Metabolite Spectra of Biofluids with Limited Mass Supply

    SciTech Connect

    Hu, Jian Zhi; Rommereim, Donald N.; Wind, Robert A.; Minard, Kevin R.; Sears, Jesse A.

    2006-11-01

    A simple approach is reported that yields high resolution, high sensitivity ¹H NMR spectra of biofluids with limited mass supply. This is achieved by spinning a capillary sample tube containing a biofluid at the magic angle at a frequency of about 80Hz. A 2D pulse sequence called ¹H PASS is then used to produce a high-resolution ¹H NMR spectrum that is free from magnetic susceptibility induced line broadening. With this new approach a high resolution ¹H NMR spectrum of biofluids with a volume less than 1.0 µl can be easily achieved at a magnetic field strength as low as 7.05T. Furthermore, the methodology facilitates easy sample handling, i.e., the samples can be directly collected into inexpensive and disposable capillary tubes at the site of collection and subsequently used for NMR measurements. In addition, slow magic angle spinning improves magnetic field shimming and is especially suitable for high throughput investigations. In this paper first results are shown obtained in a magnetic field of 7.05T on urine samples collected from mice using a modified commercial NMR probe.

  10. Mass Spectra and Yields of Intact Charged Biomolecules Ejected by Massive Cluster Impact for Bioimaging in a Time-of-Flight Secondary Ion Microscope.

    PubMed

    Zhang, Jitao; Franzreb, Klaus; Aksyonov, Sergei A; Williams, Peter

    2015-11-03

    Impacts of massive, highly charged glycerol clusters (≳10(6) Da, ≳ ± 100 charges) have been used to eject intact charged molecules of peptides, lipids, and small proteins from pure solid samples, enabling imaging using these ion species in a time-of-flight secondary ion microscope with few-micrometer spatial resolution. Here, we report mass spectra and useful ion yields (ratio of intact charged molecules detected to molecules sputtered) for several molecular species-two peptides, bradykinin and angiotensin II; two lipids, phosphatidylcholine and sphingomyelin; Irganox 1010 (a detergent); insulin; and rhodamine B-and show that useful ion yields are high enough to enable bioimaging of peptides and lipids in biological samples with few-micrometer resolution and acceptable signals. For example, several hundred molecular ion counts should be detectable from a 3 × 3 μm(2) area of a pure lipid bilayer given appropriate instrumentation or tens of counts from a minor constituent of such a layer.

  11. Predicting charmonium and bottomonium spectra with a quark harmonic oscillator

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Badavi, F. F.; Townsend, L. W.

    1986-01-01

    The nonrelativistic quark model is applied to heavy (nonrelativistic) meson (two-body) systems to obtain sufficiently accurate predictions of the spin-averaged mass levels of the charmonium and bottomonium spectra as an example of the three-dimensional harmonic oscillator. The present calculations do not include any spin dependence, but rather, mass values are averaged for different spins. Results for a charmed quark mass value of 1500 MeV/c-squared show that the simple harmonic oscillator model provides good agreement with experimental values for 3P states, and adequate agreement for the 3S1 states.

  12. Advances in structure elucidation of small molecules using mass spectrometry

    PubMed Central

    Fiehn, Oliver

    2010-01-01

    The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

  13. H2CN+ and H2CNH+: New insight into the structure and dynamics from mass-selected threshold photoelectron spectra

    NASA Astrophysics Data System (ADS)

    Holzmeier, Fabian; Lang, Melanie; Hader, Kilian; Hemberger, Patrick; Fischer, Ingo

    2013-06-01

    In this paper, we reinvestigate the photoionization of nitrogen containing reactive intermediates of the composition H2CN and H2CNH, molecules of importance in astrochemistry and biofuel combustion. In particular, H2CN is also of considerable interest to theory, because of its complicated potential energy surface. The species were generated by flash pyrolysis, ionized with vacuum ultraviolet synchrotron radiation, and studied by mass-selected threshold photoelectron (TPE) spectroscopy. In the mass-selected TPE-spectrum of m/z = 28, contributions of all four isomers of H2CN were identified. The excitation energy to the triplet cation of the methylene amidogen radical H2CN was determined to be 12.32 eV. Considerable activity in the C-N mode of the cation is visible. Furthermore, we derived values for excitation into the triplet cations of 11.72 eV for cis-HCNH, 12.65 eV for trans-HCNH, and 11.21 eV for H2NC. The latter values are probably accurate to within one vibrational quantum. The spectrum features an additional peak at 10.43 eV that corresponds to excitation into the C2v-symmetric H2CN+. As this structure constitutes a saddle point, the peak is assigned to an activated complex on the singlet potential energy surface of the cation, corresponding to a hydrogen atom migration. For methanimine, H2CNH, the adiabatic ionization energy IEad was determined to be 9.99 eV and the vibrational structure of the spectrum was analyzed in detail. The uncertainty of earlier values that simply assigned the signal onset to the IEad is thus considerably reduced. The spectrum is dominated by the H-N-C bending mode ν1+ and the rocking mode ν3+. All experimental data were supported by calculations and Franck-Condon simulations.

  14. Driving efficiency in a high-throughput metabolic stability assay through a generic high-resolution accurate mass method and automated data mining.

    PubMed

    Shui, Wenqing; Lin, Song; Zhang, Allen; Chen, Yan; Huang, Yingying; Sanders, Mark

    2011-08-01

    Improving analytical throughput is the focus of many quantitative workflows being developed for early drug discovery. For drug candidate screening, it is common practice to use ultra-high performance liquid chromatography (U-HPLC) coupled with triple quadrupole mass spectrometry. This approach certainly results in short analytical run time; however, in assessing the true throughput, all aspects of the workflow needs to be considered, including instrument optimization and the necessity to re-run samples when information is missed. Here we describe a high-throughput metabolic stability assay with a simplified instrument set-up which significantly improves the overall assay efficiency. In addition, as the data is acquired in a non-biased manner, high information content of both the parent compound and metabolites is gathered at the same time to facilitate the decision of which compounds to proceed through the drug discovery pipeline.

  15. Accurate determination of ¹²⁹I concentrations and ¹²⁹I/¹³⁷Cs ratios in spent nuclear resins by Accelerator Mass Spectrometry.

    PubMed

    Nottoli, Emmanuelle; Bienvenu, Philippe; Labet, Alexandre; Bourlès, Didier; Arnold, Maurice; Bertaux, Maité

    2014-04-01

    Determining long-lived radionuclide concentrations in radioactive waste has fundamental implications for the long-term management of storage sites. This paper focuses on the measurement of low (129)I contents in ion exchange resins used for primary fluid purification in Pressurised Water Reactors (PWR). Iodine-129 concentrations were successfully determined using Accelerator Mass Spectrometry (AMS) following a chemical procedure which included (1) acid digestion of resin samples in HNO3/HClO4, (2) radioactive decontamination by selective iodine extraction using a new chromatographic resin (CL Resin), and (3) AgI precipitation. Measured (129)I concentrations ranged from 4 to 12 ng/g, i.e. from 0.03 to 0.08 Bq/g. The calculation of (129)I/(137)Cs activity ratios used for routine waste management produced values in agreement with the few available data for PWR resin samples.

  16. Development of a Rapid and Accurate Identification Method for Citrobacter Species Isolated from Pork Products Using a Matrix-Assisted Laser-Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS).

    PubMed

    Kwak, Hye-Lim; Han, Sun-Kyung; Park, Sunghoon; Park, Si Hong; Shim, Jae-Yong; Oh, Mihwa; Ricke, Steven C; Kim, Hae-Yeong

    2015-09-01

    Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDI-TOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

  17. A comprehensive profiling of sulfatides in myelin from mouse brain using liquid chromatography coupled to high-resolution accurate tandem mass spectrometry.

    PubMed

    Pintado-Sierra, M; García-Álvarez, I; Bribián, A; Medina-Rodríguez, E M; Lebrón-Aguilar, R; Garrido, L; de Castro, F; Fernández-Mayoralas, A; Quintanilla-López, J E

    2017-01-25

    Sulfatides are sulfoglycolipids found in the myelin sheath. The composition ratio of sulfatide molecular species changes with age, and it has also been associated with the pathogenesis of various human central nervous system diseases. However, profiling sulfatides in biological samples is difficult, due to the great variety of molecular species. In this work, a new, easy and reliable liquid chromatography-electrospray tandem mass spectrometry (LC-ESI(+)-MS/MS) method has been developed to profile sulfatide content in biological samples of myelin. The 'wrong-way-round' ionization effect has been described for this type of molecules for the first time, making it possible to correctly identify as many as 37 different sulfatides in mouse brain myelin samples, including molecules with different fatty acid chain lengths and varying degrees of unsaturation and hydroxylation. A chemometric analysis of their relative abundances showed that the main difference among individuals of different ages was the content of sulfatides with odd-numbered fatty acid chains, in addition to hydroxylated species.

