High Resolution Mass Spectra Analysis with a Programmable Calculator.

ERIC Educational Resources Information Center

Holdsworth, David K.

1980-01-01

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

Characterization of the sources and processes of organic and inorganic aerosols in New York City with a high-resolution time-of-flight aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Sun, Y.-L.; Zhang, Q.; Schwab, J. J.; Demerjian, K. L.; Chen, W.-N.; Bae, M.-S.; Hung, H.-M.; Hogrefe, O.; Frank, B.; Rattigan, O. V.; Lin, Y.-C.

2010-10-01

Submicron aerosol particles (PM1) were measured in-situ using a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) during the summer 2009 Field Intensive Study at Queens College in New York City. Organic aerosol (OA) and sulfate are the two dominant species, accounting for 54% and 24%, respectively, of total PM1 mass on average. The average mass size distribution of OA presents a small mode peaking at ~150 nm (Dva) in addition to an accumulation mode (~550 nm) that is internally mixed with sulfate, nitrate, and ammonium. The diurnal cycles of sulfate and OA both show pronounced peaks between 01:00-02:00 p.m. EST due to photochemical production. The average (±1σ) oxygen-to-carbon (O/C), hydrogen-to-carbon (H/C), and nitrogen-to-carbon (N/C) ratios of OA in NYC are 0.36 (±0.09), 1.49 (±0.08), and 0.012(±0.005), respectively, corresponding to an average organic mass-to-carbon (OM/OC) ratio of 1.62(±0.11). Positive matrix factorization (PMF) of the high resolution mass spectra identified five OA components: a hydrocarbon-like OA (HOA), two types of oxygenated OA (OOA) including a low-volatility OOA (LV-OOA) and a semi-volatile OOA (SV-OOA), a cooking-emission related OA (COA), and a unique nitrogen-enriched OA (NOA). HOA appears to represent primary OA (POA) from urban traffic emissions. It comprises primarily of reduced species (H/C=1.83; O/C=0.06) and shows a mass spectral pattern very similar to those of POA from fossil fuel combustion, and correlates tightly with traffic emission tracers including elemental carbon and NOx. LV-OOA, which is highly oxidized (O/C=0.63) and correlates well with sulfate, appears to be representative for regional, aged secondary OA (SOA). SV-OOA, which is less oxidized (O/C=0.38) and correlates well with non-refractory chloride, likely represents less photo-chemically aged, semi-volatile SOA. COA shows a similar spectral pattern to the reference spectra of POA from cooking emissions and a distinct diurnal pattern

OAS :: Our History

Science.gov Websites

institutions in different spheres. The Conferences of American States met at varying intervals until, in 1970 English Español Português Français Search OAS Logo OAS Logo Home button About the OAS Who We Are What We Do Our Structure Our Locations Contact Us Access to Information Offices in the Member

Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra.

PubMed

Yang, Xiaoyu; Neta, Pedatsur; Stein, Stephen E

2017-11-01

Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS 2 spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS 3 and MS 4 spectra. These can assist the chemical identification process. A simple density-based clustering algorithm was used to cluster all significant precursor ions from MS 1 scans for an analyte acquired during an infusion experiment. The MS 2 spectra associated with these precursor ions were grouped into the same precursor clusters. Subsequently, a new top-down hierarchical divisive clustering algorithm was developed for clustering the spectra from fragmentation of ions in each precursor cluster, including the MS 2 spectra of the original precursors and of the in-source fragments as well as the MS n spectra. This algorithm starts with all the spectra of one precursor in one cluster and then separates them into sub-clusters of similar spectra based on the fragment patterns. Herein, we describe the algorithms and spectral evaluation methods for extending the library. The new library features were demonstrated by searching the high resolution spectra of E. coli extracts against the extended library, allowing identification of compounds and their in-source fragment ions in a manner that was not possible before. Graphical Abstract ᅟ.

Reanalysis of Tyrannosaurus rex Mass Spectra.

PubMed

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

2009-09-01

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

Reanalysis of Tyrannosaurus rex Mass Spectra

PubMed Central

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

2009-01-01

Asara et al. reported the detection of collagen peptides in a 68-million-year-old T. rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen. PMID:19603827

Automatic Preocessing of Impact Ionization Mass Spectra Obtained by Cassini CDA

NASA Astrophysics Data System (ADS)

Villeneuve, M.

2015-12-01

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

ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging

PubMed Central

Ma, Ze-Qiang; Chambers, Matthew C.; Ham, Amy-Joan L.; Cheek, Kristin L.; Whitwell, Corbin W.; Aerni, Hans-Rudolf; Schilling, Birgit; Miller, Aaron W.; Caprioli, Richard M.; Tabb, David L.

2011-01-01

In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search, but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu. PMID:21520941

Multispectra CWT-based algorithm (MCWT) in mass spectra for peak extraction.

PubMed

Hsueh, Huey-Miin; Kuo, Hsun-Chih; Tsai, Chen-An

2008-01-01

An important objective in mass spectrometry (MS) is to identify a set of biomarkers that can be used to potentially distinguish patients between distinct treatments (or conditions) from tens or hundreds of spectra. A common two-step approach involving peak extraction and quantification is employed to identify the features of scientific interest. The selected features are then used for further investigation to understand underlying biological mechanism of individual protein or for development of genomic biomarkers to early diagnosis. However, the use of inadequate or ineffective peak detection and peak alignment algorithms in peak extraction step may lead to a high rate of false positives. Also, it is crucial to reduce the false positive rate in detecting biomarkers from ten or hundreds of spectra. Here a new procedure is introduced for feature extraction in mass spectrometry data that extends the continuous wavelet transform-based (CWT-based) algorithm to multiple spectra. The proposed multispectra CWT-based algorithm (MCWT) not only can perform peak detection for multiple spectra but also carry out peak alignment at the same time. The author' MCWT algorithm constructs a reference, which integrates information of multiple raw spectra, for feature extraction. The algorithm is applied to a SELDI-TOF mass spectra data set provided by CAMDA 2006 with known polypeptide m/z positions. This new approach is easy to implement and it outperforms the existing peak extraction method from the Bioconductor PROcess package.

Dereplication of peptidic natural products through database search of mass spectra

PubMed Central

Mohimani, Hosein; Gurevich, Alexey; Mikheenko, Alla; Garg, Neha; Nothias, Louis-Felix; Ninomiya, Akihiro; Takada, Kentaro; Dorrestein, Pieter C.; Pevzner, Pavel A.

2016-01-01

Peptidic Natural Products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. While recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers utilize dereplication strategies that identify known PNPs and lead to the discovery of new ones even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enabled high-throughput PNP identification and that is compatible with large-scale mass spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts. PMID:27820803

AN ION CORRELATION PROGRAM FOR DECONVOLUTING COMPOSITE MASS SPECTRA ACQUIRED USING A DIRECT SURFACE IONIZATION SOURCE INTERFACED TO A TIME-OF-FLIGHT MASS SPECTROMETER

EPA Science Inventory

The rapid sampling provided by the DART in ambient air will allow rapid delineation of areas of dispersed chemicals after natural or man-made disasters. Exact masses and RIAs of dimer, precursor, and product ions measured by the oa-TOFMS entered dinto the Ion Correlation Program...

The laser desorption/laser ionization mass spectra of some anti-inflammatory drugs

NASA Astrophysics Data System (ADS)

Milnes, John; Rogers, Kevin; Jones, Sian; Gormally, John

1994-03-01

The IR laser desorption/ultraviolet laser ionization time-of-flight mass spectra are reported for the anti-inflammatory drugs indomethacin, acemetacin, ibuprofen, flurbiprofen, diflunisal and mefenamic acid. It is found that the six compounds can be readily ionized by two photon absorption at a fixed wavelength of 266 nm. Mass spectra have been obtained under conditions of high ionizing irradiance and the observed fragmentation behaviour is discussed.

Aerosol mass spectrometric features of biogenic SOA: observations from a plant chamber and in rural atmospheric environments.

PubMed

Kiendler-Scharr, Astrid; Zhang, Qi; Hohaus, Thorsten; Kleist, Einhard; Mensah, Amewu; Mentel, Thomas F; Spindler, Christian; Uerlings, Ricarda; Tillmann, Ralf; Wildt, Jürgen

2009-11-01

Secondary organic aerosol (SOA) is known to form from a variety of anthropogenic and biogenic precursors. Current estimates of global SOA production vary over 2 orders of magnitude. Since no direct measurement technique for SOA exists, quantifying SOA remains a challenge for atmospheric studies. The identification of biogenic SOA (BSOA) based on mass spectral signatures offers the possibility to derive source information of organic aerosol (OA) with high time resolution. Here we present data from simulation experiments. The BSOA from tree emissions was characterized with an Aerodyne quadrupole aerosol mass spectrometer (Q-AMS). Collection efficiencies were close to 1, and effective densities of the BSOA were found to be 1.3 +/- 0.1 g/cm(3). The mass spectra of SOA from different trees were found to be highly similar. The average BSOA mass spectrum from tree emissions is compared to a BSOA component spectrum extracted from field data. It is shown that overall the spectra agree well and that the mass spectral features of BSOA are distinctively different from those of OA components related to fresh fossil fuel and biomass combustions. The simulation chamber mass spectrum may potentially be useful for the identification and interpretation of biogenic SOA components in ambient data sets.

Reproducing impact ionization mass spectra of E and F ring ice grains at different impact speeds

NASA Astrophysics Data System (ADS)

Klenner, F.; Reviol, R.; Postberg, F.

2017-09-01

As impact speeds of E and F ring ice grains impinging onto the target of impact ionization mass spectrometers in space can vary greatly, the resulting cationic or anionic mass spectra can have very different appearances. The mass spectra can be accurately reproduced with an analog experimental setup IR-FL-MALDI-ToF-MS (Infrared Free Liquid Matrix Assisted Laser Desorption and Ionization Time of Flight Mass Spectrometry). We compare mass spectra of E and F ring ice grains taken by the Cosmic Dust Analyzer (CDA) onboard Cassini recorded at different impact speeds with our analog spectra and prove the capability of the analog experiment.

Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madar, Inamul Hasan; Ko, Seung-Ik; Kim, Hokeun

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. Themore » method, “multiplexed post-experiment monoisotopic mass refinement” (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/ MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, mPE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods.« less

TANDEM: matching proteins with tandem mass spectra.

PubMed

Craig, Robertson; Beavis, Ronald C

2004-06-12

Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.

Mass spectra and decay properties of the c\\bar{c} meson

NASA Astrophysics Data System (ADS)

Chaturvedi, Raghav; Kumar Rai, Ajay

2018-06-01

In this article we present the result of c\\bar{c} meson mass calculation by solving the Schrödinger equation numerically considering the Coulomb plus linear potential. The spin-hyperfine, spin-orbit and tensor components of one-gluon-exchange interactions are employed to obtain the mass spectra of c\\bar{c} meson. The calculated mass spectra are compared with the latest results of PDG and are found to be in good accordance. The Regge trajectories of the calculated mass spectra have also been constructed. The values of the wave function are extracted and employed to calculate the leptonic decay constant, γγ, gg, e+e-, light hadron (LH) and γγγ decay widths of S-wave 0^{-+} and 1^{- -} states of c\\bar{c} meson, the widths have been calculated by Van Royen-Weisskopf formula and by NRQCD mechanism incorporating relativistic corrections of order ν2. The γγ and gg decay widths of χ0 and χ2 states of c\\bar{c} meson have also been calculated. The calculated decay constants and widths have been compared with the experimental results.

NIST Libraries of Peptide Fragmentation Mass Spectra Databass

National Institute of Standards and Technology Data Gateway

SRD 4 NIST Libraries of Peptide Fragmentation Mass Spectra Databass (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

STRAPS v1.0: Evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Topping, David; Allan, James; Alfarra, Rami; Aumont, Bernard

2017-04-01

Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA) formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS) are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and O:C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof of concept study, the ability to train supervised methods to predict electron impact ionisation (EI) mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS), is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m/z) channels are fit as a function of molecular structure before the relative peak height for each channel is similarly fit using a range of regression methods. The widely-used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Initial results suggest the generic public 'MACCS' fingerprints provide the most accurate trained model when combined with both decision trees and random forests with median

How to Compute Electron Ionization Mass Spectra from First Principles.

PubMed

Bauer, Christoph Alexander; Grimme, Stefan

2016-06-02

The prediction of electron ionization (EI) mass spectra (MS) from first principles has been a major challenge for quantum chemistry (QC). The unimolecular reaction space grows rapidly with increasing molecular size. On the one hand, statistical models like Eyring's quasi-equilibrium theory and Rice-Ramsperger-Kassel-Marcus theory have provided valuable insight, and some predictions and quantitative results can be obtained from such calculations. On the other hand, molecular dynamics-based methods are able to explore automatically the energetically available regions of phase space and thus yield reaction paths in an unbiased way. We describe in this feature article the status of both methodologies in relation to mass spectrometry for small to medium sized molecules. We further present results obtained with the QCEIMS program developed in our laboratory. Our method, which incorporates stochastic and dynamic elements, has been a significant step toward the reliable routine calculation of EI mass spectra.

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

PubMed Central

2015-01-01

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification.

PubMed

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

2016-08-02

We describe a tool, competitive fragmentation modeling for electron ionization (CFM-EI) that, given a chemical structure (e.g., in SMILES or InChI format), computationally predicts an electron ionization mass spectrum (EI-MS) (i.e., the type of mass spectrum commonly generated by gas chromatography mass spectrometry). The predicted spectra produced by this tool can be used for putative compound identification, complementing measured spectra in reference databases by expanding the range of compounds able to be considered when availability of measured spectra is limited. The tool extends CFM-ESI, a recently developed method for computational prediction of electrospray tandem mass spectra (ESI-MS/MS), but unlike CFM-ESI, CFM-EI can handle odd-electron ions and isotopes and incorporates an artificial neural network. Tests on EI-MS data from the NIST database demonstrate that CFM-EI is able to model fragmentation likelihoods in low-resolution EI-MS data, producing predicted spectra whose dot product scores are significantly better than full enumeration "bar-code" spectra. CFM-EI also outperformed previously reported results for MetFrag, MOLGEN-MS, and Mass Frontier on one compound identification task. It also outperformed MetFrag in a range of other compound identification tasks involving a much larger data set, containing both derivatized and nonderivatized compounds. While replicate EI-MS measurements of chemical standards are still a more accurate point of comparison, CFM-EI's predictions provide a much-needed alternative when no reference standard is available for measurement. CFM-EI is available at https://sourceforge.net/projects/cfm-id/ for download and http://cfmid.wishartlab.com as a web service.

Automated tandem mass spectrometry by orthogonal acceleration TOF data acquisition and simultaneous magnet scanning for the characterization of petroleum mixtures.

PubMed

Roussis, S G

2001-08-01

The automated acquisition of the product ion spectra of all precursor ions in a selected mass range by using a magnetic sector/orthogonal acceleration time-of-flight (oa-TOF) tandem mass spectrometer for the characterization of complex petroleum mixtures is reported. Product ion spectra are obtained by rapid oa-TOF data acquisition and simultaneous scanning of the magnet. An analog signal generator is used for the scanning of the magnet. Slow magnet scanning rates permit the accurate profiling of precursor ion peaks and the acquisition of product ion spectra for all isobaric ion species. The ability of the instrument to perform both high- and low-energy collisional activation experiments provides access to a large number of dissociation pathways useful for the characterization of precursor ions. Examples are given that illustrate the capability of the method for the characterization of representative petroleum mixtures. The structural information obtained by the automated MS/MS experiment is used in combination with high-resolution accurate mass measurement results to characterize unknown components in a polar extract of a refinery product. The exhaustive mapping of all precursor ions in representative naphtha and middle-distillate fractions is presented. Sets of isobaric ion species are separated and their structures are identified by interpretation from first principles or by comparison with standard 70-eV EI libraries of spectra. The utility of the method increases with the complexity of the samples.

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.

PubMed

Falkner, Jayson; Andrews, Philip

2005-05-15

Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. This problem deserves attention as new mass spectrometers provide the ability for higher throughput and as known protein datasets rapidly grow in size. New software algorithms need to be devised in order to address the performance issues of conventional MSMS protein dataset-based protein identification. This paper describes a novel algorithm based on converting a collection of monoisotopic, centroided spectra to a new data structure, named 'peptide finite state machine' (PFSM), which may be used to rapidly search a known dataset of protein sequences, regardless of the number of spectra searched or the number of potential modifications examined. The algorithm is verified using a set of commercially available tryptic digest protein standards analyzed using an ABI 4700 MALDI TOFTOF mass spectrometer, and a free, open source PFSM implementation. It is illustrated that a PFSM can accurately search large collections of spectra against large datasets of protein sequences (e.g. NCBI nr) using a regular desktop PC; however, this paper only details the method for identifying peptide and subsequently protein candidates from a dataset of known protein sequences. The concept of using a PFSM as a peptide pre-screening technique for MSMS-based search engines is validated by using PFSM with Mascot and XTandem. Complete source code, documentation and examples for the reference PFSM implementation are freely available at the Proteome Commons, http://www.proteomecommons.org and source code may be used both commercially and non-commercially as long as the original authors are credited for their work.

OAS -- Americas Magazine

Science.gov Websites

performance in promoting the ideals and goals of the OAS. Américas will continue to fulfill requests for back English Español Americas Magazine Banner Americas Magazine Main Site OAS Main Site Home Back magazine. The last issue published was Volume 64, Number 3 (May/June) 2012. Beginning in 1949, Américas, a

Optical and Near-infrared Spectra of σ Orionis Isolated Planetary-mass Objects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zapatero Osorio, M. R.; Béjar, V. J. S.; Ramírez, K. Peña, E-mail: mosorio@cab.inta-csic.es, E-mail: vbejar@iac.es, E-mail: karla.pena@uantof.cl

We have obtained low-resolution optical (0.7–0.98 μ m) and near-infrared (1.11–1.34 μ m and 0.8–2.5 μ m) spectra of 12 isolated planetary-mass candidates ( J = 18.2–19.9 mag) of the 3 Myr σ Orionis star cluster with the aim of determining the spectroscopic properties of very young, substellar dwarfs and assembling a complete cluster mass function. We have classified our targets by visual comparison with high- and low-gravity standards and by measuring newly defined spectroscopic indices. We derived L0–L4.5 and M9–L2.5 using high- and low-gravity standards, respectively. Our targets reveal clear signposts of youth, thus corroborating their cluster membership andmore » planetary masses (6–13 M {sub Jup}). These observations complete the σ Orionis mass function by spectroscopically confirming the planetary-mass domain to a confidence level of ∼75%. The comparison of our spectra with BT-Settl solar metallicity model atmospheres yields a temperature scale of 2350–1800 K and a low surface gravity of log g ≈ 4.0 [cm s{sup −2}], as would be expected for young planetary-mass objects. We discuss the properties of the cluster’s least-massive population as a function of spectral type. We have also obtained the first optical spectrum of S Ori 70, a T dwarf in the direction of σ Orionis. Our data provide reference optical and near-infrared spectra of very young L dwarfs and a mass function that may be used as templates for future studies of low-mass substellar objects and exoplanets. The extrapolation of the σ Orionis mass function to the solar neighborhood may indicate that isolated planetary-mass objects with temperatures of ∼200–300 K and masses in the interval 6–13 M {sub Jup} may be as numerous as very low-mass stars.« less

Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra.

PubMed

Jaeger, Carsten; Méret, Michaël; Schmitt, Clemens A; Lisec, Jan

2017-08-15

A bottleneck in metabolic profiling of complex biological extracts is confident, non-supervised annotation of ideally all contained, chemically highly diverse small molecules. Recent computational strategies combining sum formula prediction with in silico fragmentation achieve confident de novo annotation, once the correct neutral mass of a compound is known. Current software solutions for automated adduct ion assignment, however, are either publicly unavailable or have been validated against only few experimental electrospray ionization (ESI) mass spectra. We here present findMAIN (find Main Adduct IoN), a new heuristic approach for interpreting ESI mass spectra. findMAIN scores MS 1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related ionization products and annotates peaks of the (de)protonated molecule and adduct ions. The approach was validated against 1141 ESI positive mode spectra of chemically diverse standard compounds acquired on different high-resolution mass spectrometric instruments (Orbitrap and time-of-flight). Robustness against impure spectra was evaluated. Correct adduct ion assignment was achieved for up to 83% of the spectra. Performance was independent of compound class and mass spectrometric platform. The algorithm proved highly tolerant against spectral contamination as demonstrated exemplarily for co-eluting compounds as well as systematically by pairwise mixing of spectra. When used in conjunction with MS-FINDER, a state-of-the-art sum formula tool, correct sum formulas were obtained for 77% of spectra. It outperformed both 'brute force' approaches and current state-of-the-art annotation packages tested as potential alternatives. Limitations of the heuristic pertained to poorly ionizing compounds and cationic compounds forming [M] + ions. A new, validated approach for interpreting ESI mass spectra is presented, filling a gap in the nontargeted metabolomics workflow. It is freely available

Unexpected peaks in tandem mass spectra due to reaction of product ions with residual water in mass spectrometer collision cells.

PubMed

Neta, Pedatsur; Farahani, Mahnaz; Simón-Manso, Yamil; Liang, Yuxue; Yang, Xiaoyu; Stein, Stephen E

2014-12-15

Certain product ions in electrospray ionization tandem mass spectrometry are found to react with residual water in the collision cell. This reaction often leads to the formation of ions that cannot be formed directly from the precursor ions, and this complicates the mass spectra and may distort MRM (multiple reaction monitoring) results. Various drugs, pesticides, metabolites, and other compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, IT, and Orbitrap HCD). Certain product ions were found to react with residual water in collision cells. The reaction was confirmed by MS(n) studies and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Examples of product ions reacting with water include phenyl and certain substituted phenyl cations, benzoyl-type cations formed from protonated folic acid and similar compounds by loss of the glutamate moiety, product ions formed from protonated cyclic siloxanes by loss of methane, product ions formed from organic phosphates, and certain negative ions. The reactions of product ions with residual water varied greatly in their rate constant and in the extent of reaction (due to isomerization). Various types of product ions react with residual water in mass spectrometer collision cells. As a result, tandem mass spectra may contain unexplained peaks and MRM results may be distorted by the occurrence of such reactions. These often unavoidable reactions must be taken into account when annotating peaks in tandem mass spectra and when interpreting MRM results. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

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

PubMed

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

2015-12-01

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

Elemental ratio measurements of organic compounds using aerosol mass spectrometry: characterization, improved calibration, and implications

DOE PAGES

Canagaratna, M. R.; Jimenez, J. L.; Kroll, J. H.; ...

2014-07-31

Elemental compositions of organic aerosol (OA) particles provide useful constraints on OA sources, chemical evolution, and effects. The Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA elemental composition. This study evaluates AMS measurements of atomic oxygen-to-carbon (O : C), hydrogen-to-carbon (H : C), organic mass-to-organic carbon (OM : OC), and carbon oxidation state (OS C) for a vastly expanded laboratory dataset of multifunctional oxidized OA standards. For the expanded standard dataset, the "Aiken-Explicit" method (Aiken et al., 2008), which uses experimentally measured ion intensities at all ions to determine elemental ratios, reproduces known molecular Omore » : C and H : C ratio values within 20% (average absolute value of relative errors) and 12% respectively. The more commonly used "Aiken-Ambient" method, which uses empirically estimated H 2O + and CO + ion intensities to avoid gas phase air interferences at these ions, reproduces O : C and H : C of multifunctional oxidized species within 28% and 14% of known values. These values are systematically biased low, however, with larger biases observed for alcohols and simple diacids. A detailed examination of the H 2O +, CO +, and CO 2 + fragments in the high-resolution mass spectra of the standard compounds indicates that the Aiken-Ambient method underestimates the CO + and H 2O + produced from many oxidized species. Combined AMS-vacuum ultraviolet (VUV) ionization measurements indicate that these ions are produced by dehydration and decarboxylation on the AMS vaporizer (usually operated at 600 °C). Thermal decomposition is observed to be efficient at vaporizer temperatures down to 200 °C. These results are used together to develop an "Improved-Ambient" elemental analysis method for AMS spectra measured in air. The Improved-Ambient method reduces the systematic biases and reproduces O : C (H : C) ratios of individual oxidized standards

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

NASA Astrophysics Data System (ADS)

Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra.

PubMed

Hogan, John D; Klein, Joshua A; Wu, Jiandong; Chopra, Pradeep; Boons, Geert-Jan; Carvalho, Luis; Lin, Cheng; Zaia, Joseph

2018-04-03

Glycosaminoglycans (GAGs) covalently linked to proteoglycans (PGs) are characterized by repeating disaccharide units and variable sulfation patterns along the chain. GAG length and sulfation patterns impact disease etiology, cellular signaling, and structural support for cells. We and others have demonstrated the usefulness of tandem mass spectrometry (MS2) for assigning the structures of GAG saccharides; however, manual interpretation of tandem mass spectra is time-consuming, so computational methods must be employed. In the proteomics domain, the identification of monoisotopic peaks and charge states relies on algorithms that use averagine, or the average building block of the compound class being analyzed. While these methods perform well for protein and peptide spectra, they perform poorly on GAG tandem mass spectra, due to the fact that a single average building block does not characterize the variable sulfation of GAG disaccharide units. In addition, it is necessary to assign product ion isotope patterns in order to interpret the tandem mass spectra of GAG saccharides. To address these problems, we developed GAGfinder, the first tandem mass spectrum peak finding algorithm developed specifically for GAGs. We define peak finding as assigning experimental isotopic peaks directly to a given product ion composition, as opposed to deconvolution or peak picking, which are terms more accurately describing the existing methods previously mentioned. GAGfinder is a targeted, brute force approach to spectrum analysis that utilizes precursor composition information to generate all theoretical fragments. GAGfinder also performs peak isotope composition annotation, which is typically a subsequent step for averagine-based methods. Data are available via ProteomeXchange with identifier PXD009101. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Fast Airborne Aerosol Size and Chemistry Measurements with the High Resolution Aerosol Mass Spectrometer during the MILAGRO Campaign

NASA Technical Reports Server (NTRS)

DeCarlo, P. F.; Dunlea, E. J.; Kimmel, J. R.; Aiken, A. C.; Sueper, D.; Crounse, J.; Wennberg, P. O.; Emmons, L.; Shinozuka, Y.; Clarke, A.;

Chemical characterization of long-range transport biomass burning emissions to the Himalayas: insights from high-resolution aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Xinghua; Xu, Jianzhong; Kang, Shichang; Liu, Yanmei; Zhang, Qi

2018-04-01

An intensive field measurement was conducted at a remote, background, high-altitude site (Qomolangma Station, QOMS, 4276 m a.s.l.) in the northern Himalayas, using an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) along with other collocated instruments. The field measurement was performed from 12 April to 12 May 2016 to chemically characterize the high time-resolved submicron particulate matter (PM1) and obtain the dynamic processes (emissions, transport, and chemical evolution) of biomass burning (BB), frequently transported from South Asia to the Himalayas during pre-monsoon season. Overall, the average (±1σ) PM1 mass concentration was 4.44 (±4.54) µg m-3 for the entire study, which is comparable with those observed at other remote sites worldwide. Organic aerosol (OA) was the dominant PM1 species (accounting for 54.3 % of total PM1 on average) followed by black carbon (BC) (25.0 %), sulfate (9.3 %), ammonium (5.8 %), nitrate (5.1 %), and chloride (0.4 %). The average size distributions of PM1 species all peaked at an overlapping accumulation mode (˜ 500 nm), suggesting that aerosol particles were internally well-mixed and aged during long-range transport. Positive matrix factorization (PMF) analysis on the high-resolution organic mass spectra identified three distinct OA factors, including a BB-related OA (BBOA, 43.7 %), a nitrogen-containing OA (NOA, 13.9 %) and a more-oxidized oxygenated OA (MO-OOA, 42.4 %). Two polluted episodes with enhanced PM1 mass loadings and elevated BBOA contributions from the west and southwest of QOMS during the study were observed. A typical BB plume was investigated in detail to illustrate the chemical evolution of aerosol characteristics under distinct air mass origins, meteorological conditions, and atmospheric oxidation processes.

Determination of effective mass of heavy hole from phonon-assisted excitonic luminescence spectra in ZnO

NASA Astrophysics Data System (ADS)

Shi, S. L.; Xu, S. J.

2011-03-01

Longitudinal optical (LO) phonon-assisted luminescence spectra of free excitons in high-quality ZnO crystal were investigated both experimentally and theoretically. By using the rigorous Segall-Mahan model based on the Green's function, good agreement between the experimental emission spectra involving one or two LO phonons and theoretical spectra can be achieved when only one adjustable parameter (effective mass of heavy hole) was adopted. This leads to determination of the heavy-hole effective mass mh⊥ = (0.8 m0 and mh∥ = 5.0 m0) in ZnO. Influence of anisotropic effective masses of heavy holes on the phonon sidebands is also discussed.

Pre-processing liquid chromatography/high-resolution mass spectrometry data: extracting pure mass spectra by deconvolution from the invariance of isotopic distribution.

PubMed

Krishnan, Shaji; Verheij, Elwin E R; Bas, Richard C; Hendriks, Margriet W B; Hankemeier, Thomas; Thissen, Uwe; Coulier, Leon

2013-05-15

Mass spectra obtained by deconvolution of liquid chromatography/high-resolution mass spectrometry (LC/HRMS) data can be impaired by non-informative mass-over-charge (m/z) channels. This impairment of mass spectra can have significant negative influence on further post-processing, like quantification and identification. A metric derived from the knowledge of errors in isotopic distribution patterns, and quality of the signal within a pre-defined mass chromatogram block, has been developed to pre-select all informative m/z channels. This procedure results in the clean-up of deconvoluted mass spectra by maintaining the intensity counts from m/z channels that originate from a specific compound/molecular ion, for example, molecular ion, adducts, (13) C-isotopes, multiply charged ions and removing all m/z channels that are not related to the specific peak. The methodology has been successfully demonstrated for two sets of high-resolution LC/MS data. The approach described is therefore thought to be a useful tool in the automatic processing of LC/HRMS data. It clearly shows the advantages compared to other approaches like peak picking and de-isotoping in the sense that all information is retained while non-informative data is removed automatically. Copyright © 2013 John Wiley & Sons, Ltd.

Mass spectra features of biomass burning boiler and coal burning boiler emitted particles by single particle aerosol mass spectrometer.

PubMed

Xu, Jiao; Li, Mei; Shi, Guoliang; Wang, Haiting; Ma, Xian; Wu, Jianhui; Shi, Xurong; Feng, Yinchang

2017-11-15

In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges. In conclusion, BBB sample mostly consists of OC and EC containing particles, and a small fraction of K-rich particles in the size range of 0.2-0.5μm. In 0.5-1.0μm, BBB sample consists of EC, OC, K-rich and Al_Silicate containing particles; CBB sample consists of EC, ECOC containing particles, while Al_Silicate (including Al_Ca_Ti_Silicate, Al_Ti_Silicate, Al_Silicate) containing particles got higher fractions as size increase. The similarity of single particle mass spectrum signatures between two samples were studied by analyzing the dot product, results indicated that part of the single particle mass spectra of two samples in the same size range are similar, which bring challenge to the future source apportionment activity by using single particle aerosol mass spectrometer. Results of this study will provide physicochemical information of important sources which contribute to particle pollution, and will support source apportionment activities. Copyright © 2017. Published by Elsevier B.V.

STRAPS v1.0: evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Topping, David O.; Allan, James; Rami Alfarra, M.; Aumont, Bernard

2017-06-01

Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA) formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS) are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and the O : C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof-of-concept study, the ability to train supervised methods to predict electron impact ionisation (EI) mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS) is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m/z) channels is fitted as a function of molecular structure before the relative peak height for each channel is similarly fitted using a range of regression methods. The widely used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Our approach relies on using supervised methods to automatically optimise the relationship between spectral characteristics and these molecular fingerprints. Therefore

Associations Between Fat Mass, Lean Mass, and Knee Osteoarthritis: The Fifth Korean National Health and Nutrition Examination Survey (KNHANES V).

