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Sample records for accurate mass analysis

  1. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

    PubMed Central

    Weisbrod, Chad R.; Eng, Jimmy K.; Hoopmann, Michael R.; Baker, Tahmina; Bruce, James E.

    2012-01-01

    FT All Reaction Monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum in order to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails due to fragmenting multiple overlapping precursors. The sensitivity, robustness and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides. PMID:22288382

  2. Accurate mass tag retention time database for urine proteome analysis by chromatography--mass spectrometry.

    PubMed

    Agron, I A; Avtonomov, D M; Kononikhin, A S; Popov, I A; Moshkovskii, S A; Nikolaev, E N

    2010-05-01

    Information about peptides and proteins in urine can be used to search for biomarkers of early stages of various diseases. The main technology currently used for identification of peptides and proteins is tandem mass spectrometry, in which peptides are identified by mass spectra of their fragmentation products. However, the presence of the fragmentation stage decreases sensitivity of analysis and increases its duration. We have developed a method for identification of human urinary proteins and peptides. This method based on the accurate mass and time tag (AMT) method does not use tandem mass spectrometry. The database of AMT tags containing more than 1381 AMT tags of peptides has been constructed. The software for database filling with AMT tags, normalizing the chromatograms, database application for identification of proteins and peptides, and their quantitative estimation has been developed. The new procedures for peptide identification by tandem mass spectra and the AMT tag database are proposed. The paper also lists novel proteins that have been identified in human urine for the first time. PMID:20632944

  3. 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

  4. Quantitation and accurate mass analysis of pesticides in vegetables by LC/TOF-MS.

    PubMed

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

    2005-05-01

    A quantitative method consisting of solvent extraction followed by liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) analysis was developed for the identification and quantitation of three chloronicotinyl pesticides (imidacloprid, acetamiprid, thiacloprid) commonly used on salad vegetables. Accurate mass measurements within 3 ppm error were obtained for all the pesticides studied in various vegetable matrixes (cucumber, tomato, lettuce, pepper), which allowed an unequivocal identification of the target pesticides. Calibration curves covering 2 orders of magnitude were linear over the concentration range studied, thus showing the quantitative ability of TOF-MS as a monitoring tool for pesticides in vegetables. Matrix effects were also evaluated using matrix-matched standards showing no significant interferences between matrixes and clean extracts. Intraday reproducibility was 2-3% relative standard deviation (RSD) and interday values were 5% RSD. The precision (standard deviation) of the mass measurements was evaluated and it was less than 0.23 mDa between days. Detection limits of the chloronicotinyl insecticides in salad vegetables ranged from 0.002 to 0.01 mg/kg. These concentrations are equal to or better than the EU directives for controlled pesticides in vegetables showing that LC/TOF-MS analysis is a powerful tool for identification of pesticides in vegetables. Robustness and applicability of the method was validated for the analysis of market vegetable samples. Concentrations found in these samples were in the range of 0.02-0.17 mg/kg of vegetable. PMID:15859598

  5. 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. PMID:24420979

  6. 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.

  7. 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.

  8. 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

  9. 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

    2014-10-01

    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. PMID:25164376

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

    SciTech Connect

    Zimmer, Jennifer S.; Monroe, Matthew E.; Qian, Weijun; Smith, Richard D.

    2006-01-20

    Proteomics, and the larger field of systems biology, have recently demonstrated utility in both the understanding of cellular processes on the molecular level and the identification of potential biomarkers of various disease states. The large amount of data generated by utilizing high mass accuracy mass spectrometry for high-throughput proteomics analyses presents a challenge in data processing, analysis and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics analysis and the accompanying data processing tools that have been developed in order to interpret and display the large volumes of data produced.

  11. 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

  12. Simultaneous measurement in mass and mass/mass mode for accurate qualitative and quantitative screening analysis of pharmaceuticals in river water.

    PubMed

    Martínez Bueno, M J; Ulaszewska, Maria M; Gomez, M J; Hernando, M D; Fernández-Alba, A R

    2012-09-21

    A new approach for the analysis of pharmaceuticals (target and non-target) in water by LC-QTOF-MS is described in this work. The study has been designed to assess the performance of the simultaneous quantitative screening of target compounds, and the qualitative analysis of non-target analytes, in just one run. The features of accurate mass full scan mass spectrometry together with high MS/MS spectral acquisition rates - by means of information dependent acquisition (IDA) - have demonstrated their potential application in this work. Applying this analytical strategy, an identification procedure is presented based on library searching for compounds which were not included a priori in the analytical method as target compounds, thus allowing their characterization by data processing of accurate mass measurements in MS and MS/MS mode. The non-target compounds identified in river water samples were ketorolac, trazodone, fluconazole, metformin and venlafaxine. Simultaneously, this strategy allowed for the identification of other compounds which were not included in the library by screening the highest intensity peaks detected in the samples and by analysis of the full scan TOF-MS, isotope pattern and MS/MS spectra - the example of loratadine (histaminergic) is described. The group of drugs of abuse selected as target compounds for evaluation included analgesics, opioids and psychostimulants. Satisfactory results regarding sensitivity and linearity of the developed method were obtained. Limits of detection for the selected target compounds were from 0.003 to 0.01 μg/L and 0.01 to 0.5 μg/L, in MS and MS/MS mode, respectively - by direct sample injection of 100 μL.

  13. 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...

  14. 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...

  15. 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...

  16. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    proteins can also be extensively modified by PTMs26-31 or by their interactions with other biomolecules or small molecules.32,33 Thus, it is highly desirable that proteins, the primary functional macromolecules involved in almost all biological activities, can be studied directly and systematically to determine their diverse properties and interplay. Such proteome-wide analysis is expected to provide a wealth of biological information, such as sequence, quantity, PTMs, interactions, activities, subcellular distribution and structure of proteins, which is critical to the comprehensive understanding of the biological systems. However, the de novo analysis of proteins isolated from cells, tissues or bodily fluids poses significant challenges due to the tremendous complexity and depth of the proteome, which necessitates high-throughput and highly sensitive analytical techniques. It is therefore not surprising that mass spectrometry (MS) has become an indispensable technology for proteome analysis.

  17. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

    PubMed Central

    Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.

    2008-01-01

    Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score potential identifications by evaluating the number of fragment ions matched between each peptide sequence and an observed spectrum. These systems, however, generally do not distinguish between matching an intense peak and matching a minor peak. We have developed a statistical model to score peptide matches that is based upon the multivariate hypergeometric distribution. This scorer, part of the “MyriMatch” database search engine, places greater emphasis on matching intense peaks. The probability that the best match for each spectrum has occurred by random chance can be employed to separate correct matches from random ones. We evaluated this software on data sets from three different laboratories employing three different ion trap instruments. Employing a novel system for testing discrimination, we demonstrate that stratifying peaks into multiple intensity classes improves the discrimination of scoring. We compare MyriMatch results to those of Sequest and X!Tandem, revealing that it is capable of higher discrimination than either of these algorithms. When minimal peak filtering is employed, performance plummets for a scoring model that does not stratify matched peaks by intensity. On the other hand, we find that MyriMatch discrimination improves as more peaks are retained in each spectrum. MyriMatch also scales well to tandem mass spectra from high-resolution mass analyzers. These findings may indicate limitations for existing database search scorers that count matched peaks without differentiating them by intensity. This software and source code is available under Mozilla Public License at this URL: http://www.mc.vanderbilt.edu/msrc/bioinformatics/. PMID:17269722

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  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. PMID:26820234

  4. Accurate masses for dispersion-supported galaxies

    NASA Astrophysics Data System (ADS)

    Wolf, Joe; Martinez, Gregory D.; Bullock, James S.; Kaplinghat, Manoj; Geha, Marla; Muñoz, Ricardo R.; Simon, Joshua D.; Avedo, Frank F.

    2010-08-01

    We derive an accurate mass estimator for dispersion-supported stellar systems and demonstrate its validity by analysing resolved line-of-sight velocity data for globular clusters, dwarf galaxies and elliptical galaxies. Specifically, by manipulating the spherical Jeans equation we show that the mass enclosed within the 3D deprojected half-light radius r1/2 can be determined with only mild assumptions about the spatial variation of the stellar velocity dispersion anisotropy as long as the projected velocity dispersion profile is fairly flat near the half-light radius, as is typically observed. We find M1/2 = 3 G-1< σ2los > r1/2 ~= 4 G-1< σ2los > Re, where < σ2los > is the luminosity-weighted square of the line-of-sight velocity dispersion and Re is the 2D projected half-light radius. While deceptively familiar in form, this formula is not the virial theorem, which cannot be used to determine accurate masses unless the radial profile of the total mass is known a priori. We utilize this finding to show that all of the Milky Way dwarf spheroidal galaxies (MW dSphs) are consistent with having formed within a halo of a mass of approximately 3 × 109 Msolar, assuming a Λ cold dark matter cosmology. The faintest MW dSphs seem to have formed in dark matter haloes that are at least as massive as those of the brightest MW dSphs, despite the almost five orders of magnitude spread in luminosity between them. We expand our analysis to the full range of observed dispersion-supported stellar systems and examine their dynamical I-band mass-to-light ratios ΥI1/2. The ΥI1/2 versus M1/2 relation for dispersion-supported galaxies follows a U shape, with a broad minimum near ΥI1/2 ~= 3 that spans dwarf elliptical galaxies to normal ellipticals, a steep rise to ΥI1/2 ~= 3200 for ultra-faint dSphs and a more shallow rise to ΥI1/2 ~= 800 for galaxy cluster spheroids.

  5. 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

  6. 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

    2015-01-01

    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

  7. 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.

  8. 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.

  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. 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

  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. Metabolite identification of artemether by data-dependent accurate mass spectrometric analysis using an LTQ-Orbitrap hybrid mass spectrometer in combination with the online hydrogen/deuterium exchange technique.

    PubMed

    Liu, Tian; Du, Fuying; Zhu, Fanping; Xing, Jie

    2011-11-15

    Artemether (ARM), the O-methyl ether prodrug of dihydroartemisinin (DHA), is a first-line antimalarial drug used in areas of multi-drug resistance. Artemisinin drugs can be metabolized extensively in vivo and this seems related to their autoinduction pharmacokinetics. In the present study, the metabolite identification of ARM was performed by the generic data-dependent accurate mass spectrometric analysis, using high-resolution (HR) liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) and tandem mass spectrometry (MS/MS) LTQ-Orbitrap hybrid mass spectrometer in conjunction with online hydrogen (H)/deuterium (D) exchange for rapid structural characterization. The LC separation was improved allowing the separation of ARM parent drugs and their metabolites from their diastereomers. A total of 77 phase I metabolites of ARM were identified in rat liver microsomal incubates and rat urine, including dihydroartemisinin and artemisinin. In rat bile, 12 phase II metabolites were found. Accurate mass data were obtained in both full scan and HR-MS/MS mode to support assignments of metabolite structures. Online H/D exchange LC/HR-ESI-MS experiments provided additional evidence in differentiating dihydroxylated deoxy-ARM from mono-hydroxylated ARM. The results showed the main phase I metabolites of artemether are hydroxylated, dehydro, demethylated and deoxy products, and they will undergo subsequent phase II glucuronidation processes. Most metabolites were reported for the first time. This study also demonstrated the effectiveness of high-resolution mass spectrometry in combination with an online H/D exchange LC/HR-MS(n) technique in rapid identification of drug metabolites. PMID:22006394

  13. CYP450 phenotyping and metabolite identification of quinine by accurate mass UPLC-MS analysis: a possible metabolic link to blackwater fever

    PubMed Central

    2013-01-01

    Background The naturally occurring alkaloid drug, quinine is commonly used for the treatment of severe malaria. Despite centuries of use, its metabolism is still not fully understood, and may play a role in the haemolytic disorders associated with the drug. Methods Incubations of quinine with CYPs 1A2, 2C9, 2C19, 2D6, and 3A4 were conducted, and the metabolites were characterized by accurate mass UPLC-MSE analysis. Reactive oxygen species generation was also measured in human erythrocytes incubated in the presence of quinine with and without microsomes. Results The metabolites 3-hydroxyquinine, 2’-oxoquininone, and O-desmethylquinine were observed after incubation with CYPs 3A4 (3-hydroxyquinine and 2’-oxoquininone) and 2D6 (O-desmethylquinine). In addition, multiple hydroxylations were observed both on the quinoline core and the quinuclidine ring system. Of the five primary abundance CYPs tested, 3A4, 2D6, 2C9, and 2C19 all demonstrated activity toward quinine, while 1A2 did not. Further, quinine produced robust dose-dependent oxidative stress in human erythrocytes in the presence of microsomes. Conclusions Taken in context, these data suggest a CYP-mediated link between quinine metabolism and the poorly understood haemolytic condition known as blackwater fever, often associated with quinine ingestion. PMID:23800033

  14. 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.

  15. An Automated High-Throughput Metabolic Stability Assay Using an Integrated High-Resolution Accurate Mass Method and Automated Data Analysis Software.

    PubMed

    Shah, Pranav; Kerns, Edward; Nguyen, Dac-Trung; Obach, R Scott; Wang, Amy Q; Zakharov, Alexey; McKew, John; Simeonov, Anton; Hop, Cornelis E C A; Xu, Xin

    2016-10-01

    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

  16. 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

  17. Accurate and reproducible determination of lignin molar mass by acetobromination.

    PubMed

    Asikkala, Janne; Tamminen, Tarja; Argyropoulos, Dimitris S

    2012-09-12

    The accurate and reproducible determination of lignin molar mass by using size exclusion chromatography (SEC) is challenging. The lignin association effects, known to dominate underivatized lignins, have been thoroughly addressed by reaction with acetyl bromide in an excess of glacial acetic acid. The combination of a concerted acetylation with the introduction of bromine within the lignin alkyl side chains is thought to be responsible for the observed excellent solubilization characteristics acetobromination imparts to a variety of lignin samples. The proposed methodology was compared and contrasted to traditional lignin derivatization methods. In addition, side reactions that could possibly be induced under the acetobromination conditions were explored with native softwood (milled wood lignin, MWL) and technical (kraft) lignin. These efforts lend support toward the use of room temperature acetobromination being a facile, effective, and universal lignin derivatization medium proposed to be employed prior to SEC measurements. PMID:22870925

  18. Selective accurate-mass-based analysis of 11 oxy-PAHs on atmospheric particulate matter by pressurized liquid extraction followed by high-performance liquid chromatography and magnetic sector mass spectrometry.

    PubMed

    Walgraeve, C; Demeestere, K; De Wispelaere, P; Dewulf, J; Lintelmann, J; Fischer, K; Van Langenhove, H

    2012-02-01

    An innovative analytical method based on high-performance liquid chromatography and atmospheric pressure chemical ionization magnetic sector mass spectrometry was developed and optimized to determine trace concentrations of 11 compounds belonging to the group of the seldom-analyzed oxy-PAHs (phenanthrene-9,10-dione, chrysene-5,6-dione, benzo[a]pyrene-4,5-dione, benzo[a]pyrene-1,6-dione, benzo[a]pyrene-3,6-dione, benzo[a]pyrene-6,12-dione, 4-oxa-benzo[def]chrysene-5-one, pyrene-1-carboxaldehyde, benzo[de]anthracene-7-one, benzo[a]anthracene-7,12-dione, and napthacene-5,12-dione) on airborne particulate matter (PM(10)). The mass spectrometer was operated in multiple ion detection mode, allowing for selective accurate mass detection (mass resolution of 12,000 full width at half maximum) of the oxy-PAHs characteristic ions. Optimization of both the vaporizer (450 °C) and capillary temperature (350 °C) resulted into instrumental detection limits in the range between 7 (benzo[a]pyrene-1,6-dione) and 926 pg (benzo[a]anthracene-7,12-dione). The advanced pressurized liquid extraction (PLE) and the more traditionally used ultrasonic extraction (USE) were compared using ethyl acetate as an extraction solvent. For both techniques, high recoveries from spiked quartz fiber filters (PLE, 82-110%; USE, 67-97%) were obtained. Recoveries obtained from real PM(10) samples were also high (76-107%), and no significant matrix effects (ME) on the ionization process (enhancement or suppression) were found (ME, 89-123%). Method limits of quantification (S/N = 10) were in the range between 2 and 336 pg/m(3). This method was used to analyze real PM samples collected at several urban and rural locations in the Antwerp area. For the first time, concentrations for Belgium are provided. Concentrations of individual oxy-PAHs are in the lower pictograms per cubic meter to 6 ng/m(3) range. High concentration differences between individual compounds are found as exemplified by the 75th percentile

  19. Maximum Mass of Strange Stars and Pulsars with the Most Accurately Measured Masses

    NASA Astrophysics Data System (ADS)

    Vartanyan, Yu. L.; Grigoryan, A. K.; Shahinyan, H. A.

    2015-06-01

    Strange quark matter (SQM) is studied using a bag model in which the transition to the SQM state takes place at energy densities of no more than twice the density in atomic nuclei. Thus, low mass neutron stars with a configuration consisting of SQM form a single family on a plot of the mass M of equilibrium superdense configurations as a function of central energy density ρ c (the M(ρ c ) curve). The bag model considered here depends on three constants: the vacuum pressure B, the quark-gluon interaction constant α c , and the strange quark mass m s . Sets of values of these constants are determined, which if used in the equation of state for SQM yield a maximal mass M max of the equilibrium quark configurations which exceeds the recently accurately determined mass of 2.01 M ⊙ for the binary radio pulsar PSR J0348+0432. The mass, radius, total baryon number, and red shift from the surface of the strange star are calculated for these configurations as a function of central energy density ρ c . The values of these integrated parameters are also calculated for each series with M max > 2.01 M ⊙ for superdense configurations with masses of 2.01, 1.97, and 1.44 solar masses, which have been determined with great accuracy from observations. It turns out that, according to the resulting equations of state, all of the three pulsars with the most accurately measured masses, may be possible candidate strange stars.

  20. Accurate Low-mass Stellar Models of KOI-126

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    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. Line gas sampling system ensures accurate analysis

    SciTech Connect

    Not Available

    1992-06-01

    Tremendous changes in the natural gas business have resulted in new approaches to the way natural gas is measured. Electronic flow measurement has altered the business forever, with developments in instrumentation and a new sensitivity to the importance of proper natural gas sampling techniques. This paper reports that YZ Industries Inc., Snyder, Texas, combined its 40 years of sampling experience with the latest in microprocessor-based technology to develop the KynaPak 2000 series, the first on-line natural gas sampling system that is both compact and extremely accurate. This means the composition of the sampled gas must be representative of the whole and related to flow. If so, relative measurement and sampling techniques are married, gas volumes are accurately accounted for and adjustments to composition can be made.

  2. 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.

  3. 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.

  4. An optimized method for neurotransmitters and their metabolites analysis in mouse hypothalamus by high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry.

    PubMed

    Yang, Zong-Lin; Li, Hui; Wang, Bing; Liu, Shu-Ying

    2016-02-15

    Neurotransmitters (NTs) and their metabolites are known to play an essential role in maintaining various physiological functions in nervous system. However, there are many difficulties in the detection of NTs together with their metabolites in biological samples. A new method for NTs and their metabolites detection by high performance liquid chromatography coupled with Q Exactive hybrid quadruple-orbitrap high-resolution accurate mass spectrometry (HPLC-HRMS) was established in this paper. This method was a great development of the applying of Q Exactive MS in the quantitative analysis. This method enabled a rapid quantification of ten compounds within 18min. Good linearity was obtained with a correlation coefficient above 0.99. The concentration range of the limit of detection (LOD) and the limit of quantitation (LOQ) level were 0.0008-0.05nmol/mL and 0.002-25.0nmol/mL respectively. Precisions (relative standard deviation, RSD) of this method were at 0.36-12.70%. Recovery ranges were between 81.83% and 118.04%. Concentrations of these compounds in mouse hypothalamus were detected by Q Exactive LC-MS technology with this method.

  5. 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.

  6. 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.

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

    PubMed

    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 . Graphical Abstract ᅟ.

  9. 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.

  10. Induced Dual-Nanospray: A Novel Internal Calibration Method for Convenient and Accurate Mass Measurement

    NASA Astrophysics Data System (ADS)

    Li, Yafeng; Zhang, Ning; Zhou, Yueming; Wang, Jianing; Zhang, Yiming; Wang, Jiyun; Xiong, Caiqiao; Chen, Suming; Nie, Zongxiu

    2013-09-01

    Accurate mass information is of great importance in the determination of unknown compounds. An effective and easy-to-control internal mass calibration method will dramatically benefit accurate mass measurement. Here we reported a simple induced dual-nanospray internal calibration device which has the following three advantages: (1) the two sprayers are in the same alternating current field; thus both reference ions and sample ions can be simultaneously generated and recorded. (2) It is very simple and can be easily assembled. Just two metal tubes, two nanosprayers, and an alternating current power supply are included. (3) With the low-flow-rate character and the versatility of nanoESI, this calibration method is capable of calibrating various samples, even untreated complex samples such as urine and other biological samples with small sample volumes. The calibration errors are around 1 ppm in positive ion mode and 3 ppm in negative ion mode with good repeatability. This new internal calibration method opens up new possibilities in the determination of unknown compounds, and it has great potential for the broad applications in biological and chemical analysis.

  11. DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

    SciTech Connect

    Mayampurath, Anoop M.; Jaitly, Navdeep; Purvine, Samuel O.; Monroe, Matthew E.; Auberry, Kenneth J.; Adkins, Joshua N.; Smith, Richard D.

    2008-04-01

    We present a new software tool for tandem MS analyses that: • accurately calculates the monoisotopic mass and charge of high–resolution parent ions • accurately operates regardless of the mass selected for fragmentation • performs independent of instrument settings • enables optimal selection of search mass tolerance for high mass accuracy experiments • is open source and thus can be tailored to individual needs • incorporates a SVM-based charge detection algorithm for analyzing low resolution tandem MS spectra • creates multiple output data formats (.dta, .MGF) • handles .RAW files and .mzXML formats • compatible with SEQUEST, MASCOT, X!Tandem

  12. 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

  13. 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...

  14. 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...

  15. 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

  16. Invited article: Time accurate mass flow measurements of solid-fueled systems.

    PubMed

    Olliges, Jordan D; Lilly, Taylor C; Joslyn, Thomas B; Ketsdever, Andrew D

    2008-10-01

    A novel diagnostic method is described that utilizes a thrust stand mass balance (TSMB) to directly measure time-accurate mass flow from a solid-fuel thruster. The accuracy of the TSMB mass flow measurement technique was demonstrated in three ways including the use of an idealized numerical simulation, verifying a fluid mass calibration with high-speed digital photography, and by measuring mass loss in more than 30 hybrid rocket motor firings. Dynamic response of the mass balance was assessed through weight calibration and used to derive spring, damping, and mass moment of inertia coefficients for the TSMB. These dynamic coefficients were used to determine the mass flow rate and total mass loss within an acrylic and gaseous oxygen hybrid rocket motor firing. Intentional variations in the oxygen flow rate resulted in corresponding variations in the total propellant mass flow as expected. The TSMB was optimized to determine mass losses of up to 2.5 g and measured total mass loss to within 2.5% of that calculated by a NIST-calibrated digital scale. Using this method, a mass flow resolution of 0.0011 g/s or 2% of the average mass flow in this study has been achieved.

  17. Main-Sequence Effective Temperatures from a Revised Mass-Luminosity Relation Based on Accurate Properties

    NASA Astrophysics Data System (ADS)

    Eker, Z.; Soydugan, F.; Soydugan, E.; Bilir, S.; Yaz Gökçe, E.; Steer, I.; Tüysüz, M.; Şenyüz, T.; Demircan, O.

    2015-04-01

    The mass-luminosity (M-L), mass-radius (M-R), and mass-effective temperature (M-{{T}eff}) diagrams for a subset of galactic nearby main-sequence stars with masses and radii accurate to ≤slant 3% and luminosities accurate to ≤slant 30% (268 stars) has led to a putative discovery. Four distinct mass domains have been identified, which we have tentatively associated with low, intermediate, high, and very high mass main-sequence stars, but which nevertheless are clearly separated by three distinct break points at 1.05, 2.4, and 7 {{M}⊙ } within the studied mass range of 0.38-32 {{M}⊙ }. Further, a revised mass-luminosity relation (MLR) is found based on linear fits for each of the mass domains identified. The revised, mass-domain based MLRs, which are classical (L\\propto {{M}α }), are shown to be preferable to a single linear, quadratic, or cubic equation representing an alternative MLR. Stellar radius evolution within the main sequence for stars with M\\gt 1 {{M}⊙ } is clearly evident on the M-R diagram, but it is not clear on the M-{{T}eff} diagram based on published temperatures. Effective temperatures can be calculated directly using the well known Stephan-Boltzmann law by employing the accurately known values of M and R with the newly defined MLRs. With the calculated temperatures, stellar temperature evolution within the main sequence for stars with M\\gt 1 {{M}⊙ } is clearly visible on the M-{{T}eff} diagram. Our study asserts that it is now possible to compute the effective temperature of a main-sequence star with an accuracy of ˜6%, as long as its observed radius error is adequately small (\\lt 1%) and its observed mass error is reasonably small (\\lt 6%).

  18. 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

    2016-02-01

    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.

  19. Accurate mass determination of short-lived isotopes by a tandem Penning-trap mass spectrometer

    SciTech Connect

    Stolzenberg, H.; Becker, S.; Bollen, G.; Kern, F.; Kluge, H.; Otto, T.; Savard, G.; Schweikhard, L. ); Audi, G. ); Moore, R.B. ); The ISOLDE Collaboration

    1990-12-17

    A mass spectrometer consisting of two Penning traps has been set up for short-lived isotopes at the on-line mass separator ISOLDE at CERN. The ion beam is collected and cooled in the first trap. After delivery to the second trap, high-accuracy direct mass measurements are made by determining the cyclotron frequency of the stored ions. Measurements have been performed for {sup 118}Cs--{sup 137}Cs. A resolving power of over 10{sup 6} and an accuracy of 1.4{times}10{sup {minus}7} have been achieved, corresponding to about 20 keV.

  20. Accurate determination of chlorine, bromine, and iodine in sedimentary rock reference samples by radiochemical neutron activation analysis and a detailed comparison with inductively coupled plasma mass spectrometry literature data.

    PubMed

    Sekimoto, Shun; Ebihara, Mitsuru

    2013-07-01

    Trace amounts of three halogens (chlorine, bromine, and iodine) were determined using radiochemical neutron activation analysis (RNAA) for nine sedimentary rocks and three rhyolite samples. To obtain high-quality analytical data, the radiochemical procedure of RNAA was improved by lowering the background in gamma-ray spectrometry and completing the chemical procedure more rapidly than in conventional procedures. A comparison of the RNAA data of Br and I with corresponding inductively coupled plasma mass spectrometry (ICPMS) literature data revealed that the values obtained by ICPMS coupled with pyrohydrolysis preconcentration were systematically lower than the RNAA data for some reference samples, suggesting that the quantitative collection of Br and I cannot always be achieved by the pyrohydrolysis for some solid samples. The RNAA data of three halogens can classify sedimentary rock reference samples into two groups (the samples from inland water and those from seawater), implying the geochemical significance of halogen data.

  1. Accurate determination of chlorine, bromine, and iodine in sedimentary rock reference samples by radiochemical neutron activation analysis and a detailed comparison with inductively coupled plasma mass spectrometry literature data.

    PubMed

    Sekimoto, Shun; Ebihara, Mitsuru

    2013-07-01

    Trace amounts of three halogens (chlorine, bromine, and iodine) were determined using radiochemical neutron activation analysis (RNAA) for nine sedimentary rocks and three rhyolite samples. To obtain high-quality analytical data, the radiochemical procedure of RNAA was improved by lowering the background in gamma-ray spectrometry and completing the chemical procedure more rapidly than in conventional procedures. A comparison of the RNAA data of Br and I with corresponding inductively coupled plasma mass spectrometry (ICPMS) literature data revealed that the values obtained by ICPMS coupled with pyrohydrolysis preconcentration were systematically lower than the RNAA data for some reference samples, suggesting that the quantitative collection of Br and I cannot always be achieved by the pyrohydrolysis for some solid samples. The RNAA data of three halogens can classify sedimentary rock reference samples into two groups (the samples from inland water and those from seawater), implying the geochemical significance of halogen data. PMID:23710630

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

    SciTech Connect

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

    2008-08-15

    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 quantitative 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. In addition, we also report on the optimization of a reversed-phase LC method for the separation of lipids in these sample types.

  3. The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics

    SciTech Connect

    Smith, Richard D. ); Anderson, Gordon A. ); Lipton, Mary S. ); Masselon, Christophe D. ); Pasa Tolic, Ljiljana ); Shen, Yufeng ); Udseth, Harold R. )

    2002-08-01

    We describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements based upon the use of peptide accurate mass tags (AMTs) produced by global protein enzymatic digestion. The two-stage strategy exploits Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry to validate peptide AMTs for a specific organism, tissue or cell type from potential mass tags identified using conventional tandem mass spectrometry (MS/MS) methods, providing greater confidence in identifications as well as the basis for subsequent measurements without the need for MS/MS, and thus with greater sensitivity and increased throughput. A single high resolution capillary liquid chromatography separation combined with high sensitivity, high resolution and ac-curate FT-ICR measurements has been shown capable of characterizing peptide mixtures of significantly more than 10 5 components with mass accuracies of -1 ppm, sufficient for broad protein identification using AMTs. Other attractions of the approach include the broad and relatively unbiased proteome coverage, the capability for exploiting stable isotope labeling methods to realize high precision for relative protein abundance measurements, and the projected potential for study of mammalian proteomes when combined with additional sample fractionation. Using this strategy, in our first application we have been able to identify AMTs for 60% of the potentially expressed proteins in the organism Deinococcus radiodurans.

  4. 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.

  5. 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

  6. Accurate hydrogen depth profiling by reflection elastic recoil detection analysis

    SciTech Connect

    Verda, R. D.; Tesmer, Joseph R.; Nastasi, Michael Anthony,; Bower, R. W.

    2001-01-01

    A technique to convert reflection elastic recoil detection analysis spectra to depth profiles, the channel-depth conversion, was introduced by Verda, et al [1]. But the channel-depth conversion does not correct for energy spread, the unwanted broadening in the energy of the spectra, which can lead to errors in depth profiling. A work in progress introduces a technique that corrects for energy spread in elastic recoil detection analysis spectra, the energy spread correction [2]. Together, the energy spread correction and the channel-depth conversion comprise an accurate and convenient hydrogen depth profiling method.

  7. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  8. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.

    PubMed

    Stanley, Jeffrey R; Adkins, Joshua N; Slysz, Gordon W; Monroe, Matthew E; Purvine, Samuel O; Karpievitch, Yuliya V; Anderson, Gordon A; Smith, Richard D; Dabney, Alan R

    2011-08-15

    Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.

  9. Dereplication of Streptomyces sp. AMC 23 polyether ionophore antibiotics by accurate-mass electrospray tandem mass spectrometry.

    PubMed

    Crevelin, Eduardo J; Crotti, Antônio E M; Zucchi, Tiago D; Melo, Itamar S; Moraes, Luiz A B

    2014-11-01

    Actinomycetes, especially those belonging to the genus Streptomyces, are economically important from a biotechnological standpoint: they produce antibiotics, anticancer compounds and a variety of bioactive substances that are potentially applicable in the agrochemical and pharmaceutical industries. This paper combined accurate-mass electrospray tandem mass spectrometry in the full scan and product ion scan modes with compounds library data to identify the major compounds in the crude extract produced by Streptomyces sp. AMC 23; it also investigated how sodiated nonactin ([M + Na](+)) fragmented. Most product ions resulted from elimination of 184 mass units due to consecutive McLafferty-type rearrangements. The data allowed identification of four macrotetrolides homologous to nonactin (monactin, isodinactin, isotrinactin/trinactin and tetranactin) as well as three related linear dimer compounds (nonactyl nonactoate, nonactyl homononactoate and homononactyl homononactoate). The major product ions of the sodiated molecules of these compounds also originated from elimination of 184 and 198 mass units. UPLC-MS/MS in the neutral loss scan mode helped to identify these compounds on the basis of the elimination of 184 and 198 mass units. This method aided monitoring of the relative production of these compounds for 32 days and revealed that the biosynthetic process began with increased production of linear dimers as compared with macrotetrolides. These data could facilitate dereplication and identification of these compounds in other microbial crude extracts.

  10. An accurate mass and radius measurement for an ultracool white dwarf

    NASA Astrophysics Data System (ADS)

    Parsons, S. G.; Gänsicke, B. T.; Marsh, T. R.; Bergeron, P.; Copperwheat, C. M.; Dhillon, V. S.; Bento, J.; Littlefair, S. P.; Schreiber, M. R.

    2012-11-01

    Studies of cool white dwarfs in the solar neighbourhood have placed a limit on the age of the Galactic disc of 8-9 billion years. However, determining their cooling ages requires the knowledge of their effective temperatures, masses, radii and atmospheric composition. So far, these parameters could only be inferred for a small number of ultracool white dwarfs for which an accurate distance is known, by fitting their spectral energy distributions in conjunction with a theoretical mass-radius relation. However, the mass-radius relation remains largely untested, and the derived cooling ages are hence model dependent. Here we report direct measurements of the mass and radius of an ultracool white dwarf in the double-lined eclipsing binary SDSS J013851.54-001621.6. We find MWD = 0.529 ± 0.010 M⊙ and RWD = 0.0131 ± 0.0003 R⊙. Our measurements are consistent with the mass-radius relation and we determine a robust cooling age of 9.5 billion years for the 3570 K white dwarf. We find that the mass and radius of the low-mass companion star, Msec = 0.132 ± 0.003 M⊙ and Rsec = 0.165 ± 0.001 R⊙, are in agreement with evolutionary models. We also find evidence that this >9.5 Gyr old M5 star is still active, far beyond the activity lifetime for a star of its spectral type. This is likely caused by the high tidally enforced rotation rate of the star. The companion star is close to filling its Roche lobe and the system will evolve into a cataclysmic variable in only 70 Myr. Our direct measurements demonstrate that this system can be used to calibrate ultracool white dwarf atmospheric models.

  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. High-resolution accurate mass measurements of biomolecules using a new electrospray ionization ion cyclotron resonance mass spectrometer.

    PubMed

    Winger, B E; Hofstadler, S A; Bruce, J E; Udseth, H R; Smith, R D

    1993-07-01

    A novel electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer based on a 7-T superconducting magnet was developed for high-resolution accurate mass measurements of large biomolecules. Ions formed at atmospheric pressure using electrospray ionization (ESI) were transmitted (through six differential pumping stages) to the trapped ion cell maintained below 10(-9) torr. The increased pumping speed attainable with cryopumping (> 10(5) L/s) allowed brief pressure excursions to above 10(-4) torr, with greatly enhanced trapping efficiencies and subsequent short pumpdown times, facilitating high-resolution mass measurements. A set of electromechanical shutters were also used to minimize the effect of the directed molecular beam produced by the ES1 source and were open only during ion injection. Coupled with the use of the pulsed-valve gas inlet, the trapped ion cell was generally filled to the space charge limit within 100 ms. The use of 10-25 ms ion injection times allowed mass spectra to be obtained from 4 fmol of bovine insulin (Mr 5734) and ubiquitin (Mr 8565, with resolution sufficient to easily resolve the isotopic envelopes and determine the charge states. The microheterogeneity of the glycoprotein ribonuclease B was examined, giving a measured mass of 14,898.74 Da for the most abundant peak in the isotopic envelope of the normally glycosylated protein (i.e., with five mannose and two N-acetylglucosamine residues (an error of approximately 2 ppm) and an average error of approximately 1 ppm for the higher glycosylated and various H3PO4 adducted forms of the protein. Time-domain signals lasting in excess of 80 s were obtained for smaller proteins, producing, for example, a mass resolution of more than 700,000 for the 4(+) charge state (m/z 1434) of insulin. PMID:24227643

  13. 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.

  14. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

    SciTech Connect

    Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2011-07-15

    High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.

  15. Accurate Universal Models for the Mass Accretion Histories and Concentrations of Dark Matter Halos

    NASA Astrophysics Data System (ADS)

    Zhao, D. H.; Jing, Y. P.; Mo, H. J.; Börner, G.

    2009-12-01

    A large amount of observations have constrained cosmological parameters and the initial density fluctuation spectrum to a very high accuracy. However, cosmological parameters change with time and the power index of the power spectrum dramatically varies with mass scale in the so-called concordance ΛCDM cosmology. Thus, any successful model for its structural evolution should work well simultaneously for various cosmological models and different power spectra. We use a large set of high-resolution N-body simulations of a variety of structure formation models (scale-free, standard CDM, open CDM, and ΛCDM) to study the mass accretion histories, the mass and redshift dependence of concentrations, and the concentration evolution histories of dark matter halos. We find that there is significant disagreement between the much-used empirical models in the literature and our simulations. Based on our simulation results, we find that the mass accretion rate of a halo is tightly correlated with a simple function of its mass, the redshift, parameters of the cosmology, and of the initial density fluctuation spectrum, which correctly disentangles the effects of all these factors and halo environments. We also find that the concentration of a halo is strongly correlated with the universe age when its progenitor on the mass accretion history first reaches 4% of its current mass. According to these correlations, we develop new empirical models for both the mass accretion histories and the concentration evolution histories of dark matter halos, and the latter can also be used to predict the mass and redshift dependence of halo concentrations. These models are accurate and universal: the same set of model parameters works well for different cosmological models and for halos of different masses at different redshifts, and in the ΛCDM case the model predictions match the simulation results very well even though halo mass is traced to about 0.0005 times the final mass, when

  16. ACCURATE UNIVERSAL MODELS FOR THE MASS ACCRETION HISTORIES AND CONCENTRATIONS OF DARK MATTER HALOS

    SciTech Connect

    Zhao, D. H.; Jing, Y. P.; Mo, H. J.; Boerner, G.

    2009-12-10

    A large amount of observations have constrained cosmological parameters and the initial density fluctuation spectrum to a very high accuracy. However, cosmological parameters change with time and the power index of the power spectrum dramatically varies with mass scale in the so-called concordance LAMBDACDM cosmology. Thus, any successful model for its structural evolution should work well simultaneously for various cosmological models and different power spectra. We use a large set of high-resolution N-body simulations of a variety of structure formation models (scale-free, standard CDM, open CDM, and LAMBDACDM) to study the mass accretion histories, the mass and redshift dependence of concentrations, and the concentration evolution histories of dark matter halos. We find that there is significant disagreement between the much-used empirical models in the literature and our simulations. Based on our simulation results, we find that the mass accretion rate of a halo is tightly correlated with a simple function of its mass, the redshift, parameters of the cosmology, and of the initial density fluctuation spectrum, which correctly disentangles the effects of all these factors and halo environments. We also find that the concentration of a halo is strongly correlated with the universe age when its progenitor on the mass accretion history first reaches 4% of its current mass. According to these correlations, we develop new empirical models for both the mass accretion histories and the concentration evolution histories of dark matter halos, and the latter can also be used to predict the mass and redshift dependence of halo concentrations. These models are accurate and universal: the same set of model parameters works well for different cosmological models and for halos of different masses at different redshifts, and in the LAMBDACDM case the model predictions match the simulation results very well even though halo mass is traced to about 0.0005 times the final mass

  17. A novel automated image analysis method for accurate adipocyte quantification

    PubMed Central

    Osman, Osman S; Selway, Joanne L; Kępczyńska, Małgorzata A; Stocker, Claire J; O’Dowd, Jacqueline F; Cawthorne, Michael A; Arch, Jonathan RS; Jassim, Sabah; Langlands, Kenneth

    2013-01-01

    Increased adipocyte size and number are associated with many of the adverse effects observed in metabolic disease states. While methods to quantify such changes in the adipocyte are of scientific and clinical interest, manual methods to determine adipocyte size are both laborious and intractable to large scale investigations. Moreover, existing computational methods are not fully automated. We, therefore, developed a novel automatic method to provide accurate measurements of the cross-sectional area of adipocytes in histological sections, allowing rapid high-throughput quantification of fat cell size and number. Photomicrographs of H&E-stained paraffin sections of murine gonadal adipose were transformed using standard image processing/analysis algorithms to reduce background and enhance edge-detection. This allowed the isolation of individual adipocytes from which their area could be calculated. Performance was compared with manual measurements made from the same images, in which adipocyte area was calculated from estimates of the major and minor axes of individual adipocytes. Both methods identified an increase in mean adipocyte size in a murine model of obesity, with good concordance, although the calculation used to identify cell area from manual measurements was found to consistently over-estimate cell size. Here we report an accurate method to determine adipocyte area in histological sections that provides a considerable time saving over manual methods. PMID:23991362

  18. 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. PMID:23856232

  19. 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

  20. Metabolic profiling of yeast culture using gas chromatography coupled with orthogonal acceleration accurate mass time-of-flight mass spectrometry: application to biomarker discovery.

    PubMed

    Kondo, Elsuida; Marriott, Philip J; Parker, Rhiannon M; Kouremenos, Konstantinos A; Morrison, Paul; Adams, Mike

    2014-01-01

    Yeast and yeast cultures are frequently used as additives in diets of dairy cows. Beneficial effects from the inclusion of yeast culture in diets for dairy mammals have been reported, and the aim of this study was to develop a comprehensive analytical method for the accurate mass identification of the 'global' metabolites in order to differentiate a variety of yeasts at varying growth stages (Diamond V XP, Yea-Sacc and Levucell). Microwave-assisted derivatization for metabolic profiling is demonstrated through the analysis of differing yeast samples developed for cattle feed, which include a wide range of metabolites of interest covering a large range of compound classes. Accurate identification of the components was undertaken using GC-oa-ToFMS (gas chromatography-orthogonal acceleration-time-of-flight mass spectrometry), followed by principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) for data reduction and biomarker discovery. Semi-quantification (fold changes in relative peak areas) was reported for metabolites identified as possible discriminative biomarkers (p-value <0.05, fold change >2), including D-ribose (four fold decrease), myo-inositol (five fold increase), L-phenylalanine (three fold increase), glucopyranoside (two fold increase), fructose (three fold increase) and threitol (three fold increase) respectively. PMID:24356230

  1. Electron Microprobe Analysis Techniques for Accurate Measurements of Apatite

    NASA Astrophysics Data System (ADS)

    Goldoff, B. A.; Webster, J. D.; Harlov, D. E.

    2010-12-01

    Apatite [Ca5(PO4)3(F, Cl, OH)] is a ubiquitous accessory mineral in igneous, metamorphic, and sedimentary rocks. The mineral contains halogens and hydroxyl ions, which can provide important constraints on fugacities of volatile components in fluids and other phases in igneous and metamorphic environments in which apatite has equilibrated. Accurate measurements of these components in apatite are therefore necessary. Analyzing apatite by electron microprobe (EMPA), which is a commonly used geochemical analytical technique, has often been found to be problematic and previous studies have identified sources of error. For example, Stormer et al. (1993) demonstrated that the orientation of an apatite grain relative to the incident electron beam could significantly affect the concentration results. In this study, a variety of alternative EMPA operating conditions for apatite analysis were investigated: a range of electron beam settings, count times, crystal grain orientations, and calibration standards were tested. Twenty synthetic anhydrous apatite samples that span the fluorapatite-chlorapatite solid solution series, and whose halogen concentrations were determined by wet chemistry, were analyzed. Accurate measurements of these samples were obtained with many EMPA techniques. One effective method includes setting a static electron beam to 10-15nA, 15kV, and 10 microns in diameter. Additionally, the apatite sample is oriented with the crystal’s c-axis parallel to the slide surface and the count times are moderate. Importantly, the F and Cl EMPA concentrations are in extremely good agreement with the wet-chemical data. We also present EMPA operating conditions and techniques that are problematic and should be avoided. J.C. Stormer, Jr. et al., Am. Mineral. 78 (1993) 641-648.

  2. 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

    2015-10-01

    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

  3. Change in body mass accurately and reliably predicts change in body water after endurance exercise.

    PubMed

    Baker, Lindsay B; Lang, James A; Kenney, W Larry

    2009-04-01

    This study tested the hypothesis that the change in body mass (DeltaBM) accurately reflects the change in total body water (DeltaTBW) after prolonged exercise. Subjects (4 men, 4 women; 22-36 year; 66 +/- 10 kg) completed 2 h of interval running (70% VO(2max)) in the heat (30 degrees C), followed by a run to exhaustion (85% VO(2max)), and then sat for a 1 h recovery period. During exercise and recovery, subjects drank fluid or no fluid to maintain their BM, increase BM by 2%, or decrease BM by 2 or 4% in separate trials. Pre- and post-experiment TBW were determined using the deuterium oxide (D(2)O) dilution technique and corrected for D(2)O lost in urine, sweat, breath vapor, and nonaqueous hydrogen exchange. The average difference between DeltaBM and DeltaTBW was 0.07 +/- 1.07 kg (paired t test, P = 0.29). The slope and intercept of the relation between DeltaBM and DeltaTBW were not significantly different from 1 and 0, respectively. The intraclass correlation coefficient between DeltaBM and DeltaTBW was 0.76, which is indicative of excellent reliability between methods. Measuring pre- to post-exercise DeltaBM is an accurate and reliable method to assess the DeltaTBW.

  4. Time-of-flight accurate mass spectrometry identification of quinoline alkaloids in honey.

    PubMed

    Rodríguez-Cabo, Tamara; Moniruzzaman, Mohammed; Rodríguez, Isaac; Ramil, María; Cela, Rafael; Gan, Siew Hua

    2015-08-01

    Time-of-flight accurate mass spectrometry (TOF-MS), following a previous chromatographic (gas or liquid chromatography) separation step, is applied to the identification and structural elucidation of quinoline-like alkaloids in honey. Both electron ionization (EI) MS and positive electrospray (ESI+) MS spectra afforded the molecular ions (M(.+) and M+H(+), respectively) of target compounds with mass errors below 5 mDa. Scan EI-MS and product ion scan ESI-MS/MS spectra permitted confirmation of the existence of a quinoline ring in the structures of the candidate compounds. Also, the observed fragmentation patterns were useful to discriminate between quinoline derivatives having the same empirical formula but different functionalities, such as aldoximes and amides. In the particular case of phenylquinolines, ESI-MS/MS spectra provided valuable clues regarding the position of the phenyl moiety attached to the quinoline ring. The aforementioned spectral information, combined with retention times matching, led to the identification of quinoline and five quinoline derivatives, substituted at carbon number 4, in honey samples. An isomer of phenyquinoline was also noticed; however, its exact structure could not be established. Liquid-liquid microextraction and gas chromatography (GC) TOF-MS were applied to the screening of the aforementioned compounds in a total of 62 honeys. Species displaying higher occurrence frequencies were 4-quinolinecarbonitrile, 4-quinolinecarboxaldehyde, 4-quinolinealdoxime, and the phenylquinoline isomer. The Pearson test revealed strong correlations among the first three compounds. PMID:26041455

  5. 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

    2016-08-01

    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.

  6. 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.

  7. Accurate evolutions of inspiralling and magnetized neutron stars: Equal-mass binaries

    SciTech Connect

    Giacomazzo, Bruno; Rezzolla, Luciano; Baiotti, Luca

    2011-02-15

    By performing new, long and numerically accurate general-relativistic simulations of magnetized, equal-mass neutron-star binaries, we investigate the role that realistic magnetic fields may have in the evolution of these systems. In particular, we study the evolution of the magnetic fields and show that they can influence the survival of the hypermassive neutron star produced at the merger by accelerating its collapse to a black hole. We also provide evidence that, even if purely poloidal initially, the magnetic fields produced in the tori surrounding the black hole have toroidal and poloidal components of equivalent strength. When estimating the possibility that magnetic fields could have an impact on the gravitational-wave signals emitted by these systems either during the inspiral or after the merger, we conclude that for realistic magnetic-field strengths B < or approx. 10{sup 12} G such effects could be detected, but only marginally, by detectors such as advanced LIGO or advanced Virgo. However, magnetically induced modifications could become detectable in the case of small-mass binaries and with the development of gravitational-wave detectors, such as the Einstein Telescope, with much higher sensitivities at frequencies larger than {approx_equal}2 kHz.

  8. 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

  9. 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

    2016-08-01

    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. PMID:27166662

  10. Accurate assessment of mass, models and resolution by small-angle scattering

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2013-01-01

    Modern small angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS based models and resolution have been inadequate. Here, we define the volume-of-correlation, Vc: a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, yet independent of concentration and the requirements of a compact, folded particle. We show Vc defines a ratio, Qr, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kDa. Furthermore, we propose a statistically robust method for assessing model-data agreements (X2free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, Rsas, for quantitative evaluation of resolution. Together, these metrics (Vc, Qr, X2free, and Rsas) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution. PMID:23619693

  11. High resolution/accurate mass (HRMS) detection of anatoxin-a in lake water using LDTD-APCI coupled to a Q-Exactive mass spectrometer.

    PubMed

    Roy-Lachapelle, Audrey; Solliec, Morgan; Sinotte, Marc; Deblois, Christian; Sauvé, Sébastien

    2015-01-01

    A new innovative analytical method combining ultra-fast analysis time with high resolution/accurate mass detection was developed to eliminate the misidentification of anatoxin-a (ANA-a), a cyanobacterial toxin, from the natural amino acid phenylalanine (PHE). This was achieved by using the laser diode thermal desorption-atmospheric pressure chemical ionization (LDTD-APCI) coupled to the Q-Exactive, a high resolution/accurate mass spectrometer (HRMS). This novel combination, the LDTD-APCI-HRMS, allowed for an ultra-fast analysis time (<15 s/sample). A comparison of two different acquisition modes (full scan and targeted ion fragmentation) was made to determine the most rigorous analytical method using the LDTD-APCI interface. Method development focused toward selectivity and sensitivity improvement to reduce the possibility of false positives and to lower detection limits. The Q-Exactive mass spectrometer operates with resolving powers between 17500 and 140000 FWHM (m/z 200). Nevertheless, a resolution of 17500FWHM is enough to dissociate ANA-a and PHE signals. Mass accuracy was satisfactory with values below 1 ppm reaching precision to the fourth decimal. Internal calibration with standard addition was achieved with the isotopically-labeled (D5) phenylalanine with good linearity (R(2)>0.999). Enhancement of signal to noise ratios relative to a standard triple-quadrupole method was demonstrated with lower detection and quantification limit values of 0.2 and 0.6 μg/L using the Q-Exactive. Accuracy and interday/intraday relative standard deviations were below 15%. The new method was applied to 8 different lake water samples with signs of cyanobacterial blooms. This work demonstrates the possibility of using an ultra-fast LDTD-APCI sample introduction system with an HRMS hybrid instrument for quantitative purposes with high selectivity in complex environmental matrices.

  12. Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data

    SciTech Connect

    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

    2010-10-15

    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, and 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 and multiple charge states of it in an MS scan to determine precursor mass. By combining the synergistic features of each of method, iPE MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. iPE MMR also allows incorporating additional data processing step(s) or skipping step(s), if necessary, to enable new developments or applications of the tools, as each step of iPE MMR produces output data in a common and conventional format used in proteomics data processing.

  13. 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.

  14. STELLAR MASS-TO-LIGHT RATIOS FROM GALAXY SPECTRA: HOW ACCURATE CAN THEY BE?

    SciTech Connect

    Gallazzi, Anna; Bell, Eric F. E-mail: ericbell@umich.edu

    2009-12-01

    Stellar masses play a crucial role in the exploration of galaxy properties and the evolution of the galaxy population. In this paper, we explore the minimum possible uncertainties in stellar mass-to-light ratios (M {sub *}/L) from the assumed star formation history (SFH) and metallicity distribution, with the goals of providing a minimum set of requirements for observational studies. We use a large Monte Carlo library of SFHs to study as a function of galaxy spectral type and signal-to-noise ratio (S/N) the statistical uncertainties of M {sub *}/L values using either absorption-line data or broadband colors. The accuracy of M {sub *}/L estimates can be significantly improved by using metal-sensitive indices in combination with age-sensitive indices, in particular for galaxies with intermediate-age or young stellar populations. While M {sub *}/L accuracy clearly depends on the spectral S/N, there is no significant gain in improving the S/N much above 50 pixel{sup -1} and limiting uncertainties of {approx}0.03 dex are reached. Assuming that dust is accurately corrected or absent and that the redshift is known, color-based M {sub *}/L estimates are only slightly more uncertain than spectroscopic estimates (at comparable spectroscopic and photometric quality), but are more easily affected by systematic biases. This is the case in particular for galaxies with bursty SFHs (high H{delta} {sub A} at fixed D4000 {sub n}), the M {sub *}/L of which cannot be constrained any better than {approx}0.15 dex with any indicators explored here. Finally, we explore the effects of the assumed prior distribution in SFHs and metallicity, finding them to be higher for color-based estimates.