  18. An Automated High-Throughput Metabolic Stability Assay Using an Integrated High-Resolution Accurate Mass Method and Automated Data Analysis Software

    PubMed Central

    Shah, Pranav; Kerns, Edward; Nguyen, Dac-Trung; Obach, R. Scott; Wang, Amy Q.; Zakharov, Alexey; McKew, John; Simeonov, Anton; Hop, Cornelis E. C. A.

    2016-01-01

    Advancement of in silico tools would be enabled by the availability of data for metabolic reaction rates and intrinsic clearance (CLint) of a diverse compound structure data set by specific metabolic enzymes. Our goal is to measure CLint for a large set of compounds with each major human cytochrome P450 (P450) isozyme. To achieve our goal, it is of utmost importance to develop an automated, robust, sensitive, high-throughput metabolic stability assay that can efficiently handle a large volume of compound sets. The substrate depletion method [in vitro half-life (t1/2) method] was chosen to determine CLint. The assay (384-well format) consisted of three parts: 1) a robotic system for incubation and sample cleanup; 2) two different integrated, ultraperformance liquid chromatography/mass spectrometry (UPLC/MS) platforms to determine the percent remaining of parent compound, and 3) an automated data analysis system. The CYP3A4 assay was evaluated using two long t1/2 compounds, carbamazepine and antipyrine (t1/2 > 30 minutes); one moderate t1/2 compound, ketoconazole (10 < t1/2 < 30 minutes); and two short t1/2 compounds, loperamide and buspirone (t½ < 10 minutes). Interday and intraday precision and accuracy of the assay were within acceptable range (∼12%) for the linear range observed. Using this assay, CYP3A4 CLint and t1/2 values for more than 3000 compounds were measured. This high-throughput, automated, and robust assay allows for rapid metabolic stability screening of large compound sets and enables advanced computational modeling for individual human P450 isozymes. PMID:27417180

  19. Inequality spectra

    NASA Astrophysics Data System (ADS)

    Eliazar, Iddo

    2017-03-01

    Inequality indices are widely applied in economics and in the social sciences as quantitative measures of the socioeconomic inequality of human societies. The application of inequality indices extends to size-distributions at large, where these indices can be used as general gauges of statistical heterogeneity. Moreover, as inequality indices are plentiful, arrays of such indices facilitate high-detail quantification of statistical heterogeneity. In this paper we elevate from arrays of inequality indices to inequality spectra: continuums of inequality indices that are parameterized by a single control parameter. We present a general methodology of constructing Lorenz-based inequality spectra, apply the general methodology to establish four sets of inequality spectra, investigate the properties of these sets, and show how these sets generalize known inequality gauges such as: the Gini index, the extended Gini index, the Rényi index, and hill curves.

  20. Accurate nuclear radii and binding energies from a chiral interaction

    DOE PAGES

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; ...

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shellmore » nuclei are in reasonable agreement with experiment.« less

  1. Accurate nuclear radii and binding energies from a chiral interaction

    SciTech Connect

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; Hagen, Gaute; Papenbrock, Thomas F.; Carlsson, Boris; Forssen, Christian; Hjorth-Jensen, M.; Navratil, Petr; Nazarewicz, Witold

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  2. Accurate identification and quantification of 11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid in urine drug testing: evaluation of a direct high efficiency liquid chromatographic-mass spectrometric method.

    PubMed

    Stephanson, Nikolai; Josefsson, Martin; Kronstrand, Robert; Beck, Olof

    2008-08-01

    A direct liquid chromatographic-tandem mass spectrometric (LC-MS/MS) method for measurement of urinary Delta(9)-tetrahydrocannabinol carboxylic acid (THCA) was developed. The method involved dilution of the urine sample with water containing (2)H(9)-deuterated analogue as internal standard, hydrolysis with ammonia, reversed phase chromatography using a Waters ultra-performance liquid chromatography (UPLC) equipment with gradient elution, negative electrospray ionization, and monitoring of two product ions in selected reaction monitoring mode. The measuring range was 2-1000 ng/mL for THCA, and the intra- and inter-assay imprecision, expressed as the coefficient of variation, was below 5%. Influence from urine matrix on ionization efficiency was noted in infusion experiments, but was compensated for by the internal standard. Comparison with established gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry methods in authentic patient samples demonstrated accuracy in both qualitative and quantitative results. A small difference in mean ratios (~15%) may be explained by the use of different hydrolysis procedures between methods. In conclusion, the high efficiency LC-MS/MS method was capable of accurately identify and quantify THCA in urine with a capacity of 14 samples per hour.

  3. Accurate simulations of TEPC neutron spectra using Geant4

    NASA Astrophysics Data System (ADS)

    Taylor, G. C.; Hawkes, N. P.; Shippen, A.

    2015-11-01

    A Geant4 model of a tissue-equivalent proportional counter (TEPC) has been developed in which the calculated output spectrum exhibits unparalleled agreement with experiment for monoenergetic neutron fields at several energies below 20 MeV. The model uses the standard release of the Geant4 9.6 p2 code, but with a non-standard neutron cross section file as provided by Mendoza et al., and with the environment variable options recommended by the same authors. This configuration was found to produce significant improvements in the alpha-dominated region of the calculated response. In this paper, these improvements are presented, and the post-processing required to convert deposited energy into the number of ion pairs (which is the quantity actually measured experimentally) is discussed.

  4. Evaluation and validation of an accurate mass screening method for the analysis of pesticides in fruits and vegetables using liquid chromatography-quadrupole-time of flight-mass spectrometry with automated detection.

    PubMed

    López, Mónica García; Fussell, Richard J; Stead, Sara L; Roberts, Dominic; McCullagh, Mike; Rao, Ramesh

    2014-12-19

    This study reports the development and validation of a screening method for the detection of pesticides in 11 different fruit and vegetable commodities. The method was based on ultra performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-QTOF-MS). The objective was to validate the method in accordance with the SANCO guidance document (12571/2013) on analytical quality control and validation procedures for pesticide residues analysis in food and feed. Samples were spiked with 199 pesticides, each at two different concentrations (0.01 and 0.05 mg kg(-1)) and extracted using the QuEChERS approach. Extracts were analysed by UPLC-QTOF-MS using generic acquisition parameters. Automated detection and data filtering were performed using the UNIFI™ software and the peaks detected evaluated against a proprietary scientific library containing information for 504 pesticides. The results obtained using different data processing parameters were evaluated for 4378 pesticide/commodities combinations at 0.01 and 0.05 mg kg(-1). Using mass accuracy (± 5 ppm) with retention time (± 0.2 min) and a low response threshold (100 counts) the validated Screening Detection Limits (SDLs) were 0.01 mg kg(-1) and 0.05 mg kg(-1) for 57% and 79% of the compounds tested, respectively, with an average of 10 false detects per sample analysis. Excluding the most complex matrices (onion and leek) the detection rates increased to 69% and 87%, respectively. The use of additional parameters such as isotopic pattern and fragmentation information further reduced the number of false detects but compromised the detection rates, particularly at lower residue concentrations. The challenges associated with the validation and subsequent implementation of a pesticide multi-residue screening method are also discussed.

  5. Mass loss

    NASA Technical Reports Server (NTRS)

    Goldberg, Leo

    1987-01-01

    Observational evidence for mass loss from cool stars is reviewed. Spectra line profiles are used for the derivation of mass-loss rates with the aid of the equation of continuity. This equation implies steady mass loss with spherical symmetry. Data from binary stars, Mira variables, and red giants in globular clusters are examined. Silicate emission is discussed as a useful indicator of mass loss in the middle infrared spectra. The use of thermal millimeter-wave radiation, Very Large Array (VLA) measurement of radio emission, and OH/IR masers are discussed as a tool for mass loss measurement. Evidence for nonsteady mass loss is also reviewed.

  6. A Bayesian method for analysing relaxation spectra

    NASA Astrophysics Data System (ADS)

    Ciocci Brazzano, L.; Pellizza, L. J.; Matteo, C. L.; Sorichetti, P. A.

    2016-01-01

    The knowledge of electrical and mechanical properties of material, relies on a precise analysis of the relaxation spectra. We explore the ability of a Bayesian method to achieve an accurate estimation of spectral parameters. We implemented a parallel-tempering Markov-chain Monte Carlo algorithm and used it to fit simulated and measured spectra. An exhaustive testing of the code shows that it presents an extremely good performance, accurately fitting complex spectra under strong noise and overlapping components. We conclude that this technique is quite suitable for relaxation spectra analysis, complementing classical methods.