PubMed

Kim, Seong Rae; Choi, Kyung-Hyun; Jung, Go-Un; Shin, Doosup; Kim, Kyuwoong; Park, Sang Min

2016-12-01

As little is known about the associations between body composition (fat mass and lean mass) and knee OA, especially regarding body parts (upper body and lower limbs), the purpose of this study was to identify the association between the former and the prevalence of the latter according to body parts. This study was designed as a cross-sectional analysis, with 4194 people (1801 men and 2393 women) from the fifth Korean National Health and Nutrition Examination Survey (KNHANES V, 2010-2011) included. Body composition (fat mass and lean mass) was measured by using dual-energy X-ray absorptiometry, and knee OA was diagnosed based on the level of Kellgren-Lawrence grade. In multivariate logistic regression analysis, upper body composition was not significantly correlated with radiographic knee OA (P > 0.05), while participants with higher lean mass of lower limbs were less likely to have radiographic knee OA (aOR 0.57; 95 % CI 0.32-0.99). In stratified analysis, participants with higher lean mass of lower limbs were less likely to have a radiographic knee OA in 40-54 kg (P for trend = 0.05) and 55-70 kg stratum (P for trend = 0.03), while this trend slightly attenuated in 70-85 kg stratum (P for trend = 0.15). In conclusion, the increase in lean mass of lower limbs is inversely related to the prevalence of knee OA while upper body composition is not. This study suggests that the lean mass of lower limbs might be associated with reduction in the risk of knee OA.

Mono-isotope Prediction for Mass Spectra Using Bayes Network.

PubMed

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

2014-12-01

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

The role of imaging in early hip OA.

PubMed

Siebelt, M; Agricola, R; Weinans, H; Kim, Y J

2014-10-01

Hip osteoarthritis (OA) is characterized by cartilage degradation, subchondral bone sclerosis and osteophyte formation. Nowadays, OA is thought to develop via different etiologies that all lead to a similar form of end stage joint degradation. One of these subtypes is related to an abnormal shaped hip joint, like acetabular dysplasia and a cam deformity. These bony abnormalities are highly predictive for development of hip OA, but they are likely to already be present from childhood. This suggests that these deformations induce OA changes in the hip, well before extensive hip degradation becomes present three to four decades later. Accurate detection and successful characterization of these early OA events might lead to better treatment options for hip OA besides nowadays available invasive joint replacement surgery. However, current diagnostic imaging techniques like radiographs or plain magnetic resonance imaging (MRI), are not sensitive enough to detect these subtle early OA changes. Nor are they able to disentangle intertwined and overlapping cascades from different OA subtypes, and neither can they predict OA progression. New and more sensitive imaging techniques might enable us to detect first OA changes on a cellular level, providing us with new opportunities for early intervention. In this respect, shape analysis using radiography, MRI, computed tomography (CT), single photon emission computed tomography (SPECT)/CT, and positron emission tomography (PET) might prove promising techniques and be more suited to detect early pathological changes in the hip joint. A broad application of these techniques might give us more understanding what can be considered physiological adaptation of the hip, or when early OA really starts. With a more clear definition of early OA, more homogenous patient populations can be selected and help with the development of new disease modifying OA interventions. Copyright © 2014 Osteoarthritis Research Society International

Influence of site and soil properties on the DRIFT spectra of northern cold-region soils [Influence of site and soil properties on the mid-infrared spectra of northern cold-region soils

DOE PAGES

Matamala, Roser; Calderon, Francisco J.; Jastrow, Julie D.; ...

2017-06-05

Here, we investigated the influence of site characteristics and soil properties on the chemical composition of organic matter in soils collected from a latitudinal transect across Alaska through analysis of diffuse reflectance Fourier transform mid infrared (MidIR) spectra of bulk soils. The study included 119 soil samples collected from 28 sites including tundra, boreal forest, and grassland ecosystems. Organic, mineral, and cryoturbated soil horizons, both seasonally and perennially frozen, from a variety of depths and edaphic conditions were examined. The amount and chemical composition of organic matter as well as site and soil properties exerted a strong influence on themore » MidIR spectra. The spectra were highly sensitive to the extent of organic matter decomposition, enabling the ordination of Oi, Oe and Oa organic horizons. Differences in absorbance intensity for several spectral bands indicated that Oi horizons contained greater abundance of relatively fresh residues, phenolic-OH compounds, aliphatic compounds (waxes, lipids and fats), and carbohydrates. In contrast, Oa horizons had a greater presence of amide groups (possibly from microbial residues), aromatics, C=C bonds, carboxylates and carboxylic acids. Another significant factor differentiating these horizons was the incorporation of clays and silicates into the decomposing organic matter of Oa horizons. Calculated height peak ratios showed a clear trend to greater decomposition among Oi, Oe and Oa. The MidIR spectra were related to many site/soil attributes including land cover type, parent material, and associated factors, such as permafrost presence/absence, soil drainage, horizon depth, bulk density, cation exchange capacity, and pH. Single MidIR spectral bands were identified that might be used in future studies to quickly estimate the organic and inorganic carbon, total nitrogen, and carbon:nitrogen ratios of soils from northern latitudes. Lastly, our results demonstrate that the

Influence of site and soil properties on the DRIFT spectra of northern cold-region soils [Influence of site and soil properties on the mid-infrared spectra of northern cold-region soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matamala, Roser; Calderon, Francisco J.; Jastrow, Julie D.

Here, we investigated the influence of site characteristics and soil properties on the chemical composition of organic matter in soils collected from a latitudinal transect across Alaska through analysis of diffuse reflectance Fourier transform mid infrared (MidIR) spectra of bulk soils. The study included 119 soil samples collected from 28 sites including tundra, boreal forest, and grassland ecosystems. Organic, mineral, and cryoturbated soil horizons, both seasonally and perennially frozen, from a variety of depths and edaphic conditions were examined. The amount and chemical composition of organic matter as well as site and soil properties exerted a strong influence on themore » MidIR spectra. The spectra were highly sensitive to the extent of organic matter decomposition, enabling the ordination of Oi, Oe and Oa organic horizons. Differences in absorbance intensity for several spectral bands indicated that Oi horizons contained greater abundance of relatively fresh residues, phenolic-OH compounds, aliphatic compounds (waxes, lipids and fats), and carbohydrates. In contrast, Oa horizons had a greater presence of amide groups (possibly from microbial residues), aromatics, C=C bonds, carboxylates and carboxylic acids. Another significant factor differentiating these horizons was the incorporation of clays and silicates into the decomposing organic matter of Oa horizons. Calculated height peak ratios showed a clear trend to greater decomposition among Oi, Oe and Oa. The MidIR spectra were related to many site/soil attributes including land cover type, parent material, and associated factors, such as permafrost presence/absence, soil drainage, horizon depth, bulk density, cation exchange capacity, and pH. Single MidIR spectral bands were identified that might be used in future studies to quickly estimate the organic and inorganic carbon, total nitrogen, and carbon:nitrogen ratios of soils from northern latitudes. Lastly, our results demonstrate that the

Long-range transport biomass burning emissions to the Himalayas: insights from high-resolution aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Xu, J.; Zhang, X.; Liu, Y.; Shichang, K.; Ma, Y.

2017-12-01

An intensive measurement was conducted at a remote, background, and high-altitude site (Qomolangma station, QOMS, 4276 m a.s.l.) in the northern Himalayas, using an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) along with other collocated instruments. The field measurement was performed from April 12 to May 12, 2016 to chemically characterize high time-resolved submicron particulate matter (PM1) and obtain the influence of biomass burning emissions to the Himalayas, frequently transported from south Asia during pre-monsoon season. Two high aerosol loading periods were observed during the study. Overall, the average (± 1σ) PM1 mass concentration was 4.44 (± 4.54) µg m-3 for the entire study, comparable with those observed at other remote sites worldwide. Organic aerosols (OA) was the dominant PM1 species (accounting for 54.3% of total PM1 mass on average) and its contribution increased with the increase of total PM1 mass loading. The average size distributions of PM1 species all peaked at an overlapping accumulation mode ( 500 nm), suggesting that aerosol particles were internally well-mixed and aged during long-range transportations. Positive matrix factorization (PMF) analysis on the high-resolution organic mass spectra identified three distinct OA factors, including a biomass burning related OA (BBOA, 43.7%) and two oxygenated OA (Local-OOA and LRT-OOA; 13.9% and 42.4%) represented sources from local emissions and long-range transportations, respectively. Two polluted air mass origins (generally from the west and southwest of QOMS) and two polluted episodes with enhanced PM1 mass loadings and elevated BBOA contributions were observed, respectively, suggesting the important sources of wildfires from south Asia. One of polluted aerosol plumes was investigated in detail to illustrate the evolution of aerosol characteristics at QOMS driving by different impacts of wildfires, air mass origins, meteorological conditions and

Elemental ratio measurements of organic compounds using aerosol mass spectrometry: Characterization, improved calibration, and implications

DOE PAGES

Canagaratna, M. R.; Jimenez, J. L.; Kroll, J. H.; ...

2015-01-12

Elemental compositions of organic aerosol (OA) particles provide useful constraints on OA sources, chemical evolution, and effects. The Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA elemental composition. This study evaluates AMS measurements of atomic oxygen-to-carbon (O : C), hydrogen-to-carbon (H : C), and organic mass-to-organic carbon (OM : OC) ratios, and of carbon oxidation state (OS C) for a vastly expanded laboratory data set of multifunctional oxidized OA standards. For the expanded standard data set, the method introduced by Aiken et al. (2008), which uses experimentally measured ion intensities at all ions to determinemore » elemental ratios (referred to here as "Aiken-Explicit"), reproduces known O : C and H : C ratio values within 20% (average absolute value of relative errors) and 12%, respectively. The more commonly used method, which uses empirically estimated H 2O + and CO + ion intensities to avoid gas phase air interferences at these ions (referred to here as "Aiken-Ambient"), reproduces O : C and H : C of multifunctional oxidized species within 28 and 14% of known values. The values from the latter method are systematically biased low, however, with larger biases observed for alcohols and simple diacids. A detailed examination of the H 2O +, CO +, and CO 2 + fragments in the high-resolution mass spectra of the standard compounds indicates that the Aiken-Ambient method underestimates the CO + and especially H 2O + produced from many oxidized species. Combined AMS–vacuum ultraviolet (VUV) ionization measurements indicate that these ions are produced by dehydration and decarboxylation on the AMS vaporizer (usually operated at 600 °C). Thermal decomposition is observed to be efficient at vaporizer temperatures down to 200 °C. These results are used together to develop an "Improved-Ambient" elemental analysis method for AMS spectra measured in air. The Improved-Ambient method uses

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

EPA Science Inventory

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

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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. Copyright © 2011 John Wiley & Sons, Ltd.

Activation of the 2-5OAS/RNase L pathway in CVB1 or HAV/18f infected FRhK-4 cells does not require induction of OAS1 or OAS2 expression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulka, Michael, E-mail: michael.kulka@fda.hhs.go; Calvo, Mona S., E-mail: mona.calvo@fda.hhs.go; Ngo, Diana T., E-mail: diana.ngo@fda.hhs.go

2009-05-25

The latent, constitutively expressed protein RNase L is activated in coxsackievirus and HAV strain 18f infected FRhK-4 cells. Endogenous oligoadenylate synthetase (OAS) from uninfected and virus infected cell extracts synthesizes active forms of the triphosphorylated 2-5A oligomer (the only known activator of RNase L) in vitro and endogenous 2-5A is detected in infected cell extracts. However, only the largest OAS isoform, OAS3, is readily detected throughout the time course of infection. While IFNbeta treatment results in an increase in the level of all three OAS isoforms in FRhK-4 cells, IFNbeta pretreatment does not affect the temporal onset or enhancement ofmore » RNase L activity nor inhibit virus replication. Our results indicate that CVB1 and HAV/18f activate the 2-5OAS/RNase L pathway in FRhK-4 cells during permissive infection through endogenous levels of OAS, but contrary to that reported for some picornaviruses, CVB1 and HAV/18f replication is insensitive to this activated antiviral pathway.« less

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

PubMed Central

2011-01-01

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods. PMID:22182234

Simultaneous separation and identification of limonoids from citrus using liquid chromatography-collision-induced dissociation mass spectra.

PubMed

Jayaprakasha, Guddadarangavvanahally K; Dandekar, Deepak V; Tichy, Shane E; Patil, Bhimanagouda S

2011-01-01

Limonoids are considered as potential cancer chemopreventive agents and are widely distributed in the Citrus genus as aglycones and glucosides. In the present study, reversed-phase HPLC coupled with CID mass spectra was developed for the simultaneous separation and identification of aglycones and glucosides of limonoids from citrus. Five aglycones such as limonin, deacetyl nomilin, ichangin, isolimonoic acid and nomilin were identified by positive ion CID MS/MS, whereas five glucosides, viz. limonin glucoside, isoobacunoic acid glucoside, obacunone glucoside, deacetyl nomilinic acid glucoside and nomilinic acid glucoside were analyzed by negative ion CID mass spectra. The developed method was successfully applied to complex citrus samples for the separation and identification of aglycones and glucosides. Citrus seeds were extracted with methanol and partially purified and analyzed by LC-CID mass spectra. The separation was achieved by C-18 column; eight limonoids were identified by comparing the retention times and mass spectral fragmentation. To the best of our knowledge, this is the first report on the identification of citrus limonoids using CID technique. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Baran, Richard; Northen, Trent R

2013-10-15

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

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

PubMed

Griss, Johannes; Perez-Riverol, Yasset; The, Matthew; Käll, Lukas; Vizcaíno, Juan Antonio

2018-05-04

In the recent benchmarking article entitled "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra", Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the authors clustered only single MS/MS runs. In one of the reported analyses, three MS/MS runs were processed together, which already led to computational performance issues in many of the tested approaches. This fact highlights the difficulties of using many of the tested algorithms on the nowadays produced average proteomics data sets. Second, the authors only processed identified spectra when merging MS runs. Thereby, all unidentified spectra that are of lower quality were already removed from the data set and could not influence the clustering results. Next, we found that the authors did not analyze the effect of chimeric spectra on the clustering results. In our analysis, we found that 3% of the spectra in the used data sets were chimeric, and this had marked effects on the behavior of the different clustering algorithms tested. Finally, the authors' choice to evaluate the MS-Cluster and spectra-cluster algorithms using a precursor tolerance of 5 Da for high-resolution Orbitrap data only was, in our opinion, not adequate to assess the performance of MS/MS clustering approaches.

Elemental ratio measurements of organic compounds using aerosol mass spectrometry: characterization, improved calibration, and implications

NASA Astrophysics Data System (ADS)

Canagaratna, M. R.; Jimenez, J. L.; Kroll, J. H.; Chen, Q.; Kessler, S. H.; Massoli, P.; Hildebrandt Ruiz, L.; Fortner, E.; Williams, L. R.; Wilson, K. R.; Surratt, J. D.; Donahue, N. M.; Jayne, J. T.; Worsnop, D. R.

2014-07-01

Elemental compositions of organic aerosol (OA) particles provide useful constraints on OA sources, chemical evolution, and effects. The Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA elemental composition. This study evaluates AMS measurements of atomic oxygen-to-carbon (O : C), hydrogen-to-carbon (H : C), organic mass-to-organic carbon (OM : OC), and carbon oxidation state (OSC) for a vastly expanded laboratory dataset of multifunctional oxidized OA standards. For the expanded standard dataset, the "Aiken-Explicit" method (Aiken et al., 2008), which uses experimentally measured ion intensities at all ions to determine elemental ratios, reproduces known molecular O : C and H : C ratio values within 20% (average absolute value of relative errors) and 12% respectively. The more commonly used "Aiken-Ambient" method, which uses empirically estimated H2O+ and CO+ ion intensities to avoid gas phase air interferences at these ions, reproduces O : C and H : C of multifunctional oxidized species within 28% and 14% of known values. These values are systematically biased low, however, with larger biases observed for alcohols and simple diacids. A detailed examination of the H2O+, CO+, and CO2+ fragments in the high-resolution mass spectra of the standard compounds indicates that the Aiken-Ambient method underestimates the CO+ and H2O+ produced from many oxidized species. Combined AMS-vacuum ultraviolet (VUV) ionization measurements indicate that these ions are produced by dehydration and decarboxylation on the AMS vaporizer (usually operated at 600 °C). Thermal decomposition is observed to be efficient at vaporizer temperatures down to 200 °C. These results are used together to develop an "Improved-Ambient" elemental analysis method for AMS spectra measured in air. The Improved-Ambient method reduces the systematic biases and reproduces O : C (H : C) ratios of

Development of OA Abroad and Its Inspirations

ERIC Educational Resources Information Center

Bi, Jing

2010-01-01

This study introduces the concept and characteristics of open access (OA), analyses the status quo and development of OA in foreign countries, and discusses its inspiration to its future development in China.

A new application of hierarchical cluster analysis to investigate organic peaks in bulk mass spectra obtained with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Middlebrook, A. M.; Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

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

NASA Technical Reports Server (NTRS)

Moshinsky, M.; Loyola, G.

1993-01-01

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

Separate Spectra of the Components of the Low-mass Binary L722-22

NASA Astrophysics Data System (ADS)

Chance, D.; Hershey, J.

1996-12-01

Separate spectra have been acquired of the components of the low-mass binary L722-22A,B. Using the Hubble Space Telescope Faint Object Spectrograph in the same manner described in BAAS 27,1341 for Ross 614A,B a small aperture was placed on each star, excluding the light from the other. L722-22 was discovered to be a binary by Ianna (1988, AJ 95,1226) from a small photographic photocentric orbit found in parallax observations. The ground-based work indicated L722-22B might have a mass in the brown-dwarf range, at 0.06 M_⊙ which motivated the FOS observations. However, current HST astrometric work indicates L722-22B is at the 0.1 M_⊙ level (Taff, Hershey Space Telescope Astrometry Team 75th Meeting Report, Apr 1996). Ground based CCD spectra of M dwarf standards have been provided to us by J. Davy Kirkpatrick in the 6300 to 8500 Angstroms range. Apart from the telluric lines the FOS spectra interpolate very closely into the ground-based series across this spectral range. A classification program has been written which defines a series of spectral interval ratios, does fits for the indices of the standards as a function of spectral subtype across the M3 to M7 range of standards, and inverts the fits for the four unknown spectra of Ross 614A,B and L722-22A,B. The internal formal error of the mean from the series of indices is a small fraction of a spectral subtype. The spectral types of L722-22A and B are found to be earlier by about 3/4 of a spectral subtype than Ross 614A and B, respectively. The HST astrometry and spectroscopy yield points for these 4 binary members which lie in a very narrow locus in the mass-spectral type plane and imply that single stars of types dM6 and later, have masses less than 0.08 M_⊙, presumably substellar. Support for this work was provided by NASA through grant number 06048 from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS5-26555.

A Pivotal Study of Optoacoustic Imaging to Diagnose Benign and Malignant Breast Masses: A New Evaluation Tool for Radiologists.

PubMed

Neuschler, Erin I; Butler, Reni; Young, Catherine A; Barke, Lora D; Bertrand, Margaret L; Böhm-Vélez, Marcela; Destounis, Stamatia; Donlan, Pamela; Grobmyer, Stephen R; Katzen, Janine; Kist, Kenneth A; Lavin, Philip T; Makariou, Erini V; Parris, Tchaiko M; Schilling, Kathy J; Tucker, F Lee; Dogan, Basak E

2018-05-01

Purpose To compare the diagnostic utility of an investigational optoacoustic imaging device that fuses laser optical imaging (OA) with grayscale ultrasonography (US) to grayscale US alone in differentiating benign and malignant breast masses. Materials and Methods This prospective, 16-site study of 2105 women (study period: 12/21/2012 to 9/9/2015) compared Breast Imaging Reporting and Data System (BI-RADS) categories assigned by seven blinded independent readers to benign and malignant breast masses using OA/US versus US alone. BI-RADS 3, 4, or 5 masses assessed at diagnostic US with biopsy-proven histologic findings and BI-RADS 3 masses stable at 12 months were eligible. Independent readers reviewed US images obtained with the OA/US device, assigned a probability of malignancy (POM) and BI-RADS category, and locked results. The same independent readers then reviewed OA/US images, scored OA features, and assigned OA/US POM and a BI-RADS category. Specificity and sensitivity were calculated for US and OA/US. Benign and malignant mass upgrade and downgrade rates, positive and negative predictive values, and positive and negative likelihood ratios were compared. Results Of 2105 consented subjects with 2191 masses, 100 subjects (103 masses) were analyzed separately as a training population and excluded. An additional 202 subjects (210 masses) were excluded due to technical failures or incomplete imaging, 72 subjects (78 masses) due to protocol deviations, and 41 subjects (43 masses) due to high-risk histologic results. Of 1690 subjects with 1757 masses (1079 [61.4%] benign and 678 [38.6%] malignant masses), OA/US downgraded 40.8% (3078/7535) of benign mass reads, with a specificity of 43.0% (3242/7538, 99% confidence interval [CI]: 40.4%, 45.7%) for OA/US versus 28.1% (2120/7543, 99% CI: 25.8%, 30.5%) for the internal US of the OA/US device. OA/US exceeded US in specificity by 14.9% (P < .0001; 99% CI: 12.9, 16.9%). Sensitivity for biopsied malignant masses was 96

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

NASA Astrophysics Data System (ADS)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

Elemental ratio measurements of organic compounds using aerosol mass spectrometry: characterization, improved calibration, and implications

NASA Astrophysics Data System (ADS)

Canagaratna, M. R.; Jimenez, J. L.; Kroll, J. H.; Chen, Q.; Kessler, S. H.; Massoli, P.; Hildebrandt Ruiz, L.; Fortner, E.; Williams, L. R.; Wilson, K. R.; Surratt, J. D.; Donahue, N. M.; Jayne, J. T.; Worsnop, D. R.

2015-01-01

Elemental compositions of organic aerosol (OA) particles provide useful constraints on OA sources, chemical evolution, and effects. The Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA elemental composition. This study evaluates AMS measurements of atomic oxygen-to-carbon (O : C), hydrogen-to-carbon (H : C), and organic mass-to-organic carbon (OM : OC) ratios, and of carbon oxidation state (OS C) for a vastly expanded laboratory data set of multifunctional oxidized OA standards. For the expanded standard data set, the method introduced by Aiken et al. (2008), which uses experimentally measured ion intensities at all ions to determine elemental ratios (referred to here as "Aiken-Explicit"), reproduces known O : C and H : C ratio values within 20% (average absolute value of relative errors) and 12%, respectively. The more commonly used method, which uses empirically estimated H2O+ and CO+ ion intensities to avoid gas phase air interferences at these ions (referred to here as "Aiken-Ambient"), reproduces O : C and H : C of multifunctional oxidized species within 28 and 14% of known values. The values from the latter method are systematically biased low, however, with larger biases observed for alcohols and simple diacids. A detailed examination of the H2O+, CO+, and CO2+ fragments in the high-resolution mass spectra of the standard compounds indicates that the Aiken-Ambient method underestimates the CO+ and especially H2O+ produced from many oxidized species. Combined AMS-vacuum ultraviolet (VUV) ionization measurements indicate that these ions are produced by dehydration and decarboxylation on the AMS vaporizer (usually operated at 600 °C). Thermal decomposition is observed to be efficient at vaporizer temperatures down to 200 °C. These results are used together to develop an "Improved-Ambient" elemental analysis method for AMS spectra measured in air

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.

2009-12-16

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

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

PubMed Central

2011-01-01

Background Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs. Results We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods. Conclusions This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra. PMID:22373085

A mass spectrometric system for analyzing thermal desorption spectra of ion-implanted argon and cesium in tungsten. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Wood, G. M., Jr.

1974-01-01

A mass spectrometric system for determining the characteristics of materials used in instrumental development and aerospace applications was developed. The desorption spectra of cesium that was ion-implanted into polycrystalline tungsten and the effects on the spectra of bombardment of the tungsten by low energy (70 eV) electrons were investigated. Work function changes were measured by the retarding potential diode method. Flash desorption characteristics were observed and gas-reaction mechanisms of the surface of heated metal filaments were studied. Desorption spectra were measured by linearly increasing the sample temperature at a selected rate, the temperature cycling being generated from a ramp-driven dc power supply, with the mass spectrometer tuned to a mass number of interest. Results of the study indicate an anomolous desorption mechanism following an electron bombardment of the sample surface. The enhanced spectra are a function of the post-bombardment time and energy and are suggestive of an increased concentration of cesium atoms, up to 10 or more angstroms below the surface.

Formation and reactions of negative ions relevant to chemical ionization mass spectrometry. I. Cl mass spectra of organic compounds produced by F− reactions

PubMed Central

Tiernan, T. O.; Chang, C.; Cheng, C. C.

1980-01-01

A systematic study of the negative-ion chemical ionization mass spectra produced by the reaction of F− with a wide variety of organic compounds has been accomplished. A time-of-flight mass spectrometer fitted with a modified high pressure ion source was employed for these experiments. The F− reagent ion was generated from CF3H or NF3, typically at an ion source pressure of 100 μm. In pure NF3, F− is the major ion formed and constitutes more than 90% of the total ion intensity. While F− is also the major primary ion formed in pure CF3H, it undergoes rapid ion-molecule reactions at elevated source pressures, yielding (HF)nF− (n = 1−3) ions, which makes CF3H less suitable as a chemical ionization reagent gas. Among the organic compounds investigated were carboxylic acids, ketones, aldehydes, esters, alcohols, phenols, halides, nitriles, nitrobenzene, ethers, amines and hydrocarbons. An intense (M − 1)− ion was observed in the F− chemical ionization mass spectra of carboxylic acids, ketones, aldehydes and phenols. Alcohols yield only (M + F)− ions upon reaction with F−. A weaker (M + F)− ion was also detected in the F− chemical ionization spectra of carboxylic acids, aldehydes, ketones and nitriles. The F− chemical ionization mass spectra of esters, halides, nitriles, nitrobenzene and ethers are characterized primarily by the ions, RCOO−, X−, CN−, NO2−, and OR−, respectively. In addition, esters show a very weak (M − 1)− ion (except formates). In the F− chemical ionization spectra of some aliphatic alkanes and o-xylene, a very weak (M + F)− ion was observed. Amines and aliphatic alkenes exhibit only insignificant fragment ions under similar conditions, while aromatic hydrocarbons, such as benzene and toluene are not reactive at all with the F− ion. The mechanisms of the various reactions mentioned are discussed, and several experimental complications are noted. In still other studies, the effects of varying several

Transformation of chlorinated paraffins to olefins during metal work and thermal exposure - Deconvolution of mass spectra and kinetics.

PubMed

Schinkel, Lena; Lehner, Sandro; Knobloch, Marco; Lienemann, Peter; Bogdal, Christian; McNeill, Kristopher; Heeb, Norbert V

2018-03-01

Chlorinated paraffins (CPs) are high production volume chemicals widely used as additives in metal working fluids. Thereby, CPs are exposed to hot metal surfaces which may induce degradation processes. We hypothesized that the elimination of hydrochloric acid would transform CPs into chlorinated olefins (COs). Mass spectrometry is widely used to detect CPs, mostly in the selected ion monitoring mode (SIM) evaluating 2-3 ions at mass resolutions R < 20'000. This approach is not suited to detected COs, because their mass spectra strongly overlap with CPs. We applied a mathematical deconvolution method based on full-scan MS data to separate interfered CP/CO spectra. Metal drilling indeed induced HCl-losses. CO proportions in exposed mixtures of chlorotridecanes increased. Thermal exposure of chlorotridecanes at 160, 180, 200 and 220 °C also induced dehydrohalogenation reactions and CO proportions also increased. Deconvolution of respective mass spectra is needed to study the CP transformation kinetics without bias from CO interferences. Apparent first-order rate constants (k app ) increased up to 0.17, 0.29 and 0.46 h -1 for penta-, hexa- and heptachloro-tridecanes exposed at 220 °C. Respective half-life times (τ 1/2 ) decreased from 4.0 to 2.4 and 1.5 h. Thus, higher chlorinated paraffins degrade faster than lower chlorinated ones. In conclusion, exposure of CPs during metal drilling and thermal treatment induced HCl losses and CO formation. It is expected that CPs and COs are co-released from such processes. Full-scan mass spectra and subsequent deconvolution of interfered signals is a promising approach to tackle the CP/CO problem, in case of insufficient mass resolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of Growth Medium on Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectra: a Case Study of Acetic Acid Bacteria

PubMed Central

Wieme, Anneleen D.; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita

2014-01-01

The effect of the growth medium used on the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectra generated and its consequences for species and strain level differentiation of acetic acid bacteria (AAB) were determined by using a set of 25 strains. The strains were grown on five different culture media that yielded a total of more than 600 mass spectra, including technical and biological replicates. The results demonstrate that the culture medium can have a profound effect on the mass spectra of AAB as observed in the presence and varying signal intensities of peak classes, in particular when culture media do not sustain optimal growth. The observed growth medium effects do not disturb species level differentiation but strongly affect the potential for strain level differentiation. The data prove that a well-constructed and robust MALDI-TOF mass spectrometry identification database should comprise mass spectra of multiple reference strains per species grown on different culture media to facilitate species and strain level differentiation. PMID:24362425

Protein mass spectra data analysis for clinical biomarker discovery: a global review.

PubMed

Roy, Pascal; Truntzer, Caroline; Maucort-Boulch, Delphine; Jouve, Thomas; Molinari, Nicolas

2011-03-01

The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. In recent years there has been a growing interest in using high throughput technologies for the detection of such biomarkers. In particular, mass spectrometry appears as an exciting tool with great potential. However, to extract any benefit from the massive potential of clinical proteomic studies, appropriate methods, improvement and validation are required. To better understand the key statistical points involved with such studies, this review presents the main data analysis steps of protein mass spectra data analysis, from the pre-processing of the data to the identification and validation of biomarkers.

Cluster Analysis of the Organic Peaks in Bulk Mass Spectra Obtained During the 2002 New England Air Quality Study with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M.; Bertman, S. B.; Middlebrook, A. M.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel R. H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Cluster analysis of the organic peaks in bulk mass spectra obtained during the 2002 New England Air Quality Study with an Aerodyne aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.; Middlebrook, A. M.

2006-06-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter most probably originating from both, anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent as much as 5 µg/m3 organic aerosol mass - 17% of the total organic mass - that can be attributed to biogenic sources. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

41 CFR 102-85.60 - Who can execute an OA?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Who can execute an OA... GSA SPACE Occupancy Agreement § 102-85.60 Who can execute an OA? Authorized GSA and customer agency officials who can commit or obligate the funds of their respective agencies can execute an OA. Higher level...

OAS1 Polymorphisms Are Associated with Susceptibility to West Nile Encephalitis in Horses

PubMed Central

Rios, Jonathan J.; Fleming, JoAnn G. W.; Bryant, Uneeda K.; Carter, Craig N.; Huber, John C.; Long, Maureen T.; Spencer, Thomas E.; Adelson, David L.

2010-01-01

West Nile virus, first identified within the United States in 1999, has since spread across the continental states and infected birds, humans and domestic animals, resulting in numerous deaths. Previous studies in mice identified the Oas1b gene, a member of the OAS/RNASEL innate immune system, as a determining factor for resistance to West Nile virus (WNV) infection. A recent case-control association study described mutations of human OAS1 associated with clinical susceptibility to WNV infection. Similar studies in horses, a particularly susceptible species, have been lacking, in part, because of the difficulty in collecting populations sufficiently homogenous in their infection and disease states. The equine OAS gene cluster most closely resembles the human cluster, with single copies of OAS1, OAS3 and OAS2 in the same orientation. With naturally occurring susceptible and resistant sub-populations to lethal West Nile encephalitis, we undertook a case-control association study to investigate whether, similar to humans (OAS1) and mice (Oas1b), equine OAS1 plays a role in resistance to severe WNV infection. We identified naturally occurring single nucleotide mutations in equine (Equus caballus) OAS1 and RNASEL genes and, using Fisher's Exact test, we provide evidence that mutations in equine OAS1 contribute to host susceptibility. Virtually all of the associated OAS1 polymorphisms were located within the interferon-inducible promoter, suggesting that differences in OAS1 gene expression may determine the host's ability to resist clinical manifestations associated with WNV infection. PMID:20479874

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

EPA Science Inventory

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

Quantitative determination of carbonaceous particle mixing state in Paris using single particle mass spectrometer and aerosol mass spectrometer measurements

NASA Astrophysics Data System (ADS)

Healy, R. M.; Sciare, J.; Poulain, L.; Crippa, M.; Wiedensohler, A.; Prévôt, A. S. H.; Baltensperger, U.; Sarda-Estève, R.; McGuire, M. L.; Jeong, C.-H.; McGillicuddy, E.; O'Connor, I. P.; Sodeau, J. R.; Evans, G. J.; Wenger, J. C.