  15. Accurate and precise measurement of selenium by instrumental neutron activation analysis.

    PubMed

    Kim, In Jung; Watson, Russell P; Lindstrom, Richard M

    2011-05-01

    An accurate and precise measurement of selenium in Standard Reference Material (SRM) 3149, a primary calibration standard for the quantitative determination of selenium, has been accomplished by instrumental neutron activation analysis (INAA) in order to resolve a question arising during the certification process of the standard. Each limiting factor of the uncertainty in the activation analysis, including the sample preparation, irradiation, and γ-ray spectrometry steps, has been carefully monitored to minimize the uncertainty in the determined mass fraction. Neutron and γ-ray self-shielding within the elemental selenium INAA standards contributed most significantly to the uncertainty of the measurement. An empirical model compensating for neutron self-shielding and reducing the self-shielding uncertainty was successfully applied to these selenium standards. The mass fraction of selenium in the new lot of SRM 3149 was determined with a relative standard uncertainty of 0.6%.

  16. Toward an Accurate Prediction of the Arrival Time of Geomagnetic-Effective Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Shi, T.; Wang, Y.; Wan, L.; Cheng, X.; Ding, M.; Zhang, J.

    2015-12-01

    Accurately predicting the arrival of coronal mass ejections (CMEs) to the Earth based on remote images is of critical significance for the study of space weather. Here we make a statistical study of 21 Earth-directed CMEs, specifically exploring the relationship between CME initial speeds and transit times. The initial speed of a CME is obtained by fitting the CME with the Graduated Cylindrical Shell model and is thus free of projection effects. We then use the drag force model to fit results of the transit time versus the initial speed. By adopting different drag regimes, i.e., the viscous, aerodynamics, and hybrid regimes, we get similar results, with a least mean estimation error of the hybrid model of 12.9 hr. CMEs with a propagation angle (the angle between the propagation direction and the Sun-Earth line) larger than their half-angular widths arrive at the Earth with an angular deviation caused by factors other than the radial solar wind drag. The drag force model cannot be reliably applied to such events. If we exclude these events in the sample, the prediction accuracy can be improved, i.e., the estimation error reduces to 6.8 hr. This work suggests that it is viable to predict the arrival time of CMEs to the Earth based on the initial parameters with fairly good accuracy. Thus, it provides a method of forecasting space weather 1-5 days following the occurrence of CMEs.

  17. Progress toward accurate high spatial resolution actinide analysis by EPMA

    NASA Astrophysics Data System (ADS)

    Jercinovic, M. J.; Allaz, J. M.; Williams, M. L.

    2010-12-01

    High precision, high spatial resolution EPMA of actinides is a significant issue for geochronology, resource geochemistry, and studies involving the nuclear fuel cycle. Particular interest focuses on understanding of the behavior of Th and U in the growth and breakdown reactions relevant to actinide-bearing phases (monazite, zircon, thorite, allanite, etc.), and geochemical fractionation processes involving Th and U in fluid interactions. Unfortunately, the measurement of minor and trace concentrations of U in the presence of major concentrations of Th and/or REEs is particularly problematic, especially in complexly zoned phases with large compositional variation on the micro or nanoscale - spatial resolutions now accessible with modern instruments. Sub-micron, high precision compositional analysis of minor components is feasible in very high Z phases where scattering is limited at lower kV (15kV or less) and where the beam diameter can be kept below 400nm at high current (e.g. 200-500nA). High collection efficiency spectrometers and high performance electron optics in EPMA now allow the use of lower overvoltage through an exceptional range in beam current, facilitating higher spatial resolution quantitative analysis. The U LIII edge at 17.2 kV precludes L-series analysis at low kV (high spatial resolution), requiring careful measurements of the actinide M series. Also, U-La detection (wavelength = 0.9A) requires the use of LiF (220) or (420), not generally available on most instruments. Strong peak overlaps of Th on U make highly accurate interference correction mandatory, with problems compounded by the ThMIV and ThMV absorption edges affecting peak, background, and interference calibration measurements (especially the interference of the Th M line family on UMb). Complex REE bearing phases such as monazite, zircon, and allanite have particularly complex interference issues due to multiple peak and background overlaps from elements present in the activation

  18. 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.

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

    PubMed

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

    2016-08-01

    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 .

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

    PubMed

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

    2016-08-01

    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 . PMID:27397138

  1. Development and evaluation of a liquid chromatography-mass spectrometry method for rapid, accurate quantitation of malondialdehyde in human plasma.

    PubMed

    Sobsey, Constance A; Han, Jun; Lin, Karen; Swardfager, Walter; Levitt, Anthony; Borchers, Christoph H

    2016-09-01

    Malondialdhyde (MDA) is a commonly used marker of lipid peroxidation in oxidative stress. To provide a sensitive analytical method that is compatible with high throughput, we developed a multiple reaction monitoring-mass spectrometry (MRM-MS) approach using 3-nitrophenylhydrazine chemical derivatization, isotope-labeling, and liquid chromatography (LC) with electrospray ionization (ESI)-tandem mass spectrometry assay to accurately quantify MDA in human plasma. A stable isotope-labeled internal standard was used to compensate for ESI matrix effects. The assay is linear (R(2)=0.9999) over a 20,000-fold concentration range with a lower limit of quantitation of 30fmol (on-column). Intra- and inter-run coefficients of variation (CVs) were <2% and ∼10% respectively. The derivative was stable for >36h at 5°C. Standards spiked into plasma had recoveries of 92-98%. When compared to a common LC-UV method, the LC-MS method found near-identical MDA concentrations. A pilot project to quantify MDA in patient plasma samples (n=26) in a study of major depressive disorder with winter-type seasonal pattern (MDD-s) confirmed known associations between MDA concentrations and obesity (p<0.02). The LC-MS method provides high sensitivity and high reproducibility for quantifying MDA in human plasma. The simple sample preparation and rapid analysis time (5x faster than LC-UV) offers high throughput for large-scale clinical applications. PMID:27437618

  2. Crux: rapid open source protein tandem mass spectrometry analysis.

    PubMed

    McIlwain, Sean; Tamura, Kaipo; Kertesz-Farkas, Attila; Grant, Charles E; Diament, Benjamin; Frewen, Barbara; Howbert, J Jeffry; Hoopmann, Michael R; Käll, Lukas; Eng, Jimmy K; MacCoss, Michael J; Noble, William Stafford

    2014-10-01

    Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit ( http://cruxtoolkit.sourceforge.net ) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

  3. THE EFFECT OF STARSPOTS ON ACCURATE RADIUS DETERMINATION OF THE LOW-MASS DOUBLE-LINED ECLIPSING BINARY GU Boo

    SciTech Connect

    Windmiller, G.; Orosz, J. A.; Etzel, P. B. E-mail: orosz@sciences.sdsu.ed

    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. Lopez-Morales and Ribas present a comprehensive analysis of multi-color light and radial velocity curves for this system. The GU Boo light curves presented by Lopez-Morales and Ribas had substantial asymmetries, which were attributed to large spots. In spite of the asymmetry, Lopez-Morales and Ribas derived masses and radii accurate to {approx_equal}2%. 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 Lopez-Morales and Ribas using models with and without spots. We derived a radius of the primary of 0.6329 +- 0.0026 R{sub sun}, 0.6413 +- 0.0049 R{sub sun}, and 0.6373 +- 0.0029 R{sub sun} from the CCD, photoelectric, and Lopez-Morales and Ribas data, respectively. Each of these measurements agrees with the value reported by Lopez-Morales and Ribas (R{sub 1} = 0.623 +- 0.016 R{sub sun}) at the level of {approx}2%. In addition, the spread in these values is {approx}1%-2% from the mean. For the secondary, we derive radii of 0.6074 +- 0.0035 R{sub sun}, 0.5944 +- 0.0069 R{sub sun}, and 0.5976 +- 0.0059 R{sub sun} from the three respective data sets. The Lopez-Morales and Ribas value is R{sub 2} = 0.620 +- 0.020 R{sub sun}, which is {approx}2%-3% larger than each of the three values we found. The spread in these values is {approx}2% from the mean. The systematic difference between our three determinations of the secondary radius and that of Lopez-Morales and 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

  4. Accurate screening for synthetic preservatives in beverage using high performance liquid chromatography with time-of-flight mass spectrometry.

    PubMed

    Li, Xiu Qin; Zhang, Feng; Sun, Yan Yan; Yong, Wei; Chu, Xiao Gang; Fang, Yan Yan; Zweigenbaum, Jerry

    2008-02-11

    In this study, liquid chromatography time-of-flight mass spectrometry (HPLC/TOF-MS) is applied to qualitation and quantitation of 18 synthetic preservatives in beverage. The identification by HPLC/TOF-MS is accomplished with the accurate mass (the subsequent generated empirical formula) of the protonated molecules [M+H]+ or the deprotonated molecules [M-H]-, along with the accurate mass of their main fragment ions. In order to obtain sufficient sensitivity for quantitation purposes (using the protonated or deprotonated molecule) and additional qualitative mass spectrum information provided by the fragments ions, segment program of fragmentor voltages is designed in positive and negative ion mode, respectively. Accurate mass measurements are highly useful in the complex sample analyses since they allow us to achieve a high degree of specificity, often needed when other interferents are present in the matrix. The mass accuracy typically obtained is routinely better than 3 ppm. The 18 compounds behave linearly in the 0.005-5.0mg.kg(-1) concentration range, with correlation coefficient >0.996. The recoveries at the tested concentrations of 1.0mg.kg(-1)-100mg.kg(-1) are 81-106%, with coefficients of variation <7.5%. Limits of detection (LODs) range from 0.0005 to 0.05 mg.kg(-1), which are far below the required maximum residue level (MRL) for these preservatives in foodstuff. The method is suitable for routine quantitative and qualitative analyses of synthetic preservatives in foodstuff.

  5. Enhancing accurate data collection in mass fatality kinship identifications: lessons learned from Hurricane Katrina.

    PubMed

    Donkervoort, Sandra; Dolan, Siobhan M; Beckwith, Michelle; Northrup, Tammy Pruet; Sozer, Amanda

    2008-09-01

    A mass fatality DNA identification effort is a complex process in which direct matching and kinship analysis is used for identifying human remains. Kinship DNA identification is an important tool in the identification process in which victim's DNA profiles are compared to the profiles of "known" biologically related reference samples. Experience from the 9/11 World Trade Center DNA identification efforts showed that forms used to record biological relationships are important and that inaccurately documented information may hamper the kinship analysis and DNA identification process. In the identification efforts following Hurricane Katrina, a Family and/or Donor Reference Collection (FDRC) form was used as a means to document the reported relationship between the reference DNA donor and the purported missing individual. This FDRC form was developed based upon lessons learned from 9/11 and the Tsunami identification efforts. This paper analyses the effectiveness of the FDRC form used in the Hurricane Katrina kinship DNA identification efforts and proposes an improved sample collection form for kinship and other donor reference samples. The data presented can be used to enhance the accuracy of the data collection process through an improved sample collection form, streamlining the DNA kinship identification process and decreasing the burden on valuable resources.

  6. 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.

  7. Accurate determination of selected pesticides in soya beans by liquid chromatography coupled to isotope dilution mass spectrometry.

    PubMed

    Huertas Pérez, J F; Sejerøe-Olsen, B; Fernández Alba, A R; Schimmel, H; Dabrio, M

    2015-05-01

    A sensitive, accurate and simple liquid chromatography coupled with mass spectrometry method for the determination of 10 selected pesticides in soya beans has been developed and validated. The method is intended for use during the characterization of selected pesticides in a reference material. In this process, high accuracy and appropriate uncertainty levels associated to the analytical measurements are of utmost importance. The analytical procedure is based on sample extraction by the use of a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction and subsequent clean-up of the extract with C18, PSA and Florisil. Analytes were separated on a C18 column using gradient elution with water-methanol/2.5 mM ammonium acetate mobile phase, and finally identified and quantified by triple quadrupole mass spectrometry in the multiple reaction monitoring mode (MRM). Reliable and accurate quantification of the analytes was achieved by means of stable isotope-labelled analogues employed as internal standards (IS) and calibration with pure substance solutions containing both, the isotopically labelled and native compounds. Exceptions were made for thiodicarb and malaoxon where the isotopically labelled congeners were not commercially available at the time of analysis. For the quantification of those compounds methomyl-(13)C2(15)N and malathion-D10 were used respectively. The method was validated according to the general principles covered by DG SANCO guidelines. However, validation criteria were set more stringently. Mean recoveries were in the range of 86-103% with RSDs lower than 8.1%. Repeatability and intermediate precision were in the range of 3.9-7.6% and 1.9-8.7% respectively. LODs were theoretically estimated and experimentally confirmed to be in the range 0.001-0.005 mg kg(-1) in the matrix, while LOQs established as the lowest spiking mass fractionation level were in the range 0.01-0.05 mg kg(-1). The method reliably identifies and quantifies the

  8. 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

  9. Accurate stellar masses for SB2 components: Interferometric observations for Gaia validation

    NASA Astrophysics Data System (ADS)

    Halbwachs, J.-L.; Boffin, H. M. J.; Le Bouquin, J.-B.; Famaey, B.; Salomon, J.-B.; Arenou, F.; Pourbaix, D.; Anthonioz, F.; Grellmann, R.; Guieu, S.; Guillout, P.; Jorissen, A.; Kiefer, F.; Lebreton, Y.; Mazeh, T.; Nebot Gómez-Morán, A.; Sana, H.; Tal-Or, L.

    2015-12-01

    A sample of about 70 double-lined spectroscopic binaries (SB2) is followed with radial velocity (RV) measurements, in order to derive the masses of their components when the astrometric measurements of Gaia will be available. A subset of 6 SB2 was observed in interferometry with VLTI/PIONIER, and the components were separated for each binary. The RV measurements already obtained were combined with the interferometric observations and the masses of the components were derived. The accuracies of the 12 masses are presently between 0.4 and 7 %, but they will still be improved in the future. These masses will be used to validate the masses which will be obtained from Gaia. In addition, the parallaxes derived from the combined visual+spectroscopic orbits are compared to that of Hipparcos, and a mass-luminosity relation is derived in the infrared H band.

  10. Improvements in Accurate GPS Positioning Using Time Series Analysis

    NASA Astrophysics Data System (ADS)

    Koyama, Yuichiro; Tanaka, Toshiyuki

    Although the Global Positioning System (GPS) is used widely in car navigation systems, cell phones, surveying, and other areas, several issues still exist. We focus on the continuous data received in public use of GPS, and propose a new positioning algorithm that uses time series analysis. By fitting an autoregressive model to the time series model of the pseudorange, we propose an appropriate state-space model. We apply the Kalman filter to the state-space model and use the pseudorange estimated by the filter in our positioning calculations. The results of the authors' positioning experiment show that the accuracy of the proposed method is much better than that of the standard method. In addition, as we can obtain valid values estimated by time series analysis using the state-space model, the proposed state-space model can be applied to several other fields.

  11. Accurate feature detection and estimation using nonlinear and multiresolution analysis

    NASA Astrophysics Data System (ADS)

    Rudin, Leonid; Osher, Stanley

    1994-11-01

    A program for feature detection and estimation using nonlinear and multiscale analysis was completed. The state-of-the-art edge detection was combined with multiscale restoration (as suggested by the first author) and robust results in the presence of noise were obtained. Successful applications to numerous images of interest to DOD were made. Also, a new market in the criminal justice field was developed, based in part, on this work.

  12. Reduction procedures for accurate analysis of MSX surveillance experiment data

    NASA Technical Reports Server (NTRS)

    Gaposchkin, E. Mike; Lane, Mark T.; Abbot, Rick I.

    1994-01-01

    Technical challenges of the Midcourse Space Experiment (MSX) science instruments require careful characterization and calibration of these sensors for analysis of surveillance experiment data. Procedures for reduction of Resident Space Object (RSO) detections will be presented which include refinement and calibration of the metric and radiometric (and photometric) data and calculation of a precise MSX ephemeris. Examples will be given which support the reduction, and these are taken from ground-test data similar in characteristics to the MSX sensors and from the IRAS satellite RSO detections. Examples to demonstrate the calculation of a precise ephemeris will be provided from satellites in similar orbits which are equipped with S-band transponders.

  13. An experimental correction proposed for an accurate determination of mass diffusivity of wood in steady regime

    NASA Astrophysics Data System (ADS)

    Zohoun, Sylvain; Agoua, Eusèbe; Degan, Gérard; Perre, Patrick

    2002-08-01

    This paper presents an experimental study of the mass diffusion in the hygroscopic region of four temperate species and three tropical ones. In order to simplify the interpretation of the phenomena, a dimensionless parameter called reduced diffusivity is defined. This parameter varies from 0 to 1. The method used is firstly based on the determination of that parameter from results of the measurement of the mass flux which takes into account the conditions of operating standard device (tightness, dimensional variations and easy installation of samples of wood, good stability of temperature and humidity). Secondly the reasons why that parameter has to be corrected are presented. An abacus for this correction of mass diffusivity of wood in steady regime has been plotted. This work constitutes an advanced deal nowadays for characterising forest species.

  14. Active contour approach for accurate quantitative airway analysis

    NASA Astrophysics Data System (ADS)

    Odry, Benjamin L.; Kiraly, Atilla P.; Slabaugh, Greg G.; Novak, Carol L.; Naidich, David P.; Lerallut, Jean-Francois

    2008-03-01

    Chronic airway disease causes structural changes in the lungs including peribronchial thickening and airway dilatation. Multi-detector computed tomography (CT) yields detailed near-isotropic images of the lungs, and thus the potential to obtain quantitative measurements of lumen diameter and airway wall thickness. Such measurements would allow standardized assessment, and physicians to diagnose and locate airway abnormalities, adapt treatment, and monitor progress over time. However, due to the sheer number of airways per patient, systematic analysis is infeasible in routine clinical practice without automation. We have developed an automated and real-time method based on active contours to estimate both airway lumen and wall dimensions; the method does not require manual contour initialization but only a starting point on the targeted airway. While the lumen contour segmentation is purely region-based, the estimation of the outer diameter considers the inner wall segmentation as well as local intensity variation, in order anticipate the presence of nearby arteries and exclude them. These properties make the method more robust than the Full-Width Half Maximum (FWHM) approach. Results are demonstrated on a phantom dataset with known dimensions and on a human dataset where the automated measurements are compared against two human operators. The average error on the phantom measurements was 0.10mm and 0.14mm for inner and outer diameters, showing sub-voxel accuracy. Similarly, the mean variation from the average manual measurement was 0.14mm and 0.18mm for inner and outer diameters respectively.

  15. ACCURATE MASSES FOR THE PRIMARY AND SECONDARY IN THE ECLIPSING WHITE DWARF BINARY NLTT 11748

    SciTech Connect

    Kilic, Mukremin; Brown, Warren R.; Kenyon, S. J.; Allende Prieto, Carlos; Agueeros, M. A.; Camilo, Fernando

    2010-10-01

    We measure the radial velocity curve of the eclipsing detached white dwarf binary NLTT 11748. The primary exhibits velocity variations with a semi-amplitude of 273 km s{sup -1} and an orbital period of 5.641 hr. We do not detect any spectral features from the secondary star or any spectral changes during the secondary eclipse. We use our composite spectrum to constrain the temperature and surface gravity of the primary to be T {sub eff} = 8690 {+-} 140 K and log g = 6.54 {+-} 0.05, which correspond to a mass of 0.18 M {sub sun}. For an inclination angle of 89.{sup 0}9 derived from the eclipse modeling, the mass function requires a 0.76 M {sub sun} companion. The merger time for the system is 7.2 Gyr. However, due to the extreme mass ratio of 0.24, the binary will most likely create an AM CVn system instead of a merger.

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

    PubMed

    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 ((2)A2), 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(2v) symmetry through the C-N axis.

  17. 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.

  18. How Accurate Is the Science News We Receive from the Mass Media?

    ERIC Educational Resources Information Center

    Molitor, Fred

    One day before a health study appeared in the "New England Journal of Medicine (NEJM)" the study was reported media. A content analysis of the top 5 national newspapers examined the accuracy of this news reporting. The NEJM study found that men who took aspirin had 50% fewer heart attacks than men who received a placebo. Analysis of the original…

  19. Accurate mass measurements of short-lived isotopes with the MISTRAL* rf spectrometer

    SciTech Connect

    Toader, C.; Audi, G.; Doubre, H.; Jacotin, M.; Henry, S.; Kepinski, J.-F.; Le Scornet, G.; Lunney, D.; Monsanglant, C.; Saint Simon, M. de; Thibault, C.; Borcea, C.; Duma, M.; Lebee, G.

    1999-01-15

    The MISTRAL* experiment has measured its first masses at ISOLDE. Installed in May 1997, this radiofrequency transmission spectrometer is to concentrate on nuclides with particularly short half-lives. MISTRAL received its first stable beam in October and first radioactive beam in November 1997. These first tests, with a plasma ion source, resulted in excellent isobaric separation and reasonable transmission. Further testing and development enabled first data taking in July 1998 on neutron-rich Na isotopes having half-lives as short as 31 ms.

  20. 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.

  1. Assessment of gas chromatography time-of-flight accurate mass spectrometry for identification of volatile and semi-volatile compounds in honey.

    PubMed

    Moniruzzaman, M; Rodríguez, I; Ramil, M; Cela, R; Sulaiman, S A; Gan, S H

    2014-11-01

    The performance of gas chromatography (GC) combined with a hybrid quadrupole time-of-flight (QTOF) mass spectrometry (MS) system for the determination of volatile and semi-volatile compounds in honey samples is evaluated. After headspace (HS) solid-phase microextraction (SPME) of samples, the accurate mass capabilities of the above system were evaluated for compounds identification. Accurate scan electron impact (EI) MS spectra allowed discriminating compounds displaying the same nominal masses, but having different empirical formulae. Moreover, the use of a mass window with a width of 0.005 Da provided highly specific chromatograms for selected ions, avoiding the contribution of interferences to their peak areas. Additional information derived from positive chemical ionization (PCI) MS spectra and ion product scan MS/MS spectra permitted confirming the identity of novel compounds. The above possibilities are illustrated with examples of honey aroma compounds, belonging to different chemical classes and containing different elements in their molecules. Examples of compounds whose structures could not be described are also provided. Overall, 84 compounds, from a total of 89 species, could be identified in 19 honey samples from 3 different geographic areas in the world. The suitability of responses measured for selected ions, corresponding to above species, for authentication purposes is assessed through principal components analysis. PMID:25127626

  2. Accurate mass screening of pharmaceuticals and fungicides in water by U-HPLC-Exactive Orbitrap MS.

    PubMed

    Chitescu, Carmen Lidia; Oosterink, Efraim; de Jong, Jacob; Linda Stolker, Alida Adriana Maria

    2012-07-01

    The use of pharmaceuticals in livestock production is a potential source of surface water, groundwater and soil contamination. Possible impacts of antibiotics on the environment include toxicity and the emergence of antibiotic resistance. Monitoring programs are required to record the presence of these substances in the environment. A rapid, versatile and selective multi-method was developed and validated for screening 43 pharmaceutical and fungicides compounds, in surface and groundwater, in one single full-scan MS method, using benchtop U-HPLC-Exactive Orbitrap MS at 50,000 (FWHM) resolution. Detection was based on calculated exact masses and on retention time. Sample volume, pH conditions and solid-phase extraction (SPE) sample clean-up conditions were optimized. In the final method, 74 % of the compounds had recoveries higher than 80 %, 15 % of the compounds had recoveries between 60 % and 80 %, and 7 % of the compounds had recoveries between 40 % and 50 %. One of the compounds (itraconazole) had a recovery lower than 10 % and nystatin was not detected. The level of detection was 10 ng L(-1) for 61 % of the compounds, 50 ng L(-1) for 32 % and 100 ng L(-1) for 5%. In-house validation, based on EU guidelines, proves that the detection capability CCβ is lower than 10 ng L(-1) (for β error 5 %) for 37 % of the compounds, lower than 50 ng L(-1) for 35 % of the compounds and lower than 100 ng L(-1) for 14 % of compounds. This study demonstrates that the ultra-high resolution and reliable mass accuracy of Exactive Orbitrap MS permits the detection of pharmaceutical residues in a concentration range of 10-100 ng L(-1), applying a post target screening approach, in the multi-method conditions.

  3. A feasibility study of UHPLC-HRMS accurate-mass screening methods for multiclass testing of organic contaminants in food.

    PubMed

    Pérez-Ortega, Patricia; Lara-Ortega, Felipe J; García-Reyes, Juan F; Gilbert-López, Bienvenida; Trojanowicz, Marek; Molina-Díaz, Antonio

    2016-11-01

    The feasibility of accurate-mass multi-residue screening methods using liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) using time-of-flight mass spectrometry has been evaluated, including over 625 multiclass food contaminants as case study. Aspects such as the selectivity and confirmation capability provided by HRMS with different acquisition modes (full-scan or full-scan combined with collision induced dissociation (CID) with no precursor ion isolation), and chromatographic separation along with main limitations such as sensitivity or automated data processing have been examined. Compound identification was accomplished with retention time matching and accurate mass measurements of the targeted ions for each analyte (mainly (de)protonated molecules). Compounds with the same nominal mass (isobaric species) were very frequent due to the large number of compounds included. Although 76% of database compounds were involved in isobaric groups, they were resolved in most cases (99% of these isobaric species were distinguished by retention time, resolving power, isotopic profile or fragment ions). Only three pairs could not be resolved with these tools. In-source CID fragmentation was evaluated in depth, although the results obtained in terms of information provided were not as thorough as those obtained using fragmentation experiments without precursor ion isolation (all ion mode). The latter acquisition mode was found to be the best suited for this type of large-scale screening method instead of classic product ion scan, as provided excellent fragmentation information for confirmatory purposes for an unlimited number of compounds. Leaving aside the sample treatment limitations, the main weaknesses noticed are basically the relatively low sensitivity for compounds which does not map well against electrospray ionization and also quantitation issues such as those produced by signal suppression due to either matrix effects from coeluting matrix or from

  4. A feasibility study of UHPLC-HRMS accurate-mass screening methods for multiclass testing of organic contaminants in food.

    PubMed

    Pérez-Ortega, Patricia; Lara-Ortega, Felipe J; García-Reyes, Juan F; Gilbert-López, Bienvenida; Trojanowicz, Marek; Molina-Díaz, Antonio

    2016-11-01

    The feasibility of accurate-mass multi-residue screening methods using liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) using time-of-flight mass spectrometry has been evaluated, including over 625 multiclass food contaminants as case study. Aspects such as the selectivity and confirmation capability provided by HRMS with different acquisition modes (full-scan or full-scan combined with collision induced dissociation (CID) with no precursor ion isolation), and chromatographic separation along with main limitations such as sensitivity or automated data processing have been examined. Compound identification was accomplished with retention time matching and accurate mass measurements of the targeted ions for each analyte (mainly (de)protonated molecules). Compounds with the same nominal mass (isobaric species) were very frequent due to the large number of compounds included. Although 76% of database compounds were involved in isobaric groups, they were resolved in most cases (99% of these isobaric species were distinguished by retention time, resolving power, isotopic profile or fragment ions). Only three pairs could not be resolved with these tools. In-source CID fragmentation was evaluated in depth, although the results obtained in terms of information provided were not as thorough as those obtained using fragmentation experiments without precursor ion isolation (all ion mode). The latter acquisition mode was found to be the best suited for this type of large-scale screening method instead of classic product ion scan, as provided excellent fragmentation information for confirmatory purposes for an unlimited number of compounds. Leaving aside the sample treatment limitations, the main weaknesses noticed are basically the relatively low sensitivity for compounds which does not map well against electrospray ionization and also quantitation issues such as those produced by signal suppression due to either matrix effects from coeluting matrix or from

  5. An improved method for accurate prediction of mass flows through combustor liner holes

    SciTech Connect

    Adkins, R.C.; Gueroui, D.

    1986-01-01

    The objective of this paper is to present a simple approach to the solution of flow through combustor liner holes which can be used by practicing combustor engineers as well as providing the specialist modeler with a convenient boundary condition. For modeling, suppose that all relevant details of the incoming jets can be readily predicted, then the computational boundary can be limited to the inner wall of the liner and to the jets themselves. The scope of this paper is limited to the derivation of a simple analysis, the development of a reliable test technique, and to the correlation of data for plane holes having a diameter which is large when compared to the liner wall thickness. The effect of internal liner flow on the performance of the holes is neglected; this is considered to be justifiable because the analysis terminates at a short distance downstream of the hole and the significantly lower velocities inside the combustor have had little opportunity to have taken any effect. It is intended to extend the procedure to more complex hole forms and flow configurations in later papers.

  6. 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.

  7. A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry

    PubMed Central

    Hong, Sun Pyo; Ji, Seung Il; Rhee, Hwanseok; Shin, Soo Kyeong; Hwang, Sun Young; Lee, Seung Hwan; Lee, Soong Deok; Oh, Heung-Bum; Yoo, Wangdon; Kim, Soo-Ok

    2008-01-01

    Background We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS. Results The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing. Conclusion The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories. PMID:18538037

  8. 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

  9. Mass Spectrometry-based Workflow for Accurate Quantification of Escherichia coli Enzymes: How Proteomics Can Play a Key Role in Metabolic Engineering*

    PubMed Central

    Trauchessec, Mathieu; Jaquinod, Michel; Bonvalot, Aline; Brun, Virginie; Bruley, Christophe; Ropers, Delphine; de Jong, Hidde; Garin, Jérôme; Bestel-Corre, Gwenaëlle; Ferro, Myriam

    2014-01-01

    Metabolic engineering aims to design high performance microbial strains producing compounds of interest. This requires systems-level understanding; genome-scale models have therefore been developed to predict metabolic fluxes. However, multi-omics data including genomics, transcriptomics, fluxomics, and proteomics may be required to model the metabolism of potential cell factories. Recent technological advances to quantitative proteomics have made mass spectrometry-based quantitative assays an interesting alternative to more traditional immuno-affinity based approaches. This has improved specificity and multiplexing capabilities. In this study, we developed a quantification workflow to analyze enzymes involved in central metabolism in Escherichia coli (E. coli). This workflow combined full-length isotopically labeled standards with selected reaction monitoring analysis. First, full-length 15N labeled standards were produced and calibrated to ensure accurate measurements. Liquid chromatography conditions were then optimized for reproducibility and multiplexing capabilities over a single 30-min liquid chromatography-MS analysis. This workflow was used to accurately quantify 22 enzymes involved in E. coli central metabolism in a wild-type reference strain and two derived strains, optimized for higher NADPH production. In combination with measurements of metabolic fluxes, proteomics data can be used to assess different levels of regulation, in particular enzyme abundance and catalytic rate. This provides information that can be used to design specific strains used in biotechnology. In addition, accurate measurement of absolute enzyme concentrations is key to the development of predictive kinetic models in the context of metabolic engineering. PMID:24482123

  10. 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

  11. Fast and accurate procedure for the determination of Cr(VI) in solid samples by isotope dilution mass spectrometry.

    PubMed

    Fabregat-Cabello, Neus; Rodríguez-González, Pablo; Castillo, Ángel; Malherbe, Julien; Roig-Navarro, Antoni F; Long, Stephen E; García Alonso, J Ignacio

    2012-11-20

    We present here a new environmental measurement method for the rapid extraction and accurate quantification of Cr(VI) in solid samples. The quantitative extraction of Cr(VI) is achieved in 10 minutes by means of focused microwave assisted extraction using 50 mmol/L Ethylendiamintetraacetic acid (EDTA) at pH 10 as extractant. In addition, it enables the separation of Cr species by anion exchange chromatography using a mobile phase which is a 1:10 dilution of the extracting solution. Thus, neutralization or acidification steps which are prone to cause interconversion of Cr species are not needed. Another benefit of using EDTA is that it allows to measure Cr(III)-EDTA complex and Cr(VI) simultaneously in an alkaline extraction solution. The application of a 10 minutes focused microwave assisted extraction (5 min at 90 °C plus 5 min at 110 °C) has been shown to quantitatively extract all forms of hexavalent chromium from the standard reference materials (SRM) candidate NIST 2700 and NIST 2701. A double spike isotope dilution mass spectrometry (IDMS) procedure was employed to study chromium interconversion reactions. It was observed that the formation of a Cr(III)-EDTA complex avoided Cr(III) oxidation for these two reference materials. Thus, the use of a double spiking strategy for quantification is not required and a single spike IDMS procedure using isotopically enriched Cr(VI) provided accurate results.

  12. Multiclass semi-volatile compounds determination in wine by gas chromatography accurate time-of-flight mass spectrometry.

    PubMed

    Rodríguez-Cabo, T; Rodríguez, I; Ramil, M; Silva, A; Cela, R

    2016-04-15

    The performance of gas chromatography (GC) with accurate, high resolution mass spectrometry (HRMS) for the determination of a group of 39 semi-volatile compounds related to wine quality (pesticide residues, phenolic off-flavours, phenolic pollutants and bioactive stilbenes) is investigated. Solid-phase extraction (SPE) was used as extraction technique, previously to acetylation (phenolic compounds) and dispersive liquid-liquid microextraction (DLLME) concentration. Compounds were determined by GC coupled to a quadrupole time-of-flight (QTOF) MS system through an electron ionization (EI) source. The final method attained limits of quantification (LOQs) at the very low ng mL(-1) level, covering the range of expected concentrations for target compounds in red and white wines. For 38 out of 39 compounds, performance of sample preparation and determination steps were hardly affected by the wine matrix; thus, accurate recoveries were achieved by using pseudo-external calibration. Levels of target compounds in a set of 25 wine samples are reported. The capabilities of the described approach for the post-run identification of species not considered during method development, without retention time information, are illustrated and discussed with selected examples of compounds from different classes.

  13. 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

  14. 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.

  15. 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. PMID:26633821

  16. 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.

  17. Galaxy And Mass Assembly (GAMA): spectroscopic analysis

    NASA Astrophysics Data System (ADS)

    Hopkins, A. M.; Driver, S. P.; Brough, S.; Owers, M. S.; Bauer, A. E.; Gunawardhana, M. L. P.; Cluver, M. E.; Colless, M.; Foster, C.; Lara-López, M. A.; Roseboom, I.; Sharp, R.; Steele, O.; Thomas, D.; Baldry, I. K.; Brown, M. J. I.; Liske, J.; Norberg, P.; Robotham, A. S. G.; Bamford, S.; Bland-Hawthorn, J.; Drinkwater, M. J.; Loveday, J.; Meyer, M.; Peacock, J. A.; Tuffs, R.; Agius, N.; Alpaslan, M.; Andrae, E.; Cameron, E.; Cole, S.; Ching, J. H. Y.; Christodoulou, L.; Conselice, C.; Croom, S.; Cross, N. J. G.; De Propris, R.; Delhaize, J.; Dunne, L.; Eales, S.; Ellis, S.; Frenk, C. S.; Graham, Alister W.; Grootes, M. W.; Häußler, B.; Heymans, C.; Hill, D.; Hoyle, B.; Hudson, M.; Jarvis, M.; Johansson, J.; Jones, D. H.; van Kampen, E.; Kelvin, L.; Kuijken, K.; López-Sánchez, Á.; Maddox, S.; Madore, B.; Maraston, C.; McNaught-Roberts, T.; Nichol, R. C.; Oliver, S.; Parkinson, H.; Penny, S.; Phillipps, S.; Pimbblet, K. A.; Ponman, T.; Popescu, C. C.; Prescott, M.; Proctor, R.; Sadler, E. M.; Sansom, A. E.; Seibert, M.; Staveley-Smith, L.; Sutherland, W.; Taylor, E.; Van Waerbeke, L.; Vázquez-Mata, J. A.; Warren, S.; Wijesinghe, D. B.; Wild, V.; Wilkins, S.

    2013-04-01

    The Galaxy And Mass Assembly (GAMA) survey is a multiwavelength photometric and spectroscopic survey, using the AAOmega spectrograph on the Anglo-Australian Telescope to obtain spectra for up to ˜300 000 galaxies over 280 deg2, to a limiting magnitude of rpet < 19.8 mag. The target galaxies are distributed over 0 < z ≲ 0.5 with a median redshift of z ≈ 0.2, although the redshift distribution includes a small number of systems, primarily quasars, at higher redshifts, up to and beyond z = 1. The redshift accuracy ranges from σv ≈ 50 km s-1 to σv ≈ 100 km s-1 depending on the signal-to-noise ratio of the spectrum. Here we describe the GAMA spectroscopic reduction and analysis pipeline. We present the steps involved in taking the raw two-dimensional spectroscopic images through to flux-calibrated one-dimensional spectra. The resulting GAMA spectra cover an observed wavelength range of 3750 ≲ λ ≲ 8850 Å at a resolution of R ≈ 1300. The final flux calibration is typically accurate to 10-20 per cent, although the reliability is worse at the extreme wavelength ends, and poorer in the blue than the red. We present details of the measurement of emission and absorption features in the GAMA spectra. These measurements are characterized through a variety of quality control analyses detailing the robustness and reliability of the measurements. We illustrate the quality of the measurements with a brief exploration of elementary emission line properties of the galaxies in the GAMA sample. We demonstrate the luminosity dependence of the Balmer decrement, consistent with previously published results, and explore further how Balmer decrement varies with galaxy mass and redshift. We also investigate the mass and redshift dependencies of the [N II]/Hα versus [O III]/Hβ spectral diagnostic diagram, commonly used to discriminate between star forming and nuclear activity in galaxies.

  18. Accurate measurement of pancreatic islet beta-cell mass using a second-generation fluorescent exendin-4 analog.

    PubMed

    Reiner, Thomas; Thurber, Greg; Gaglia, Jason; Vinegoni, Claudio; Liew, Chong Wee; Upadhyay, Rabi; Kohler, Rainer H; Li, Li; Kulkarni, Rohit N; Benoist, Christophe; Mathis, Diane; Weissleder, Ralph

    2011-08-01

    The hallmark of type 1 diabetes is autoimmune destruction of the insulin-producing β-cells of the pancreatic islets. Autoimmune diabetes has been difficult to study or treat because it is not usually diagnosed until substantial β-cell loss has already occurred. Imaging agents that permit noninvasive visualization of changes in β-cell mass remain a high-priority goal. We report on the development and testing of a near-infrared fluorescent β-cell imaging agent. Based on the amino acid sequence of exendin-4, we created a neopeptide via introduction of an unnatural amino acid at the K(12) position, which could subsequently be conjugated to fluorophores via bioorthogonal copper-catalyzed click-chemistry. Cell assays confirmed that the resulting fluorescent probe (E4(×12)-VT750) had a high binding affinity (~3 nM). Its in vivo properties were evaluated using high-resolution intravital imaging, histology, whole-pancreas visualization, and endoscopic imaging. According to intravital microscopy, the probe rapidly bound to β-cells and, as demonstrated by confocal microscopy, it was internalized. Histology of the whole pancreas showed a close correspondence between fluorescence and insulin staining, and there was an excellent correlation between imaging signals and β-cell mass in mice treated with streptozotocin, a β-cell toxin. Individual islets could also be visualized by endoscopic imaging. In short, E4(×12)-VT750 showed strong and selective binding to glucose-like peptide-1 receptors and permitted accurate measurement of β-cell mass in both diabetic and nondiabetic mice. This near-infrared imaging probe, as well as future radioisotope-labeled versions of it, should prove to be important tools for monitoring diabetes, progression, and treatment in both experimental and clinical contexts. PMID:21768367

  19. Accurate measurement of pancreatic islet β-cell mass using a second-generation fluorescent exendin-4 analog

    PubMed Central

    Reiner, Thomas; Thurber, Greg; Gaglia, Jason; Vinegoni, Claudio; Liew, Chong Wee; Upadhyay, Rabi; Kohler, Rainer H.; Kulkarni, Rohit N.; Benoist, Christophe; Mathis, Diane; Weissleder, Ralph

    2011-01-01

    The hallmark of type 1 diabetes is autoimmune destruction of the insulin-producing β-cells of the pancreatic islets. Autoimmune diabetes has been difficult to study or treat because it is not usually diagnosed until substantial β-cell loss has already occurred. Imaging agents that permit noninvasive visualization of changes in β-cell mass remain a high-priority goal. We report on the development and testing of a near-infrared fluorescent β-cell imaging agent. Based on the amino acid sequence of exendin-4, we created a neopeptide via introduction of an unnatural amino acid at the K12 position, which could subsequently be conjugated to fluorophores via bioorthogonal copper-catalyzed click-chemistry. Cell assays confirmed that the resulting fluorescent probe (E4×12-VT750) had a high binding affinity (∼3 nM). Its in vivo properties were evaluated using high-resolution intravital imaging, histology, whole-pancreas visualization, and endoscopic imaging. According to intravital microscopy, the probe rapidly bound to β-cells and, as demonstrated by confocal microscopy, it was internalized. Histology of the whole pancreas showed a close correspondence between fluorescence and insulin staining, and there was an excellent correlation between imaging signals and β-cell mass in mice treated with streptozotocin, a β-cell toxin. Individual islets could also be visualized by endoscopic imaging. In short, E4×12-VT750 showed strong and selective binding to glucose-like peptide-1 receptors and permitted accurate measurement of β-cell mass in both diabetic and nondiabetic mice. This near-infrared imaging probe, as well as future radioisotope-labeled versions of it, should prove to be important tools for monitoring diabetes, progression, and treatment in both experimental and clinical contexts. PMID:21768367

  20. The potential of inductively coupled plasma mass spectrometry detection for high-performance liquid chromatography combined with accurate mass measurement of organic pharmaceutical compounds.

    PubMed

    Axelsson, B O; Jörnten-Karlsson, M; Michelsen, P; Abou-Shakra, F

    2001-01-01

    Quantification of unknown components in pharmaceutical, metabolic and environmental samples is an important but difficult task. Most commonly used detectors (like UV, RI or MS) require standards of each analyte for accurate quantification. Even if the chemical structure or elemental composition is known, the response from these detectors is difficult to predict with any accuracy. In inductively coupled plasma mass spectrometry (ICP-MS) compounds are atomised and ionised irrespective of the chemical structure(s) incorporating the element of interest. Liquid chromatography coupled with inductively coupled plasma mass spectrometry (LC/ICP-MS) has been shown to provide a generic detection for structurally non-correlated compounds with common elements like phosphorus and iodine. Detection of selected elements gives a better quantification of tested 'unknowns' than UV and organic mass spectrometric detection. It was shown that the ultrasonic nebuliser did not introduce any measurable dead volume and preserves the separation efficiency of the system. ICP-MS can be used in combination with many different mobile phases ranging from 0-100% organic modifier. The dynamic range was found to exceed 2.5 orders of magnitude. The application of LC/ICP-MS to pharmaceutical drugs and formulations has shown that impurities can be quantified below the 0.1 mol-% level.

  1. 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

    2012-08-01

    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

  2. Investigation of low-abundant in vitro metabolites of stable isotope-labelled BAL4815 by accurate mass capillary-LC-ESI-qTof-MS and MS/MS.

    PubMed

    Wind, Mathias; Spickermann, Jochen; Schleimer, Michael; Donzelli, Massimiliano; Gebhardt, Klaus; Sturm-Haurany, Rima; Klauer, Dominique; Fullhardt, Pascal; Schmitt-Hoffmann, Anne

    2006-07-01

    The metabolic profile of BAL4815, an antifungal azole drug, was determined using in vitro rat hepatocyte incubations and subsequent analysis by capillary LC-qTof-MS and MS/MS including accurate mass determination. For the detection of the metabolites, a mixture of the drug and its deuterium-labelled analogue was used for incubations. Metabolic stability of BAL4815 was high in cultured rat hepatocytes. However, several low-abundant metabolites were detected by the use of capillary LC-qTof-MS and manual investigation of the data. The peak intensity of the most abundant metabolite was close to the limit of detection. Except for an apparent oxidation product, the masses of the other detected metabolites could not be assigned to a single and frequently occurring biotransformation. Accurate mass determination and possible elemental compositions suggested that metabolism occurred through a combination of glutathionylation and defluorination. This was verified using accurate mass MS/MS. The use of accurate mass measurements and the derived suggestions for the elemental compositions were essential to elucidate this atypical metabolic pathway. A mass accuracy better than 8 ppm could be achieved for most assigned MS and MS/MS signals with intensities less than 6 cps in the spectra.

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

    PubMed

    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.

  4. 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

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

    PubMed

    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

  6. An accurate, convective energy equation based automated meshing technique for analysis of blood vessels and tissues.

    PubMed

    White, J A; Dutton, A W; Schmidt, J A; Roemer, R B

    2000-01-01

    An automated three-element meshing method for generating finite element based models for the accurate thermal analysis of blood vessels imbedded in tissue has been developed and evaluated. The meshing method places eight noded hexahedral elements inside the vessels where advective flows exist, and four noded tetrahedral elements in the surrounding tissue. The higher order hexahedrals are used where advective flow fields occur, since high accuracy is required and effective upwinding algorithms exist. Tetrahedral elements are placed in the remaining tissue region, since they are computationally more efficient and existing automatic tetrahedral mesh generators can be used. Five noded pyramid elements connect the hexahedrals and tetrahedrals. A convective energy equation (CEE) based finite element algorithm solves for the temperature distributions in the flowing blood, while a finite element formulation of a generalized conduction equation is used in the surrounding tissue. Use of the CEE allows accurate solutions to be obtained without the necessity of assuming ad hoc values for heat transfer coefficients. Comparisons of the predictions of the three-element model to analytical solutions show that the three-element model accurately simulates temperature fields. Energy balance checks show that the three-element model has small, acceptable errors. In summary, this method provides an accurate, automatic finite element gridding procedure for thermal analysis of irregularly shaped tissue regions that contain important blood vessels. At present, the models so generated are relatively large (in order to obtain accurate results) and are, thus, best used for providing accurate reference values for checking other approximate formulations to complicated, conjugated blood heat transfer problems.

  7. 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. PMID:27428379

  8. 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.

  9. Ultra-performance liquid chromatography/tandem mass spectrometry for accurate quantification of global DNA methylation in human sperms.

    PubMed

    Wang, Xiaoli; Suo, Yongshan; Yin, Ruichuan; Shen, Heqing; Wang, Hailin

    2011-06-01

    Aberrant DNA methylation in human sperms has been proposed to be a possible mechanism associated with male infertility. We developed an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) method for rapid, sensitive, and specific detection of global DNA methylation level in human sperms. Multiple-reaction monitoring (MRM) mode was used in MS/MS detection for accurate quantification of DNA methylation. The intra-day and inter-day precision values of this method were within 1.50-5.70%. By using 2-deoxyguanosine as an internal standard, UPLC-MS/MS method was applied for the detection of global DNA methylation levels in three cultured cell lines. DNA methyltransferases inhibitor 5-aza-2'-deoxycytidine can significantly reduce global DNA methylation levels in treated cell lines, showing the reliability of our method. We further examined global DNA methylation levels in human sperms, and found that global methylation values varied from 3.79% to 4.65%. The average global DNA methylation level of sperm samples washed only by PBS (4.03%) was relatively lower than that of sperm samples in which abnormal and dead sperm cells were removed by density gradient centrifugation (4.25%), indicating the possible aberrant DNA methylation level in abnormal sperm cells. Clinical application of UPLC-MS/MS method in global DNA methylation detection of human sperms will be useful in human sperm quality evaluation and the study of epigenetic mechanisms responsible for male infertility.

  10. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    SciTech Connect

    Nakhleh, Luay

    2014-03-12

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

  11. Gravitational waves from compact binaries inspiralling along post-Newtonian accurate eccentric orbits: Data analysis implications

    SciTech Connect

    Tessmer, Manuel; Gopakumar, Achamveedu

    2008-10-15

    Compact binaries inspiralling along eccentric orbits are plausible gravitational-wave (GW) sources for the ground-based laser interferometers. We explore the losses in the event rates incurred when searching for GWs from compact binaries inspiralling along post-Newtonian accurate eccentric orbits with certain obvious nonoptimal search templates. For the present analysis, GW signals having 2.5 post-Newtonian (PN) accurate orbital evolution are modeled following the phasing formalism, presented by T. Damour, A. Gopakumar, and B. R. Iyer [Phys. Rev. D 70, 064028 (2004)]. We demonstrate that the search templates that model in a gauge-invariant manner GWs from compact binaries inspiralling under quadrupolar radiation reaction along 2PN accurate circular orbits are very efficient in capturing our somewhat realistic GW signals. However, three types of search templates based on the adiabatic, complete adiabatic, and gauge-dependent complete nonadiabatic approximants, detailed in P. Ajith, B. R. Iyer, C. A. K. Robinson, and B. S. Sathyaprakash, Phys. Rev. D 71, 044029 (2005), relevant for the circular inspiral under the quadrupolar radiation reaction were found to be inefficient in capturing the above-mentioned eccentric signal. We conclude that further investigations will be required to probe the ability of various types of PN accurate circular templates, employed to analyze the LIGO/VIRGO data, to capture GWs from compact binaries having tiny orbital eccentricities.

  12. Gravitational waves from compact binaries inspiralling along post-Newtonian accurate eccentric orbits: Data analysis implications

    NASA Astrophysics Data System (ADS)

    Tessmer, Manuel; Gopakumar, Achamveedu

    2008-10-01

    Compact binaries inspiralling along eccentric orbits are plausible gravitational-wave (GW) sources for the ground-based laser interferometers. We explore the losses in the event rates incurred when searching for GWs from compact binaries inspiralling along post-Newtonian accurate eccentric orbits with certain obvious nonoptimal search templates. For the present analysis, GW signals having 2.5 post-Newtonian (PN) accurate orbital evolution are modeled following the phasing formalism, presented by T. Damour, A. Gopakumar, and B. R. Iyer [Phys. Rev. D 70, 064028 (2004)PRVDAQ0556-282110.1103/PhysRevD.70.064028]. We demonstrate that the search templates that model in a gauge-invariant manner GWs from compact binaries inspiralling under quadrupolar radiation reaction along 2PN accurate circular orbits are very efficient in capturing our somewhat realistic GW signals. However, three types of search templates based on the adiabatic, complete adiabatic, and gauge-dependent complete nonadiabatic approximants, detailed in P. Ajith, B. R. Iyer, C. A. K. Robinson, and B. S. Sathyaprakash, Phys. Rev. D 71, 044029 (2005)PRVDAQ0556-282110.1103/PhysRevD.71.044029, relevant for the circular inspiral under the quadrupolar radiation reaction were found to be inefficient in capturing the above-mentioned eccentric signal. We conclude that further investigations will be required to probe the ability of various types of PN accurate circular templates, employed to analyze the LIGO/VIRGO data, to capture GWs from compact binaries having tiny orbital eccentricities.

  13. Inorganic trace analysis by mass spectrometry

    NASA Astrophysics Data System (ADS)

    Becker, Johanna Sabine; Dietze, Hans-Joachim

    1998-10-01

    Mass spectrometric methods for the trace analysis of inorganic materials with their ability to provide a very sensitive multielemental analysis have been established for the determination of trace and ultratrace elements in high-purity materials (metals, semiconductors and insulators), in different technical samples (e.g. alloys, pure chemicals, ceramics, thin films, ion-implanted semiconductors), in environmental samples (waters, soils, biological and medical materials) and geological samples. Whereas such techniques as spark source mass spectrometry (SSMS), laser ionization mass spectrometry (LIMS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), glow discharge mass spectrometry (GDMS), secondary ion mass spectrometry (SIMS) and inductively coupled plasma mass spectrometry (ICP-MS) have multielemental capability, other methods such as thermal ionization mass spectrometry (TIMS), accelerator mass spectrometry (AMS) and resonance ionization mass spectrometry (RIMS) have been used for sensitive mono- or oligoelemental ultratrace analysis (and precise determination of isotopic ratios) in solid samples. The limits of detection for chemical elements using these mass spectrometric techniques are in the low ng g -1 concentration range. The quantification of the analytical results of mass spectrometric methods is sometimes difficult due to a lack of matrix-fitted multielement standard reference materials (SRMs) for many solid samples. Therefore, owing to the simple quantification procedure of the aqueous solution, inductively coupled plasma mass spectrometry (ICP-MS) is being increasingly used for the characterization of solid samples after sample dissolution. ICP-MS is often combined with special sample introduction equipment (e.g. flow injection, hydride generation, high performance liquid chromatography (HPLC) or electrothermal vaporization) or an off-line matrix separation and enrichment of trace impurities (especially for characterization of

  14. Negative chemical ionization gas chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry and automated accurate mass data processing for determination of pesticides in fruit and vegetables.