  7. A REVISED CALIBRATION OF THE VIRIAL MASS ESTIMATOR FOR BLACK HOLES IN ACTIVE GALAXIES BASED ON SINGLE-EPOCH Hβ SPECTRA

    SciTech Connect

    Ho, Luis C.; Kim, Minjin

    2015-08-20

    The masses of supermassive black holes (BHs) in broad-line active galactic nuclei (AGNs) can be measured through reverberation mapping, but this method currently cannot be applied to very large samples or to high-redshift AGNs. As a practical alternative, one can devise empirical scaling relations, based on the correlation between broad-line region size and AGN luminosity and the relation between BH mass and bulge stellar velocity dispersion, to estimate the virial masses of BHs from single-epoch spectroscopy. We present a revised calibration of the BH mass estimator for the commonly used Hβ emission line. Our new calibration takes into account the recent determination of the virial coefficient for pseudo and classical bulges.

  8. DETERMINATION OF ION AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF PRODUCT ION MASS SPECTRA USING AN ORTHOGONAL ACCELERATION, TIME-OF-FLIGHT MASS SPECTROMETER AND AN ION CORRELATION PROGRAM

    EPA Science Inventory

    Exact masses of monoisotopic ions and the relative isotopic abundances (RIAs) of ions greater in mass by 1 and 2 Da than the monoisotopic ion are independent and complementary physical properties useful for istinguishing among ion compositions possible for a given nominal mass. U...

  9. Accurate, Direct, and High-Throughput Analyses of a Broad Spectrum of Endogenously Generated DNA Base Modifications with Isotope-Dilution Two-Dimensional Ultraperformance Liquid Chromatography with Tandem Mass Spectrometry: Possible Clinical Implication.

    PubMed

    Gackowski, Daniel; Starczak, Marta; Zarakowska, Ewelina; Modrzejewska, Martyna; Szpila, Anna; Banaszkiewicz, Zbigniew; Olinski, Ryszard

    2016-12-20

    Our hereby presented methodology is suitable for reliable assessment of the most common unavoidable DNA modifications which arise as a product of fundamental metabolic processes. 8-Oxoguanine, one of the oxidatively modified DNA bases, is a typical biomarker of oxidative stress. A noncanonical base, uracil, may be also present in small quantities in DNA. A set of ten-eleven translocation (TET) proteins are involved in oxidation of 5-methylcytosine to 5-hydroxymethylcytosine which can be further oxidized to 5-formylcytosine and 5-carboxycytosine. 5-Hydroxymethyluracil may be formed in deamination reaction of 5-hydroxymethylcytosine or can be also generated by TET enzymes. All of the aforementioned modifications seem to play some regulatory roles. We applied isotope-dilution automated online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS) for direct measurement of the 5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, 5-carboxy-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxyuridine, 2'-deoxyuridine, and 8-oxo-2'-deoxyguanosine. Analyses of DNA extracted from matched human samples showed that the 5-(hydroxymethyl)-2'-deoxycytidine level was 5-fold lower in colorectal carcinoma tumor in comparison with the normal one from the tumor's margin; also 5-formyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine were lower in colorectal carcinoma tissue (ca. 2.5- and 3.5-fold, respectively). No such differences was found for 2'-deoxyuridine and 5-(hydroxymethyl)-2'-deoxyuridine. The presented methodology is suitable for fast, accurate, and complex evaluation of an array of endogenously generated DNA deoxynucleosides modifications. This novel technique could be used for monitoring of cancer and other diseases related to oxidative stress, aberrant metabolism, and environmental exposure. Furthermore, the fully automated two-dimensional separation is extremely useful for analysis of material

  10. Countercurrent chromatography separation of saponins by skeleton type from Ampelozizyphus amazonicus for off-line ultra-high-performance liquid chromatography/high resolution accurate mass spectrometry analysis and characterisation.

    PubMed

    de Souza Figueiredo, Fabiana; Celano, Rita; de Sousa Silva, Danila; das Neves Costa, Fernanda; Hewitson, Peter; Ignatova, Svetlana; Piccinelli, Anna Lisa; Rastrelli, Luca; Guimarães Leitão, Suzana; Guimarães Leitão, Gilda

    2017-01-20

    Ampelozizyphus amazonicus Ducke (Rhamnaceae), a medicinal plant used to prevent malaria, is a climbing shrub, native to the Amazonian region, with jujubogenin glycoside saponins as main compounds. The crude extract of this plant is too complex for any kind of structural identification, and HPLC separation was not sufficient to resolve this issue. Therefore, the aim of this work was to obtain saponin enriched fractions from the bark ethanol extract by countercurrent chromatography (CCC) for further isolation and identification/characterisation of the major saponins by HPLC and MS. The butanol extract was fractionated by CCC with hexane - ethyl acetate - butanol - ethanol - water (1:6:1:1:6; v/v) solvent system yielding 4 group fractions. The collected fractions were analysed by UHPLC-HRMS (ultra-high-performance liquid chromatography/high resolution accurate mass spectrometry) and MS(n). Group 1 presented mainly oleane type saponins, and group 3 showed mainly jujubogenin glycosides, keto-dammarane type triterpene saponins and saponins with C31 skeleton. Thus, CCC separated saponins from the butanol-rich extract by skeleton type. A further purification of group 3 by CCC (ethyl acetate - ethanol - water (1:0.2:1; v/v)) and HPLC-RI was performed in order to obtain these unusual aglycones in pure form.

  11. REPS: REscaled Power Spectra for initial conditions with massive neutrinos

    NASA Astrophysics Data System (ADS)

    Zennaro, Matteo; Bel, Julien; Villaescusa-Navarro, Francisco; Carbone, Carmelita; Sefusatti, Emiliano; Guzzo, Luigi

    2016-12-01

    REPS (REscaled Power Spectra) provides accurate, one-percent level, numerical simulations of the initial conditions for massive neutrino cosmologies, rescaling the late-time linear power spectra to the simulation initial redshift.

  12. Zero kinetic energy spectroscopy: mass-analyzed threshold ionization spectra of chromium sandwich complexes with alkylbenzenes, (η(6)-RPh)(2)Cr (R = Me, Et, i-Pr, t-Bu).

    PubMed

    Ketkov, Sergey Y; Selzle, Heinrich L; Cloke, F Geoffrey N; Markin, Gennady V; Shevelev, Yury A; Domrachev, Georgy A; Schlag, Edward W

    2010-10-28

    For over 25 years zero kinetic energy (ZEKE) spectroscopy has yielded a rich foundation of high-resolution results of molecular ions. This was based on the discovery in the late 60's of long-lived ion states throughout the ionization continuum of molecular ions. Here, an example is chosen from another fundamental system pioneered at this university. The mass-analyzed threshold ionization (MATI) spectra of jet-cooled chromium bisarene complexes (η(6)-RPh)(2)Cr (R = Me (1), Et (2), i-Pr (3), and t-Bu (4)) have been measured and interpreted on the basis of DFT calculations. The MATI spectra of complexes 1 and 2 appear to reveal features arising from ionizations of the isomers formed by the rotation of one arene ring relative to the other. The 1 and 2 MATI spectra show two intense peaks corresponding to the 0(0)(0) ionizations with inverse intensity ratios. As indicated by the DFT calculations, the intensity ratio change on going from 1 to 2 results from different isomers contributing to each MATI peak. The ionization energies corresponding to the 0(0)(0) peaks are 42746 ± 5 and 42809 ± 5 cm(-1) for compound 1 and 42379 ± 5 and 42463 ± 5 cm(-1) for complex 2. The 1 and 2 spectra show also the weaker features representing transitions to the vibrationally excited cationic levels, the signals of individual rotamers being detected and assigned on the basis of calculated vibrational frequencies. The MATI spectra of compounds 3 and 4 reveal only one strong peak because of close ionization potentials of the isomers contributing to the MATI signal. The 3 and 4 ionization energies are 42104 ± 5 and 41917 ± 5 cm(-1), respectively. The precise values of ionization energies obtained from the MATI spectra reveal a nonlinear dependence of the IE on the number of Me groups in the alkyl substituents of (η(6)-RPh)(2)Cr. This can be explained by an increase in the molecular zero point energies on methylation of the substituents.

  13. Ion Mobility Mass Spectrometry for Extracting Spectra of N-Glycans Directly from Incubation Mixtures Following Glycan Release: Application to Glycans from Engineered Glycoforms of Intact, Folded HIV gp120

    NASA Astrophysics Data System (ADS)

    Harvey, David J.; Sobott, Frank; Crispin, Max; Wrobel, Antoni; Bonomelli, Camille; Vasiljevic, Snezana; Scanlan, Christopher N.; Scarff, Charlotte A.; Thalassinos, Konstantinos; Scrivens, James H.