2013-04-01

Single particle mixing state information can be a powerful tool for assessing the relative impact of local and regional sources of ambient particulate matter in urban environments. However, quantitative mixing state data are challenging to obtain using single particle mass spectrometers. In this study, the quantitative chemical composition of carbonaceous single particles has been estimated using an aerosol time-of-flight mass spectrometer (ATOFMS) as part of the MEGAPOLI 2010 winter campaign in Paris, France. Relative peak areas of marker ions for elemental carbon (EC), organic aerosol (OA), ammonium, nitrate, sulphate and potassium were compared with concurrent measurements from an Aerodyne high resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), a thermal/optical OCEC analyser and a particle into liquid sampler coupled with ion chromatography (PILS-IC). ATOFMS-derived mass concentrations reproduced the variability of these species well (R2 = 0.67-0.78), and ten discrete mixing states for carbonaceous particles were identified and quantified. Potassium content was used to identify particles associated with biomass combustion. The chemical mixing state of HR-ToF-AMS organic aerosol factors, resolved using positive matrix factorization, was also investigated through comparison with the ATOFMS dataset. The results indicate that hydrocarbon-like OA (HOA) detected in Paris is associated with two EC-rich mixing states which differ in their relative sulphate content, while fresh biomass burning OA (BBOA) is associated with two mixing states which differ significantly in their OA/EC ratios. Aged biomass burning OA (OOA2-BBOA) was found to be significantly internally mixed with nitrate, while secondary, oxidized OA (OOA) was associated with five particle mixing states, each exhibiting different relative secondary inorganic ion content. Externally mixed secondary organic aerosol was not observed. These findings demonstrate the heterogeneity of primary and

Quantitative determination of carbonaceous particle mixing state in Paris using single-particle mass spectrometer and aerosol mass spectrometer measurements

NASA Astrophysics Data System (ADS)

Healy, R. M.; Sciare, J.; Poulain, L.; Crippa, M.; Wiedensohler, A.; Prévôt, A. S. H.; Baltensperger, U.; Sarda-Estève, R.; McGuire, M. L.; Jeong, C.-H.; McGillicuddy, E.; O'Connor, I. P.; Sodeau, J. R.; Evans, G. J.; Wenger, J. C.

2013-09-01

Single-particle mixing state information can be a powerful tool for assessing the relative impact of local and regional sources of ambient particulate matter in urban environments. However, quantitative mixing state data are challenging to obtain using single-particle mass spectrometers. In this study, the quantitative chemical composition of carbonaceous single particles has been determined using an aerosol time-of-flight mass spectrometer (ATOFMS) as part of the MEGAPOLI 2010 winter campaign in Paris, France. Relative peak areas of marker ions for elemental carbon (EC), organic aerosol (OA), ammonium, nitrate, sulfate and potassium were compared with concurrent measurements from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), a thermal-optical OCEC analyser and a particle into liquid sampler coupled with ion chromatography (PILS-IC). ATOFMS-derived estimated mass concentrations reproduced the variability of these species well (R2 = 0.67-0.78), and 10 discrete mixing states for carbonaceous particles were identified and quantified. The chemical mixing state of HR-ToF-AMS organic aerosol factors, resolved using positive matrix factorisation, was also investigated through comparison with the ATOFMS dataset. The results indicate that hydrocarbon-like OA (HOA) detected in Paris is associated with two EC-rich mixing states which differ in their relative sulfate content, while fresh biomass burning OA (BBOA) is associated with two mixing states which differ significantly in their OA / EC ratios. Aged biomass burning OA (OOA2-BBOA) was found to be significantly internally mixed with nitrate, while secondary, oxidised OA (OOA) was associated with five particle mixing states, each exhibiting different relative secondary inorganic ion content. Externally mixed secondary organic aerosol was not observed. These findings demonstrate the range of primary and secondary organic aerosol mixing states in Paris. Examination of the temporal

OAS :: Press Releases

Science.gov Websites

General Assembly Governance H Human Development Human Rights I Indigenous Peoples Integral Development Scholarships School of Governance Science and Technology Social Development Summits of the Americas Sustainable : 1 2 Next » S-022/18 May 25, 2018 FACT SHEET: OAS School of Governance S-021/18 May 24, 2018 FACT

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of

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

EPA Science Inventory

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

OA-7 Service Module Arrival

NASA Image and Video Library

2017-02-01

The Orbital ATK OA-7 Cygnus spacecraft's service module arrives inside the Space Station Processing Facility of NASA's Kennedy Space Center in Florida. The service module is sealed in an environmentally controlled shipping container, pulled in by truck on a low-boy flatbed trailer. Scheduled to launch on March 19, 2017, the Orbital ATK OA-7 mission will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

OA-7 Cargo Module Arrival

NASA Image and Video Library

2017-01-09

The Orbital ATK OA-7 Cygnus spacecraft's pressurized cargo module (PCM) arrives at the Space Station Processing Facility of NASA's Kennedy Space Center in Florida. The PCM is sealed in an environmentally controlled shipping container, pulled in by truck on a low-boy flatbed trailer. Scheduled to launch in March 2017, the Orbital ATK OA-7 mission will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

Can we prevent OA? Epidemiology and public health insights and implications.

PubMed

Runhaar, Jos; Zhang, Yuqing

2018-05-01

This narrative review discusses the potential of prevention of OA in different stages of the disease. The theoretical background for primary prevention (i.e. prevention of occurrence of definite structural or clinical OA in subjects free of the disease) and secondary prevention (i.e. prevention of progression of the disease in subjects with pre-clinical pathological changes to the joint) is provided and evidence for effective strategies is discussed. Since direct evidence for the prevention of OA development and progression is scarce, indirect evidence enhancing our current knowledge on the potential of OA prevention is additionally discussed. Also, implications of preventive strategies for study design and public health are considered. Prevention of OA has great potential, but as deliberated in the current review, there are still large gaps in our current knowledge and the implications of preventive strategies for the development and progression of OA require consideration.

Quantitative regional and sub-regional analysis of femoral and tibial subchondral bone mineral density (sBMD) using computed tomography (CT): comparison of non-osteoarthritic (OA) and severe OA knees.

PubMed

Omoumi, P; Babel, H; Jolles, B M; Favre, J

2017-11-01

This study aimed to compare subchondral bone mineral density (sBMD) between non-radiographic osteoarthritic (OA) and medial femorotibial OA knees, using computed tomography (CT). CT exams from 16 non-radiographic OA (KL grade < 2) and 16 severe medial OA (KL grade ≥ 3) knees (average age of 61.7 ± 3 and 62.2 ± 5 years old respectively, 50% male in each group), were retrospectively analyzed. CT exams were segmented and 3D maps of sBMD based on the CT number in the most superficial 3 mm of femoral and tibial subchondral bone were computed. Average sBMD and medial-to-lateral sBMD ratios were calculated for total load-bearing regions and for sub-regions of interest in the femur and tibia. The analysis of total load-bearing regions did not reveal any significant difference between groups, except for the lateral tibia, where OA knees had lower sBMD. Sub-regional analysis unveiled differences with some sub-regions of the femur and tibia presenting significantly lower (in the lateral compartment) or higher (in the medial compartment) sBMD in OA knees compared to non-OA knees. The M/L sBMD ratios were significantly higher for OA knees compared to non-OA knees for all regions and sub-regions, except for the internal sub-regions. sBMD locally differs between non-OA and OA knees, in agreement with prior knowledge on biomechanics. CT proved to be a valuable tool for 3D analysis of femoral and tibial sBMD, which can be used in future studies to describe the chronology of sBMD alterations and improve our understanding of the role of subchondral bone in knee OA. Copyright © 2017 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

NASA Astrophysics Data System (ADS)

Hong, Pengyu; Sun, Hui; Sha, Long; Pu, Yi; Khatri, Kshitij; Yu, Xiang; Tang, Yang; Lin, Cheng

2017-08-01

A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. [Figure not available: see fulltext.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

A candidate gene for X-linked Ocular Albinism (OA1)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bassi, M.T.; Schiaffino, V.; Rugarli, E.

1994-09-01

Ocular Albinism of the Nettleship-Fall type 1 (OA1) is the most common form of ocular albinism. It is transmitted as an X-linked recessive trait with affected males showing severe reduction of visual acuity, nystagmus, strabismus, photophobia. Ophthalmologic examination reveals foveal hypoplasia, hypopigmentation of the retina and iris translucency. Microscopic examination of melanocytes suggests that the underlying defect in OA1 is an abnormality in melanosome formation. Recently we assembled a 350 kb cosmid contig spanning the entire critical region on Xp22.3, which measures approximately 110 kb. A minimum set of cosmids was used to identify transcribed sequences using both cDNA selectionmore » and exon amplification. Two putative exons recovered by exon amplification strategy were found to be highly conserved throughout evolution and, therefore, they were used as probes for the screening of fetal and adult retina cDNA libraries. This led to the isolation of clones spanning a full-length cDNA which measures 7.6 kb. Sequence analysis revealed that the predicted protein product shows homology with syntrophines and a Xenopus laevis apical protein. The gene covers approximately 170 kb of DNA and spans the entire critical region for OA1, being deleted in two patients with contiguous gene deletion including OA1 and in one patient with isolated OA1. Therefore, this new gene represents a very strong candidate for involvement in OA1 (an alternative, but unlikely possibility to be considered is that the true OA1 gene lies within an intron of the former). Northern analysis revealed very high level of expression in retina and melanoma. Unlike most Xp22.3 genes, this gene is conserved in the mouse. We are currently performing SSCP analysis and direct sequencing of exons on DNAs from approximately 60 unrelated patients with OA1 for mutation detection.« less

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

PubMed Central

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

2013-01-01

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

Matrix effect in matrix-assisted laser desorption/ionization mass spectra of derivatized oligomeric polyols.

PubMed

Borisov, Roman S; Polovkov, Nikolai Yu; Zhilyaev, Dmitry I; Zaikin, Vladimir G

2013-01-30

Herein we describe a strong matrix effect observed in the matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectra of silylated glycerol alkoxylates and manifested in the loss of the silyl groups in the presence of carboxyl-containing matrices. Commercially available glycerol alkoxylates containing three end OH groups as well as three matrices - 2,5-dihydroxybenzoic acid (DHB), 3-indoleacrylic acid (IAA) and 1,8,9-anthracenetriol (dithranol) - were chosen for the investigation. N,O-Bis(trimethylsilyl)trifluoroacetamide containing 1% trimethylchlorosilane, acetic anhydride and a formylation mixture (formic acid/acetyl chloride) were used for derivatization. Initial oligomers and derivatized products were analyzed by MALDI-ToF-mass spectrometry (MS) on an Autoflex II instrument, equipped with a nitrogen laser (λ 337 nm), in positive ion reflectron mode. Only [M + Na](+) ions were observed for underivatized polymers and for completely derivatized polymers in the presence of DHB and dithranol, respectively. In the case of IAA the mass spectra revealed sets of peaks for underivatized, and for partially and completely derivatized oligomers. No similar 'matrix effect' was observed in the case of acylated glycerol alkoxylates (acyl = formyl, acetyl): only peaks for completely derivatized oligomers were obtained in all matrices: DHB, IAA and dithranol. Using 1,9-nonandiol, we showed that the 'matrix effect' was due to trans-silylation of carboxyl-containing matrices (DHB and IAA) during co-crystallization of silylated oligomers and matrices. The obtained results show that matrix molecules can participate as reactive species in MALDI-ToF-MS experiments. The matrix should be carefully chosen when a derivatization approach is applied because the analysis of spectra of the completely derivatized products is particularly desirable in the quantitative determination of functional end-groups. Copyright © 2012 John Wiley & Sons, Ltd.

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

PubMed

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

2016-06-09

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

Modeling of Dolichol Mass Spectra Isotopic Envelopes as a Tool to Monitor Isoprenoid Biosynthesis.

PubMed

Jozwiak, Adam; Lipko, Agata; Kania, Magdalena; Danikiewicz, Witold; Surmacz, Liliana; Witek, Agnieszka; Wojcik, Jacek; Zdanowski, Konrad; Pączkowski, Cezary; Chojnacki, Tadeusz; Poznanski, Jaroslaw; Swiezewska, Ewa

2017-06-01

The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis ( Arabidopsis thaliana ). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes. © 2017 American Society of Plant Biologists. All Rights Reserved.

Submicron particles influenced by mixed biogenic and anthropogenic emissions: high-resolution aerosol mass spectrometry results from the Carbonaceous Aerosols and Radiative Effects Study (CARES)

NASA Astrophysics Data System (ADS)

Setyan, A.; Zhang, Q.; Merkel, M.; Knighton, W. B.; Sun, Y.; Song, C.; Shilling, J. E.; Onasch, T. B.; Herndon, S. C.; Worsnop, D. R.; Fast, J. D.; Zaveri, R. A.; Berg, L. K.; Wiedensohler, A.; Flowers, B. A.; Dubey, M. K.; Subramanian, R.

2012-02-01

The Carbonaceous Aerosols and Radiative Effects Study (CARES) took place in the Sacramento Valley of California in summer 2010. We present results obtained at Cool, CA, the T1 site of the project (~40 km downwind of urban emissions from Sacramento), where we deployed an Aerodyne high resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) in parallel with complementary instrumentation to characterize the sources and processes of submicron particles (PM1). Cool is located at the foothill of the Sierra Nevada Mountains, where intense biogenic emissions are periodically mixed with urban outflow transported by daytime southwesterly winds from the Sacramento metropolitan area. The particle mass loading was low (3.0 μg m-3 on average) and dominated by organics (80 % of the PM1 mass) followed by sulfate (9.9 %). Organics and sulfate appeared to be externally mixed, as suggested by their different time series (r2 = 0.13) and size distributions. Sulfate showed a bimodal distribution with a droplet mode peaking at ˜400 nm in vacuum aerodynamic diameter (Dva), and a condensation mode at ~150 nm, while organics generally displayed a broad distribution in 60-600 nm (Dva). New particle formation and growth events were observed almost every day, emphasizing the roles of organics and sulfate in new particle growth, especially that of organics. The organic aerosol (OA) had a~nominal formula of C1H1.38N0.004O0.44, thus an average organic mass-to-carbon (OM/OC) ratio of 1.70. Two different oxygenated OA (OOA, 90 % of total OA mass) and a hydrocarbon-like OA (HOA, 10 %) were identified by Positive matrix factorization (PMF) of the high-resolution mass spectra. The more oxidized MO-OOA (O/C = 0.54) corresponded to secondary OA (SOA) primarily influenced by biogenic emissions, while the less oxidized LO-OOA (O/C = 0.42) corresponded to SOA associated with urban transport. The HOA factor corresponded to primary emissions mainly due to local traffic. Twenty three periods of

Establishment of reliable mass spectra and retention indices library: identification of fatty acids in human plasma without authentic standards.

PubMed

Zhang, Liangxiao; Tan, Binbin; Zeng, Maomao; Lu, Hongmei; Liang, Yizeng

2012-01-15

Gas chromatography mass spectrometry (GC-MS) is routinely employed to analyze small molecules in various samples. The more challenge of GC-MS data processing is to identify the unknown compounds in samples. Mass spectra and retention indices library searching are commonly used method. However, the current libraries are often built through collecting data from different groups. To unknown compounds with similar mass spectra and retention indices (e.g. geometric (cis/trans) isomers), the inaccurate results sometime are supplied. In this case, the costly standard compounds have to be used in every analysis. In this report, taking identification of fatty acids as an example, we proposed a strategy of establishment of special database constructed by equivalent chain length (ECL) values in uniform conditions and mass spectra of fatty acid methyl esters (FAMEs). The mass spectral characteristics were firstly used to identify all expected straight saturated fatty acids, and subsequently calculate the ECL for fatty acids in the sample. Finally, the ECL values of fatty acids in the sample were compared with those of fatty acids in the customized database to identify their structures. The results showed that the method developed in this report could effectively identify similar unknown compounds (FAMEs in the human plasma) after validated by the authentic standards. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed

Roussis, Stilianos G; Proulx, Richard

2003-03-15

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

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

PubMed Central

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

2014-01-01

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

Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra*

PubMed Central

Richards, Alicia L.; Vincent, Catherine E.; Guthals, Adrian; Rose, Christopher M.; Westphall, Michael S.; Bandeira, Nuno; Coon, Joshua J.

2013-01-01

We report the use of neutron-encoded (NeuCode) stable isotope labeling of amino acids in cell culture for the purpose of C-terminal product ion annotation. Two NeuCode labeling isotopologues of lysine, 13C615N2 and 2H8, which differ by 36 mDa, were metabolically embedded in a sample proteome, and the resultant labeled proteins were combined, digested, and analyzed via liquid chromatography and mass spectrometry. With MS/MS scan resolving powers of ∼50,000 or higher, product ions containing the C terminus (i.e. lysine) appear as a doublet spaced by exactly 36 mDa, whereas N-terminal fragments exist as a single m/z peak. Through theory and experiment, we demonstrate that over 90% of all y-type product ions have detectable doublets. We report on an algorithm that can extract these neutron signatures with high sensitivity and specificity. In other words, of 15,503 y-type product ion peaks, the y-type ion identification algorithm correctly identified 14,552 (93.2%) based on detection of the NeuCode doublet; 6.8% were misclassified (i.e. other ion types that were assigned as y-type products). Searching NeuCode labeled yeast with PepNovo+ resulted in a 34% increase in correct de novo identifications relative to searching through MS/MS only. We use this tool to simplify spectra prior to database searching, to sort unmatched tandem mass spectra for spectral richness, for correlation of co-fragmented ions to their parent precursor, and for de novo sequence identification. PMID:24043425

Applications and limitations of constrained high-resolution peak fitting on low resolving power mass spectra from the ToF-ACSM

DOE PAGES

Timonen, Hilkka; Cubison, Mike; Aurela, Minna; ...

2016-07-25

The applicability, methods and limitations of constrained peak fitting on mass spectra of low mass resolving power ( m/Δ m 50~500) recorded with a time-of-flight aerosol chemical speciation monitor (ToF-ACSM) are explored. Calibration measurements as well as ambient data are used to exemplify the methods that should be applied to maximise data quality and assess confidence in peak-fitting results. Sensitivity analyses and basic peak fit metrics such as normalised ion separation are employed to demonstrate which peak-fitting analyses commonly performed in high-resolution aerosol mass spectrometry are appropriate to perform on spectra of this resolving power. Information on aerosol sulfate, nitrate,more » sodium chloride, methanesulfonic acid as well as semi-volatile metal species retrieved from these methods is evaluated. The constants in a commonly used formula for the estimation of the mass concentration of hydrocarbon-like organic aerosol may be refined based on peak-fitting results. Lastly, application of a recently published parameterisation for the estimation of carbon oxidation state to ToF-ACSM spectra is validated for a range of organic standards and its use demonstrated for ambient urban data.« less

Format Aside: Applying Beall's Criteria to Assess the Predatory Nature of Both OA and Non-OA Library and Information Science Journals

ERIC Educational Resources Information Center

Olivarez, Joseph D.; Bales, Stephen; Sare, Laura; vanDuinkerken, Wyoma

2018-01-01

Jeffrey Beall's blog listing of potential predatory journals and publishers, as well as his "Criteria for Determining Predatory Open-Access (OA) Publishers" are often looked at as tools to help researchers avoid publishing in predatory journals. While these "Criteria" have brought a greater awareness of OA predatory journals,…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fast, J; Zhang, Q; Tilp, A

Significantly improved returns in their aerosol chemistry data can be achieved via the development of a value-added product (VAP) of deriving OA components, called Organic Aerosol Components (OACOMP). OACOMP is primarily based on multivariate analysis of the measured organic mass spectral matrix. The key outputs of OACOMP are the concentration time series and the mass spectra of OA factors that are associated with distinct sources, formation and evolution processes, and physicochemical properties.

Corona discharge ion mobility spectrometry with orthogonal acceleration time of flight mass spectrometry for monitoring of volatile organic compounds.

PubMed

Sabo, Martin; Matejčík, Štefan

2012-06-19

We demonstrate the application of corona discharge ion mobility spectrometry with orthogonal acceleration time of flight mass spectrometry (CD IMS-oaTOF) for volatile organic compounds (VOCs) monitoring. Two-dimensional (2D) IMS-oaTOF spectra of VOCs were recorded in nearly real time. The corona discharge atmospheric pressure chemical ionization (APCI) source was operated in positive mode in nitrogen and air. The CD ion source generates in air H(3)O(+)(H(2)O)(n) and NO(+). The NO(+) offers additional possibility for selective ionization and for an increase of the sensitivity of monoaromatic compounds. In addition to H(3)O(+)(H(2)O)(n) and NO(+), we have carried out ionization of VOCs using acetone as dopant gas ((CH(3))(2)COH(+)). Sixteen model VOCs (tetrahydrofuran, butanol, n-propanol, iso-propano, acetone, methanol, ethanol, toluene, benzene, amomnia, dioxan, triethylamine, acetonitrile, formaldehyde, m-xylene, 2,2,2-trifluoroethylamine) were tested using these ionization techniques.

Establishment of reference intervals for osteoarthritis-related soluble biomarkers: the FNIH/OARSI OA Biomarkers Consortium.

PubMed

Kraus, Virginia B; Hargrove, David E; Hunter, David J; Renner, Jordan B; Jordan, Joanne M

2017-01-01

To establish reference intervals for osteoarthritis (OA)-related biomarkers used in the Foundation for the National Institutes of Health (FNIH) OA Biomarkers Consortium Project. A total of 129 'multijoint controls' were selected from 2722 African-American and Caucasian men and women in the Johnston County Osteoarthritis Project. The majority (79%) of those eligible (with biospecimens and baseline data) also had one or more follow-up evaluations 5-15 years later. Multijoint controls were selected to be free of radiographic hand, hip, knee and lumbar spine osteoarthritis (OA), to have no knee or hip symptoms, and minimal hand and spine symptoms at all available time points. Eighteen biomarkers were evaluated in serum (s) and/or urine (u) by ELISA. Reference intervals and partitioning by gender and race were performed with EP Evaluator software. Controls were 64% women, 33% African-Americans, mean age 59 years and mean body mass index 29 kg/m 2 . Three biomarkers were associated with age: sHyaluronan (positively), sN-terminal propeptide of collagen IIA (positively) and sCol2-3/4 C-terminal cleavage product of types I and II collagen (negatively). Exploratory analyses suggested that separate reference intervals may be warranted on the basis of gender for uC-terminal cross-linked telopeptide of type II collagen (uCTXII), sMatrix metalloproteinase-3, uNitrated type II collagen degradation fragment (uCol2-1 NO2) and sHyaluronan, and on the basis of race for uCTXII, sCartilage oligomeric matrix protein, sC-terminal cross-linked telopeptide of type I collagen and uCol2-1 NO2. To our knowledge, this represents the best and most stringent control group ever assayed for OA-related biomarkers. These well-phenotyped controls, representing a similar age demographic to that of the OA Initiative-FNIH main study sample, provide a context for interpretation of OA subject biomarker data. The freely available data set also provides a reference for future human studies. Published

Mass spectra and radiative transitions of doubly heavy baryons in a relativized quark model

NASA Astrophysics Data System (ADS)

Lü, Qi-Fang; Wang, Kai-Lei; Xiao, Li-Ye; Zhong, Xian-Hui

2017-12-01

We study the mass spectra and radiative decays of doubly heavy baryons within the diquark picture in a relativized quark model. The mass of the JP=1 /2+ Ξc c ground state is predicted to be 3606 MeV, which is consistent with the mass of Ξcc ++(3621 ) newly observed by the LHCb Collaboration. The predicted mass gap between two S -wave states, Ξcc * (JP=3 /2+) and Ξc c (JP=1 /2+), is 69 MeV. Furthermore, the radiative transitions of doubly heavy baryons are also estimated by using the realistic wave functions obtained from relativized quark model. The radiative decay widths of Ξcc *++→Ξcc ++γ and Ξcc *+→Ξcc +γ are predicted to be about 7 and 4 keV, respectively. These predictions of doubly heavy baryons can provide helpful information for future experimental searches.

41 CFR 102-85.25 - What is the basic principle governing OAs?

Code of Federal Regulations, 2010 CFR

2010-07-01

... principle governing OAs? 102-85.25 Section 102-85.25 Public Contracts and Property Management Federal... POLICY FOR OCCUPANCY IN GSA SPACE Pricing Policy-General § 102-85.25 What is the basic principle governing OAs? The basic principle governing OAs is to adopt the private sector practice of capturing in a...

Proximity effects in the electron impact mass spectra of 2-substituted benzazoles

NASA Astrophysics Data System (ADS)

Chantler, Thomas; Perrin, Victoria L.; Donkor, Rachel E.; Cawthorne, Richard S.; Bowen, Richard D.

2004-08-01

The 70 eV electron impact mass spectra of a wide range of 2-substituted benzazoles are reported and discussed. Particular attention is paid to the mechanistic significance and analytical utility of [M-H]+ and [M-X]+ signals in the spectra of benzazoles in which the 2-substituent contains a terminal aryl group with one or more substituents, X. Loss of H[radical sign] or X[radical sign] occurs preferentially from an ortho-position from ionized 2-benzylbenzimidazoles, 2-phenethylbenzimidazoles, 2-styrylbenzimidazoles, 2-styrylbenzoxazoles and 2-styrylbenzothiazoles. In the three styrylbenzazole series, the [M-H]+ and/or [M-X]+ signals dominate the spectra. This unusually facile loss of H[radical sign] or X[radical sign] may be attributed to a proximity effect, in which cyclization of the ionized molecule is followed by elimination of an ortho-substituent to give an exceptionally stable polycyclic ion. Formation of a new five- or six-membered ring by the proximity effect occurs rapidly; cyclization to a seven-membered ring takes place rather less readily; but formation of a ring with only four atoms or more than seven atoms is not observed to a significant extent. The proximity effect competes effectively with loss of a methyl radical by simple cleavage of an ethyl, isopropyl and even a t-butyl group in the pendant aromatic ring of ionized 2-(4-alkylstyryl)benzazoles.

Mechanical Properties of Plant Cell Walls Probed by Relaxation Spectra1[W][OA

PubMed Central

Hansen, Steen Laugesen; Ray, Peter Martin; Karlsson, Anders Ola; Jørgensen, Bodil; Borkhardt, Bernhard; Petersen, Bent Larsen; Ulvskov, Peter

2011-01-01

Transformants and mutants with altered cell wall composition are expected to display a biomechanical phenotype due to the structural role of the cell wall. It is often quite difficult, however, to distinguish the mechanical behavior of a mutant's or transformant's cell walls from that of the wild type. This may be due to the plant’s ability to compensate for the wall modification or because the biophysical method that is often employed, determination of simple elastic modulus and breakstrength, lacks the resolving power necessary for detecting subtle mechanical phenotypes. Here, we apply a method, determination of relaxation spectra, which probes, and can separate, the viscoelastic properties of different cell wall components (i.e. those properties that depend on the elastic behavior of load-bearing wall polymers combined with viscous interactions between them). A computer program, BayesRelax, that deduces relaxation spectra from appropriate rheological measurements is presented and made accessible through a Web interface. BayesRelax models the cell wall as a continuum of relaxing elements, and the ability of the method to resolve small differences in cell wall mechanical properties is demonstrated using tuber tissue from wild-type and transgenic potatoes (Solanum tuberosum) that differ in rhamnogalacturonan I side chain structure. PMID:21075961

Comparison of the new biometer OA-1000 with IOLMaster and Tomey AL-3000.

PubMed

Goebels, Susanne Christiane; Seitz, Berthold; Langenbucher, Achim

2013-09-01

The OA-1000 (Tomey, Japan) is a new optical biometer, which allows measurements of axial length (AL), anterior chamber depth (ACD) and corneal thickness (CT) due to partial coherence interferometry (PCI) technology. The aim of this study was to compare the OA-1000 results with those obtained with the IOLMaster and contact applanation A-scan ultrasonography. We examined 133 eyes of 75 patients with age related cataract. Mean age was 72.0 ± 9.5 years. Biometry measurements of AL and ACD were performed with the Tomey OA-1000 based on PCI, the IOLMaster based on PCI (AL) and slit projection (ACD), and the Tomey AL-3000 based on contact applanation A-scan ultrasonography. Mean AL using the IOLMaster was 23.21 ± 1.08 mm, using the AL-3000 was 22.79 ± 1.04 mm, using the OA-1000 it was 22.97 ± 1.1 mm. Mean ACD using the IOLMaster was 2.99 ± 0.41 mm, using the OA-1000 3.40 ± 0.46 mm, using the Tomey AL-3000 it was 2.93 ± 0.43 mm. Mean difference between the AL and ACD measured with the OA-1000 and the IOLMaster was 0.22 ± 0.047 mm and 0.40 ± 0.33 mm, between OA-1000 and the AL-3000 it was 0.19 ± 0.23 mm and 0.47 ± 0.33 mm, and between IOLMaster and AL-3000 it was 0.42 ± 0.23 and 0.09 ± 0.36 mm. For AL the correlation coefficient R between IOLMaster and OA-1000 was 0.999, between IOLMaster and AL-3000 it was 0.976, between AL-3000 and OA-1000 it was 0.977. For ACD R between IOLMaster and OA-1000 was 0.735, between IOLMaster and AL-3000 it was 0.822, between AL-3000 and OA-1000 it was 0.716 (all p < 0.001). Compared with other used clinical instruments the OA-1000 generates accurate results. Although differences were found, the OA-1000 provided results that correlated well with the values of IOLMaster and AL-3000.

Protein and peptide cross sections and mass spectra in an electrostatic ion beam trap

NASA Astrophysics Data System (ADS)

Fradkin, Z.; Strasser, D.; Heber, O.; Rappaport, M. L.; Sharon, M.; Thomson, B. A.; Rahinov, I.; Toker, Y.; Zajfman, D.

2017-05-01

Among the advantages of an electrostatic ion beam trap (EIBT), which is based on purely electrostatic fields, are mass-unlimited trapping and ease of operation. We have developed a new system that couples an electrospray ion source to an EIBT. Between the source and EIBT there is a Paul trap in which the ions are accumulated before being extracted and accelerated. After the ion bunch has entered the EIBT, the ions are trapped by rapidly raising the voltages on the entrance mirror. The oscillations of the bunch are detected by amplifying the charge induced on a pickup ring in the center of the trap, the ion mass being directly proportional to the square of the oscillation period. The trapping of biomolecules in the RF-bunching mode of the EIBT is used for measurement of mass spectra and collision cross sections. Coalescence of bunches of ions of nearby mass in the self-bunching mode is also demonstrated.

The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles.

PubMed

Piwowar, Heather; Priem, Jason; Larivière, Vincent; Alperin, Juan Pablo; Matthias, Lisa; Norlander, Bree; Farley, Ashley; West, Jevin; Haustein, Stefanie

2018-01-01

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.

The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles

PubMed Central

Larivière, Vincent; Alperin, Juan Pablo; Matthias, Lisa; Norlander, Bree; Farley, Ashley; West, Jevin; Haustein, Stefanie

2018-01-01

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice. PMID:29456894

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

PubMed

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

2006-07-01

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

Accuracy of Mass and Radius Determination for Neutron Stars in X-ray Bursters from Simulated LOFT Spectra

NASA Astrophysics Data System (ADS)

Majczyna, A.; Madej, J.; Różańska, A.; Należyty, M.