    PubMed

    Besil, Natalia; Uclés, Samanta; Mezcúa, Milagros; Heinzen, Horacio; Fernández-Alba, Amadeo R

    2015-08-01

    Gas chromatography coupled to high resolution hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS), operating in negative chemical ionization (NCI) mode and combining full scan with MSMS experiments using accurate mass analysis, has been explored for the automated determination of pesticide residues in fruit and vegetables. Seventy compounds were included in this approach where 50 % of them are not approved by the EU legislation. A global 76 % of the analytes could be identified at 1 μg kg(-1). Recovery studies were developed at three concentration levels (1, 5, and 10 μg kg(-1)). Seventy-seven percent of the detected pesticides at the lowest level yielded recoveries within the 70 %-120 % range, whereas 94 % could be quantified at 5 μg kg(-1), and the 100 % were determined at 10 μg kg(-1). Good repeatability, expressed as relative standard deviation (RSD <20 %), was obtained for all compounds. The main drawback of the method was the limited dynamic range that was observed for some analytes that can be overcome either diluting the sample or lowering the injection volume. A home-made database was developed and applied to an automatic accurate mass data processing. Measured mass accuracies of the generated ions were mainly less than 5 ppm for at least one diagnostic ion. When only one ion was obtained in the single-stage NCI-MS, a representative product ion from MSMS experiments was used as identification criterion. A total of 30 real samples were analyzed and 67 % of the samples were positive for 12 different pesticides in the range 1.0-1321.3 μg kg(-1). PMID:25694145

  15. Broadband Analysis of Bioagents by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Fenselau, Catherine; Wynne, Colin; Edwards, Nathan

    Mass spectrometry was first reported to provide analysis of intact metabolite biomarkers from whole cells in 1975.1 Since then advances in ionization techniques have extended our capabilities to polar lipids and, eventually, to proteins.2, 3 Mass spectrometry provides a broadband detection system, which, however, has great specificity. Bioinformatics plays an important role in providing flexible and rapid characterization of species, based on protein and peptide mass spectra collected in the field.

  16. Accurate near-field calculation in the rigorous coupled-wave analysis method

    NASA Astrophysics Data System (ADS)

    Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.

    2015-12-01

    The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.

  17. Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis.

    PubMed Central

    Sieracki, M E; Reichenbach, S E; Webb, K L

    1989-01-01

    The accurate measurement of bacterial and protistan cell biomass is necessary for understanding their population and trophic dynamics in nature. Direct measurement of fluorescently stained cells is often the method of choice. The tedium of making such measurements visually on the large numbers of cells required has prompted the use of automatic image analysis for this purpose. Accurate measurements by image analysis require an accurate, reliable method of segmenting the image, that is, distinguishing the brightly fluorescing cells from a dark background. This is commonly done by visually choosing a threshold intensity value which most closely coincides with the outline of the cells as perceived by the operator. Ideally, an automated method based on the cell image characteristics should be used. Since the optical nature of edges in images of light-emitting, microscopic fluorescent objects is different from that of images generated by transmitted or reflected light, it seemed that automatic segmentation of such images may require special considerations. We tested nine automated threshold selection methods using standard fluorescent microspheres ranging in size and fluorescence intensity and fluorochrome-stained samples of cells from cultures of cyanobacteria, flagellates, and ciliates. The methods included several variations based on the maximum intensity gradient of the sphere profile (first derivative), the minimum in the second derivative of the sphere profile, the minimum of the image histogram, and the midpoint intensity. Our results indicated that thresholds determined visually and by first-derivative methods tended to overestimate the threshold, causing an underestimation of microsphere size. The method based on the minimum of the second derivative of the profile yielded the most accurate area estimates for spheres of different sizes and brightnesses and for four of the five cell types tested. A simple model of the optical properties of fluorescing objects and

  18. 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.

  19. Analysis of low resolution mass spectra

    NASA Technical Reports Server (NTRS)

    Babst, R. W.; Shapiro, H.

    1971-01-01

    Computer program determines gas constituents from measurements of mass/peak-height spectrum from residual gas analyzer. Applications of program include residual gas analysis for work in space environmental simulators, space environment contamination, and air pollution monitoring.

  20. An optimized method for the accurate determination of patulin in apple products by isotope dilution-liquid chromatography/mass spectrometry.

    PubMed

    Seo, Miyeong; Kim, Byungjoo; Baek, Song-Yee

    2015-07-01

    Patulin, a mycotoxin produced by several molds in fruits, has been frequently detected in apple products. Therefore, regulatory bodies have established recommended maximum permitted patulin concentrations for each type of apple product. Although several analytical methods have been adopted to determine patulin in food, quality control of patulin analysis is not easy, as reliable certified reference materials (CRMs) are not available. In this study, as a part of a project for developing CRMs for patulin analysis, we developed isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC/MS/MS) as a higher-order reference method for the accurate value-assignment of CRMs. (13)C7-patulin was used as internal standard. Samples were extracted with ethyl acetate to improve recovery. For further sample cleanup with solid-phase extraction (SPE), the HLB SPE cartridge was chosen after comparing with several other types of SPE cartridges. High-performance liquid chromatography was performed on a multimode column for proper retention and separation of highly polar and water-soluble patulin from sample interferences. Sample extracts were analyzed by LC/MS/MS with electrospray ionization in negative ion mode with selected reaction monitoring of patulin and (13)C7-patulin at m/z 153→m/z 109 and m/z 160→m/z 115, respectively. The validity of the method was tested by measuring gravimetrically fortified samples of various apple products. In addition, the repeatability and the reproducibility of the method were tested to evaluate the performance of the method. The method was shown to provide accurate measurements in the 3-40 μg/kg range with a relative expanded uncertainty of around 1%.

  1. Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion trap mass spectrometer

    PubMed Central

    Vincent, Catherine E.; Rensvold, Jarred W.; Westphall, Michael S.; Pagliarini, David J.; Coon, Joshua J.

    2012-01-01

    Isobaric tagging enables the acquisition of highly-multiplexed proteome quantification but is hindered by the pervasive problem of precursor interference. The elimination of co-isolated contaminants prior to reporter tag generation can be achieved through the use of gas-phase purification via proton transfer ion/ion reactions (QuantMode); however, the original QuantMode technique was implemented on the high resolution linear ion trap-Orbitrap hybrid mass spectrometer enabled with electron transfer dissociation (ETD). Here we extend this technology to stand-alone linear ion trap systems (trapQuantMode). Facilitated by the use of inlet beam-type activation (i.e., trapHCD) for production and observation of the low mass-to-charge reporter region, this scan sequence comprises three separate events to maximize peptide identifications, minimize duty cycle requirements, and increase quantitative accuracy, precision, and dynamic range. Significant improvements in quantitative accuracy were attained over standard methods when using trapQuantMode (trapQM) to analyze an interference model system comprising tryptic peptides of yeast that we contaminated with human peptides. Finally, we demonstrate practical benefits of this method by analysis of the proteomic changes that occur during mouse skeletal muscle myoblast differentiation. While trapQM’s reduced duty cycle led to the identification of fewer proteins than conventional operation (4,050 vs. 2,964), trapQM identified more significant differences (>1.5 fold, 1,362 vs 1,132, respectively; P<0.05) between the proteomes of undifferentiated myoblasts and differentiated myotubes and nearly ten-fold more differences with changes greater than 5-fold (96 vs. 12). We further show that our trapQM dataset is superior for identifying changes in protein abundance that are consistent with the metabolic and structural changes known to accompany myotube formation. PMID:23046161

  2. Accurate analysis of blood vessel sizes and stenotic lesions using stereoscopic DSA system.

    PubMed

    Fencil, L E; Doi, K; Hoffman, K R

    1988-01-01

    We have developed a technique to determine accurately the magnification factor and three-dimensional orientation of a vessel segment from a stereoscopic pair of digital subtraction angiograms (DSA). Our DSA system includes a stereoscopic x-ray tube with a 25-mm focal spot shift. The magnification and orientation of a selected vessel segment are determined from the distance and direction of the focal spot shift and the stereoscopic discrepancy in image positions for that segment. Our results indicate that the accuracies of determining the magnification and orientation are less than 1% and approximately 5 degrees, respectively. After the magnification and orientation are determined accurately, an iterative deconvolution technique for the measurement of vessel image size is applied to the selected vessel segment. This iterative deconvolution technique provides the best estimate of vessel image size by taking into account the unsharpness of the digital system. With this technique, the vessel image size can be determined to an accuracy of approximately 1.0 mm, which corresponds to one third the pixel size of our DSA system. Information derived from stereoscopic analysis and iterative deconvolution thus allows accurate calculation of actual vascular dimensions from DSA images.

  3. Nonlinear Aeroelastic Analysis Using a Time-Accurate Navier-Stokes Equations Solver

    NASA Technical Reports Server (NTRS)

    Kuruvila, Geojoe; Bartels, Robert E.; Hong, Moeljo S.; Bhatia, G.

    2007-01-01

    A method to simulate limit cycle oscillation (LCO) due to control surface freeplay using a modified CFL3D, a time-accurate Navier-Stokes computational fluid dynamics (CFD) analysis code with structural modeling capability, is presented. This approach can be used to analyze aeroelastic response of aircraft with structural behavior characterized by nonlinearity in the force verses displacement curve. A limited validation of the method, using very low Mach number experimental data for a three-degrees-of-freedom (pitch/plunge/flap deflection) airfoil model with flap freeplay, is also presented.

  4. Dual electrospray ionization source for confident generation of accurate mass tags using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Nepomuceno, Angelito I; Muddiman, David C; Bergen, H Robert; Craighead, James R; Burke, Michael J; Caskey, Patrick E; Allan, Jonathan A

    2003-07-15

    resulting in mass accuracies of 1.08 ppm +/- 0.11 ppm (mean +/- confidence interval of the mean at 95% confidence; N = 160). In addition, the analysis of a tryptic digest of apomyoglobin by nanoLC-dual ESI-FT-ICR afforded an average MMA of -1.09 versus -74.5 ppm for externally calibrated data. Furthermore, we demonstrate that the amplitude of a peptide being electrosprayed at 25 nM can be linearly increased, ultimately allowing for dynamic analyte/IMC abundance modulation. Finally, we demonstrate that this source can reliably be used for multiplexing measurements from two (eventually more) flow streams.

  5. The analysis of comet mass spectrometric data

    NASA Astrophysics Data System (ADS)

    Balm, S. P.; Hare, J. P.; Kroto, H. W.

    1991-04-01

    The mass spectra from the Giotto PICCA experiment have been studied using computer simulations based on tabulated mass spectrometric data. It is shown that random mixtures of organic compounds give rise to mass spectra with peaks at about 45, 60, 75, and 90 amu; i.e., separated by about 15 amu. In particular it is shown that the products of Urey-Miller type experiments give mass spectra which can match the observed Giotto data closely. The analysis indicates that the material consists mainly of C/H/O/N (i.e., it is organic), but that the assignment to any well defined organic material is less certain. It is not clear that mass spectrometric studies of complex mixtures have the prospect of yielding this type of information without some form of preseparation.

  6. Biological particle analysis by mass spectrometry

    NASA Technical Reports Server (NTRS)

    Vilker, V. L.; Platz, R. M.

    1983-01-01

    An instrument that analyzes the chemical composition of biological particles in aerosol or hydrosol form was developed. Efforts were directed toward the acquisition of mass spectra from aerosols of biomolecules and bacteria. The filament ion source was installed on the particle analysis by mass spectrometry system. Modifications of the vacuum system improved the sensitivity of the mass spectrometer. After the modifications were incorporated, detailed mass spectra of simple compounds from the three major classes of biomolecules, proteins, nucleic acids, and carbohydrates were obtained. A method of generating bacterial aerosols was developed. The aerosols generated were collected and examined in the scanning electron microscope to insure that the bacteria delivered to the mass spectrometer were intact and free from debris.

  7. Mass Spectrometric Analysis of Histone Proteoforms

    PubMed Central

    Yuan, Zuo-Fei; Arnaudo, Anna M.; Garcia, Benjamin A.

    2014-01-01

    Histones play important roles in chromatin, due to various post-translational modifications and sequence variants, which are called histone proteoforms. Investigating modifications and variants is an on-going challenge. Previous methods are based on antibodies and because they usually detect only one modification at a time, they are not suitable to study the various combinations of modifications on histones. Fortunately, mass spectrometry has emerged as a high-throughput technology for histone analysis and does not require prior knowledge about any modifications. From the data generated by mass spectrometers, both identification and quantification of modifications and variants can be easily obtained. Based on this information, the functions of histones in various cellular contexts can be revealed. Therefore, mass spectrometry continues to play an important role in the study of histone proteoforms. In this review, we will discuss the analysis strategies of mass spectrometry, their applications on histones, and some key remaining challenges. PMID:24896311

  8. A convenient method for calculation of ionic diffusion coefficients for accurate selected ion flow tube mass spectrometry, SIFT-MS

    NASA Astrophysics Data System (ADS)

    Dryahina, K.; Spanel, P.

    2005-07-01

    A method to calculate diffusion coefficients of ions important for the selected ion flow tube mass spectrometry, SIFT-MS, is presented. The ions, on which this method is demonstrated, include the SIFT-MS precursors H3O+(H2O)0,1,2,3, NO.+(H2O)0,1,2 and O2+ and the product ions relevant to analysis of breath trace metabolites ammonia (NH3+(H2O)0,1,2, NH4+(H2O)0,1,2), acetaldehyde (C2H4OH+(H2O)0,1,2), acetone (CH3CO+, (CH3)2CO+, (CH3)2COH+(H2O)0,1, (CH3)2CO.NO+), ethanol (C2H5OHH+(H2O)0,1,2) and isoprene (C5H7+, C5H8+, C5H9+). Theoretical model of the (12, 4) potential for interaction between the ions and the helium atoms is used, with the repulsive part approximated by the mean hard-sphere cross section and the attractive part describing ion-induced dipole interactions. The reduced zero-field mobilities at 300 K are calculated using the Viehland and Mason theory [L.A. Viehland, S.L. Lin, E.A. Mason, At. Data Nucl. Data Tables, 60 (1995) 37-95], parameterised by a simple formula as a function of the mean hard-sphere cross section, and converted to diffusion coefficients using the Einstein relation. The method is tested on a set of experimental data for simple ions and cluster ions.

  9. DNA sequence analysis by MALDI mass spectrometry.

    PubMed Central

    Kirpekar, F; Nordhoff, E; Larsen, L K; Kristiansen, K; Roepstorff, P; Hillenkamp, F

    1998-01-01

    Conventional DNA sequencing is based on gel electrophoretic separation of the sequencing products. Gel casting and electrophoresis are the time limiting steps, and the gel separation is occasionally imperfect due to aberrant mobility of certain fragments, leading to erroneous sequence determination. Furthermore, illegitimately terminated products frequently cannot be distinguished from correctly terminated ones, a phenomenon that also obscures data interpretation. In the present work the use of MALDI mass spectrometry for sequencing of DNA amplified from clinical samples is implemented. The unambiguous and fast identification of deletions and substitutions in DNA amplified from heterozygous carriers realistically suggest MALDI mass spectrometry as a future alternative to conventional sequencing procedures for high throughput screening for mutations. Unique features of the method are demonstrated by sequencing a DNA fragment that could not be sequenced conventionally because of gel electrophoretic band compression and the presence of multiple non-specific termination products. Taking advantage of the accurate mass information provided by MALDI mass spectrometry, the sequence was deduced, and the nature of the non-specific termination could be determined. The method described here increases the fidelity in DNA sequencing, is fast, compatible with standard DNA sequencing procedures, and amenable to automation. PMID:9592136

  10. Accurate palm vein recognition based on wavelet scattering and spectral regression kernel discriminant analysis

    NASA Astrophysics Data System (ADS)

    Elnasir, Selma; Shamsuddin, Siti Mariyam; Farokhi, Sajad

    2015-01-01

    Palm vein recognition (PVR) is a promising new biometric that has been applied successfully as a method of access control by many organizations, which has even further potential in the field of forensics. The palm vein pattern has highly discriminative features that are difficult to forge because of its subcutaneous position in the palm. Despite considerable progress and a few practical issues, providing accurate palm vein readings has remained an unsolved issue in biometrics. We propose a robust and more accurate PVR method based on the combination of wavelet scattering (WS) with spectral regression kernel discriminant analysis (SRKDA). As the dimension of WS generated features is quite large, SRKDA is required to reduce the extracted features to enhance the discrimination. The results based on two public databases-PolyU Hyper Spectral Palmprint public database and PolyU Multi Spectral Palmprint-show the high performance of the proposed scheme in comparison with state-of-the-art methods. The proposed approach scored a 99.44% identification rate and a 99.90% verification rate [equal error rate (EER)=0.1%] for the hyperspectral database and a 99.97% identification rate and a 99.98% verification rate (EER=0.019%) for the multispectral database.

  11. Accurate determination of protein methionine oxidation by stable isotope labeling and LC-MS analysis.

    PubMed

    Liu, Hongcheng; Ponniah, Gomathinayagam; Neill, Alyssa; Patel, Rekha; Andrien, Bruce

    2013-12-17

    Methionine (Met) oxidation is a major modification of proteins, which converts Met to Met sulfoxide as the common product. It is challenging to determine the level of Met sulfoxide, because it can be generated during sample preparation and analysis as an artifact. To determine the level of Met sulfoxide in proteins accurately, an isotope labeling and LC-MS peptide mapping method was developed. Met residues in proteins were fully oxidized using hydrogen peroxide enriched with (18)O atoms before sample preparation. Therefore, it was impossible to generate Met sulfoxide as an artifact during sample preparation. The molecular weight difference of 2 Da between Met sulfoxide with the (16)O atom and Met sulfoxide with the (18)O atom was used to differentiate and calculate the level of Met sulfoxide in the sample originally. Using a recombinant monoclonal antibody as a model protein, much lower levels of Met sulfoxide were detected for the two susceptible Met residues with this new method compared to a typical peptide mapping procedure. The results demonstrated efficient elimination of the analytical artifact during LC-MS peptide mapping for the measurement of Met sulfoxide. This method can thus be used when accurate determination of the level of Met sulfoxide is critical.

  12. Fast and accurate sensitivity analysis of IMPT treatment plans using Polynomial Chaos Expansion

    NASA Astrophysics Data System (ADS)

    Perkó, Zoltán; van der Voort, Sebastian R.; van de Water, Steven; Hartman, Charlotte M. H.; Hoogeman, Mischa; Lathouwers, Danny

    2016-06-01

    The highly conformal planned dose distribution achievable in intensity modulated proton therapy (IMPT) can severely be compromised by uncertainties in patient setup and proton range. While several robust optimization approaches have been presented to address this issue, appropriate methods to accurately estimate the robustness of treatment plans are still lacking. To fill this gap we present Polynomial Chaos Expansion (PCE) techniques which are easily applicable and create a meta-model of the dose engine by approximating the dose in every voxel with multidimensional polynomials. This Polynomial Chaos (PC) model can be built in an automated fashion relatively cheaply and subsequently it can be used to perform comprehensive robustness analysis. We adapted PC to provide among others the expected dose, the dose variance, accurate probability distribution of dose-volume histogram (DVH) metrics (e.g. minimum tumor or maximum organ dose), exact bandwidths of DVHs, and to separate the effects of random and systematic errors. We present the outcome of our verification experiments based on 6 head-and-neck (HN) patients, and exemplify the usefulness of PCE by comparing a robust and a non-robust treatment plan for a selected HN case. The results suggest that PCE is highly valuable for both research and clinical applications.

  13. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

    2001-01-01

    A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

  14. Forensic analysis of explosions: Inverse calculation of the charge mass.

    PubMed

    van der Voort, M M; van Wees, R M M; Brouwer, S D; van der Jagt-Deutekom, M J; Verreault, J

    2015-07-01

    Forensic analysis of explosions consists of determining the point of origin, the explosive substance involved, and the charge mass. Within the EU FP7 project Hyperion, TNO developed the Inverse Explosion Analysis (TNO-IEA) tool to estimate the charge mass and point of origin based on observed damage around an explosion. In this paper, inverse models are presented based on two frequently occurring and reliable sources of information: window breakage and building damage. The models have been verified by applying them to the Enschede firework disaster and the Khobar tower attack. Furthermore, a statistical method has been developed to combine the various types of data, in order to determine an overall charge mass distribution. In relatively open environments, like for the Enschede firework disaster, the models generate realistic charge masses that are consistent with values found in forensic literature. The spread predicted by the IEA tool is however larger than presented in the literature for these specific cases. This is also realistic due to the large inherent uncertainties in a forensic analysis. The IEA-models give a reasonable first order estimate of the charge mass in a densely built urban environment, such as for the Khobar tower attack. Due to blast shielding effects which are not taken into account in the IEA tool, this is usually an under prediction. To obtain more accurate predictions, the application of Computational Fluid Dynamics (CFD) simulations is advised. The TNO IEA tool gives unique possibilities to inversely calculate the TNT equivalent charge mass based on a large variety of explosion effects and observations. The IEA tool enables forensic analysts, also those who are not experts on explosion effects, to perform an analysis with a largely reduced effort.

  15. Forensic analysis of explosions: Inverse calculation of the charge mass.

    PubMed

    van der Voort, M M; van Wees, R M M; Brouwer, S D; van der Jagt-Deutekom, M J; Verreault, J

    2015-07-01

    Forensic analysis of explosions consists of determining the point of origin, the explosive substance involved, and the charge mass. Within the EU FP7 project Hyperion, TNO developed the Inverse Explosion Analysis (TNO-IEA) tool to estimate the charge mass and point of origin based on observed damage around an explosion. In this paper, inverse models are presented based on two frequently occurring and reliable sources of information: window breakage and building damage. The models have been verified by applying them to the Enschede firework disaster and the Khobar tower attack. Furthermore, a statistical method has been developed to combine the various types of data, in order to determine an overall charge mass distribution. In relatively open environments, like for the Enschede firework disaster, the models generate realistic charge masses that are consistent with values found in forensic literature. The spread predicted by the IEA tool is however larger than presented in the literature for these specific cases. This is also realistic due to the large inherent uncertainties in a forensic analysis. The IEA-models give a reasonable first order estimate of the charge mass in a densely built urban environment, such as for the Khobar tower attack. Due to blast shielding effects which are not taken into account in the IEA tool, this is usually an under prediction. To obtain more accurate predictions, the application of Computational Fluid Dynamics (CFD) simulations is advised. The TNO IEA tool gives unique possibilities to inversely calculate the TNT equivalent charge mass based on a large variety of explosion effects and observations. The IEA tool enables forensic analysts, also those who are not experts on explosion effects, to perform an analysis with a largely reduced effort. PMID:25933424

  16. D{O} top quark mass analysis

    SciTech Connect

    Strovink, M.

    1995-07-01

    Based on (44-48 pb{sup -1}) of lepton + jets data, we review D0`s initial analysis of the top quark mass. The result, M{sub top} = 199 {+-} 19/21 (stat.) {+-} 22 (syst.) GeV/c{sup 2}, is insensitive to background normalization. The errors are based on ISAJET top Monte Carlo, with its more severe gluon radiation, and allow for ISAJET/HERWIG differences. Good progress is being made in reducing the systematic error. We present a new study based on two-dimensional distributions of reconstructed top quark vs. dijet mass. With 98.7% confidence we observe a peak in the top mass - dijet mass plane. The peak and its projections are similar both in shape and magnitude to expectations based on the decay sequence 1 {yields} bW, W {yields} jj.

  17. Accurate abundance analysis of late-type stars: advances in atomic physics

    NASA Astrophysics Data System (ADS)

    Barklem, Paul S.

    2016-05-01

    The measurement of stellar properties such as chemical compositions, masses and ages, through stellar spectra, is a fundamental problem in astrophysics. Progress in the understanding, calculation and measurement of atomic properties and processes relevant to the high-accuracy analysis of F-, G-, and K-type stellar spectra is reviewed, with particular emphasis on abundance analysis. This includes fundamental atomic data such as energy levels, wavelengths, and transition probabilities, as well as processes of photoionisation, collisional broadening and inelastic collisions. A recurring theme throughout the review is the interplay between theoretical atomic physics, laboratory measurements, and astrophysical modelling, all of which contribute to our understanding of atoms and atomic processes, as well as to modelling stellar spectra.

  18. Aero-Thermo-Dynamic Mass Analysis

    NASA Astrophysics Data System (ADS)

    Shiba, Kota; Yoshikawa, Genki

    2016-07-01

    Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis.

  19. Aero-Thermo-Dynamic Mass Analysis.

    PubMed

    Shiba, Kota; Yoshikawa, Genki

    2016-07-14

    Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis.

  20. Aero-Thermo-Dynamic Mass Analysis.

    PubMed

    Shiba, Kota; Yoshikawa, Genki

    2016-01-01

    Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis. PMID:27412335

  1. Aero-Thermo-Dynamic Mass Analysis

    PubMed Central

    Shiba, Kota; Yoshikawa, Genki

    2016-01-01

    Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis. PMID:27412335

  2. Automated system for fast and accurate analysis of SF6 injected in the surface ocean.

    PubMed

    Koo, Chul-Min; Lee, Kitack; Kim, Miok; Kim, Dae-Ok

    2005-11-01

    This paper describes an automated sampling and analysis system for the shipboard measurement of dissolved sulfur hexafluoride (SF6) in surface marine environments into which SF6 has been deliberately released. This underway system includes a gas chromatograph associated with an electron capture detector, a fast and highly efficient SF6-extraction device, a global positioning system, and a data acquisition system based on Visual Basic 6.0/C 6.0. This work is distinct from previous studies in that it quantifies the efficiency of the SF6-extraction device and its carryover effect and examines the effect of surfactant on the SF6-extraction efficiency. Measurements can be continuously performed on seawater samples taken from a seawater line installed onboard a research vessel. The system runs on an hourly cycle during which one set of four SF6 standards is measured and SF6 derived from the seawater stream is subsequently analyzed for the rest of each 1 h period. This state-of-art system was successfully used to trace a water mass carrying Cochlodinium polykrikoides, which causes harmful algal blooms (HAB) in the coastal waters of southern Korea. The successful application of this analysis system in tracing the HAB-infected water mass suggests that the SF6 detection method described in this paper will improve the quality of the future study of biogeochemical processes in the marine environment. PMID:16294883

  3. Automated system for fast and accurate analysis of SF6 injected in the surface ocean.

    PubMed

    Koo, Chul-Min; Lee, Kitack; Kim, Miok; Kim, Dae-Ok

    2005-11-01

    This paper describes an automated sampling and analysis system for the shipboard measurement of dissolved sulfur hexafluoride (SF6) in surface marine environments into which SF6 has been deliberately released. This underway system includes a gas chromatograph associated with an electron capture detector, a fast and highly efficient SF6-extraction device, a global positioning system, and a data acquisition system based on Visual Basic 6.0/C 6.0. This work is distinct from previous studies in that it quantifies the efficiency of the SF6-extraction device and its carryover effect and examines the effect of surfactant on the SF6-extraction efficiency. Measurements can be continuously performed on seawater samples taken from a seawater line installed onboard a research vessel. The system runs on an hourly cycle during which one set of four SF6 standards is measured and SF6 derived from the seawater stream is subsequently analyzed for the rest of each 1 h period. This state-of-art system was successfully used to trace a water mass carrying Cochlodinium polykrikoides, which causes harmful algal blooms (HAB) in the coastal waters of southern Korea. The successful application of this analysis system in tracing the HAB-infected water mass suggests that the SF6 detection method described in this paper will improve the quality of the future study of biogeochemical processes in the marine environment.

  4. 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.

  5. Analysis of tear glucose concentration with electrospray ionization mass spectrometry.

    PubMed

    Taormina, Christopher R; Baca, Justin T; Asher, Sanford A; Grabowski, Joseph J; Finegold, David N

    2007-02-01

    We have developed a mass spectrometry-based method that allows one to accurately determine the glucose concentration of tear fluid. We used a 1 microL micro-capillary to collect tear fluid from the tear meniscus with minimal irritation of the eye. We analyzed the 1 muL volume of collected tear fluid with liquid-chromatography electrospray ionization mass spectrometry with the use of D-glucose-6,6-d2 as an internal standard. Repeated measurements and a recovery experiment on pooled, onion-induced tears showed that the analysis of the glucose in tears was precise (4% relative standard deviation) and provided 100% recovery. We found the tear glucose concentration of one fasting nondiabetic subject to be 13 to 51 microM while the onion-induced tear glucose concentration of a different nondiabetic subject to be 211 to 256 microM. PMID:17084090

  6. Analysis of Tear Glucose Concentration with Electrospray Ionization Mass Spectrometry

    PubMed Central

    Taormina, Christopher R.; Baca, Justin T.; Finegold, David N.; Asher, Sanford A.; Grabowski, Joseph J.

    2007-01-01

    We have developed a mass spectrometry-based method which allows one to accurately determine the glucose concentration of tear fluid. We used a 1 μL micro-capillary to collect tear fluid from the tear meniscus with minimal irritation of the eye. We analyzed the 1 μL volume of collected tear fluid with liquid-chromatography electrospray ionization mass spectrometry with the use of D-glucose-6,6-d2 as an internal standard. Repeated measurements and a recovery experiment on pooled, onion-induced tears showed that the analysis of the glucose in tears was precise (4% relative standard deviation) and provided 100% recovery. We found the tear glucose concentration of one fasting non-diabetic subject to be 13 to 51 μM while the onion-induced tear glucose concentration of a different non-diabetic subject to be 211 to 256 μM. PMID:17084090

  7. Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

    PubMed

    Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

    2012-12-01

    Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance.

  8. Accurate measurement of bromine contents in plastic samples by instrumental neutron activation analysis.

    PubMed

    Kim, I J; Lee, K S; Hwang, E; Min, H S; Yim, Y H

    2013-03-26

    Accurate measurements of bromine contents in plastic samples were made by the direct comparator instrumental neutron activation analysis (INAA). Individual factors affecting the measurements were comprehensively evaluated and compensated, including the volatility loss of bromine from standard comparators, the background bromine level in the filter papers used for preparation of the standard comparators, nuclear interference, γ-ray spectral interference and the variance among replicates of the samples. Uncertainty contributions from those factors were thoroughly evaluated and included in the uncertainty budgeting of the INAA measurement. (81)Br was chosen as the target isotope, and the INAA measurements for bromine were experimentally confirmed to exhibit good linearity within a bromine content range of 10-170 μg. The established method has been applied to the analysis of eight plastic samples: four commercially available certified reference materials (CRMs) of polyethylene and polystyrene and four acrylonitrile butadiene styrene (ABS) samples prepared as the candidate reference materials (KRISS CRM 113-01-012, -013, -014 and -015). The bromine contents of the samples were calculated at three different γ-ray energies and compared, showing good agreement. The results of the four CRMs also showed good consistency with their certified values within the stated uncertainties. Finally, the bromine contents of the ABS samples were determined with expanded uncertainties (at a 95% level of confidence) between 2.5% and 5% in a bromine content range of 25-900 mg kg(-1).

  9. An accurate skull stripping method based on simplex meshes and histogram analysis for magnetic resonance images.

    PubMed

    Galdames, Francisco J; Jaillet, Fabrice; Perez, Claudio A

    2012-01-01

    Skull stripping methods are designed to eliminate the non-brain tissue in magnetic resonance (MR) brain images. Removal of non-brain tissues is a fundamental step in enabling the processing of brain MR images. The aim of this study is to develop an automatic accurate skull stripping method based on deformable models and histogram analysis. A rough-segmentation step is used to find the optimal starting point for the deformation and is based on thresholds and morphological operators. Thresholds are computed using comparisons with an atlas, and modeling by Gaussians. The deformable model is based on a simplex mesh and its deformation is controlled by the image local gray levels and the information obtained on the gray level modeling of the rough-segmentation. Our Simplex Mesh and Histogram Analysis Skull Stripping (SMHASS) method was tested on the following international databases commonly used in scientific articles: BrainWeb, Internet Brain Segmentation Repository (IBSR), and Segmentation Validation Engine (SVE). A comparison was performed against three of the best skull stripping methods previously published: Brain Extraction Tool (BET), Brain Surface Extractor (BSE), and Hybrid Watershed Algorithm (HWA). Performance was measured using the Jaccard index (J) and Dice coefficient (κ). Our method showed the best performance and differences were statistically significant (p<0.05): J=0.904 and κ=0.950 on BrainWeb; J=0.905 and κ=0.950 on IBSR; J=0.946 and κ=0.972 on SVE.

  10. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  11. Accurate measurement of bromine contents in plastic samples by instrumental neutron activation analysis.

    PubMed

    Kim, I J; Lee, K S; Hwang, E; Min, H S; Yim, Y H

    2013-03-26

    Accurate measurements of bromine contents in plastic samples were made by the direct comparator instrumental neutron activation analysis (INAA). Individual factors affecting the measurements were comprehensively evaluated and compensated, including the volatility loss of bromine from standard comparators, the background bromine level in the filter papers used for preparation of the standard comparators, nuclear interference, γ-ray spectral interference and the variance among replicates of the samples. Uncertainty contributions from those factors were thoroughly evaluated and included in the uncertainty budgeting of the INAA measurement. (81)Br was chosen as the target isotope, and the INAA measurements for bromine were experimentally confirmed to exhibit good linearity within a bromine content range of 10-170 μg. The established method has been applied to the analysis of eight plastic samples: four commercially available certified reference materials (CRMs) of polyethylene and polystyrene and four acrylonitrile butadiene styrene (ABS) samples prepared as the candidate reference materials (KRISS CRM 113-01-012, -013, -014 and -015). The bromine contents of the samples were calculated at three different γ-ray energies and compared, showing good agreement. The results of the four CRMs also showed good consistency with their certified values within the stated uncertainties. Finally, the bromine contents of the ABS samples were determined with expanded uncertainties (at a 95% level of confidence) between 2.5% and 5% in a bromine content range of 25-900 mg kg(-1). PMID:23498117

  12. Analysis of Electroblotted Proteins by Mass Spectrometry

    PubMed Central

    Luque-Garcia, Jose L.; Neubert, Thomas A.

    2015-01-01

    Summary Identification of proteins by mass spectrometry is crucial for better understanding of many biological, biochemical, and biomedical processes. Here we describe two methods for the identification of electroblotted proteins by on-membrane digestion prior to analysis by mass spectrometry. These on-membrane methods take approximately half the time of in-gel digestion and provide better digestion efficiency, due to the better accessibility of the protease to the proteins adsorbed onto the nitrocellulose, and better protein sequence coverage, especially for membrane proteins where large and hydrophobic peptides are commonly present. PMID:26139272

  13. Mass spectrometry for pectin structure analysis.

    PubMed

    Ralet, Marie-Christine; Lerouge, Patrice; Quéméner, Bernard

    2009-09-28

    Pectin are extremely complex biopolymers made up of different structural domains. Enzymatic degradation followed by purification and structural analysis of the degradation products proved to be efficient tools for the understanding of pectin fine structure, including covalent interactions between pectic structural domains or with other cell wall polysaccharides. Due to its high sensitivity, high throughput and capacity to analyze mixtures, mass spectrometry has gained more and more importance as a tool for oligosaccharides structural characterization in the past 10 years. This review will focus on the combined use of mass spectrometry and enzymatic digestion for pectins structural characterization. PMID:19058795

  14. 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.

  15. CLASH-VLT: CONSTRAINTS ON THE DARK MATTER EQUATION OF STATE FROM ACCURATE MEASUREMENTS OF GALAXY CLUSTER MASS PROFILES

    SciTech Connect

    Sartoris, Barbara; Borgani, Stefano; Girardi, Marisa; Biviano, Andrea; Balestra, Italo; Nonino, Mario; Umetsu, Keiichi; Czakon, Nicole; Bartelmann, Matthias; Grillo, Claudio; Lemze, Doron; Medezinski, Elinor; Zitrin, Adi; Mercurio, Amata; Broadhurst, Tom; Melchior, Peter; and others

    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 <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 = (p{sub r} + 2 p{sub t} )/(3 c {sup 2}ρ) = 0.00 ± 0.15 (stat) ± 0.08 (syst), averaged over the radial range 0.5 Mpc ≤ r ≤ r {sub 200}, where p{sub r} and p{sub t} 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.

  16. [Imaging Mass Spectrometry in Histopathologic Analysis].

    PubMed

    Yamazaki, Fumiyoshi; Seto, Mitsutoshi

    2015-04-01

    Matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS) enables visualization of the distribution of a range of biomolecules by integrating biochemical information from mass spectrometry with positional information from microscopy. IMS identifies a target molecule. In addition, IMS enables global analysis of biomolecules containing unknown molecules by detecting the ratio of the molecular weight to electric charge without any target, which makes it possible to identify novel molecules. IMS generates data on the distribution of lipids and small molecules in tissues, which is difficult to visualize with either conventional counter-staining or immunohistochemistry. In this review, we firstly introduce the principle of imaging mass spectrometry and recent advances in the sample preparation method. Secondly, we present findings regarding biological samples, especially pathological ones. Finally, we discuss the limitations and problems of the IMS technique and clinical application, such as in drug development. PMID:26536781

  17. Development and validation of a sensitive solid phase extraction/hydrophilic interaction liquid chromatography/mass spectrometry method for the accurate determination of glucosamine in dog plasma.

    PubMed

    Hubert, C; Houari, S; Lecomte, F; Houbart, V; De Bleye, C; Fillet, M; Piel, G; Rozet, E; Hubert, Ph

    2010-05-01

    A sensitive and accurate LC/MS method was developed for the monitoring of glucosamine (GLcN) dog plasmatic concentration. In this scope, relatively low plasmatic concentrations of GLcN were expected, ranging from 50 to 1000 ng/mL. Liquid chromatography coupled to simple quadrupole mass spectrometry detection (LC/MS) was selected bringing the selectivity and the sensitivity needed for this application. Additionally, a solid phase extraction (SPE) step was performed to reduce matrix and ion suppression effects. Due to the ionisable character of the compound of interest, a mixed-mode strong cation exchange (Plexa PCX) disposable extraction cartridge (DEC) was selected. The separation was carried out on a Zorbax SB-CN column (5 microm, 4.6mm i.d. x 250 mm), considering hydrophilic interaction liquid chromatography (HILIC). Indeed, the mobile phase was made of methanol and 5mM ammonium hydrogen carbonate buffer at pH 7.5 (95/5, v/v). The detection was led at m/z ratios of 180.0 and 417.0, for GLcN and IS, respectively. Reliability of the results was demonstrated through the validation of the method using an approach based on the accuracy profile allowing managing the risk associated to the use of these methods in routine analysis: it is thus guaranteed that each future result will fall in the +/-30% acceptance limits with a probability of at least 90%. Successful application of the method to a preliminary pharmacokinetic study illustrated the usefulness of the method for pre-clinical studies.

  18. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms

    PubMed Central

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F.

    2016-01-01

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7–76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment. PMID:27645567

  19. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    SciTech Connect

    Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

    2015-03-15

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  20. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms.

    PubMed

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F

    2016-09-20

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7-76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment.

  1. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms.

    PubMed

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F

    2016-01-01

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7-76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment. PMID:27645567

  2. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for (Exo-)Planetary Retrieval Models

    NASA Astrophysics Data System (ADS)

    Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.

    2015-12-01

    Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work

  3. Accurate means of detecting and characterizing abnormal patterns of ventricular activation by phase image analysis

    SciTech Connect

    Botvinick, E.H.; Frais, M.A.; Shosa, D.W.; O'Connell, J.W.; Pacheco-Alvarez, J.A.; Scheinman, M.; Hattner, R.S.; Morady, F.; Faulkner, D.B.

    1982-08-01

    The ability of scintigraphic phase image analysis to characterize patterns of abnormal ventricular activation was investigated. The pattern of phase distribution and sequential phase changes over both right and left ventricular regions of interest were evaluated in 16 patients with normal electrical activation and wall motion and compared with those in 8 patients with an artificial pacemaker and 4 patients with sinus rhythm with the Wolff-Parkinson-White syndrome and delta waves. Normally, the site of earliest phase angle was seen at the base of the interventricular septum, with sequential change affecting the body of the septum and the cardiac apex and then spreading laterally to involve the body of both ventricles. The site of earliest phase angle was located at the apex of the right ventricle in seven patients with a right ventricular endocardial pacemaker and on the lateral left ventricular wall in one patient with a left ventricular epicardial pacemaker. In each case the site corresponded exactly to the position of the pacing electrode as seen on posteroanterior and left lateral chest X-ray films, and sequential phase changes spread from the initial focus to affect both ventricles. In each of the patients with the Wolff-Parkinson-White syndrome, the site of earliest ventricular phase angle was located, and it corresponded exactly to the site of the bypass tract as determined by endocardial mapping. In this way, four bypass pathways, two posterior left paraseptal, one left lateral and one right lateral, were correctly localized scintigraphically. On the basis of the sequence of mechanical contraction, phase image analysis provides an accurate noninvasive method of detecting abnormal foci of ventricular activation.

  4. Methods for applying accurate digital PCR analysis on low copy DNA samples.

    PubMed

    Whale, Alexandra S; Cowen, Simon; Foy, Carole A; Huggett, Jim F

    2013-01-01

    Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA.

  5. Mass Spectrometric Analysis of Histone Proteoforms

    NASA Astrophysics Data System (ADS)

    Yuan, Zuo-Fei; Arnaudo, Anna M.; Garcia, Benjamin A.

    2014-06-01

    Histones play important roles in chromatin, in the forms of various posttranslational modifications (PTMs) and sequence variants, which are called histone proteoforms. Investigating modifications and variants is an ongoing challenge. Previous methods are based on antibodies, and because they usually detect only one modification at a time, they are not suitable for studying the various combinations of modifications on histones. Fortunately, mass spectrometry (MS) has emerged as a high-throughput technology for histone analysis and does not require prior knowledge about any modifications. From the data generated by mass spectrometers, both identification and quantification of modifications, as well as variants, can be obtained easily. On the basis of this information, the functions of histones in various cellular contexts can be revealed. Therefore, MS continues to play an important role in the study of histone proteoforms. In this review, we discuss the analysis strategies of MS, their applications on histones, and some key remaining challenges.

  6. 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. PMID:24144617

  7. Utility of accurate monoisotopic mass measurements to confidently identify lambda exonuclease generated single-stranded amplicons containing 7-deaza analogs by electrospray ionization FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Frahm, Jennifer L.; Mason, Christopher J.; Muddiman, David C.

    2004-05-01

    A 53-base pair region on the long arm of chromosome 22 was amplified using PCR with 7-deaza-modified deoxynucleotides. Increased amplification efficiency was achieved by doubling the concentration of the modified deoxynucleotide triphosphates. Incorporation of 7-deaza purines has been previously shown to selectively eliminate fragmentation pathways during gas-phase sequencing of nucleic acids by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation. However, 7-deaza analogs result in significant duplex stability precluding interrogation of the single-stranded species by tandem mass spectrometry. Herein, we demonstrate the use of lambda exonuclease to successfully overcome this problem and are able to obtain single-stranded PCR products containing 7-deaza adenine and guanine nucleobases. Mass accuracy was used as our metric to determine complete incorporation of 7-deaza residues in PCR products>15 kDa; <= 3 ppm neutral monoisotopic mass measurement accuracies were routinely achieved. High mass measurement accuracy was obtained using a dual electrospray source and subsequently, using an isotopic fitting algorithm, the best fit between the theoretical and experimental isotopic distributions was determined using a chi-square value. Theoretical isotopic distributions were generated using an average nucleotide (averatide) chemical formula developed herein which was based on the relative frequencies of AT and GC base pairs in the human genome. Single-stranded PCR products were fragmented using SORI-CID and as expected, cleavage at the 7-deaza modified sites was not observed. Collectively, this integrated approach can facilitate top-down sequencing of PCR products by a variety of tandem mass spectrometry methods.

  8. 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.

  9. Matrix-assisted laser desorption ionization-time of flight mass spectrometry can accurately differentiate Aeromonas dhakensis from A. hydrophila, A. caviae, and A. veronii.

    PubMed

    Chen, Po-Lin; Lee, Tai-Fen; Wu, Chi-Jung; Teng, Shih-Hua; Teng, Lee-Jene; Ko, Wen-Chien; Hsueh, Po-Ren

    2014-07-01

    Among 217 Aeromonas isolates identified by sequencing analysis of their rpoB genes, the accuracy rates of identification of A. dhakensis, A. hydrophila, A. veronii, and A. caviae were 96.7%, 90.0%, 96.7%, and 100.0%, respectively, by the cluster analysis of spectra generated by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

  10. 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

  11. 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

  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. Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis

    SciTech Connect

    Manuel J. Manard, Stephan Weeks, Kevin Kyle

    2010-05-27

    The nuclear forensics community is currently engaged in the analysis of illicit nuclear or radioactive material for the purposes of non-proliferations and attribution. One technique commonly employed for gathering nuclear forensics information is isotope analysis. At present, the state-of-the-art methodology for obtaining isotopic distributions is thermal ionization mass spectrometry (TIMS). Although TIMS is highly accurate at determining isotope distributions, the technique requires an elementally pure sample to perform the measurement. The required radiochemical separations give rise to sample preparation times that can be in excess of one to two weeks. Clearly, the nuclear forensics community is in need of instrumentation and methods that can expedite their decision making process in the event of a radiological release or nuclear detonation. Accordingly, we are developing instrumentation that couples a high resolution IM drift cell to the front end of a MS. The IM cell provides a means of separating ions based upon their collision cross-section and mass-to-charge ratio (m/z). Two analytes with the same m/z, but with different collision cross-sections (shapes) would exit the cell at different times, essentially enabling the cell to function in a similar manner to a gas chromatography (GC) column. Thus, molecular and atomic isobaric interferences can be effectively removed from the ion beam. The mobility selected chemical species could then be introduced to a MS for high-resolution mass analysis to generate isotopic distributions of the target analytes. The outcome would be an IM/MS system capable of accurately measuring isotopic distributions while concurrently eliminating isobaric interferences and laboratory radiochemical sample preparation. The overall objective of this project is developing instrumentation and methods to produce near real-time isotope distributions with a modular mass spectrometric system that performs the required gas-phase chemistry and

  14. Quantitative mass spectrometry methods for pharmaceutical analysis.

    PubMed

    Loos, Glenn; Van Schepdael, Ann; Cabooter, Deirdre

    2016-10-28

    Quantitative pharmaceutical analysis is nowadays frequently executed using mass spectrometry. Electrospray ionization coupled to a (hybrid) triple quadrupole mass spectrometer is generally used in combination with solid-phase extraction and liquid chromatography. Furthermore, isotopically labelled standards are often used to correct for ion suppression. The challenges in producing sensitive but reliable quantitative data depend on the instrumentation, sample preparation and hyphenated techniques. In this contribution, different approaches to enhance the ionization efficiencies using modified source geometries and improved ion guidance are provided. Furthermore, possibilities to minimize, assess and correct for matrix interferences caused by co-eluting substances are described. With the focus on pharmaceuticals in the environment and bioanalysis, different separation techniques, trends in liquid chromatography and sample preparation methods to minimize matrix effects and increase sensitivity are discussed. Although highly sensitive methods are generally aimed for to provide automated multi-residue analysis, (less sensitive) miniaturized set-ups have a great potential due to their ability for in-field usage.This article is part of the themed issue 'Quantitative mass spectrometry'.

  15. MIA: non-targeted mass isotopolome analysis

    PubMed Central

    Weindl, Daniel; Wegner, Andre; Hiller, Karsten

    2016-01-01

    Summary: MIA detects and visualizes isotopic enrichment in gas chromatography electron ionization mass spectrometry (GC–EI-MS) datasets in a non-targeted manner. It provides an easy-to-use graphical user interface that allows for visual mass isotopomer distribution analysis across multiple datasets. MIA helps to reveal changes in metabolic fluxes, visualizes metabolic proximity of isotopically enriched compounds and shows the fate of the applied stable isotope labeled tracer. Availability and Implementation: Linux and Windows binaries, documentation, and sample data are freely available for download at http://massisotopolomeanalyzer.lu. MIA is a stand-alone application implemented in C ++  and based on Qt5, NTFD and the MetaboliteDetector framework. Contact: karsten.hiller@uni.lu PMID:27273671

  16. Calcium isotope analysis by mass spectrometry.

    PubMed

    Boulyga, Sergei F

    2010-01-01

    The variations in the isotopic composition of calcium caused by fractionation in heterogeneous systems and by nuclear reactions can provide insight into numerous biological, geological, and cosmic processes, and therefore isotopic analysis finds a wide spectrum of applications in cosmo- and geochemistry, paleoclimatic, nutritional, and biomedical studies. The measurement of calcium isotopic abundances in natural samples has challenged the analysts for more than three decades. Practically all Ca isotopes suffer from significant isobaric interferences, whereas low-abundant isotopes can be particularly affected by neighboring major isotopes. The extent of natural variations of stable isotopes appears to be relatively limited, and highly precise techniques are required to resolve isotopic effects. Isotope fractionation during sample preparation and measurements and instrumental mass bias can significantly exceed small isotope abundance variations in samples, which have to be investigated. Not surprisingly, a TIMS procedure developed by Russell et al. (Russell et al., 1978. Geochim Cosmochim Acta 42: 1075-1090) for Ca isotope measurements was considered as revolutionary for isotopic measurements in general, and that approach is used nowadays (with small modifications) for practically all isotopic systems and with different mass spectrometric techniques. Nevertheless, despite several decades of calcium research and corresponding development of mass spectrometers, the available precision and accuracy is still not always sufficient to achieve the challenging goals. The present article discusses figures of merits of presently used analytical methods and instrumentation, and attempts to critically assess their limitations. In Sections 2 and 3, mass spectrometric methods applied to precise stable isotope analysis and to the determination of (41)Ca are described. Section 4 contains a short summary of selected applications, and includes tracer experiments and the potential use

  17. Accurate Free Vibration Analysis of the Completely Free Rectangular Mindlin Plate

    NASA Astrophysics Data System (ADS)

    Gorman, D. J.; Ding, Wei

    1996-01-01

    The superposition method is exploited to obtain accurate solutions for the natural frequencies and mode shapes of the completely free Mindlin plate. Computed eigenvalues are tabulated for a number of plate aspect and thickness ratios. Steps taken to avoid computational instability are described. Difficulties associated with choosing mode shape functions, particularly when free edges are involved, have always hindered researchers utilizing the Rayleigh-Ritz method. Such difficulties are obviated here. To the authors' knowledge, this represents the first accurate comprehensive solution to this important plate vibration problem.

  18. A DPF Analysis Yields Quantum Mechanically Accurate Analytic Potential Energy Functions for the a ^1Σ^+ and X ^1Σ^+ States of NaH

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine

    2013-06-01

    Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).

  19. Higher-order mass defect analysis for mass spectra of complex organic mixtures.

    PubMed

    Roach, Patrick J; Laskin, Julia; Laskin, Alexander

    2011-06-15

    Higher-order mass defect analysis is introduced as a unique formula assignment and visualization method for the analysis of complex mass spectra. This approach is an extension of the concepts of Kendrick mass transformation widely used for identification of homologous compounds differing only by a number of base units (e.g., CH(2), H(2), O, CH(2)O, etc.) in complex mixtures. We present an iterative renormalization routine for defining higher-order homologous series and multidimensional clustering of mass spectral features. This approach greatly simplifies visualization of complex mass spectra and increases the number of chemical formulas that can be confidently assigned for given mass accuracy. The potential for using higher-order mass defects for data reduction and visualization is shown. Higher-order mass defect analysis is described and demonstrated through third-order analysis of a deisotoped high-resolution mass spectrum of crude oil containing nearly 13,000 peaks. PMID:21526851

  20. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2).