    2011-03-01

    The analysis of glycosylation from native biological sources is often frustrated by the low abundances of available material. Here, ion mobility combined with electrospray ionization mass spectrometry have been used to extract the spectra of N-glycans released with PNGase F from a serial titration of recombinantly expressed envelope glycoprotein, gp120, from the human immunodeficiency virus (HIV). Analysis was also performed on gp120 expressed in the α-mannosidase inhibitor, and in a matched mammalian cell line deficient in GlcNAc transferase I. Without ion mobility separation, ESI spectra frequently contained no observable ions from the glycans whereas ions from other compounds such as detergents and residual buffer salts were abundant. After ion mobility separation on a Waters T-wave ion mobility mass spectrometer, the N-glycans fell into a unique region of the ion mobility/ m/z plot allowing their profiles to be extracted with good signal:noise ratios. This method allowed N-glycan profiles to be extracted from crude incubation mixtures with no clean-up even in the presence of surfactants such as NP40. Furthermore, this technique allowed clear profiles to be obtained from sub-microgram amounts of glycoprotein. Glycan profiles were similar to those generated by MALDI-TOF MS although they were more susceptible to double charging and fragmentation. Structural analysis could be accomplished by MS/MS experiments in either positive or negative ion mode but negative ion mode gave the most informative spectra and provided a reliable approach to the analysis of glycans from small amounts of glycoprotein.

  14. A sensitive and accurate method for the determination of perfluoroalkyl and polyfluoroalkyl substances in human serum using a high performance liquid chromatography-online solid phase extraction-tandem mass spectrometry.

    PubMed

    Yu, Chang Ho; Patel, Bhupendra; Palencia, Marilou; Fan, Zhihua Tina

    2017-01-13

    A selective, sensitive, and accurate analytical method for the measurement of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in human serum, utilizing LC-MS/MS (liquid chromatography-tandem mass spectrometry), was developed and validated according to the Centers for Disease Control and Prevention (CDC) guidelines for biological sample analysis. Tests were conducted to determine the optimal analytical column, mobile phase composition and pH, gradient program, and cleaning procedure. The final analytical column selected for analysis was an extra densely bonded silica-packed reverse-phase column (Agilent XDB-C8, 3.0×100mm, 3.5μm). Mobile phase A was an aqueous buffer solution containing 10mM ammonium acetate (pH=4.3). Mobile phase B was a mixture of methanol and acetonitrile (1:1, v/v). The gradient program was programmed by initiating a fast elution (%B, from 40 to 65%) between 1.0 and 1.5min, followed by a slow elution (%B: 65-80%) in the period of 1.5-7.5min. The cleanup procedures were augmented by cleaning with (1) various solvents (isopropyl alcohol, methanol, acetonitrile, and reverse osmosis-purified water); (2) extensive washing steps for the autosampler and solid phase extraction (SPE) cartridge; and (3) a post-analysis cleaning step for the whole system. Under the above conditions, the resolution and sensitivity were significantly improved. Twelve target PFASs were baseline-separated (2.5-7.0min) within a 10-min of acquisition time. The limits of detection (LODs) were 0.01ng/mL or lower for all of the target compounds, making this method 5 times more sensitive than previously published methods. The newly developed method was validated in the linear range of 0.01-50ng/mL, and the accuracy (recovery between 80 and 120%) and precision (RSD<20%) were acceptable at three spiked levels (0.25, 2.5, and 25ng/mL). The method development and validation results demonstrated that this method was precise, accurate, and robust, with high-throughput (∼10min per

  15. Storm Spectra

    NASA Technical Reports Server (NTRS)

    2007-01-01

    portion is defined by the day/night boundary (known as the terminator).

    These two images illustrate only a small fraction of the information contained in a single LEISA scan, highlighting just one aspect of the power of infrared spectra for atmospheric studies.

  16. NASA Fuse Cycle 1 Program A100. FUV Spectra of Evolved Late-K and M Stars: Mass Loss revisited and Stellar Activity

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2002-01-01

    Program A100 was awarded 50 ksec of FUSE observing time. Targets alpha TrA (K3 II) and gamma Cru (N13 III) were originally assigned 25 ksec each, to be observed in the medium aperture. Once the in-flight performance and telescope alignment problems were known, the observations were reprogrammed to optimized the scientific return of the program. alpha TrA was scheduled for 25 ksec observations in both the medium and large apertures. The principle aim of this program was to measure the stellar FUV line and continuum emission, in order to estimate the photoionization radiation field and to determine the level of stellar activity through the fluxes in the collisionally excited high temperature diagnostics: C III 977A and O VI 1032,1038A doublet. The medium aperture observations were obtained successfully while the large aperture observations were thought by Johns Hopkins University (JHU)to be lost to satellite problems. There was insufficient signal-to noise in the medium aperture short wavelength SiC channels to do quantitative science. The long wavelength LiF spectra are of high signal-to-noise (SN) and show pronounced emission lines near lambdalambda1100 - 1140A. Emission had been observed at these wavelength in low resolution and low SN ORFEUS-SPAS 11 spectra obtained by Dupree & Brickhouse (1998 ApJ 500, L33), however, they were unable to identify these features. One of the first problems faced in the early FUSE mission was establishing a reliable wavelength scale, especially between the different channels. With the medium aperture data in hand we decided to identify the features and thereby establish an absolute wavelength scale for the channels where the emission occurred. We first established that the emission was fluorescent. and then we constructed a fluorescent line formation model for all neutrals. and singly ionized species with atomic numbers up to 28, and the H2 molecule. We used datasets of radiative rates and energy levels which were as complete as

  17. Use of Ga for mass bias correction for the accurate determination of copper isotope ratio in the NIST SRM 3114 Cu standard and geological samples by MC-ICP MS

    NASA Astrophysics Data System (ADS)

    Zhang, T.; Zhou, L.; Tong, S.

    2015-12-01

    The absolute determination of the Cu isotope ratio in NIST SRM 3114 based on a regression mass bias correction model is performed for the first time with NIST SRM 944 Ga as the calibrant. A value of 0.4471±0.0013 (2SD, n=37) for the 65Cu/63Cu ratio was obtained with a value of +0.18±0.04 ‰ (2SD, n=5) for δ65Cu relative to NIST 976.The availability of the NIST SRM 3114 material, now with the absolute value of the 65Cu/63Cu ratio and a δ65Cu value relative to NIST 976 makes it suitable as a new candidate reference material for Cu isotope studies. In addition, a protocol is described for the accurate and precise determination of δ65Cu values of geological reference materials. Purification of Cu from the sample matrix was performed using the AG MP-1M Bio-Rad resin. The column recovery for geological samples was found to be 100±2% (2SD, n=15).A modified method of standard-sample bracketing with internal normalization for mass bias correction was employed by adding natural Ga to both the sample and the solution of NIST SRM 3114, which was used as the bracketing standard. An absolute value of 0.4471±0.0013 (2SD, n=37) for 65Cu/63Cu quantified in this study was used to calibrate the 69Ga/71Ga ratio in the two adjacent bracketing standards of SRM 3114,their average value of 69Ga/71Ga was then used to correct the 65Cu/63Cu ratio in the sample. Measured δ65Cu values of 0.18±0.04‰ (2SD, n=20),0.13±0.04‰ (2SD, n=9),0.08±0.03‰ (2SD, n=6),0.01±0.06‰(2SD, n=4) and 0.26±0.04‰ (2SD, n=7) were obtained for five geological reference materials of BCR-2,BHVO-2,AGV-2,BIR-1a,and GSP-2,respectively,in agreement with values obtained in previous studies.

  18. Bootstrap classification and point-based feature selection from age-staged mouse cerebellum tissues of matrix assisted laser desorption/ionization mass spectra using a fuzzy rule-building expert system.

    PubMed

    Harrington, Peter B; Laurent, Claudine; Levinson, Douglas F; Levitt, Pat; Markey, Sanford P

    2007-09-19

    A bootstrap method for point-based detection of candidate biomarker peaks has been developed from pattern classifiers. Point-based detection methods are advantageous in comparison to peak-based methods. Peak determination and selection are problematic when spectral peaks are not baseline resolved or on a varying baseline. The benefit of point-based detection is that peaks can be globally determined from the characteristic features of the entire data set (i.e., subsets of candidate points) as opposed to the traditional method of selecting peaks from individual spectra and then combining the peak list into a data set. The point-based method is demonstrated to be more effective and efficient using a synthetic data set when compared to using Mahalanobis distance for feature selection. In addition, probabilities that characterize the uniqueness of the peaks are determined. This method was applied for detecting peaks that characterize age-specific patterns of protein expression of developing and adult mouse cerebella from matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) data. The mice comprised three age groups: 42 adults, 19 14-day-old pups, and 16 7-day-old pups. Three sequential spectra were obtained from each tissue section to yield 126, 57 and 48 spectra for adult, 14-day-old pup, and 7-day-old pup spectra, respectively. Each spectrum comprised 71,879 mass measurements in a range of 3.5-50 kDa. A previous study revealed that 846 unique peaks were detected that were consistent for 50% of the mice in each age group (C. Laurent, D.F. Levinson, S.A. Schwartz, P.B. Harrington, S.P. Markey, R.M. Caprioli, P. Levitt, Direct profiling of the cerebellum by MALDI MS: a methodological study in postnatal and adult mouse, J. Neurosci. Res. 81 (2005) 613-621.). A fuzzy rule-building expert system (FuRES) was applied to investigate the correlation of age with features in the MS data. FuRES detected two outlier pup-14 spectra. Prediction was evaluated

  19. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    PubMed

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs.