2017-06-01

We present a simulation of an X-ray spectrum of a hot neutron star, as would be seen by the LAD detector on board of LOFT satellite. We also compute a grid of theoretical spectra corresponding to a range of effective temperatures Teff and surface gravities log g with values corresponding to compact stars in Type I X-ray bursters. A neutron star with the mass M=1.64 M⊙ and the radius R=11.95 km (which yields the surface gravity log g=14.30 [cgs] and the surface redshift z=0.30) is used in simulation. Accuracy of mass and radius determination by fitting theoretical spectra to the observed one is found to be M=1.64+0.16-0.02 M⊙ and R=11.95+1.57-0.40 km (2σ). The confidence contours for these two variables are narrow but elongated, and therefore the resulting constraints on the EOS cannot be strong. Note, that in this paper we aim to discuss error contours of NS mass and radius, whereas discussion of EOS is beyond the scope of this work.

Organic aerosol source apportionment by offline-AMS over a full year in Marseille

NASA Astrophysics Data System (ADS)

Bozzetti, Carlo; El Haddad, Imad; Salameh, Dalia; Daellenbach, Kaspar Rudolf; Fermo, Paola; Gonzalez, Raquel; Cruz Minguillón, María; Iinuma, Yoshiteru; Poulain, Laurent; Elser, Miriam; Müller, Emanuel; Gates Slowik, Jay; Jaffrezo, Jean-Luc; Baltensperger, Urs; Marchand, Nicolas; Prévôt, André Stephan Henry

2017-07-01

We investigated the seasonal trends of OA sources affecting the air quality of Marseille (France), which is the largest harbor of the Mediterranean Sea. This was achieved by measurements of nebulized filter extracts using an aerosol mass spectrometer (offline-AMS). In total 216 PM2. 5 (particulate matter with an aerodynamic diameter < 2.5 µm) filter samples were collected over 1 year from August 2011 to July 2012. These filters were used to create 54 composite samples which were analyzed by offline-AMS. The same samples were also analyzed for major water-soluble ions, metals, elemental and organic carbon (EC / OC), and organic markers, including n-alkanes, hopanes, polycyclic aromatic hydrocarbons (PAHs), lignin and cellulose pyrolysis products, and nitrocatechols. The application of positive matrix factorization (PMF) to the water-soluble AMS spectra enabled the extraction of five factors, related to hydrocarbon-like OA (HOA), cooking OA (COA), biomass burning OA (BBOA), oxygenated OA (OOA), and an industry-related OA (INDOA). Seasonal trends and relative contributions of OA sources were compared with the source apportionment of OA spectra collected from the AMS field deployment at the same station but in different years and for shorter monitoring periods (February 2011 and July 2008). Online- and offline-AMS source apportionment revealed comparable seasonal contribution of the different OA sources. Results revealed that BBOA was the dominant source during winter, representing on average 48 % of the OA, while during summer the main OA component was OOA (63 % of OA mass on average). HOA related to traffic emissions contributed on a yearly average 17 % to the OA mass, while COA was a minor source contributing 4 %. The contribution of INDOA was enhanced during winter (17 % during winter and 11 % during summer), consistent with an increased contribution from light alkanes, light PAHs (fluoranthene, pyrene, phenanthrene), and selenium, which is commonly considered as

Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias

PubMed Central

Imperlini, Esther; Santorelli, Lucia; Orrù, Stefania; Scolamiero, Emanuela; Ruoppolo, Margherita

2016-01-01

Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs. PMID:27403441

Eight previously unidentified mutations found in the OA1 ocular albinism gene

PubMed Central

Mayeur, Hélène; Roche, Olivier; Vêtu, Christelle; Jaliffa, Carolina; Marchant, Dominique; Dollfus, Hélène; Bonneau, Dominique; Munier, Francis L; Schorderet, Daniel F; Levin, Alex V; Héon, Elise; Sutherland, Joanne; Lacombe, Didier; Said, Edith; Mezer, Eedy; Kaplan, Josseline; Dufier, Jean-Louis; Marsac, Cécile; Menasche, Maurice; Abitbol, Marc

2006-01-01

Background Ocular albinism type 1 (OA1) is an X-linked ocular disorder characterized by a severe reduction in visual acuity, nystagmus, hypopigmentation of the retinal pigmented epithelium, foveal hypoplasia, macromelanosomes in pigmented skin and eye cells, and misrouting of the optical tracts. This disease is primarily caused by mutations in the OA1 gene. Methods The ophthalmologic phenotype of the patients and their family members was characterized. We screened for mutations in the OA1 gene by direct sequencing of the nine PCR-amplified exons, and for genomic deletions by PCR-amplification of large DNA fragments. Results We sequenced the nine exons of the OA1 gene in 72 individuals and found ten different mutations in seven unrelated families and three sporadic cases. The ten mutations include an amino acid substitution and a premature stop codon previously reported by our team, and eight previously unidentified mutations: three amino acid substitutions, a duplication, a deletion, an insertion and two splice-site mutations. The use of a novel Taq polymerase enabled us to amplify large genomic fragments covering the OA1 gene. and to detect very likely six distinct large deletions. Furthermore, we were able to confirm that there was no deletion in twenty one patients where no mutation had been found. Conclusion The identified mutations affect highly conserved amino acids, cause frameshifts or alternative splicing, thus affecting folding of the OA1 G protein coupled receptor, interactions of OA1 with its G protein and/or binding with its ligand. PMID:16646960

Modeling of Dolichol Mass Spectra Isotopic Envelopes as a Tool to Monitor Isoprenoid Biosynthesis1[OPEN

PubMed Central

Kania, Magdalena; Witek, Agnieszka; Wojcik, Jacek; Zdanowski, Konrad; Pączkowski, Cezary; Chojnacki, Tadeusz; Poznanski, Jaroslaw

2017-01-01

The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes. PMID:28385729

Operational results for the experimental DOE/NASA Mod-OA wind turbine project

NASA Astrophysics Data System (ADS)

Shaltens, R. K.; Birchenough, A. G.

The Mod-OA wind turbine project which was to gain early experience in the operation of large wind turbines in a utility environment is discussed. The Mod-OA wind turbines were a first generation design, and even though not cost effective, the operating experience and performance characteristics had a significant effect on the design and development of the second and third generation machines. The Mod-OA machines were modified as a result of the operational experience, particularly the blade development and control system strategy. The results of study to investigate the interaction of a Mod-OA wind turbine with an isolated diesel generation system are discussed. The machine configuration, its advantages and disadvantages and the machine performance and availability are discussed.

Operational results for the experimental DOE/NASA Mod-OA wind turbine project

NASA Technical Reports Server (NTRS)

Shaltens, R. K.; Birchenough, A. G.

1983-01-01

The Mod-OA wind turbine project which was to gain early experience in the operation of large wind turbines in a utility environment is discussed. The Mod-OA wind turbines were a first generation design, and even though not cost effective, the operating experience and performance characteristics had a significant effect on the design and development of the second and third generation machines. The Mod-OA machines were modified as a result of the operational experience, particularly the blade development and control system strategy. The results of study to investigate the interaction of a Mod-OA wind turbine with an isolated diesel generation system are discussed. The machine configuration, its advantages and disadvantages and the machine performance and availability are discussed.

Analysis of steranes and triterpanes in geolipid extracts by automatic classification of mass spectra

NASA Technical Reports Server (NTRS)

Wardroper, A. M. K.; Brooks, P. W.; Humberston, M. J.; Maxwell, J. R.

1977-01-01

A computer method is described for the automatic classification of triterpanes and steranes into gross structural type from their mass spectral characteristics. The method has been applied to the spectra obtained by gas-chromatographic/mass-spectroscopic analysis of two mixtures of standards and of hydrocarbon fractions isolated from Green River and Messel oil shales. Almost all of the steranes and triterpanes identified previously in both shales were classified, in addition to a number of new components. The results indicate that classification of such alkanes is possible with a laboratory computer system. The method has application to diagenesis and maturation studies as well as to oil/oil and oil/source rock correlations in which rapid screening of large numbers of samples is required.

Comparison of FTIR and Particle Mass Spectrometry for the Measurement of Paticulate Organic Nitrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruns, Emily; Perraud, Veronique; Zelenyuk, Alla

2010-02-01

While multifunctional organic nitrates are formed during the atmospheric oxidation of volatile organic compounds, relatively little is known about their signatures in particle mass spectrometers. High resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS) was applied to NH4NO3, NaNO3 and isosorbide 5-mononitrate (IMN) particles, and to secondary organic aerosol (SOA) from NO3 radical reactions at 22 C and 1 atm in air with and pinene, 3-carene, limonene and isoprene. For comparison, single particle laser ablation mass spectra (SPLAT II) were also obtained for IMN and SOA from the pinene reaction. The mass spectra of all particles exhibit significant intensity at m/z 30,more » and for the SOA, weak peaks corresponding to various organic fragments containing nitrogen [CxHyNzOa]+ were identified using HR-ToF-AMS. The NO+/NO2+ ratios from HR-ToF-AMS were 10-15 for IMN and the SOA from the and pinene, 3-carene and limonene reactions, ~5 for the isoprene reaction, 2.4 for NH4NO3 and 80 for NaNO3. The N/H ratios from HR-ToF-AMS for the SOA were smaller by a factor of 2 to 4 than the -ONO2/C-H ratios measured using FTIR on particles impacted on ZnSe windows. While the NO+/NO2+ ratio may provide a generic indication of organic nitrates under some conditions, specific identification of particulate organic nitrates awaits further development of particle mass spectrometry techniques.« less

Diagnostic index: an open-source tool to classify TMJ OA condyles

NASA Astrophysics Data System (ADS)

Paniagua, Beatriz; Pascal, Laura; Prieto, Juan; Vimort, Jean Baptiste; Gomes, Liliane; Yatabe, Marilia; Ruellas, Antonio Carlos; Budin, Francois; Pieper, Steve; Styner, Martin; Benavides, Erika; Cevidanes, Lucia

2017-03-01

Osteoarthritis (OA) of temporomandibular joints (TMJ) occurs in about 40% of the patients who present TMJ disorders. Despite its prevalence, OA diagnosis and treatment remain controversial since there are no clear symptoms of the disease, especially in early stages. Quantitative tools based on 3D imaging of the TMJ condyle have the potential to help characterize TMJ OA changes. The goals of the tools proposed in this study are to ultimately develop robust imaging markers for diagnosis and assessment of treatment efficacy. This work proposes to identify differences among asymptomatic controls and different clinical phenotypes of TMJ OA by means of Statistical Shape Modeling (SSM), obtained via clinical expert consensus. From three different grouping schemes (with 3, 5 and 7 groups), our best results reveal that that the majority (74.5%) of the classifications occur in agreement with the groups assigned by consensus between our clinical experts. Our findings suggest the existence of different disease-based phenotypic morphologies in TMJ OA. Our preliminary findings with statistical shape modeling based biomarkers may provide a quantitative staging of the disease. The methodology used in this study is included in an open source image analysis toolbox, to ensure reproducibility and appropriate distribution and dissemination of the solution proposed.

Chemical Characteristics of Organic Aerosols in Shanghai: A Study by Ultrahigh-Performance Liquid Chromatography Coupled With Orbitrap Mass Spectrometry

NASA Astrophysics Data System (ADS)

Wang, Xinke; Hayeck, Nathalie; Brüggemann, Martin; Yao, Lei; Chen, Hangfei; Zhang, Ci; Emmelin, Corinne; Chen, Jianmin; George, Christian; Wang, Lin

2017-11-01

Particulate matter 2.5 (PM2.5) filter samples were collected in July and October 2014 and January and April 2015 in urban Shanghai and analyzed using ultrahigh-performance liquid chromatography coupled to Orbitrap mass spectrometry. The measured chromatogram-mass spectra were processed by a nontarget screening approach to identify significant signals. In total, 810-1,510 chemical formulas of organic compounds in the negative polarity (negative electrospray ionization (ESI-)) and 860-1,790 in the positive polarity (ESI+), respectively, were determined. The chemical characteristics of organic aerosols (OAs) in Shanghai varied among different months and between daytime and nighttime. In the January samples, organics were generally richer in terms of both number and abundance, whereas those in the July samples were far lower. More CHO- (compounds containing only carbon, hydrogen, and oxygen and detected in ESI-) and CHOS- (sulfur-containing organics) were found in the daytime samples, suggesting a photochemical source, whereas CHONS- (nitrogen- and sulfur-containing organics) were more abundant in the nighttime samples, due to nocturnal nitrate radical chemistry. A significant number of monocyclic and polycyclic aromatic compounds, and nitrogen- and sulfur-containing heterocyclic compounds, were detected in all samples, indicating that biomass burning and fossil fuel combustion made important contributions to the OAs in urban Shanghai. Additionally, precursor-product pair analysis indicates that the epoxide pathway is an important formation route for organosulfates observed in Shanghai. Moreover, a similar analysis suggests that 35-57% of nitrogen-containing compounds detected in ESI+ could be formed through reactions between ammonia and carbonyls. Our study presents a comprehensive overview of OAs in urban Shanghai, which helps to understand their characteristics and sources.

Proposal and Evaluation of Subordinate Standard Solar Irradiance Spectra: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habte, Aron M; Wilbert, Stefan; Jessen, Wilko

This paper introduces a concept for global tilted irradiance (GTI) subordinate standard spectra to supplement the current standard spectra used in solar photovoltaic applications as defined in ASTM G173 and IEC60904. The proposed subordinate standard spectra correspond to atmospheric conditions and tilt angles that depart significantly from the main standard spectrum, and they can be used to more accurately represent various local conditions. For the definition of subordinate standard spectra cases with an elevation 1.5 km above sea level, the question arises whether the air mass should be calculated including a pressure correction or not. This study focuses on themore » impact of air mass used in standard spectra, and it uses data from 29 locations to examine which air mass is most appropriate for GTI and direct normal irradiance (DNI) spectra. Overall, it is found that the pressure-corrected air mass of 1.5 is most appropriate for DNI spectra. For GTI, a non-pressure-corrected air mass of 1.5 was found to be more appropriate.« less

Computer-aided discovery of biological activity spectra for anti-aging and anti-cancer olive oil oleuropeins.

PubMed

Corominas-Faja, Bruna; Santangelo, Elvira; Cuyàs, Elisabet; Micol, Vicente; Joven, Jorge; Ariza, Xavier; Segura-Carretero, Antonio; García, Jordi; Menendez, Javier A

2014-09-01

Aging is associated with common conditions, including cancer, diabetes, cardiovascular disease, and Alzheimer's disease. The type of multi-targeted pharmacological approach necessary to address a complex multifaceted disease such as aging might take advantage of pleiotropic natural polyphenols affecting a wide variety of biological processes. We have recently postulated that the secoiridoids oleuropein aglycone (OA) and decarboxymethyl oleuropein aglycone (DOA), two complex polyphenols present in health-promoting extra virgin olive oil (EVOO), might constitute a new family of plant-produced gerosuppressant agents. This paper describes an analysis of the biological activity spectra (BAS) of OA and DOA using PASS (Prediction of Activity Spectra for Substances) software. PASS can predict thousands of biological activities, as the BAS of a compound is an intrinsic property that is largely dependent on the compound's structure and reflects pharmacological effects, physiological and biochemical mechanisms of action, and specific toxicities. Using Pharmaexpert, a tool that analyzes the PASS-predicted BAS of substances based on thousands of "mechanism-effect" and "effect-mechanism" relationships, we illuminate hypothesis-generating pharmacological effects, mechanisms of action, and targets that might underlie the anti-aging/anti-cancer activities of the gerosuppressant EVOO oleuropeins.

Seasonal variability in chemical composition and source apportionment of sub-micron aerosol over a high altitude site in Western Ghats, India

NASA Astrophysics Data System (ADS)

Mukherjee, Subrata; Singla, Vyoma; Pandithurai, Govindan; Safai, P. D.; Meena, G. S.; Dani, K. K.; Anil Kumar, V.

2018-05-01

This manuscript reports the seasonal variation of chemically speciated sub-micron aerosol particles (diameter < 1 μm). An Aerosol Chemical Speciation Monitor (ACSM) was used to measure the mass concentration of non-refractory particulate matter (NR-PM1) at a high-altitude site in the Western Ghats, India from March 2016 to February 2017. The mass concentration of NR-PM1 averaged at 7.5 ± 6.5 μgm-3, with major contributions from organics (59%) and sulfates (23%). Positive matrix factorization (PMF) was applied on the measured mass spectra of organic aerosol (OA) to derive the sources distinctive of each season (Summer, Monsoon, Post-Monsoon and Winter). The four OA factors (two primary OA and two oxygenated OA) resolved during summer, post-monsoon and winter season. However, only one oxygenated factor resolved during monsoon and contributed only 20% to the total OA. The factors associated with primary emissions dominated during the monsoon, whereas factors related to secondary formation dominated in other three seasons. During summer, an isoprene derived SOA - IEPOX-OA (isoprene-epoxydiol OA) contributed ∼17% to the total OA. Cluster and concentration weighted trajectory (CWT) analyses were performed to identify the possible source regions of NR-PM1 mass concentration observed at the receptor site. The analysis identifies Central India as the potential source region of transported aerosol during post-monsoon and winter season. Our study suggests that contributions from both local sources and regional transport are important in governing mass concentration of PM1 over Mahabaleshwar.

Otolith mass asymmetry: natural, and after weightlessness and hypergravity

NASA Astrophysics Data System (ADS)

Lychakov, Dmitri

It is believed that otolith mass asymmetry (OA) can play an essential role in genesis of vestibular space disturbances in human subjects and fish. This review poster presents data on values and characters of OA in animals of various species and classes and on the effect of weightlessness and hypergravity on OA; the issue of the effect of OA on vestibular and auditory functions also is considered (Lychakov, Rebane, 2004, 2005; Lychakov et al., 2006, 2008). In symmetric vertebrates, OA was shown to be fluctuating, its coefficient chiχ ranges from - 0.2 to + 0.2 (±± 20%). It should be stressed that in the overwhelming majority of individuals absolute values of chiχ << 0.06. The low OA level enables the paired otolith organs to work in coordination; this is why the OA level is equally low regardless of the individual taxonomic and ecological position, size, age, and otolith growth rate. Individuals with the abnormally high OA level can experience difficulties in analyzing auditory and vestibular stimuli; therefore, most of such individuals are eliminated by natural selection. Unlike symmetric vertebrates, labyrinths of many Pleuronectiformes have pronounced OA. Otoliths in the lower labyrinth, on average, are significantly heavier than those in the upper labyrinth. The organs of flatfish represent the only example when OA, being directional, seem to play an essential role in lateralized behavior and are suggested to be used in the spatial localization of the source of sound. The short-term weightlessness and relatively weak hypergravity (<< 2g) do not affect OA. However, it cannot be ruled out that the long-term weightlessness and hypergravity >> 3g as well as some diseases and age-related changes can indirectly enhance OA and cause some functional disturbances. This work was partly supported by Russian grant RFFI 14-04-00601.

Proteinase-activated receptor 2 modulates OA-related pain, cartilage and bone pathology.

PubMed

Huesa, Carmen; Ortiz, Ana C; Dunning, Lynette; McGavin, Laura; Bennett, Louise; McIntosh, Kathryn; Crilly, Anne; Kurowska-Stolarska, Mariola; Plevin, Robin; van 't Hof, Rob J; Rowan, Andrew D; McInnes, Iain B; Goodyear, Carl S; Lockhart, John C; Ferrell, William R

2016-11-01

Proteinase-activated receptor 2 (PAR2) deficiency protects against cartilage degradation in experimental osteoarthritis (OA). The wider impact of this pathway upon OA-associated pathologies such as osteophyte formation and pain is unknown. Herein, we investigated early temporal bone and cartilage changes in experimental OA in order to further elucidate the role of PAR2 in OA pathogenesis. OA was induced in wild-type (WT) and PAR2-deficient (PAR2 -/- ) mice by destabilisation of the medial meniscus (DMM). Inflammation, cartilage degradation and bone changes were monitored using histology and microCT. In gene rescue experiments, PAR2 -/- mice were intra-articularly injected with human PAR2 (hPAR2)-expressing adenovirus. Dynamic weight bearing was used as a surrogate of OA-related pain. Osteophytes formed within 7 days post-DMM in WT mice but osteosclerosis was only evident from 14 days post induction. Importantly, PAR2 was expressed in the proliferative/hypertrophic chondrocytes present within osteophytes. In PAR2 -/- mice, osteophytes developed significantly less frequently but, when present, were smaller and of greater density; no osteosclerosis was observed in these mice up to day 28. The pattern of weight bearing was altered in PAR2 -/- mice, suggesting reduced pain perception. The expression of hPAR2 in PAR2 -/- mice recapitulated osteophyte formation and cartilage damage similar to that observed in WT mice. However, osteosclerosis was absent, consistent with lack of hPAR2 expression in subchondral bone. This study clearly demonstrates PAR2 plays a critical role, via chondrocytes, in osteophyte development and subchondral bone changes, which occur prior to PAR2-mediated cartilage damage. The latter likely occurs independently of OA-related bone changes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Proteinase-activated receptor 2 modulates OA-related pain, cartilage and bone pathology

PubMed Central

Huesa, Carmen; Ortiz, Ana C; Dunning, Lynette; McGavin, Laura; Bennett, Louise; McIntosh, Kathryn; Crilly, Anne; Kurowska-Stolarska, Mariola; Plevin, Robin; van ‘t Hof, Rob J; Rowan, Andrew D; McInnes, Iain B; Goodyear, Carl S; Lockhart, John C; Ferrell, William R

2016-01-01

Objective Proteinase-activated receptor 2 (PAR2) deficiency protects against cartilage degradation in experimental osteoarthritis (OA). The wider impact of this pathway upon OA-associated pathologies such as osteophyte formation and pain is unknown. Herein, we investigated early temporal bone and cartilage changes in experimental OA in order to further elucidate the role of PAR2 in OA pathogenesis. Methods OA was induced in wild-type (WT) and PAR2-deficient (PAR2−/−) mice by destabilisation of the medial meniscus (DMM). Inflammation, cartilage degradation and bone changes were monitored using histology and microCT. In gene rescue experiments, PAR2−/− mice were intra-articularly injected with human PAR2 (hPAR2)-expressing adenovirus. Dynamic weight bearing was used as a surrogate of OA-related pain. Results Osteophytes formed within 7 days post-DMM in WT mice but osteosclerosis was only evident from 14 days post induction. Importantly, PAR2 was expressed in the proliferative/hypertrophic chondrocytes present within osteophytes. In PAR2−/− mice, osteophytes developed significantly less frequently but, when present, were smaller and of greater density; no osteosclerosis was observed in these mice up to day 28. The pattern of weight bearing was altered in PAR2−/− mice, suggesting reduced pain perception. The expression of hPAR2 in PAR2−/− mice recapitulated osteophyte formation and cartilage damage similar to that observed in WT mice. However, osteosclerosis was absent, consistent with lack of hPAR2 expression in subchondral bone. Conclusions This study clearly demonstrates PAR2 plays a critical role, via chondrocytes, in osteophyte development and subchondral bone changes, which occur prior to PAR2-mediated cartilage damage. The latter likely occurs independently of OA-related bone changes. PMID:26698846

Mass spectra and fusion cross sections for /sup 20/Ne+/sup 24/Mg interaction at 55 and 85 MeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grotowski, K.; Belery, P.; Delbar, T.

1981-06-01

Inclusive ..gamma.. spectra from the /sup 20/Ne+/sup 24/Mg interaction have been measured using 55- and 85-MeV /sup 20/Ne ions. The identification of ..gamma.. lines allows the determination of mass spectra in the region 12< or =A< or =43. Experimental results are compared with statistical model calculations. The total reaction and fusion cross sections are extracted. Cross sections for inelastic scattering, few nucleon transfers, and deep inelastic scattering are estimated.

Inorganic Salt Interference on CO2+ in Aerodyne AMS and ACSM Organic Aerosol Composition Studies.

PubMed

Pieber, Simone M; El Haddad, Imad; Slowik, Jay G; Canagaratna, Manjula R; Jayne, John T; Platt, Stephen M; Bozzetti, Carlo; Daellenbach, Kaspar R; Fröhlich, Roman; Vlachou, Athanasia; Klein, Felix; Dommen, Josef; Miljevic, Branka; Jiménez, José L; Worsnop, Douglas R; Baltensperger, Urs; Prévôt, André S H

2016-10-04

Aerodyne aerosol mass spectrometer (AMS) and Aerodyne aerosol chemical speciation monitor (ACSM) mass spectra are widely used to quantify organic aerosol (OA) elemental composition, oxidation state, and major environmental sources. The OA CO 2 + fragment is among the most important measurements for such analyses. Here, we show that a non-OA CO 2 + signal can arise from reactions on the particle vaporizer, ion chamber, or both, induced by thermal decomposition products of inorganic salts. In our tests (eight instruments, n = 29), ammonium nitrate (NH 4 NO 3 ) causes a median CO 2 + interference signal of +3.4% relative to nitrate. This interference is highly variable between instruments and with measurement history (percentiles P 10-90 = +0.4 to +10.2%). Other semi-refractory nitrate salts showed 2-10 times enhanced interference compared to that of NH 4 NO 3 , while the ammonium sulfate ((NH 4 ) 2 SO 4 ) induced interference was 3-10 times lower. Propagation of the CO 2 + interference to other ions during standard AMS and ACSM data analysis affects the calculated OA mass, mass spectra, molecular oxygen-to-carbon ratio (O/C), and f 44 . The resulting bias may be trivial for most ambient data sets but can be significant for aerosol with higher inorganic fractions (>50%), e.g., for low ambient temperatures, or laboratory experiments. The large variation between instruments makes it imperative to regularly quantify this effect on individual AMS and ACSM systems.

Examination of segmental average mass spectra from liquid chromatography-tandem mass spectrometric (LC-MS/MS) data enables screening of multiple types of protein modifications.

PubMed

Liu, Nai-Yu; Lee, Hsiao-Hui; Chang, Zee-Fen; Tsay, Yeou-Guang

2015-09-10

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1-3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra ((sa)MS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography-mass spectrometric (LC-MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC-MS map, we have implemented a set of computer programs, or the (sa)MS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC-MS/MS data. Copyright © 2015 Elsevier B.V. All rights reserved.

Muscle mass and composition of the hip, thigh and abdominal muscles in women with and without hip osteoarthritis.

PubMed

Fukumoto, Yoshihiro; Ikezoe, Tome; Tateuchi, Hiroshige; Tsukagoshi, Rui; Akiyama, Haruhiko; So, Kazutaka; Kuroda, Yutaka; Yoneyama, Tomohide; Ichihashi, Noriaki

2012-09-01

The objective of this study was to compare muscle mass and composition between individuals with and without hip osteoarthritis. Twenty-four women with hip osteoarthritis (OA group) and 16 healthy women (healthy group) participated in this study. Muscle thickness (MT) and echo intensity (EI) were measured as indices of muscle mass and composition, respectively, using ultrasound imaging. Seven muscles were examined: gluteus maximus, gluteus medius, quadriceps femoris, rectus abdominis, external oblique, internal oblique and transversus abdominis. MT of only quadriceps femoris in the OA group was significantly thinner than that in the healthy group. EIs of gluteus medius, quadriceps femoris and rectus abdominis were significantly higher in the OA group than those in the healthy group. Thus, actual contractile tissue of gluteus medius and rectus abdominis substantially decreased, although muscle mass was similar, whereas both quantitative and qualitative changes occurred in quadriceps femoris in patients with hip OA. Copyright © 2012 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Quercetin attenuates mitochondrial dysfunction and biogenesis via upregulated AMPK/SIRT1 signaling pathway in OA rats.

PubMed

Qiu, Linan; Luo, Yuju; Chen, Xiaojuan

2018-07-01

Despite the severity of osteoarthritis (OA), current medical therapy strategies for OA aim at symptom control and pain reduction, as there is no ideal drug for effective OA treatment. OA rat model was used to explore the therapeutic function of quercetin on remission of OA, by determining the reactive oxygen species (ROS) levels, mitochondrial function and extracellular matrix integrity. Quercetin could attenuate ROS generation and augment the glutathione (GSH) and glutathione peroxidase (GPx) expression levels in OA rat. Quercetin not only enhanced mitochondrial membrane potential, oxygen consumption, adenosine triphosphate (ATP) levels in mitochondria, but also increased the mitochondrial copy number. Furthermore, the interlukin (IL)-1β-induced accumulation of nitric oxide (NO), matrixmetalloproteinase (MMP)-3) and MMP-13 could be suppressed by quercetin. Finally, we confirmed that the therapeutic properties of quercetin on OA might function through the adenosine monophosphate-activated protein kinase/sirtuin 1 (AMPK/SIRT1) signaling pathway. In summary, quercetin could alleviate OA through attenuating the ROS levels, reversing the mitochondrial dysfunction and keeping the integrality of extracellular matrix of joint cartilage. The underlying mechanism might involve the regulation of AMPK/SIRT1 signaling pathway. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Multivariate Analysis of Electron Detachment Dissociation and Infrared Multiphoton Dissociation Mass Spectra of Heparan Sulfate Tetrasaccharides Differing Only in Hexuronic acid Stereochemistry

NASA Astrophysics Data System (ADS)

Oh, Han Bin; Leach, Franklin E.; Arungundram, Sailaja; Al-Mafraji, Kanar; Venot, Andre; Boons, Geert-Jan; Amster, I. Jonathan

2011-03-01

The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture.

Method for calibrating mass spectrometers

DOEpatents

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

2002-12-24

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

Polymer Analysis by Liquid Chromatography/Electrospray Ionization Time-of-Flight Mass Spectrometry.

PubMed

Nielen, M W; Buijtenhuijs, F A

1999-05-01

Hyphenation of liquid chromatography (LC) techniques with electrospray ionization (ESI) orthogonal acceleration time-of-flight (oa-TOF) mass spectrometry (MS) provides both MS-based structural information and LC-based quantitative data in polymer analysis. In one experimental setup, three different LC modes are interfaced with MS:  size-exclusion chromatography (SEC/MS), gradient polymer elution chromatography (GPEC/MS), and liquid chromatography at the critical point of adsorption (LCCC/MS). In SEC/MS, both absolute mass calibration of the SEC column based on the polymer itself and determination of monomers and end groups from the mass spectra are achieved. GPEC/MS shows detailed chemical heterogeneity of the polymer and the chemical composition distribution within oligomer groups. In LCCC/MS, the retention behavior is primarily governed by chemical heterogeneities, such as different end group functionalities, and quantitative end group calculations can be easily made. The potential of these methods and the benefit of time-of-flight analyzers in polymer analysis are discussed using SEC/MS of a polydisperse poly(methyl methacrylate) sample, GPEC/MS of dipropoxylated bisphenol A/adipic acid polyester resin, LCCC/MS of alkylated poly(ethylene glycol), and LCCC/MS of terephthalic acid/neopentyl glycol polyester resin.

Short communication: Evaluation of MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci.

PubMed

Cameron, M; Perry, J; Middleton, J R; Chaffer, M; Lewis, J; Keefe, G P

2018-01-01

This study evaluated MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci (CNS). A total of 861 CNS isolates were used in the study, covering 21 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 804) and the remainder were identified by sequencing of hsp60 (n = 56) and tuf (n = 1). The genotypic identification was considered the gold standard identification. Using a direct transfer protocol and the existing commercial database, MALDI-TOF mass spectrometry showed a typeability of 96.5% (831/861) and an accuracy of 99.2% (824/831). Using a custom reference spectra expanded database, which included an additional 13 in-house created reference spectra, isolates were identified by MALDI-TOF mass spectrometry with 99.2% (854/861) typeability and 99.4% (849/854) accuracy. Overall, MALDI-TOF mass spectrometry using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Formation of Oxidized Organic Aerosol (OOA) through Fog Processing in the Po Valley

NASA Astrophysics Data System (ADS)

Gilardoni, S.; Paglione, M.; Rinaldi, M.; Giulianelli, L.; Massoli, P.; Hillamo, R. E.; Carbone, S.; Lanconelli, C.; Laaksonen, A. J.; Russell, L. M.; Poluzzi, V.; Fuzzi, S.; Facchini, C.