  1. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). PMID:24704185

  2. Accurate determination of the thickness or mass per unit area of thin foils and single-crystal wafers for x-ray attenuation measurements

    NASA Astrophysics Data System (ADS)

    Tran, C. Q.; Chantler, C. T.; Barnea, Z.; de Jonge, M. D.

    2004-09-01

    The determination of the local mass per unit area m/A=∫ρdt and the thickness of a specimen is an important aspect of its characterization and is often required for material quality control in fabrication. We discuss common methods which have been used to determine the local thickness of thin specimens. We then propose an x-ray technique which is capable of determining the local thickness and the x-ray absorption profile of a foil or wafer to high accuracy. This technique provides an accurate integration of the column density which is not affected by the presence of voids and internal defects in the material. The technique is best suited to specimens with thickness substantially greater than the dimensions of the surface and void structure. We also show that the attenuation of an x-ray beam by a nonuniform specimen is significantly different from that calculated by using a simple linear average of the mass per unit area and quantify this effect. For much thinner specimens or in the presence of a very structured surface profile we propose a complementary technique capable of attaining high accuracy by the use of a secondary standard. The technique is demonstrated by absolute measurements of the x-ray mass attenuation coefficient of copper and silver.

  3. Accurate determination of the thickness or mass per unit area of thin foils and single-crystal wafers for x-ray attenuation measurements

    SciTech Connect

    Tran, C.Q.; Chantler, C.T.; Barnea, Z.; Jonge, M.D. de

    2004-09-01

    The determination of the local mass per unit area m/A={integral}{rho}dt and the thickness of a specimen is an important aspect of its characterization and is often required for material quality control in fabrication. We discuss common methods which have been used to determine the local thickness of thin specimens. We then propose an x-ray technique which is capable of determining the local thickness and the x-ray absorption profile of a foil or wafer to high accuracy. This technique provides an accurate integration of the column density which is not affected by the presence of voids and internal defects in the material. The technique is best suited to specimens with thickness substantially greater than the dimensions of the surface and void structure. We also show that the attenuation of an x-ray beam by a nonuniform specimen is significantly different from that calculated by using a simple linear average of the mass per unit area and quantify this effect. For much thinner specimens or in the presence of a very structured surface profile we propose a complementary technique capable of attaining high accuracy by the use of a secondary standard. The technique is demonstrated by absolute measurements of the x-ray mass attenuation coefficient of copper and silver.

  4. 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…

  5. Revisit to three-dimensional percolation theory: Accurate analysis for highly stretchable conductive composite materials

    PubMed Central

    Kim, Sangwoo; Choi, Seongdae; Oh, Eunho; Byun, Junghwan; Kim, Hyunjong; Lee, Byeongmoon; Lee, Seunghwan; Hong, Yongtaek

    2016-01-01

    A percolation theory based on variation of conductive filler fraction has been widely used to explain the behavior of conductive composite materials under both small and large deformation conditions. However, it typically fails in properly analyzing the materials under the large deformation since the assumption may not be valid in such a case. Therefore, we proposed a new three-dimensional percolation theory by considering three key factors: nonlinear elasticity, precisely measured strain-dependent Poisson’s ratio, and strain-dependent percolation threshold. Digital image correlation (DIC) method was used to determine actual Poisson’s ratios at various strain levels, which were used to accurately estimate variation of conductive filler volume fraction under deformation. We also adopted strain-dependent percolation threshold caused by the filler re-location with deformation. When three key factors were considered, electrical performance change was accurately analyzed for composite materials with both isotropic and anisotropic mechanical properties. PMID:27694856

  6. An Accurate Scene Segmentation Method Based on Graph Analysis Using Object Matching and Audio Feature

    NASA Astrophysics Data System (ADS)

    Yamamoto, Makoto; Haseyama, Miki

    A method for accurate scene segmentation using two kinds of directed graph obtained by object matching and audio features is proposed. Generally, in audiovisual materials, such as broadcast programs and movies, there are repeated appearances of similar shots that include frames of the same background, object or place, and such shots are included in a single scene. Many scene segmentation methods based on this idea have been proposed; however, since they use color information as visual features, they cannot provide accurate scene segmentation results if the color features change in different shots for which frames include the same object due to camera operations such as zooming and panning. In order to solve this problem, scene segmentation by the proposed method is realized by using two novel approaches. In the first approach, object matching is performed between two frames that are each included in different shots. By using these matching results, repeated appearances of shots for which frames include the same object can be successfully found and represented as a directed graph. The proposed method also generates another directed graph that represents the repeated appearances of shots with similar audio features in the second approach. By combined use of these two directed graphs, degradation of scene segmentation accuracy, which results from using only one kind of graph, can be avoided in the proposed method and thereby accurate scene segmentation can be realized. Experimental results performed by applying the proposed method to actual broadcast programs are shown to verify the effectiveness of the proposed method.

  7. Sectional power-law correction for the accurate determination of lutetium by isotope dilution multiple collector-inductively coupled plasma-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Yuan, Hong-Lin; Gao, Shan; Zong, Chun-Lei; Dai, Meng-Ning

    2009-11-01

    In this study, we employ a sectional power-law (SPL) correction that provides accurate and precise measurements of 176Lu/ 175Lu ratios in geological samples using multiple collector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Three independent power laws were adopted based on the 176Lu/ 176Yb ratios of samples measured after chemical chromatography. Using isotope dilution (ID) techniques and the SPL correction method, the measured lutetium contents of United States Geological Survey rock standards (BHVO-1, BHVO-2, BCR-2, AGV-1, and G-2) agree well with the recommended values. Results obtained by conventional ICP-MS and INAA are generally higher than those obtained by ID-TIMS and ID-MC-ICP-MS; this discrepancy probably reflects oxide interference and inaccurate corrections.

  8. In situ secondary ion mass spectrometry analysis

    SciTech Connect

    Groenewold, G.S.; Applehans, A.D.; Ingram, J.C.; Delmore, J.E.; Dahl, D.A.

    1993-01-01

    The direct detection of tributyl phosphate (TBP) on rocks using molecular beam surface analysis [MBSA or in situ secondary ion mass spectrometry (SIMS)] is demonstrated. Quantities as low as 250 ng were detected on basalt and sandstone with little or no sample preparation. Detection of TBP on soil has proven to be more problematic and requires further study. Ethylenediaminetetraacetic acid (EDTA) is more difficult to detect because it is very reactive with surfaces of interest. Nevertheless, it is possible to detect EDTA if the acidity of the surface is controlled. The detection of EDTA-metal complexes is currently an open question, but evidence is presented for the detection of ions arising from a EDTA-lead complex. Carboxylic acids (i.e., citric, ascorbic, malic, succinic, malonic, and oxalic) give characteristic SIM spectra, but their detection on sample surfaces awaits evaluation.

  9. 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

  10. RELATIONSHIP BETWEEN MASS FLUX REDUCTION AND SOURCE-ZONE MASS REMOVAL: ANALYSIS OF FIELD DATA

    PubMed Central

    DiFilippo, Erica L.

    2010-01-01

    The magnitude of contaminant mass flux reduction associated with a specific amount of contaminant mass removed is a key consideration for evaluating the effectiveness of a source-zone remediation effort. Thus, there is great interest in characterizing, estimating, and predicting relationships between mass flux reduction and mass removal. Published data collected for several field studies were examined to evaluate relationships between mass flux reduction and source-zone mass removal. The studies analyzed herein represent a variety of source-zone architectures, immiscible-liquid compositions, and implemented remediation technologies. There are two general approaches to characterizing the mass-flux-reduction/mass-removal relationship, end-point analysis and time-continuous analysis. End-point analysis, based on comparing masses and mass fluxes measured before and after a source-zone remediation effort, was conducted for 21 remediation projects. Mass removals were greater than 60% for all but three of the studies. Mass flux reductions ranging from slightly less than to slightly greater than one-to-one were observed for the majority of the sites. However, these single-snapshot characterizations are limited in that the antecedent behavior is indeterminate. Time-continuous analysis, based on continuous monitoring of mass removal and mass flux, was performed for two sites, both for which data were obtained under water-flushing conditions. The reductions in mass flux were significantly different for the two sites (90% vs. ~8%) for similar mass removals (~40%). These results illustrate the dependence of the mass-flux-reduction/mass-removal relationship on source-zone architecture and associated mass-transfer processes. Minimal mass flux reduction was observed for a system wherein mass removal was relatively efficient (ideal mass transfer and displacement). Conversely, a significant degree of mass flux reduction was observed for a site wherein mass removal was inefficient

  11. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear-Layer. Part 2

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Lockard, David P.

    2002-01-01

    Unsteady computational simulations of a multi-element, high-lift configuration are performed. Emphasis is placed on accurate spatiotemporal resolution of the free shear layer in the slat-cove region. The excessive dissipative effects of the turbulence model, so prevalent in previous simulations, are circumvented by switching off the turbulence-production term in the slat cove region. The justifications and physical arguments for taking such a step are explained in detail. The removal of this excess damping allows the shear layer to amplify large-scale structures, to achieve a proper non-linear saturation state, and to permit vortex merging. The large-scale disturbances are self-excited, and unlike our prior fully turbulent simulations, no external forcing of the shear layer is required. To obtain the farfield acoustics, the Ffowcs Williams and Hawkings equation is evaluated numerically using the simulated time-accurate flow data. The present comparison between the computed and measured farfield acoustic spectra shows much better agreement for the amplitude and frequency content than past calculations. The effect of the angle-of-attack on the slat's flow features radiated acoustic field are also simulated presented.

  12. Mass Media Representation of Teaching: A Behaviour Analysis Approach.

    ERIC Educational Resources Information Center

    Hobbs, Sandy; Mackie, Stirling

    Although psychological studies of the mass media have been dominated by cognitivist and psychodynamic concepts, a study of the mass media using a behavior analysis method may be used to analyze the content of the mass media. By applying that analysis to fictional teacher-learner interactions an interpretation of those relationships can be made and…

  13. Letter: High-mass capabilities of positive-ion and negative-ion direct analysis in real time mass spectrometry.

    PubMed

    Gross, Jürgen H

    2016-01-01

    Of the ionic liquid 1-butyl-3-methylimidazolium (C(+)) tricyanomethide (A(-)) high-mass cluster ions of both positive ([C(n)A(n-1)](+)) and negative ([C(n-1)A(n)](-)) charge were generated and detected by direct analysis in real time (DART) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). After optimization of the settings of the DART ionization source and of the mass analyzer ions of m/z values unprecedented in DART-MS were detected. Thus, the upper m/z limits of positive-ion and negative-ion DART- MS were substantially expanded. Negative-ion DART-MS delivered cluster ions up to [C(15)A(16)](-), m/z 3527 (nominal mass of monoisotopic ion), while positive-ion DART-MS even yielded ions up to [C(30)A(29)](+), m/z 6784. The identification of the cluster ions is supported by their accurate mass and exact mass differences corresponding to CA between adjacent cluster ion peaks.

  14. A novel isotope analysis of oxygen in uranium oxides: comparison of secondary ion mass spectrometry, glow discharge mass spectrometry and thermal ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Pajo, L.; Tamborini, G.; Rasmussen, G.; Mayer, K.; Koch, L.

    2001-05-01

    The natural variation of the oxygen isotopic composition is used among geologists to determine paleotemperatures and the origin of minerals. In recent studies, oxygen isotopic composition has been recognized as a possible tool for identification of the origin of seized uranium oxides in nuclear forensic science. In the last 10 years, great effort has been made to develop new direct and accurate n( 18O)/ n( 16O) measurements methods. Traditionally, n( 18O)/ n( 16O) analyses are performed by gas mass spectrometry. In this work, a novel oxygen isotope analysis by thermal ionization mass spectrometry (TIMS), using metal oxide ion species (UO +), is compared to the direct methods: glow discharge mass spectrometry (GDMS) and secondary ion mass spectrometry (SIMS). Because of the possible application of the n( 18O)/ n( 16O) ratio in nuclear forensics science, the samples were solid, pure UO 2 or U 3O 8 particles. The precision achieved using TIMS analysis was 0.04%, which is similar or even better than the one obtained using the SIMS technique (0.05%), and clearly better if compared to that of GDMS (0.5%). The samples used by TIMS are micrograms in size. The suitability of TIMS as a n( 18O)/ n( 16O) measurement method is verified by SIMS measurements. In addition, TIMS results have been confirmed by characterizing the n( 18O)/ n( 16O) ratio of UO 2 sample also by the traditional method of static vacuum mass spectrometry at the University of Chicago.

  15. The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

    NASA Astrophysics Data System (ADS)

    López-Sanjuan, C.; Cenarro, A. J.; Varela, J.; Viironen, K.; Molino, A.; Benítez, N.; Arnalte-Mur, P.; Ascaso, B.; Díaz-García, L. A.; Fernández-Soto, A.; Jiménez-Teja, Y.; Márquez, I.; Masegosa, J.; Moles, M.; Pović, M.; Aguerri, J. A. L.; Alfaro, E.; Aparicio-Villegas, T.; Broadhurst, T.; Cabrera-Caño, J.; Castander, F. J.; Cepa, J.; Cerviño, M.; Cristóbal-Hornillos, D.; Del Olmo, A.; González Delgado, R. M.; Husillos, C.; Infante, L.; Martínez, V. J.; Perea, J.; Prada, F.; Quintana, J. M.

    2015-04-01

    Aims: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. Methods: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections. We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. Results: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20-1.1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2.7 ± 0.5) than for red galaxies (n = 1.3 ± 0.4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nmred = 0.57 ± 0.05 for red galaxies and Nmblue = 0.26 ± 0.02 for blue galaxies. Conclusions: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (CSIC).The catalogues, probabilities, and figures of the ALHAMBRA close pairs detected in Sect. 5.1 are available at http://https://cloud.iaa.csic.es/alhambra/catalogues/ClosePairs

  16. Quantitative analysis of LISA pathfinder test-mass noise

    NASA Astrophysics Data System (ADS)

    Ferraioli, Luigi; Congedo, Giuseppe; Hueller, Mauro; Vitale, Stefano; Hewitson, Martin; Nofrarias, Miquel; Armano, Michele

    2011-12-01

    LISA Pathfinder (LPF) is a mission aiming to test the critical technology for the forthcoming space-based gravitational-wave detectors. The main scientific objective of the LPF mission is to demonstrate test masses free falling with residual accelerations below 3×10-14ms-2/Hz at 1 mHz. Reaching such an ambitious target will require a significant amount of system optimization and characterization, which will in turn require accurate and quantitative noise analysis procedures. In this paper, we discuss two main problems associated with the analysis of the data from LPF: i) excess noise detection and ii) noise parameter identification. The mission is focused on the low-frequency region ([0.1, 10] mHz) of the available signal spectrum. In such a region, the signal is dominated by the force noise acting on test masses. At the same time, the mission duration is limited to 90 days and typical data segments will be 24 hours in length. Considering those constraints, noise analysis is expected to deal with a limited amount of non-Gaussian data, since the spectrum statistics will be far from Gaussian and the lowest available frequency is limited by the data length. In this paper, we analyze the details of the expected statistics for spectral data and develop two suitable excess noise estimators. One is based on the statistical properties of the integrated spectrum, the other is based on the Kolmogorov-Smirnov test. The sensitivity of the estimators is discussed theoretically for independent data, then the algorithms are tested on LPF synthetic data. The test on realistic LPF data allows the effect of spectral data correlations on the efficiency of the different noise excess estimators to be highlighted. It also reveals the versatility of the Kolmogorov-Smirnov approach, which can be adapted to provide reasonable results on correlated data from a modified version of the standard equations for the inversion of the test statistic. Closely related to excess noise detection, the

  17. TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology

    PubMed Central

    Hong, Dongwan; Park, Sung-Soo; Ju, Young Seok; Kim, Sheehyun; Shin, Jong-Yeon; Kim, Sujung; Yu, Saet-Byeol; Lee, Won-Chul; Lee, Seungbok; Park, Hansoo; Kim, Jong-Il; Seo, Jeong-Sun

    2011-01-01

    High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research. PMID:21051338

  18. Guided resonances on lithium niobate for extremely small electric field detection investigated by accurate sensitivity analysis.

    PubMed

    Qiu, Wentao; Ndao, Abdoulaye; Lu, Huihui; Bernal, Maria-Pilar; Baida, Fadi Issam

    2016-09-01

    We present a theoretical study of guided resonances (GR) on a thin film lithium niobate rectangular lattice photonic crystal by band diagram calculations and 3D Finite Difference Time Domain (FDTD) transmission investigations which cover a broad range of parameters. A photonic crystal with an active zone as small as 13μm×13μm×0.7μm can be easily designed to obtain a resonance Q value in the order of 1000. These resonances are then employed in electric field (E-field) sensing applications exploiting the electro optic (EO) effect of lithium niobate. A local field factor that is calculated locally for each FDTD cell is proposed to accurately estimate the sensitivity of GR based E-field sensor. The local field factor allows well agreement between simulations and reported experimental data therefore providing a valuable method in optimizing the GR structure to obtain high sensitivities. When these resonances are associated with sub-picometer optical spectrum analyzer and high field enhancement antenna design, an E-field probe with a sensitivity of 50 μV/m could be achieved. The results of our simulations could be also exploited in other EO based applications such as EEG (Electroencephalography) or ECG (Electrocardiography) probe and E-field frequency detector with an 'invisible' probe to the field being detected etc. PMID:27607627

  19. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

    PubMed Central

    Wang, Yi; Lu, James; Yu, Jin; Gibbs, Richard A.; Yu, Fuli

    2013-01-01

    Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical modeling of sequencing data; (2) variance ratio scoring, a variance-based statistic that discovers polymorphic loci with high sensitivity and specificity; and (3) BAM-specific binomial mixture modeling (BBMM), a clustering algorithm that generates robust genotype likelihoods from heterogeneous sequencing data. Last, we develop an imputation engine that refines raw genotype likelihoods to produce high-quality phased genotypes/haplotypes. Designed for large population studies, SNPTools' input/output (I/O) and storage aware design leads to improved computing performance on large sequencing data sets. We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray. PMID:23296920

  20. Accurate reliability analysis method for quantum-dot cellular automata circuits

    NASA Astrophysics Data System (ADS)

    Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo

    2015-10-01

    Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.

  1. Mechanical Analysis and Hierarchies of Multi-digit Synergies during Accurate Object Rotation

    PubMed Central

    Zhang, Wei; Olafsdottir, Halla B.; Zatsiorsky, Vladimir M.; Latash, Mark L.

    2009-01-01

    We studied the mechanical variables (the grip force and the total moment of force) and multi-digit synergies at two levels (the virtual finger-thumb level, VF-TH, and the individual finger level, IMRL) of a hypothetical control hierarchy during accurate rotation of a hand-held instrumented handle. Synergies were defined as co-varied changes in elemental variables (forces and moments of force) that stabilize the output at a particular level. Indices of multi-digit synergies showed higher values at the hierarchically higher level (VF-TH) for both normal and tangential forces. The moment of force was stabilized at both hierarchical levels during the steady-state phases but not during the movement. The results support the principles of superposition and of mechanical advantage. They also support an earlier hypothesis on an inherent trade-off between synergies at the two hierarchical levels, although the controller showed more subtle and versatile synergic control than the one hypothesized earlier. PMID:19799165

  2. Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry

    PubMed Central

    Potgieter, Matthys G.; Nakedi, Kehilwe C.; Ambler, Jon M.; Nel, Andrew J. M.; Garnett, Shaun; Soares, Nelson C.; Mulder, Nicola; Blackburn, Jonathan M.

    2016-01-01

    Biochemical evidence is vital for accurate genome annotation. The integration of experimental data collected at the proteome level using high resolution mass spectrometry allows for improvements in genome annotation by providing evidence for novel gene models, while validating or modifying others. Here, we report the results of a proteogenomic analysis of a reference strain of Mycobacterium smegmatis (mc2155), a fast growing model organism for the pathogenic Mycobacterium tuberculosis—the causative agent for Tuberculosis. By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to a Reference protein, and 63 ORFs not previously annotated to a Reference protein. Further, the translational start site (TSS) was validated for 558 Reference proteome gene models, while upstream translational evidence was identified for 81. In addition, N-terminus derived peptide identifications allowed for downstream TSS modification of a further 24 gene models. We validated the existence of six previously described interrupted coding sequences at the peptide level, and provide evidence for four novel frameshift positions. Analysis of peptide posterior error probability (PEP) scores indicates high-confidence novel peptide identifications and shows that the genome of M. smegmatis mc2155 is not yet fully annotated. Data are available via ProteomeXchange with identifier PXD003500. PMID:27092112

  3. A Nanoengineered Conductometric Device for Accurate Analysis of Elemental Mercury Vapor.

    PubMed

    Griffin, Matthew J; Kabir, K M Mohibul; Coyle, Victoria E; Kandjani, Ahmad Esmaielzadeh; Sabri, Ylias M; Ippolito, Samuel J; Bhargava, Suresh K

    2016-02-01

    We developed a novel conductometric device with nanostructured gold (Au) sensitive layer which showed high-performance for elemental mercury (Hg(0)) vapor detection under simulated conditions that resemble harsh industrial environments. That is, the Hg(0) vapor sensing performance of the developed sensor was investigated under different operating temperatures (30-130 °C) and working conditions (i.e., humid) as well as in the presence of various interfering gas species, including ammonia (NH3), hydrogen sulfide (H2S), nitric oxide (NO), carbon mono-oxide (CO), carbon dioxide (CO2), sulfur dioxide (SO2), hydrogen (H2), methane (CH4), and volatile organic compounds (VOCs) such as ethylmercaptan (EM), acetaldehyde (MeCHO) and methyl ethyl ketone (MEK) among others. The results indicate that the introduction of Au nanostructures (referred to as nanospikes) on the sensor's surface enhanced the sensitivity toward Hg(0) vapor by up-to 450%. The newly developed sensor exhibited a limit of detection (LoD) (∼35 μg/m(3)), repeatability (∼94%), desorption efficiency (100%) and selectivity (∼93%) when exposed to different concentrations of Hg(0) vapor (0.5 to 9.1 mg/m(3)) and interfering gas species at a chosen operating temperature of 105 °C. Furthermore, the sensor was also found to show 91% average selectivity when exposed toward harsher industrial gases such as NO, CO, CO2, and SO2 along with same concentrations of Hg(0) vapor in similar operating conditions. In fact, this is the first time a conductometric sensor is shown to have high selectivity toward Hg(0) vapor even in the presence of H2S. Overall results indicate that the developed sensor has immense potential to be used as accurate online Hg(0) vapor monitoring technology within industrial processes.

  4. Accurate and noninvasive embryos screening during in vitro fertilization (IVF) assisted by Raman analysis of embryos culture medium Accurate and noninvasive embryos screening during IVF

    NASA Astrophysics Data System (ADS)

    Shen, A. G.; Peng, J.; Zhao, Q. H.; Su, L.; Wang, X. H.; Hu, J. M.; Yang, J.

    2012-04-01

    In combination with morphological evaluation tests, we employ Raman spectroscopy to select higher potential reproductive embryos during in vitro fertilization (IVF) based on chemical composition of embryos culture medium. In this study, 57 Raman spectra are acquired from both higher and lower quality embryos culture medium (ECM) from 10 patients which have been preliminarily confirmed by clinical assay. Data are fit by using a linear combination model of least squares method in which 12 basis spectra represent the chemical features of ECM. The final fitting coefficients provide insight into the chemical compositions of culture medium samples and are subsequently used as criterion to evaluate the quality of embryos. The relative fitting coefficients ratios of sodium pyruvate/albumin and phenylalanine/albumin seem act as key roles in the embryo screening, attaining 85.7% accuracy in comparison with clinical pregnancy. The good results demonstrate that Raman spectroscopy therefore is an important candidate for an accurate and noninvasive screening of higher quality embryos, which potentially decrease the time-consuming clinical trials during IVF.

  5. Can Raters with Reduced Job Descriptive Information Provide Accurate Position Analysis Questionnaire (PAQ) Ratings?

    ERIC Educational Resources Information Center

    Friedman, Lee; Harvey, Robert J.

    1986-01-01

    Job-naive raters provided with job descriptive information made Position Analysis Questionnaire (PAQ) ratings which were validated against ratings of job analysts who were also job content experts. None of the reduced job descriptive information conditions enabled job-naive raters to obtain either acceptable levels of convergent validity with…

  6. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  7. Solid rocket booster internal flow analysis by highly accurate adaptive computational methods

    NASA Technical Reports Server (NTRS)

    Huang, C. Y.; Tworzydlo, W.; Oden, J. T.; Bass, J. M.; Cullen, C.; Vadaketh, S.

    1991-01-01

    The primary objective of this project was to develop an adaptive finite element flow solver for simulating internal flows in the solid rocket booster. Described here is a unique flow simulator code for analyzing highly complex flow phenomena in the solid rocket booster. New methodologies and features incorporated into this analysis tool are described.

  8. 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). PMID:23106487

  9. 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.

  10. Analysis of radioactive metals by spark source mass spectrometry.

    PubMed

    Johnson, A J; Kozy, A; Morris, R N

    1969-04-01

    A spark source mass spectrograph with photographic plate recording has been adapted for the analysis of plutonium and americium metals. Over seventy elements can be determined simultaneously in these metals. A comparison has been made between results obtained by mass spectrography and by conventional methods for impurity elements. The operations involved in handling radioactive materials in the mass spectrograph are also discussed. PMID:18960537

  11. Determination of T-2 and HT-2 toxins from maize by direct analysis in real time mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Direct analysis in real time (DART) ionization coupled to mass spectrometry (MS) was used for the rapid quantitative analysis of T-2 toxin, and the related HT-2 toxin, extracted from corn. Sample preparation procedures and instrument parameters were optimized to obtain sensitive and accurate determi...

  12. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    PubMed

    Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

    2016-08-30

    High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease. PMID:27575624

  13. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    PubMed

    Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

    2016-08-30

    High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

  14. 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. PMID:26141269

  15. 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.

  16. Apparatus for use in rapid and accurate controlled-potential coulometric analysis

    DOEpatents

    Frazzini, Thomas L.; Holland, Michael K.; Pietri, Charles E.; Weiss, Jon R.

    1981-01-01

    An apparatus for controlled-potential coulometric analysis of a solution includes a cell to contain the solution to be analyzed and a plurality of electrodes to contact the solution in the cell. Means are provided to stir the solution and to control the atmosphere above it. A potentiostat connected to the electrodes controls potential differences among the electrodes. An electronic circuit connected to the potentiostat provides analog-to-digital conversion and displays a precise count of charge transfer during a desired chemical process. This count provides a measure of the amount of an unknown substance in the solution.

  17. Accurate RT-qPCR gene expression analysis on cell culture lysates

    PubMed Central

    Van Peer, Gert; Mestdagh, Pieter; Vandesompele, Jo

    2012-01-01

    Gene expression quantification on cultured cells using the reverse transcription quantitative polymerase chain reaction (RT-qPCR) typically involves an RNA purification step that limits sample processing throughput and precludes parallel analysis of large numbers of samples. An approach in which cDNA synthesis is carried out on crude cell lysates instead of on purified RNA samples can offer a fast and straightforward alternative. Here, we evaluate such an approach, benchmarking Ambion's Cells-to-CT kit with the classic workflow of RNA purification and cDNA synthesis, and demonstrate its good accuracy and superior sensitivity. PMID:22355736

  18. Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics

    PubMed Central

    Xu, Xiayu; Ding, Wenxiang; Wang, Xuemin; Cao, Ruofan; Zhang, Maiye; Lv, Peilin; Xu, Feng

    2016-01-01

    Retinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries. PMID:27698369

  19. High Resolution Melting Analysis: A Rapid and Accurate Method to Detect CALR Mutations

    PubMed Central

    Moreno, Melania; Torres, Laura; Santana-Lopez, Gonzalo; Rodriguez-Medina, Carlos; Perera, María; Bellosillo, Beatriz; de la Iglesia, Silvia; Molero, Teresa; Gomez-Casares, Maria Teresa

    2014-01-01

    Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations. PMID:25068507

  20. Tritium speciation in nuclear reactor bioshield concrete and its impact on accurate analysis.

    PubMed

    Kim, Dae Ji; E Warwick, Phillip; Croudace, Ian W

    2008-07-15

    Tritium ((3)H) is produced in nuclear reactors via several neutron-induced reactions [(2)H(n, gamma)(3)H, (6)Li(n, alpha)(3)H, (10)B(n, 2alpha)(3)H, (14)N(n, (3)H)(12)C, and ternary fission (fission yield <0.01%)]. Typically, (3)H is present as tritiated water (HTO) and can become adsorbed into structural concrete from the surface inward where it will be held in a weakly bound form. However, a systematic analysis of a sequence of subsamples taken from a reactor bioshield using combustion and liquid scintillation analysis has identified two forms of (3)H, one weakly bound and one strongly bound. The strongly bound tritium, which originates from neutron capture on trace lithium ((6)Li) within mineral phases, requires temperatures in excess of 350 degrees C to achieve quantitative recovery. The weakly bound form of tritium can be liberated at significantly lower temperatures (100 degrees C) as HTO and is associated with dehydration of hydrous mineral components. Without an appreciation that two forms of tritium can exist in reactor bioshields, the (3)H content of samples may be severely underestimated using conventional analytical approaches. These findings exemplify the need to develop robust radioactive waste characterization procedures in support of nuclear decommissioning programs. PMID:18543953

  1. Tritium speciation in nuclear reactor bioshield concrete and its impact on accurate analysis.

    PubMed

    Kim, Dae Ji; E Warwick, Phillip; Croudace, Ian W

    2008-07-15

    Tritium ((3)H) is produced in nuclear reactors via several neutron-induced reactions [(2)H(n, gamma)(3)H, (6)Li(n, alpha)(3)H, (10)B(n, 2alpha)(3)H, (14)N(n, (3)H)(12)C, and ternary fission (fission yield <0.01%)]. Typically, (3)H is present as tritiated water (HTO) and can become adsorbed into structural concrete from the surface inward where it will be held in a weakly bound form. However, a systematic analysis of a sequence of subsamples taken from a reactor bioshield using combustion and liquid scintillation analysis has identified two forms of (3)H, one weakly bound and one strongly bound. The strongly bound tritium, which originates from neutron capture on trace lithium ((6)Li) within mineral phases, requires temperatures in excess of 350 degrees C to achieve quantitative recovery. The weakly bound form of tritium can be liberated at significantly lower temperatures (100 degrees C) as HTO and is associated with dehydration of hydrous mineral components. Without an appreciation that two forms of tritium can exist in reactor bioshields, the (3)H content of samples may be severely underestimated using conventional analytical approaches. These findings exemplify the need to develop robust radioactive waste characterization procedures in support of nuclear decommissioning programs.

  2. Mass quantity gauging by RF mode analysis

    NASA Technical Reports Server (NTRS)

    Collier, R. S.; Ellerbruch, D.; Cruz, J. E.; Stokes, R. W.; Luft, P. E.; Peterson, R. G.; Hiester, A. E.

    1973-01-01

    Work done to date is reported concerning Radio Frequency Mass Quantity Gauging. Experimental apparatus has been designed and tested which measures the resonant frequencies of a tank in the time domain. These frequencies correspond to the total mass of fluid within the tank. Experimental results are discussed for nitrogen and hydrogen in normal gravity both in the supercritical state and also in the two phase (liquid-gas) region. Theoretical discussions for more general cases are given.

  3. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  4. Simulating Expert Clinical Comprehension: Adapting Latent Semantic Analysis to Accurately Extract Clinical Concepts from Psychiatric Narrative

    PubMed Central

    Cohen, Trevor; Blatter, Brett; Patel, Vimla

    2008-01-01

    Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested. PMID:18455483

  5. Computer-implemented system and method for automated and highly accurate plaque analysis, reporting, and visualization

    NASA Technical Reports Server (NTRS)

    Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)

    2008-01-01

    A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.

  6. Quantum analysis of a bandpass Purcell filter for accurate qubit readout

    NASA Astrophysics Data System (ADS)

    Sete, Eyob A.; Martinis, John M.; Korotkov, Alexander N.

    2015-03-01

    In a circuit QED setup the readout fidelity of a superconducting qubit is partially limited by the qubit relaxation through the resonator into a transmission line, which is also known as the Purcell effect. One way to suppress this effect is to employ a filter, which impedes microwave propagation at the qubit frequency. We present a quantum analysis for the bandpass Purcell filter that was recently realized by E. Jeffrey et al. [1]. Using experimental parameters, we show that the bandpass filter suppresses the qubit relaxation rate by two orders of magnitude while keeping the measurement rate the same. We also show that in the presence of a microwave drive the qubit relaxation rate further decreases with increasing drive strength.

  7. A Method for the Identification of Lipid Classes Based on Referenced Kendrick Mass Analysis

    PubMed Central

    Lerno, Larry A.; German, J. Bruce; Lebrilla, Carlito B.

    2010-01-01

    A rapid method for the determination of lipid classes with high sensitivity is described. The referenced Kendrick mass defect (RKMD) and RKMD plots are novel adaptations of the Kendrick mass defect analysis that allows for the rapid identification of members of a homologous series in addition to identifying the lipid class. Assignment of lipid classes by the RKMD method is accomplished by conversion of the lipid masses to the Kendrick mass scale and then referencing the converted masses to each lipid class. Referencing of the masses to a given lipid class is achieved by first subtracting the heteroatom and lipid backbone contributions to the mass defect, leaving behind the contribution to the mass by the fatty acid constituents. The final step in the referencing makes use of spacing differences in mass defects between members of the same Kendrick class to identify members of the lipid class being referenced. The end result of this is that a lipid belonging to the class being referenced will have an integer RKMD with the value of the integer being the degrees of unsaturation in the lipid. The RKMD method was able to successfully identify the lipids in an idealized data set consisting of 160 lipids drawn from the glyceride and phosphoglyceride classes. As a real world example the lipid extract from bovine milk was analyzed using both accurate mass measurements and the RKMD method. PMID:20426402

  8. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

    PubMed Central

    2010-01-01

    High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

  9. Wind effect on PV module temperature: Analysis of different techniques for an accurate estimation.

    NASA Astrophysics Data System (ADS)

    Schwingshackl, Clemens; Petitta, Marcello; Ernst Wagner, Jochen; Belluardo, Giorgio; Moser, David; Castelli, Mariapina; Zebisch, Marc; Tetzlaff, Anke

    2013-04-01

    In this abstract a study on the influence of wind to model the PV module temperature is presented. This study is carried out in the framework of the PV-Alps INTERREG project in which the potential of different photovoltaic technologies is analysed for alpine regions. The PV module temperature depends on different parameters, such as ambient temperature, irradiance, wind speed and PV technology [1]. In most models, a very simple approach is used, where the PV module temperature is calculated from NOCT (nominal operating cell temperature), ambient temperature and irradiance alone [2]. In this study the influence of wind speed on the PV module temperature was investigated. First, different approaches suggested by various authors were tested [1], [2], [3], [4], [5]. For our analysis, temperature, irradiance and wind data from a PV test facility at the airport Bolzano (South Tyrol, Italy) from the EURAC Institute of Renewable Energies were used. The PV module temperature was calculated with different models and compared to the measured PV module temperature at the single panels. The best results were achieved with the approach suggested by Skoplaki et al. [1]. Preliminary results indicate that for all PV technologies which were tested (monocrystalline, amorphous, microcrystalline and polycrystalline silicon and cadmium telluride), modelled and measured PV module temperatures show a higher agreement (RMSE about 3-4 K) compared to standard approaches in which wind is not considered. For further investigation the in-situ measured wind velocities were replaced with wind data from numerical weather forecast models (ECMWF, reanalysis fields). Our results show that the PV module temperature calculated with wind data from ECMWF is still in very good agreement with the measured one (R² > 0.9 for all technologies). Compared to the previous analysis, we find comparable mean values and an increasing standard deviation. These results open a promising approach for PV module

  10. Accurate analysis of taurine, anserine, carnosine and free amino acids in a cattle muscle biopsy sample.

    PubMed

    Imanari, Mai; Higuchi, Mikito; Shiba, Nobuya; Watanabe, Akira

    2010-06-01

    We have established an analysis method for some free amino acids (FAAs), as well as taurine (Tau), anserine (Ans) and carnosine (Car), in a fresh biopsy sample from cattle muscle. A series of model biopsy samples, corresponding to the mixtures of lean meat, fat and connective tissue, was prepared and showed high correlation coefficients between the compound concentration and the 3-methylhistidine (3-MeHis) content derived from hydrolysis of the biopsy sample (r = 0.74-0.95, P < 0.01). Interference from blood contamination could not be neglected, because the concentration of some FAAs in blood was comparable to that in muscle. However, it was possible to control the contamination of Tau, Ans, Car, glutamic acid, glutamine, asparatic acid and alanine to less than 5.0% when the blood contamination was controlled to less than 23%.These results suggest the necessity of measuring 3-MeHis as an index of lean meat and hemoglobin as an index of blood contamination when compounds in muscle biopsy samples are evaluated. We have carried out a series of these analyses using one biopsy sample and reveal differences in Tau, Ans, Car and some FAAs in beef muscle after different feeding regimes.

  11. Photo-detachment signal analysis to accurately determine electronegativity, electron temperature, and charged species density

    NASA Astrophysics Data System (ADS)

    Oudini, N.; Sirse, N.; Taccogna, F.; Ellingboe, A. R.; Bendib, A.

    2016-09-01

    Laser pulse induced photo-detachment combined with Langmuir probing has been introduced to diagnose plasma electronegativity. This technique uses a laser pulse to convert negative ions into electron-atom pairs and tracks the change of electron saturation current by a Langmuir probe. The existing model determines plasma electronegativity as the ratio of electron saturation current before and after detachment. However, this model depends on various assumptions and neglects the formation of a potential barrier between the laser channel and surrounding electronegative plasma. In this letter, we present a new analytical model to analyze photo-detachment signals in order to improve the accuracy of electronegativity measurements and extend this technique for measuring electron temperature and charged species density. This analytical model is supported by Particle-In-Cell simulation of electronegative plasma dynamics following laser photo-detachment. The analysis of the signal, detected on a simulated probe, shows that the present analytical model determines electronegativity, electron temperature, and plasma density with a relative error of ˜20%, ˜20%, and ˜50%, respectively, whereas the electronegativity obtained from a previous model is underestimated by an order of magnitude.

  12. A Cost-Benefit and Accurate Method for Assessing Microalbuminuria: Single versus Frequent Urine Analysis

    PubMed Central

    Hemmati, Roholla; Gharipour, Mojgan; Khosravi, Alireza; Jozan, Mahnaz

    2013-01-01

    Background. The purpose of this study was to answer the question whether a single testing for microalbuminuria results in a reliable conclusion leading costs saving. Methods. This current cross-sectional study included a total of 126 consecutive persons. Microalbuminuria was assessed by collection of two fasting random urine specimens on arrival to the clinic as well as one week later in the morning. Results. In overall, 17 out of 126 participants suffered from microalbuminuria that, among them, 12 subjects were also diagnosed as microalbuminuria once assessing this factor with a sensitivity of 70.6%, a specificity of 100%, a PPV of 100%, a NPV of 95.6%, and an accuracy of 96.0%. The measured sensitivity, specificity, PVV, NPV, and accuracy in hypertensive patients were 73.3%, 100%, 100%, 94.8%, and 95.5%, respectively. Also, these rates in nonhypertensive groups were 50.0%, 100%, 100%, 97.3%, and 97.4%, respectively. According to the ROC curve analysis, a single measurement of UACR had a high value for discriminating defected from normal renal function state (c = 0.989). Urinary albumin concentration in a single measurement had also high discriminative value for diagnosis of damaged kidney (c = 0.995). Conclusion. The single testing of both UACR and urine albumin level rather frequent testing leads to high diagnostic sensitivity, specificity, and accuracy as well as high predictive values in total population and also in hypertensive subgroups. PMID:24455207

  13. Borehole flowmeter logging for the accurate design and analysis of tracer tests.

    PubMed

    Basiricò, Stefano; Crosta, Giovanni B; Frattini, Paolo; Villa, Alberto; Godio, Alberto

    2015-04-01

    Tracer tests often give ambiguous interpretations that may be due to the erroneous location of sampling points and/or the lack of flow rate measurements through the sampler. To obtain more reliable tracer test results, we propose a methodology that optimizes the design and analysis of tracer tests in a cross borehole mode by using vertical borehole flow rate measurements. Experiments using this approach, herein defined as the Bh-flow tracer test, have been performed by implementing three sequential steps: (1) single-hole flowmeter test, (2) cross-hole flowmeter test, and (3) tracer test. At the experimental site, core logging, pumping tests, and static water-level measurements were previously carried out to determine stratigraphy, fracture characteristics, and bulk hydraulic conductivity. Single-hole flowmeter testing makes it possible to detect the presence of vertical flows as well as inflow and outflow zones, whereas cross-hole flowmeter testing detects the presence of connections along sets of flow conduits or discontinuities intercepted by boreholes. Finally, the specific pathways and rates of groundwater flow through selected flowpaths are determined by tracer testing. We conclude that the combined use of single and cross-borehole flowmeter tests is fundamental to the formulation of the tracer test strategy and interpretation of the tracer test results. PMID:25417730

  14. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing

    PubMed Central

    Guo, Xiaoge; Lehner, Kevin; O’Connell, Karen; Zhang, Jenny; Dave, Sandeep S.; Jinks-Robertson, Sue

    2015-01-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  15. An analysis of space power system masses

    NASA Technical Reports Server (NTRS)

    Kenny, Barbara H.; Cull, Ronald C.; Kankam, M. David

    1990-01-01

    Various space electrical power system masses are analyzed with particular emphasis on the power management and distribution (PMAD) portion. The electrical power system (EPS) is divided into functional blocks: source, interconnection, storage, transmission, distribution, system control and load. The PMAD subsystem is defined as all the blocks between the source, storage and load, plus the power conditioning equipment required for the source, storage and load. The EPS mass of a wide range of spacecraft is then classified as source, storage or PMAD and tabulated in a database. The intent of the database is to serve as a reference source for PMAD masses of existing and in-design spacecraft. The PMAD masses in the database range from 40 kg/kW to 183 kg/kW across the spacecraft systems studied. Factors influencing the power system mass are identified. These include the total spacecraft power requirements, total amount of load capacity and physical size of the spacecraft. It is found that a new utility class of power systems, represented by Space Station Freedom, is evolving.

  16. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed Central

    Tyson, G. H.; Chen, Y.; Li, C.; Mukherjee, S.; Young, S.; Lam, C.; Folster, J. P.; Whichard, J. M.; McDermott, P. F.

    2015-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  17. Method for the Compound Annotation of Conjugates in Nontargeted Metabolomics Using Accurate Mass Spectrometry, Multistage Product Ion Spectra and Compound Database Searching.

    PubMed

    Ogura, Tairo; Bamba, Takeshi; Tai, Akihiro; Fukusaki, Eiichiro

    2015-01-01

    Owing to biotransformation, xenobiotics are often found in conjugated form in biological samples such as urine and plasma. Liquid chromatography coupled with accurate mass spectrometry with multistage collision-induced dissociation provides spectral information concerning these metabolites in complex materials. Unfortunately, compound databases typically do not contain a sufficient number of records for such conjugates. We report here on the development of a novel protocol, referred to as ChemProphet, to annotate compounds, including conjugates, using compound databases such as PubChem and ChemSpider. The annotation of conjugates involves three steps: 1. Recognition of the type and number of conjugates in the sample; 2. Compound search and annotation of the deconjugated form; and 3. In silico evaluation of the candidate conjugate. ChemProphet assigns a spectrum to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum. When finished, it annotates the candidates assigning a rank for each candidate based on the calculated score that ranks its relative likelihood. We assessed our protocol by annotating a benchmark dataset by including the product ion spectra for 102 compounds, annotating the commercially available standard for quercetin 3-glucuronide, and by conducting a model experiment using urine from mice that had been administered a green tea extract. The results show that by using the ChemProphet approach, it is possible to annotate not only the deconjugated molecules but also the conjugated molecules using an automatic interpretation method based on deconjugation that involves multistage collision-induced dissociation and in silico calculated conjugation.

  18. Mass Spectral Analysis of PAMPRE Tholins

    NASA Astrophysics Data System (ADS)

    Horst, Sarah; Adams, R.; Carrasco, N.; Djevahirdjian, L.; Pernot, P.; Sciamma-O'Brien, E.; Szopa, C.; Thissen, R.; Vuitton, V.; Yelle, R. V.

    2009-09-01

    The destruction of N2 and CH4 and subsequent complex chemical processes lead to the formation of organic aerosols in Titan's atmosphere. To further the understanding of the formation and composition of these aerosols, laboratory experiments have been designed to produce aerosols under Titan atmospheric conditions. We have characterized tholins generated by the PAMPRE (Production d'Aérosols en Microgravité par Plasma REactif) experiment. The PAMPRE experiment uses capacitively coupled RF plasma discharge to initiate the chemistry between N2 and CH4 that leads to the production of solid particles (tholins). The tholins form and grow while levitated in the plasma, which minimizes any possible wall effects. Tholins were generated using 3 different N2/CH4 gas mixtures: 98/2, 95/5, 90/10. The tholins were characterized using the LTQ-Orbitrap XL mass spectrometer, which has a resolving power of 1.e5 at 400 amu and accuracy in exact mass determination of 2 ppm. Thousands of molecules have been identified ranging in mass from 50 to 800 amu. The spectra exhibit groups of peaks with a mass periodicity of 13.5, which provides insight into the chemical processes involved in tholin synthesis. The application of the knowledge gained from these experiments to the study of corresponding processes on Titan will be briefly discussed.

  19. In situ mass analysis of particles by surface ionization mass spectrometry

    NASA Technical Reports Server (NTRS)

    Lassiter, W. S.; Moen, A. L.

    1974-01-01

    A qualitative study of the application of surface ionization and mass spectrometry to the in situ detection and constituent analysis of atmospheric particles was conducted. The technique consists of mass analysis of ions formed as a result of impingement of a stream of particles on a hot filament where, it is presumed, surface ionization takes place. Laboratory air particles containing K, Ca, and possibly hydrocarbons were detected. Other known particles such as Al2O3, Pb(NO3)2, and Cr2O3 were analyzed by detecting the respective metal atoms making up the particles. In some cases, mass numbers indicative of compounds making up the particles were detected showing surface ionization of particles sometimes leads to chemical analysis as well as to elemental analysis. Individual particles were detected, and it was shown that the technique is sensitive to Al2O3 particles with a mass of a few nanograms.

  20. Identification and Characterization of Indole and Oxindole Alkaloids from Leaves of Mitragyna speciosa Korth Using Liquid Chromatography-Accurate QToF Mass Spectrometry.

    PubMed

    Avula, Bharathi; Sagi, Satyanarayanaraju; Wang, Yan-Hong; Wang, Mei; Ali, Zulfiqar; Smillie, Troy J; Zweigenbaum, Jerry; Khan, Ikhlas A

    2015-01-01

    Alkaloids have been reported to be the major physiologically active constituents in Mitragyna. An analytical method was developed to provide an alternative, fast method for characterization of alkaloids from various M. speciosa samples. The separation was achieved using an RP octylsilyl (C8) column, MS detection, and a water-acetonitrile with formic acid gradient as the mobile phase. Ultra-HPLC/quadrupole time-of-flight MS analysis and characterization were performed on 12 corynanthe-type indole/oxindole alkaloids obtained from the leaves of M. speciosa Korth. The indoles and oxindoles had an open E ring with or without substitution occurring at the C9 position. The full single mass spectrum of alkaloids showed a strong signal for the protonated molecule [M+H]+. The product ion spectrum of mitragynine type of alkaloids showed strong response at m/z=174.0901 suggestive of an ion containing an odd number of nitrogen atoms corresponding to formula C11H12NO, which is characteristic of indole alkaloids. A multivariate statistical analysis technique, principal component analysis, was used to show discrimination between the M. speciosa samples. The results indicated that the analytical method is suitable for QC testing of various Mitragyna commercial samples and can be used to evaluate market products purported to contain M. speciosa. PMID:25857873

  1. Identification and Characterization of Indole and Oxindole Alkaloids from Leaves of Mitragyna speciosa Korth Using Liquid Chromatography-Accurate QToF Mass Spectrometry.

    PubMed

    Avula, Bharathi; Sagi, Satyanarayanaraju; Wang, Yan-Hong; Wang, Mei; Ali, Zulfiqar; Smillie, Troy J; Zweigenbaum, Jerry; Khan, Ikhlas A

    2015-01-01

    Alkaloids have been reported to be the major physiologically active constituents in Mitragyna. An analytical method was developed to provide an alternative, fast method for characterization of alkaloids from various M. speciosa samples. The separation was achieved using an RP octylsilyl (C8) column, MS detection, and a water-acetonitrile with formic acid gradient as the mobile phase. Ultra-HPLC/quadrupole time-of-flight MS analysis and characterization were performed on 12 corynanthe-type indole/oxindole alkaloids obtained from the leaves of M. speciosa Korth. The indoles and oxindoles had an open E ring with or without substitution occurring at the C9 position. The full single mass spectrum of alkaloids showed a strong signal for the protonated molecule [M+H]+. The product ion spectrum of mitragynine type of alkaloids showed strong response at m/z=174.0901 suggestive of an ion containing an odd number of nitrogen atoms corresponding to formula C11H12NO, which is characteristic of indole alkaloids. A multivariate statistical analysis technique, principal component analysis, was used to show discrimination between the M. speciosa samples. The results indicated that the analytical method is suitable for QC testing of various Mitragyna commercial samples and can be used to evaluate market products purported to contain M. speciosa.

  2. Particle analysis using laser ablation mass spectroscopy

    DOEpatents

    Parker, Eric P.; Rosenthal, Stephen E.; Trahan, Michael W.; Wagner, John S.

    2003-09-09

    The present invention provides a method of quickly identifying bioaerosols by class, even if the subject bioaerosol has not been previously encountered. The method begins by collecting laser ablation mass spectra from known particles. The spectra are correlated with the known particles, including the species of particle and the classification (e.g., bacteria). The spectra can then be used to train a neural network, for example using genetic algorithm-based training, to recognize each spectra and to recognize characteristics of the classifications. The spectra can also be used in a multivariate patch algorithm. Laser ablation mass specta from unknown particles can be presented as inputs to the trained neural net for identification as to classification. The description below first describes suitable intelligent algorithms and multivariate patch algorithms, then presents an example of the present invention including results.

  3. Herbal medicine analysis by liquid chromatography/time-of-flight mass spectrometry.

    PubMed

    Zhou, Jian-Liang; Qi, Lian-Wen; Li, Ping

    2009-10-30

    The fact that the effects of herbal medicines (HMs) are brought about by their chemical constituents has created a critical demand for powerful analytical tools performing the chemical analysis to assure their efficacy, safety and quality. Liquid chromatography coupled to mass spectrometry (LC-MS) is an excellent technique to analyze multi-components in complex herbal matrices. Due to its inherent characteristics of accurate mass measurements and high resolution, time-of-flight (TOF) MS is well-suited to this field, especially for qualitative applications. The purpose of this article is to provide an overview on the potential of TOF, including the hybrid quadrupole- and ion trap-TOF (QTOF and IT-TOF), hyphenated to LC for chemical analysis in HMs or HM-treated biological samples. The peculiarities of LC-(Q/IT)TOF-MS for the analysis of HMs are discussed first, including applied stationary phase, mobile-phase selection, accurate mass measurements, fragmentation and selectivity. The final section is devoted to describing the applicability of LC-(Q/IT)TOF-MS to routine analysis of multi-components, including target and non-target (unknown) compounds, in herbal samples, emphasizing both the advantages and limitations of this approach for qualitative and quantitative purposes. The potential and future trends of fast high-performance liquid chromatography (HPLC) (e.g. rapid resolution LC and ultra-performance LC) coupled to (Q)TOF-MS for chemical analysis of HMs are highlighted.