  20. Chemical profiling and quantification of monacolins and citrinin in red yeast rice commercial raw materials and dietary supplements using liquid chromatography-accurate QToF mass spectrometry: Chemometrics application.

    PubMed

    Avula, Bharathi; Cohen, Pieter A; Wang, Yan-Hong; Sagi, Satyanarayanaraju; Feng, Wei; Wang, Mei; Zweigenbaum, Jerry; Shuangcheng, Ma; Khan, Ikhlas A

    2014-11-01

    Red yeast rice (RYR) is prepared by fermenting rice with various strains of the yeast Monascus spp of the Aspergillaceae family. Depending on the Monascus strains and the fermentation conditions, the products may contain monacolins, pigments and citrinin as secondary metabolites. Authentic and commercial RYR samples were analyzed using UHPLC-DAD-QToF-MS for monacolins, pigments and citrinin. A separation by UHPLC was achieved using a reversed-phase column and a gradient of water/acetonitrile each containing formic acid as the mobile phase. Accurate mass QToF spectrometry was used to distinguish isobaric monacolins. Principle component analysis (PCA), a chemometric technique was used to discriminate between authentic RYR, commercial RYR raw materials and dietary supplements. Three authentic RYR samples, 31 commercial RYR raw materials and 14 RYR dietary supplements were analyzed. Monacolin K content in 600mg of authentic RYR samples ranged from 1.2mg to 1.38mg. Amounts of monacolin K in dietary supplements labeled as containing 600mg of RYR varied more than 40-fold from 0.03mg to 2.18mg. Monacolin K content of dietary supplements labeled as containing 1200mg RYR varied more than 20-fold from 0.22mg to 5.23mg. In addition to large variations in quantity of monacolin K found in dietary supplements, RYR dietary supplements contained ratios of monacolins that differed significantly from authentic samples. The results indicated that RYR commercial products are of variable quality and the analytical method is suitable for quality control testing of a variety of RYR products.

  1. Prediction of collision-induced dissociation spectra of common N-glycopeptides for glycoform identification.

    PubMed

    Zhang, Zhongqi; Shah, Bhavana

    2010-12-15

    Confident identification of the glycan moieties in glycopeptides by collision-induced dissociation (CID) requires accurate prediction of the CID spectrum of the glycopeptides. In this Article, the kinetic model for the prediction of peptide CID spectra is extended to predict the CID spectra of N-glycopeptides. The model was trained with 1831 ion-trap CID spectra of N-glycopeptides and is able to predict ion-trap CID spectra with excellent accuracy in ion intensities for N-glycopeptides up to 8000 u in mass. A total of 524 common glycoforms including complex N-glycans with 2-4 antennas, plus high-mannose type and hybrid type, can be predicted.

  2. Interpretation of the ion mass spectra in the mass per charge range 25-35 amu/e obtained in the inner coma of Halley's comet by the HIS-sensor of the Giotto IMS experiment

    NASA Technical Reports Server (NTRS)

    Geiss, J.; Altwegg, K.; Anders, E.; Balsiger, H.; Meier, A.; Shelley, E. G.; Ip, W.-H.; Rosenbauer, H.; Neugebauer, M.

    1991-01-01

    The IMS-HIS double-focusing mass spectrometer that flew on the Giotto spacecraft covered the mass per charge range from 12 to 56 (amu/e). By comparing flight data, calibration data and results of model calculations of the ion population in the inner coma, the absolute mass scale is established, and ions in the mass range 25 to 35 are identified. Ions resulting from protonation of molecules with high proton affinity are relatively abundant, enabling us to estimate relative source strengths for H2CO, CH3OH, HCN, and H2S, providing for the first time a positive in situ measurement of methanol. Also, upper limits for NO and some hydrocarbons are derived.

  3. Interpretation of the ion mass spectra in the mass range 25-35 obtained in the inner coma of Halley's comet by the HIS-sensor of the Giotto IMS Experiment

    NASA Technical Reports Server (NTRS)

    Geiss, J.; Altwegg, K.; Anders, E.; Balsiger, H.; Ip, W.-H.; Meier, A.; Neugebauer, M.; Rosenbauer, H.; Shelley, E. G.

    1991-01-01

    The IMS-HIS double-focussing mass spectrometer that flew on the Giotto spacecraft covered the mass per charge range from 12 to 56 (AMU/e). By comparing flight data, calibration data, and results of model calculations of the ion population in the inner coma, the absolute mass scale is established, and ions in the mass range 25 to 35 are identified. Ions resulting from protonation of molecules with high proton affinity are relatively abundant, enabling us to estimate relative source strengths for H2CO, CH3OH, HCN, and H2S, providing for the first time a positive in situ measurement of methanol. Also, upper limits for NO and some hydrocarbons are derived.

  4. Mass spectra of the heavy baryons {lambda}{sub Q} and {sigma}{sub Q}{sup (*)} from QCD sum rules

    SciTech Connect

    Zhang Jianrong; Huang Mingqiu

    2008-05-01

    We use QCD sum rule approach to calculate the masses of the ground-state {lambda}{sub Q} and {sigma}{sub Q}{sup (*)} baryons. Contributions of the operators up to dimension six are included in operator product expansion. The resulting heavy baryonic masses from the calculations are m{sub {lambda}{sub b}}=5.69{+-}0.13 GeV, and m{sub {lambda}{sub c}}=2.31{+-}0.19 GeV for {lambda}{sub Q}; m{sub {sigma}{sub b}}=5.73{+-}0.21 GeV, m{sub {sigma}{sub b}}{sub *}=5.81{+-}0.19 GeV, m{sub {sigma}{sub c}}=2.40{+-}0.31 GeV and m{sub {sigma}{sub c}}{sub *}=2.56{+-}0.24 GeV for {sigma}{sub Q}{sup (*)}, respectively, which are in good agreement with the experimental values.

  5. Profiling and classification of French propolis by combined multivariate data analysis of planar chromatograms and scanning direct analysis in real time mass spectra.

    PubMed

    Chasset, Thibaut; Häbe, Tim T; Ristivojevic, Petar; Morlock, Gertrud E

    2016-09-23

    Quality control of propolis is challenging, as it is a complex natural mixture of compounds, and thus, very difficult to analyze and standardize. Shown on the example of 30 French propolis samples, a strategy for an improved quality control was demonstrated in which high-performance thin-layer chromatography (HPTLC) fingerprints were evaluated in combination with selected mass signals obtained by desorption-based scanning mass spectrometry (MS). The French propolis sample extracts were separated by a newly developed reversed phase (RP)-HPTLC method. The fingerprints obtained by two different detection modes, i.e. after (1) derivatization and fluorescence detection (FLD) at UV 366nm and (2) scanning direct analysis in real time (DART)-MS, were analyzed by multivariate data analysis. Thus, RP-HPTLC-FLD and RP-HPTLC-DART-MS fingerprints were explored and the best classification was obtained using both methods in combination with pattern recognition techniques, such as principal component analysis. All investigated French propolis samples were divided in two types and characteristic patterns were observed. Phenolic compounds such as caffeic acid, p-coumaric acid, chrysin, pinobanksin, pinobanksin-3-acetate, galangin, kaempferol, tectochrysin and pinocembrin were identified as characteristic marker compounds of French propolis samples. This study expanded the research on the European poplar type of propolis and confirmed the presence of two botanically different types of propolis, known as the blue and orange types.

  6. Estimating modal abundances from the spectra of natural and laboratory pyroxene mixtures using the modified Gaussian model

    NASA Astrophysics Data System (ADS)

    Sunshine, J. M.; Pieters, C. M.

    1993-05-01

    The modified Gaussian model (MGM) is used to explore spectra of samples containing multiple pyroxene components as a function of modal abundance. The MGM allows spectra to be analyzed directly, without the use of actual or assumed end-member spectra and therefore holds great promise for remote applications. A series of mass fraction mixtures created from several different particle size fractions are analyzed with the MGM to quantify the properties of pyroxene mixtures as a function of both modal abundance and grain size. Band centers, band widths, and relative band strengths of absorptions from individual pyroxenes in mixture spectra are found to be largely independent of particle size. Spectral properties of both zoned and exsolved pyroxene components are resolved in exsolved samples using the MGM, and modal abundances are accurately estimated to within 5-10 percent without predetermined knowledge of the end-member spectra.

  7. Estimating modal abundances from the spectra of natural and laboratory pyroxene mixtures using the modified Gaussian model

    NASA Technical Reports Server (NTRS)

    Sunshine, Jessica M.; Pieters, Carle M.