2014-12-01

Aqueous phase chemistry might be responsible for the formation of a significant fraction of the organic aerosol (OA) observed in the atmosphere, and could explain some of the discrepancies between OA concentration and properties predicted by models and observed in the environment. Aerosol - fog interaction and its effect on submicron aerosol properties were investigated in the Po Valley (northern Italy) during fall 2011, in the framework of the Supersite project (ARPA Emilia Romagna). Composition and physical properties of submicron aerosol were measured online by a High Resolution- Time of Flight - Aerosol Mass Spectrometer (HR-TOF-AMS), a Soot Photometer - Aerosol Mass Spectrometer (SP-AMS), and a Tandem Differential Mobility Particle Sizer (TDMPS). Organic functional group analysis was performed off-line by Hydrogen - Nuclear Magnetic Resonance (H-NMR) spectrometry and by Fourier Transform Infrared (FTIR) spectrometry. Aerosol absorption, scattering, and total extinction were measured simultaneously with a Particle Soot Absorption Photometer (PSAP), a Nephelometer, and a Cavity Attenuated Phase Shift Spectrometer particle extinction monitor (CAPS PMex), respectively. Water-soluble organic carbon in fog-water was characterized off-line by HR-TOF-AMS. Fourteen distinct fog events were observed. Fog dissipation left behind an aerosol enriched in particles larger than 400 nm, typical of fog and cloud processing, and dominated by secondary species, including ammonium nitrate, ammonium sulfate and oxidized OA (OOA). Source apportionment of OA allowed us to identify OOA as the difference between total OA and primary OA (hydrocarbon like OA and biomass burning OA). The formation of OOA through fog processing is proved by the correlation of OOA concentration with hydroxyl methyl sulfonate signal and by the similarity of OOA spectra with organic mass spectra obtained by re-aerosolization of fog water samples. The oxygen to carbon ratio and the hydrogen to carbon ratio of

Laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF): performance, reference spectra and classification of atmospheric samples

NASA Astrophysics Data System (ADS)

Shen, Xiaoli; Ramisetty, Ramakrishna; Mohr, Claudia; Huang, Wei; Leisner, Thomas; Saathoff, Harald

2018-04-01

The laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF, AeroMegt GmbH) is able to identify the chemical composition and mixing state of individual aerosol particles, and thus is a tool for elucidating their impacts on human health, visibility, ecosystem, and climate. The overall detection efficiency (ODE) of the instrument we use was determined to range from ˜ (0.01 ± 0.01) to ˜ (4.23 ± 2.36) % for polystyrene latex (PSL) in the size range of 200 to 2000 nm, ˜ (0.44 ± 0.19) to ˜ (6.57 ± 2.38) % for ammonium nitrate (NH4NO3), and ˜ (0.14 ± 0.02) to ˜ (1.46 ± 0.08) % for sodium chloride (NaCl) particles in the size range of 300 to 1000 nm. Reference mass spectra of 32 different particle types relevant for atmospheric aerosol (e.g. pure compounds NH4NO3, K2SO4, NaCl, oxalic acid, pinic acid, and pinonic acid; internal mixtures of e.g. salts, secondary organic aerosol, and metallic core-organic shell particles; more complex particles such as soot and dust particles) were determined. Our results show that internally mixed aerosol particles can result in spectra with new clusters of ions, rather than simply a combination of the spectra from the single components. An exemplary 1-day ambient data set was analysed by both classical fuzzy clustering and a reference-spectra-based classification method. Resulting identified particle types were generally well correlated. We show how a combination of both methods can greatly improve the interpretation of single-particle data in field measurements.

“Let’s Talk about OA Pain”: A Qualitative Analysis of the Perceptions of People Suffering from OA. Towards the Development of a Specific Pain OA-Related Questionnaire, the Osteoarthritis Symptom Inventory Scale (OASIS)

PubMed Central

Cedraschi, Christine; Delézay, Sylvie; Marty, Marc; Berenbaum, Francis; Bouhassira, Didier; Henrotin, Yves; Laroche, Françoise; Perrot, Serge

2013-01-01

Introduction Pain is the primary outcome measurement in osteoarthritis, and its assessment is mostly based on its intensity. The management of this difficult chronic condition could be improved by using pain descriptors to improve analyses of painful sensations. This should help to define subgroups of patients based on pain phenotype, for more adapted treatment. This study draws upon patients’ descriptions of their pain, to identify and understand their perception of osteoarthritis pain and to categorize pain dimensions. Methods This qualitative study was conducted with representative types of patients suffering from osteoarthritis. Two focus groups were conducted with a sample of 14 participants, with either recent or chronic OA, at one or multiple sites. Focus groups were semi-structured and used open-ended questions addressing personal experiences to explore the experiences of patients with OA pain and the meanings they attributed to these pains. Results Two main points emerged from content analyses: -A major difficulty in getting patients to describe their osteoarthritis pain: perception that nobody wants to hear about it; necessity to preserve one’s self and social image; notion of self-imposed stoicism; and perception of osteoarthritis as a complex, changing, illogical disease associated with aging. -Osteoarthritis pains were numerous and differed in intensity, duration, depth, type of occurrence, impact and rhythm, but also in painful sensations and associated symptoms. Based on analyses of the verbatim interviews, seven dimensions of OA pain emerged: pain sensory description, OA-related symptoms, pain variability profile, pain-triggering factors, pain and physical activity, mood and image, general physical symptoms. Summary In osteoarthritis, pain analysis should not be restricted to intensity. Our qualitative study identified pain descriptors and defined seven dimensions of osteoarthritis pain. Based on these dimensions, we aim to develop a specific

Source apportionment of submicron organic aerosol collected from Atlanta, Georgia, during 2014-2015 using the aerosol chemical speciation monitor (ACSM)

NASA Astrophysics Data System (ADS)

Rattanavaraha, Weruka; Canagaratna, Manjula R.; Budisulistiorini, Sri Hapsari; Croteau, Philip L.; Baumann, Karsten; Canonaco, Francesco; Prevot, Andre S. H.; Edgerton, Eric S.; Zhang, Zhenfa; Jayne, John T.; Worsnop, Douglas R.; Gold, Avram; Shaw, Stephanie L.; Surratt, Jason D.

2017-10-01

The Aerodyne Aerosol Chemical Speciation Monitor (ACSM) was redeployed at the Jefferson Street (JST) site in downtown Atlanta, Georgia (GA) for 1 year (March 20, 2014-February 08, 2015) to chemically characterize non-refractory submicron particulate matter (NR-PM1) in near real-time and to assess whether organic aerosol (OA) types and amounts change from year-to-year. Submicron organic aerosol (OA) mass spectra were analyzed by season using multilinear engine (ME-2) to apportion OA subtypes to potential sources and chemical processes. A suite of real-time collocated measurements from the Southeastern Aerosol Research and Characterization (SEARCH) network was compared with ME-2 factor solutions to aid in the interpretation of OA subtypes during each season. OA tracers measured from high-volume filter samples using gas chromatography interfaced with electron ionization-mass spectrometry (GC/EI-MS) also aided in identifying OA sources. The initial application of ME-2 to the yearlong ACSM dataset revealed that OA source apportionment by season was required to better resolve sporadic OA types. Spring and fall OA mass spectral datasets were separated into finer periods to capture potential OA sources resulting from non-homogeneous emissions during transitioning periods. NR-PM1 was highest in summer (16.7 ± 8.4 μg m-3) and lowest in winter (8.0 ± 5.7 μg m-3), consistent with prior studies. OA dominated NR-PM1 mass (56-74% on average) in all seasons. Hydrocarbon-like OA (HOA) from primary emissions was observed in all seasons, averaging 5-22% of total OA mass. Strong correlations of HOA with carbon monoxide (CO) (R = 0.71-0.88) and oxides of nitrogen (NOx) (R = 0.55-0.79) indicated that vehicular traffic was the likely source. Biomass burning OA (BBOA) was observed in all seasons, with lower contributions (2%) in summer and higher in colder seasons (averaging 8-20% of total OA mass). BBOA correlated strongly with levoglucosan (R = 0.78-0.95) during colder seasons

Ion mobility mass spectrometry for ion recovery and clean-up of MS and MS/MS spectra obtained from low abundance viral samples

PubMed Central

Harvey, David J.; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H.

2016-01-01

Graphical abstract Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This paper describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-Glycans were released enzymatically from within SDS-PAGE gels, from the representative glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer. Clean profiles of singly, doubly and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up showing that the extra dimension provided by ion mobility was invaluable for studies of this type. PMID:26204966

Identification of 19-epi-okadaic acid, a new diarrhetic shellfish poisoning toxin, by liquid chromatography with mass spectrometry detection.

PubMed

Paz, Beatriz; Daranas, Antonio H; Cruz, Patricia G; Franco, José M; Norte, Manuel; Fernández, José J

2008-01-01

Okadaic acid (1) (OA) and its congeners are mainly responsible for diarrhetic shellfish poisoning (DSP) syndrome. The presence of several OA derivatives have already been confirmed in Prorocentrum and Dinophysis spp. In this paper, we report on the detection and identification of a new DSP toxin, the OA isomer 19-epi-okadaic acid (2) (19-epi-OA), isolated from cultures of Prorocentrum belizeanum, by determining its retention time (RT) and fragmentation pattern using liquid chromatography coupled with mass spectrometry (LC-MS/MS).

Measurement of Dielectron Invariant Mass Spectra in Au + Au Collisions at p sNN = 200GeV with HBD in PHENIX

NASA Astrophysics Data System (ADS)

Sun, Jiayin

Dileptons are emitted throughout the entire space-time evolution of heavy ion collisions. Being colorless, these electromagnetic probes do not participate in the final-state strong interactions during the passage through the hot medium, and retain the information on the conditions of their creation. This characteristic renders them valuable tools for studying the properties of the Quark Gluon Plasma created during ultra-relativistic heavy ion collisions. The invariant mass spectra of dileptons contain a wealth of information on every stage of the evolution of heavy ion collisions. At low mass, dilepton spectra consist mainly of light meson decays. The medium modification of the light vector mesons gives insight on the chiral symmetry restoration in heavy ion collisions. At intermediate and high mass, there are significant contributions from charm and bottom, with a minor contribution from QGP thermal radiation. The region was utilized to measure cross sections of open charm and open bottom, as well as quarkonium suppression as demonstrated by PHENIX. An earlier PHENIX measurement of dielectron spectra in heavy ion collisions, using data taken in 2004, shows significant deviations from the hadronic decay expectations. The measurement, however, suffered from an unfavorable signal to background ratio. Random combination of electron-positron pairs from unrelated sources, mostly Dalitz decay of pi0 and external conversion of decay photon to electrons, is the main contributor to the background. Mis-identified hadrons are another major background source. To improve the situation, the Hadron Blind Detector (HBD), a windowless proximity focusing Cerenkov detector, is designed to reduce this background by identifying electron tracks from photon conversions and pi. 0 Dalitzdecays. The detector has been installed and operated in PHENIX in 2009 and 2010, where reference p+p and Au+Au data sets were successfully taken. We will present the dielectron results from the analysis of

Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs.

PubMed

Yan, Yan; Zhang, Kaizhong

2016-12-23

De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance of de novo sequencing is greatly improved. Currently, with large amount of spectra sequenced everyday, spectra libraries containing tens of thousands of annotated experimental MS/MS spectra become available. These libraries provide information of the spectra properties, thus have the potential to be used with de novo sequencing to improve its performance. In this study, an improved de novo sequencing method assisted with spectra library is proposed. It uses spectra libraries as training datasets and introduces significant scores of the features used in our previous de novo sequencing method for HCD and ETD spectra pairs. Two pairs of HCD and ETD spectral datasets were used to test the performance of the proposed method and our previous method. The results show that this proposed method achieves better sequencing accuracy with higher ranked correct sequences and less computational time. This paper proposed an advanced de novo sequencing method for HCD and ETD spectra pair and used information from spectra libraries and significant improved previous similar methods.

Clinically important improvement in function is common in people with or at high risk of knee OA: the MOST study

PubMed Central

White, Daniel K.; Keysor, Julie J.; LaValley, Michael P.; Lewis, Cora E.; Torner, James C.; Nevitt, Michael C.; Felson, David T.

2010-01-01

To calculate the frequency of clinically important improvement in function over 30 months and identify risk factors in people who have or are at risk of knee OA. Subjects were from MOST, a longitudinal study of persons with or at high risk of knee OA. We defined Minimal Clinically Important Improvement (MCII) with WOMAC physical function using three different methods. Baseline risk factors tested for improvement included age, gender, educational attainment, presence of radiographic knee OA (ROA), the number of comorbidities, Body Mass Index (BMI), knee pain, walking speed, isokinetic knee extensor strength, depressive symptoms, physical activity, and medication usage. We used logistic regression to evaluate the association of baseline risk factors with MCII. Of the 1801 subjects (age= 63, BMI= 31, 63% female), most had mild limitations in baseline function (WOMAC = 19 +/− 11). Regardless how defined, a substantial percentage of subjects (24%–39%) reached MCII at 30 months. Compared to their counterparts, people with MCII were less likely to have ROA and to use medications, and were more likely to have a lower BMI, less knee pain, a faster walking speed, more knee strength, and fewer depressive symptoms. After adjustment, MCII was 40% to 50% less likely in those with ROA, and 1.9 to 2.0 times more likely in those walking 1.0 m/s faster than counterparts. Clinically important improvement is frequent in people with or at high risk of knee OA. The absence of ROA and a faster walking speed appear to be associated with clinically important improvements. PMID:20395640

Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

PubMed Central

Chandler, Kevin Brown; Pompach, Petr; Goldman, Radoslav

2013-01-01

Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something which detached N-glycan and de-glycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy which takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false-discovery-rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at false-discovery-rate 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at false-discovery-rate 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http

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

PubMed

Raznikova, M O; Raznikov, V V

2015-01-01

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

OA-7 Cargo Module Move from Airlock to Highbay

NASA Image and Video Library

2017-01-10

Inside an environmentally controlled shipping container the Orbital ATK OA-7 Cygnus spacecraft's pressurized cargo module (PCM) moves from an airlock to the high bay of the Space Station Processing Facility of NASA's Kennedy Space Center in Florida. Scheduled to launch on March 19, 2017, the Orbital ATK OA-7 mission will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

OA-7 Cargo Module Move from Airlock to Highbay

NASA Image and Video Library

2017-01-10

The Orbital ATK OA-7 Cygnus spacecraft's pressurized cargo module (PCM) arrives at the Space Station Processing Facility of NASA's Kennedy Space Center in Florida. The PCM is sealed in an environmentally controlled shipping container. Scheduled to launch on March 19, 2017, the Orbital ATK OA-7 mission will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

Identification of 19-epi-okadaic Acid, a New Diarrhetic Shellfish Poisoning Toxin, by Liquid Chromatography with Mass Spectrometry Detection

PubMed Central

Paz, Beatriz; Daranas, Antonio H.; Cruz, Patricia G.; Franco, José M.; Norte, Manuel; Fernández, José J.

2008-01-01

Okadaic acid (1) (OA) and its congeners are mainly responsible for diarrhetic shellfish poisoning (DSP) syndrome. The presence of several OA derivatives have already been confirmed in Prorocentrum and Dinophysis spp. In this paper, we report on the detection and identification of a new DSP toxin, the OA isomer 19-epi-okadaic acid (2) (19-epi-OA), isolated from cultures of Prorocentrum belizeanum, by determining its retention time (RT) and fragmentation pattern using liquid chromatography coupled with mass spectrometry (LC–MS/MS). PMID:19005581

Time of flight mass spectra of ions in plasmas produced by hypervelocity impacts of organic and mineralogical microparticles on a cosmic dust analyser

NASA Astrophysics Data System (ADS)

Goldsworthy, B. J.; Burchell, M. J.; Cole, M. J.; Armes, S. P.; Khan, M. A.; Lascelles, S. F.; Green, S. F.; McDonnell, J. A. M.; Srama, R.; Bigger, S. W.

2003-10-01

The ionic plasma produced by a hypervelocity particle impact can be analysed to determine compositional information for the original particle by using a time-of-flight mass spectrometer. Such methods have been adopted on interplanetary dust detectors to perform in-situ analyses of encountered grains, for example, the Cassini Cosmic Dust Analyser (CDA). In order to more fully understand the data returned by such instruments, it is necessary to study their response to impacts in the laboratory. Accordingly, data are shown here for the mass spectra of ionic plasmas, produced through the acceleration of microparticles via a 2 MV van de Graaff accelerator and their impact on a dimensionally correct CDA model with a rhodium target. The microparticle dusts examined have three different chemical compositions: metal (iron), organic (polypyrrole and polystyrene latex) and mineral (aluminosilicate clay). These microparticles have mean diameters in the range 0.1 to 1.6 mu m and their velocities range from 1-50 km s-1. They thus cover a wide range of compositions, sizes and speeds expected for dust particles encountered by spacecraft in the Solar System. The advent of new low-density, microparticles with highly controllable attributes (composition, size) has enabled a number of new investigations in this area. The key is the use of a conducting polymer, either as the particle itself or as a thin overlayer on organic (or inorganic) core particles. This conductive coating permits efficient electrostatic charging and acceleration. Here, we examine how the projectile's chemical composition influences the ionic plasma produced after the hypervelocity impact. This study thus extends our understanding of impact plasma formation and detection. The ionization yield normalized to particle mass was found to depend on impact speed to the power (3.4 +/- 0.1) for iron and (2.9 +/- 0.1) for polypyrrole coated polystyrene and aluminosilicate clay. The ioization signal rise time was found to

Baseline Vitamin D Status is Predictive of Longitudinal Change in Tibial BMD in Knee Osteoarthritis (OA)

USDA-ARS?s Scientific Manuscript database

With its lack of effective treatment and high prevalence, the public health impact of OA is substantial. Peri-articular bone in OA can be evaluated with the medial:lateral tibial BMD ratio (M:L BMD) obtained from dual x-ray absorptiometry (DXA). Higher M:L BMD is associated with medial OA features...

Subgroup analyses of the effectiveness of oral glucosamine for knee and hip osteoarthritis: a systematic review and individual patient data meta-analysis from the OA trial bank.

PubMed

Runhaar, Jos; Rozendaal, Rianne M; van Middelkoop, Marienke; Bijlsma, Hans J W; Doherty, Michael; Dziedzic, Krysia S; Lohmander, L Stefan; McAlindon, Timothy; Zhang, Weiya; Bierma Zeinstra, Sita

2017-11-01

To evaluate the effectiveness of oral glucosamine in subgroups of people with hip or knee osteoarthritis (OA) based on baseline pain severity, body mass index (BMI), sex, structural abnormalities and presence of inflammation using individual patient data. After a systematic search of the literature and clinical trial registries, all randomised controlled trials (RCTs) evaluating the effect of any oral glucosamine substance in patients with clinically or radiographically defined hip or knee OA were contacted. As a minimum, pain, age, sex and BMI at baseline and pain as an outcome measure needed to be assessed. Of 21 eligible studies, six (n=1663) shared their trial data with the OA Trial Bank. Five trials (all independent of industry, n=1625) compared glucosamine with placebo, representing 55% of the total number of participants in all published placebo-controlled RCTs. Glucosamine was no better than placebo for pain or function at short (3 months) and long-term (24 months) follow-up. Glucosamine was also no better than placebo among the predefined subgroups. Stratification for knee OA and type of glucosamine did not alter these results. Although proposed and debated for several years, open trial data are not widely made available for studies of glucosamine for OA, especially those sponsored by industry. Currently, there is no good evidence to support the use of glucosamine for hip or knee OA and an absence of evidence to support specific consideration of glucosamine for any clinically relevant OA subgroup according to baseline pain severity, BMI, sex, structural abnormalities or presence of inflammation. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

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

DOE PAGES

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

2016-04-26

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

Systematic review of the concurrent and predictive validity of MRI biomarkers in OA

PubMed Central

Hunter, D.J.; Zhang, W.; Conaghan, Philip G.; Hirko, K.; Menashe, L.; Li, L.; Reichmann, W.M.; Losina, E.

2012-01-01

SUMMARY Objective To summarize literature on the concurrent and predictive validity of MRI-based measures of osteoarthritis (OA) structural change. Methods An online literature search was conducted of the OVID, EMBASE, CINAHL, PsychInfo and Cochrane databases of articles published up to the time of the search, April 2009. 1338 abstracts obtained with this search were preliminarily screened for relevance by two reviewers. Of these, 243 were selected for data extraction for this analysis on validity as well as separate reviews on discriminate validity and diagnostic performance. Of these 142 manuscripts included data pertinent to concurrent validity and 61 manuscripts for the predictive validity review. For this analysis we extracted data on criterion (concurrent and predictive) validity from both longitudinal and cross-sectional studies for all synovial joint tissues as it relates to MRI measurement in OA. Results Concurrent validity of MRI in OA has been examined compared to symptoms, radiography, histology/pathology, arthroscopy, CT, and alignment. The relation of bone marrow lesions, synovitis and effusion to pain was moderate to strong. There was a weak or no relation of cartilage morphology or meniscal tears to pain. The relation of cartilage morphology to radiographic OA and radiographic joint space was inconsistent. There was a higher frequency of meniscal tears, synovitis and other features in persons with radiographic OA. The relation of cartilage to other constructs including histology and arthroscopy was stronger. Predictive validity of MRI in OA has been examined for ability to predict total knee replacement (TKR), change in symptoms, radiographic progression as well as MRI progression. Quantitative cartilage volume change and presence of cartilage defects or bone marrow lesions are potential predictors of TKR. Conclusion MRI has inherent strengths and unique advantages in its ability to visualize multiple individual tissue pathologies relating to pain

Integration of the B-52G Offensive Avionics System (OAS) with the Global Positioning System (GPS)

NASA Astrophysics Data System (ADS)

Foote, A. L.; Pluntze, S. C.

Integration of the B-52G OAS with the GPS has been accomplished by modification of existing OAS software. GPS derived position and velocity data are used to enhance the quality of the OAS inertial and dead reckoning navigation systems. The engineering design and the software development process used to implement this design are presented.

Unassigned MS/MS Spectra: Who Am I?

PubMed

Pathan, Mohashin; Samuel, Monisha; Keerthikumar, Shivakumar; Mathivanan, Suresh

2017-01-01

Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process. In a typical MS data analysis, about 60 % of the MS/MS spectra remains unassigned. While some of these could attribute to the low quality of the MS/MS spectra, a proportion can be classified as high quality. Further analysis may reveal how much of the unassigned MS spectra attribute to search space, sequence annotation errors, mutations, and/or posttranslational modifications. In this chapter, the tools used to identify proteins and ways to assign unassigned tandem MS spectra are discussed.

VIRIAL BLACK HOLE MASS ESTIMATES FOR 280,000 AGNs FROM THE SDSS BROADBAND PHOTOMETRY AND SINGLE-EPOCH SPECTRA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozłowski, Szymon, E-mail: simkoz@astrouw.edu.pl

2017-01-01

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

Pathomechanics of Post-Traumatic OA Development in the Military Following Articular Fracture

DTIC Science & Technology

2017-10-01

AWARD NUMBER: W81XWH-15-2-0087 TITLE: Pathomechanics of Post -Traumatic OA Development in the Military Following Articular Fracture PRINCIPAL...Sep 2017 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Pathomechanics of Post -Traumatic OA Development in the Military Following Articular Fracture 5b...develop new models for predicting the risk of post -traumatic osteoarthritis (PTOA) following intra-articular fracture (IAF). We have analyzed pre

Electronic Absorption Spectra of Mass-Selected Hydrocarbon Cations in Solid Neon: C_nH_4+ (n=5-8,10,12)

NASA Astrophysics Data System (ADS)

Nagy, A.; Fulara, J.; Garkusha, I.; Maier, J. P.

2011-05-01

Small, unsaturated hydrocarbons, C_nH_m (n,m≤6), play an important role in astrochemical models as they have been detected in various space objects such as the interstellar medium or envelopes of carbon-rich stars. Although identification of most of these species was based on rotational studies, they are candidate carriers of the infamous diffuse interstellar bands. It has been proposed that corresponding cationic species formed upon UV radiation may also be of astrophysical relevance; therefore, their optical spectra need to be determined. In this contribution, electronic absorption spectra of mass-selected C_nH_4+ (n=5-8,10,12) ions trapped in neon matrices are presented. The cations were produced in a hot-cathode discharge source, guided through a series of electrostatic lenses, mass filtered and co-deposited with excess of neon onto a rhodium-coated sapphire plate held at 6 K. In the same experiments, neutral species were generated from the cations by a photobleaching procedure.

Body mass index affects knee joint mechanics during gait differently with and without moderate knee osteoarthritis.

PubMed

Harding, Graeme T; Hubley-Kozey, Cheryl L; Dunbar, Michael J; Stanish, William D; Astephen Wilson, Janie L

2012-11-01

Obesity is a highly cited risk factor for knee osteoarthritis (OA), but its role in knee OA pathogenesis and progression is not as clear. Excess weight may contribute to an increased mechanical burden and altered dynamic movement and loading patterns at the knee. The objective of this study was to examine the interacting role of moderate knee OA disease presence and obesity on knee joint mechanics during gait. Gait analysis was performed on 104 asymptomatic and 140 individuals with moderate knee OA. Each subject group was divided into three body mass categories based on body mass index (BMI): healthy weight (BMI<25), overweight (25≤BMI≤30), and obese (BMI>30). Three-dimensional knee joint angles and net external knee joint moments were calculated and waveform principal component analysis (PCA) was applied to extract major patterns of variability from each. PC scores for major patterns were compared between groups using a two-factor ANOVA. Significant BMI main effects were found in the pattern of the knee adduction moment, the knee flexion moment, and the knee rotation moment during gait. Two interaction effects between moderate OA disease presence and BMI were also found that described different changes in the knee flexion moment and the knee flexion angle with increased BMI with and without knee OA. Our results suggest that increased BMI is associated with different changes in biomechanical patterns of the knee joint during gait depending on the presence of moderate knee OA. Copyright © 2012 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Prevalence of radiographic hip osteoarthritis is increased in high bone mass.

PubMed

Hardcastle, S A; Dieppe, P; Gregson, C L; Hunter, D; Thomas, G E R; Arden, N K; Spector, T D; Hart, D J; Laugharne, M J; Clague, G A; Edwards, M H; Dennison, E M; Cooper, C; Williams, M; Davey Smith, G; Tobias, J H

2014-08-01

Epidemiological studies have shown an association between increased bone mineral density (BMD) and osteoarthritis (OA), but whether this represents cause or effect remains unclear. In this study, we used a novel approach to investigate this question, determining whether individuals with High Bone Mass (HBM) have a higher prevalence of radiographic hip OA compared with controls. HBM cases came from the UK-based HBM study: HBM was defined by BMD Z-score. Unaffected relatives of index cases were recruited as family controls. Age-stratified random sampling was used to select further population controls from the Chingford and Hertfordshire cohort studies. Pelvic radiographs were pooled and assessed by a single observer blinded to case-control status. Analyses used logistic regression, adjusted for age, gender and body mass index (BMI). 530 HBM hips in 272 cases (mean age 62.9 years, 74% female) and 1702 control hips in 863 controls (mean age 64.8 years, 84% female) were analysed. The prevalence of radiographic OA, defined as Croft score ≥3, was higher in cases compared with controls (20.0% vs 13.6%), with adjusted odds ratio (OR) [95% CI] 1.52 [1.09, 2.11], P = 0.013. Osteophytes (OR 2.12 [1.61, 2.79], P < 0.001) and subchondral sclerosis (OR 2.78 [1.49, 5.18], P = 0.001) were more prevalent in cases. However, no difference in the prevalence of joint space narrowing (JSN) was seen (OR 0.97 [0.72, 1.33], P = 0.869). An increased prevalence of radiographic hip OA and osteophytosis was observed in HBM cases compared with controls, in keeping with a positive association between HBM and OA and suggesting that OA in HBM has a hypertrophic phenotype. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

The ambient aerosol characterization during the prescribed bushfire season in Brisbane 2013.

PubMed

Milic, A; Miljevic, B; Alroe, J; Mallet, M; Canonaco, F; Prevot, A S H; Ristovski, Z D

2016-08-01

Prescribed burnings are conducted in Queensland each year from August until November aiming to decrease the impact of bushfire hazards and maintain the health of vegetation. This study reports chemical characteristics of the ambient aerosol, with a focus on source apportionment of the organic aerosol (OA) fraction, during the prescribed biomass burning (BB) season in Brisbane 2013. All measurements were conducted within the International Laboratory for Air Quality and Health (ILAQH) located in Brisbane's Central Business District. Chemical composition, degree of ageing and the influence of BB emission on the air quality of central Brisbane were characterized using a compact Time of Flight Aerosol Mass Spectrometer (cToF-AMS). AMS loadings were dominated by OA (64%), followed by, sulfate (17%), ammonium (14%) and nitrates (5%). Source apportionment was applied on the AMS OA mass spectra via the multilinear engine solver (ME-2) implementation within the recently developed Source Finder (SoFi) interface. Six factors were extracted including hydrocarbon-like OA (HOA), cooking-related OA (COA), biomass burning OA (BBOA), low-volatility oxygenated OA (LV-OOA), semivolatile oxygenated OA (SV-OOA), and nitrogen-enriched OA (NOA). The aerosol fraction that was attributed to BB factor was 9%, on average over the sampling period. The high proportion of oxygenated OA (72%), typically representing aged emissions, could possess a fraction of oxygenated species transfored from BB components on their way to the sampling site. Copyright © 2016 Elsevier B.V. All rights reserved.

Comprehensive identification and structural characterization of target components from Gelsemium elegans by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry based on accurate mass databases combined with MS/MS spectra.

PubMed

Liu, Yan-Chun; Xiao, Sa; Yang, Kun; Ling, Li; Sun, Zhi-Liang; Liu, Zhao-Ying

2017-06-01

This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data-dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC-QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans, but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds.

PubMed

Milman, Boris L

2005-01-01

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers. 2005 John

Pathomechanics of Post-Traumatic OA Development in the Military Following Articular Fracture

DTIC Science & Technology

2016-10-01

post -op CT) associated with IAFs, but more patient data are needed to make the risk models clinically useful. Prospective studies of PTOA...AWARD NUMBER: W81XWH-15-2-0087 TITLE: Pathomechanics of Post -Traumatic OA Development in the Military Following Articular Fracture PRINCIPAL...29 Sep 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Pathomechanics of Post -Traumatic OA Development in the Military Following Articular Fracture

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be

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

PubMed

Turewicz, Michael; Deutsch, Eric W

2011-01-01

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

Mass loss

NASA Technical Reports Server (NTRS)

Goldberg, Leo

1987-01-01

Observational evidence for mass loss from cool stars is reviewed. Spectra line profiles are used for the derivation of mass-loss rates with the aid of the equation of continuity. This equation implies steady mass loss with spherical symmetry. Data from binary stars, Mira variables, and red giants in globular clusters are examined. Silicate emission is discussed as a useful indicator of mass loss in the middle infrared spectra. The use of thermal millimeter-wave radiation, Very Large Array (VLA) measurement of radio emission, and OH/IR masers are discussed as a tool for mass loss measurement. Evidence for nonsteady mass loss is also reviewed.

Simultaneous detection of low and high molecular weight carbonylated compounds derived from lipid peroxidation by electrospray ionization-tandem mass spectrometry.