  4. PTMSearchPlus: Software Tool for Automated Protein Identification and Post-Translational and Post-Translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-Up Mass Spectrometric Data Searches

    SciTech Connect

    Kertesz, Vilmos; Connelly, Heather M; Erickson, Brian K; Hettich, Robert {Bob} L

    2009-01-01

    PTMSearchPlus is a software tool for the automated integration of accurate intact protein mass (AIPM) and bottom-up (BU) mass spectra searches/data in order to both confidently identify the intact proteins and to characterize their post-translational modifications (PTMs). The development of PTMSearchPlus was motivated by the desire to effectively integrate high-resolution intact protein molecular masses with bottom-up peptide MS/MS data. PTMSearchPlus requires as input both intact protein and proteolytic peptide mass spectra collected from the same protein mixture, a FASTA protein database, and a selection of possible PTMs, the types and ranges of which can be specified. The output of PTMSearchPlus is a list of intact and modified proteins matching the AIPM data concomitant with their respective peptides found by the BU search. This list also contains protein and peptide sequence coverage information, scores, etc. that can be used for further evaluation or refiltering of the results. Corresponding and annotated AIPM and BU mass spectra are also displayed for visual inspection when a listed protein or a peptide is selected. These and other controls ensure that the user can manually evaluate, modify (e.g., remove obvious false positives, low quality spectra etc.), and save the results of the automated search if necessary. Driven by the exponential growth in the number of possible peptide candidates in a BU search when multiple PTMs are probed, the advantages on search speed by limiting the total number of possible PTMs on a peptide in the BU search or by performing an AIPM predicted BU search are also discussed in addition to the integration approach. The features of PTMSearchPlus are demonstrated using both a protein standard mixture and a complex protein mixture from Escherichia coli. Experimental data revealed a unique advantage of coupling AIPM and the BU data sets that is mutually beneficial for both approaches. Namely, AIPM data can confirm that no PTM peptides

  5. PTMSearchPlus: A Software Tool for Automated Protein Identification and Post-Translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-Up Mass Spectrometric Data Searches

    SciTech Connect

    Kertesz, Vilmos; Connelly, Heather M; Erickson, Brian K; Hettich, Robert {Bob} L

    2009-01-01

    PTMSearchPlus is a software tool for the automated integration of accurate intact protein mass (AIPM) and bottom-up (BU) mass spectra searches/data in order to both confidently identify the intact proteins and to characterize their post-translational modifications (PTMs). The development of PTMSearchPlus was motivated by the desire to effectively integrate high resolution intact protein molecular masses with bottom-up peptide MS/MS data. PTMSearchPlus requires as input both intact protein and proteolytic peptide mass spectra collected from the same protein mixture, a FASTA protein database, and a selection of possible PTMs, the types and ranges of which can be specified. The output of PTMSearchPlus is a list of intact and modified proteins matching the AIPM data concomitant with their respective peptides found by the BU search. This list also contains protein and peptide sequence coverage information, scores, etc. that can be used for further evaluation or refiltering of the results. Corresponding and annotated AIPM and BU mass spectra are also displayed for visual inspection when a listed protein or a peptide is selected. These and other controls ensure that the user can manually evaluate, modify (e.g. remove obvious false positives, low quality spectra etc.), and save the results of the automated search if necessary. Driven by the exponential growth in the number of possible peptide candidates in a BU search when multiple PTMs are probed, the advantages on search speed by limiting the total number of possible PTMs on a peptide in the BU search or by performing an AIPM predicted BU search are also discussed in addition to the integration approach. The features of PTMSearchPlus are demonstrated using both a protein standard mixture and a complex protein mixture from Escherichia coli. Experimental data revealed a unique advantage of coupling AIPM and the BU datasets that is mutually beneficial for both approaches. Namely, AIPM data can confirm that no PTM peptides

  6. Mass spectrometric analysis of monolayer protected nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhu, Zhengjiang

    Monolayer protected nanoparticles (NPs) include an inorganic core and a monolayer of organic ligands. The wide variety of core materials and the tunable surface monolayers make NPs promising materials for numerous applications. Concerns related to unforeseen human health and environmental impacts of NPs have also been raised. In this thesis, new analytical methods based on mass spectrometry are developed to understand the fate, transport, and biodistributions of NPs in the complex biological systems. A laser desorption/ionization mass spectrometry (LDI-MS) method has been developed to characterize the monolayers on NP surface. LDI-MS allows multiple NPs taken up by cells to be measured and quantified in a multiplexed fashion. The correlations between surface properties of NPs and cellular uptake have also been explored. LDI-MS is further coupled with inductively coupled plasma mass spectrometry (ICP-MS) to quantitatively measure monolayer stability of gold NPs (AuNPs) and quantum dots (QDs), respectively, in live cells. This label-free approach allows correlating monolayer structure and particle size with NP stability in various cellular environments. Finally, uptake, distribution, accumulation, and excretion of NPs in higher order organisms, such as fish and plants, have been investigated to understand the environmental impact of nanomaterials. The results indicate that surface chemistry is a primary determinant. NPs with hydrophilic surfaces are substantially less toxic and present a lower degree of bioaccumulation, making these nanomaterials attractive for sustainable nanotechnology.

  7. 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.

  8. A Simple and Accurate Analysis of Conductivity Loss in Millimeter-Wave Helical Slow-Wave Structures

    NASA Astrophysics Data System (ADS)

    Datta, S. K.; Kumar, Lalit; Basu, B. N.

    2009-04-01

    Electromagnetic field analysis of a helix slow-wave structure was carried out and a closed form expression was derived for the inductance per unit length of the transmission-line equivalent circuit of the structure, taking into account the actual helix tape dimensions and surface current on the helix over the actual metallic area of the tape. The expression of the inductance per unit length, thus obtained, was used for estimating the increment in the inductance per unit length caused due to penetration of the magnetic flux into the conducting surfaces following Wheeler’s incremental inductance rule, which was subsequently interpreted for the attenuation constant of the propagating structure. The analysis was computationally simple and accurate, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The approach was benchmarked against measurement for two practical structures, and excellent agreement was observed. The analysis was subsequently applied to demonstrate the effects of conductivity on the attenuation constant of a typical broadband millimeter-wave helical slow-wave structure with respect to helix materials and copper plating on the helix, surface finish of the helix, dielectric loading effect and effect of high temperature operation - a comparative study of various such aspects are covered.

  9. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.

    PubMed

    Mackie, David M; Jahnke, Justin P; Benyamin, Marcus S; Sumner, James J

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users' purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells.

  10. Accurate Enumeration of Aspergillus brasiliensis in Hair Color and Mascara by Time-Lapse Shadow Image Analysis.

    PubMed

    Ogawa, Hiroyuki; Matsuoka, Hideaki; Saito, Mikako

    2015-01-01

    The growth of black mold (Aspergillus brasiliensis) in black-colored samples such as hair color and mascara was measured with an automatic count system based on time-lapse shadow image analysis (TSIA). A. brasiliensis suspended in a lecithin and polysorbate (LP) solution of each sample (hair color or mascara) was spread on a potato dextrose agar medium plate containing LP. The background image darkness of the agar plate could be adjusted to attain accurate colony counts. 95 colonies in hair color and 22 colonies in mascara could be automatically determined at 48 h. The accuracy of the colony counts could be confirmed from the timelapse image data. In contrast, conventional visual counting at a specified time could not determine the number of colonies or led to false colony counts.

  11. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples

    PubMed Central

    Mackie, David M.; Jahnke, Justin P.; Benyamin, Marcus S.; Sumner, James J.

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users’ purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells. PMID:26977411

  12. Assessment of tandem mass spectrometry and high-resolution mass spectrometry for the analysis of bupivacaine in plasma.

    PubMed

    Gaudette, Fleur; Benito, Javier; Steagall, Paulo; Beaudry, Francis

    2015-11-01

    Triple quadrupole mass spectrometers coupled with high performance liquid chromatography are workhorses in quantitative bioanalyses. They provide substantial benefits including reproducibility, sensitivity and selectivity for trace analysis. Selected reaction monitoring allows targeted assay development but datasets generated contain very limited information. Data mining and analysis of nontargeted high-resolution mass spectrometry profiles of biological samples offer the opportunity to perform more exhaustive assessments, including quantitative and qualitative analysis. The objectives of this study were to test method precision and accuracy, to statistically compare bupivacaine drug concentration in real study samples and to verify if high-resolution and accurate mass data collected in scan mode can actually permit retrospective data analysis, more specifically, extract metabolite related information. The precision and accuracy data presented using both instruments provided equivalent results. Overall, the accuracy ranged from 106.2 to 113.2% and the precision observed was from 1.0 to 3.7%. Statistical comparisons using a linear regression between both methods revealed a coefficient of determination (R(2)) of 0.9996 and a slope of 1.02, demonstrating a very strong correlation between the two methods. Individual sample comparison showed differences from -4.5 to 1.6%, well within the accepted analytical error. Moreover, post-acquisition extracted ion chromatograms at m/z 233.1648 ± 5 ppm (M - 56) and m/z 305.2224 ± 5 ppm (M + 16) revealed the presence of desbutyl-bupivacaine and three distinct hydroxylated bupivacaine metabolites. Post-acquisition analysis allowed us to produce semi-quantitative evaluations of the concentration-time profiles for bupicavaine metabolites.

  13. 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

  14. freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

    PubMed

    Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

    2015-01-01

    Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

  15. The expanding universe of mass analyzer configurations for biological analysis.

    PubMed

    Calvete, Juan J

    2014-01-01

    Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge ratio of electrically charged gas-phase particles. All mass spectrometers combine ion formation, mass analysis, and ion detection. Although mass analyzers can be regarded as sophisticated devices that manipulate ions in space and time, the rich diversity of possible ways to combine ion separation, focusing, and detection in dynamic mass spectrometers accounts for the large number of instrument designs. A historical perspective of the progress in mass spectrometry that since 1965 until today have contributed to position this technique as an indispensable tool for biological research has been recently addressed by a privileged witness of this golden age of MS (Gelpí J. Mass Spectrom 43:419-435, 2008; Gelpí J. Mass Spectrom 44:1137-1161, 2008). The aim of this chapter is to highlight the view that the operational principles of mass spectrometry can be understood by a simple mathematical language, and that an understanding of the basic concepts of mass spectrometry is necessary to take the most out of this versatile technique.

  16. The expanding universe of mass analyzer configurations for biological analysis.

    PubMed

    Calvete, Juan J

    2014-01-01

    Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge ratio of electrically charged gas-phase particles. All mass spectrometers combine ion formation, mass analysis, and ion detection. Although mass analyzers can be regarded as sophisticated devices that manipulate ions in space and time, the rich diversity of possible ways to combine ion separation, focusing, and detection in dynamic mass spectrometers accounts for the large number of instrument designs. A historical perspective of the progress in mass spectrometry that since 1965 until today have contributed to position this technique as an indispensable tool for biological research has been recently addressed by a privileged witness of this golden age of MS (Gelpí J. Mass Spectrom 43:419-435, 2008; Gelpí J. Mass Spectrom 44:1137-1161, 2008). The aim of this chapter is to highlight the view that the operational principles of mass spectrometry can be understood by a simple mathematical language, and that an understanding of the basic concepts of mass spectrometry is necessary to take the most out of this versatile technique. PMID:24136515

  17. Applications of Mass Spectrometry to Structural Analysis of Marine Oligosaccharides

    PubMed Central

    Lang, Yinzhi; Zhao, Xia; Liu, Lili; Yu, Guangli

    2014-01-01

    Marine oligosaccharides have attracted increasing attention recently in developing potential drugs and biomaterials for their particular physical and chemical properties. However, the composition and sequence analysis of marine oligosaccharides are very challenging for their structural complexity and heterogeneity. Mass spectrometry (MS) has become an important technique for carbohydrate analysis by providing more detailed structural information, including molecular mass, sugar constituent, sequence, inter-residue linkage position and substitution pattern. This paper provides an overview of the structural analysis based on MS approaches in marine oligosaccharides, which are derived from some biologically important marine polysaccharides, including agaran, carrageenan, alginate, sulfated fucan, chitosan, glycosaminoglycan (GAG) and GAG-like polysaccharides. Applications of electrospray ionization mass spectrometry (ESI-MS) are mainly presented and the general applications of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are also outlined. Some technical challenges in the structural analysis of marine oligosaccharides by MS have also been pointed out. PMID:24983643

  18. Dual parallel mass spectrometry for lipid and vitamin D analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are numerous options for mass spectrometric analysis of lipids, including different types of ionization, and a wide variety of experiments using different scan modes that can be conducted. Atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) provide complementary ...

  19. Applications of Mass Spectrometry for Cellular Lipid Analysis

    PubMed Central

    Wang, Chunyan; Wang, Miao; Han, Xianlin

    2015-01-01

    Mass spectrometric analysis of cellular lipids is an enabling technology for lipidomics, which is a rapidly-developing research field. In this review, we briefly discuss the principles, advantages, and possible limitations of electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based methodologies for the analysis of lipid species. The applications of these methodologies to lipidomic research are also summarized. PMID:25598407

  20. Compact mass spectrometer for plasma discharge ion analysis

    DOEpatents

    Tuszewski, Michel G.

    1997-01-01

    A mass spectrometer and methods for mass spectrometry which are useful in characterizing a plasma. This mass spectrometer for determining type and quantity of ions present in a plasma is simple, compact, and inexpensive. It accomplishes mass analysis in a single step, rather than the usual two-step process comprised of ion extraction followed by mass filtering. Ions are captured by a measuring element placed in a plasma and accelerated by a known applied voltage. Captured ions are bent into near-circular orbits by a magnetic field such that they strike a collector, producing an electric current. Ion orbits vary with applied voltage and proton mass ratio of the ions, so that ion species may be identified. Current flow provides an indication of quantity of ions striking the collector.

  1. Compact mass spectrometer for plasma discharge ion analysis

    DOEpatents

    Tuszewski, M.G.

    1997-07-22

    A mass spectrometer and methods are disclosed for mass spectrometry which are useful in characterizing a plasma. This mass spectrometer for determining type and quantity of ions present in a plasma is simple, compact, and inexpensive. It accomplishes mass analysis in a single step, rather than the usual two-step process comprised of ion extraction followed by mass filtering. Ions are captured by a measuring element placed in a plasma and accelerated by a known applied voltage. Captured ions are bent into near-circular orbits by a magnetic field such that they strike a collector, producing an electric current. Ion orbits vary with applied voltage and proton mass ratio of the ions, so that ion species may be identified. Current flow provides an indication of quantity of ions striking the collector. 7 figs.

  2. Accurate Analysis of the Change in Volume, Location, and Shape of Metastatic Cervical Lymph Nodes During Radiotherapy

    SciTech Connect

    Takao, Seishin; Tadano, Shigeru; Taguchi, Hiroshi; Yasuda, Koichi; Onimaru, Rikiya; Ishikawa, Masayori; Bengua, Gerard; Suzuki, Ryusuke; Shirato, Hiroki

    2011-11-01

    Purpose: To establish a method for the accurate acquisition and analysis of the variations in tumor volume, location, and three-dimensional (3D) shape of tumors during radiotherapy in the era of image-guided radiotherapy. Methods and Materials: Finite element models of lymph nodes were developed based on computed tomography (CT) images taken before the start of treatment and every week during the treatment period. A surface geometry map with a volumetric scale was adopted and used for the analysis. Six metastatic cervical lymph nodes, 3.5 to 55.1 cm{sup 3} before treatment, in 6 patients with head and neck carcinomas were analyzed in this study. Three fiducial markers implanted in mouthpieces were used for the fusion of CT images. Changes in the location of the lymph nodes were measured on the basis of these fiducial markers. Results: The surface geometry maps showed convex regions in red and concave regions in blue to ensure that the characteristics of the 3D tumor geometries are simply understood visually. After the irradiation of 66 to 70 Gy in 2 Gy daily doses, the patterns of the colors had not changed significantly, and the maps before and during treatment were strongly correlated (average correlation coefficient was 0.808), suggesting that the tumors shrank uniformly, maintaining the original characteristics of the shapes in all 6 patients. The movement of the gravitational center of the lymph nodes during the treatment period was everywhere less than {+-}5 mm except in 1 patient, in whom the change reached nearly 10 mm. Conclusions: The surface geometry map was useful for an accurate evaluation of the changes in volume and 3D shapes of metastatic lymph nodes. The fusion of the initial and follow-up CT images based on fiducial markers enabled an analysis of changes in the location of the targets. Metastatic cervical lymph nodes in patients were suggested to decrease in size without significant changes in the 3D shape during radiotherapy. The movements of the

  3. Mesoscale and severe storms (Mass) data management and analysis system

    NASA Technical Reports Server (NTRS)

    Hickey, J. S.; Karitani, S.; Dickerson, M.

    1984-01-01

    Progress on the Mesoscale and Severe Storms (MASS) data management and analysis system is described. An interactive atmospheric data base management software package to convert four types of data (Sounding, Single Level, Grid, Image) into standard random access formats is implemented and integrated with the MASS AVE80 Series general purpose plotting and graphics display data analysis software package. An interactive analysis and display graphics software package (AVE80) to analyze large volumes of conventional and satellite derived meteorological data is enhanced to provide imaging/color graphics display utilizing color video hardware integrated into the MASS computer system. Local and remote smart-terminal capability is provided by installing APPLE III computer systems within individual scientist offices and integrated with the MASS system, thus providing color video display, graphics, and characters display of the four data types.

  4. New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets.

    PubMed

    Zhu, Zhikai; Su, Xiaomeng; Go, Eden P; Desaire, Heather

    2014-09-16

    Glycoproteins are biologically significant large molecules that participate in numerous cellular activities. In order to obtain site-specific protein glycosylation information, intact glycopeptides, with the glycan attached to the peptide sequence, are characterized by tandem mass spectrometry (MS/MS) methods such as collision-induced dissociation (CID) and electron transfer dissociation (ETD). While several emerging automated tools are developed, no consensus is present in the field about the best way to determine the reliability of the tools and/or provide the false discovery rate (FDR). A common approach to calculate FDRs for glycopeptide analysis, adopted from the target-decoy strategy in proteomics, employs a decoy database that is created based on the target protein sequence database. Nonetheless, this approach is not optimal in measuring the confidence of N-linked glycopeptide matches, because the glycopeptide data set is considerably smaller compared to that of peptides, and the requirement of a consensus sequence for N-glycosylation further limits the number of possible decoy glycopeptides tested in a database search. To address the need to accurately determine FDRs for automated glycopeptide assignments, we developed GlycoPep Evaluator (GPE), a tool that helps to measure FDRs in identifying glycopeptides without using a decoy database. GPE generates decoy glycopeptides de novo for every target glycopeptide, in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides, are scored against the ETD data, from which FDRs can be calculated accurately based on the number of decoy matches and the ratio of the number of targets to decoys, for small data sets. GPE is freely accessible for download and can work with any search engine that interprets ETD data of N-linked glycopeptides. The software is provided at https://desairegroup.ku.edu/research.

  5. Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using the Vitek MS System for Rapid and Accurate Identification of Dermatophytes on Solid Cultures

    PubMed Central

    Monnin, Valérie; Girard, Victoria; Welker, Martin; Arsac, Maud; Cellière, Béatrice; Durand, Géraldine; Bosshard, Philipp P.; Farina, Claudio; Passera, Marco; Van Belkum, Alex; Petrini, Orlando; Tonolla, Mauro

    2014-01-01

    The objective of this research was to extend the Vitek MS fungal knowledge base version 2.0.0 to allow the robust identification of clinically relevant dermatophytes, using a variety of strains, incubation times, and growth conditions. First, we established a quick and reliable method for sample preparation to obtain a reliable and reproducible identification independently of the growth conditions. The Vitek MS V2.0.0 fungal knowledge base was then expanded using 134 well-characterized strains belonging to 17 species in the genera Epidermophyton, Microsporum, and Trichophyton. Cluster analysis based on mass spectrum similarity indicated good species discrimination independently of the culture conditions. We achieved a good separation of the subpopulations of the Trichophyton anamorph of Arthroderma benhamiae and of anthropophilic and zoophilic strains of Trichophyton interdigitale. Overall, the 1,130 mass spectra obtained for dermatophytes gave an estimated identification performance of 98.4%. The expanded fungal knowledge base was then validated using 131 clinical isolates of dermatophytes belonging to 13 taxa. For 8 taxa all strains were correctly identified, and for 3 the rate of successful identification was >90%; 75% (6/8) of the M. gypseum strains were correctly identified, whereas only 47% (18/38) of the African T. rubrum population (also called T. soudanense) were recognized accurately, with a large quantity of strains misidentified as T. violaceum, demonstrating the close relationship of these two taxa. The method of sample preparation was fast and efficient and the expanded Vitek MS fungal knowledge base reliable and robust, allowing reproducible dermatophyte identifications in the routine laboratory. PMID:25297329

  6. 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

  7. Development and experimental verification of a finite element method for accurate analysis of a surface acoustic wave device

    NASA Astrophysics Data System (ADS)

    Mohibul Kabir, K. M.; Matthews, Glenn I.; Sabri, Ylias M.; Russo, Salvy P.; Ippolito, Samuel J.; Bhargava, Suresh K.

    2016-03-01

    Accurate analysis of surface acoustic wave (SAW) devices is highly important due to their use in ever-growing applications in electronics, telecommunication and chemical sensing. In this study, a novel approach for analyzing the SAW devices was developed based on a series of two-dimensional finite element method (FEM) simulations, which has been experimentally verified. It was found that the frequency response of the two SAW device structures, each having slightly different bandwidth and center lobe characteristics, can be successfully obtained utilizing the current density of the electrodes via FEM simulations. The two SAW structures were based on XY Lithium Niobate (LiNbO3) substrates and had two and four electrode finger pairs in both of their interdigital transducers, respectively. Later, SAW devices were fabricated in accordance with the simulated models and their measured frequency responses were found to correlate well with the obtained simulations results. The results indicated that better match between calculated and measured frequency response can be obtained when one of the input electrode finger pairs was set at zero volts and all the current density components were taken into account when calculating the frequency response of the simulated SAW device structures.

  8. Analysis and accurate reconstruction of incomplete data in X-ray differential phase-contrast computed tomography.

    PubMed

    Fu, Jian; Tan, Renbo; Chen, Liyuan

    2014-01-01

    X-ray differential phase-contrast computed tomography (DPC-CT) is a powerful physical and biochemical analysis tool. In practical applications, there are often challenges for DPC-CT due to insufficient data caused by few-view, bad or missing detector channels, or limited scanning angular range. They occur quite frequently because of experimental constraints from imaging hardware, scanning geometry, and the exposure dose delivered to living specimens. In this work, we analyze the influence of incomplete data on DPC-CT image reconstruction. Then, a reconstruction method is developed and investigated for incomplete data DPC-CT. It is based on an algebraic iteration reconstruction technique, which minimizes the image total variation and permits accurate tomographic imaging with less data. This work comprises a numerical study of the method and its experimental verification using a dataset measured at the W2 beamline of the storage ring DORIS III equipped with a Talbot-Lau interferometer. The numerical and experimental results demonstrate that the presented method can handle incomplete data. It will be of interest for a wide range of DPC-CT applications in medicine, biology, and nondestructive testing.

  9. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

    PubMed

    Kapp, Eugene A; Schütz, Frédéric; Connolly, Lisa M; Chakel, John A; Meza, Jose E; Miller, Christine A; Fenyo, David; Eng, Jimmy K; Adkins, Joshua N; Omenn, Gilbert S; Simpson, Richard J

    2005-08-01

    MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X!Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, PeptideProphet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X!Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of "consensus scoring", i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.

  10. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and Specificity analysis.

    SciTech Connect

    Kapp, Eugene; Schutz, Frederick; Connolly, Lisa M.; Chakel, John A.; Meza, Jose E.; Miller, Christine A.; Fenyo, David; Eng, Jimmy K.; Adkins, Joshua N.; Omenn, Gilbert; Simpson, Richard

    2005-08-01

    MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X-Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, Peptide Prophet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X-Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of ''consensus scoring'', i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.

  11. Mathematical analysis and algorithms for efficiently and accurately implementing stochastic simulations of short-term synaptic depression and facilitation.

    PubMed

    McDonnell, Mark D; Mohan, Ashutosh; Stricker, Christian

    2013-01-01

    The release of neurotransmitter vesicles after arrival of a pre-synaptic action potential (AP) at cortical synapses is known to be a stochastic process, as is the availability of vesicles for release. These processes are known to also depend on the recent history of AP arrivals, and this can be described in terms of time-varying probabilities of vesicle release. Mathematical models of such synaptic dynamics frequently are based only on the mean number of vesicles released by each pre-synaptic AP, since if it is assumed there are sufficiently many vesicle sites, then variance is small. However, it has been shown recently that variance across sites can be significant for neuron and network dynamics, and this suggests the potential importance of studying short-term plasticity using simulations that do generate trial-to-trial variability. Therefore, in this paper we study several well-known conceptual models for stochastic availability and release. We state explicitly the random variables that these models describe and propose efficient algorithms for accurately implementing stochastic simulations of these random variables in software or hardware. Our results are complemented by mathematical analysis and statement of pseudo-code algorithms.

  12. Sampling and analysis method for measuring airborne coal dust mass in mixtures with limestone (rock) dust.

    PubMed

    Barone, T L; Patts, J R; Janisko, S J; Colinet, J F; Patts, L D; Beck, T W; Mischler, S E

    2016-01-01

    Airborne coal dust mass measurements in underground bituminous coal mines can be challenged by the presence of airborne limestone dust, which is an incombustible dust applied to prevent the propagation of dust explosions. To accurately measure the coal portion of this mixed airborne dust, the National Institute for Occupational Safety and Health (NIOSH) developed a sampling and analysis protocol that used a stainless steel cassette adapted with an isokinetic inlet and the low temperature ashing (LTA) analytical method. The Mine Safety and Health Administration (MSHA) routinely utilizes this LTA method to quantify the incombustible content of bulk dust samples collected from the roof, floor, and ribs of mining entries. The use of the stainless steel cassette with isokinetic inlet allowed NIOSH to adopt the LTA method for the analysis of airborne dust samples. Mixtures of known coal and limestone dust masses were prepared in the laboratory, loaded into the stainless steel cassettes, and analyzed to assess the accuracy of this method. Coal dust mass measurements differed from predicted values by an average of 0.5%, 0.2%, and 0.1% for samples containing 20%, 91%, and 95% limestone dust, respectively. The ability of this method to accurately quantify the laboratory samples confirmed the validity of this method and allowed NIOSH to successfully measure the coal fraction of airborne dust samples collected in an underground coal mine.

  13. Aerosol Analysis via Electrostatic Precipitation-Electrospray Ionization Mass Spectrometry.

    PubMed

    He, Siqin; Li, Lin; Duan, Hongxu; Naqwi, Amir; Hogan, Christopher J

    2015-07-01

    Electrospray ionization (ESI) is the preferred mode of ion generation for mass analysis of many organic species, as alternative ionization techniques can lead to appreciable analyte fragmentation. For this reason, ESI is an ideal method for the analysis of species within aerosol particles. However, because of their low concentrations (∼10 μg/m(3)) in most environments, ESI has been applied sparingly in aerosol particle analysis; aerosol mass spectrometers typically employ analyte volatilization followed by electron ionization or chemical ionization, which can lead to a considerable degree of analyte fragmentation. Here, we describe an approach to apply ESI to submicrometer and nanometer scale aerosol particles, which utilizes unipolar ionization to charge particles, electrostatic precipitation to collect particles on the tip of a Tungsten rod, and subsequently, by flowing liquid over the rod, ESI and mass analysis of the species composing collected particles. This technique, which we term electrostatic precipitation-ESI-MS (EP-ESI-MS), is shown to enable analysis of nanogram quantities of collected particles (from aerosol phase concentrations as low as 10(2) ng m(-3)) composed of cesium iodide, levoglucosan, and levoglucosan within a carbon nanoparticle matrix. With EP-ESI-MS, the integrated mass spectrometric signals are found to be a monotonic function of the mass concentration of analyte in the aerosol phase. We additionally show that EP-ESI-MS has a dynamic range of close to 5 orders of magnitude in mass, making it suitable for molecular analysis of aerosol particles in laboratory settings with upstream particle size classification, as well as analysis of PM 2.5 particles in ambient air. PMID:26024017

  14. New Applications of Mass Spectrometry in Lipid Analysis*

    PubMed Central

    Murphy, Robert C.; Gaskell, Simon J.

    2011-01-01

    Mass spectrometry has emerged as a powerful tool for the analysis of all lipids. Lipidomic analysis of biological systems using various approaches is now possible with a quantitative measurement of hundreds of lipid molecular species. Although availability of reference and internal standards lags behind the field, approaches using stable isotope-labeled derivative tagging permit precise determination of specific phospholipids in an experimental series. The use of reactivity of ozone has enabled assessment of double bond positions in fatty acyl groups even when species remain in complex lipid mixtures. Rapid scanning tandem mass spectrometers are capable of quantitative analysis of hundreds of targeted lipids at high sensitivity in a single on-line chromatographic separation. Imaging mass spectrometry of lipids in tissues has opened new insights into the distribution of lipid molecular species with promising application to study pathophysiological events and diseases. PMID:21632539

  15. Improved analytic extreme-mass-ratio inspiral model for scoping out eLISA data analysis

    NASA Astrophysics Data System (ADS)

    Chua, Alvin J. K.; Gair, Jonathan R.

    2015-12-01

    The space-based gravitational-wave detector eLISA has been selected as the ESA L3 mission, and the mission design will be finalized by the end of this decade. To prepare for mission formulation over the next few years, several outstanding and urgent questions in data analysis will be addressed using mock data challenges, informed by instrument measurements from the LISA Pathfinder satellite launching at the end of 2015. These data challenges will require accurate and computationally affordable waveform models for anticipated sources such as the extreme-mass-ratio inspirals (EMRIs) of stellar-mass compact objects into massive black holes. Previous data challenges have made use of the well-known analytic EMRI waveforms of Barack and Cutler, which are extremely quick to generate but dephase relative to more accurate waveforms within hours, due to their mismatched radial, polar and azimuthal frequencies. In this paper, we describe an augmented Barack-Cutler model that uses a frequency map to the correct Kerr frequencies, along with updated evolution equations and a simple fit to a more accurate model. The augmented waveforms stay in phase for months and may be generated with virtually no additional computational cost.

  16. High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis.

    PubMed

    Gilar, M; Belenky, A; Wang, B H

    2001-06-29

    In the last 10 years mass spectrometry (MS) has become an important method for analysis of peptides, proteins and DNA. It was recently utilized for accurate high-throughput protein identification, sequencing and DNA genotyping. The presence of non-volatile buffers compromises sensitivity and accuracy of MS biopolymer analysis; it is essential to remove sample contaminants prior to analysis. We have developed a fast and efficient method for desalting of DNA oligonucleotides and peptides using 96-well solid-phase extraction plates packed with 5 mg of Waters Oasis HLB sorbent (Waters, Milford, MA, USA). This reversed-phase sorbent retains the biopolymer analytes, while non-retained inorganic ions are washed out with pure deionized water. DNA oligonucleotides or peptides are eluted using a small amount (20-100 microl) of acetonitrile-water (70:30, v/v) solution. The SPE desalting performance meets the requirements for MS applications such as protein digest analysis and DNA genotyping. PMID:11461010

  17. Lumped mass modelling for the dynamic analysis of aircraft structures

    NASA Technical Reports Server (NTRS)

    Abu-Saba, Elias G.; Shen, Ji Yao; Mcginley, William M.; Montgomery, Raymond C.

    1992-01-01

    Aircraft structures may be modelled by lumping the masses at particular strategic points and the flexibility or stiffness of the structure is obtained with reference to these points. Equivalent moments of inertia for the section at these positions are determined. The lumped masses are calculated based on the assumption that each point will represent the mass spread on one half of the space on each side. Then these parameters are used in the differential equation of motion and the eigen characteristics are determined. A comparison is made with results obtained by other established methods. The lumped mass approach in the dynamic analysis of complicated structures provides an easier means of predicting the dynamic characteristics of these structures. It involves less computer time and avoids computational errors that are inherent in the numerical solution of complicated systems.

  18. Accurate determination of human serum transferrin isoforms: Exploring metal-specific isotope dilution analysis as a quantitative proteomic tool.

    PubMed

    Busto, M Estela del Castillo; Montes-Bayón, Maria; Sanz-Medel, Alfredo

    2006-12-15

    Carbohydrate-deficient transferrin (CDT) measurements are considered a reliable marker for chronic alcohol consumption, and its use is becoming extensive in forensic medicine. However, CDT is not a single molecular entity but refers to a group of sialic acid-deficient transferrin isoforms from mono- to trisialotransferrin. Thus, the development of methods to analyze accurately and precisely individual transferrin isoforms in biological fluids such as serum is of increasing importance. The present work illustrates the use of ICPMS isotope dilution analysis for the quantification of transferrin isoforms once saturated with iron and separated by anion exchange chromatography (Mono Q 5/50) using a mobile phase consisting of a gradient of ammonium acetate (0-250 mM) in 25 mM Tris-acetic acid (pH 6.5). Species-specific and species-unspecific spikes have been explored. In the first part of the study, the use of postcolumn addition of a solution of 200 ng mL(-1) isotopically enriched iron (57Fe, 95%) in 25 mM sodium citrate/citric acid (pH 4) permitted the quantification of individual sialoforms of transferrin (from S2 to S5) in human serum samples of healthy individuals as well as alcoholic patients. Second, the species-specific spike method was performed by synthesizing an isotopically enriched standard of saturated transferrin (saturated with 57Fe). The characterization of the spike was performed by postcolumn reverse isotope dilution analysis (this is, by postcolumn addition of a solution of 200 ng mL(-1) natural iron in sodium citrate/citric acid of pH 4). Also, the stability of the transferrin spike was tested during one week with negligible species transformation. Finally, the enriched transferrin was used to quantify the individual isoforms in the same serum samples obtaining results comparative to those of postcolumn isotope dilution and to those previously published in the literature, demonstrating the suitability of both strategies for quantitative transferrin

  19. Molecular-genetic analysis is essential for accurate classification of renal carcinoma resembling Xp11.2 translocation carcinoma.

    PubMed

    Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej

    2015-03-01

    tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614

  20. Multiple mass analysis using an ion trap array (ITA) mass analyzer.

    PubMed

    Yu, Xiao; Chu, Yanqiu; Ling, Xing; Ding, Zhengzhi; Xu, Chongsheng; Ding, Li; Ding, Chuan-Fan

    2013-09-01

    A novel ion trap array (ITA) mass analyzer with six ion trapping and analyzing channels was investigated. It is capable of analyzing multiple samples simultaneously. The ITA was built with several planar electrodes made of stainless steel and 12 identical parallel zirconia ceramic substrates plated with conductive metal layers. Each two of the opposing ceramic electrode plates formed a boundary of an ion trap channel and six identical ion trapping and analyzing channels were placed in parallel without physical electrode between any two adjacent channels. The electric field distribution inside each channel was studied with simulation. The new design took the advantage of high precision machining attributable to the rigidity of ceramic, and the convenience of surface patterning technique. The ITA system was tested by using a two-channel electrospray ionization source, a multichannel simultaneous quadruple ion guide, and two detectors. The simultaneous analysis of two different samples with two adjacent ITA channels was achieved and independent mass spectra were obtained. For each channel, the mass resolution was tested. Additional ion trap functions such as mass-selected ion isolation and collision-induced dissociation (CID) were also tested. The results show that one ITA is well suited for multiple simultaneous mass analyses. PMID:23797864

  1. Multiple Mass Analysis Using an Ion Trap Array (ITA) Mass Analyzer

    NASA Astrophysics Data System (ADS)

    Xiao, Yu; Chu, Yanqiu; Ling, Xing; Ding, Zhengzhi; Xu, Chongsheng; Ding, Li; Ding, Chuan-Fan

    2013-09-01

    A novel ion trap array (ITA) mass analyzer with six ion trapping and analyzing channels was investigated. It is capable of analyzing multiple samples simultaneously. The ITA was built with several planar electrodes made of stainless steel and 12 identical parallel zirconia ceramic substrates plated with conductive metal layers. Each two of the opposing ceramic electrode plates formed a boundary of an ion trap channel and six identical ion trapping and analyzing channels were placed in parallel without physical electrode between any two adjacent channels. The electric field distribution inside each channel was studied with simulation. The new design took the advantage of high precision machining attributable to the rigidity of ceramic, and the convenience of surface patterning technique. The ITA system was tested by using a two-channel electrospray ionization source, a multichannel simultaneous quadruple ion guide, and two detectors. The simultaneous analysis of two different samples with two adjacent ITA channels was achieved and independent mass spectra were obtained. For each channel, the mass resolution was tested. Additional ion trap functions such as mass-selected ion isolation and collision-induced dissociation (CID) were also tested. The results show that one ITA is well suited for multiple simultaneous mass analyses.

  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. On-Line Synthesis and Analysis by Mass Spectrometry

    ERIC Educational Resources Information Center

    Bain, Ryan M.; Pulliam, Christopher J.; Raab, Shannon A.; Cooks, R. Graham

    2015-01-01

    In this laboratory experiment, students learn how to use ESI to accelerate chemical synthesis and to couple it with on-line mass spectrometry for structural analysis. The Hantzsch synthesis of symmetric 1,4-dihydropyridines is a classic example of a one-pot reaction in which multiple intermediates can serve to indicate the progress of the reaction…

  4. THE APPLICATION OF MASS SPECTROMETRY TO PROTEIN ANALYSIS

    EPA Science Inventory

    The purpose of this presentation is to give our NHEERL collaborators a brief introduction to the use of mass spectrometric (MS) techniques in the analysis of proteins. The basic principles of electrospray ionization and matrix-assisted laser desorption ionization will be discuss...

  5. Fundamentals of Biomolecule Analysis by Electrospray Ionization Mass Spectrometry

    ERIC Educational Resources Information Center

    Weinecke, Andrea; Ryzhov, Victor

    2005-01-01

    Electrospray ionization (ESI) is a soft ionization technique that allows transfer of fragile biomolecules directly from solution into the gas phase. An instrumental analysis laboratory experiment is designed that would introduce the students to the ESI technique, major parameters of the ion trap mass spectrometers and some caveats in…

  6. Multiple parallel mass spectrometry for lipid and vitamin D analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Liquid chromatography (LC) coupled to mass spectrometry (MS) has become the method of choice for analysis of complex lipid samples. Two types of ionization sources have emerged as the most commonly used to couple LC to MS: atmospheric pressure chemical ionization (APCI) and electrospray ionization ...

  7. Mass spectrometric peptide mapping analysis and structural characterization of dihydrodiol dehydrogenase isoenzymes.

    PubMed Central

    Gauss, C; Klein, J; Post, K; Suckau, D; Schneider, K; Thomas, H; Oesch, F; Przybylski, M

    1990-01-01

    The direct molecular weight determination and structural analysis of polypeptides and peptide mixtures have become amenable by the recent development of fast atom bombardment (FABMS) and 252Cf-plasma desorption (PDMS) mass spectrometry. FABMS and PDMS peptide mapping, i.e., the direct analysis of peptide mixtures resulting from proteolytic digestion, have been developed as powerful methods for the structural characterization of epoxide-metabolizing isoenzymes. The major advantage of this approach is provided by the selectivity of the endoproteolytic cleavage, combined with the specific and accurate molecular weight determination of complex digest mixtures containing peptides up to several thousands daltons in size. Furthermore, the mass spectrometric peptide mapping analysis can be combined with a range of protein-chemical modification reactions and with sequential degradation such as by carboxypeptidases. Both FABMS and PDMS peptide mapping have already been successfully applied to the structural differentiation of glutathione transferase and epoxide hydrolase isoenzymes in cases where references sequence data for at least one isoenzyme form was available. In the application described here, for a series of dihydrodiol dehydrogenase (DDH) isoenzymes with hitherto undetermined primary structures, a direct correlation between the structural differentiation from peptide mapping data and differences in their substrate specificities could be demonstrated. The mass spectrometric peptide mapping analysis of isoenzymes proved to be an efficient basis for the elucidation of the structure of one major DDH isoenzyme form; partial sequence data for this protein are reported. PMID:2272334

  8. Evaluation on mass sensitivity of SAW sensors for different piezoelectric materials using finite-element analysis.

    PubMed

    Abdollahi, Amir; Jiang, Zhongwei; Arabshahi, Sayyed Alireza

    2007-12-01

    The mass sensitivity of the piezoelectric surface acoustic wave (SAW) sensors is an important factor in the selection of the best gravimetric sensors for different applications. To determine this value without facing the practical problems and the long theoretical calculation time, we have shown that the mass sensitivity of SAW sensors can be calculated by a simple three-dimensional (3-D) finite-element analysis (FEA) using a commercial finite-element platform. The FEA data are used to calculate the wave propagation speed, surface particle displacements, and wave energy distribution on different cuts of various piezoelectric materials. The results are used to provide a simple method for evaluation of their mass sensitivities. Meanwhile, to calculate more accurate results from FEA data, surface and bulk wave reflection problems are considered in the analyses. In this research, different cuts of lithium niobate, quartz, lithium tantalate, and langasite piezoelectric materials are applied to investigate their acoustic wave properties. Our analyses results for these materials have a good agreement with other researchers' results. Also, the mass sensitivity value for the novel cut of langasite was calculated through these analyses. It was found that its mass sensitivity is higher than that of the conventional Rayleigh mode quartz sensor.

  9. Analysis of proteins and proteomes by mass spectrometry.

    PubMed

    Mann, M; Hendrickson, R C; Pandey, A

    2001-01-01

    A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolecules, mass spectrometry has become a powerful tool in protein analysis and the key technology in the emerging field of proteomics. The success of mass spectrometry is driven both by innovative instrumentation designs, especially those operating on the time-of-flight or ion-trapping principles, and by large-scale biochemical strategies, which use mass spectrometry to detect the isolated proteins. Any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry. As has already happened in genomics, increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data. Protein-protein interactions can be analyzed directly by precipitation of a tagged bait followed by mass spectrometric identification of its binding partners. By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies.

  10. Inferences on active faults at the Southern Alps-Liguria basin junction from accurate analysis of low energy seismicity

    NASA Astrophysics Data System (ADS)

    Turino, Chiara; Scafidi, Davide; Eva, Elena; Solarino, Stefano

    2009-10-01

    Seismotectonic studies concern themselves with understanding the distribution of earthquakes in space, time, size and style. Therefore, the better these parameters are known, the most correct the association of any seismic event with the faulting structure that caused it will result. The use of accurate location methods is especially required when dealing with very complex areas, where several faulting systems or relatively small seismogenic structures exist. In fact, even though routinely determined epicentres are capable of revealing the rough picture of the seismicity, they are not suitable for studies of the fine structure of the causative fault, as their location uncertainties are often larger than the source dimension itself. In this work the probabilistic approach of the "Non Linear Localization" has been used to compute precise locations for earthquakes occurred in the last twenty years nearby the Saorge-Taggia line, a complex fault system situated in Western Liguria, close to the border between Italy and France. Together with the Breil-Sospel-Monaco and the Peille-Laghet faults, this line is responsible for the seismic activity of the area. The seismotectonic study is completed through a local tomographic study and the analysis of the focal mechanisms computed for an enlarged area. The results show that the seismicity associated with this fault system is confined within the first 10 km depth. Many clusters of seismic events are identified along the Saorge-Taggia line. The existence of a not previously mapped branch perpendicular to the Saorge-Taggia line is also recognized. Although its position may suggest it to be the continuation of the Breil-Sospel-Monaco fault system towards NE, our finding would rather suggest no association with the fault. The overall results confirm the complexity of the area; in particular the hypothesis that the Saorge-Taggia system may represent the eastward limit of a subalpine crustal block comprised within the Nice Arc, the

  11. Uncertainty analysis for determination of plutonium mass by neutron multiplicity counting

    SciTech Connect

    Carrillo, L.A.; Ensslin, N.; Krick, M.S.; Langner, D.G.; Rudy, C.R.

    1998-12-31

    This paper describes an uncertainty analysis carried out in association with the use of neutron multiplicity counting to collect data, and assign a total plutonium mass. During 1997, the Los Alamos Safeguards Science and Technology Group carried out careful calorimetry and neutron multiplicity certification measurements on two {sup 239}Pu metal foils used as reference standards at the Idaho National Environmental Engineering Laboratory (INEEL). The foils were measured using a five ring neutron multiplicity counter designed for neutron measurement control activities. This multiplicity counter is well characterized, and the detector parameters were reaffirmed before the measurements were made using several well-known Los Alamos standards. Then, the {sup 240}Pu effective mass of the foils was determined directly from the multiplicity analysis without a conventional calibration curve based on representative standards. Finally, the {sup 240}Pu effective mass fraction and the total plutonium mass was calculated using gamma ray isotopics. Errors from statistical data collection, background subtraction, cosmic ray interaction, dead time corrections, calibration constants, sample geometry, and sample position were carefully estimated and propagated. The authors describe these error sources, the final calculated relative error in the foil assay, and the comparison with very accurate calorimetry measurements.

  12. 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.

  13. Surrogate markers of visceral adiposity in young adults: waist circumference and body mass index are more accurate than waist hip ratio, model of adipose distribution and visceral adiposity index.

    PubMed

    Borruel, Susana; Moltó, José F; Alpañés, Macarena; Fernández-Durán, Elena; Álvarez-Blasco, Francisco; Luque-Ramírez, Manuel; Escobar-Morreale, Héctor F

    2014-01-01

    Surrogate indexes of visceral adiposity, a major risk factor for metabolic and cardiovascular disorders, are routinely used in clinical practice because objective measurements of visceral adiposity are expensive, may involve exposure to radiation, and their availability is limited. We compared several surrogate indexes of visceral adiposity with ultrasound assessment of subcutaneous and visceral adipose tissue depots in 99 young Caucasian adults, including 20 women without androgen excess, 53 women with polycystic ovary syndrome, and 26 men. Obesity was present in 7, 21, and 7 subjects, respectively. We obtained body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), model of adipose distribution (MOAD), visceral adiposity index (VAI), and ultrasound measurements of subcutaneous and visceral adipose tissue depots and hepatic steatosis. WC and BMI showed the strongest correlations with ultrasound measurements of visceral adiposity. Only WHR correlated with sex hormones. Linear stepwise regression models including VAI were only slightly stronger than models including BMI or WC in explaining the variability in the insulin sensitivity index (yet BMI and WC had higher individual standardized coefficients of regression), and these models were superior to those including WHR and MOAD. WC showed 0.94 (95% confidence interval 0.88-0.99) and BMI showed 0.91 (0.85-0.98) probability of identifying the presence of hepatic steatosis according to receiver operating characteristic curve analysis. In conclusion, WC and BMI not only the simplest to obtain, but are also the most accurate surrogate markers of visceral adiposity in young adults, and are good indicators of insulin resistance and powerful predictors of the presence of hepatic steatosis.

  14. Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry.

    PubMed

    Thüring, Kathrin; Schmid, Katharina; Keller, Patrick; Helm, Mark

    2016-09-01

    The analysis of RNA modifications is of high importance in order to address a wide range of biological questions. Therefore, a highly sensitive and accurate method such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) has to be available. By using different LC-MS/MS procedures, it is not only possible to quantify very low amounts of RNA modifications, but also to detect probably unknown modified nucleosides. For these cases the dynamic multiple reaction monitoring and the neutral loss scan are the most common techniques. Here, we provide the whole workflow for analyzing RNA samples regarding their modification content. This includes an equipment list, the preparation of required solutions/enzymes and the creation of an internal standard or nucleoside stocks for internal or external calibration. Furthermore, we describe the preparation of RNA samples for the subsequent LC-MS/MS analysis and the corresponding analysis process. PMID:27020891

  15. Mass biased partitioning to enhance middle down proteomics analysis

    PubMed Central

    Cannon, Joe R.; Edwards, Nathan J.; Fenselau, Catherine

    2013-01-01

    A strategy is presented for enhancing the middle-down analysis of higher mass peptides recovered from complex protein mixtures. Following a 30 min digestion of multiple myeloma cell lysate by an acid cleavage reaction that is selective for aspartic acid, a 3000 Da membrane filter is used to bifurcate the peptide product mixture, and the heavier fraction is subjected to collisional activation with precursor selection that excludes charge states below +4. Filtration and charge state selection are shown to provide significant increases in the number of peptides identified in the mass range above 3000 Da and in information about protein sequences. PMID:23494789

  16. Advances in liquid chromatography-high-resolution mass spectrometry for quantitative and qualitative environmental analysis.

    PubMed

    Aceña, Jaume; Stampachiacchiere, Serena; Pérez, Sandra; Barceló, Damià

    2015-08-01

    This review summarizes the advances in environmental analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) during the last decade and discusses different aspects of their application. LC-HRMS has become a powerful tool for simultaneous quantitative and qualitative analysis of organic pollutants, enabling their quantitation and the search for metabolites and transformation products or the detection of unknown compounds. LC-HRMS provides more information than low-resolution (LR) MS for each sample because it can accurately determine the mass of the molecular ion and its fragment ions if it can be used for MS-MS. Another advantage is that the data can be processed using either target analysis, suspect screening, retrospective analysis, or non-target screening. With the growing popularity and acceptance of HRMS analysis, current guidelines for compound confirmation need to be revised for quantitative and qualitative purposes. Furthermore, new commercial software and user-built libraries are required to mine data in an efficient and comprehensive way. The scope of this critical review is not to provide a comprehensive overview of the many studies performed with LC-HRMS in the field of environmental analysis, but to reveal its advantages and limitations using different workflows. PMID:26138893

  17. Advances in liquid chromatography-high-resolution mass spectrometry for quantitative and qualitative environmental analysis.

    PubMed

    Aceña, Jaume; Stampachiacchiere, Serena; Pérez, Sandra; Barceló, Damià

    2015-08-01

    This review summarizes the advances in environmental analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) during the last decade and discusses different aspects of their application. LC-HRMS has become a powerful tool for simultaneous quantitative and qualitative analysis of organic pollutants, enabling their quantitation and the search for metabolites and transformation products or the detection of unknown compounds. LC-HRMS provides more information than low-resolution (LR) MS for each sample because it can accurately determine the mass of the molecular ion and its fragment ions if it can be used for MS-MS. Another advantage is that the data can be processed using either target analysis, suspect screening, retrospective analysis, or non-target screening. With the growing popularity and acceptance of HRMS analysis, current guidelines for compound confirmation need to be revised for quantitative and qualitative purposes. Furthermore, new commercial software and user-built libraries are required to mine data in an efficient and comprehensive way. The scope of this critical review is not to provide a comprehensive overview of the many studies performed with LC-HRMS in the field of environmental analysis, but to reveal its advantages and limitations using different workflows.

  18. Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: compound class targeting in a metabolomics workflow.

    PubMed

    Bobeldijk, Ivana; Hekman, Maarten; de Vries-van der Weij, Jitske; Coulier, Leon; Ramaker, Raymond; Kleemann, Robert; Kooistra, Teake; Rubingh, Carina; Freidig, Andreas; Verheij, Elwin

    2008-08-15

    We report a sensitive, generic method for quantitative profiling of bile acids and other endogenous metabolites in small quantities of various biological fluids and tissues. The method is based on a straightforward sample preparation, separation by reversed-phase high performance liquid-chromatography mass spectrometry (HPLC-MS) and electrospray ionisation in the negative ionisation mode (ESI-). Detection is performed in full scan using the linear ion trap Fourier transform mass spectrometer (LTQ-FTMS) generating data for many (endogenous) metabolites, not only bile acids. A validation of the method in urine, plasma and liver was performed for 17 bile acids including their taurine, sulfate and glycine conjugates. The method is linear in the 0.01-1 microM range. The accuracy in human plasma ranges from 74 to 113%, in human urine 77 to 104% and in mouse liver 79 to 140%. The precision ranges from 2 to 20% for pooled samples even in studies with large number of samples (n>250). The method was successfully applied to a multi-compartmental APOE*3-Leiden mouse study, the main goal of which was to analyze the effect of increasing dietary cholesterol concentrations on hepatic cholesterol homeostasis and bile acid synthesis. Serum and liver samples from different treatment groups were profiled with the new method. Statistically significant differences between the diet groups were observed regarding total as well as individual bile acid concentrations.

  19. Direct tandem mass spectrometric analysis of amino acids in plasma using fluorous derivatization and monolithic solid-phase purification.