    1993-01-01

    The modified Gaussian model (MGM) is used to explore spectra of samples containing multiple pyroxene components as a function of modal abundance. The MGM allows spectra to be analyzed directly, without the use of actual or assumed end-member spectra and therefore holds great promise for remote applications. A series of mass fraction mixtures created from several different particle size fractions are analyzed with the MGM to quantify the properties of pyroxene mixtures as a function of both modal abundance and grain size. Band centers, band widths, and relative band strengths of absorptions from individual pyroxenes in mixture spectra are found to be largely independent of particle size. Spectral properties of both zoned and exsolved pyroxene components are resolved in exsolved samples using the MGM, and modal abundances are accurately estimated to within 5-10 percent without predetermined knowledge of the end-member spectra.

  8. A search of new samples of active galactic nuclei with low-mass black holes from SDSS

    NASA Astrophysics Data System (ADS)

    Liu, H.; Yuan, W.; Zhou, H.; Dong, X.-B.

    2016-02-01

    We report on the progress of our on-going work to search for low-mass black holes (LMBHs) in active galactic nuclei. The masses of black holes are estimated using the broad line width and luminosity obtained from one-epoch optical spectra. As the first step, we fitted the spectra of 1263 objects in the quasar catalog of the SDSS DR10 and obtained accurate measurement of the emission lines. Two AGNs are found to have M BH ~ 106 M⊙. The next step is to analyze the spectra of the DR10 galaxy sample, from which a much larger sample of low-mass AGNs is expected to be obtained.

  9. Charged hadron spectra in gold-on-gold collisions at centre-of-mass energy per nucleon pair of 130 GeV

    NASA Astrophysics Data System (ADS)

    Calderon de La Barca Sanchez, Manuel

    The collision of high energy heavy ions is the most promising laboratory for the study of nuclear matter at high energy density and for creation of the Quark-Gluon Plasma. A new era in this field began with the operation and first collisions of Au nuclei in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory during 2000. This work concentrates on measurement of global hadronic observables in Au + Au interactions at a centre-of-mass energy of sNN = 130 GeV, which mainly address conditions in the final state of the collision. The minimum bias multiplicity distribution, the transverse momentum (p⊥), and pseudorapidity (η) distributions for charged hadrons (h-, h+) are presented. Results on identified π- transverse mass ( m⊥) and rapidity (y) distributions are also discussed. The data were taken with the STAR detector with emphasis on particles near mid-rapidity. We find that the multiplicity density at mid-rapidity for the 5% most central interactions is dNh- /dh|h=0 = 280 +/- 1stat +/- 20syst, an increase per participant of 38% relative to pp¯ collisions at similar energy. The mean transverse momentum is 0.508 +/- 0.012 GeV/c and is larger than in Pb + Pb collisions at lower energies. The scaling of the h- yield per participant nucleon pair, obtained via a ratio of Au + Au to pp¯ p ⊥ distributions, is a strong function of p ⊥. The pseudorapidity distribution is almost constant within |η| < 1. The π- rapidity distribution is also flat around mid-rapidity in the region |y| < 0.8, with a yield of pions for central collisions of dNp- /dy|y=0 = 287 +/- 1stat +/- 21syst. However, the slope of the m⊥ distributions is not the same for different rapidity bins, suggesting that boost-invariance is not fully achieved in the collisions.

  10. Predicting ambient aerosol Thermal Optical Reflectance (TOR) measurements from infrared spectra: organic carbon

    NASA Astrophysics Data System (ADS)

    Dillner, A. M.; Takahama, S.

    2014-11-01

    Organic carbon (OC) can constitute 50% or more of the mass of atmospheric particulate matter. Typically, the organic carbon concentration is measured using thermal methods such as Thermal-Optical Reflectance (TOR) from quartz fiber filters. Here, methods are presented whereby Fourier Transform Infrared (FT-IR) absorbance spectra from polytetrafluoroethylene (PTFE or Teflon) filters are used to accurately predict TOR OC. Transmittance FT-IR analysis is rapid, inexpensive, and non-destructive to the PTFE filters. To develop and test the method, FT-IR absorbance spectra are obtained from 794 samples from seven Interagency Monitoring of PROtected Visual Environment (IMPROVE) sites sampled during 2011. Partial least squares regression is used to calibrate sample FT-IR absorbance spectra to artifact-corrected TOR OC. The FTIR spectra are divided into calibration and test sets by sampling site and date which leads to precise and accurate OC predictions by FT-IR as indicated by high coefficient of determination (R2; 0.96), low bias (0.02 μg m-3, all μg m-3 values based on the nominal IMPROVE sample volume of 32.8 m-3), low error (0.08 μg m-3) and low normalized error (11%). These performance metrics can be achieved with various degrees of spectral pretreatment (e.g., including or excluding substrate contributions to the absorbances) and are comparable in precision and accuracy to collocated TOR measurements. FT-IR spectra are also divided into calibration and test sets by OC mass and by OM / OC which reflects the organic composition of the particulate matter and is obtained from organic functional group composition; this division also leads to precise and accurate OC predictions. Low OC concentrations have higher bias and normalized error due to TOR analytical errors and artifact correction errors, not due to the range of OC mass of the samples in the calibration set. However, samples with low OC mass can be used to predict samples with high OC mass indicating that the

  11. Towards understanding the tandem mass spectra of protonated oligopeptides. 2: The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp).

    PubMed

    Bleiholder, Christian; Suhai, Sándor; Harrison, Alex G; Paizs, Béla

    2011-06-01

    The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.

  12. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  13. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  14. Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques.

    PubMed

    Peng, Wen-Ping; Chou, Szu-Wei; Patil, Avinash A

    2014-07-21

    Large biomolecules and bioparticles play a vital role in biology, chemistry, biomedical science and physics. Mass is a critical parameter for the characterization of large biomolecules and bioparticles. To achieve mass analysis, choosing a suitable ion source is the first step and the instruments for detecting ions, mass analyzers and detectors should also be considered. Abundant mass spectrometric techniques have been proposed to determine the masses of large biomolecules and bioparticles and these techniques can be divided into two categories. The first category measures the mass (or size) of intact particles, including single particle quadrupole ion trap mass spectrometry, cell mass spectrometry, charge detection mass spectrometry and differential mobility mass analysis; the second category aims to measure the mass and tandem mass of biomolecular ions, including quadrupole ion trap mass spectrometry, time-of-flight mass spectrometry, quadrupole orthogonal time-of-flight mass spectrometry and orbitrap mass spectrometry. Moreover, algorithms for the mass and stoichiometry assignment of electrospray mass spectra are developed to obtain accurate structure information and subunit combinations.

  15. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

    PubMed

    Shilov, Ignat V; Seymour, Sean L; Patel, Alpesh A; Loboda, Alex; Tang, Wilfred H; Keating, Sean P; Hunter, Christie L; Nuwaysir, Lydia M; Schaeffer, Daniel A

    2007-09-01

    The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.

  16. Mass spectra of tetrahydroisoquinoline-fused 1,3,2-O,N,P- and 1,2,3-O,S,N-heterocycles: influence of ring size and fusion, of present heteroatoms, substituent effects and of the stereochemistry on fragmentation.

    PubMed

    Starke, Ines; Schuster, Ildikó; Fülöp, Ferenc; Kleinpeter, Erich

    2008-05-01

    The electron ionization (EI) mass spectra of a variety of stereoisomeric tricyclic 1,3,2-oxazaphosphino[4,3-a]isoquinolines (1-4), 1,2,3-oxathiazino[4,3-a]isoquinoline-4-oxides (5-7) and the -4,4-dioxides (8-10) of oxazaphospholo- and oxathiazolo[4,3-a]- (11, 12, 15 and 16) and -[3,4-b]isoquinolines (13, 14 and 17) were recorded. Ring size and fusion, the different heteroatoms (P and S) and substituents on the ring systems strongly influence the mass spectra. In addition, mass spectra of the stereoisomers of compounds 1, 2 and 13, 14 revealed stereochemically relevant differences which are not observed for the other pairs of isomers.

  17. Search for narrow resonances in dilepton mass spectra in proton-proton collisions at $\\sqrt{s}$ = 13 TeV and combination with 8 TeV data

    SciTech Connect

    Khachatryan, Vardan; et al.

    2016-09-17

    A search for narrow resonances in dielectron and dimuon invariant mass spectra has been performed using data obtained from proton-proton collisions at $ \\sqrt{s} = $ 13 TeV collected with the CMS detector. The integrated luminosity for the dielectron sample is 2.7 fb$^{-1}$ and for the dimuon sample 2.9 fb$^{-1}$. The sensitivity of the search is increased by combining these data with a previously analysed set of data obtained at $ \\sqrt{s} = $ 8 TeV and corresponding to a luminosity of 20 fb$^{-1}$. No evidence for non-standard-model physics is found, either in the 13 TeV data set alone, or in the combined data set. Upper limits on the product of production cross section and branching fraction have also been calculated in a model-independent manner to enable interpretation in models predicting a narrow dielectron or dimuon resonance structure. Limits are set on the masses of hypothetical particles that could appear in new-physics scenarios. For the $\\mathrm{Z}'_{\\text{SSM}}$ particle, which arises in the sequential standard model, and for the superstring inspired $\\mathrm{Z}'_{\\psi}$ particle, 95% confidence level lower mass limits for the combined data sets and combined channels are found to be 3.37 and 2.82 TeV, respectively. The corresponding limits for Kaluza-Klein gravitons arising in the Randall-Sundrum model of extra dimensions with coupling parameters 0.01 and 0.10 are 1.46 and 3.11 TeV, respectively. These results significantly extend previous limits.