PubMed

Milic, Ivana; Hoffmann, Ralf; Fedorova, Maria

2013-01-02

Reactive oxygen species (ROS) and other oxidative agents such as free radicals can oxidize polyunsaturated fatty acids (PUFA) as well as PUFA in lipids. The oxidation products can undergo consecutive reactions including oxidative cleavages to yield a chemically diverse group of products, such as lipid peroxidation products (LPP). Among them are aldehydes and ketones ("reactive carbonyls") that are strong electrophiles and thus can readily react with nucleophilic side chains of proteins, which can alter the protein structure, function, cellular distribution, and antigenicity. Here, we report a novel technique to specifically derivatize both low molecular and high molecular weight carbonylated LPP with 7-(diethylamino)coumarin-3-carbohydrazide (CHH) and analyze all compounds by electrospray ionization-mass spectrometry (ESI-MS) in positive ion mode. CHH-derivatized compounds were identified by specific neutral losses or fragment ions. The fragment ion spectra displayed additional signals that allowed unambiguous identification of the lipid, fatty acids, cleavage sites, and oxidative modifications. Oxidation of docosahexaenoic (DHA, 22:6), arachidonic (AA, 20:4), linoleic (LA, 18:2), and oleic acids (OA, 18:1) yielded 69 aliphatic carbonyls, whose structures were all deduced from the tandem mass spectra. When four phosphatidylcholine (PC) vesicles containing the aforementioned unsaturated fatty acids were oxidized, we were able to deduce the structures of 122 carbonylated compounds from the tandem mass spectra of a single shotgun analysis acquired within 15 min. The high sensitivity (LOD ∼ 1 nmol/L for 4-hydroxy-2-nonenal, HNE) and a linear range of more than 3 orders of magnitude (10 nmol/L to 10 μmol/L for HNE) will allow further studies on complex biological samples including plasma.

High-Resolution Electrospray Ionization Mass Spectrometry Analysis of Water- Soluble Organic Aerosols Collected with a Particle into Liquid Sampler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bateman, Adam P.; Nizkorodov, Serguei; Laskin, Julia

2010-10-01

This work demonstrates the utility of a particle-into-liquid sampler (PILS) a technique traditionally used for identification of inorganic ions present in ambient or laboratory aerosols for the analysis of water soluble organic aerosol (OA) using high resolution electrospray ionization mass spectrometry (HR ESI-MS). Secondary organic aerosol (SOA) was produced from 0.5 ppm mixing ratios of limonene and ozone in a 5 m3 Teflon chamber. SOA was collected simultaneously using a traditional filter sampler and a PILS. The filter samples were later extracted with either water or acetonitrile, while the aqueous PILS samples were analyzed directly. In terms of peak intensities,more » types of detectable compounds, average O:C ratios, and organic mass to organic carbon ratios, the resulting high resolution mass spectra were essentially identical for the PILS and filter based samples. SOA compounds extracted from both filter/acetonitrile extraction and PILS/water extraction accounted for >95% of the total ion current in ESI mass spectra. This similarity was attributed to high solubility of limonene SOA in water. In contrast, significant differences in detected ions and peak abundances were observed for pine needle biomass burning organic aerosol (BBOA) collected with PILS and filter sampling. The water soluble fraction of BBOA is considerably smaller than for SOA, and a number of unique peaks were detectable only by the filter/acetonitrile method. The combination of PILS collection with HR-ESI-MS analysis offers a new approach for molecular analysis of the water-soluble organic fraction in biogenic SOA, aged photochemical smog, and BBOA.« less

Urban increments of gaseous and aerosol pollutants and their sources using mobile aerosol mass spectrometry measurements

NASA Astrophysics Data System (ADS)

Elser, Miriam; Bozzetti, Carlo; El-Haddad, Imad; Maasikmets, Marek; Teinemaa, Erik; Richter, Rene; Wolf, Robert; Slowik, Jay G.; Baltensperger, Urs; Prévôt, André S. H.

2016-06-01

Air pollution is one of the main environmental concerns in urban areas, where anthropogenic emissions strongly affect air quality. This work presents the first spatially resolved detailed characterization of PM2.5 (particulate matter with aerodynamic equivalent diameter daero ≤ 2.5 µm) in two major Estonian cities, Tallinn and Tartu. The measurements were performed in March 2014 using a mobile platform. In both cities, the non-refractory (NR)-PM2.5 was characterized by a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) using a recently developed lens which increases the transmission of super-micron particles. Equivalent black carbon (eBC) and several trace gases including carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were also measured. The chemical composition of PM2.5 was found to be very similar in the two cities. Organic aerosol (OA) constituted the largest fraction, explaining on average about 52 to 60 % of the PM2.5 mass. Four sources of OA were identified using positive matrix factorization (PMF): hydrocarbon-like OA (HOA, from traffic emissions), biomass burning OA (BBOA, from biomass combustion), residential influenced OA (RIOA, probably mostly from cooking processes with possible contributions from waste and coal burning), and oxygenated OA (OOA, related to secondary aerosol formation). OOA was the major OA source during nighttime, explaining on average half of the OA mass, while during daytime mobile measurements the OA was affected by point sources and dominated by the primary fraction. A strong increase in the secondary organic and inorganic components was observed during periods with transport of air masses from northern Germany, while the primary local emissions accumulated during periods with temperature inversions. Mobile measurements offered the identification of different source regions within the urban areas and the assessment of the extent to which pollutants concentrations exceeded regional background

Chemical characteristics of submicron particles at the central Tibetan Plateau: insights from aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Xu, Jianzhong; Zhang, Qi; Shi, Jinsen; Ge, Xinlei; Xie, Conghui; Wang, Junfeng; Kang, Shichang; Zhang, Ruixiong; Wang, Yuhang

2018-01-01

Recent studies have revealed a significant influx of anthropogenic aerosol from South Asia to the Himalayas and Tibetan Plateau (TP) during pre-monsoon period. In order to characterize the chemical composition, sources, and transport processes of aerosol in this area, we carried out a field study during June 2015 by deploying a suite of online instruments including an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-AMS) and a multi-angle absorption photometer (MAAP) at Nam Co station (90°57' E, 30°46' N; 4730 m a.s.l.) at the central of the TP. The measurements were made at a period when the transition from pre-monsoon to monsoon occurred. The average ambient mass concentration of submicron particulate matter (PM1) over the whole campaign was ˜ 2.0 µg m-3, with organics accounting for 68 %, followed by sulfate (15 %), black carbon (8 %), ammonium (7 %), and nitrate (2 %). Relatively higher aerosol mass concentration episodes were observed during the pre-monsoon period, whereas persistently low aerosol concentrations were observed during the monsoon period. However, the chemical composition of aerosol during the higher aerosol concentration episodes in the pre-monsoon season was on a case-by-case basis, depending on the prevailing meteorological conditions and air mass transport routes. Most of the chemical species exhibited significant diurnal variations with higher values occurring during afternoon and lower values during early morning, whereas nitrate peaked during early morning in association with higher relative humidity and lower air temperature. Organic aerosol (OA), with an oxygen-to-carbon ratio (O / C) of 0.94, was more oxidized during the pre-monsoon period than during monsoon (average O / C ratio of 0.72), and an average O / C was 0.88 over the entire campaign period, suggesting overall highly oxygenated aerosol in the central TP. Positive matrix factorization of the high-resolution mass spectra of OA identified two oxygenated

Rapid, Automated Determination of Elemental Compositions of Ions in Mass Spectra Obtained with an Open-Air Ion Source (2 of 2)

EPA Science Inventory

An inexpensive autosampler for a DART/TOFMS provides mass spectra from analytes absorbed on 76 cotton swab, wipe samples in 7.5 min. A field sample carrier simplifies sample collection and provides swabs nearly ready for analysis to the lab. Applications of the high throughput pr...

Reactions and mass spectra of complex particles using Aerosol CIMS

NASA Astrophysics Data System (ADS)

Hearn, John D.; Smith, Geoffrey D.

2006-12-01

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

Performance optimisation of a new-generation orthogonal-acceleration quadrupole-time-of-flight mass spectrometer.

PubMed

Bristow, Tony; Constantine, Jill; Harrison, Mark; Cavoit, Fabien

2008-04-01

Orthogonal-acceleration quadrupole time-of-flight (oa-QTOF) mass spectrometers, employed for accurate mass measurement, have been commercially available for well over a decade. A limitation of the early instruments of this type was the narrow ion abundance range over which accurate mass measurements could be made with a high degree of certainty. Recently, a new generation of oa-QTOF mass spectrometers has been developed and these allow accurate mass measurements to be recorded over a much greater range of ion abundances. This development has resulted from new ion detection technology and improved electronic stability or by accurate control of the number of ions reaching the detector. In this report we describe the results from experiments performed to evaluate the mass measurement performance of the Bruker micrOTOF-Q, a member of the new-generation oa-QTOFs. The relationship between mass accuracy and ion abundance has been extensively evaluated and mass measurement accuracy remained stable (+/-1.5 m m/z units) over approximately 3-4 orders of magnitude of ion abundance. The second feature of the Bruker micrOTOF-Q that was evaluated was the SigmaFit function of the software. This isotope pattern-matching algorithm provides an exact numerical comparison of the theoretical and measured isotope patterns as an additional identification tool to accurate mass measurement. The smaller the value, the closer the match between theoretical and measured isotope patterns. This information is then employed to reduce the number of potential elemental formulae produced from the mass measurements. A relationship between the SigmaFit value and ion abundance has been established. The results from the study for both mass accuracy and SigmaFit were employed to define the performance criteria for the micrOTOF-Q. This provided increased confidence in the selection of elemental formulae resulting from accurate mass measurements.

Broad screening and identification of β-agonists in feed and animal body fluid and tissues using ultra-high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry combined with spectra library search.

PubMed

Li, Tingting; Cao, Jingjing; Li, Zhen; Wang, Xian; He, Pingli

2016-02-01

Broad screening and identification of β-agonists in feed, serum, urine, muscle and liver samples was achieved in a quick and highly sensitive manner using ultra high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) combined with a spectra library search. Solid-phase extraction technology was employed for sample purification and enrichment. After extraction and purification, the samples were analyzed using a Q-Orbitrap high-resolution mass spectrometer under full-scan and data-dependent MS/MS mode. The acquired mass spectra were compared with an in-house library (compound library and MS/MS mass spectral library) built with TraceFinder Software which contained the M/Z of the precursor ion, chemical formula, retention time, character fragment ions and the entire MS/MS spectra of 32 β-agonist standards. Screening was achieved by comparing 5 key mass spectral results and positive matches were marked. Using the developed method, the identification results from 10 spiked samples and 238 actual samples indicated that only 2% of acquired mass spectra produced false identities. The method validation results showed that the limit of detection ranged from 0.021-3.854 μg kg(-1)and 0.015-1.198 ng mL(-1) for solid and liquid samples, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra.

PubMed

Liu, Yi; Ma, Bin; Zhang, Kaizhong; Lajoie, Gilles

2017-01-01

Mixture spectra occur quite frequently in a typical wet-lab mass spectrometry experiment, which result from the concurrent fragmentation of multiple precursors. The ability to efficiently and confidently identify mixture spectra is essential to alleviate the existent bottleneck of low mass spectra identification rate. However, most of the traditional computational methods are not suitable for interpreting mixture spectra, because they still take the assumption that the acquired spectra come from the fragmentation of a single precursor. In this manuscript, we formulate the mixture spectra de novo sequencing problem mathematically, and propose a dynamic programming algorithm for the problem. Additionally, we use both simulated and real mixture spectra data sets to verify the merits of the proposed algorithm.

OA-7 Veggie Series 1 Processing

NASA Image and Video Library

2017-02-15

Charles Spern, project manager on the Engineering Services Contract (ESC), and Glenn Washington, ESC quality assurance specialist, perform final inspections of the Veggie Series 1 plant experiment inside a laboratory in the Space Station Processing Facility at NASA's Kennedy Space Center in Florida. The Series 1 experiment is being readied for flight aboard Orbital ATK's Cygnus module on its seventh (OA-7) Commercial Resupply Services mission to the International Space Station. The Veggie system is on the space station.

Sources and atmospheric processing of winter aerosols in Seoul, Korea: insights from real-time measurements using a high-resolution aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Kim, Hwajin; Zhang, Qi; Bae, Gwi-Nam; Kim, Jin Young; Bok Lee, Seung

2017-02-01

Highly time-resolved chemical characterization of nonrefractory submicrometer particulate matter (NR-PM1) was conducted in Seoul, the capital and largest metropolis of Korea, using an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). The measurements were performed during winter, when elevated particulate matter (PM) pollution events are often observed. This is the first time that detailed real-time aerosol measurement results have been reported from Seoul, Korea, and they reveal valuable insights into the sources and atmospheric processes that contribute to PM pollution in this region. The average concentration of submicron aerosol (PM1 = NR-PM1+ black carbon (BC)) was 27.5 µg m-3, and the total mass was dominated by organics (44 %), followed by nitrate (24 %) and sulfate (10 %). The average atomic ratios of oxygen to carbon (O / C), hydrogen to carbon (H / C), and nitrogen to carbon (N / C) of organic aerosols (OA) were 0.37, 1.79, and 0.018, respectively, which result in an average organic mass-to-carbon (OM / OC) ratio of 1.67. The concentrations (2.6-90.7 µg m-3) and composition of PM1 varied dynamically during the measurement period due to the influences of different meteorological conditions, emission sources, and air mass origins. Five distinct sources of OA were identified via positive matrix factorization (PMF) analysis of the HR-ToF-AMS data: vehicle emissions represented by a hydrocarbon-like OA factor (HOA, O / C = 0.06), cooking activities represented by a cooking OA factor (COA, O / C = 0.14), wood combustion represented by a biomass burning OA factor (BBOA, O / C = 0.34), and secondary organic aerosol (SOA) represented by a semivolatile oxygenated OA factor (SV-OOA, O / C = 0.56) and a low-volatility oxygenated OA factor (LV-OOA, O / C = 0.68). On average, primary OA (POA = HOA + COA + BBOA) accounted for 59 % the OA mass, whereas SV-OOA and LV-OOA contributed 15 and 26 %, respectively. Our results indicate that air

Chandra Observations of Associates of η Carinae. II. Spectra

NASA Astrophysics Data System (ADS)

Evans, Nancy Remage; Schlegel, Eric M.; Waldron, Wayne L.; Seward, Frederick D.; Krauss, Miriam I.; Nichols, Joy; Wolk, Scott J.

2004-09-01

The low-resolution X-ray spectra around η Car covering Trumpler 16 and part of Trumpler 14 have been extracted from a Chandra CCD ACIS image. Various analysis techniques have been applied to the spectra based on their count rates. The spectra with the greatest number of counts (HD 93162 = WR 25, HD 93129 AB, and HD 93250) have been fitted with a wind model, which uses several components with different temperatures and depths in the wind. Weaker spectra have been fitted with Raymond-Smith models. The weakest spectra are simply intercompared with strong spectra. In general, fits produce reasonable parameters based on knowledge of the extinction from optical studies and on the range of temperatures for high- and low-mass stars. Direct comparisons of spectra confirm the consistency of the fitting results and also hardness ratios for cases of unusually large extinction in the clusters. The spectra of the low-mass stars are harder than the more massive stars. Stars in the sequence evolving from the main sequence (HD 93250) through the system containing the O supergiant (HD 93129 AB) and then through the Wolf-Rayet stage (HD 93162), presumably ending in the extreme example of η Car, share the property of being unusually luminous and hard in X-rays. For these X-ray-luminous stars, their high mass and evolutionary status (from the very last stages of the main sequence and beyond) is the common feature. Their binary status is mixed, and their magnetic status is still uncertain. Based on observations made with the Chandra X-Ray Observatory.

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

DOE PAGES

Schenke, Björn; Schlichting, Sören; Tribedy, Prithwish; ...

2016-10-14

The mass ordering of mean transverse momentummore » $$\\langle$$p T$$\\rangle$$ and of the Fourier harmonic coefficient v 2 (p T) of azimuthally anisotropic particle distributions in high energy hadron collisions is often interpreted as evidence for the hydrodynamic flow of the matter produced. We investigate an alternative initial state interpretation of this pattern in high-multiplicity proton-proton collisions at the LHC. The QCD Yang-Mills equations describing the dynamics of saturated gluons are solved numerically with initial conditions obtained from the color-glass-condensate-based impact-parameter-dependent glasma model. The gluons are subsequently fragmented into various hadron species employing the well established Lund string fragmentation algorithm of the pythia event generator. Lastly, we find that this initial state approach reproduces characteristic features of bulk spectra, in particular, the particle mass dependence of $$\\langle$$p T$$\\rangle$$ and v 2 (p T).« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madronich, Sasha; Kleinman, Larry; Conley, Andrew

Gas-to-particle partitioning of organic aerosols (OA) is represented in most models by Raoult’s law, and depends on the existing mass of particles into which organic gases can dissolve. This raises the possibility of non-linear response of particle-phase OA to the emissions of precursor volatile organic compounds (VOCs) that contribute to this partitioning mass. Implications for air quality management are evident: A strong non-linear dependence would suggest that reductions in VOC emission would have a more-than-proportionate benefit in lowering ambient OA concentrations. Chamber measurements on simple VOC mixtures generally confirm the non-linear scaling between OA and VOCs, usually stated as amore » mass-dependence of the measured OA yields. However, for realistic ambient conditions including urban settings, no single component dominates the composition of the organic particles, and deviations from linearity are presumed to be small. Here we re-examine the linearity question using volatility spectra from several sources: (1) chamber studies of selected aerosols, (2) volatility inferred for aerosols sampled in two megacities, Mexico City and Paris, and (3) an explicit chemistry model (GECKO-A). These few available volatility distributions suggest that urban OA may be only slightly super-linear, with most values of the sensitivity exponent in the range 1.1-1.3, also substantially lower than seen in chambers for some specific aerosols. Furthermore, the rather low values suggest that OA concentrations in megacities are not an inevitable convergence of non-linear effects, but can be addressed (much like in smaller urban areas) by proportionate reductions in emissions.« less

FDATMOS16 non-linear partitioning and organic volatility distributions in urban aerosols

DOE PAGES

Madronich, Sasha; Kleinman, Larry; Conley, Andrew; ...

2015-12-17

Gas-to-particle partitioning of organic aerosols (OA) is represented in most models by Raoult’s law, and depends on the existing mass of particles into which organic gases can dissolve. This raises the possibility of non-linear response of particle-phase OA to the emissions of precursor volatile organic compounds (VOCs) that contribute to this partitioning mass. Implications for air quality management are evident: A strong non-linear dependence would suggest that reductions in VOC emission would have a more-than-proportionate benefit in lowering ambient OA concentrations. Chamber measurements on simple VOC mixtures generally confirm the non-linear scaling between OA and VOCs, usually stated as amore » mass-dependence of the measured OA yields. However, for realistic ambient conditions including urban settings, no single component dominates the composition of the organic particles, and deviations from linearity are presumed to be small. Here we re-examine the linearity question using volatility spectra from several sources: (1) chamber studies of selected aerosols, (2) volatility inferred for aerosols sampled in two megacities, Mexico City and Paris, and (3) an explicit chemistry model (GECKO-A). These few available volatility distributions suggest that urban OA may be only slightly super-linear, with most values of the sensitivity exponent in the range 1.1-1.3, also substantially lower than seen in chambers for some specific aerosols. Furthermore, the rather low values suggest that OA concentrations in megacities are not an inevitable convergence of non-linear effects, but can be addressed (much like in smaller urban areas) by proportionate reductions in emissions.« less

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra

PubMed Central

Deepaisarn, S; Tar, P D; Thacker, N A; Seepujak, A; McMahon, A W

2018-01-01

Abstract Motivation Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian. Results We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth. Availability and implementation Software is available via the open source image analysis system TINA Vision, www.tina-vision.net. Contact paul.tar@manchester.ac.uk Supplementary information Supplementary data are available at Bioinformatics online. PMID:29091994

OAS proteins and cGAS: unifying concepts in sensing and responding to cytosolic nucleic acids.

PubMed

Hornung, Veit; Hartmann, Rune; Ablasser, Andrea; Hopfner, Karl-Peter

2014-08-01

Recent discoveries in the field of innate immunity have highlighted the existence of a family of nucleic acid-sensing proteins that have similar structural and functional properties. These include the well-known oligoadenylate synthase (OAS) family proteins and the recently identified OAS homologue cyclic GMP-AMP (cGAMP) synthase (cGAS). The OAS proteins and cGAS are template-independent nucleotidyltransferases that, once activated by double-stranded nucleic acids in the cytosol, produce unique classes of 2'-5'-linked second messenger molecules, which - through distinct mechanisms - have crucial antiviral functions. 2'-5'-linked oligoadenylates limit viral propagation through the activation of the enzyme RNase L, which degrades host and viral RNA, and 2'-5'-linked cGAMP activates downstream signalling pathways to induce de novo antiviral gene expression. In this Progress article, we describe the striking functional and structural similarities between OAS proteins and cGAS, and highlight their roles in antiviral immunity.

BOREAS TF-1 SSA-OA Soil Characteristics Data

NASA Technical Reports Server (NTRS)

Black, T. Andrew; Chen, Z; Nesic, Z.; Hall, Forrest G. (Editor); Papagno, Andrea (Editor)

2000-01-01

The BOREAS TF-1 team collected several data sets in support of its efforts to characterize and interpret soil information at the SSA-OA tower site in 1994 as part of BOREAS. Data sets collected include soil respiration, temperature, moisture, and gravimetric data. The data are stored in tabular ASCII format.

OAS single-nucleotide polymorphisms and haplotypes are associated with variations in immune responses to rubella vaccine

PubMed Central

Haralambieva, Iana H.; Dhiman, Neelam; Ovsyannikova, Inna G.; Vierkant, Robert A.; Pankratz, V. Shane; Jacobson, Robert M.; Poland, Gregory A.

2010-01-01

Interferon (IFN)-induced antiviral genes are crucial players in innate antiviral defense and potential determinants of immune response heterogeneity. We selected 114 candidate SNPs from 12 antiviral genes using an LD tagSNP selection approach and genotyped them in a cohort of 738 schoolchildren immunized with two doses of rubella vaccine. Associations between SNPs/haplotypes and rubella virus-specific immune measures were assessed using linear regression methodologies. We identified 23 significant associations (p<0.05) between polymorphisms within the 2′-5′-oligoadenylate synthetase (OAS) gene cluster, and rubella virus-specific IL-2, IL-10, IL-6 secretion and antibody levels. The minor allele variants of three OAS1 SNPs (rs3741981/Ser162Gly, rs1051042/Thr361Arg, rs2660), located in a linkage disequilibrium block of functional importance, were significantly associated with an increase in rubella virus-specific IL-2/Th1 response (p≤0.024). Seven OAS1 and OAS3 promoter/regulatory SNPs were similarly associated with IL-2 secretion. Importantly, two SNPs (rs3741981 and rs10774670), independently cross-regulated rubella virus-specific IL-10 secretion levels (p≤0.031). Furthermore, both global tests and individual haplotype analyses revealed significant associations between OAS1 haplotypes and rubella virus-specific cytokine secretion. Our results suggest that innate immunity and OAS genetic variations are likely involved in modulating the magnitude and quality of the adaptive immune responses to live attenuated rubella vaccine. PMID:20079393

Argon offline-AMS source apportionment of organic aerosol over yearly cycles for an urban, rural, and marine site in northern Europe

NASA Astrophysics Data System (ADS)

Bozzetti, Carlo; Sosedova, Yuliya; Xiao, Mao; Daellenbach, Kaspar R.; Ulevicius, Vidmantas; Dudoitis, Vadimas; Mordas, Genrik; Byčenkienė, Steigvilė; Plauškaitė, Kristina; Vlachou, Athanasia; Golly, Benjamin; Chazeau, Benjamin; Besombes, Jean-Luc; Baltensperger, Urs; Jaffrezo, Jean-Luc; Slowik, Jay G.; El Haddad, Imad; Prévôt, André S. H.

2017-01-01

The widespread use of Aerodyne aerosol mass spectrometers (AMS) has greatly improved real-time organic aerosol (OA) monitoring, providing mass spectra that contain sufficient information for source apportionment. However, AMS field deployments remain expensive and demanding, limiting the acquisition of long-term datasets at many sampling sites. The offline application of aerosol mass spectrometry entailing the analysis of nebulized water extracted filter samples (offline-AMS) increases the spatial coverage accessible to AMS measurements, being filters routinely collected at many stations worldwide. PM1 (particulate matter with an aerodynamic diameter < 1 µm) filter samples were collected during an entire year in Lithuania at three different locations representative of three typical environments of the southeast Baltic region: Vilnius (urban background), Rūgšteli\\vskis (rural terrestrial), and Preila (rural coastal). Aqueous filter extracts were nebulized in Ar, yielding the first AMS measurements of water-soluble atmospheric organic aerosol (WSOA) without interference from air fragments. This enables direct measurement of the CO+ fragment contribution, whose intensity is typically assumed to be equal to that of CO2+. Offline-AMS spectra reveal that the water-soluble CO2+ : CO+ ratio not only shows values systematically > 1 but is also dependent on season, with lower values in winter than in summer. AMS WSOA spectra were analyzed using positive matrix factorization (PMF), which yielded four factors. These factors included biomass burning OA (BBOA), local OA (LOA) contributing significantly only in Vilnius, and two oxygenated OA (OOA) factors, summer OOA (S-OOA) and background OOA (B-OOA), distinguished by their seasonal variability. The contribution of traffic exhaust OA (TEOA) was not resolved by PMF due to both low concentrations and low water solubility. Therefore, the TEOA concentration was estimated using a chemical mass balance approach, based on the

Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes

PubMed Central

Rios, Jonathan J; Perelygin, Andrey A; Long, Maureen T; Lear, Teri L; Zharkikh, Andrey A; Brinton, Margo A; Adelson, David L

2007-01-01

Background The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. Results Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. Conclusion In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases. PMID:17822564

Variability of aerosol, gaseous pollutants and meteorological characteristics associated with changes in air mass origin at the SW Atlantic coast of Iberia

NASA Astrophysics Data System (ADS)

Diesch, J.-M.; Drewnick, F.; Zorn, S. R.; von der Weiden-Reinmüller, S.-L.; Martinez, M.; Borrmann, S.

2012-04-01

. In all air masses passing the continent the organic aerosol fraction dominated the total NR-PM1. For this reason, using Positive Matrix Factorization (PMF) four organic aerosol (OA) classes that can be associated with various aerosol sources and components were identified: a highly-oxygenated OA is the major component (43% OA) while semi-volatile OA accounts for 23%. A hydrocarbon-like OA mainly resulting from industries, traffic and shipping emissions as well as particles from wood burning emissions also contribute to total OA and depend on the air mass origin. A significant variability of ozone was observed that depends on the impact of different air mass types and solar radiation.

UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra

NASA Astrophysics Data System (ADS)

Rosenberg, Jake; Parker, W. Ryan; Cammarata, Michael B.; Brodbelt, Jennifer S.

2018-04-01

UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu. UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT. [Figure not available: see fulltext.

UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

PubMed

Rosenberg, Jake; Parker, W Ryan; Cammarata, Michael B; Brodbelt, Jennifer S

2018-06-01

UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu . UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT . Graphical Abstract.

Mass Spectra of Ds and Ωc in Lattice QCD with Nf = 2 + 1 + 1 Domain-Wall Quarks

NASA Astrophysics Data System (ADS)

Chiu, Ting-Wai

2018-03-01

We perform hybrid Monte Carlo simulation of lattice QCD with Nf = 2+1+1 optimal domain-wall quarks on the 323 × 64 lattice with lattice spacing a 0:06 fm, and generate a gauge ensemble with physical s and c quarks, and pion mass 280 MeV. Using 2-quark (meson) and 3-quark (baryon) interpolating operators, the mass spectra of the lowest-lying states containing s and c quarks (Ds and Ωc) are extracted [1], which turn out in good agreement with the high energy experimental values, together with the predictions of the charmed baryons which have not been observed in experiments. For the five new narrow c states observed by the LHCb Collaboration [2], the lowest-lying Ωc(3000) agrees with our predicted mass 3015(29)(34) MeV of the lowest-lying Ωc with JP = 1/2-. This implies that JP of Ωc(3000) is 1/2-.

Insights into characteristics, sources, and evolution of submicron aerosols during harvest seasons in the Yangtze River delta region, China

NASA Astrophysics Data System (ADS)

Zhang, Y. J.; Tang, L. L.; Wang, Z.; Yu, H. X.; Sun, Y. L.; Liu, D.; Qin, W.; Canonaco, F.; Prévôt, A. S. H.; Zhang, H. L.; Zhou, H. C.

2015-02-01

Atmospheric submicron particulate matter (PM1) is one of the most significant pollution components in China. Despite its current popularity in the studies of aerosol chemistry, the characteristics, sources and evolution of atmospheric PM1 species are still poorly understood in China, particularly for the two harvest seasons, namely, the summer wheat harvest and autumn rice harvest. An Aerodyne Aerosol Chemical Speciation Monitor (ACSM) was deployed for online monitoring of PM1 components during summer and autumn harvest seasons in urban Nanjing, in the Yangtze River delta (YRD) region of China. PM1 components were shown to be dominated by organic aerosol (OA, 39 and 41%) and nitrate (23 and 20%) during the harvest seasons (the summer and autumn harvest). Positive matrix factorization (PMF) analysis of the ACSM OA mass spectra resolved four OA factors: hydrocarbon-like mixed with cooking-related OA (HOA + COA), fresh biomass-burning OA (BBOA), oxidized biomass-burning-influenced OA (OOA-BB), and highly oxidized OA (OOA); in particular the oxidized BBOA contributes ~80% of the total BBOA loadings. Both fresh and oxidized BBOA exhibited apparent diurnal cycles with peak concentration at night, when the high ambient relative humidity and low temperature facilitated the partitioning of semi-volatile organic species into the particle phase. The fresh BBOA concentrations for the harvests are estimated as BBOA = 15.1 × (m/z 60-0.26% × OA), where m/z (mass-to-charge ratio) 60 is a marker for levoglucosan-like species. The (BBOA + OOA-BB)/ΔCO, (ΔCO is the CO minus background CO), decreases as a function of f44 (fraction of m/z 44 in OA signal), which might indicate that BBOA was oxidized to less volatile OOA, e.g., more aged and low volatility OOA (LV-OOA) during the aging process. Analysis of air mass back trajectories indicates that the high BB pollutant concentrations are linked to the air masses from the western (summer harvest) and southern (autumn harvest) areas.

Differences of Cd uptake and expression of OAS and IRT genes in two varieties of ryegrasses.

PubMed

Chi, Sunlin; Qin, Yuli; Xu, Weihong; Chai, Yourong; Feng, Deyu; Li, Yanhua; Li, Tao; Yang, Mei; He, Zhangmi

2018-06-16

Pot experiment was conducted to study the difference of cadmium uptake and OAS and IRT genes' expression between the two ryegrass varieties under cadmium stress. The results showed that with the increase of cadmium levels, the dry weights of roots of the two ryegrass varieties, and the dry weights of shoots and plants of Abbott first increased and then decreased. When exposed to 75 mg kg -1 Cd, the dry weights of shoot and plant of Abbott reached the maximum, which increased by 11.13 and 10.67% compared with the control. At 75 mg kg -1 Cd, cadmium concentrations in shoot of the two ryegrass varieties were higher than the critical value of Cd hyperaccumulator (100 mg kg -1 ), 111.19 mg kg -1 (Bond), and 133.69 mg kg -1 (Abbott), respectively. The OAS gene expression in the leaves of the two ryegrass varieties showed a unimodal curve, which was up to the highest at the cadmium level of 150 mg kg -1 , but fell back at high cadmium levels of 300 and 600 mg kg -1 . The OAS gene expression in Bond and Abbott roots showed a bimodal curve. The OAS gene expression in Bond root and Abbott stem mainly showed a unimodal curve. The expression of IRT genes family in the leaves of ryegrass varieties was basically in line with the characteristics of unimodal curve, which was up to the highest at cadmium level of 75 or 150 mg kg -1 , respectively. The IRT expression in the ryegrass stems showed characteristics of bimodal and unimodal curves, while that in the roots was mainly unimodal. The expression of OAS and IRT genes was higher in Bond than that in Abbott due to genotype difference between the two varieties. The expression of OAS and IRT was greater in leaves than that in roots and stems. Ryegrass tolerance to cadmium can be increased by increasing the expression of OAS and IRT genes in roots and stems, and transfer of cadmium from roots and stems to the leaves can be enhanced by increasing expression OAS and IRT in leaves.

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...