    PubMed

    Tamashima, Erina; Hayama, Tadashi; Yoshida, Hideyuki; Imakyure, Osamu; Yamaguchi, Masatoshi; Nohta, Hitoshi

    2015-11-10

    In this study, we developed a novel direct tandem mass spectrometric method for rapid and accurate analysis of amino acids utilizing a fluorous derivatization and purification technique. Amino acids were perfluoroalkylated with 2H,2H,3H,3H-perfluoroundecan-1-al in the presence of 2-picoline borane via reductive amination. The derivatives were purified by perfluoroalkyl-modified silica-based monolithic solid-phase extraction (monolithic F-SPE), and directly analyzed by tandem mass spectrometry using electrospray ionization without liquid chromatographic separation. The perfluoroalkyl derivatives could be sufficiently distinguished from non-fluorous compounds, i.e. the biological matrix, due to their fluorous interaction. Thus, rapid and accurate determination of amino acids was accomplished. The method was validated with human plasma samples and applied to the analysis of amino acids in the plasma of mice with maple syrup urine disease or phenylketonuria. PMID:26222276

  20. Direct tandem mass spectrometric analysis of amino acids in plasma using fluorous derivatization and monolithic solid-phase purification.

    PubMed

    Tamashima, Erina; Hayama, Tadashi; Yoshida, Hideyuki; Imakyure, Osamu; Yamaguchi, Masatoshi; Nohta, Hitoshi

    2015-11-10

    In this study, we developed a novel direct tandem mass spectrometric method for rapid and accurate analysis of amino acids utilizing a fluorous derivatization and purification technique. Amino acids were perfluoroalkylated with 2H,2H,3H,3H-perfluoroundecan-1-al in the presence of 2-picoline borane via reductive amination. The derivatives were purified by perfluoroalkyl-modified silica-based monolithic solid-phase extraction (monolithic F-SPE), and directly analyzed by tandem mass spectrometry using electrospray ionization without liquid chromatographic separation. The perfluoroalkyl derivatives could be sufficiently distinguished from non-fluorous compounds, i.e. the biological matrix, due to their fluorous interaction. Thus, rapid and accurate determination of amino acids was accomplished. The method was validated with human plasma samples and applied to the analysis of amino acids in the plasma of mice with maple syrup urine disease or phenylketonuria.

  1. 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. PMID:24525301

  2. 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.

  3. Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

    PubMed Central

    2015-01-01

    As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performance of multiplexed quantitative phosphoproteomics on the Orbitrap Fusion mass spectrometer. Utilizing a two-phosphoproteome model of precursor ion interference, we assessed the accuracy of phosphopeptide quantitation across a variety of experimental approaches. These methods included the use of synchronous precursor selection (SPS) to enhance TMT reporter ion intensity and accuracy. We found that (i) ratio distortion remained a problem for phosphopeptide analysis in multiplexed quantitative workflows, (ii) ratio distortion can be overcome by the use of an SPS-MS3 scan, (iii) interfering ions generally possessed a different charge state than the target precursor, and (iv) selecting only the phosphate neutral loss peak (single notch) for the MS3 scan still provided accurate ratio measurements. Remarkably, these data suggest that the underlying cause of interference may not be due to coeluting and cofragmented peptides but instead from consistent, low level background fragmentation. Finally, as a proof-of-concept 10-plex experiment, we compared phosphopeptide levels from five murine brains to five livers. In total, the SPS-MS3 method quantified 38 247 phosphopeptides, corresponding to 11 000 phosphorylation sites. With 10 measurements recorded for each phosphopeptide, this equates to more than 628 000 binary comparisons collected in less than 48 h. PMID:25521595

  4. Petroleomics by Direct Analysis in Real Time-Mass Spectrometry.

    PubMed

    Romão, Wanderson; Tose, Lilian V; Vaz, Boniek G; Sama, Sara G; Lobinski, Ryszard; Giusti, Pierre; Carrier, Hervé; Bouyssiere, Brice

    2016-01-01

    The analysis of crude oil and its fractions by applying ambient ionization techniques remains underexplored in mass spectrometry (MS). Direct analysis in real time (DART) in the positive-ion mode was coupled to a linear quadrupole ion trap Orbitrap mass spectrometer (LTQ Orbitrap) to analyze crude oil, paraffin samples, and porphyrin standard compounds. The ionization parameters of DART-MS were optimized for crude oil analysis. DART-MS rendered the optimum conditions of the operation using paper as the substrate, T = 400°C, helium as the carrier gas, and a sample concentration ≥6 mg mL(-1). In the crude oils analysis, the DART(+)-Orbitrap mass spectra detected the typical N, NO, and O-containing compounds. In the paraffin samples, oxidized hydrocarbon species (Ox classes, where x = 1-4) with double-bond equivalent of 1-4 were detected, and their structures and connectivity were confirmed by collision-induced dissociation (CID) experiments. DART(+)-MS has identified the porphyrin standard compounds as [M + H](+) ions of m/z 615.2502 and 680.1763, where M = C44H30N4 and C44H28N4OV, respectively, based on the formula assignment and by phenyl losses observed on CID experiments. PMID:26432579

  5. Petroleomics by Direct Analysis in Real Time-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Romão, Wanderson; Tose, Lilian V.; Vaz, Boniek G.; Sama, Sara G.; Lobinski, Ryszard; Giusti, Pierre; Carrier, Hervé; Bouyssiere, Brice

    2016-01-01

    The analysis of crude oil and its fractions by applying ambient ionization techniques remains underexplored in mass spectrometry (MS). Direct analysis in real time (DART) in the positive-ion mode was coupled to a linear quadrupole ion trap Orbitrap mass spectrometer (LTQ Orbitrap) to analyze crude oil, paraffin samples, and porphyrin standard compounds. The ionization parameters of DART-MS were optimized for crude oil analysis. DART-MS rendered the optimum conditions of the operation using paper as the substrate, T = 400°C, helium as the carrier gas, and a sample concentration ≥6 mg mL-1. In the crude oils analysis, the DART(+)-Orbitrap mass spectra detected the typical N, NO, and O-containing compounds. In the paraffin samples, oxidized hydrocarbon species (Ox classes, where x = 1-4) with double-bond equivalent of 1-4 were detected, and their structures and connectivity were confirmed by collision-induced dissociation (CID) experiments. DART(+)-MS has identified the porphyrin standard compounds as [M + H]+ ions of m/ z 615.2502 and 680.1763, where M = C44H30N4 and C44H28N4OV, respectively, based on the formula assignment and by phenyl losses observed on CID experiments.

  6. How effective are traditional methods of compositional analysis in providing an accurate material balance for a range of softwood derived residues?

    PubMed Central

    2013-01-01

    Background Forest residues represent an abundant and sustainable source of biomass which could be used as a biorefinery feedstock. Due to the heterogeneity of forest residues, such as hog fuel and bark, one of the expected challenges is to obtain an accurate material balance of these feedstocks. Current compositional analytical methods have been standardised for more homogenous feedstocks such as white wood and agricultural residues. The described work assessed the accuracy of existing and modified methods on a variety of forest residues both before and after a typical pretreatment process. Results When “traditional” pulp and paper methods were used, the total amount of material that could be quantified in each of the six softwood-derived residues ranged from 88% to 96%. It was apparent that the extractives present in the substrate were most influential in limiting the accuracy of a more representative material balance. This was particularly evident when trying to determine the lignin content, due to the incomplete removal of the extractives, even after a two stage water-ethanol extraction. Residual extractives likely precipitated with the acid insoluble lignin during analysis, contributing to an overestimation of the lignin content. Despite the minor dissolution of hemicellulosic sugars, extraction with mild alkali removed most of the extractives from the bark and improved the raw material mass closure to 95% in comparison to the 88% value obtained after water-ethanol extraction. After pretreatment, the extent of extractive removal and their reaction/precipitation with lignin was heavily dependent on the pretreatment conditions used. The selective removal of extractives and their quantification after a pretreatment proved to be even more challenging. Regardless of the amount of extractives that were originally present, the analytical methods could be refined to provide reproducible quantification of the carbohydrates present in both the starting material and

  7. Lacunarity and multifractal analysis of the large DLA mass distribution

    NASA Astrophysics Data System (ADS)

    Rodriguez-Romo, Suemi; Sosa-Herrera, Antonio

    2013-08-01

    We show the methodology used to analyze fractal and mass-multifractal properties of very large Diffusion-Limited Aggregation (DLA) clusters with a maximum of 109 particles for 2D aggregates and 108 particles for 3D clusters, to support our main result; the scaling behavior obtained by our experimental results corresponds to the expected performance of monofractal objects. In order to estimate lacunarity measures for large DLA clusters, we develop a variant of the gliding-box algorithm which reduces the computer time needed to obtain experimental results. We show how our mass multifractal data have a tendency to present monofractal behavior for the mass distribution of the cases presented in this paper in the limit of very large clusters. Lacunarity analysis shows, provided we study small clusters mass distributions, data which might be interpreted as two different values of fractal dimensions while the cluster grows; however, this effect tends to vanish when the cluster size increases further, in such a way that monofractality is achieved. The outcomes of this paper lead us to conclude that the previously reported mass multifractality behavior (Vicsek et al., 1990 [13]) detected for DLA clusters is a consequence of finite size effects and floating point precision limitations and not an intrinsic feature of the phenomena, since the scaling behavior of our DLA clusters space corresponds to monofractal objects, being this situation remarkably noticeable in the limit of very large clusters.

  8. Use of Tritium Accelerator Mass Spectrometry for Tree Ring Analysis

    PubMed Central

    LOVE, ADAM H.; HUNT, JAMES R.; ROBERTS, MARK L.; SOUTHON, JOHN R.; CHIARAPPA - ZUCCA, MARINA L.; DINGLEY, KAREN H.

    2010-01-01

    Public concerns over the health effects associated with low-level and long-term exposure to tritium released from industrial point sources have generated the demand for better methods to evaluate historical tritium exposure levels for these communities. The cellulose of trees accurately reflects the tritium concentration in the source water and may contain the only historical record of tritium exposure. The tritium activity in the annual rings of a tree was measured using accelerator mass spectrometry to reconstruct historical annual averages of tritium exposure. Milligram-sized samples of the annual tree rings from a Tamarix located at the Nevada Test Site are used for validation of this methodology. The salt cedar was chosen since it had a single source of tritiated water that was well-characterized as it varied over time. The decay-corrected tritium activity of the water in which the salt cedar grew closely agrees with the organically bound tritium activity in its annual rings. This demonstrates that the milligram-sized samples used in tritium accelerator mass spectrometry are suited for reconstructing anthropogenic tritium levels in the environment. PMID:12144257

  9. Field gas chromatography-mass spectrometry for fast analysis.

    PubMed

    Makas, Alexei L; Troshkov, Mikhail L

    2004-02-01

    The objective of this presentation is to demonstrate the original device and procedure for fast gas chromatography-mass spectrometry (GC-MS) analysis of gaseous and liquid samples and to discuss its features and capabilities. The concept was developed in order to expand the range of compounds suitable for GC separation and to reduce the time of analysis. Field GC-MS, consisting of original "concentrator-thermodesorber" (CTD) unit, multiple module GC system and compact magnetic mass spectrometer with powerful two-stage vacuum system and multicollector ion detector, is represented. The whole weight of the device is 90 kg. Power consumption is 250 W. The device and analytical procedures allow high speed screening of toxic substances in air and extracts within 100 s per sample. The examples of applications are described, including fast screening of tributyl phosphate (TBP) in air at low ppt level at the rate 1 sample/min.

  10. Field gas chromatography-mass spectrometry for fast analysis.

    PubMed

    Makas, Alexei L; Troshkov, Mikhail L

    2004-02-01

    The objective of this presentation is to demonstrate the original device and procedure for fast gas chromatography-mass spectrometry (GC-MS) analysis of gaseous and liquid samples and to discuss its features and capabilities. The concept was developed in order to expand the range of compounds suitable for GC separation and to reduce the time of analysis. Field GC-MS, consisting of original "concentrator-thermodesorber" (CTD) unit, multiple module GC system and compact magnetic mass spectrometer with powerful two-stage vacuum system and multicollector ion detector, is represented. The whole weight of the device is 90 kg. Power consumption is 250 W. The device and analytical procedures allow high speed screening of toxic substances in air and extracts within 100 s per sample. The examples of applications are described, including fast screening of tributyl phosphate (TBP) in air at low ppt level at the rate 1 sample/min. PMID:14698236

  11. Determination of densified biomass mass properties using 3D laser scanning and image analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biomass densification is viewed as the indispensable feedstock preprocessing operation for efficient transport, storage, material flow through machines, and handling activities. Accurate mass properties of densified biomass such as surface area, volume, and envelope density form fundamental data for...

  12. A mass spectrometric analysis of {gamma}-GPS films

    SciTech Connect

    Dillingham, R.G.; Boerio, F.J.; Bertelsen, C.; Savina, M.R.; Lykke, K.R.; Calaway, W.F.

    1996-06-01

    {gamma}-glycidoxypropyltrimethoxysilane ({gamma}-GPS) is used for pre-treatment of grit-blasted aluminum before adhesive bonding. This paper discusses analysis of non-reflective grit-blasted surfaces using mass spectrometry of species that were either sputtered off using an ion beam or thermally desorbed as neutrals using a pulsed laser and then post-ionized using a secondary laser. Results show that fragmentation is excessive and structural information is difficult to obtain from the spectra.

  13. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  14. A more accurate and penetrating method to measure the enrichment and mass of UF6 storage containers using passive neutron self-interrogation

    SciTech Connect

    Menlove, Howard O; Swinhoe, Martyn T; Miller, Karen A

    2010-01-01

    This paper describes an unattended mode neutron measurement that can provide the enrichment of the uranium in UF{sub 6} cylinders. The new passive neutron measurement provides better penetration into the uranium mass than prior gamma-ray enrichment measurement methods. The Passive Neutron Enrichment Monitor (PNEM) provides a new measurement technique that uses passive neutron totals and coincidence counting together with neutron self-interrogation to measure the enrichment in the cylinders. The measurement uses the neutron rates from two detector pods. One of the pods has a bare polyethylene surface next to the cylinder and the other polyethylene surface is covered with Cd to prevent thermal neutrons from returning to the cylinder. The primary neutron source from the enriched UF{sub 6} is the alpha-particle decay from the {sub 234}U that interacts with the fluorine to produce random neutrons. The singles neutron counting rate is dominated by the {sub 234}U neutrons with a minor contribution from the induced fissions in the {sub 235}U. However, the doubles counting rate comes primarily from the induced fissions (i.e., multiplication) in the {sub 235}U in enriched uranium. The PNEM concept makes use of the passive neutrons that are initially produced from the {sub 234}U reactions that track the {sub 235}U enrichment during the enrichment process. The induced fission reactions from the thermal-neutron albedo are all from the {sub 235}U and provide a measurement of the {sub 235}U. The Cd ratio has the desirable feature that all of the thermal-neutron-induced fissions in {sub 235}U are independent of the original neutron source. Thus, the ratio is independent of the uranium age, purity, and prior reactor history.

  15. Keto acid profiling analysis as ethoxime/tert-butyldimethylsilyl derivatives by gas chromatography-mass spectrometry.

    PubMed

    Nguyen, Duc-Toan; Lee, Gwang; Paik, Man-Jeong

    2013-01-15

    Organic acids, including keto acids, are key intermediates of central pathways in cellular metabolism. In this study, a comprehensive and reliable method was developed and optimized for the simultaneous measurement of 17 keto acids in various biological samples. The keto acids were converted to solvent extractable forms by ethoximation followed by tert-butyldimethylsilylation for direct analysis by gas chromatography-mass spectrometry in selected ion monitoring mode. The proposed method was precise (0.05-8.3, % RSD) and accurate (-10.5 to 5.3, % RE) with low limit of detection (0.01-0.5ng/mL) and good linearity (r>0.995) in the range of 0.01-5.0μg/mL. This was suitable for profiling analysis of targeted keto acids in human plasma, urine and rat brain tissue.

  16. Analysis of volatile mouse pheromones by gas chromatography mass spectrometry.

    PubMed

    Novotny, Milos V; Soini, Helena A

    2013-01-01

    High-precision quantitative profiling of volatile organic constituents in rodent physiological fluids and glandular secretions is needed to relate olfactory signals to physiology and behavior. Whereas capillary gas chromatography-mass spectrometry (GC-MS) analysis has become the most widely applied in such investigations, the extraction and preconcentration of volatile organics is arguably the most critical step in the overall analytical task. In this chapter, we describe technical details of two main sample extraction procedures used in our laboratory: dynamic headspace trapping, and stir bar sorptive extraction (SBSE). They have been demonstrated here for the chromatographic analysis of mouse urine, serum, saliva, and preputial gland specimens.

  17. Mass spectrometry-based quantitative analysis and biomarker discovery.

    PubMed

    Suzuki, Naoto

    2011-01-01

      Mass spectrometry-based quantitative analysis and biomarker discovery using metabolomics approach represent one of the major platforms in clinical fields including for the prognosis or diagnosis, assessment of severity and response to therapy in a number of clinical disease states as well as therapeutic drug monitoring (TDM). This review first summarizes our mass spectrometry-based research strategy and some results on relationship between cysteinyl leukotriene (cysLT), thromboxane (TX), 12-hydroxyeicosatetraenoic acid (12-HETE) and other metabolites of arachidonic acid and diseases such as atopic dermatitis, rheumatoid arthritis and diabetes mellitus. For the purpose of evaluating the role of these metabolites of arachidonic acid in disease status, we have developed sensitive determination methods with simple solid-phase extraction and applied in clinical settings. In addition to these endogenous compounds, using mass spectrometry, we have developed actually applicable quantitative methods for TDM. Representative example was a method of TDM for sirolimus, one of the immunosuppressant agents for a recipient of organ transplant, which requires rigorous monitoring of blood level. As we recognized great potential in mass spectrometry during these researches, we have become interested in metabolomics as the non-targeted analysis of metabolites. Now, established strategy for the metabolomics investigation applies to samples from cells, animals and humans to separate groups based on altered patterns of metabolites in biological fluids and to identify metabolites as potential biomarkers discriminating groups. We would be honored if our research using mass spectrometry would contribute to provide useful information in the field of medical pharmacy. PMID:21881303

  18. Mass Spectrometry and Fourier Transform Infrared Spectroscopy for Analysis of Biological Materials

    SciTech Connect

    Anderson, Timothy J.

    2014-12-01

    Time-of-flight mass spectrometry along with statistical analysis was utilized to study metabolic profiles among rats fed resistant starch (RS) diets. Fischer 344 rats were fed four starch diets consisting of 55% (w/w, dbs) starch. A control starch diet consisting of corn starch was compared against three RS diets. The RS diets were high-amylose corn starch (HA7), HA7 chemically modified with octenyl succinic anhydride, and stearic-acid-complexed HA7 starch. A subgroup received antibiotic treatment to determine if perturbations in the gut microbiome were long lasting. A second subgroup was treated with azoxymethane (AOM), a carcinogen. At the end of the eight week study, cecal and distal-colon contents samples were collected from the sacrificed rats. Metabolites were extracted from cecal and distal colon samples into acetonitrile. The extracts were then analyzed on an accurate-mass time-of-flight mass spectrometer to obtain their metabolic profile. The data were analyzed using partial least-squares discriminant analysis (PLS-DA). The PLS-DA analysis utilized a training set and verification set to classify samples within diet and treatment groups. PLS-DA could reliably differentiate the diet treatments for both cecal and distal colon samples. The PLS-DA analyses of the antibiotic and no antibiotic treated subgroups were well classified for cecal samples and modestly separated for distal-colon samples. PLS-DA analysis had limited success separating distal colon samples for rats given AOM from those not treated; the cecal samples from AOM had very poor classification. Mass spectrometry profiling coupled with PLS-DA can readily classify metabolite differences among rats given RS diets.

  19. Feasibility of ultra-high performance liquid and gas chromatography coupled to mass spectrometry for accurate determination of primary and secondary phthalate metabolites in urine samples.

    PubMed

    Herrero, Laura; Calvarro, Sagrario; Fernández, Mario A; Quintanilla-López, Jesús Eduardo; González, María José; Gómara, Belén

    2015-01-01

    Phthalates (PAEs) are ubiquitous toxic chemical compounds. During the last few years, some phthalate metabolites (MPAEs) have been proposed as appropriate biomarkers in human urine samples to determine PAE human intake and exposure. So, it is necessary to have fast, easy, robust and validated analytical methods to determine selected MPAEs in urine human samples. Two different instrumental methods based on gas (GC) and ultra-high performance liquid (UHPLC) chromatography coupled to mass spectrometry (MS) have been optimized, characterized and validated for the simultaneous determination of nine primary and secondary phthalate metabolites in urine samples. Both instrumental methods have similar sensitivity (detection limits ranged from 0.03 to 8.89 pg μL(-1) and from 0.06 to 0.49 pg μL(-1) in GC-MS and UHPLC-MS(2), respectively), precision (repeatability, expressed as relative standard deviation, which was lower than 8.4% in both systems, except for 5OH-MEHP in the case of GC-MS) and accuracy. But some advantages of the UHPLC-MS(2) method, such as more selectivity and lower time in the chromatographic runs (6.8 min vs. 28.5 min), have caused the UHPLC-MS(2) method to be chosen to analyze the twenty one human urine samples from the general Spanish population. Regarding these samples, MEP showed the highest median concentration (68.6 μg L(-1)), followed by MiBP (23.3 μg L(-1)), 5cx-MEPP (22.5 μg L(-1)) and MBP (19.3μgL(-1)). MMP (6.99 μg L(-1)), 5oxo-MEHP (6.15 μg L(-1)), 5OH-MEHP (5.30 μg L(-1)) and MEHP (4.40 μg L(-1)) showed intermediate levels. Finally, the lowest levels were found for MBzP (2.55 μg L(-1)). These data are within the same order of magnitude as those found in other similar populations. PMID:25467512

  20. Feasibility of ultra-high performance liquid and gas chromatography coupled to mass spectrometry for accurate determination of primary and secondary phthalate metabolites in urine samples.

    PubMed

    Herrero, Laura; Calvarro, Sagrario; Fernández, Mario A; Quintanilla-López, Jesús Eduardo; González, María José; Gómara, Belén

    2015-01-01

    Phthalates (PAEs) are ubiquitous toxic chemical compounds. During the last few years, some phthalate metabolites (MPAEs) have been proposed as appropriate biomarkers in human urine samples to determine PAE human intake and exposure. So, it is necessary to have fast, easy, robust and validated analytical methods to determine selected MPAEs in urine human samples. Two different instrumental methods based on gas (GC) and ultra-high performance liquid (UHPLC) chromatography coupled to mass spectrometry (MS) have been optimized, characterized and validated for the simultaneous determination of nine primary and secondary phthalate metabolites in urine samples. Both instrumental methods have similar sensitivity (detection limits ranged from 0.03 to 8.89 pg μL(-1) and from 0.06 to 0.49 pg μL(-1) in GC-MS and UHPLC-MS(2), respectively), precision (repeatability, expressed as relative standard deviation, which was lower than 8.4% in both systems, except for 5OH-MEHP in the case of GC-MS) and accuracy. But some advantages of the UHPLC-MS(2) method, such as more selectivity and lower time in the chromatographic runs (6.8 min vs. 28.5 min), have caused the UHPLC-MS(2) method to be chosen to analyze the twenty one human urine samples from the general Spanish population. Regarding these samples, MEP showed the highest median concentration (68.6 μg L(-1)), followed by MiBP (23.3 μg L(-1)), 5cx-MEPP (22.5 μg L(-1)) and MBP (19.3μgL(-1)). MMP (6.99 μg L(-1)), 5oxo-MEHP (6.15 μg L(-1)), 5OH-MEHP (5.30 μg L(-1)) and MEHP (4.40 μg L(-1)) showed intermediate levels. Finally, the lowest levels were found for MBzP (2.55 μg L(-1)). These data are within the same order of magnitude as those found in other similar populations.

  1. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    Watrous, Matthew George; Adamic, Mary Louise; Olson, John Eric; Baeck, D. L.; Fox, R. V.; Hahn, P. A.; Jenson, D. D.; Lister, T. E.

    2015-09-01

    The goal of the project, New Paradigms for Isotope Ratio Mass Spectrometry: Raising the Scientific Profile and Improved Performance for Accelerator Mass Spectrometry (AMS) and Thermal Ionization Mass Spectrometry (TIMS), is to ensure that the ongoing isotope ratio determination capability within the U.S. Department of Energy complex is the world’s best for application to nonproliferation. This report spells out the progress of Task 4, Transition of TIMS to AMS for Iodine Analysis, of the larger project. The subtasks under Task 4 and the accomplishments throughout the three year project life cycle are presented in this report. Progress was made in optimization of chemical extraction, determination of a detection limit for 127Iodine, production of standard materials for AMS analysis quality assurance, facilitation of knowledge exchange with respect to analyzing iodine on an AMS, cross comparison with a world-leading AMS laboratory, supercritical fluid extraction of iodine for AMS analysis and electrodeposition of seawater as a direct method of preparation for iodine analysis by AMS--all with the goal of minimizing the time required to stand up an AMS capability for iodine analysis of exposed air filters at INL. An effective extraction method has been developed and demonstrated for iodine analysis of exposed air filters. Innovative techniques to accomplish the cathode preparation for AMS analysis were developed and demonstrated and published. The known gap of a lack of available materials for reference standards in the analysis of iodine by AMS was filled by the preparation of homogenous materials that were calibrated against NIST materials. A minimum limit on the amount of abundant isotope in a sample was determined for AMS analysis. The knowledge exchange occurred with fantastic success. Scientists engaged the international AMS community at conferences, as well as in their laboratories for collaborative work. The supercritical fluid extraction work has positive

  2. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

    PubMed Central

    Wong, Michael Thomas

    2016-01-01

    Single-cell mass cytometry significantly increases the dimensionality of cytometry analysis as compared to fluorescence flow cytometry, providing unprecedented resolution of cellular diversity in tissues. However, analysis and interpretation of these high-dimensional data poses a significant technical challenge. Here, we present cytofkit, a new Bioconductor package, which integrates both state-of-the-art bioinformatics methods and in-house novel algorithms to offer a comprehensive toolset for mass cytometry data analysis. Cytofkit provides functions for data pre-processing, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets. This pipeline also provides a graphical user interface (GUI) for ease of use, as well as a shiny application (APP) for interactive visualization of cell subpopulations and progression profiles of key markers. Applied to a CD14−CD19− PBMCs dataset, cytofkit accurately identified different subsets of lymphocytes; applied to a human CD4+ T cell dataset, cytofkit uncovered multiple subtypes of TFH cells spanning blood and tonsils. Cytofkit is implemented in R, licensed under the Artistic license 2.0, and freely available from the Bioconductor website, https://bioconductor.org/packages/cytofkit/. Cytofkit is also applicable for flow cytometry data analysis. PMID:27662185

  3. Qualitative nontarget analysis of landfill leachate using gas chromatography time-of-flight mass spectrometry.

    PubMed

    Jernberg, Joonas; Pellinen, Jukka; Rantalainen, Anna-Lea

    2013-01-15

    Nontarget analysis means that a sample is analysed without preselection of the studied analytes. While target analysis attempts to determine whether certain selected compounds are present in the sample, nontarget analysis is performed to explore what unknown compounds can be found. We developed a nontarget method using a landfill leachate sample as a complex test sample. The method was based on the use of a gas chromatograph-time-of-flight mass spectrometer (GC-TOF-MS) for final analysis and a deconvolution computer application for data processing. This nontarget analysis method was tested and validated by applying it to a landfill leachate sample spiked with 11 organic pollutants that were treated as unknowns. Sensitivity was found to be the most critical parameter affecting the success of nontarget analysis. The limit of identification (LOI) was 2500 ng L(-1) for four of the 11 compounds, 500 ng L(-1) for three compounds and 100 ng L(-1) for one compound. Three compounds were not detected in any of the spiked samples. A six-stage identification process was developed based on the spiking experiments. The process was based on the forward fit value of the library hit, the number of deconvoluted ions and the accurate mass scoring of the measured ions. The process was applied to an unspiked leachate water sample. Altogether, 44 compounds were tentatively identified in the sample. Elemental compositions of 36 components were additionally determined for which an unequivocal compound identification could not be given. Nontarget analysis with GC-TOF-MS is a promising method for the qualitative analysis of complex water samples. However, we conclude that the computer application for nontarget analysis needs improvement to decrease the amount of manual work needed in the identification process.

  4. Mercury mass measurement in fluorescent lamps via neutron activation analysis

    NASA Astrophysics Data System (ADS)

    Viererbl, L.; Vinš, M.; Lahodová, Z.; Fuksa, A.; Kučera, J.; Koleška, M.; Voljanskij, A.

    2015-11-01

    Mercury is an essential component of fluorescent lamps. Not all fluorescent lamps are recycled, resulting in contamination of the environment with toxic mercury, making measurement of the mercury mass used in fluorescent lamps important. Mercury mass measurement of lamps via instrumental neutron activation analysis (NAA) was tested under various conditions in the LVR-15 research reactor. Fluorescent lamps were irradiated in different positions in vertical irradiation channels and a horizontal channel in neutron fields with total fluence rates from 3×108 cm-2 s-1 to 1014 cm-2 s-1. The 202Hg(n,γ)203Hg nuclear reaction was used for mercury mass evaluation. Activities of 203Hg and others induced radionuclides were measured via gamma spectrometry with an HPGe detector at various times after irradiation. Standards containing an Hg2Cl2 compound were used to determine mercury mass. Problems arise from the presence of elements with a large effective cross section in luminescent material (europium, antimony and gadolinium) and glass (boron). The paper describes optimization of the NAA procedure in the LVR-15 research reactor with particular attention to influence of neutron self-absorption in fluorescent lamps.

  5. Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis.

    PubMed

    Yoon, Sung Hwan; Huang, Yue; Edgar, J Scott; Ting, Ying S; Heron, Scott R; Kao, Yuchieh; Li, Yanyan; Masselon, Christophe D; Ernst, Robert K; Goodlett, David R

    2012-08-01

    Surface acoustic wave nebulization (SAWN) is a novel method to transfer nonvolatile analytes directly from the aqueous phase to the gas phase for mass spectrometric analysis. The lower ion energetics of SAWN and its planar nature make it appealing for analytically challenging lipid samples. This challenge is a result of their amphipathic nature, labile nature, and tendency to form aggregates, which readily precipitate clogging capillaries used for electrospray ionization (ESI). Here, we report the use of SAWN to characterize the complex glycolipid, lipid A, which serves as the membrane anchor component of lipopolysaccharide (LPS) and has a pronounced tendency to clog nano-ESI capillaries. We also show that unlike ESI SAWN is capable of ionizing labile phospholipids without fragmentation. Lastly, we compare the ease of use of SAWN to the more conventional infusion-based ESI methods and demonstrate the ability to generate higher order tandem mass spectral data of lipid A for automated structure assignment using our previously reported hierarchical tandem mass spectrometry (HiTMS) algorithm. The ease of generating SAWN-MS(n) data combined with HiTMS interpretation offers the potential for high throughput lipid A structure analysis.

  6. Nonlinear Pressure Wave Analysis by Concentrated Mass Model

    NASA Astrophysics Data System (ADS)

    Ishikawa, Satoshi; Kondou, Takahiro; Matsuzaki, Kenichiro

    A pressure wave propagating in a tube often changes to a shock wave because of the nonlinear effect of fluid. Analyzing this phenomenon by the finite difference method requires high computational cost. To lessen the computational cost, a concentrated mass model is proposed. This model consists of masses, connecting nonlinear springs, connecting dampers, and base support dampers. The characteristic of a connecting nonlinear spring is derived from the adiabatic change of fluid, and the equivalent mass and equivalent damping coefficient of the base support damper are derived from the equation of motion of fluid in a cylindrical tube. Pressure waves generated in a hydraulic oil tube, a sound tube and a plane-wave tube are analyzed numerically by the proposed model to confirm the validity of the model. All numerical computational results agree very well with the experimental results carried out by Okamura, Saenger and Kamakura. Especially, the numerical analysis reproduces the phenomena that a pressure wave with large amplitude propagating in a sound tube or in a plane tube changes to a shock wave. Therefore, it is concluded that the proposed model is valid for the numerical analysis of nonlinear pressure wave problem.

  7. Size and concentration determination of (functionalised) fullerenes in surface and sewage water matrices using field flow fractionation coupled to an online accurate mass spectrometer: method development and validation.

    PubMed

    Herrero, Pol; Bäuerlein, Patrick S; Emke, Erik; Marcé, Rosa M; de Voogt, Pim

    2015-04-29

    In order to assess the environmental risks of a compound it is imperative to have suitable and reliable techniques for its determination in environmental matrices. In this paper, we focused on a method development for the recently introduced online coupling of a field flow fractionation (FFF) system to an Orbitrap-HRMS, that allows the simultaneous size and concentration determination of different aqueous fullerene aggregates and their concentrations in different size fractions. A 0.05% NH4OH solution in water was identified as the best carrier liquid for the analysis of the three different aqueous fullerene suspensions (C60 [60], [6,6]-phenyl-C61 butyric acid methyl ester ([60]PCBM) and [6,6]-(bis)phenyl-C61 butyric acid methyl ester ([60]bisPCBM)). The multi-angle light scattering (MALS) data received after employing the ammonia solution was consistent with both the theory and calibration using well defined Au and latex particles. The LODs obtained using Orbitrap HRMS detection were 0.1 μg L(-1) for an injection volume of 100 μL which are significantly better than the LODs obtained by using UV (20 μg L(-1)) and MALS detectors (5 μg L(-1)). However, these LODs can be further improved as in theory there is no limit to the amount of sample that can be injected into the FFF. Environmental samples (river and sewage water) were spiked with fullerenes and the fractograms obtained for these samples revealed that the matrix does affect the size of fullerene aggregates. Information on the size distribution can be useful for the risk assessment of these particles.

  8. Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

    NASA Astrophysics Data System (ADS)

    Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

  9. An automated proteomic data analysis workflow for mass spectrometry

    PubMed Central

    2009-01-01

    Background Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be integrated and quantitatively analyzed. The Sequest™ search algorithm is a commonly used algorithm for identifying peptides and proteins from two dimensional liquid chromatography electrospray ionization tandem mass spectrometry (2-D LC ESI MS2) data. A number of proteomic pipelines that facilitate high throughput 'post data acquisition analysis' are described in the literature. However, these pipelines need to be updated to accommodate the rapidly evolving data analysis methods. Here, we describe a proteomic data analysis pipeline that specifically addresses two main issues pertinent to protein identification and differential expression analysis: 1) estimation of the probability of peptide and protein identifications and 2) non-parametric statistics for protein differential expression analysis. Our proteomic analysis workflow analyzes replicate datasets from a single experimental paradigm to generate a list of identified proteins with their probabilities and significant changes in protein expression using parametric and non-parametric statistics. Results The input for our workflow is Bioworks™ 3.2 Sequest (or a later version, including cluster) output in XML format. We use a decoy database approach to assign probability to peptide identifications. The user has the option to select "quality thresholds" on peptide identifications based on the P value. We also estimate probability for protein identification. Proteins identified with peptides at a user-specified threshold value from biological experiments are grouped as either control or treatment for further analysis in ProtQuant. ProtQuant utilizes a parametric (ANOVA) method, for calculating differences in protein expression based on the quantitative measure ΣXcorr. Alternatively Prot

  10. Analysis of EDZ Development of Columnar Jointed Rock Mass in the Baihetan Diversion Tunnel

    NASA Astrophysics Data System (ADS)

    Hao, Xian-Jie; Feng, Xia-Ting; Yang, Cheng-Xiang; Jiang, Quan; Li, Shao-Jun

    2016-04-01

    Due to the time dependency of the crack propagation, columnar jointed rock masses exhibit marked time-dependent behaviour. In this study, in situ measurements, scanning electron microscope (SEM), back-analysis method and numerical simulations are presented to study the time-dependent development of the excavation damaged zone (EDZ) around underground diversion tunnels in a columnar jointed rock mass. Through in situ measurements of crack propagation and EDZ development, their extent is seen to have increased over time, despite the fact that the advancing face has passed. Similar to creep behaviour, the time-dependent EDZ development curve also consists of three stages: a deceleration stage, a stabilization stage, and an acceleration stage. A corresponding constitutive model of columnar jointed rock mass considering time-dependent behaviour is proposed. The time-dependent degradation coefficient of the roughness coefficient and residual friction angle in the Barton-Bandis strength criterion are taken into account. An intelligent back-analysis method is adopted to obtain the unknown time-dependent degradation coefficients for the proposed constitutive model. The numerical modelling results are in good agreement with the measured EDZ. Not only that, the failure pattern simulated by this time-dependent constitutive model is consistent with that observed in the scanning electron microscope (SEM) and in situ observation, indicating that this model could accurately simulate the failure pattern and time-dependent EDZ development of columnar joints. Moreover, the effects of the support system provided and the in situ stress on the time-dependent coefficients are studied. Finally, the long-term stability analysis of diversion tunnels excavated in columnar jointed rock masses is performed.

  11. Intact MicroRNA Analysis Using High Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kullolli, Majlinda; Knouf, Emily; Arampatzidou, Maria; Tewari, Muneesh; Pitteri, Sharon J.

    2014-01-01

    MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that post-transcriptionally regulate gene expression, and play key roles in the regulation of a variety of cellular processes and in disease. New tools to analyze miRNAs will add understanding of the physiological origins and biological functions of this class of molecules. In this study, we investigate the utility of high resolution mass spectrometry for the analysis of miRNAs through proof-of-concept experiments. We demonstrate the ability of mass spectrometry to resolve and separate miRNAs and corresponding 3' variants in mixtures. The mass accuracy of the monoisotopic deprotonated peaks from various miRNAs is in the low ppm range. We compare fragmentation of miRNA by collision-induced dissociation (CID) and by higher-energy collisional dissociation (HCD) which yields similar sequence coverage from both methods but additional fragmentation by HCD versus CID. We measure the linear dynamic range, limit of detection, and limit of quantitation of miRNA loaded onto a C18 column. Lastly, we explore the use of data-dependent acquisition of MS/MS spectra of miRNA during online LC-MS and demonstrate that multiple charge states can be fragmented, yielding nearly full sequence coverage of miRNA on a chromatographic time scale. We conclude that high resolution mass spectrometry allows the separation and measurement of miRNAs in mixtures and a standard LC-MS setup can be adapted for online analysis of these molecules.

  12. Solution of the surface Euler equations for accurate three-dimensional boundary-layer analysis of aerodynamic configurations

    NASA Technical Reports Server (NTRS)

    Iyer, V.; Harris, J. E.

    1987-01-01

    The three-dimensional boundary-layer equations in the limit as the normal coordinate tends to infinity are called the surface Euler equations. The present paper describes an accurate method for generating edge conditions for three-dimensional boundary-layer codes using these equations. The inviscid pressure distribution is first interpolated to the boundary-layer grid. The surface Euler equations are then solved with this pressure field and a prescribed set of initial and boundary conditions to yield the velocities along the two surface coordinate directions. Results for typical wing and fuselage geometries are presented. The smoothness and accuracy of the edge conditions obtained are found to be superior to the conventional interpolation procedures.

  13. Analysis of continuous oxygen saturation data for accurate representation of retinal exposure to oxygen in the preterm infant.

    PubMed

    Cirelli, Josie; McGregor, Carolyn; Graydon, Brenda; James, Andrew

    2013-01-01

    Maintaining blood oxygen saturation within the intended target range for preterm infants receiving neonatal intensive care is challenging. Supplemental oxygen is believed to lead to increased risk of retinopathy of prematurity and hence managing the level of oxygen within this population is important within their care. Current quality improvement activities use coarse hourly spot readings to measure supplemental oxygen levels as associated with targeted ranges that vary based on gestational age. In this research we use Artemis, a real-time online healthcare analytics platform to ascertain if the collection of second by second data provides a better representation of retinal exposure to oxygen than an infrequent, intermittent spot reading. We show that Artemis is capable of producing more accurate information from the higher frequency data, as it includes all the episodic events in the activity of the hour, which provides a better understanding of oxygen fluctuation ranges which affect the physiological status of the infant.

  14. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. PMID:24889823

  15. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.

  16. Analysis of algebraic reconstruction technique for accurate imaging of gas temperature and concentration based on tunable diode laser absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Hui-Hui, Xia; Rui-Feng, Kan; Jian-Guo, Liu; Zhen-Yu, Xu; Ya-Bai, He

    2016-06-01

    An improved algebraic reconstruction technique (ART) combined with tunable diode laser absorption spectroscopy(TDLAS) is presented in this paper for determining two-dimensional (2D) distribution of H2O concentration and temperature in a simulated combustion flame. This work aims to simulate the reconstruction of spectroscopic measurements by a multi-view parallel-beam scanning geometry and analyze the effects of projection rays on reconstruction accuracy. It finally proves that reconstruction quality dramatically increases with the number of projection rays increasing until more than 180 for 20 × 20 grid, and after that point, the number of projection rays has little influence on reconstruction accuracy. It is clear that the temperature reconstruction results are more accurate than the water vapor concentration obtained by the traditional concentration calculation method. In the present study an innovative way to reduce the error of concentration reconstruction and improve the reconstruction quality greatly is also proposed, and the capability of this new method is evaluated by using appropriate assessment parameters. By using this new approach, not only the concentration reconstruction accuracy is greatly improved, but also a suitable parallel-beam arrangement is put forward for high reconstruction accuracy and simplicity of experimental validation. Finally, a bimodal structure of the combustion region is assumed to demonstrate the robustness and universality of the proposed method. Numerical investigation indicates that the proposed TDLAS tomographic algorithm is capable of detecting accurate temperature and concentration profiles. This feasible formula for reconstruction research is expected to resolve several key issues in practical combustion devices. Project supported by the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 61205151), the National Key Scientific Instrument and Equipment Development Project of China (Grant

  17. Analysis of algebraic reconstruction technique for accurate imaging of gas temperature and concentration based on tunable diode laser absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Hui-Hui, Xia; Rui-Feng, Kan; Jian-Guo, Liu; Zhen-Yu, Xu; Ya-Bai, He

    2016-06-01

    An improved algebraic reconstruction technique (ART) combined with tunable diode laser absorption spectroscopy(TDLAS) is presented in this paper for determining two-dimensional (2D) distribution of H2O concentration and temperature in a simulated combustion flame. This work aims to simulate the reconstruction of spectroscopic measurements by a multi-view parallel-beam scanning geometry and analyze the effects of projection rays on reconstruction accuracy. It finally proves that reconstruction quality dramatically increases with the number of projection rays increasing until more than 180 for 20 × 20 grid, and after that point, the number of projection rays has little influence on reconstruction accuracy. It is clear that the temperature reconstruction results are more accurate than the water vapor concentration obtained by the traditional concentration calculation method. In the present study an innovative way to reduce the error of concentration reconstruction and improve the reconstruction quality greatly is also proposed, and the capability of this new method is evaluated by using appropriate assessment parameters. By using this new approach, not only the concentration reconstruction accuracy is greatly improved, but also a suitable parallel-beam arrangement is put forward for high reconstruction accuracy and simplicity of experimental validation. Finally, a bimodal structure of the combustion region is assumed to demonstrate the robustness and universality of the proposed method. Numerical investigation indicates that the proposed TDLAS tomographic algorithm is capable of detecting accurate temperature and concentration profiles. This feasible formula for reconstruction research is expected to resolve several key issues in practical combustion devices. Project supported by the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 61205151), the National Key Scientific Instrument and Equipment Development Project of China (Grant

  18. Rosiglitazone: can meta-analysis accurately estimate excess cardiovascular risk given the available data? Re-analysis of randomized trials using various methodologic approaches

    PubMed Central

    Friedrich, Jan O; Beyene, Joseph; Adhikari, Neill KJ

    2009-01-01

    statistically significant. Conclusion We have shown that alternative reasonable methodological approaches to the rosiglitazone meta-analysis can yield increased or decreased risks that are either statistically significant or not significant at the p = 0.05 level for both myocardial infarction and cardiovascular death. Completion of ongoing trials may help to generate more accurate estimates of rosiglitazone's effect on cardiovascular outcomes. However, given that almost all point estimates suggest harm rather than benefit and the availability of alternative agents, the use of rosiglitazone may greatly decline prior to more definitive safety data being generated. PMID:19134216

  19. Isotope ratio analysis of individual sub-micrometer plutonium particles with inductively coupled plasma mass spectrometry.

    PubMed

    Esaka, Fumitaka; Magara, Masaaki; Suzuki, Daisuke; Miyamoto, Yutaka; Lee, Chi-Gyu; Kimura, Takaumi

    2010-12-15

    Information on plutonium isotope ratios in individual particles is of great importance for nuclear safeguards, nuclear forensics and so on. Although secondary ion mass spectrometry (SIMS) is successfully utilized for the analysis of individual uranium particles, the isobaric interference of americium-241 to plutonium-241 makes difficult to obtain accurate isotope ratios in individual plutonium particles. In the present work, an analytical technique by a combination of chemical separation and inductively coupled plasma mass spectrometry (ICP-MS) is developed and applied to isotope ratio analysis of individual sub-micrometer plutonium particles. The ICP-MS results for individual plutonium particles prepared from a standard reference material (NBL SRM-947) indicate that the use of a desolvation system for sample introduction improves the precision of isotope ratios. In addition, the accuracy of the (241)Pu/(239)Pu isotope ratio is much improved, owing to the chemical separation of plutonium and americium. In conclusion, the performance of the proposed ICP-MS technique is sufficient for the analysis of individual plutonium particles. PMID:21111176

  20. Isotope ratio analysis of individual sub-micrometer plutonium particles with inductively coupled plasma mass spectrometry.

    PubMed

    Esaka, Fumitaka; Magara, Masaaki; Suzuki, Daisuke; Miyamoto, Yutaka; Lee, Chi-Gyu; Kimura, Takaumi

    2010-12-15

    Information on plutonium isotope ratios in individual particles is of great importance for nuclear safeguards, nuclear forensics and so on. Although secondary ion mass spectrometry (SIMS) is successfully utilized for the analysis of individual uranium particles, the isobaric interference of americium-241 to plutonium-241 makes difficult to obtain accurate isotope ratios in individual plutonium particles. In the present work, an analytical technique by a combination of chemical separation and inductively coupled plasma mass spectrometry (ICP-MS) is developed and applied to isotope ratio analysis of individual sub-micrometer plutonium particles. The ICP-MS results for individual plutonium particles prepared from a standard reference material (NBL SRM-947) indicate that the use of a desolvation system for sample introduction improves the precision of isotope ratios. In addition, the accuracy of the (241)Pu/(239)Pu isotope ratio is much improved, owing to the chemical separation of plutonium and americium. In conclusion, the performance of the proposed ICP-MS technique is sufficient for the analysis of individual plutonium particles.

  1. Laser desorption mass spectrometry for fast DNA analysis

    SciTech Connect

    Chen, C.H.; Ch`ang, L.Y.; Taranenko, N.I.; Allman, S.L.; Tang, K.; Matteson, K.J.

    1995-09-01

    During the past few years, major effort has been directed toward developing mass spectrometry to measure biopolymers because of the great potential benefit to biomedical research. Hellenkamp and his co-workers were the first to report that large polypeptide molecules can be ionized and detected without significant fragmentation when a greater number of nicotinic acid molecules are used as a matrix. This method is now well known as matrix-assisted laser desorption/ionization (MALDI). Since then, various groups have reported measurements of very large proteins by MALDI. Reliable protein analysis by MALDI is more or less well established. However, the application of MALDI to nucleic acids analysis has been found to be much more difficult. Most research on the measurement of nucleic acid by MALDI were stimulated by the Human Genome Project. Up to now, the only method for reliable routine analysis of nucleic acid is gel electrophoresis. Different sizes of nucleic acids can be separated in gel medium when a high electric field is applied to the gel. However, the time needed to separate different sizes of DNA segments usually takes from several minutes to several hours. If MALDI can be successfully used for nucleic acids analysis, the analysis time can be reduced to less than I millisecond. In addition, no tagging with radioactive materials or chemical dyes is needed. In this work, we will review recent progress related to MALDI for DNA analysis.

  2. Stereophotogrammetrie Mass Distribution Parameter Determination Of The Lower Body Segments For Use In Gait Analysis

    NASA Astrophysics Data System (ADS)

    Sheffer, Daniel B.; Schaer, Alex R.; Baumann, Juerg U.

    1989-04-01

    Inclusion of mass distribution information in biomechanical analysis of motion is a requirement for the accurate calculation of external moments and forces acting on the segmental joints during locomotion. Regression equations produced from a variety of photogrammetric, anthropometric and cadaeveric studies have been developed and espoused in literature. Because of limitations in the accuracy of predicted inertial properties based on the application of regression equation developed on one population and then applied on a different study population, the employment of a measurement technique that accurately defines the shape of each individual subject measured is desirable. This individual data acquisition method is especially needed when analyzing the gait of subjects with large differences in their extremity geo-metry from those considered "normal", or who may possess gross asymmetries in shape in their own contralateral limbs. This study presents the photogrammetric acquisition and data analysis methodology used to assess the inertial tensors of two groups of subjects, one with spastic diplegic cerebral palsy and the other considered normal.

  3. Isotope dilution mass spectrometry for quantitative elemental analysis of powdered samples by radiofrequency pulsed glow discharge time of flight mass spectrometry.

    PubMed

    Alvarez-Toral, Aitor; Fernandez, Beatriz; Malherbe, Julien; Claverie, Fanny; Molloy, John L; Pereiro, Rosario; Sanz-Medel, Alfredo

    2013-10-15

    In recent years particular effort is being devoted to the development of pulsed glow discharges (PGDs) for mass spectrometry because this powering operation mode could offer important ionization analytical advantages. However, the capabilities of radiofrequency (RF) PGD coupled to a time of flight mass spectrometry (ToFMS) for accurate isotope ratio measurements have not been demonstrated yet. This work is focused on investigating different time positions along the pulse profile for the accurate measurement of isotope ratios. As a result, a method has been developed for the direct and simultaneous multielement determination of trace elements in powdered geological samples by RF-PGD-ToFMS in combination with isotope dilution mass spectrometry (IDMS) as an absolute measurement method directly traceable to the International System of Units. Optimized operating conditions were 70 W of applied radiofrequency power, 250 Pa of pressure, 2 ms of pulse width and 4 ms of pulse period, being argon the plasma gas used. To homogeneously distribute the added isotopically-enriched standards, lithium borate fusion of powdered solid samples was used as sample preparation approach. In this way, Cu, Zn, Ba and Pb were successfully determined by RF-PGD-ToF(IDMS) in two NIST Standard Reference Materials (SRM 2586 and SRM 2780) representing two different matrices of geological interest (soil and rock samples). Cu, Zn, Ba and Pb concentrations determined by RF-PGD-ToF(IDMS) were well in agreement with the certified values at 95% confidence interval and precisions below 12% relative standard deviation were observed for three independent analyses. Elemental concentrations investigated were in the range of 81-5770 mg/kg, demonstrating the potential of RF-PGD-ToF(IDMS) for a sensitive, accurate and robust analysis of powdered samples.

  4. Isotope dilution mass spectrometry for quantitative elemental analysis of powdered samples by radiofrequency pulsed glow discharge time of flight mass spectrometry.