  18. Search for narrow resonances in dilepton mass spectra in proton-proton collisions at $$\\sqrt{s}$$ = 13 TeV and combination with 8 TeV data

    DOE PAGES

    Khachatryan, Vardan

    2017-02-14

    A search for narrow resonances in dielectron and dimuon invariant mass spectra has been performed using data obtained from proton-proton collisions atmore » $$ \\sqrt{s} = $$ 13 TeV collected with the CMS detector. The integrated luminosity for the dielectron sample is 2.7 fb$$^{-1}$$ and for the dimuon sample 2.9 fb$$^{-1}$$. The sensitivity of the search is increased by combining these data with a previously analysed set of data obtained at $$ \\sqrt{s} = $$ 8 TeV and corresponding to a luminosity of 20 fb$$^{-1}$$. No evidence for non-standard-model physics is found, either in the 13 TeV data set alone, or in the combined data set. Upper limits on the product of production cross section and branching fraction have also been calculated in a model-independent manner to enable interpretation in models predicting a narrow dielectron or dimuon resonance structure. Limits are set on the masses of hypothetical particles that could appear in new-physics scenarios. For the $$\\mathrm{Z}'_{\\text{SSM}}$$ particle, which arises in the sequential standard model, and for the superstring inspired $$\\mathrm{Z}'_{\\psi}$$ particle, 95% confidence level lower mass limits for the combined data sets and combined channels are found to be 3.37 and 2.82 TeV, respectively. The corresponding limits for Kaluza-Klein gravitons arising in the Randall-Sundrum model of extra dimensions with coupling parameters 0.01 and 0.10 are 1.46 and 3.11 TeV, respectively. Lastly, these results significantly extend previous limits.« less

  19. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  20. Elucidation of the mass fragmentation pathways of potato glycoalkaloids and aglycons using Orbitrap mass spectrometry.

    PubMed

    Cahill, Michael G; Caprioli, Giovanni; Vittori, Sauro; James, Kevin J

    2010-09-01

    The mass fragmentation of potato glycoalkaloids, α-solanine and α-chaconine, and the aglycons, demissidine and solasodine were studied using the Orbitrap Fourier transform (FT) mass spectrometer. Using the linear ion trap (LIT) mass spectrometry, multistage collisional-induced dissociation (CID) experiments (MS(n)) on the [M + H](+) precursor ions were performed to aid the elucidation of the mass fragmentation pathways. In addition, higher energy collisional-induced dissociation (HCD) mass spectra were generated for these toxins at a high resolution setting [100,000 FWHM (full width at half maximum)] using the Orbitrap. This hybrid mass spectrometry instrumentation was exploited to produce MS(3) spectra by selecting MS(2) product ions, generated using LIT MS, and fragmentation using HCD. The accurate mass data in the MS(3) spectra aided the confirmation of proposed product ion formulae. The precursor and product ions from glycoalkaloids lost up to four sugars from different regions during MS(n) experiments. Mass fragmentation of the six-ring aglycons were similar, generating major product ions that resulted from cleavages at the B-rings and E-rings.

  1. Miniaturized Linear Wire Ion Trap Mass Analyzer.

    PubMed

    Wu, Qinghao; Li, Ailin; Tian, Yuan; Zare, Richard N; Austin, Daniel E

    2016-08-02

    We report a linear ion trap (LIT) in which the electric field is formed by fine wires held under tension and accurately positioned using holes drilled in two end plates made of plastic. The coordinates of the hole positions were optimized in simulation. The stability diagram and mass spectra using boundary ejection were compared between simulation and experiment and good agreement was found. The mass spectra from experiments show peak widths (fwhm) in units of mass-to-charge of around 0.38 Th using a scan rate of 3830 Th/s. The limits of detection are 137 ppbv and 401 ppbv for benzene and toluene, respectively. Different sizes of the wire ion trap can be easily fabricated by drilling holes in scaled positions. Other distinguishing features, such as high ion and photon transmission, low capacitance, high tolerance to mechanical and assembly error, and low weight, are discussed.

  2. Photon spectra from WIMP annihilation

    SciTech Connect

    Cembranos, J. A. R.; Cruz-Dombriz, A. de la; Dobado, A.; Maroto, A. L.; Lineros, R. A.

    2011-04-15

    If the present dark matter in the Universe annihilates into standard model particles, it must contribute to the fluxes of cosmic rays that are detected on the Earth and, in particular, to the observed gamma-ray fluxes. The magnitude of such a contribution depends on the particular dark matter candidate, but certain features of the produced photon spectra may be analyzed in a rather model-independent fashion. In this work we provide the complete photon spectra coming from WIMP annihilation into standard model particle-antiparticle pairs obtained by extensive Monte Carlo simulations. We present results for each individual annihilation channel and provide analytical fitting formulas for the different spectra for a wide range of WIMP masses.

  3. Suspected-target pesticide screening using gas chromatography-quadrupole time-of-flight mass spectrometry with high resolution deconvolution and retention index/mass spectrum library.

    PubMed

    Zhang, Fang; Wang, Haoyang; Zhang, Li; Zhang, Jing; Fan, Ruojing; Yu, Chongtian; Wang, Wenwen; Guo, Yinlong

    2014-10-01

    A strategy for suspected-target screening of pesticide residues in complicated matrices was exploited using gas chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS). The screening workflow followed three key steps of, initial detection, preliminary identification, and final confirmation. The initial detection of components in a matrix was done by a high resolution mass spectrum deconvolution; the preliminary identification of suspected pesticides was based on a special retention index/mass spectrum (RI/MS) library that contained both the first-stage mass spectra (MS(1) spectra) and retention indices; and the final confirmation was accomplished by accurate mass measurements of representative ions with their response ratios from the MS(1) spectra or representative product ions from the second-stage mass spectra (MS(2) spectra). To evaluate the applicability of the workflow in real samples, three matrices of apple, spinach, and scallion, each spiked with 165 test pesticides in a set of concentrations, were selected as the models. The results showed that the use of high-resolution TOF enabled effective extractions of spectra from noisy chromatograms, which was based on a narrow mass window (5 mDa) and suspected-target compounds identified by the similarity match of deconvoluted full mass spectra and filtering of linear RIs. On average, over 74% of pesticides at 50 ng/mL could be identified using deconvolution and the RI/MS library. Over 80% of pesticides at 5 ng/mL or lower concentrations could be confirmed in each matrix using at least two representative ions with their response ratios from the MS(1) spectra. In addition, the application of product ion spectra was capable of confirming suspected pesticides with specificity for some pesticides in complicated matrices. In conclusion, GC-QTOF MS combined with the RI/MS library seems to be one of the most efficient tools for the analysis of suspected-target pesticide residues

  4. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    EPA Pesticide Factsheets

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  5. QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

    SciTech Connect

    Sanchez Almeida, J.; Morales-Luis, A. B.; Terlevich, R.; Terlevich, E.; Cid Fernandes, R. E-mail: abml@iac.es E-mail: eterlevi@inaoep.mx

    2012-09-10

    We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

  6. Synthesis and Mass Spectra of Butenyltin Compounds

    DTIC Science & Technology

    1989-03-01

    California 92152-5000 E . G. SCHWEIZER, CAPT, USN R. M . HILLYER Commander Technical Director ADMINISTRATIVE INFORMATION This work was funded by the Office...to m /z intensities .................................... 8 Accesion For _ NTIS GRA&I 6~ Unannounced By coy .. / A,-’iabdl;ty C,.ts " t0IAvail ai,dlo...12.5 m by 0.2 mm-I.D. HP-1 fused-silica capillary column with a 0.33-gm coating thickness. Helium carrier gas was used at a head pressure of 40 kPa

  7. Accurate spectral color measurements

    NASA Astrophysics Data System (ADS)

    Hiltunen, Jouni; Jaeaeskelaeinen, Timo; Parkkinen, Jussi P. S.