Development and practical application of a library of CID accurate mass spectra of more than 2,500 toxic compounds for systematic toxicological analysis by LC-QTOF-MS with data-dependent acquisition.

PubMed

Broecker, Sebastian; Herre, Sieglinde; Wüst, Bernhard; Zweigenbaum, Jerry; Pragst, Fritz

2011-04-01

A library of collision-induced dissociation (CID) accurate mass spectra has been developed for efficient use of liquid chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) as a tool in systematic toxicological analysis. The mass spectra (Δm < 3 ppm) of more than 2,500 illegal and therapeutic drugs, pesticides, alkaloids, other toxic chemicals and metabolites were measured, by use of an Agilent 6530 instrument, by flow-injection of 1 ng of the pure substances in aqueous ammonium formate-formic acid-methanol, with positive and negative electrospray-ionization (ESI), selection of the protonated or deprotonated molecules [M+H](+) or [M-H](-) by the quadrupole, and collision induced dissociation (CID) with nitrogen as collision gas at CID energies of 10, 20, and 40 eV. The fragment mass spectra were controlled for structural plausibility, corrected by recalculation to the theoretical fragment masses and added to a database of accurate mass data and molecular formulas of more than 7,500 toxicologically relevant substances to form the "database and library of toxic compounds". For practical evaluation, blood and urine samples were spiked with a mixture of 33 drugs at seven concentrations between 0.5 and 500 ng mL(-1), prepared by dichloromethane extraction or protein precipitation, and analyzed by LC-QTOF-MS in data-dependent acquisition mode. Unambiguous identification by library search was possible for typical basic drugs down to 0.5-2 ng mL(-1) and for benzodiazepines down to 2-20 ng mL(-1). The efficiency of the method was also demonstrated by re-analysis of venous blood samples from 50 death cases and comparison with previous results. In conclusion, LC-QTOF-MS in data-dependent acquisition mode combined with an accurate mass database and CID spectra library seemed to be one of the most efficient tools for systematic toxicological analysis.

AmeriFlux CA-Oas Saskatchewan - Western Boreal, Mature Aspen

DOE Data Explorer

Black, T. Andrew [The University of British Columbia

2017-01-01

This is the AmeriFlux version of the carbon flux data for the site CA-Oas Saskatchewan - Western Boreal, Mature Aspen. Site Description - 53.62889° N, 106.19779° W, elabation of 600.63 m,BOREAS 1994, 1996, BERMS climate and flux measurements began Dec. 1996

Organic aerosol in the summertime southeastern United States: components and their link to volatility distribution, oxidation state and hygroscopicity

NASA Astrophysics Data System (ADS)

Kostenidou, Evangelia; Karnezi, Eleni; Hite, James R., Jr.; Bougiatioti, Aikaterini; Cerully, Kate; Xu, Lu; Ng, Nga L.; Nenes, Athanasios; Pandis, Spyros N.

2018-04-01

The volatility distribution of the organic aerosol (OA) and its sources during the Southern Oxidant and Aerosol Study (SOAS; Centreville, Alabama) was constrained using measurements from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) and a thermodenuder (TD). Positive matrix factorization (PMF) analysis was applied on both the ambient and thermodenuded high-resolution mass spectra, leading to four factors: more oxidized oxygenated OA (MO-OOA), less oxidized oxygenated OA (LO-OOA), an isoprene epoxydiol (IEPOX)-related factor (isoprene-OA) and biomass burning OA (BBOA). BBOA had the highest mass fraction remaining (MFR) at 100 °C, followed by the isoprene-OA, and the LO-OOA. Surprisingly the MO-OOA evaporated the most in the TD. The estimated effective vaporization enthalpies assuming an evaporation coefficient equal to unity were 58 ± 13 kJ mol-1 for the LO-OOA, 89 ± 10 kJ mol-1 for the MO-OOA, 55 ± 11 kJ mol-1 for the BBOA, and 63 ± 15 kJ mol-1 for the isoprene-OA. The estimated volatility distribution of all factors covered a wide range including both semi-volatile and low-volatility components. BBOA had the lowest average volatility of all factors, even though it had the lowest O : C ratio among all factors. LO-OOA was the more volatile factor and its high MFR was due to its low enthalpy of vaporization according to the model. The isoprene-OA factor had intermediate volatility, quite higher than suggested by a few other studies. The analysis suggests that deducing the volatility of a factor only from its MFR could lead to erroneous conclusions. The oxygen content of the factors can be combined with their estimated volatility and hygroscopicity to provide a better view of their physical properties.

GHRS Spectra of the Very Low Mass Star VB 10 (M8 Ve)

NASA Astrophysics Data System (ADS)

Linsky, J. L.; Wood, B.; Brown, A.

1994-12-01

We report on ultraviolet spectra of the M8 Ve star VB10 = Gl 752B, probably the coolest and lowest mass star observed so far in the ultraviolet. This star is of great interest because it lies almost at the end of the main sequence where stars are thought to be fully convective and solar-type dynamo processes should not be present. On 1994 October 12 we observed the brighter companion Gl 752A (M3 Ve) and then offset to VB10. Both stars were observed with the G140L grating on the HST Goddard High Resolution Spectrograph. The spectrum of Gl 752A shows the expected transition region lines of solar-type stars consisting of C III 1175 Angstroms, H I Lyman-alpha , N V 1240 Angstroms, O I 1304 Angstroms, C II 1335 Angstroms, Si IV 1400 Angstroms, C IV 1550 Angstroms, He II 1640 Angstroms, and others. The spectrum of VB10, on the other hand, provided a surprise. Our spectra of this star consists of 11 integrations, each of about 5 minutes duration. The first 10 integrations show no emission features with very small upper limits to the surface fluxes in the transition region lines. The last integration, however, shows strong emission in the C II, Si IV, and C IV lines, which we interpret as a flare. The VB10 spectra imply that there is little if any continuous heating of the transition regions of the very coolest M dwarf stars. Instead, there is only transient emission during major realignments of the magnetic field. By contrast, hotter stars show continuous emission in the transition region lines, indicating a continuous heating process or a large number of small flares (microflaring). This change in behavior may be due to the absence of radiative cores in the coolest M dwarfs and the inability of the solar-type alpha -omega dynamo to operate in stars without an interface between a radiative core and a convective envelope. Our data indicate that the coolest M dwarfs nevertheless do have magnetic fields. This work is supported by NASA Interagency Transfer S-56460-D to the

Effect of antiresorptive and anabolic bone therapy on development of osteoarthritis in a posttraumatic rat model of OA.

PubMed

Bagi, Cedo M; Berryman, Edwin; Zakur, David E; Wilkie, Dean; Andresen, Catharine J

2015-11-06

Osteoarthritis (OA) is a leading cause of disability, but despite the high unmet clinical need and extensive research seeking dependable therapeutic interventions, no proven disease-modifying treatment for OA is currently available. Due to the close interaction and interplay between the articular cartilage and the subchondral bone plate, it has been hypothesized that antiresorptive drugs can also reduce cartilage degradation, inhibit excessive turnover of the subchondral bone plate, prevent osteophyte formation, and/or that bone anabolic drugs might also stimulate cartilage synthesis by chondrocytes and preserve cartilage integrity. The benefit of intensive zoledronate (Zol) and parathyroid hormone (PTH) therapy for bone and cartilage metabolism was evaluated in a rat model of OA. Medial meniscectomy (MM) was used to induce OA in male Lewis rats. Therapy with Zol and human PTH was initiated immediately after surgery. A dynamic weight-bearing (DWB) system was deployed to evaluate the weight-bearing capacity of the front and hind legs. At the end of the 10-week study, the rats were euthanized and the cartilage pathology was evaluated by contrast (Hexabrix)-enhanced μCT imaging and traditional histology. Bone tissue was evaluated at the tibial metaphysis and epiphysis, including the subchondral bone. Histological techniques and dynamic histomorphometry were used to evaluate cartilage morphology and bone mineralization. The results of this study highlight the complex changes in bone metabolism in different bone compartments influenced by local factors, including inflammation, pain and mechanical loads. Surgery caused severe and extensive deterioration of the articular cartilage at the medial tibial plateau, as evidenced by contrast-enhanced μCT and histology. The study results showed the negative impact of MM surgery on the weight-bearing capacity of the operated limb, which was not corrected by treatment. Although both Zol and PTH improved subchondral bone mass and

Activation of TRPC channels contributes to OA-NO2-induced responses in guinea-pig dorsal root ganglion neurons

PubMed Central

Zhang, Xiulin; Beckel, Jonathan M; Daugherty, Stephanie L; Wang, Ting; Woodcock, Stephen R; Freeman, Bruce A; de Groat, William C

2014-01-01

Effects of nitro-oleic acid (OA-NO2) on TRP channels were examined in guinea-pig dissociated dorsal root ganglia (DRG) neurons using calcium imaging and patch clamp techniques. OA-NO2 increased intracellular Ca2+ in 60–80% DRG neurons. 1-Oleoyl-2acetyl-sn-glycerol (OAG), a TRPC agonist, elicited responses in 36% of OA-NO2-sensitive neurons while capsaicin (TRPV1 agonist) or allyl-isothiocyanate (AITC, TRPA1 agonist) elicited responses in only 16% and 10%, respectively, of these neurons. A TRPV1 antagonist (diarylpiperazine, 5 μm) in combination with a TRPA1 antagonist (HC-030031, 30 μm) did not change the amplitude of the Ca2+ transients or percentage of neurons responding to OA-NO2; however, a reducing agent DTT (50 mm) or La3+ (50 μm) completely abolished OA-NO2 responses. OA-NO2 also induced a transient inward current associated with a membrane depolarization followed by a prolonged outward current and hyperpolarization in 80% of neurons. The reversal potentials of inward and outward currents were approximately −20 mV and −60 mV, respectively. Inward current was reduced when extracellular Na+ was absent, but unchanged by niflumic acid (100 μm), a Cl− channel blocker. Outward current was abolished in the absence of extracellular Ca2+ or a combination of two Ca2+-activated K+ channel blockers (iberiotoxin, 100 nm and apamin, 1 μm). BTP2 (1 or 10 μm), a broad spectrum TRPC antagonist, or La3+ (50 μm) completely abolished OA-NO2 currents. RT-PCR performed on mRNA extracted from DRGs revealed the expression of all seven subtypes of TRPC channels. These results support the hypothesis that OA-NO2 activates TRPC channels other than the TRPV1 and TRPA1 channels already known to be targets in rat and mouse sensory neurons and challenge the prevailing view that electrophilic compounds act specifically on TRPA1 or TRPV1 channels. The modulation of sensory neuron excitability via actions on multiple TRP channels can contribute to the anti-inflammatory effect

The Attractiveness Halo Effect and the Babyface Stereotype in Older and Younger Adults: Similarities, Own-Age Accentuation, and OA Positivity Effects

PubMed Central

Zebrowitz, Leslie A; Franklin, Robert G.

2014-01-01

Background Two well-documented phenomena in person perception are the attractiveness halo effect (more positive impressions of more attractive people), and the babyface stereotype (more childlike impressions of more babyfaced people), shown by children, young adults (YA) and people from diverse cultures. This is the first study to systematically investigate these face stereotypes in older adults (OA) and to compare effects for younger and older adult faces. Method YA and OA judges rated competence, health, hostility, untrustworthiness, attractiveness, and babyfaceness of older and younger neutral expression faces. Multilevel modeling assessed effects of rater age and face age on appearance stereotypes. Results Like YA, OA showed both the attractiveness halo effect and the babyface stereotype. However, OA showed weaker effects of attractiveness on impressions of untrustworthiness, and only OA associated higher babyfaceness with greater competence. There also was own-age accentuation, with both OA and YA showing stronger face stereotypes for faces closer to their own age. Age differences in the strength of the stereotypes reflected an OA positivity effect shown in more influence of positive facial qualities on impressions or less influence of negative ones, rather than vice versa. Conclusions OA own-age biases, previously shown in emotion, age, and identity recognition, and OA positivity effects, previously revealed in attention, memory, and social judgments, also influence age differences in the strength and content of appearance stereotypes. Future research should assess implications of these results for age-related differences in susceptibility to appearance biases that YA have shown in socially significant domains, such as judicial and personnel decisions. PMID:24785596

OA-7 Cargo Module Arrival

NASA Image and Video Library

2017-01-09

Still sealed in its environmentally controlled shipping container, the Orbital ATK OA-7 Cygnus spacecraft's pressurized cargo module (PCM) has arrived inside the Space Station Processing Facility at NASA's Kennedy Space Center in Florida. Once the Cygnus spacecraft is removed from its shipping container, engineers and technicians will begin preparing for launch scheduled for March 2017. Orbital ATK CRS-7 will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

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

PubMed

Todua, Nino G; Mikaia, Anzor I

2016-01-01

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

Orbitally excited spectra and decay of cc¯ meson

NASA Astrophysics Data System (ADS)

Chaturvedi, Raghav; Rai, A. K.

2018-05-01

We use the hydrogen like trial wave function for computation of the mass spectra and decay properties of charmonia within the framework of phenomenological quark anti-quark Coulomb plus power potential with varying potential index from 0.5 to 2.0. The spin-spin hyperfine interaction is considered to incorporate splitting of the ground and radially excited states energy levels, further spin-orbit and tensor interactions are employed to calculate the masses of orbitally excited states. We construct the Regge trajectories from the mass spectra in (J, M2) and (nr, M2) planes. We also compute γγ decay width of P wave states of cc¯.

De novo peptide sequencing using CID and HCD spectra pairs.

PubMed

Yan, Yan; Kusalik, Anthony J; Wu, Fang-Xiang

2016-10-01

In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision-induced dissociation (CID) higher energy collisional dissociation (HCD), electron-capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full-length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Uptake of Semivolatile Secondary Organic Aerosol Formed from α-Pinene into Nonvolatile Polyethylene Glycol Probe Particles.

PubMed

Ye, Penglin; Ding, Xiang; Ye, Qing; Robinson, Ellis S; Donahue, Neil M

2016-03-10

Semivolatile organic compounds (SVOCs) play an essential role in secondary organic aerosol (SOA) formation, chemical aging, and mixing of organic aerosol (OA) from different sources. Polyethylene glycol (PEG400) particles are liquid, polar, and nearly nonvolatile; they provide a new vehicle to study the interaction between SVOCs with OA. With a unique fragment ion C4H9O2(+) (m/z 89), PEG400 can be easily separated from α-pinene SOA in aerosol mass spectra. By injecting separately prepared PEG probe particles into a chamber containing SOA coated on ammonium sulfate seeds, we show that a substantial pool of SVOCs exists in equilibrium with the original SOA particles. Quantitative findings are based on bulk mass spectra, size-dependent composition, and the evolution of individual particle mass spectra, which we use to separate the two particle populations. We observed a larger fraction of SVOC vapors with increased amounts of reacted α-pinene. For the same amount of reacted α-pinene, the SOA formed from α-pinene oxidized by OH radicals had a higher fraction of SOA vapors than SOA formed by α-pinene ozonolysis. Compared to the PEG400 probe particles, we observed a lower mass fraction of SVOCs in poly(ethylene glycol) dimethyl ether (MePEG500) probe particles under otherwise identical conditions; this may be due to the lower polarity of the MePEG500 or caused by esterification reactions between the PEG400 and organic acids in the SOA.

GPNMB/OA protein increases the invasiveness of human metastatic prostate cancer cell lines DU145 and PC3 through MMP-2 and MMP-9 activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fiorentini, Chiara; Bodei, Serena; Bedussi, Francesca

2014-04-15

Non-metastatic glycoprotein melanoma protein B (GPNMB), also known as osteoactivin (OA) is expressed in a wide array of tumors and represents an emerging target for drug development. In this study, we investigated the role of GPNMB/OA in the progression of human metastatic DU145 and PC3 prostate cancer cells. GPNMB/OA contribution in PCa malignant phenotype has been analyzed by small interfering RNA-induced GPNMB/OA silencing. We found that following GPNMB/OA silencing the migration capability of both DU145 and PC3 cells, evaluated by using in vitro invasivity assay, as well as the metalloproteinases MMP-2 and MMP-9 activity were equally strongly inhibited. By contrastmore » knocking down GPNMB/OA weakly attenuated cell proliferation rate of DU145, an effect that paralleled with an increase number of apoptotic cells. However, PC3 cell growth seems to be not affected by GPNMB/OA. Together, these data reveal that GPNMB/OA acts as a critical molecular mediator promoting the acquisition of the more aggressive, pro-metastatic phenotype distinctive of human DU145 and PC3 cell lines. - Highlights: • GPNMB/OA expression correlates with DU145 and PC3 cells malignant phenotype. • GPNMB/OA silencing affects the migration capability of both DU145 and PC3 cells. • GPNMB/OA increases invasiveness by up-regulating MMPs activity. • GPNMB/OA promotes DU145 and PC3 cells progression into a more aggressive phenotype.« less

Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.

PubMed

Mantini, Dante; Petrucci, Francesca; Del Boccio, Piero; Pieragostino, Damiana; Di Nicola, Marta; Lugaresi, Alessandra; Federici, Giorgio; Sacchetta, Paolo; Di Ilio, Carmine; Urbani, Andrea

2008-01-01

Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra. The comparison on peak detection with an open-source and two commercial methods shows its superior reliability in reducing the false discovery rate of protein peak masses. Moreover, the integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state. This data-driven approach demonstrates to be a promising tool for biomarker-discovery studies based on MALDI-TOF MS technology. The MATLAB implementation of the method described in the article and both simulated and experimental data are freely available at http://www.unich.it/proteomica/bioinf/.

Electromagnetic fluctuation spectra of collective oscillations in magnetized Maxwellian equal mass plasmas for low-frequency waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vafin, S.; Schlickeiser, R.; Yoon, P. H.

Recently, the general electromagnetic fluctuation theory for magnetized plasmas has been used to study the steady-state fluctuation spectra and the total intensity of low-frequency collective weakly damped modes for parallel wave vectors in Maxwellian plasmas. Now, we address the same question with respect to an arbitrary direction of the wave-vector. Here, we analyze this problem for equal mass plasmas. These plasmas are a very good tool to study various plasma phenomena, as they considerably facilitate the theoretical consideration and at the same time provide with their clear physical picture. Finally, we compare our results in the limiting case of parallelmore » wave vectors with the previous study.« less

High-resolution 18 CM spectra of OH/IR stars

NASA Astrophysics Data System (ADS)

Fix, John D.

1987-02-01

High-velocity-resolution, high-signal-to-noise spectra have been obtained for the 18 cm maser emission lines from a number of optically visible OH/IR stars. The spectra have been interpreted in terms of a recent model by Alcock and Ross (1986), in which OH/IR stars lose mass in discrete elements rather than by a continuous wind. Comparison of the observed spectra with synthetic spectra shows that the lines are the composite emission from thousands or tens of thousands of individual elements.

High-field FT-ICR-MS and aromaticity equivalent approach for structural identification of water soluble organic compounds (WSOC)

NASA Astrophysics Data System (ADS)

Harir, Mourad; Yassine, Mahmoud M.; Dabek-Zlotorzynska, Ewa; Hertkorn, Norbert; Schmitt-Kopplin, Philippe

2015-04-01

Organic aerosol (OA) makes up a large and often dominant fraction, (20 to 90%) of the submicron atmospheric particulate mass, and its effects are becoming increasingly important in determining climatic and health effects of atmospheric aerosols. Despite the abundance of OA, our understanding of the sources, formation processes and atmospheric properties of OA is limited. Atmospheric OA has both primary (directly emitted) and secondary (formed in the atmosphere from precursor gases) sources, which can be natural (e.g. vegetation) and/or anthropogenic (e.g. fossil-based vehicle exhaust or biomass burning). A significant fraction of OA contains as much as 20-70% of water soluble organic compounds (WSOC). The WSOC fraction is a very complex mixture of low volatility, polyfunctional aliphatic and aromatic compounds containing carboxyl, alcohol, carbonyl, sulfo, nitro, and other functionalities. This high degree of chemical complexity of atmospheric organics has inspired a number of sophisticated approaches that are capable of identifying and detecting a variety of different analytes in OA. Accordingly, one of the most challenging areas of atmospheric particulate matter (PM) analysis is to comprehend the molecular complexity of the OA, especially WSOC fraction, a significant component of atmospheric fine PM (PM2.5). The sources of WSOC are not well understood, especially the relative contributions of primary vs. secondary organic aerosol. Therefore, the molecular characterization of WSOC is important because it allows gaining insight into aerosol sources and underlying mechanisms of secondary organic aerosols (SOA) formation and transformation. In this abstract, molecular characterization of WSOC was achieved using high-field mass spectrometry FT-ICR-MS and aromaticity equivalent approach. Aromaticity equivalent (Xc), defined recently as a new parameter calculated from the assigned molecular formulas (complementary to the aromaticity index [1]), is introduced to improve

Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis.

PubMed

Baldwin, M A; Medzihradszky, K F; Lock, C M; Fisher, B; Settineri, T A; Burlingame, A L

2001-04-15

The design and operation of a novel UV-MALDI ionization source on a commercial QqoaTOF mass spectrometer (Applied Biosystem/MDS Sciex QSTAR Pulsar) is described. Samples are loaded on a 96-well target plate, the movement of which is under software control and can be readily automated. Unlike conventional high-energy MALDI-TOF, the ions are produced with low energies (5-10 eV) in a region of relatively low vacuum (8 mTorr). Thus, they are cooled by extensive low-energy collisions before selection in the quadrupole mass analyzer (Q1), potentially giving a quasi-continuous ion beam ideally suited to the oaTOF used for mass analysis of the fragment ions, although ion yields from individual laser shots may vary widely. Ion dissociation is induced by collisions with argon in an rf-only quadrupole cell, giving typical low-energy CID spectra for protonated peptide ions. Ions separated in the oaTOF are registered by a four-anode detector and time-to-digital converter and accumulated in "bins" that are 625 ps wide. Peak shapes depend upon the number of ion counts in adjacent bins. As expected, the accuracy of mass measurement is shown to be dependent upon the number of ions recorded for a particular peak. With internal calibration, mass accuracy better than 10 ppm is attainable for peaks that contain sufficient ions to give well-defined Gaussian profiles. By virtue of its high resolution, capability for accurate mass measurements, and sensitivity in the low-femotomole range, this instrument is ideally suited to protein identification for proteomic applications by generation of peptide tags, manual sequence interpretation, identification of modifications such as phosphorylation, and protein structural elucidation. Unlike the multiply charged ions typical of electrospray ionization, the singly charged MALDI-generated peptide ions show a linear dependence of optimal collision energy upon molecular mass, which is advantageous for automated operation. It is shown that the novel

Storage and retrieval of mass spectral information

NASA Technical Reports Server (NTRS)

Hohn, M. E.; Humberston, M. J.; Eglinton, G.

1977-01-01

Computer handling of mass spectra serves two main purposes: the interpretation of the occasional, problematic mass spectrum, and the identification of the large number of spectra generated in the gas-chromatographic-mass spectrometric (GC-MS) analysis of complex natural and synthetic mixtures. Methods available fall into the three categories of library search, artificial intelligence, and learning machine. Optional procedures for coding, abbreviating and filtering a library of spectra minimize time and storage requirements. Newer techniques make increasing use of probability and information theory in accessing files of mass spectral information.

Stage-specific differences in secretory profile of mesenchymal stromal cells (MSCs) subjected to early- vs late-stage OA synovial fluid.

PubMed

Gómez-Aristizábal, A; Sharma, A; Bakooshli, M A; Kapoor, M; Gilbert, P M; Viswanathan, S; Gandhi, R

2017-05-01

Although, mesenchymal stromal cells (MSCs) are being clinically investigated for their use in osteoarthritis (OA), it is unclear whether their postulated therapeutic properties are equally effective in the early- and late-stages of OA. In this study we investigated MSC cytokine secretion post-exposure to synovial fluid (SF), obtained from early- vs late-stage knee OA patients to justify a potential patient stratification strategy to maximize MSC-mediated treatment effects. Subjects were recruited and categorized into early- [Kellgren-Lawrence (KL) grade I/II, n = 12] and late-stage (KL-III/IV, n = 12) knee OA groups. SF samples were obtained, and their proteome was tested using multiplex assays, after 3-days culture, with and without MSCs. SFs cultured without MSCs were used as a baseline to identify MSC-secreted factors into SFs cultured with MSCs. Linear mixed-effect models and non-parametric tests were used to identify alterations in the MSC secretome during exposure to OA SF (3-days). MSCs cultured for 3-days in 0.5% fetal bovine serum (FBS)-supplemented medium were used to compare SF results with culture medium. Following exposure to OA SF, the MSC secretome contained proteins that are involved in tissue repair, angiogenesis, chemotaxis, matrix remodeling and the clotting process. However, chemokine (C-X-C motif) ligand-8 (CXCL8; chemoattractant), interleukin-6 (IL6) and chemokine (C-C motif) ligand 2 (CCL2) were elevated in the MSC-secretome in response to early- vs late-stage OA SF. Early- vs late-stage OA SF samples elicit a differential MSC secretome response, arguing for stratification of OA patients to maximize MSC-mediated therapeutic effects. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

Sources and Characterization of Submicron Aerosols in a Rural Forest During the PROPHET-AMOS 2016 Campaign

NASA Astrophysics Data System (ADS)

Bui, A. T.; Wallace, H. W., IV; Alvarez, S. L.; Erickson, M.; Alwe, H. D.; May, N.; Cook, R.; Connor, M.; Slade, J. H., Jr.; Shi, Q.; Kavassalis, S.; Tyndall, G. S.; Shepson, P. B.; Pratt, K.; Ault, A. P.; Millet, D. B.; Murphy, J. G.; Usenko, S.; Sheesley, R. J.; Flynn, J. H., III; Griffin, R. J.; Wang, W.

2017-12-01

Forests are a rich source of biogenic volatile organic compounds (BVOCs). Oxidation of BVOCs can result in the formation of secondary organic aerosol (SOA) and in the presence of NOx (NO+NO2) produce organic nitrate-containing particles. However, the distribution of both BVOCs and oxidants can be dramatically altered by the physical barriers provided by a forest canopy. Global models currently neglect the effect of these canopies on SOA formation in forested regions. In this work, we characterize non-refractory submicron aerosol (NR-PM1) using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) during the 2016 Program on Oxidants: Photochemistry, Emissions, and Transport-Atmospheric Measurements of Oxidants in Summer (PROPHET-AMOS) campaign. This site is located in a rural forest in northern Michigan and features a tower that allowed for both above and below canopy measurements. Our results indicate that organic aerosols (OA) account for a substantial portion of the NR-PM1 measured at this site. Organic nitrate aerosol can contribute up to 18% of the total OA and an average of 75% of the total measured nitrate aerosol. Episodes of above- and below-canopy NR-PM1 concentration differences indicate that above-canopy OA concentrations can be up to 40% greater than below-canopy, which represents an increase of up to 1.5 µg/m3. Organic fragment ions such as CxHy, CxHyOz, and CxHyO1 contribute to enhanced above-canopy OA concentrations. Positive matrix factorization analysis of the high-resolution OA mass spectra identified three SOA factors: low volatility oxygenated OA (LVOOA), isoprene-derived OOA (ISOOA), and oxygenated organic aerosol. Analysis of air mass backward trajectories and correlations with external data indicate that LVOOA correlates well with sulfate and aged, urban-influenced air masses, whereas ISOOA correlates well with isoprene SOA tracers and air masses originating from semi-remote areas. Our results indicate that the OA at this

Burning of olive tree branches: a major organic aerosol source in the Mediterranean

NASA Astrophysics Data System (ADS)

Kostenidou, E.; Kaltsonoudis, C.; Tsiflikiotou, M.; Louvaris, E.; Russell, L. M.; Pandis, S. N.

2013-09-01

Aerosol produced during the burning of olive tree branches was characterized with both direct source sampling (using a mobile smog chamber) and with ambient measurements during the burning season. The fresh particles were composed of 80% organic matter, 8-10% black carbon (BC), 5% potassium, 3-4% sulfate, 2-3% nitrate and 0.8% chloride. Almost half of the fresh olive tree branches burning organic aerosol (otBB-OA) consisted of alkane groups. Their mode diameter was close to 70 nm. The oxygen to carbon (O : C) ratio of the fresh otBB-OA was 0.29 ± 0.04. The mass fraction of levoglucosan in PM1 was 0.034-0.043, relatively low in comparison with most fuel types. This may lead to an underestimation of the otBB-OA contribution if levoglucosan is being used as a wood burning tracer. Chemical aging was observed during smog chamber experiments, as f44 and O : C ratio increased, due to reactions with OH radicals and O3. The otBB-OA AMS mass spectrum differs from the other published biomass burning spectra, with a main difference at m/z 60, used as levoglucosan tracer. In addition to particles, volatile organic compounds (VOCs) such as methanol, acetonitrile, acrolein, benzene, toluene and xylenes are also emitted. Positive matrix factorization (PMF) was applied to the ambient organic aerosol data and 3 factors could be identified: OOA (oxygenated organic aerosol, 55%), HOA (hydrocarbon-like organic aerosol, 11.3%) and otBB-OA 33.7%. The fresh chamber otBB-OA AMS spectrum is close to the PMF otBB-OA spectrum and resembles the ambient mass spectrum during olive tree branches burning periods. We estimated an otBB-OA emission factor of 3.5 ± 0.9 g kg-1. Assuming that half of the olive tree branches pruned is burned in Greece, 2300 ± 600 tons of otBB-OA are emitted every year. This activity is one of the most important fine aerosol sources during the winter months in Mediterranean countries.

Burning of olive tree branches: a major organic aerosol source in the Mediterranean

NASA Astrophysics Data System (ADS)

Kostenidou, E.; Kaltsonoudis, C.; Tsiflikiotou, M.; Louvaris, E.; Russell, L. M.; Pandis, S. N.

2013-03-01

Aerosol produced during the burning of olive tree branches was characterized with both direct source-sampling (using a mobile smog chamber) and with ambient measurements during the burning season. The fresh particles were composed of 80% organic matter, 8-10% black carbon (BC), 5% potassium, 3-4% sulfate, 2-3% nitrate and 0.8% chloride. Almost half of the fresh olive tree branches burning organic aerosol (otBB-OA) consisted of alkane groups. Their mode diameter was close to 70 nm. The oxygen to carbon (O:C) ratio of the fresh otBB-OA was 0.29 ± 0.04. The mass fraction of levoglucosan in PM1 was 0.034-0.043, relatively low in comparison with most fuel types. This may lead to an underestimation of the otBB-OA contribution if levoglucosan is being used as a wood burning tracer. Chemical aging was observed during smog chamber experiments, as f44 and O:C ratio increased, due to reactions with OH radicals and O3. The otBB-OA AMS mass spectrum differs from the other published biomass burning spectra, with a main difference at m/z 60, used as levoglucosan tracer. In addition to particles, volatile organic compounds (VOCs) such as methanol, acetonitrile, acrolein, benzene, toluene and xylenes are also emitted. Positive matrix factorization (PMF) was applied to the ambient organic aerosol data and 3 factors could be identified: OOA (oxygenated organic aerosol, 55%), HOA (hydrocarbon-like organic aerosol, 11.3%) and otBB-OA 33.7%. The fresh chamber otBB-OA AMS spectrum is close to the PMF otBB-OA spectrum and resembles the ambient mass spectrum during olive tree branches burning periods. We estimated an otBB-OA emission factor of 3.5 ± 0.2 g kg-1. Assuming that half of the olive tree branches pruned is burned in Greece 2280 ± 140 tons of otBB-OA are emitted every year. This activity is one of the most important fine aerosol sources during the winter months in the Mediterranean countries.

Aerosol characterization over the southeastern United States using high resolution aerosol mass spectrometry: spatial and seasonal variation of aerosol composition, sources, and organic nitrates

NASA Astrophysics Data System (ADS)

Xu, L.; Suresh, S.; Guo, H.; Weber, R. J.; Ng, N. L.