    PubMed

    Alvarez-Toral, Aitor; Fernandez, Beatriz; Malherbe, Julien; Claverie, Fanny; Molloy, John L; Pereiro, Rosario; Sanz-Medel, Alfredo

    2013-10-15

    In recent years particular effort is being devoted to the development of pulsed glow discharges (PGDs) for mass spectrometry because this powering operation mode could offer important ionization analytical advantages. However, the capabilities of radiofrequency (RF) PGD coupled to a time of flight mass spectrometry (ToFMS) for accurate isotope ratio measurements have not been demonstrated yet. This work is focused on investigating different time positions along the pulse profile for the accurate measurement of isotope ratios. As a result, a method has been developed for the direct and simultaneous multielement determination of trace elements in powdered geological samples by RF-PGD-ToFMS in combination with isotope dilution mass spectrometry (IDMS) as an absolute measurement method directly traceable to the International System of Units. Optimized operating conditions were 70 W of applied radiofrequency power, 250 Pa of pressure, 2 ms of pulse width and 4 ms of pulse period, being argon the plasma gas used. To homogeneously distribute the added isotopically-enriched standards, lithium borate fusion of powdered solid samples was used as sample preparation approach. In this way, Cu, Zn, Ba and Pb were successfully determined by RF-PGD-ToF(IDMS) in two NIST Standard Reference Materials (SRM 2586 and SRM 2780) representing two different matrices of geological interest (soil and rock samples). Cu, Zn, Ba and Pb concentrations determined by RF-PGD-ToF(IDMS) were well in agreement with the certified values at 95% confidence interval and precisions below 12% relative standard deviation were observed for three independent analyses. Elemental concentrations investigated were in the range of 81-5770 mg/kg, demonstrating the potential of RF-PGD-ToF(IDMS) for a sensitive, accurate and robust analysis of powdered samples. PMID:24054645

  5. Recent Advances in Water Analysis with Gas Chromatograph Mass Spectrometers

    NASA Technical Reports Server (NTRS)

    MacAskill, John A.; Tsikata, Edem

    2014-01-01

    We report on progress made in developing a water sampling system for detection and analysis of volatile organic compounds in water with a gas chromatograph mass spectrometer (GCMS). Two approaches are described herein. The first approach uses a custom water pre-concentrator for performing trap and purge of VOCs from water. The second approach uses a custom micro-volume, split-splitless injector that is compatible with air and water. These water sampling systems will enable a single GC-based instrument to analyze air and water samples for VOC content. As reduced mass, volume, and power is crucial for long-duration, manned space-exploration, these water sampling systems will demonstrate the ability of a GCMS to monitor both air and water quality of the astronaut environment, thereby reducing the amount of required instrumentation for long duration habitation. Laboratory prototypes of these water sampling systems have been constructed and tested with a quadrupole ion trap mass spectrometer as well as a thermal conductivity detector. Presented herein are details of these water sampling system with preliminary test results.

  6. Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates

    NASA Astrophysics Data System (ADS)

    Martin, Nicholas J.; Griffiths, Rian L.; Edwards, Rebecca L.; Cooper, Helen J.

    2015-08-01

    Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2 4H] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The `contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.

  7. a Modal Expansion Analysis of Noise Transmission Through Circular Cylindrical Shell Structures with Blocking Masses

    NASA Astrophysics Data System (ADS)

    GARDONIO, P.; FERGUSON, N. S.; FAHY, F. J.

    2001-07-01

    This paper covers the development and application of a modal interaction analysis (MIA) to investigate the plane wave transmission characteristics of a circular cylindrical sandwich shell of the type used in the aerospace industry for satellite launch vehicles. The model is capable of handling many high order structural and acoustic modes, and can be used to investigate the sensitivity to different structural stiffness configurations, angles of incidence, damping and cavity absorption. The model has been developed to predict the structural response and transmitted noise when a number of discrete masses are applied to the shell. The study presented considers a set of cases where blocking masses, having a total weight equal to 8% of the cylinder weight, are attached to the cylinder. The simulations carried out show a substantial reduction of the sound transmission in many of the first 15 one-third octave frequency bands (frequency range 22·4-707 Hz). The blocking masses act on the shape of the cylinder normal modes and their orientations with respect to the plane of the incident wavenumber vector. In particular, the circumferential re-orientation reduces the coupling between the incident acoustic field and the structural modes of the cylinder. The modification of the structural mode shapes, both in axial and circumferential directions, also reduces the coupling between the cylinder modes and the acoustic modes of the interior.Simulations show the effect of the number of structural and acoustic modes included on the calculated frequency response, and indicate the number necessary for an accurate prediction of the resonant and non-resonant sound transmission through the structure. In particular, the effect of neglecting off-resonance acoustic and structural modes is investigated. It is shown that restricting the acoustic and structural modes to those having natural frequencies within an interval of ±40 and ±60 Hz, respectively, of the excitation frequency produces

  8. Two-timescale analysis of extreme mass ratio inspirals in Kerr spacetime: Orbital motion

    SciTech Connect

    Hinderer, Tanja; Flanagan, Eanna E.

    2008-09-15

    Inspirals of stellar-mass compact objects into massive black holes are an important source for future gravitational wave detectors such as Advanced LIGO and LISA. The detection and analysis of these signals rely on accurate theoretical models of the binary dynamics. We cast the equations describing binary inspiral in the extreme mass ratio limit in terms of action-angle variables, and derive properties of general solutions using a two-timescale expansion. This provides a rigorous derivation of the prescription for computing the leading order orbital motion. As shown by Mino, this leading order or adiabatic motion requires only knowledge of the orbit-averaged, dissipative piece of the self-force. The two-timescale method also gives a framework for calculating the post-adiabatic corrections. For circular and for equatorial orbits, the leading order corrections are suppressed by one power of the mass ratio, and give rise to phase errors of order unity over a complete inspiral through the relativistic regime. These post-1-adiabatic corrections are generated by the fluctuating, dissipative piece of the first order self-force, by the conservative piece of the first order self-force, and by the orbit-averaged, dissipative piece of the second order self-force. We also sketch a two-timescale expansion of the Einstein equation, and deduce an analytic formula for the leading order, adiabatic gravitational waveforms generated by an inspiral.

  9. [Analysis of Trace Inorganic Elements in Castor Oil by Inductively Coupled Plasma Mass Spectrometry].

    PubMed

    Li, Tan-ping; Xie, Hua-lin; Nie, Xi-du

    2015-10-01

    A method for the determination of Na, Mg, Si, P, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Sr, Mo, Cd, Hg and Pb in castor oil after direct dilution with ethanol by inductively coupled plasma mass spectrometry (ICP-MS) was established. The sample was diluted by ethanol before ICP-MS determination. The condensation and deposition of high concentrations of carbon in mass cone interface and ion lens, which will decrease the sensitivity of element analysis, were avoided effectively by introducing O2 to plasma. The mass spectral interferences were eliminated by octopole reaction system (ORS). The matrix effects were calibrated to using Sc, Ge, Rh and Ir as internal standard elements. Au standard solution, which could form amalgam alloy with Hg, was dropped to eliminate the memory effect of Hg. The results show that the correlation coefficient for analyte is no less than 0.999 5, the detection limits is in the range of 0.06 - 20.1 ng x L(-1), the recovery is in the range of 990.4% - 110.2%, and the RSD is less than 4.8%. This method was very fast, simple and accurate to simultaneously analyze multi-elements in castor oil.

  10. Meta-Analysis of Mass Balances Examining Chemical Fate during Wastewater Treatment

    PubMed Central

    2008-01-01

    Mass balances are an instructive means for investigating the fate of chemicals during wastewater treatment. In addition to the aqueous-phase removal efficiency (Φ), they can inform on chemical partitioning, transformation, and persistence, as well as on the chemical loading to streams and soils receiving, respectively, treated effluent and digested sewage sludge (biosolids). Release rates computed on a per-capita basis can serve to extrapolate findings to a larger scale. This review examines over a dozen mass balances conducted for various organic wastewater contaminants, including prescription drugs, estrogens, fragrances, antimicrobials, and surfactants of differing sorption potential (hydrophobicity), here expressed as the 1-octanol−water partition coefficient (KOW) and the organic carbon normalized sorption coefficient (KOC). Major challenges to mass balances are the collection of representative samples and accurate quantification of chemicals in sludge. A meta-analysis of peer-reviewed data identified sorption potential as the principal determinant governing chemical persistence in biosolids. Occurrence data for organic wastewater compounds detected in digested sludge followed a simple nonlinear model that required only KOW or KOC as the input and yielded a correlation coefficient of 0.9 in both instances. The model predicted persistence in biosolids for the majority (>50%) of the input load of organic wastewater compounds featuring a log10KOW value of greater than 5.2 (log10KOC > 4.4). In contrast, hydrophobicity had no or only limited value for estimating, respectively, Φ and the overall persistence of a chemical during conventional wastewater treatment. PMID:18800497

  11. Fibre Diffraction Analysis of Skin Offers a Very Early and Extremely Accurate Diagnostic Test for Prostate Cancer

    DOE PAGES

    James, Veronica J.; O’Malley Ford, Judith M.

    2014-01-01

    Double blind analysis of a batch of thirty skin tissue samples from potential prostate cancer sufferers correctly identified all “control” patients, patients with high and low grade prostate cancers, the presence of benign prostate hyperplasia (BPH), perineural invasions, and the one lymphatic invasion. Identification was by analysis of fibre diffraction patterns interpreted using a schema developed from observations in nine previous studies. The method, schema, and specific experiment results are reported in this paper, with some implications then drawn.

  12. Authenticity assessment of beef origin by principal component analysis of matrix-assisted laser desorption/ionization mass spectrometric data.

    PubMed

    Zaima, Nobuhiro; Goto-Inoue, Naoko; Hayasaka, Takahiro; Enomoto, Hirofumi; Setou, Mitsutoshi

    2011-06-01

    It has become necessary to assess the authenticity of beef origin because of concerns regarding human health hazards. In this study, we used a metabolomic approach involving matrix-assisted laser desorption/ionization imaging mass spectrometry to assess the authenticity of beef origin. Highly accurate data were obtained for samples of extracted lipids from beef of different origin; the samples were grouped according to their origin. The analysis of extracted lipids in this study ended within 10 min, suggesting this approach can be used as a simple authenticity assessment before a definitive identification by isotope analysis.

  13. Extraction, chromatographic and mass spectrometric methods for lipid analysis.

    PubMed

    Pati, Sumitra; Nie, Ben; Arnold, Robert D; Cummings, Brian S

    2016-05-01

    Lipids make up a diverse subset of biomolecules that are responsible for mediating a variety of structural and functional properties as well as modulating cellular functions such as trafficking, regulation of membrane proteins and subcellular compartmentalization. In particular, phospholipids are the main constituents of biological membranes and play major roles in cellular processes like transmembrane signaling and structural dynamics. The chemical and structural variety of lipids makes analysis using a single experimental approach quite challenging. Research in the field relies on the use of multiple techniques to detect and quantify components of cellular lipidomes as well as determine structural features and cellular organization. Understanding these features can allow researchers to elucidate the biochemical mechanisms by which lipid-lipid and/or lipid-protein interactions take place within the conditions of study. Herein, we provide an overview of essential methods for the examination of lipids, including extraction methods, chromatographic techniques and approaches for mass spectrometric analysis.

  14. Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis

    NASA Astrophysics Data System (ADS)

    Chen, C. H. Winston; Taranenko, N. I.; Golovlev, V. V.; Isola, N. R.; Allman, S. L.

    1998-03-01

    Rapid DNA sequencing and/or analysis is critically important for biomedical research. In the past, gel electrophoresis has been the primary tool to achieve DNA analysis and sequencing. However, gel electrophoresis is a time-consuming and labor-extensive process. Recently, we have developed and used laser desorption mass spectrometry (LDMS) to achieve sequencing of ss-DNA longer than 100 nucleotides. With LDMS, we succeeded in sequencing DNA in seconds instead of hours or days required by gel electrophoresis. In addition to sequencing, we also applied LDMS for the detection of DNA probes for hybridization LDMS was also used to detect short tandem repeats for forensic applications. Clinical applications for disease diagnosis such as cystic fibrosis caused by base deletion and point mutation have also been demonstrated. Experimental details will be presented in the meeting. abstract.

  15. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    M. L. Adamic; J. E. Olson; D. D. Jenson; J. G. Eisenmenger; M. G. Watrous

    2012-09-01

    This NA 22 funded research project investigated the transition of iodine isotopic analyses from thermal ionization mass spectrometry (TIMS) to an accelerator mass spectrometry (AMS) system. Previous work (Fiscal Year 2010) had demonstrated comparable data from TIMS and AMS. With AMS providing comparable data with improved background levels and vastly superior sample throughput, improvement in the sample extraction from environmental sample matrices was needed to bring sample preparation throughput closer to the operation level of the instrument. Previous research used an extraction chemistry that was not optimized for yield or refined for reduced labor to prove the principle. This research was done to find an extraction with better yield using less labor per sample to produce a sample ready for the AMS instrument. An extraction method using tetramethyl ammonium hydroxide (TMAH) was developed for removal of iodine species from high volume air filters. The TMAH with gentle heating was superior to the following three extraction methods: ammonium hydroxide aided by sonication, acidic and basic extraction aided by microwave, and ethanol mixed with sodium hydroxide. Taking the iodine from the extraction solvent to being ready for AMS analysis was accomplished by a direct precipitation, as well as, using silver wool to harvest the iodine from the TMAH. Portions of the same filters processed in FY 2010 were processed again with the improved extraction scheme followed by successful analysis by AMS at the Swiss Federal Institute of Technology. The data favorably matched the data obtained in 2010. The time required for analysis has been reduced over the aqueous extraction/AMS approach developed in FY 2010. For a hypothetical batch of 30 samples, the AMS methodology is about 10 times faster than the traditional gas phase chemistry and TIMS analysis. As an additional benefit, background levels for the AMS method are about 1000 times lower than TIMS. This results from the

  16. A Comprehensive Analysis of Uncertainties Affecting the Stellar Mass-Halo Mass Relation for 0

    SciTech Connect

    Behroozi, Peter S.; Conroy, Charlie; Wechsler, Risa H.

    2010-06-07

    We conduct a comprehensive analysis of the relationship between central galaxies and their host dark matter halos, as characterized by the stellar mass - halo mass (SM-HM) relation, with rigorous consideration of uncertainties. Our analysis focuses on results from the abundance matching technique, which assumes that every dark matter halo or subhalo above a specific mass threshold hosts one galaxy. We provide a robust estimate of the SM-HM relation for 0 < z < 1 and discuss the quantitative effects of uncertainties in observed galaxy stellar mass functions (GSMFs) (including stellar mass estimates and counting uncertainties), halo mass functions (including cosmology and uncertainties from substructure), and the abundance matching technique used to link galaxies to halos (including scatter in this connection). Our analysis results in a robust estimate of the SM-HM relation and its evolution from z=0 to z=4. The shape and evolution are well constrained for z < 1. The largest uncertainties at these redshifts are due to stellar mass estimates (0.25 dex uncertainty in normalization); however, failure to account for scatter in stellar masses at fixed halo mass can lead to errors of similar magnitude in the SM-HM relation for central galaxies in massive halos. We also investigate the SM-HM relation to z = 4, although the shape of the relation at higher redshifts remains fairly unconstrained when uncertainties are taken into account. We find that the integrated star formation at a given halo mass peaks at 10-20% of available baryons for all redshifts from 0 to 4. This peak occurs at a halo mass of 7 x 10{sup 11} M{sub {circle_dot}} at z = 0 and this mass increases by a factor of 5 to z = 4. At lower and higher masses, star formation is substantially less efficient, with stellar mass scaling as M{sub *} {approx} M{sub h}{sup 2.3} at low masses and M{sub *} {approx} M{sub h}{sup 0.29} at high masses. The typical stellar mass for halos with mass less than 10{sup 12} M

  17. Sewage sludge toxicity assessment using earthworm Eisenia fetida: can biochemical and histopathological analysis provide fast and accurate insight?

    PubMed

    Babić, S; Barišić, J; Malev, O; Klobučar, G; Popović, N Topić; Strunjak-Perović, I; Krasnići, N; Čož-Rakovac, R; Klobučar, R Sauerborn

    2016-06-01

    Sewage sludge (SS) is a complex organic by-product of wastewater treatment plants. Deposition of large amounts of SS can increase the risk of soil contamination. Therefore, there is an increasing need for fast and accurate assessment of SS toxic potential. Toxic effects of SS were tested on earthworm Eisenia fetida tissue, at the subcellular and biochemical level. Earthworms were exposed to depot sludge (DS) concentration ratio of 30 or 70 %, to undiluted and to 100 and 10 times diluted active sludge (AS). The exposure to DS lasted for 24/48 h (acute exposure), 96 h (semi-acute exposure) and 7/14/28 days (sub-chronic exposure) and 48 h for AS. Toxic effects were tested by the measurements of multixenobiotic resistance mechanism (MXR) activity and lipid peroxidation levels, as well as the observation of morphological alterations and behavioural changes. Biochemical markers confirmed the presence of MXR inhibitors in the tested AS and DS and highlighted the presence of SS-induced oxidative stress. The MXR inhibition and thiobarbituric acid reactive substance (TBARS) concentration in the whole earthworm's body were higher after the exposition to lower concentration of the DS. Furthermore, histopathological changes revealed damage to earthworm body wall tissue layers as well as to the epithelial and chloragogen cells in the typhlosole region. These changes were proportional to SS concentration in tested soils and to exposure duration. Obtained results may contribute to the understanding of SS-induced toxic effects on terrestrial invertebrates exposed through soil contact and to identify defence mechanisms of earthworms. PMID:26971513

  18. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    PubMed

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.

  19. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    PubMed

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing. PMID:26072424

  20. An automated gas chromatography time-of-flight mass spectrometry instrument for the quantitative analysis of halocarbons in air

    NASA Astrophysics Data System (ADS)

    Obersteiner, F.; Bönisch, H.; Engel, A.

    2015-09-01

    We present the characterization and application of a new gas chromatography-time-of-flight mass spectrometry instrument (GC-TOFMS) for the quantitative analysis of halocarbons in air samples. The setup comprises three fundamental enhancements compared to our earlier work (Hoker et al., 2015): (1) full automation, (2) a mass resolving power R = m/Δ m of the TOFMS (Tofwerk AG, Switzerland) increased up to 4000 Th/Th and (3) a fully accessible data format of the mass spectrometric data. Automation in combination with the accessible data allowed an in-depth characterization of the instrument. Mass accuracy was found around 5 ppm after automatic recalibration of the mass axis in each measurement. A TOFMS configuration giving R = 3500 was chosen to provide an R-to-sensitivity ratio suitable for our purpose. Calculated detection limits were as low as a few femtograms as mass traces could be made highly specific for selected molecule fragments with the accurate mass information. The precision for substance quantification was 0.15 % at the best for an individual measurement and in general mainly determined by the signal-to-noise ratio of the chromatographic peak. The TOFMS was found to be linear within a concentration range from about 1 pg to 1 ng of analyte per Liter of air. At higher concentrations, non-linearities of a few percent were observed (precision level: 0.2 %) but could be attributed to a potential source within the detection system. A straight-forward correction for those non-linearities was applied in data processing, again by exploiting the accurate mass information. Based on the overall characterization results, the GC-TOFMS instrument was found to be very well-suited for the task of quantitative halocarbon trace gas observation and a big step forward compared to scanning, low resolution quadrupole MS and a TOFMS technique reported to be non-linear and restricted by a small dynamical range.

  1. An automated gas chromatography time-of-flight mass spectrometry instrument for the quantitative analysis of halocarbons in air

    NASA Astrophysics Data System (ADS)

    Obersteiner, F.; Bönisch, H.; Engel, A.

    2016-01-01

    We present the characterization and application of a new gas chromatography time-of-flight mass spectrometry instrument (GC-TOFMS) for the quantitative analysis of halocarbons in air samples. The setup comprises three fundamental enhancements compared to our earlier work (Hoker et al., 2015): (1) full automation, (2) a mass resolving power R = m/Δm of the TOFMS (Tofwerk AG, Switzerland) increased up to 4000 and (3) a fully accessible data format of the mass spectrometric data. Automation in combination with the accessible data allowed an in-depth characterization of the instrument. Mass accuracy was found to be approximately 5 ppm in mean after automatic recalibration of the mass axis in each measurement. A TOFMS configuration giving R = 3500 was chosen to provide an R-to-sensitivity ratio suitable for our purpose. Calculated detection limits are as low as a few femtograms by means of the accurate mass information. The precision for substance quantification was 0.15 % at the best for an individual measurement and in general mainly determined by the signal-to-noise ratio of the chromatographic peak. Detector non-linearity was found to be insignificant up to a mixing ratio of roughly 150 ppt at 0.5 L sampled volume. At higher concentrations, non-linearities of a few percent were observed (precision level: 0.2 %) but could be attributed to a potential source within the detection system. A straightforward correction for those non-linearities was applied in data processing, again by exploiting the accurate mass information. Based on the overall characterization results, the GC-TOFMS instrument was found to be very well suited for the task of quantitative halocarbon trace gas observation and a big step forward compared to scanning, quadrupole MS with low mass resolving power and a TOFMS technique reported to be non-linear and restricted by a small dynamical range.

  2. How accurate are interpretations of curriculum-based measurement progress monitoring data? Visual analysis versus decision rules.

    PubMed

    Van Norman, Ethan R; Christ, Theodore J

    2016-10-01

    Curriculum based measurement of oral reading (CBM-R) is used to monitor the effects of academic interventions for individual students. Decisions to continue, modify, or terminate these interventions are made by interpreting time series CBM-R data. Such interpretation is founded upon visual analysis or the application of decision rules. The purpose of this study was to compare the accuracy of visual analysis and decision rules. Visual analysts interpreted 108 CBM-R progress monitoring graphs one of three ways: (a) without graphic aids, (b) with a goal line, or (c) with a goal line and a trend line. Graphs differed along three dimensions, including trend magnitude, variability of observations, and duration of data collection. Automated trend line and data point decision rules were also applied to each graph. Inferential analyses permitted the estimation of the probability of a correct decision (i.e., the student is improving - continue the intervention, or the student is not improving - discontinue the intervention) for each evaluation method as a function of trend magnitude, variability of observations, and duration of data collection. All evaluation methods performed better when students made adequate progress. Visual analysis and decision rules performed similarly when observations were less variable. Results suggest that educators should collect data for more than six weeks, take steps to control measurement error, and visually analyze graphs when data are variable. Implications for practice and research are discussed. PMID:27586069

  3. How accurate are interpretations of curriculum-based measurement progress monitoring data? Visual analysis versus decision rules.

    PubMed

    Van Norman, Ethan R; Christ, Theodore J

    2016-10-01

    Curriculum based measurement of oral reading (CBM-R) is used to monitor the effects of academic interventions for individual students. Decisions to continue, modify, or terminate these interventions are made by interpreting time series CBM-R data. Such interpretation is founded upon visual analysis or the application of decision rules. The purpose of this study was to compare the accuracy of visual analysis and decision rules. Visual analysts interpreted 108 CBM-R progress monitoring graphs one of three ways: (a) without graphic aids, (b) with a goal line, or (c) with a goal line and a trend line. Graphs differed along three dimensions, including trend magnitude, variability of observations, and duration of data collection. Automated trend line and data point decision rules were also applied to each graph. Inferential analyses permitted the estimation of the probability of a correct decision (i.e., the student is improving - continue the intervention, or the student is not improving - discontinue the intervention) for each evaluation method as a function of trend magnitude, variability of observations, and duration of data collection. All evaluation methods performed better when students made adequate progress. Visual analysis and decision rules performed similarly when observations were less variable. Results suggest that educators should collect data for more than six weeks, take steps to control measurement error, and visually analyze graphs when data are variable. Implications for practice and research are discussed.

  4. High-Resolution Analysis of Atmospheric Mass Spectra: Identification, Resolution, Assignment of complex mass spectra

    NASA Astrophysics Data System (ADS)

    Stark, H.; Yatavelli, R. L. N.; Thompson, S.; Mazzoleni, L. R.; Kimmel, J.; Cubison, M.; Day, D. A.; Campuzano Jost, P.; Palm, B. B.; Chhabra, P. S.; Canagaratna, M. R.; Jayne, J. T.; Worsnop, D. R.; Jimenez, J. L.

    2015-12-01

    The troposphere can contain thousands of organic molecules with widely varying carbon numbers and levels of oxidation. Unraveling this complex molecular mixture gives new insights into key processes such as atmospheric processing, secondary aerosol formation, radiative properties as well as implications for human health. High-resolution time-of-flight chemical ionization mass spectrometry (HRToF-CIMS) is a powerful technique with the potential to provide many insights into this complex mix of molecules. We have developed new data analysis techniques to identify the most likely ions present in complex mass spectra in which individual peaks strongly overlap. New ancillary algorithms will also be presented to first develop a list of all possible formulas for this particular ion chemistry and then to automatically assign possible ions to the likely peak positions. Spectral simulation experiments confirm that bulk elemental properties such as oxidation state and carbon number can be reliably extracted from this method. Comparison of results from a CIMS operated during the 2011 BEACHON-RoMBAS campaign in the Colorado Rocky Mountains to electrospray-ultra-high-resolution mass spectrometry data from compounds measured in another forest in the Rockies allows a comparison of the compounds and compound classes measured by both techniques. We will also address the problem of quantifying ion signals from the organic molecule mix encountered in this study by a new method to calculate approximate sensitivities for acetate ionization chemistry to help quantifying concentrations of atmospheric compounds. We applied the above methods to a dataset from the micro-orifice volatilization impactor (MOVI)-CIMS collected during August 2011 as part of the BEACHON campaign. Calculated atmospheric bulk elemental parameters such as diurnal cycles of carbon number and oxidation state from both gas phase and aerosols from a pine forest environment will be presented and compared to data from

  5. Mass spectrometric analysis with cluster projectiles and coincidence counting

    SciTech Connect

    Cox, B.D.

    1992-01-01

    Methods for maximizing the amount of secondary ion information, per primary projectile, are described. The method is based on time-of-flight mass spectrometry and event-by-event coincidence counting. The information obtained from coincidence counting time-of-flight mass spectrometry includes: (a) surface composition, (b) relative concentrations, and (c) degree of intermolecular mixing. The technique was applied to the study of an important new class of polymers: polymer blends. Secondary ion mass spectrometry, when applied to the analysis of synthetic polymers, induces backbone fragmentation which is characteristic of the homopolymer. The characteristic fingerprint peaks from polystyrene and poly(vinyl methyl ether) were used to identify the presence of these two polymers in a polymer blend. The percent coincidence between the characteristic secondary ions from each component of the blend were used to determine both the relative concentration and the degree of molecular mixing. Results indicate molecular segregation of the two polymers on the film surface. The largest degree of segregation was determined for the phase separated blends. The performance of this technique depends on the desorption efficiency of the primary projectiles. In practice one seeks primary ions which are surface sensitive, have controllable parameters such as size, velocity, and charge state, and generate high secondary ion yields. Focus was placed on the use of keV organic cluster projectiles to meet these criteria. Of interest to this study were C[sub 18] (chrysene), C[sub 24] (coronene), and C[sub 60] (buckminster-fulleren). Results indicate enhanced secondary ion yields for C[sub 60]. For example, when CsI is bombarded with 30 keV C[sub 60], the yields for I[sup [minus

  6. A mass spectroscopic analysis of {gamma}-GPS films

    SciTech Connect

    Dillingham, R.G.; Boerio, F.J.; Bertelsen, C.; Savina, M.R.; Lykke, K.; Calaway, W.

    1996-12-31

    Preparation of substrates for painting or adhesive bonding frequently includes roughening through sanding, chemical etching, or gritblasting. Increased roughness can improve interfacial strength and durability due to increased mechanical interlocking, increased surface area, and improved wettability of the substrate. The chemical reactivity of the surface with the organic phase may be affected as well, perhaps related to the strain energy stored in the surface regions through the intense plastic deformation that occurs. Unfortunately, the chemistry of interactions taking place near a surface that has been roughened is difficult to access analytically by some of the more useful techniques such as infrared spectroscopy. This paper discusses analysis of nonreflective grit-blasted surfaces using mass spectroscopy of species which were either sputtered off using an ion beam (Static Secondary Ion Mass Spectroscopy, or SSIMS) or thermally desorbed as neutrals using a pulsed laser and then post-ionized using a secondary laser (Laser Desorption-Laser Ionization Mass Spectroscopy, or LDLIMS). Both of these techniques exhibit sub-nanometer sensitivity and provide significant information as to the chemistry and structure of the surface regions. In a current application of {gamma}-glycidoxypropyltrimethoxysilane ({gamma}-GPS) for the pre-treatment of grit-blasted aluminum before adhesive bonding, certain factors related to the handling of the primer solution and to the application technique were found to significantly affect the performance of the adhesive bond under long-term aging conditions including stress and humidity. To understand why these parameters are important and to potentially improve the pretreatment process even further, the authors have been investigating how the structure and reactivity of these silane films are related to the application techniques.

  7. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    J. E. Delmore

    2010-09-01

    Funding was received from NA-22 to investigate transitioning iodine isotopic analyses to an accelerator mass spectrometry (AMS) system. The present method uses gas-phase chemistry followed by thermal ionization mass spectrometry (TIMS). It was anticipated that the AMS approach could provide comparable data, with improved background levels and superior sample throughput. An aqueous extraction method was developed for removal of iodine species from high-volume air filters. Ethanol and sodium hydroxide, plus heating and ultrasonic treatment, were used to successfully extract iodine from loaded high-volume air filters. Portions of the same filters were also processed in the traditional method and analyzed by TIMS for comparison. Aliquot parts of the aqueous extracts were analyzed by AMS at the Swiss Federal Institute of Technology. Idaho National Laboratory (INL) personnel visited several AMS laboratories in the US, Spain, and Switzerland. Experience with AMS systems from several manufacturers was gained, and relationships were developed with key personnel at the laboratories. Three batches of samples were analyzed in Switzerland, and one in Spain. Results show that the INL extraction method successfully extracted enough iodine from high-volume air filters to allow AMS analysis. Comparison of the AMS and TIMS data is very encouraging; while the TIMS showed about forty percent more atoms of 129I, the 129/127 ratios tracked each other very well between the two methods. The time required for analysis is greatly reduced for the aqueous extraction/AMS approach. For a hypothetical batch of thirty samples, the AMS methodology is about five times faster than the traditional gas-phase chemistry and TIMS analysis. As an additional benefit, background levels for the AMS method are about 1000 times lower than for TIMS. This results from the fundamental mechanisms of ionization in the AMS system and cleanup of molecular interferences. We showed that an aqueous extraction of high

  8. Analysis of hazardous biological material by MALDI mass spectrometry

    SciTech Connect

    KL Wahl; KH Jarman; NB Valentine; MT Kingsley; CE Petersen; ST Cebula; AJ Saenz

    2000-03-21

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) has become a valuable tool for analyzing microorganisms. The speed with which data can be obtained from MALDI-MS makes this a potentially important tool for biological health hazard monitoring and forensic applications. The excitement in the mass spectrometry community in this potential field of application is evident by the expanding list of research laboratories pursuing development of MALDI-MS for bacterial identification. Numerous research groups have demonstrated the ability to obtain unique MALDI-MS spectra from intact bacterial cells and bacterial cell extracts. The ability to differentiate strains of the same species has been investigated. Reproducibility of MALDI-MS spectra from bacterial species under carefully controlled experimental conditions has also been demonstrated. Wang et al. have reported on interlaboratory reproducibility of the MALDI-MS analysis of several bacterial species. However, there are still issues that need to be addressed, including the careful control of experimental parameters for reproducible spectra and selection of optimal experimental parameters such as solvent and matrix.

  9. Mass spectrometric analysis of lens [beta]-crystallins

    NASA Astrophysics Data System (ADS)

    Smith, Jean B.; Miesbauer, Laura R.; Leeds, Jonathan; Smith, David L.; Loo, Joseph A.; Smith, Richard D.; Edmonds, Charles G.

    1991-12-01

    A combination of electrospray ionization mass spectrometry (ESIMS), fast atom bombardment mass spectrometry (FABMS), and sodium dodecylsulfate-polyacrylamide get electrophoresis (SDS-PAGE) was used to determine the homegeneity of chromatographic fractions of [beta]-crystallins, separated by reversed-phase HPLC. The molecular weight of the major component of [beta]-crystallins, [beta]B2, was found by ESIMS to be 23 215, in agreement with the accepted value of 23 209. The practical utility of improved resolution and accuracy of ESIMS relative to SDS-PAGE of identifying proteins is discussed. The component [beta]B2 was found in more than one HPLC fraction, suggesting that it migrates through the HPLC column aggregated with itself or other [beta]-crystallins. Several proteins with different molecular weights were found to be unique to each of the two classes of [beta]-crystallins. Tryptic digest of the major HPLC fractions were analyzed by FABMS, on-line HPLC continuous-flow FABMS--MS to give detailed information about the primary structure of [beta]B2. Peptides related to all but one portion of the proposed amino acid sequence of [beta]B2 were found in the tryptic digest, suggesting that the proposed sequence is correct. On-line HPLC continuous-flow FABMS analysis of the proteolytic digest was particularly attractive because it gave a nearly complete peptide molecular weight map in 20 min.

  10. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli

    PubMed Central

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1α and TUB were the most stable genes for abiotic stresses, whereas EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley. PMID:27746803

  11. Accurate analysis of prevalence of coccidiosis in individually identified wild cranes in inhabiting and migrating populations in Japan.

    PubMed

    Honma, Hajime; Suyama, Yoshihisa; Watanabe, Yuki; Matsumoto, Fumio; Nakai, Yutaka

    2011-11-01

    Eimeria gruis and E. reichenowi cause coccidiosis, a major parasitic disease of cranes. By non-invasive molecular approaches, we investigated the prevalence and genetic characterization of pathogens in two Japanese crane habitats; one is Hokkaido inhabited by the endangered red-crowned crane, and the other is Izumi in Kyushu where populations that consist mainly of vulnerable hooded and white-naped cranes migrate in winter. The non-invasively collected faecal samples from each wintering population were first subjected to host genomic DNA-targeted analyses to determine the sample origin and avoid sample redundancy. Extremely high prevalence was observed in the Izumi populations (> 90%) compared with the Hokkaido population (18-30%) by examining 470 specimens by microscopy and PCR-based capillary electrophoresis (PCR-CE), using genetic markers in the second internal transcribed spacer (ITS2). Correspondence analysis of PCR-CE data revealed differences in community composition of coccidia between hooded and white-naped cranes. 18S rRNA and ITS2 sequences were determined from single oocysts excreted by red-crowned and hooded cranes. Phylogenetic analysis of 18S rRNA suggested that E. reichenowi was polyphyletic while E. gruis was monophyletic. Together with PCR-CE data, these results indicate different host specificity among the E. reichenowi type. Our data suggest that E. reichenowi comprises multiple species. PMID:21895916

  12. Laser-based mass spectrometry for in situ chemical composition analysis of planetary surfaces

    NASA Astrophysics Data System (ADS)

    Frey, Samira; Neuland, Maike B.; Grimaudo, Valentine; Moreno-García, Pavel; Riedo, Andreas; Tulej, Marek; Broekmann, Peter; Wurz, Peter

    2016-04-01

    Mass spectrometry is an important analytical technique in space research. The chemical composition of planetary surface material is a key scientific question on every space mission to a planet, moon or asteroid. Chemical composition measurements of rocky material on the surface are of great importance to understand the origin and evolution of the planetary body.[1] A miniature laser ablation/ionisation reflectron- type time-of-flight mass spectrometer (instrument name LMS) was designed and built at the University of Bern for planetary research.[2] Despite its small size and light weight, the LMS instrument still maintains the same capabilities as large laboratory systems, which makes it suitable for its application on planetary space missions.[3-5] The high dynamic range of about eight orders of magnitude, high lateral (μm-level) and vertical (sub-nm level) resolution and high detection sensitivity for almost all elements (10 ppb, atomic fraction) make LMS a versatile instrument for various applications. LMS is a suitable instrument for in situ measurements of elemental and isotope composition with high precision and accuracy. Measurements of Pb- isotope abundances can be used for dating of planetary material. Measurements of bio-relevant elements allow searching for past or present life on a planetary surface. The high spatial resolution, both in lateral and vertical direction, is of considerable interest, e.g. for analysis of inhomogeneous, extraterrestrial samples as well as weathering processes of planetary material. References [1] P. Wurz, D. Abplanalp, M. Tulej, M. Iakovleva, V.A. Fernandes, A. Chumikov, and G. Managadze, "Mass Spectrometric Analysis in Planetary Science: Investigation of the Surface and the Atmosphere", Sol. Sys. Res., 2012, 46, 408. [2] U. Rohner, J.A. Whitby, P. Wurz, "A miniature laser ablation time of flight mass spectrometer for in situ planetary exploration" Meas. Sci. Tch., 2003, 14, 2159. [3] M. Tulej, A. Riedo, M.B. Neuland, S

  13. Sensitive and accurate identification of protein–DNA binding events in ChIP-chip assays using higher order derivative analysis

    PubMed Central

    Barrett, Christian L.; Cho, Byung-Kwan

    2011-01-01

    Immuno-precipitation of protein–DNA complexes followed by microarray hybridization is a powerful and cost-effective technology for discovering protein–DNA binding events at the genome scale. It is still an unresolved challenge to comprehensively, accurately and sensitively extract binding event information from the produced data. We have developed a novel strategy composed of an information-preserving signal-smoothing procedure, higher order derivative analysis and application of the principle of maximum entropy to address this challenge. Importantly, our method does not require any input parameters to be specified by the user. Using genome-scale binding data of two Escherichia coli global transcription regulators for which a relatively large number of experimentally supported sites are known, we show that ∼90% of known sites were resolved to within four probes, or ∼88 bp. Over half of the sites were resolved to within two probes, or ∼38 bp. Furthermore, we demonstrate that our strategy delivers significant quantitative and qualitative performance gains over available methods. Such accurate and sensitive binding site resolution has important consequences for accurately reconstructing transcriptional regulatory networks, for motif discovery, for furthering our understanding of local and non-local factors in protein–DNA interactions and for extending the usefulness horizon of the ChIP-chip platform. PMID:21051353

  14. Development of a miniaturized mass-flow meter for an axial flow blood pump based on computational analysis.

    PubMed

    Kosaka, Ryo; Nishida, Masahiro; Maruyama, Osamu; Yamane, Takashi

    2011-09-01

    In order to monitor the condition of patients with implantable left ventricular assist systems (LVAS), it is important to measure pump flow rate continuously and noninvasively. However, it is difficult to measure the pump flow rate, especially in an implantable axial flow blood pump, because the power consumption has neither linearity nor uniqueness with regard to the pump flow rate. In this study, a miniaturized mass-flow meter for discharged patients with an implantable axial blood pump was developed on the basis of computational analysis, and was evaluated in in-vitro tests. The mass-flow meter makes use of centrifugal force produced by the mass-flow rate around a curved cannula. An optimized design was investigated by use of computational fluid dynamics (CFD) analysis. On the basis of the computational analysis, a miniaturized mass-flow meter made of titanium alloy was developed. A strain gauge was adopted as a sensor element. The first strain gauge, attached to the curved area, measured both static pressure and centrifugal force. The second strain gauge, attached to the straight area, measured static pressure. By subtracting the output of the second strain gauge from the output of the first strain gauge, the mass-flow rate was determined. In in-vitro tests using a model circulation loop, the mass-flow meter was compared with a conventional flow meter. Measurement error was less than ±0.5 L/min and average time delay was 0.14 s. We confirmed that the miniaturized mass-flow meter could accurately measure the mass-flow rate continuously and noninvasively. PMID:21537972

  15. Purification of SUMO Conjugates from Arabidopsis for Mass Spectrometry Analysis.

    PubMed

    Rytz, Thérèse C; Miller, Marcus J; Vierstra, Richard D

    2016-01-01

    The posttranslational modification of proteins with small ubiquitin-related modifier (SUMO) is a rapid, robust, and reversible mechanism that impacts a host of eukaryotic processes important to both normal cellular functions and survival during various abiotic and biotic challenges. Essential to defining the breadth of events impacted by SUMOylation is the development of full catalogues of protein targets. Here, we describe a stringent affinity method to purify native SUMO conjugates from the model plant Arabidopsis thaliana based on the expression of modified SUMOs bearing epitope tags. When combined with standard and quantitative mass spectrometric methods, deep datasets of SUMOylated proteins can be acquired. Functional analysis of these lists links SUMO to numerous regulatory events, with an emphasis on those associated with transcription, DNA replication and repair, and chromatin assembly/accessibility. PMID:27631811

  16. Imaging Mass Spectrometric Analysis of Neurotransmitters: A Review

    PubMed Central

    Romero-Perez, Gustavo A.; Takei, Shiro; Yao, Ikuko

    2014-01-01

    Imaging mass spectrometry (IMS) is a toolbox of versatile techniques that enable us to investigate analytes in samples at molecular level. In recent years, IMS, and especially matrix-assisted laser desorption/ionisation (MALDI), has been used to visualise a wide range of metabolites in biological samples. Simultaneous visualisation of the spatial distribution of metabolites in a single sample with little tissue disruption can be considered as one important advantage of MALDI over other techniques. However, several technical hurdles including low concentrations and rapid degradation rates of small molecule metabolites, matrix interference of signals and poor ionisation, need to be addressed before MALDI can be considered as a reliable tool for the analysis of metabolites such as neurotransmitters in brain tissues from different sources including humans. In the present review we will briefly describe current MALDI IMS techniques used to study neurotransmitters and discuss their current status, challenges, as well as future prospects. PMID:26819893

  17. In situ secondary ion mass spectrometry analysis. 1992 Summary report

    SciTech Connect

    Groenewold, G.S.; Applehans, A.D.; Ingram, J.C.; Delmore, J.E.; Dahl, D.A.

    1993-01-01

    The direct detection of tributyl phosphate (TBP) on rocks using molecular beam surface analysis [MBSA or in situ secondary ion mass spectrometry (SIMS)] is demonstrated. Quantities as low as 250 ng were detected on basalt and sandstone with little or no sample preparation. Detection of TBP on soil has proven to be more problematic and requires further study. Ethylenediaminetetraacetic acid (EDTA) is more difficult to detect because it is very reactive with surfaces of interest. Nevertheless, it is possible to detect EDTA if the acidity of the surface is controlled. The detection of EDTA-metal complexes is currently an open question, but evidence is presented for the detection of ions arising from a EDTA-lead complex. Carboxylic acids (i.e., citric, ascorbic, malic, succinic, malonic, and oxalic) give characteristic SIM spectra, but their detection on sample surfaces awaits evaluation.

  18. Ion attachment mass spectrometry combined with infrared image furnace for thermal analysis: evolved gas analysis studies.

    PubMed

    Kitahara, Yuki; Takahashi, Seiji; Kuramoto, Noriyuki; Sala, Martin; Tsugoshi, Takahisa; Sablier, Michel; Fujii, Toshihiro

    2009-04-15

    A well-established ion attachment mass spectrometer (IAMS) is combined with an in-house single-atom infrared image furnace (IIF) specifically for thermal analysis studies. Besides the detection of many chemical species at atmospheric pressure, including free radical intermediates, the ion attachment mass spectrometer can also be used for the analysis of products emanating from temperature-programmed pyrolysis. The performance and applicability of the IIF-IAMS is illustrated with poly(tetrafluoroethylene) (PTFE) samples. The potential of the system for the analysis of oxidative pyrolysis is also considered. Temperature-programmed decomposition of PTFE gave constant slopes of the plots of temperature versus signal intensity in a defined region and provided an apparent activation energy of 28.8 kcal/mol for the PTFE decomposition product (CF(2))(3). A brief comparison with a conventional pyrolysis gas chromatography/mass spectrometry system is also given.

  19. Accurate extraction of Lagrangian coherent structures over finite domains with application to flight data analysis over Hong Kong International Airport.

    PubMed

    Tang, Wenbo; Chan, Pak Wai; Haller, George

    2010-03-01

    Locating Lagrangian coherent structures (LCS) for dynamical systems defined on a spatially limited domain present a challenge because trajectory integration must be stopped at the boundary for lack of further velocity data. This effectively turns the domain boundary into an attractor, introduces edge effects resulting in spurious ridges in the associated finite-time Lyapunov exponent (FTLE) field, and causes some of the real ridges of the FTLE field to be suppressed by strong spurious ridges. To address these issues, we develop a finite-domain FTLE method that renders LCS with an accuracy and fidelity that is suitable for automated feature detection. We show the application of this technique to the analysis of velocity data from aircraft landing at the Hong Kong International Airport.

  20. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose. PMID:27410113

  1. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose.

  2. Accurate discrimination of Alzheimer's disease from other dementia and/or normal subjects using SPECT specific volume analysis

    NASA Astrophysics Data System (ADS)

    Iyatomi, Hitoshi; Hashimoto, Jun; Yoshii, Fumuhito; Kazama, Toshiki; Kawada, Shuichi; Imai, Yutaka

    2014-03-01

    Discrimination between Alzheimer's disease and other dementia is clinically significant, however it is often difficult. In this study, we developed classification models among Alzheimer's disease (AD), other dementia (OD) and/or normal subjects (NC) using patient factors and indices obtained by brain perfusion SPECT. SPECT is commonly used to assess cerebral blood flow (CBF) and allows the evaluation of the severity of hypoperfusion by introducing statistical parametric mapping (SPM). We investigated a total of 150 cases (50 cases each for AD, OD, and NC) from Tokai University Hospital, Japan. In each case, we obtained a total of 127 candidate parameters from: (A) 2 patient factors (age and sex), (B) 12 CBF parameters and 113 SPM parameters including (C) 3 from specific volume analysis (SVA), and (D) 110 from voxel-based analysis stereotactic extraction estimation (vbSEE). We built linear classifiers with a statistical stepwise feature selection and evaluated the performance with the leave-one-out cross validation strategy. Our classifiers achieved very high classification performances with reasonable number of selected parameters. In the most significant discrimination in clinical, namely those of AD from OD, our classifier achieved both sensitivity (SE) and specificity (SP) of 96%. In a similar way, our classifiers achieved a SE of 90% and a SP of 98% in AD from NC, as well as a SE of 88% and a SP of 86% in AD from OD and NC cases. Introducing SPM indices such as SVA and vbSEE, classification performances improved around 7-15%. We confirmed that these SPM factors are quite important for diagnosing Alzheimer's disease.

  3. A feasibility study for measuring accurate tendon displacements using an audio-based Fourier analysis of pulsed-wave Doppler ultrasound signals.

    PubMed

    Stegman, K J; Podhorodeski, R P; Park, E J

    2009-01-01

    The accuracy of Pulsed-Wave Doppler Ultrasound displacement measurements of a slow moving "tendon-like" string was investigated in this study. This was accomplished by estimating string displacements using an audio-based Fourier analysis of a Pulsed-Wave Doppler signal from a commercial ultrasound scanner. Our feasibility study showed that the proposed technique is much more accurate at estimating the actual string displacement in comparison to the scanner's onboard software. Furthermore, this study also shows that a real-time Doppler data acquisition from an ultrasound scanner is possible for the ultimate purpose of real-time biological tendon displacement monitoring.

  4. [Analysis of polycyclic aromatic hydrocarbons in air samples by gas chromatography-triple quadrupole mass spectrometry].

    PubMed

    Zhao, Bo; Li, Yuqing; Zhang, Sukun; Han, Jinglei; Xu, Zhencheng; Fang, Jiande

    2014-09-01

    A method of gas chromatography coupled to triple quadrupole tandem mass spectrometry (GC-MS/MS) has been optimized for the determination of polycyclic aromatic hydrocarbons (PAHs) in air samples. In the analysis step, isotope dilution was introduced to the quantification of PAHs. The GC-MS/MS method was applied to the analysis of the real air samples around a big petrochemical power plant in South China. The results were compared with those obtained by gas chromatography coupled to mass spectrometry (GC-MS). The results showed that better selectivity and sensitivity were obtained by GC-MS/MS. It was found that the external standard of deuterated-PAHs and internal standard of hexamethyl benzene were disturbed seriously with GC-MS, and the problems were both solved effectively by GC-MS/MS. Therefore more accurate quantification results of PAHs were obtained with GC-MS/MS. For the analysis of real samples, the RSDs of relative response factors ranged from 2.60% to 15.6% in standard curves; the recoveries of deuterated-PAHs ranged from 55.2% to 82.3%; the recoveries of spiked samples ranged from 98.9% to 111%; the RSDs of parallel specimens ranged from 6.50% to 18.4%; the concentrations of field blank samples ranged from not detected to 44.3 pg/m3; and the concentrations of library blank samples ranged from not detected to 36.5 pg/m3. The study indicated that the application of GC-MS/MS on the analysis of PAHs in air samples was recommended. PMID:25752088

  5. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  6. Combination of micro-dialysis and infrared spectroscopy: a multianalyte assay for accurate biofluid analysis and patient monitoring

    NASA Astrophysics Data System (ADS)

    Vahlsing, Thorsten; Delbeck, Sven; Budde, Janpeter; Ihrig, Dieter; Heise, H. Michael

    2016-03-01

    Micro-dialysis can be used for continuously harvesting body fluids, while a multi-component analysis of the dialysates by infrared spectrometry offers splendid opportunities for monitoring substrates and metabolites such as glucose, lactate and others small enough to penetrate the semi-permeable dialysis membranes. However, a drawback of this process are variable recovery rates, which can be observed especially for subcutaneously implanted catheters in human subjects. Isotonic perfusates were investigated with acetate and mannitol as recovery markers for the dialysis of human serum at 37°C to mimic in vivo patient monitoring. The latter non-ionic substance has been suggested for application when other ionic substances such as bicarbonate or pH are also to be determined. Simultaneously for acetate and mannitol, the depletion of the marker substances from the perfusates using different micro-dialysis devices was investigated under various flow-rates. Relationships between relative dialysate marker concentrations and glucose recovery rates were determined based on multivariate calibrations. For quantification, classical least squares with reference spectra for modelling the serum dialysates was used, rendering a basis for reliable blood glucose and lactate measurements.

  7. Analysis of sucralose and other sweeteners in water and beverage samples by liquid chromatography/time-of-flight mass spectrometry.

    PubMed

    Ferrer, Imma; Thurman, E Michael

    2010-06-18

    A methodology for the chromatographic separation and analysis of three of the most popular artificial sweeteners (aspartame, saccharin, and sucralose) in water and beverage samples was developed using liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS). The sweeteners were extracted from water samples using solid-phase extraction (SPE) cartridges. Furthermore, several beverages were analyzed by a rapid and simple method without SPE, and the presence of the sweeteners was confirmed by accurate mass measurements below 2-ppm error. The unambiguous confirmation of the compounds was based on accurate mass measurements of the protonated molecules [M+H](+), their sodium adducts and their main fragment ions. Quantitation was carried out using matrix-matched standard calibration and linearity of response over 2 orders of magnitude was demonstrated (r>0.99). A detailed fragmentation study for sucralose was carried out by time-of-flight and a characteristic spectrum fingerprint pattern was obtained for the presence of this compound in water samples. Finally, the analysis of several wastewater, surface water and groundwater samples from the US showed that sucralose can be found in the aquatic environment at concentrations up to 2.4microg/L, thus providing a good indication of wastewater input from beverage sources.

  8. Automatic Earthquake Shear Stress Measurement Method Developed for Accurate Time- Prediction Analysis of Forthcoming Major Earthquakes Along Shallow Active Faults

    NASA Astrophysics Data System (ADS)

    Serata, S.

    2006-12-01

    The Serata Stressmeter has been developed to measure and monitor earthquake shear stress build-up along shallow active faults. The development work made in the past 25 years has established the Stressmeter as an automatic stress measurement system to study timing of forthcoming major earthquakes in support of the current earthquake prediction studies based on statistical analysis of seismological observations. In early 1982, a series of major Man-made earthquakes (magnitude 4.5-5.0) suddenly occurred in an area over deep underground potash mine in Saskatchewan, Canada. By measuring underground stress condition of the mine, the direct cause of the earthquake was disclosed. The cause was successfully eliminated by controlling the stress condition of the mine. The Japanese government was interested in this development and the Stressmeter was introduced to the Japanese government research program for earthquake stress studies. In Japan the Stressmeter was first utilized for direct measurement of the intrinsic lateral tectonic stress gradient G. The measurement, conducted at the Mt. Fuji Underground Research Center of the Japanese government, disclosed the constant natural gradients of maximum and minimum lateral stresses in an excellent agreement with the theoretical value, i.e., G = 0.25. All the conventional methods of overcoring, hydrofracturing and deformation, which were introduced to compete with the Serata method, failed demonstrating the fundamental difficulties of the conventional methods. The intrinsic lateral stress gradient determined by the Stressmeter for the Japanese government was found to be the same with all the other measurements made by the Stressmeter in Japan. The stress measurement results obtained by the major international stress measurement work in the Hot Dry Rock Projects conducted in USA, England and Germany are found to be in good agreement with the Stressmeter results obtained in Japan. Based on this broad agreement, a solid geomechanical

  9. Establishment of an x-ray standard calibration curve by conventional dicentric analysis as prerequisite for accurate radiation dose assessment.