    1999-08-01

    Surface color measurement is of importance in a very wide range of industrial applications including paint, paper, printing, photography, textiles, plastics and so on. For a demanding color measurements spectral approach is often needed. One can measure a color spectrum with a spectrophotometer using calibrated standard samples as a reference. Because it is impossible to define absolute color values of a sample, we always work with approximations. The human eye can perceive color difference as small as 0.5 CIELAB units and thus distinguish millions of colors. This 0.5 unit difference should be a goal for the precise color measurements. This limit is not a problem if we only want to measure the color difference of two samples, but if we want to know in a same time exact color coordinate values accuracy problems arise. The values of two instruments can be astonishingly different. The accuracy of the instrument used in color measurement may depend on various errors such as photometric non-linearity, wavelength error, integrating sphere dark level error, integrating sphere error in both specular included and specular excluded modes. Thus the correction formulas should be used to get more accurate results. Another question is how many channels i.e. wavelengths we are using to measure a spectrum. It is obvious that the sampling interval should be short to get more precise results. Furthermore, the result we get is always compromise of measuring time, conditions and cost. Sometimes we have to use portable syste or the shape and the size of samples makes it impossible to use sensitive equipment. In this study a small set of calibrated color tiles measured with the Perkin Elmer Lamda 18 and the Minolta CM-2002 spectrophotometers are compared. In the paper we explain the typical error sources of spectral color measurements, and show which are the accuracy demands a good colorimeter should have.

  8. Delineation of Stenotrophomonas maltophilia isolates from cystic fibrosis patients by fatty acid methyl ester profiles and matrix-assisted laser desorption/ionization time-of-flight mass spectra using hierarchical cluster analysis and principal component analysis.

    PubMed

    Vidigal, Pedrina Gonçalves; Mosel, Frank; Koehling, Hedda Luise; Mueller, Karl Dieter; Buer, Jan; Rath, Peter Michael; Steinmann, Joerg

    2014-12-01

    Stenotrophomonas maltophilia is an opportunist multidrug-resistant pathogen that causes a wide range of nosocomial infections. Various cystic fibrosis (CF) centres have reported an increasing prevalence of S. maltophilia colonization/infection among patients with this disease. The purpose of this study was to assess specific fingerprints of S. maltophilia isolates from CF patients (n = 71) by investigating fatty acid methyl esters (FAMEs) through gas chromatography (GC) and highly abundant proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and to compare them with isolates obtained from intensive care unit (ICU) patients (n = 20) and the environment (n = 11). Principal component analysis (PCA) of GC-FAME patterns did not reveal a clustering corresponding to distinct CF, ICU or environmental types. Based on the peak area index, it was observed that S. maltophilia isolates from CF patients produced significantly higher amounts of fatty acids in comparison with ICU patients and the environmental isolates. Hierarchical cluster analysis (HCA) based on the MALDI-TOF MS peak profiles of S. maltophilia revealed the presence of five large clusters, suggesting a high phenotypic diversity. Although HCA of MALDI-TOF mass spectra did not result in distinct clusters predominantly composed of CF isolates, PCA revealed the presence of a distinct cluster composed of S. maltophilia isolates from CF patients. Our data suggest that S. maltophilia colonizing CF patients tend to modify not only their fatty acid patterns but also their protein patterns as a response to adaptation in the unfavourable environment of the CF lung.

  9. Accurate colorimetric feedback for RGB LED clusters

    NASA Astrophysics Data System (ADS)

    Man, Kwong; Ashdown, Ian

    2006-08-01

    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  10. Spectroscopic determination of masses (and implied ages) for red giants

    NASA Astrophysics Data System (ADS)

    Ness, Melissa; Hogg, David W.; Rix, Hans-Walter; Martig, Marie; Ho, Anna

    2016-01-01

    The mass of a star is arguably its most fundamental parameter and for red giant stars it implies a stellar evolution age. Stellar masses and ages have never been derived directly from spectra of red giants. However, using the APOGEE Kepler sample of stars, (the APOKASC sample), with high-quality spectra and astroseismic masses, we can build a data-driven spectral model using THE CANNON (arXiv:1501.07604) to infer stellar mass and therefore age from stellar spectra. We determine stellar masses to 0.07 dex from APOGEE DR12 spectra of red giants; these imply age estimates accurate to 0.2 dex (40 percent). THE CANNON constrains the ages foremost from spectral regions with particular absorption lines, elements whose surface abundances reflect mass-dependent dredge-up. We deliver an unprecedented catalog of 85,000 giants (including 20,000 red-clump stars) with mass and age estimates, spanning the entire disk (from the Galactic center to R ˜ 20 kpc). Such stellar age constraints across the Milky Way open up new avenues in Galactic archeology.

  11. Reactor Neutrino Spectra

    NASA Astrophysics Data System (ADS)

    Hayes, Anna C.; Vogel, Petr

    2016-10-01

    We present a review of the antineutrino spectra emitted from reactors. Knowledge of these spectra and their associated uncertainties is crucial for neutrino oscillation studies. The spectra used to date have been determined either by converting measured electron spectra to antineutrino spectra or by summing over all of the thousands of transitions that make up the spectra, using modern databases as input. The uncertainties in the subdominant corrections to β-decay plague both methods, and we provide estimates of these uncertainties. Improving on current knowledge of the antineutrino spectra from reactors will require new experiments. Such experiments would also address the so-called reactor neutrino anomaly and the possible origin of the shoulder observed in the antineutrino spectra measured in recent high-statistics reactor neutrino experiments.

  12. The structure of BPS spectra

    NASA Astrophysics Data System (ADS)

    Longhi, Pietro

    In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

  13. High-Precision Tungsten Isotopic Analysis by Multicollection Negative Thermal Ionization Mass Spectrometry Based on Simultaneous Measurement of W and (18)O/(16)O Isotope Ratios for Accurate Fractionation Correction.

    PubMed

    Trinquier, Anne; Touboul, Mathieu; Walker, Richard J

    2016-02-02

    Determination of the (182)W/(184)W ratio to a precision of ± 5 ppm (2σ) is desirable for constraining the timing of core formation and other early planetary differentiation processes. However, WO3(-) analysis by negative thermal ionization mass spectrometry normally results in a residual correlation between the instrumental-mass-fractionation-corrected (182)W/(184)W and (183)W/(184)W ratios that is attributed to mass-dependent variability of O isotopes over the course of an analysis and between different analyses. A second-order correction using the (183)W/(184)W ratio relies on the assumption that this ratio is constant in nature. This may prove invalid, as has already been realized for other isotope systems. The present study utilizes simultaneous monitoring of the (18)O/(16)O and W isotope ratios to correct oxide interferences on a per-integration basis and thus avoid the need for a double normalization of W isotopes. After normalization of W isotope ratios to a pair of W isotopes, following the exponential law, no residual W-O isotope correlation is observed. However, there is a nonideal mass bias residual correlation between (182)W/(i)W and (183)W/(i)W with time. Without double normalization of W isotopes and on the basis of three or four duplicate analyses, the external reproducibility per session of (182)W/(184)W and (183)W/(184)W normalized to (186)W/(183)W is 5-6 ppm (2σ, 1-3 μg loads). The combined uncertainty per session is less than 4 ppm for (183)W/(184)W and less than 6 ppm for (182)W/(184)W (2σm) for loads between 3000 and 50 ng.

  14. Mass spectrometry.

    NASA Technical Reports Server (NTRS)

    Burlingame, A. L.; Johanson, G. A.

    1972-01-01

    Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

  15. Shape effects on asteroid spectra

    NASA Astrophysics Data System (ADS)

    Davalos, J.; Carvano, J.

    2014-07-01

    The objective of this work is to probe how the shape of a body like an asteroid could be modifying its observed spectra and the derived mineralogical interfaces based on spectral modeling. To model this effect, we construct an oblate ellipsoid with triangular facets, where each facet contributes to the overall reflectance. The synthetic spectra is generated by the isotropic multiple-scattering approximation (IMSA) reflectance model of Hapke (1993). First, we obtained optical constants by inverting the spectra of meteorites, obtained from the RELAB spectral database. These optical constants were found inverting the reflectance bidirectional equation of Hapke; this is made in two steps: (i) The first inversion is to find the single-scattering albedo π (ii) in the model of Hapke, this albedo is found under the regime of the geometric optics, where the particle size is much larger than the wavelength of the incident radiation. Here we assumed a constant value for the real part of the optical constant n=1.5. With these optical constants, we can construct synthetic spectra for any particle size. The phase function used is the double Henyey-Greenstein phase function and an accurate expression for the H-functions. We started with the ellipsoidal shape a=1.0, b=c=0.5 for two particle size 50 and 250 μ m, in this part, we found good differences in the BAR parameter between the two geometric models, this was done for 100 Eucrite meteorites spectra. In this first study, we found that the BAR parameter between the two models is bigger when the particle size increases. In the second part, we started with different ellipsoidal shapes and produced synthetic spectra for material with eucrite and diogenite composition with a phase angle of 20 degrees, incidence and emission angles of 10 degrees, and particle size at 250 μ m. All spectra was generated for four parameters of phase angle b=[0.2,0.4,0.6,0.8] taking the empirical relation between the phase constants of Hapke (2012

  16. How accurately can 21cm tomography constrain cosmology?

    NASA Astrophysics Data System (ADS)

    Mao, Yi; Tegmark, Max; McQuinn, Matthew; Zaldarriaga, Matias; Zahn, Oliver

    2008-07-0