    PubMed

    Beinke, Christina; Braselmann, Herbert; Meineke, Viktor

    2010-02-01

    The dicentric assay was established to carry out cytogenetic biodosimetry after suspected radiation overexposure, including a comprehensive documentation system to record the processing of the specimen, all data, results, and stored information. As an essential prerequisite for retrospective radiation dose assessment, a dose-response curve for dicentric induction by in vitro x-ray irradiation of peripheral blood samples was produced. The accelerating potential was 240 kV (maximum photon energy: 240 keV). A total of 8,377 first-division metaphases of four healthy volunteers were analyzed after exposure to doses ranging from 0.2 to 4.0 Gy at a dose rate of 1.0 Gy min. The background level of aberrations at 0-dose was determined by the analysis of 14,522 first-division metaphases obtained from unirradiated blood samples of 10 healthy volunteers. The dose-response relationship follows a linear-quadratic equation, Y = c + alphaD + betaD, with the coefficients c = 0.0005 +/- 0.0002, alpha = 0.043 +/- 0.006, and beta = 0.063 +/- 0.004. The technical competence and the quality of the calibration curve were assessed by determination of the dose prediction accuracy in an in vitro experiment simulating whole-body exposures within a range of 0.2 to 2.0 Gy. Dose estimations were derived by scoring up to 500-1,000 metaphase spreads or more (full estimation mode) and by evaluating only 50 metaphase spreads (triage mode) per subject. The triage mode was applied by performing manifold evaluations of the full estimation data in order to test the robustness of the curve for triage purposes and to assess possible variations among the estimated doses referring to a single exposure and preparation.

  10. Importance of including small body spin effects in the modelling of intermediate mass-ratio inspirals. II. Accurate parameter extraction of strong sources using higher-order spin effects

    NASA Astrophysics Data System (ADS)

    Huerta, E. A.; Gair, Jonathan R.; Brown, Duncan A.

    2012-03-01

    We improve the numerical kludge waveform model introduced in Huerta and Gair (2011) [E. A. Huerta and J. R. Gair, Phys. Rev. D 84, 064023 (2011).PRVDAQ1550-799810.1103/PhysRevD.84.064023] in two ways. We extend the equations of motion for spinning black hole binaries derived by Saijo et al. [M. Saijo, K. Maeda, M. Shibata, and Y. Mino, Phys. Rev. D 58, 064005 (1998).PRVDAQ0556-282110.1103/PhysRevD.58.064005] using spin-orbit and spin-spin couplings taken from perturbative and post-Newtonian (PN) calculations at the highest order available. We also include first-order conservative self-force corrections for spin-orbit and spin-spin couplings, which are derived by comparison to PN results. We generate the inspiral evolution using fluxes that include the most recent calculations of small body spin corrections, spin-spin, and spin-orbit couplings and higher-order fits to solutions of the Teukolsky equation. Using a simplified version of this model in [E. A. Huerta and J. R. Gair, Phys. Rev. D 84, 064023 (2011).PRVDAQ1550-799810.1103/PhysRevD.84.064023], we found that small body spin effects could be measured through gravitational-wave observations from intermediate-mass-ratio inspirals (IMRIs) with mass ratio η≳10-3, when both binary components are rapidly rotating. In this paper, we present results of Monte Carlo simulations of parameter-estimation errors to study in detail how the spin of the small/big body affects parameter measurement using a variety of mass and spin combinations for typical IMRI sources. We have found that for IMRI events involving a moderately rotating intermediate-mass black hole (IMBH) of mass 104M⊙ and a rapidly rotating central supermassive black hole (SMBH) of mass 106M⊙, gravitational wave observations made with LISA at a signal-to-noise ratio of 1000 should be able to determine the inspiralling IMBH mass, the central SMBH mass, the SMBH spin magnitude, and the IMBH spin magnitude to within fractional errors of ˜10-3, 10-3, 10

  11. Differential mobility spectrometry-mass spectrometry for atomic analysis.

    PubMed

    Sinatra, Francy L; Wu, Tianpeng; Manolakos, Spiros; Wang, Jing; Evans-Nguyen, Theresa G

    2015-02-01

    Analysis and separation of atomic ions within a portable setting are studied in forensic applications of radiological debris analysis. Ion mobility spectrometry (IMS) may be used to show separation of atomic ions, while the related method of differential mobility spectrometry (DMS) has focused on fractionation of primarily molecular components. We set out to investigate DMS as a means for separating atomic ions. We initially derived the differential ion mobility parameter, alpha, from classic empirical IMS data of atomic ions, cesium and potassium, each showing its own distinct form of alpha. These alpha functions were applied to DMS simulations and supported by analytical treatment that suggested a means for a rapid disambiguation of atomic ions using DMS. We validated this hypothesis through the prototype cesium-potassium system investigated experimentally by DMS coupled to mass spectrometry (MS). Such a feature would be advantageous in a field portable instrument for rapid atomic analyses especially in the case of isobaric ions that cannot be distinguished by MS. Herein, we first report this novel method for the derivation of alpha from existing field dependent drift tube ion mobility data. Further, we translate experimental DMS data into alpha parameters by expanding upon existing methods. Refining the alpha parameter in this manner helps convey the interpretation of the alpha parameter particularly for those new to the DMS field.

  12. Mass-based metabolomic analysis of soybean sprouts during germination.

    PubMed

    Gu, Eun-Ji; Kim, Dong Wook; Jang, Gwang-Ju; Song, Seong Hwa; Lee, Jae-In; Lee, Sang Bong; Kim, Bo-Min; Cho, Yeongrae; Lee, Hyeon-Jeong; Kim, Hyun-Jin

    2017-02-15

    We investigated the metabolite profile of soybean sprouts at 0, 1, 2, 3, and 4days after germination using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-MS (LC-MS) to understand the relationship between germination and nutritional quality. Data were analyzed by partial least squares-discriminant analysis (PLS-DA), and sprout samples were separated successfully using their PLS-DA scores. Fifty-eight metabolites, including macromolecular derivatives related to energy production, amino acids, myo-inositol metabolites, phytosterols, antioxidants, isoflavones, and soyasaponins, contributed to the separation. Amino acids, myo-inositol metabolites, isoflavone aglycones, B soyasaponins, antioxidants, and phytosterols, associated with health benefits and/or taste quality, increased with germination time while isoflavone glycosides and DDMP soyasaponins decreased. Based on these metabolites, the metabolomic pathway associated with energy production in soybean sprouts is suggested. Our data suggest that sprouting is a useful processing step to improve soybean nutritional quality, and metabolomic analysis is useful in understanding nutritional change during sprouting. PMID:27664639

  13. In Situ Analysis of Organics with a Portable Mass Spectrometer

    NASA Technical Reports Server (NTRS)

    Soparawalla, Santosh

    2011-01-01

    The search for extra-terrestrial life starts at home. In order to find life on other planets, we start by examining life processes we understand on the earth. Though it may not be possible to see the life in the form of macroscopic organisms, telltale signs of life can exist in the form of small organic molecules such as peptides and amino acids. Our overall goal is to test a portable mass spectrometer (MS) system, the Mini 10.5, for astrobiological applications including in situ hydrocarbon analysis and sediments analysis using an additional automated sample processing system (ASPS). The collaborative research focuses on two current projects in the field of astrobiology. Both projects are geared towards examining organics distributed in extreme environments. One portion of study attempts to qualitatively analyze the effect of volatile organic compounds (VOC) produced by diesel exhaust on lichens growing in the desert. This requires measurements to be taken by bringing the instrument to the Mojave Desert and monitoring atmospheric composition of VOCs in situ. The second project is to evaluate the miniature MS system as a detector for the ASPS extraction system. A major obstacle of any chemometric in situ analysis is the suppression of analyte signal by concomitant signal from the surrounding environment. The ASPS extraction device has been developed at JPL to extract amino acids from sediment samples and elute them in solution. The solution is eluted at a high pH and needs to be conditioned to a more neutral pH so that dissolved amino acids can be readily protonated and subsequently analyzed by electrospray MS.

  14. Direct analysis of samples by mass spectrometry: From elements to bio-molecules using laser ablation inductively couple plasma mass spectrometry and laser desorption/ionization mass spectrometry

    SciTech Connect

    Perdian, David C.

    2009-01-01

    Mass spectrometric methods that are able to analyze solid samples or biological materials with little or no sample preparation are invaluable to science as well as society. Fundamental research that has discovered experimental and instrumental parameters that inhibit fractionation effects that occur during the quantification of elemental species in solid samples by laser ablation inductively coupled plasma mass spectrometry is described. Research that determines the effectiveness of novel laser desorption/ionization mass spectrometric methods for the molecular analysis of biological tissues at atmospheric pressure and at high spatial resolution is also described. A spatial resolution is achieved that is able to analyze samples at the single cell level.

  15. Levels of Analysis in Mass Media Decision Making: A Taxonomy, Research Strategy, and Illustrative Data Analysis.

    ERIC Educational Resources Information Center

    Dimmick, John; Coit, Philip

    1982-01-01

    Presents a taxonomy of influences on decision making in mass media. Illustrates the use of the taxonomy and research strategy in a quantitative analysis of influences on the decision autonomy of reporters. Results indicate that reporters' experience plays the most important role in explaining their story selection/content autonomy. (PD)

  16. High-Throughput and Comprehensive Lipidomic Analysis Using Ultrahigh-Performance Supercritical Fluid Chromatography-Mass Spectrometry.

    PubMed

    Lísa, Miroslav; Holčapek, Michal

    2015-07-21

    New analytical approach for high-throughput and comprehensive lipidomic analysis of biological samples using ultrahigh-performance supercritical fluid chromatography (UHPSFC) with electrospray ionization-mass spectrometry (ESI-MS) is presented in this work as an alternative approach to established shotgun MS or high-performance liquid chromatography-MS. The lipid class separation is performed by UHPSFC method based on 1.7 μm particle-bridged ethylene hybrid silica column with a gradient of methanol-water-ammonium acetate mixture as a modifier. All parameters of UHPSFC conditions are carefully optimized and their influence on the chromatographic behavior of lipids is discussed. The final UHPSFC/ESI-MS method enables a fast separation of 30 nonpolar and polar lipid classes within 6 min analysis covering 6 main lipid categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenols. Individual lipid species within lipid classes are identified based on positive and negative-ion full-scan and tandem mass spectra measured with high mass accuracy and high resolving power. Developed UHPSFC/ESI-MS method is applied for the analysis of porcine brain extract as a complex lipidomic sample, where 24 lipid classes containing 436 lipid species are identified. The method is validated for the quantitative analysis of lipid species in biological tissues using internal standards for each lipid class. This high-throughput, comprehensive and accurate UHPSFC/ESI-MS method is suitable for the lipidomic analysis of large sample sets in the clinical research. PMID:26095628

  17. Characterization and quantitative analysis of surfactants in textile wastewater by liquid chromatography/quadrupole-time-of-flight mass spectrometry.

    PubMed

    González, Susana; Petrović, Mira; Radetic, Maja; Jovancic, Petar; Ilic, Vesna; Barceló, Damià

    2008-05-01

    A method based on the application of ultra-performance liquid chromatography (UPLC) coupled to hybrid quadrupole-time-of-flight mass spectrometry (QqTOF-MS) with an electrospray (ESI) interface has been developed for the screening and confirmation of several anionic and non-ionic surfactants: linear alkylbenzenesulfonates (LAS), alkylsulfate (AS), alkylethersulfate (AES), dihexyl sulfosuccinate (DHSS), alcohol ethoxylates (AEOs), coconut diethanolamide (CDEA), nonylphenol ethoxylates (NPEOs), and their degradation products (nonylphenol carboxylate (NPEC), octylphenol carboxylate (OPEC), 4-nonylphenol (NP), 4-octylphenol (OP) and NPEO sulfate (NPEO-SO4). The developed methodology permits reliable quantification combined with a high accuracy confirmation based on the accurate mass of the (de)protonated molecules in the TOFMS mode. For further confirmation of the identity of the detected compounds the QqTOF mode was used. Accurate masses of product ions obtained by performing collision-induced dissociation (CID) of the (de)protonated molecules of parent compounds were matched with the ions obtained for a standard solution. The method was applied for the quantitative analysis and high accuracy confirmation of surfactants in complex mixtures in effluents from the textile industry. Positive identification of the target compounds was based on accurate mass measurement of the base peak, at least one product ion and the LC retention time of the analyte compared with that of a standard. The most frequently surfactants found in these textile effluents were NPEO and NPEO-SO4 in concentrations ranging from 0.93 to 5.68 mg/L for NPEO and 0.06 to 4.30 mg/L for NPEO-SO4. AEOs were also identified. PMID:18398847

  18. Mass spectrometric methods for the direct elemental and isotopic analysis of solid material

    NASA Astrophysics Data System (ADS)

    Ganeev, A. A.; Gubal, A. R.; Potapov, S. V.; Agafonova, N. N.; Nemets, V. M.

    2016-04-01

    Methods for the direct analysis of solids have a number of undeniable advantages over the methods that require preliminary dissolution of samples. High sensitivity and selectivity make the direct mass spectrometric techniques the most in-demand. The review concerns spark source mass spectrometry, laser ionization mass spectrometry, laser ablation inductively coupled plasma mass spectrometry, secondary ion mass spectrometry, secondary neutral mass spectrometry and glow discharge mass spectrometry. Basic principles, analytical characteristics and trends in the development of these techniques are discussed. Particular attention is given to applications of the techniques as well as to their competitive advantages and drawbacks. The bibliography includes 123 references.

  19. Meta-analysis of mass balances examining chemical fate during wastewater treatment.

    PubMed

    Heidler, Jochen; Halden, Rolf U

    2008-09-01

    Mass balances are an instructive means for investigating the fate of chemicals during wastewater treatment. In addition to the aqueous-phase removal efficiency (phi), they can inform on chemical partitioning, transformation, and persistence, as well as on the chemical loading to streams and soils receiving, respectively, treated effluent and digested sewage sludge (biosolids). Release rates computed on a per-capita basis can serve to extrapolate findings to a larger scale. This review examines over a dozen mass balances conducted for various organic wastewater contaminants, including prescription drugs, estrogens, fragrances, antimicrobials, and surfactants of differing sorption potential (hydrophobicity), here expressed as the 1-octanol-water partition coefficient (K(OW)) and the organic carbon normalized sorption coefficient (K(OC)). Major challengesto mass balances are the collection of representative samples and accurate quantification of chemicals in sludge. A meta-analysis of peer-reviewed data identified sorption potential as the principal determinant governing chemical persistence in biosolids. Occurrence data for organic wastewater compounds detected in digested sludge followed a simple nonlinear model that required only K(OW) or K(OC) as the input and yielded a correlation coefficient of 0.9 in both instances. The model predicted persistence in biosolids for the majority (> 50%) of the input load of organic wastewater compounds featuring a log10 K(OW) value of greater than 5.2 (log10 K(OC) > 4.4). In contrast, hydrophobicity had no or only limited value for estimating, respectively, phi and the overall persistence of a chemical during conventional wastewater treatment.

  20. Analysis of Mass Spectrometry Data for Nucleolar Proteomics Experiments.

    PubMed

    Nicolas, Armel; Bensaddek, Dalila; Lamond, Angus I

    2016-01-01

    With recent advances in experiment design, sample preparation, separation and instruments, mass spectrometry (MS)-based quantitative proteomics is becoming increasingly more popular. This has the potential to usher a new revolution in biology, in which the protein complement of cell populations can be described not only with increasing coverage, but also in all of its dimensions with unprecedented precision. Indeed, while earlier proteomics studies aimed solely at identifying as many as possible of the proteins present in the sample, newer, so-called Next Generation Proteomics studies add to this the aim of determining and quantifying the protein variants present in the sample, their mutual associations within complexes, their posttranslational modifications, their variation across the cell-cycle or in response to stimuli or perturbations, and their subcellular distribution. This has the potential to make MS proteomics much more useful for researchers, but will also mean that researchers with no background in MS will increasingly be confronted with the less-than trivial challenges of preparing samples for MS analysis, then processing and interpreting the results. In Chapter 20 , we described a workflow for isolating the protein contents of a specific SILAC-labeled organelle sample (the nucleolus) and processing it into peptides suitable for bottom-up MS analysis. Here, we complete this workflow by describing how to use the freely available MaxQuant software to convert the spectra stored in the Raw files into peptide- and protein-level information. We also briefly describe how to visualize the data using the free R scripting language.

  1. Analysis of Mass Spectrometry Data for Nucleolar Proteomics Experiments.

    PubMed

    Nicolas, Armel; Bensaddek, Dalila; Lamond, Angus I

    2016-01-01

    With recent advances in experiment design, sample preparation, separation and instruments, mass spectrometry (MS)-based quantitative proteomics is becoming increasingly more popular. This has the potential to usher a new revolution in biology, in which the protein complement of cell populations can be described not only with increasing coverage, but also in all of its dimensions with unprecedented precision. Indeed, while earlier proteomics studies aimed solely at identifying as many as possible of the proteins present in the sample, newer, so-called Next Generation Proteomics studies add to this the aim of determining and quantifying the protein variants present in the sample, their mutual associations within complexes, their posttranslational modifications, their variation across the cell-cycle or in response to stimuli or perturbations, and their subcellular distribution. This has the potential to make MS proteomics much more useful for researchers, but will also mean that researchers with no background in MS will increasingly be confronted with the less-than trivial challenges of preparing samples for MS analysis, then processing and interpreting the results. In Chapter 20 , we described a workflow for isolating the protein contents of a specific SILAC-labeled organelle sample (the nucleolus) and processing it into peptides suitable for bottom-up MS analysis. Here, we complete this workflow by describing how to use the freely available MaxQuant software to convert the spectra stored in the Raw files into peptide- and protein-level information. We also briefly describe how to visualize the data using the free R scripting language. PMID:27576726

  2. [Application of gas chromatography-high resolution quadrupole time of flight mass spectrometry to the analysis of benzaldehyde, benzyl alcohol acetophenone and phenylacetaldehyde in complex aromatic samples].

    PubMed

    Liu, Junyan; Cao, Zhe; Li, Jiwen; Wang, Zheming; Wang, Chuan; Gu, Songyuan

    2015-02-01

    The study focuses on the quantitative analytical characterization of benzaldehyde, benzyl alcohol, acetophenone and phenylacetaldehyde in complex aromatic samples by gas chromatography-high resolution quadrupole time of flight mass spectrometry (GC-QTOF MS). The four compounds in real sample were accurately qualified and quantified through a comprehensive analysis of the GC retention times and the accurate masses of the ion fragments obtained by the high resolution MS. The new method therefore effectively avoids the interference of the real sample substrate, which reduces the accuracy of the analysis results. The peak area of the characteristic ion fragment for each compound was used for quantitation calculation. The MS signal responses of the four compounds showed good linear relationships with the corresponding mass concentrations and the linear regression coefficients were greater than 0. 99. The method recoveries were 87. 97% - 103.01%. The limits of detection (LODs) were 0. 01, 0. 03, 0. 02 and 0. 01 mg/L for benzaldehyde, benzyl alcohol, acetophenone and phenylacetaldehyde respectively. The contents of the four compounds in three real samples were analyzed. The study provided a new strategy for oxygenate analysis in complex aromatic samples using GC-QTOF MS. By measuring the accurate masses, the new method reduces the reliance on chromatographic separation ability and makes up the shortcomings of the traditional GC-MS methods.

  3. Liquid chromatography/electrospray ionization/isotopic dilution mass spectrometry analysis of n-(phosphonomethyl) glycine and mass spectrometry analysis of aminomethyl phosphonic acid in environmental water and vegetation matrixes.

    PubMed

    Grey, L; Nguyen, B; Yang, P

    2001-01-01

    A liquid chromatography/electrospray/mass spectrometry (LC/ES/MS) method was developed for the analysis of glyphosate (n-phosphonomethyl glycine) and its metabolite, aminomethyl phosphonic acid (AMPA) using isotope-labelled glyphosate as a method surrogate. Optimized parameters were achieved to derivatize glyphosate and AMPA using 9-fluorenylmethyl chloroformate (FMOC-Cl) in borate buffer prior to a reversed-phase LC analysis. Method spike recovery data obtained using laboratory and real world sample matrixes indicated an excellent correlation between the recovery of the native and isotope-labelled glyphosate. Hence, the first performance-based, isotope dilution MS method with superior precision, accuracy, and data quality was developed for the analysis of glyphosate. There was, however, no observable correlation between the isotope-labelled glyphosate and AMPA. Thus, the use of this procedure for the accurate analysis of AMPA was not supported. Method detection limits established using standard U.S. Environmental Protection Agency protocol were 0.06 and 0.30 microg/L, respectively, for glyphosate and AMPA in water matrixes and 0.11 and 0.53 microg/g, respectively, in vegetation matrixes. Problems, solutions, and the method performance data related to the analysis of chlorine-treated drinking water samples are discussed. Applying this method to other environmental matrixes, e.g., soil, with minimum modifications is possible, assuring accurate, multimedia studies of glyphosate concentration in the environment and the delivery of useful multimedia information for regulatory applications.

  4. A Framework for the Comparative Assessment of Neuronal Spike Sorting Algorithms towards More Accurate Off-Line and On-Line Microelectrode Arrays Data Analysis.

    PubMed

    Regalia, Giulia; Coelli, Stefania; Biffi, Emilia; Ferrigno, Giancarlo; Pedrocchi, Alessandra

    2016-01-01

    Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting "building blocks" into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191

  5. A Framework for the Comparative Assessment of Neuronal Spike Sorting Algorithms towards More Accurate Off-Line and On-Line Microelectrode Arrays Data Analysis

    PubMed Central

    Pedrocchi, Alessandra

    2016-01-01

    Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting “building blocks” into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191

  6. A Mass Spectrometric Analysis Method Based on PPCA and SVM for Early Detection of Ovarian Cancer

    PubMed Central

    Wu, Jiang; Ji, Mengying; Ye, Zhuang

    2016-01-01

    Background. Surfaced-enhanced laser desorption-ionization-time of flight mass spectrometry (SELDI-TOF-MS) technology plays an important role in the early diagnosis of ovarian cancer. However, the raw MS data is highly dimensional and redundant. Therefore, it is necessary to study rapid and accurate detection methods from the massive MS data. Methods. The clinical data set used in the experiments for early cancer detection consisted of 216 SELDI-TOF-MS samples. An MS analysis method based on probabilistic principal components analysis (PPCA) and support vector machine (SVM) was proposed and applied to the ovarian cancer early classification in the data set. Additionally, by the same data set, we also established a traditional PCA-SVM model. Finally we compared the two models in detection accuracy, specificity, and sensitivity. Results. Using independent training and testing experiments 10 times to evaluate the ovarian cancer detection models, the average prediction accuracy, sensitivity, and specificity of the PCA-SVM model were 83.34%, 82.70%, and 83.88%, respectively. In contrast, those of the PPCA-SVM model were 90.80%, 92.98%, and 88.97%, respectively. Conclusions. The PPCA-SVM model had better detection performance. And the model combined with the SELDI-TOF-MS technology had a prospect in early clinical detection and diagnosis of ovarian cancer. PMID:27642365

  7. Femtosecond laser ablation-based mass spectrometry. An ideal tool for stoichiometric analysis of thin films

    DOE PAGES

    LaHaye, Nicole L.; Kurian, Jose; Diwakar, Prasoon K.; Alff, Lambert; Harilal, Sivanandan S.

    2015-08-19

    An accurate and routinely available method for stoichiometric analysis of thin films is a desideratum of modern materials science where a material’s properties depend sensitively on elemental composition. We thoroughly investigated femtosecond laser ablation-inductively coupled plasma-mass spectrometry (fs-LA-ICP-MS) as an analytical technique for determination of the stoichiometry of thin films down to the nanometer scale. The use of femtosecond laser ablation allows for precise removal of material with high spatial and depth resolution that can be coupled to an ICP-MS to obtain elemental and isotopic information. We used molecular beam epitaxy-grown thin films of LaPd(x)Sb2 and T´-La2CuO4 to demonstrate themore » capacity of fs-LA-ICP-MS for stoichiometric analysis and the spatial and depth resolution of the technique. Here we demonstrate that the stoichiometric information of thin films with a thickness of ~10 nm or lower can be determined. Furthermore, our results indicate that fs-LA-ICP-MS provides precise information on the thin film-substrate interface and is able to detect the interdiffusion of cations.« less

  8. Femtosecond laser ablation-based mass spectrometry. An ideal tool for stoichiometric analysis of thin films

    SciTech Connect

    LaHaye, Nicole L.; Kurian, Jose; Diwakar, Prasoon K.; Alff, Lambert; Harilal, Sivanandan S.

    2015-08-19

    An accurate and routinely available method for stoichiometric analysis of thin films is a desideratum of modern materials science where a material’s properties depend sensitively on elemental composition. We thoroughly investigated femtosecond laser ablation-inductively coupled plasma-mass spectrometry (fs-LA-ICP-MS) as an analytical technique for determination of the stoichiometry of thin films down to the nanometer scale. The use of femtosecond laser ablation allows for precise removal of material with high spatial and depth resolution that can be coupled to an ICP-MS to obtain elemental and isotopic information. We used molecular beam epitaxy-grown thin films of LaPd(x)Sb2 and T´-La2CuO4 to demonstrate the capacity of fs-LA-ICP-MS for stoichiometric analysis and the spatial and depth resolution of the technique. Here we demonstrate that the stoichiometric information of thin films with a thickness of ~10 nm or lower can be determined. Furthermore, our results indicate that fs-LA-ICP-MS provides precise information on the thin film-substrate interface and is able to detect the interdiffusion of cations.

  9. Femtosecond laser ablation-based mass spectrometry: An ideal tool for stoichiometric analysis of thin films

    PubMed Central

    LaHaye, Nicole L.; Kurian, Jose; Diwakar, Prasoon K.; Alff, Lambert; Harilal, Sivanandan S.

    2015-01-01

    An accurate and routinely available method for stoichiometric analysis of thin films is a desideratum of modern materials science where a material’s properties depend sensitively on elemental composition. We thoroughly investigated femtosecond laser ablation-inductively coupled plasma-mass spectrometry (fs-LA-ICP-MS) as an analytical technique for determination of the stoichiometry of thin films down to the nanometer scale. The use of femtosecond laser ablation allows for precise removal of material with high spatial and depth resolution that can be coupled to an ICP-MS to obtain elemental and isotopic information. We used molecular beam epitaxy-grown thin films of LaPd(x)Sb2 and T′-La2CuO4 to demonstrate the capacity of fs-LA-ICP-MS for stoichiometric analysis and the spatial and depth resolution of the technique. Here we demonstrate that the stoichiometric information of thin films with a thickness of ~10 nm or lower can be determined. Furthermore, our results indicate that fs-LA-ICP-MS provides precise information on the thin film-substrate interface and is able to detect the interdiffusion of cations. PMID:26285795

  10. A Mass Spectrometric Analysis Method Based on PPCA and SVM for Early Detection of Ovarian Cancer

    PubMed Central

    Wu, Jiang; Ji, Mengying; Ye, Zhuang

    2016-01-01

    Background. Surfaced-enhanced laser desorption-ionization-time of flight mass spectrometry (SELDI-TOF-MS) technology plays an important role in the early diagnosis of ovarian cancer. However, the raw MS data is highly dimensional and redundant. Therefore, it is necessary to study rapid and accurate detection methods from the massive MS data. Methods. The clinical data set used in the experiments for early cancer detection consisted of 216 SELDI-TOF-MS samples. An MS analysis method based on probabilistic principal components analysis (PPCA) and support vector machine (SVM) was proposed and applied to the ovarian cancer early classification in the data set. Additionally, by the same data set, we also established a traditional PCA-SVM model. Finally we compared the two models in detection accuracy, specificity, and sensitivity. Results. Using independent training and testing experiments 10 times to evaluate the ovarian cancer detection models, the average prediction accuracy, sensitivity, and specificity of the PCA-SVM model were 83.34%, 82.70%, and 83.88%, respectively. In contrast, those of the PPCA-SVM model were 90.80%, 92.98%, and 88.97%, respectively. Conclusions. The PPCA-SVM model had better detection performance. And the model combined with the SELDI-TOF-MS technology had a prospect in early clinical detection and diagnosis of ovarian cancer.

  11. A Mass Spectrometric Analysis Method Based on PPCA and SVM for Early Detection of Ovarian Cancer.

    PubMed

    Wu, Jiang; Ji, Yanju; Zhao, Ling; Ji, Mengying; Ye, Zhuang; Li, Suyi

    2016-01-01

    Background. Surfaced-enhanced laser desorption-ionization-time of flight mass spectrometry (SELDI-TOF-MS) technology plays an important role in the early diagnosis of ovarian cancer. However, the raw MS data is highly dimensional and redundant. Therefore, it is necessary to study rapid and accurate detection methods from the massive MS data. Methods. The clinical data set used in the experiments for early cancer detection consisted of 216 SELDI-TOF-MS samples. An MS analysis method based on probabilistic principal components analysis (PPCA) and support vector machine (SVM) was proposed and applied to the ovarian cancer early classification in the data set. Additionally, by the same data set, we also established a traditional PCA-SVM model. Finally we compared the two models in detection accuracy, specificity, and sensitivity. Results. Using independent training and testing experiments 10 times to evaluate the ovarian cancer detection models, the average prediction accuracy, sensitivity, and specificity of the PCA-SVM model were 83.34%, 82.70%, and 83.88%, respectively. In contrast, those of the PPCA-SVM model were 90.80%, 92.98%, and 88.97%, respectively. Conclusions. The PPCA-SVM model had better detection performance. And the model combined with the SELDI-TOF-MS technology had a prospect in early clinical detection and diagnosis of ovarian cancer. PMID:27642365

  12. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

    PubMed

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-11-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

  13. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes

    PubMed Central

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-01-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a ∼21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes. PMID:19740761

  14. Low pressure gas flow analysis through an effusive inlet using mass spectrometry

    NASA Technical Reports Server (NTRS)

    Brown, David R.; Brown, Kenneth G.

    1988-01-01

    A mass spectrometric method for analyzing flow past and through an effusive inlet designed for use on the tethered satellite and other entering vehicles is discussed. Source stream concentrations of species in a gaseous mixture are determined using a calibration of measured mass spectral intensities versus source stream pressure for standard gas mixtures and pure gases. Concentrations are shown to be accurate within experimental error. Theoretical explanations for observed mass discrimination effects as they relate to the various flow situations in the effusive inlet and the experimental apparatus are discussed.

  15. Accurate Analysis and Evaluation of Acidic Plant Growth Regulators in Transgenic and Nontransgenic Edible Oils with Facile Microwave-Assisted Extraction-Derivatization.

    PubMed

    Liu, Mengge; Chen, Guang; Guo, Hailong; Fan, Baolei; Liu, Jianjun; Fu, Qiang; Li, Xiu; Lu, Xiaomin; Zhao, Xianen; Li, Guoliang; Sun, Zhiwei; Xia, Lian; Zhu, Shuyun; Yang, Daoshan; Cao, Ziping; Wang, Hua; Suo, Yourui; You, Jinmao

    2015-09-16

    Determination of plant growth regulators (PGRs) in a signal transduction system (STS) is significant for transgenic food safety, but may be challenged by poor accuracy and analyte instability. In this work, a microwave-assisted extraction-derivatization (MAED) method is developed for six acidic PGRs in oil samples, allowing an efficient (<1.5 h) and facile (one step) pretreatment. Accuracies are greatly improved, particularly for gibberellin A3 (-2.72 to -0.65%) as compared with those reported (-22 to -2%). Excellent selectivity and quite low detection limits (0.37-1.36 ng mL(-1)) are enabled by fluorescence detection-mass spectrum monitoring. Results show the significant differences in acidic PGRs between transgenic and nontransgenic oils, particularly 1-naphthaleneacetic acid (1-NAA), implying the PGRs induced variations of components and genes. This study provides, for the first time, an accurate and efficient determination for labile PGRs involved in STS and a promising concept for objectively evaluating the safety of transgenic foods.

  16. Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry.

    PubMed

    Strittmatter, Nicole; Jones, Emrys A; Veselkov, Kirill A; Rebec, Monica; Bundy, Jacob G; Takats, Zoltan

    2013-07-14

    An identification system for microorganisms based on recently developed rapid evaporative ionisation mass spectrometry (REIMS) is presented. Nine bacterial species cultured on various growth media were correctly identified to family-, genus-, and species-level based on their different mass spectral fingerprints using a cross-validated maximum margin criterion model.

  17. Mass Analysis of Charged Aerosol Particles During the MASS/ECOMA Campaign

    NASA Astrophysics Data System (ADS)

    Knappmiller, S.; Robertson, S.; Horanyi, M.; Sternovsky, Z.

    2008-12-01

    . The Mesospheric Aerosol Sampling Spectrometer (MASS) instrument was launched on two sounding rockets in August 2007 from Andoya, Norway to find the masses of charged aerosol particles in the polar mesosphere in NLC/PMSE conditions (3 August) and PMSE conditions alone (6 August). We compare and contrast the four data sets from the uplegs and downlegs. The MASS instrument collected ions, cluster ions, and charged nanometer-sized particles on four pairs of electrically-biased graphite plates that collect positive and negative particles separately. Electron collection was prevented by the negative potential on the rocket body. For the 3 August upleg, the data show charged particle collection on all channels with number densities of order several thousand per cubic centimeter in the four size ranges < 0.5 nm, 0.5-1 nm, 1-2 nm, and > 3 nm. The occurrence of positively charged aerosol particles in the smallest sizes suggests positive ions as the nucleation sites because the smallest particles have negligible probability of charging by photoionization. The signals were smaller on the 3 August downleg as a consequence of the spatial variability of the cloud. For the 6 August upleg into PMSE alone, only smaller particles (< 2 nm) were detected and these were both positive and negative with number densities of several thousand per cubic centimeter. On the downleg, 1-2 nm negatively charged particles were detected, but there were no positive particles in this mass range.

  18. Evaluating a direct swabbing method for screening pesticides on fruit and vegetable surfaces using Direct Analysis in Real Time (DART) coupled to an Exactive benchtop orbitrap mass spectrometer.

    PubMed

    Crawford, Elizabeth; Musselman, Brian

    2012-07-01

    Rapid screening of pesticides present on the surfaces of fruits and vegetables has been facilitated by using a Direct Analysis in Real Time (DART(®)) open air surface desorption ionization source coupled to an Exactive(®) high-resolution accurate mass benchtop orbitrap mass spectrometer. The use of cotton and polyester cleaning swabs to collect and retain pesticides for subsequent open air desorption ionization is demonstrated by sampling the surface of various produce to which solutions of pesticides have been applied at levels 10 and 100 times below the tolerance levels established by the United States Environmental Protection Agency (US EPA). Samples analyzed include cherry tomatoes, oranges, peaches and carrots each chosen for their surface characteristics which include: smooth, pitted, fuzzy, and rough respectively. Results from the direct analysis of fungicides on store-bought oranges are also described. In all cases, the swabs were introduced directly into the heated ionizing gas of the DART source resulting in production of protonated pesticide molecules within seconds of sampling. Operation of the orbitrap mass spectrometer at 25,000 full-width half maximum resolution was sufficient to generate high-quality accurate mass data. Stable external mass calibration eliminated the need for addition of standards typically required for mass calibration, thus allowing multiple analyses to be completed without instrument recalibration. PMID:22362280

  19. Vibration analysis of rotor blades with an attached concentrated mass

    NASA Technical Reports Server (NTRS)

    Murthy, V. R.; Barna, P. S.

    1977-01-01

    The effect of an attached concentrated mass on the dynamics of helicopter rotor blades is determined. The point transmission matrix method was used to define, through three completely automated computer programs, the natural vibrational characteristics (natural frequencies and mode shapes) of rotor blades. The problems of coupled flapwise bending, chordwise bending, and torsional vibration of a twisted nonuniform blade and its special subcase pure torsional vibration are discussed. The orthogonality relations that exist between the natural modes of rotor blades with an attached concentrated mass are derived. The effect of pitch, rotation, and point mass parameters on the collective, cyclic, scissor, and pure torsional modes of a seesaw rotor blade is determined.

  20. Analysis of Soil Vapor Extraction Data to Evaluate Mass-Transfer Constraints and Estimate Source-Zone Mass Flux

    SciTech Connect

    Brusseau, Mark; Rohay, Virginia J.; Truex, Michael J.

    2010-06-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy’s Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and representing mass flux during the rebound periods, were calculated and compared. It was shown that it is possible to use the rebound data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure.

  1. ANALYSIS OF SOIL VAPOR EXTRACTION DATA TO EVALUATE MASS-TRANSFER CONSTRAINTS AND ESTIMATE SOURCE-ZONE MASS FLUX.

    PubMed

    Brusseau, Mark L; Rohay, Virginia; Truex, Michael J

    2010-01-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy's Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and during the rebound period, were calculated and compared. It was shown that it is possible to use the data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure. The mass-flux data would also be useful for risk assessments of the impact of vadose-zone sources on groundwater contamination or vapor intrusion.

  2. ANALYSIS OF SOIL VAPOR EXTRACTION DATA TO EVALUATE MASS-TRANSFER CONSTRAINTS AND ESTIMATE SOURCE-ZONE MASS FLUX

    PubMed Central

    Rohay, Virginia; Truex, Michael J.

    2013-01-01

    Methods are developed to use data collected during cyclic operation of soil vapor extraction (SVE) systems to help characterize the magnitudes and timescales of mass flux associated with vadose zone contaminant sources. Operational data collected at the Department of Energy’s Hanford site are used to illustrate the use of such data. An analysis was conducted of carbon tetrachloride vapor concentrations collected during and between SVE operations. The objective of the analysis was to evaluate changes in concentrations measured during periods of operation and non-operation of SVE, with a focus on quantifying temporal dynamics of the vadose zone contaminant mass flux, and associated source strength. Three mass-flux terms, representing mass flux during the initial period of a SVE cycle, during the asymptotic period of a cycle, and during the rebound period, were calculated and compared. It was shown that it is possible to use the data to estimate time frames for effective operation of an SVE system if a sufficient set of historical cyclic operational data exists. This information could then be used to help evaluate changes in SVE operations, including system closure. The mass-flux data would also be useful for risk assessments of the impact of vadose-zone sources on groundwater contamination or vapor intrusion. PMID:23516336

  3. 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.

  4. Accurate quantification of mercapturic acids of styrene (PHEMAs) in human urine with direct sample injection using automated column-switching high-performance liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Reska, M; Ochsmann, E; Kraus, T; Schettgen, T

    2010-08-01

    Styrene is one of the most important industrial chemicals, with an enormously high production volume worldwide. The urinary mercapturic acids of its metabolite styrene-7,8-oxide, namely N-acetyl-S-(2-hydroxy-1-phenylethyl)-L-cysteine (PHEMA 1) and N-acetyl-S-(2-hydroxy-2-phenylethyl)-L-cysteine (PHEMA 2), are specific biomarkers for the determination of individual internal exposure to this highly reactive intermediate of styrene. We have developed and validated a fast, specific and very sensitive method for the accurate determination of the sum of phenylhydroxyethyl mercapturic acids (PHEMAs) in human urine with an automated multidimensional liquid chromatography-tandem mass spectrometry method using (13)C(6)-labelled PHEMAs as internal standards. Analytes were stripped from the urinary matrix by online extraction on a restricted access material, transferred to the analytical column and subsequently determined by tandem mass spectrometry. The limit of quantification (LOQ) for the sum of PHEMAs was 0.3 microg/L urine and allowed us to quantify the background exposure of the (smoking) general population. Precision within series and between series ranged from 1.5 to 6.8% at three concentrations ranging from 3 to 30 microg/L urine; the mean accuracy was between 104 and 110%. We applied the method to spot urine samples from 40 subjects of the general population with no known occupational exposure to styrene. The median levels (range) for the sum of PHEMAs in urine of non-smokers (n = 22) were less than 0.3 microg/L (less than 0.3 to 1.1 microg/L), whereas in urine of smokers (n = 18), the median levels were 0.46 microg/L (less than 0.3 to 2.8 microg/L). Smokers showed a significantly higher excretion of the sum of PHEMAs (p = 0.02). Owing to its automation and high sensitivity, our method is well suited for application in occupational or environmental studies.

  5. Computer Analysis of Isotope Clusters in Mass Spectrometry

    ERIC Educational Resources Information Center

    Bell, Harold M.

    1974-01-01

    Describes the application of a computer program designed to produce a formula determination simultaneously accounting for both elemental composition and probable isotopic species for a measured ion mass. (SLH)

  6. Subcellular analysis by laser ablation electrospray ionization mass spectrometry

    DOEpatents

    Vertes, Akos; Stolee, Jessica A; Shrestha, Bindesh

    2014-12-02

    In various embodiments, a method of laser ablation electrospray ionization mass spectrometry (LAESI-MS) may generally comprise micro-dissecting a cell comprising at least one of a cell wall and a cell membrane to expose at least one subcellular component therein, ablating the at least one subcellular component by an infrared laser pulse to form an ablation plume, intercepting the ablation plume by an electrospray plume to form ions, and detecting the ions by mass spectrometry.

  7. Qualitative analysis of halogenated organic contaminants in American eel by gas chromatography/time-of-flight mass spectrometry.

    PubMed

    Byer, Jonathan D; Pacepavicius, Grazina; Lebeuf, Michel; Brown, R Stephen; Backus, Sean; Hodson, Peter V; Alaee, Mehran

    2014-12-01

    Target compound analysis with scanning mass spectrometers such as quadrupole or magnetic sector instruments is used extensively in environmental chemistry because of the selectivity, sensitivity, and robustness. Yet, target compound analysis selectively ignores the majority of compounds present in a sample, especially in complex matrices like fish. In this study, time-of-flight mass spectrometry was used to screen for and identify halogenated compounds in American eels (Anguilla rostrata). Individual and then pooled eel samples were analysed using electron ionization and electron capture negative ionization (ECNI) modes. Eels were differentiated by principal component analysis of chemical profiles and were grouped corresponding to their capture location, all with a single instrument injection per sample. Bromine containing compounds were further investigated by taking advantage of the selectivity of ECNI by utilizing the Br(-) ion m/z 79 and 81. A total of 51 brominated compounds were detected and their identities were attempted by authentic standards, library searching, and/or chemical formula prediction based on accurate mass measurements. Several PBDEs were identified in the samples, and the majority of the non-PBDEs identified were bromophenols, bromoanisoles, and bromobenzenes. These classes of compounds are synthesized for use in flame retardant production either as intermediates or as final products. However, their occurrence in eels was most likely the result of metabolism or break-down products of high production volume flame retardants like polybrominated diphenyl ethers and bromophenoxy compounds.

  8. An Accurate, Flexible and Small Optical Fiber Sensor: A Novel Technological Breakthrough for Real-Time Analysis of Dynamic Blood Flow Data In Vivo

    PubMed Central

    Yuan, Qiao-ying; Zhang, Ling; Xiao, Dan; Zhao, Kun; Lin, Chun; Si, Liang-yi

    2014-01-01

    Because of the limitations of existing methods and techniques for directly obtaining real-time blood data, no accurate microflow in vivo real-time analysis method exists. To establish a novel technical platform for real-time in vivo detection and to analyze average blood pressure and other blood flow parameters, a small, accurate, flexible, and nontoxic Fabry-Perot fiber sensor was designed. The carotid sheath was implanted through intubation of the rabbit carotid artery (n = 8), and the blood pressure and other detection data were determined directly through the veins. The fiber detection results were compared with test results obtained using color Doppler ultrasound and a physiological pressure sensor recorder. Pairwise comparisons among the blood pressure results obtained using the three methods indicated that real-time blood pressure information obtained through the fiber sensor technique exhibited better correlation than the data obtained with the other techniques. The highest correlation (correlation coefficient of 0.86) was obtained between the fiber sensor and pressure sensor. The blood pressure values were positively related to the total cholesterol level, low-density lipoprotein level, number of red blood cells, and hemoglobin level, with correlation coefficients of 0.033, 0.129, 0.358, and 0.373, respectively. The blood pressure values had no obvious relationship with the number of white blood cells and high-density lipoprotein and had a negative relationship with triglyceride levels, with a correlation coefficient of –0.031. The average ambulatory blood pressure measured by the fiber sensor exhibited a negative correlation with the quantity of blood platelets (correlation coefficient of −0.839, P<0.05). The novel fiber sensor can thus obtain in vivo blood pressure data accurately, stably, and in real time; the sensor can also determine the content and status of the blood flow to some extent. Therefore, the fiber sensor can obtain partially real

  9. An accurate, flexible and small optical fiber sensor: a novel technological breakthrough for real-time analysis of dynamic blood flow data in vivo.

    PubMed

    Yuan, Qiao-ying; Zhang, Ling; Xiao, Dan; Zhao, Kun; Lin, Chun; Si, Liang-yi

    2014-01-01

    Because of the limitations of existing methods and techniques for directly obtaining real-time blood data, no accurate microflow in vivo real-time analysis method exists. To establish a novel technical platform for real-time in vivo detection and to analyze average blood pressure and other blood flow parameters, a small, accurate, flexible, and nontoxic Fabry-Perot fiber sensor was designed. The carotid sheath was implanted through intubation of the rabbit carotid artery (n = 8), and the blood pressure and other detection data were determined directly through the veins. The fiber detection results were compared with test results obtained using color Doppler ultrasound and a physiological pressure sensor recorder. Pairwise comparisons among the blood pressure results obtained using the three methods indicated that real-time blood pressure information obtained through the fiber sensor technique exhibited better correlation than the data obtained with the other techniques. The highest correlation (correlation coefficient of 0.86) was obtained between the fiber sensor and pressure sensor. The blood pressure values were positively related to the total cholesterol level, low-density lipoprotein level, number of red blood cells, and hemoglobin level, with correlation coefficients of 0.033, 0.129, 0.358, and 0.373, respectively. The blood pressure values had no obvious relationship with the number of white blood cells and high-density lipoprotein and had a negative relationship with triglyceride levels, with a correlation coefficient of -0.031. The average ambulatory blood pressure measured by the fiber sensor exhibited a negative correlation with the quantity of blood platelets (correlation coefficient of -0.839, P<0.05). The novel fiber sensor can thus obtain in vivo blood pressure data accurately, stably, and in real time; the sensor can also determine the content and status of the blood flow to some extent. Therefore, the fiber sensor can obtain partially real

  10. Differential analysis of camphor wood products by desorption atmospheric pressure chemical ionization mass spectrometry.

    PubMed

    Zhu, Liang; Yan, Jianping; Zhu, Zhiqiang; Ouyang, Yongzhong; Zhang, Xinglei; Zhang, Wenjun; Dai, Ximo; Luo, Liping; Chen, Huanwen

    2013-01-23

    In the course of this study, desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI-MS) was applied to readily acquire the mass spectral fingerprints of camphor wood and other wood samples under ambient conditions. Characteristic natural analytes, such as camphor and geraniol, were successfully detected in their protonated form and then identified by tandem mass spectrometry (MS(n)). Further principal component analysis (PCA) and cluster analysis (CA) of the mass spectrometric results allow a confident discrimination of camphor wood products from inferior/fake ones. These experimental findings demonstrate that DAPCI-MS is a valuable tool for differential analysis of untreated camphor wood products with sufficient sensitivity and high throughput.

  11. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  12. Does objective measurement of tracheal tube cuff pressures minimise adverse effects and maintain accurate cuff pressures? A systematic review and meta-analysis.

    PubMed

    Ca, Hockey; Aaj, van Zundert; Jd, Paratz

    2016-09-01

    Correct inflation pressures of the tracheal cuff are recommended to ensure adequate ventilation and prevent aspiration and adverse events. However there are conflicting views on which measurement to employ. The aim of this review was to examine whether adjustment of cuff pressure guided by objective measurement, compared with subjective measurement or observation of the pressure value alone, was able to prevent patient-related adverse effects and maintain accurate cuff pressures. A search of PubMed, Web of Science, Embase, CINAHL and ScienceDirect was conducted using keywords 'cuff pressure' and 'measure*' and related synonyms. Included studies were randomised or pseudo-randomised controlled trials investigating mechanically ventilated patients both in the intensive care unit and during surgery. Outcomes included adverse effects and the comparison of pressure measurements. Pooled analyses were performed to calculate risk ratios, effect sizes and 95% confidence intervals. Meta-analysis found preliminary evidence that adjustment of cuff pressure guided by objective measurement as compared with subjective measurement or observation of the pressure value alone, has benefit in preventing adverse effects. These included cough at two hours (odds ratio [OR] 0.42, confidence interval [CI] 0.23 to 0.79, P=0.007), hoarseness at 24 hours (OR 0.49, CI 0.31 to 0.76, P <0.002), sore throat (OR 0.73, CI 0.54 to 0.97, P <0.03), lesions of the trachea and incidences of silent aspiration (P=0.001), as well as maintaining accurate cuff pressures (Hedges' g 1.61, CI 2.69 to 0.53, P=0.003). Subjective measurement to guide adjustment or observation of the pressure value alone may lead to patient-related adverse effects and inaccuracies. It is recommended that an objective form of measurement be used. PMID:27608338

  13. Does objective measurement of tracheal tube cuff pressures minimise adverse effects and maintain accurate cuff pressures? A systematic review and meta-analysis.

    PubMed

    Hockey, C A; van Zundert, A A J; Paratz, J D

    2016-09-01

    Correct inflation pressures of the tracheal cuff are recommended to ensure adequate ventilation and prevent aspiration and adverse events. However there are conflicting views on which measurement to employ. The aim of this review was to examine whether adjustment of cuff pressure guided by objective measurement, compared with subjective measurement or observation of the pressure value alone, was able to prevent patient-related adverse effects and maintain accurate cuff pressures. A search of PubMed, Web of Science, Embase, CINAHL and ScienceDirect was conducted using keywords 'cuff pressure' and 'measure*' and related synonyms. Included studies were randomised or pseudo-randomised controlled trials investigating mechanically ventilated patients both in the intensive care unit and during surgery. Outcomes included adverse effects and the comparison of pressure measurements. Pooled analyses were performed to calculate risk ratios, effect sizes and 95% confidence intervals. Meta-analysis found preliminary evidence that adjustment of cuff pressure guided by objective measurement as compared with subjective measurement or observation of the pressure value alone, has benefit in preventing adverse effects. These included cough at two hours (odds ratio [OR] 0.42, confidence interval [CI] 0.23 to 0.79, P=0.007), hoarseness at 24 hours (OR 0.49, CI 0.31 to 0.76, P <0.002), sore throat (OR 0.73, CI 0.54 to 0.97, P <0.03), lesions of the trachea and incidences of silent aspiration (P=0.001), as well as maintaining accurate cuff pressures (Hedges' g 1.61, CI 2.69 to 0.53, P=0.003). Subjective measurement to guide adjustment or observation of the pressure value alone may lead to patient-related adverse effects and inaccuracies. It is recommended that an objective form of measurement be used.

  14. Peculiarities of data interpretation upon direct tissue analysis by Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Chagovets, Vtaliy; Kononikhin, Aleksey; Starodubtseva, Nataliia; Kostyukevich, Yury; Popov, Igor; Frankevich, Vladimir; Nikolaev, Eugene

    2016-01-01

    The importance of high-resolution mass spectrometry for the correct data interpretation of a direct tissue analysis is demonstrated with an example of its clinical application for an endometriosis study. Multivariate analysis of the data discovers lipid species differentially expressed in different tissues under investigation. High-resolution mass spectrometry allows unambiguous separation of peaks with close masses that correspond to proton and sodium adducts of phosphatidylcholines and to phosphatidylcholines differing in double bond number. PMID:27553733

  15. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

    SciTech Connect

    Ting, Ying S.; Egertson, Jarrett D.; Payne, Samuel H.; Kim, Sangtae; MacLean, Brendan; Kall, Lukas; Aebersold, Ruedi; Smith, Richard D.; Noble, William; MacCoss, Michael

    2015-09-01

    In mass spectrometry-based bottom-up proteomics, data-independent acquisition (DIA) is an emerging technique due to its comprehensive and unbiased sampling of precursor ions. However, current DIA methods use wide precurs