2015-04-01

We deployed a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and an Aerosol Chemical Speciation Monitor (ACSM) to characterize the chemical composition of submicron non-refractory particles (NR-PM1) in the southeastern US. Measurements were performed in both rural and urban sites in the greater Atlanta area, GA and Centreville, AL for approximately one year, as part of Southeastern Center of Air Pollution and Epidemiology study (SCAPE) and Southern Oxidant and Aerosol Study (SOAS). Organic aerosol (OA) accounts for more than half of NR1 mass concentration regardless of sampling sites and seasons. Positive matrix factorization (PMF) analysis of HR-ToF-AMS measurements identified various OA sources, depending on location and season. Hydrocarbon-like OA (HOA) and cooking OA (COA) have important but not dominant contributions to total OA in urban sites. Biomass burning OA (BBOA) concentration shows a distinct seasonal variation with a larger enhancement in winter than summer. We find a good correlation between BBOA and brown carbon, indicating biomass burning is an important source for brown carbon, although an additional, unidentified brown carbon source is likely present at the rural Yorkville site. Isoprene-derived OA (Isoprene-OA) is only deconvolved in warmer months and contributes 18-36% of total OA. The presence of Isoprene-OA factor in urban sites is more likely from local production in the presence of NOx than transport from rural sites. More-oxidized and less-oxidized oxygenated organic aerosol (MO-OOA and LO-OOA, respectively) are dominant fractions (47-79%) of OA in all sites. MO-OOA correlates well with ozone in summer, but not in winter, indicating MO-OOA sources may vary with seasons. LO-OOA, which reaches a daily maximum at night, correlates better with estimated nitrate functionality from organic nitrates than total nitrates. Based on the HR-ToF-AMS measurements, we estimate that the nitrate functionality from organic nitrates

Alternative mass reference standards for direct analysis in real time mass spectrometry.

PubMed

Cody, Robert B; Dane, A John

2016-05-30

Mass spectra were acquired with the Direct Analysis in Real Time (DART®) ion source for an amine-terminated polyether used as positive-ion mass reference standards and for several fluorinated materials commonly used as negative-ion reference standards for mass spectrometry. A commercial time-of-flight mass spectrometer equipped with a DART ion source was used for all measurements. Mass reference standards deposited onto the sealed end of a glass melting point tube were suspended in the DART gas stream for analysis. A polyetheramine (Jeffamine® M-600) produced intense peaks corresponding to protonated molecules. Perfluorotributylamine (PFTBA), and perfluorotripentylamine, gave useful reference spectra for different m/z ranges. DART mass spectra of Ultramark 1621® resembled those previously reported for Fast Atom Bombardment (FAB) and Electrospray Ionization (ESI). Fomblin®Y, a fluorinated ether, was the most useful negative-ion reference standard of the materials tested. The material is commercially available, inexpensive, and provides reference peaks covering the m/z range 85 to >3000. Jeffamine-M600 was found to be a convenient alternative to polyethers such as polyethylene glycol (PEG) for DART positive-ion mass calibration. Fomblin Y was suitable for use as a negative-ion reference standard. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

High Bone Mass is associated with bone-forming features of osteoarthritis in non-weight bearing joints independent of body mass index.

PubMed

Gregson, C L; Hardcastle, S A; Murphy, A; Faber, B; Fraser, W D; Williams, M; Davey Smith, G; Tobias, J H

2017-04-01

High Bone Mass (HBM) is associated with (a) radiographic knee osteoarthritis (OA), partly mediated by increased BMI, and (b) pelvic enthesophytes and hip osteophytes, suggestive of a bone-forming phenotype. We aimed to establish whether HBM is associated with radiographic features of OA in non-weight-bearing (hand) joints, and whether such OA demonstrates a bone-forming phenotype. HBM cases (BMD Z-scores≥+3.2) were compared with family controls. A blinded assessor graded all PA hand radiographs for: osteophytes (0-3), joint space narrowing (JSN) (0-3), subchondral sclerosis (0-1), at the index Distal Interphalangeal Joint (DIPJ) and 1st Carpometacarpal Joint (CMCJ), using an established atlas. Analyses used a random effects logistic regression model, adjusting a priori for age and gender. Mediating roles of BMI and bone turnover markers (BTMs) were explored by further adjustment. 314 HBM cases (mean age 61.1years, 74% female) and 183 controls (54.3years, 46% female) were included. Osteophytes (grade≥1) were more common in HBM (DIPJ: 67% vs. 45%, CMCJ: 69% vs. 50%), with adjusted OR [95% CI] 1.82 [1.11, 2.97], p=0.017 and 1.89 [1.19, 3.01], p=0.007 respectively; no differences were seen in JSN. Further adjustment for BMI failed to attenuate ORs for osteophytes in HBM cases vs. controls; DIPJ 1.72 [1.05, 2.83], p=0.032, CMCJ 1.76 [1.00, 3.06], p=0.049. Adjustment for BTMs (concentrations lower amongst HBM cases) did not attenuate ORs. HBM is positively associated with OA in non-weight-bearing joints, independent of BMI. HBM-associated OA is characterised by osteophytes, consistent with a bone-forming phenotype, rather than JSN reflecting cartilage loss. Systemic factors (e.g. genetic architecture) which govern HBM may also increase bone-forming OA risk. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Apis mellifera octopamine receptor 1 (AmOA1) expression in antennal lobe networks of the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster)

PubMed Central

Sinakevitch, Irina T.; Smith, Adrian N.; Locatelli, Fernando; Huerta, Ramon; Bazhenov, Maxim; Smith, Brian H.

2013-01-01

Octopamine (OA) underlies reinforcement during appetitive conditioning in the honey bee and fruit fly, acting via different subtypes of receptors. Recently, antibodies raised against a peptide sequence of one honey bee OA receptor, AmOA1, were used to study the distribution of these receptors in the honey bee brain (Sinakevitch et al., 2011). These antibodies also recognize an isoform of the AmOA1 ortholog in the fruit fly (OAMB, mushroom body OA receptor). Here we describe in detail the distribution of AmOA1 receptors in different types of neurons in the honey bee and fruit fly antennal lobes. We integrate this information into a detailed anatomical analysis of olfactory receptor neurons (ORNs), uni- and multi-glomerular projection neurons (uPNs, and mPNs) and local interneurons (LNs) in glomeruli of the antennal lobe. These neurons were revealed by dye injection into the antennal nerve, antennal lobe, medial and lateral antenno-protocerbral tracts (m-APT and l-APT), and lateral protocerebral lobe (LPL) by use of labeled cell lines in the fruit fly or by staining with anti-GABA. We found that ORN receptor terminals and uPNs largely do not show immunostaining for AmOA1. About seventeen GABAergic mPNs leave the antennal lobe through the ml-APT and branch into the LPL. Many, but not all, mPNs show staining for AmOA1. AmOA1 receptors are also in glomeruli on GABAergic processes associated with LNs. The data suggest that in both species one important action of OA in the antennal lobe involves modulation of different types of inhibitory neurons via AmOA1 receptors. We integrated this new information into a model of circuitry within glomeruli of the antennal lobes of these species. PMID:24187534

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

PubMed

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

2016-05-01

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

Advances in structure elucidation of small molecules using mass spectrometry

PubMed Central

Fiehn, Oliver

2010-01-01

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

Variability of aerosol, gaseous pollutants and meteorological characteristics associated with continental, urban and marine air masses at the SW Atlantic coast of Iberia

NASA Astrophysics Data System (ADS)

Diesch, J.-M.; Drewnick, F.; Zorn, S. R.; von der Weiden-Reinmüller, S.-L.; Martinez, M.; Borrmann, S.

2011-12-01

air masses passing the continent the organic aerosol fraction dominated the total NR-PM1. For this reason, using Positive Matrix Factorization (PMF) four organic aerosol (OA) classes that can be associated with various aerosol sources and components were identified: a highly-oxygenated OA is the major component contributing an average of 43% of the particulate organic mass while the semi-volatile OA accounts for 23%. A hydrocarbon-like OA mainly resulting from industries, traffic and shipping emissions as well as particles from wood burning emissions also contribute to total OA dependent on the air mass origin. The variability of ozone is not only affected by different types of air masses but also significantly by the diurnal variation as a consequence of the solar radiation as well as local meteorological parameters.

Data reduction of isotope-resolved LC-MS spectra.

PubMed

Du, Peicheng; Sudha, Rajagopalan; Prystowsky, Michael B; Angeletti, Ruth Hogue

2007-06-01

Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data. LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses. It is capable of noise removal, and deconvoluting peaks that overlap in m/z, in retention time, or both, by using a novel iterative peak-picking step, a 'rescue' step, and a modified variable selection method. LCMS-2D performs well with three sets of annotated LC-MS spectra, yielding results that are better than those from PepList, msInspect and the vendor software BioAnalyst. The software LCMS-2D is available under the GNU general public license from http://www.bioc.aecom.yu.edu/labs/angellab/as a standalone C program running on LINUX.

Expert system for computer-assisted annotation of MS/MS spectra.

PubMed

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-11-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions.

Expert System for Computer-assisted Annotation of MS/MS Spectra*

PubMed Central

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-01-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147

Neutron star mass and radius measurements from atmospheric model fits to X-ray burst cooling tail spectra

NASA Astrophysics Data System (ADS)

Nättilä, J.; Miller, M. C.; Steiner, A. W.; Kajava, J. J. E.; Suleimanov, V. F.; Poutanen, J.

2017-12-01

Observations of thermonuclear X-ray bursts from accreting neutron stars (NSs) in low-mass X-ray binary systems can be used to constrain NS masses and radii. Most previous work of this type has set these constraints using Planck function fits as a proxy: the models and the data are both fit with diluted blackbody functions to yield normalizations and temperatures that are then compared with each other. For the first time, we here fit atmosphere models of X-ray bursting NSs directly to the observed spectra. We present a hierarchical Bayesian fitting framework that uses current X-ray bursting NS atmosphere models with realistic opacities and relativistic exact Compton scattering kernels as a model for the surface emission. We test our approach against synthetic data and find that for data that are well described by our model, we can obtain robust radius, mass, distance, and composition measurements. We then apply our technique to Rossi X-ray Timing Explorer observations of five hard-state X-ray bursts from 4U 1702-429. Our joint fit to all five bursts shows that the theoretical atmosphere models describe the data well, but there are still some unmodeled features in the spectrum corresponding to a relative error of 1-5% of the energy flux. After marginalizing over this intrinsic scatter, we find that at 68% credibility, the circumferential radius of the NS in 4U 1702-429 is R = 12.4±0.4 km, the gravitational mass is M = 1.9±0.3 M⊙, the distance is 5.1 < D/ kpc < 6.2, and the hydrogen mass fraction is X < 0.09.

The structure of BPS spectra

NASA Astrophysics Data System (ADS)

Longhi, Pietro

In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

Combination of lateral and PA view radiographs to study development of knee OA and associated pain

NASA Astrophysics Data System (ADS)

Minciullo, Luca; Thomson, Jessie; Cootes, Timothy F.

2017-03-01

Knee Osteoarthritis (OA) is the most common form of arthritis, affecting millions of people around the world. The effects of the disease have been studied using the shape and texture features of bones in PosteriorAnterior (PA) and Lateral radiographs separately. In this work we compare the utility of features from each view, and evaluate whether combining features from both is advantageous. We built a fully automated system to independently locate landmark points in both radiographic images using Random Forest Constrained Local Models. We extracted discriminative features from the two bony outlines using Appearance Models. The features were used to train Random Forest classifiers to solve three specific tasks: (i) OA classification, distinguishing patients with structural signs of OA from the others; (ii) predicting future onset of the disease and (iii) predicting which patients with no current pain will have a positive pain score later in a follow-up visit. Using a subset of the MOST dataset we show that the PA view has more discriminative features to classify and predict OA, while the lateral view contains features that achieve better performance in predicting pain, and that combining the features from both views gives a small improvement in accuracy of the classification compared to the individual views.

Evidence for the frequency-shift of the OA A_1g mode in Hg-based superconductors

NASA Astrophysics Data System (ADS)

Yang, In-Sang; Lee, Hye-Gyong

1996-03-01

The Hg-based superconductors, HgBa_2Ca_n-1Cu_nO_2n+2+δ (n=1,2,3) have two strong Raman peaks at ~ 570 and 590 cm-1 in the high-frequency region. From the results of Raman measurements of Tl-doped Hg-1223 system, it is concluded that the peak at ~ 570 cm-1 does not arise from the vibration of the interstitial oxygen O_δ in the Hg/Tl-O plane, but from the frequency-shift of the A_1g-type vibration of the apical oxygen O_A. The peak at 570 cm-1 is from the O_As surrounded by the O_δs in the nearest neighbor, while the 590 cm-1 mode is from the O_As without the O_δs in the immediate neighbor. The intensity of the 570 cm-1 mode increases with the O_δ content, but the Raman frequencies of both modes do not change significantly. This suggests that the increase of the frequency of the OA A_1g mode under high pressure (I.-S. Yang et al., Phys. Rev. B 51, 644 (1995)) is independent from the O_δ content, in the Hg-based superconductors.

Lunar orbital mass spectrometer experiment

NASA Technical Reports Server (NTRS)

Lord, W. P.

1971-01-01

The design, development, manufacture, test and calibration of five lunar orbital mass spectrometers with the four associated ground support equipment test sets are discussed. A mass spectrometer was installed in the Apollo 15 and one in the Apollo 16 Scientific Instrument Module within the Service Module. The Apollo 15 mass spectrometer was operated with collection of 38 hours of mass spectra data during lunar orbit and 50 hours of data were collected during transearth coast. The Apollo 16 mass spectrometer was operated with collection of 76 hours of mass spectra data during lunar orbit. However, the Apollo 16 mass spectrometer was ejected into lunar orbit upon malfunction of spacecraft boom system just prior to transearth insection and no transearth coast data was possible.

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls

PubMed Central

Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique LCT; Heeren, Ron MA; Sillevis Smitt, Peter A; Luider, Theo M

2006-01-01

Background Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. Results A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. Conclusion The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

PubMed

Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique L C T; Heeren, Ron M A; Sillevis Smitt, Peter A; Luider, Theo M

2006-09-05

Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the

Matrix assisted laser desorption ionization mass spectrometry imaging identifies markers of ageing and osteoarthritic cartilage

PubMed Central

2014-01-01

Introduction Cartilage protein distribution and the changes that occur in cartilage ageing and disease are essential in understanding the process of cartilage ageing and age related diseases such as osteoarthritis. The aim of this study was to investigate the peptide profiles in ageing and osteoarthritic (OA) cartilage sections using matrix assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Methods The distribution of proteins in young, old and OA equine cartilage was compared following tryptic digestion of cartilage slices and MALDI-MSI undertaken with a MALDI SYNAPT™ HDMS system. Protein identification was undertaken using database searches following multivariate analysis. Peptide intensity differences between young, ageing and OA cartilage were imaged with Biomap software. Analysis of aggrecanase specific cleavage patterns of a crude cartilage proteoglycan extract were used to validate some of the differences in peptide intensity identified. Immunohistochemistry studies validated the differences in protein abundance. Results Young, old and OA equine cartilage was discriminated based on their peptide signature using discriminant analysis. Proteins including aggrecan core protein, fibromodulin, and cartilage oligomeric matrix protein were identified and localised. Fibronectin peptides displayed a stronger intensity in OA cartilage. Age-specific protein markers for collectin-43 and cartilage oligomeric matrix protein were identified. In addition potential fibromodulin and biglycan peptides targeted for degradation in OA were detected. Conclusions MALDI-MSI provided a novel platform to study cartilage ageing and disease enabling age and disease specific peptides in cartilage to be elucidated and spatially resolved. PMID:24886698

Geographical and Vertical Distribution of Organic Aerosol (OA) during ATom-1 and 2: Chemical removal and aging as a function of photochemical age

NASA Astrophysics Data System (ADS)

Campuzano Jost, P.; Schroder, J. C.; Nault, B.; Day, D. A.; Jimenez, J. L.; Heald, C. L.; Hodzic, A.; Katich, J. M.; Schwarz, J. P.; Blake, N. J.; Blake, D. R.; Daube, B. C.; Wofsy, S. C.; Ray, E. A.; Bian, H.; Colarco, P. R.; Chin, M.; Pawson, S.; Newman, P. A.

2017-12-01

Submicron aerosols in the remote free troposphere (FT) originate mostly from long-range transport from distant biogenic, anthropogenic, and biomass burning sources. Very limited local production in this region heightens the sensitivity of aerosol concentrations to slow removal processes. As yet, few studies with an advanced aerosol payload have targeted the remote FT. Current global models exhibit a very large diversity in predicting aerosol concentrations in these regions of the atmosphere, particularly when trying to model organic aerosol (OA), which, together with sulfate, is the most prevalent type of non-refractory aerosol in the remote FT. As part of NASA's Atmospheric Tomography (ATom) aircraft mission, we have acquired a global dataset of organic aerosol (OA) concentration and composition over the remote Atlantic and Pacific Oceans from 0 to 12 km and from 65 S to 80 N for both Summer and Winter seasons. This dataset provides unique new constraints on the spatial distribution of OA and its contribution to the global aerosol background; of particular interest are the OA/Sulfate ratio and OA oxidation state that are critical for estimating the activity of cloud condensation nuclei (CCN) in the remote troposphere. We find that, except for the cleanest of the ATom-sampled airmasses, OA concentrations are comparable and often larger than sulfate. OA was highly oxidized, significantly more than over the continental FT, with O:C ratios often in excess of 1 (i.e. OA/OC >2.5). Using several different hydrocarbon-ratio based photochemical clocks in combination with backtrajectories to infer the age of the airmasses sampled during ATom, we estimate that the lifetime of OA in the remote FT is on the order of 10 days. This is significantly shorter than the FT lifetime assuming just wet and dry deposition as the primary loss mechanisms, and suggests a chemical removal mechanism such as heterogeneous oxidation or photolysis. This provides a key constraint for modeling of

Construction of low-cost, Mod-OA wood composite wind turbine blades

NASA Technical Reports Server (NTRS)

Lark, R. F.

1983-01-01

Two sixty-foot, low-cost, wood composite blades for service on 200 kW Mod-OA wind turbines were constructed. The blades were constructed of epoxy resin-bonded Douglas fir veneers for the leading edge sections, and paper honeycombcored, birch plywood faced panels for the afterbody sections. The blades were joined to the wind turbine hub by epoxy resin-bonded steel load take-off studs embedded into the root end of the blades. The blades were installed on the 200 kW Mod-OA wind turbine facility at Kahuku, Hawaii, The blades completed nearly 8,000 hours of operation over an 18 month period at an average power of 150 kW prior to replacement with another set of wood composite blades. The blades were replaced because of a corrosion failure of the steel shank on one stud. Inspections showed that the wood composite structure remained in excellent condition.

Restriction of spontaneous and prednisolone-induced leptin production to dedifferentiated state in human hip OA chondrocytes: role of Smad1 and β-catenin activation.

PubMed

Charlier, E; Malaise, O; Zeddou, M; Neuville, S; Cobraiville, G; Deroyer, C; Sanchez, C; Gillet, P; Kurth, W; de Seny, D; Relic, B; Malaise, M G

2016-02-01

The aetiology of OA is not fully understood although several adipokines such as leptin are known mediators of disease progression. Since leptin levels were increased in synovial fluid compared to serum in OA patients, it was suggested that joint cells themselves could produce leptin. However, exact mechanisms underlying leptin production by chondrocytes are poorly understood. Nevertheless, prednisolone, although displaying powerful anti-inflammatory properties has been recently reported to be potent stimulator of leptin and its receptor in OA synovial fibroblasts. Therefore, we investigated, in vitro, spontaneous and prednisolone-induced leptin production in OA chondrocytes, focusing on transforming growth factor-β (TGFβ) and Wnt/β-catenin pathways. We used an in vitro dedifferentiation model, comparing human freshly isolated hip OA chondrocytes cultivated in monolayer during 1 day (type II, COL2A1 +; type X, COL10A1 + and type I collagen, COL1A1 -) or 14 days (COL2A1 -; COL10A1 - and COL1A1+). Leptin expression was not detected in day1 OA chondrocytes whereas day14 OA chondrocytes produced leptin, significantly increased with prednisolone. Activin receptor-like kinase 1 (ALK1)/ALK5 ratio was shifted during dedifferentiation, from high ALK5 and phospho (p)-Smad2 expression at day1 to high ALK1, endoglin and p-Smad1/5 expression at day14. Moreover, inactive glycogen synthase kinase 3 (GSK3) and active β-catenin were only found in dedifferentiated OA chondrocytes. Smad1 and β-catenin but not endoglin stable lentiviral silencing led to a significant decrease in leptin production by dedifferentiated OA chondrocytes. Only dedifferentiated OA chondrocytes produced leptin. Prednisolone markedly enhanced leptin production, which involved Smad1 and β-catenin activation. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

DETERMINING ION COMPOSITIONS USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER

EPA Science Inventory

For the past decade, we have used double focusing mass spectrometers to determine
compositions of ions observed in mass spectra produced from compounds introduced by GC
based on measured exact masses of the ions and their +1 and +2 isotopic profiles arising from atoms of ...

A Bayesian Markov-chain-based heteroscedastic regression model for the analysis of 18O-labeled mass spectra.

PubMed

Zhu, Qi; Burzykowski, Tomasz

2011-03-01

To reduce the influence of the between-spectra variability on the results of peptide quantification, one can consider the (18)O-labeling approach. Ideally, with such labeling technique, a mass shift of 4 Da of the isotopic distributions of peptides from the labeled sample is induced, which allows one to distinguish the two samples and to quantify the relative abundance of the peptides. It is worth noting, however, that the presence of small quantities of (16)O and (17)O atoms during the labeling step can cause incomplete labeling. In practice, ignoring incomplete labeling may result in the biased estimation of the relative abundance of the peptide in the compared samples. A Markov model was developed to address this issue (Zhu, Valkenborg, Burzykowski. J. Proteome Res. 9, 2669-2677, 2010). The model assumed that the peak intensities were normally distributed with heteroscedasticity using a power-of-the-mean variance funtion. Such a dependence has been observed in practice. Alternatively, we formulate the model within the Bayesian framework. This opens the possibility to further extend the model by the inclusion of random effects that can be used to capture the biological/technical variability of the peptide abundance. The operational characteristics of the model were investigated by applications to real-life mass-spectrometry data sets and a simulation study. © American Society for Mass Spectrometry, 2011

Exchangeable hydrogen explains the pH of spodosol Oa horizons

USGS Publications Warehouse

Ross, D.S.; David, M.B.; Lawrence, G.B.; Bartlett, R.J.

1996-01-01

The chemistry of extremely acid Oa horizons does not conform to traditional pH, Al, and base saturation relationships. Results from two separate studies of northeastern U.S. forested soils were used to investigate relationships between pH in water or dilute salt solutions and other soil characteristics. In Oa horizons with pH below 4, soil pH in dilute CaCl2 solution was correlated with exchangeable H+ measured either by titration (r = -0.88, P = 0.0001, n = 142) or by electrode (r = -0.89, P = 0.0001, n = 45). Exchangeable H+ expressed as a percentage of the cation-exchange capacity (CEC) was linear with pH and showed similar slopes for data from both studies. For all samples, pHw = 4.21 - 1.80 x H+/CEC (R2 = 0.69, n = 194). The reciprocal of the H+/CEC ratio is base saturation with Al added to the bases. Because of the low pH, exchangeable Al does not appear to behave as an acid. Exchangeable H+ remains an operationally defined quantity because of the difficulty in separating exchange and hydrolysis reactions. In a variety of neutral-salt extractants, concentration of H+ were correlated with 0.1 M BaCl2-exchangeable H+ (r > 0.91, P = 0.0001, n = 26) regardless of the strength of the extract. Nine successive extractions with 0.33 mM CaCl2 removed more H+ than was removed by single batch extractions with either 1 M KCl or 0.1 M BaCl2 (average H+ of 70, 43, and 49 mmol kg-1, respectively for 26 samples). The data showed little difference in the chemical behavior of Oa horizons from a variety of geographical sites and vegetation types.

Aerosol characterization over the southeastern United States using high-resolution aerosol mass spectrometry: spatial and seasonal variation of aerosol composition and sources with a focus on organic nitrates

NASA Astrophysics Data System (ADS)

Xu, L.; Suresh, S.; Guo, H.; Weber, R. J.; Ng, N. L.

2015-07-01

We deployed a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and an Aerosol Chemical Speciation Monitor (ACSM) to characterize the chemical composition of submicron non-refractory particulate matter (NR-PM1) in the southeastern USA. Measurements were performed in both rural and urban sites in the greater Atlanta area, Georgia (GA), and Centreville, Alabama (AL), for approximately 1 year as part of Southeastern Center for Air Pollution and Epidemiology study (SCAPE) and Southern Oxidant and Aerosol Study (SOAS). Organic aerosol (OA) accounts for more than half of NR-PM1 mass concentration regardless of sampling sites and seasons. Positive matrix factorization (PMF) analysis of HR-ToF-AMS measurements identified various OA sources, depending on location and season. Hydrocarbon-like OA (HOA) and cooking OA (COA) have important, but not dominant, contributions to total OA in urban sites (i.e., 21-38 % of total OA depending on site and season). Biomass burning OA (BBOA) concentration shows a distinct seasonal variation with a larger enhancement in winter than summer. We find a good correlation between BBOA and brown carbon, indicating biomass burning is an important source for brown carbon, although an additional, unidentified brown carbon source is likely present at the rural Yorkville site. Isoprene-derived OA factor (isoprene-OA) is only deconvolved in warmer months and contributes 18-36 % of total OA. The presence of isoprene-OA factor in urban sites is more likely from local production in the presence of NOx than transport from rural sites. More-oxidized and less-oxidized oxygenated organic aerosol (MO-OOA and LO-OOA, respectively) are dominant fractions (47-79 %) of OA in all sites. MO-OOA correlates well with ozone in summer but not in winter, indicating MO-OOA sources may vary with seasons. LO-OOA, which reaches a daily maximum at night, correlates better with estimated nitrate functionality from organic nitrates than total nitrates. Based

Mass Spectrometry of Large, Fragile, and Involatile Molecules.

ERIC Educational Resources Information Center

Busch, Kenneth L.; Cooks, R. Graham

1982-01-01

Desorption ionization (DI) is used to obtain mass spectra of molecules whose vaporization by heating may lead to thermal degradation. Discusses DI techniques, characteristics of DI mass spectra, ion production, current applications of DI in mass spectroscopy, developments in DI, and prospects for future evolution of new DI techniques. (Author/JN)

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

NASA Astrophysics Data System (ADS)

Bahreini, R.; Middlebrook, A. M.; de Gouw, J. A.; Warneke, C.; Trainer, M.; Brock, C. A.; Stark, H.; Brown, S. S.; Dube, W. P.; Gilman, J. B.; Hall, K.; Holloway, J. S.; Kuster, W. C.; Perring, A. E.; Prevot, A. S. H.; Schwarz, J. P.; Spackman, J. R.; Szidat, S.; Wagner, N. L.; Weber, R. J.; Zotter, P.; Parrish, D. D.

2012-03-01

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

Laboratory Measurements of Mass Specific Absorption Spectra for Suites of Black Carbon-like, Biomass Burning and Mineral Dust Aerosols

NASA Astrophysics Data System (ADS)

Radney, J.; Zangmeister, C.

2017-12-01

Light-absorbing atmospheric aerosols can be grouped into three categories: black carbon (BC), brown carbon (BrC) or mineral dust (MD). In many cases, the absorption of these species is best quantified using a mass-specific absorption cross section (MAC) since the particles are in the Rayleigh regime (BC) or optically thin (BrC and MD); notably, MAC values are both traceable to the SI and transferrable between photoacoustic spectroscopy and filter-based absorption measurements. Here, we present laboratory measurements of MAC for all three light-absorbing aerosol classes. Particles were size- and mass-selected using a differential mobility analyzer and aerosol particle mass analyzer, respectively, with absorption coefficients (αabs) and number concentrations (N) being measured by a broadband photoacoustic spectrometer and condensation particle counter, respectively. This suite of instrumentation allows for direct quantification of MAC from the measured parameters (MAC = αabs/Nmp). Further, the measurements contained > 8 data points spanning λ = 405 nm to 840 nm allowing for spectral curvatures (i.e. the Absorption Angstrom Exponent or AAE) to be fit from many data points versus the more common 2-point interpolations. For the carbonaceous, BC-like aerosols - five samples generated from flames, spark discharge soot (i.e. fullerene soot), graphene, reduced graphene oxide (rGO), and fullerene (C60) - we found: 1) measured MAC ranged between 2.4 m2 g-1 and 8.6 m2 g-1 at λ = 550 nm, 2) most AAEs ranged between 0.5 and 1.3; C60 AAE was 7.5 ± 0.9 and 3) MAC spectra were dependent on fuel type and formation conditions. For BrC particles generated from smoldering combustion of 3 hardwood (Oak, Hickory and Mesquite) and 3 softwood species (Western redcedar, Blue spruce and Baldcypress), we found: 1) median MAC values ranged from 1.4 x 10-2 m2 g-1 to 7.9 x 10-2 m2 g-1 at λ = 550 nm, 2) AAE values ranged between 3.5 and 6.2, and 3) Oak, Western redcedar and Blue spruce

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra*

PubMed Central

Jeong, Kyowon; Kim, Sangtae; Bandeira, Nuno; Pevzner, Pavel A.

2011-01-01

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-GappedDictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-GappedDictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches. PMID:21444829

Proton Spectra from He 3 + T and He 3 + He 3 Fusion at Low Center-of-Mass Energy, with Potential Implications for Solar Fusion Cross Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zylstra, A. B.; Frenje, J. A.; Gatu Johnson, M.

Few-body nuclear physics often relies upon phenomenological models, with new efforts at the ab initio theory reported recently; both need high-quality benchmark data, particularly at low center-of-mass energies. We use high-energy-density plasmas to measure the proton spectra from 3He + T and 3He + 3He fusion. The data disagree with R -matrix predictions constrained by neutron spectra from T + T fusion. Here, we present a new analysis of the 3He + 3He proton spectrum; these benchmarked spectral shapes should be used for interpreting low-resolution data, such as solar fusion cross-section measurements.

Proton Spectra from 3He + T and 3He + 3He Fusion at Low Center-of-Mass Energy, with Potential Implications for Solar Fusion Cross Sections

NASA Astrophysics Data System (ADS)

Zylstra, A. B.; Frenje, J. A.; Gatu Johnson, M.; Hale, G. M.; Brune, C. R.; Bacher, A.; Casey, D. T.; Li, C. K.; McNabb, D.; Paris, M.; Petrasso, R. D.; Sangster, T. C.; Sayre, D. B.; Séguin, F. H.

2017-12-01

Few-body nuclear physics often relies upon phenomenological models, with new efforts at the ab initio theory reported recently; both need high-quality benchmark data, particularly at low center-of-mass energies. We use high-energy-density plasmas to measure the proton spectra from 3He +T and 3He + 3He fusion. The data disagree with R -matrix predictions constrained by neutron spectra from T +T fusion. We present a new analysis of the 3He + 3He 3 proton spectrum; these benchmarked spectral shapes should be used for interpreting low-resolution data, such as solar fusion cross-section measurements.

Proton Spectra from He 3 + T and He 3 + He 3 Fusion at Low Center-of-Mass Energy, with Potential Implications for Solar Fusion Cross Sections

DOE PAGES

Zylstra, A. B.; Frenje, J. A.; Gatu Johnson, M.; ...

2017-11-29

Few-body nuclear physics often relies upon phenomenological models, with new efforts at the ab initio theory reported recently; both need high-quality benchmark data, particularly at low center-of-mass energies. We use high-energy-density plasmas to measure the proton spectra from 3He + T and 3He + 3He fusion. The data disagree with R -matrix predictions constrained by neutron spectra from T + T fusion. Here, we present a new analysis of the 3He + 3He proton spectrum; these benchmarked spectral shapes should be used for interpreting low-resolution data, such as solar fusion cross-section measurements.

NEGATIVE-ION MASS SPECTROMETRY OF SULFONYLUREA HERBICIDES

EPA Science Inventory

Sulfonylurea herbicides have been studied using neg-ion desorption chem.-ionization (DCI) mass spectrometry (MS) and DCI-MS/MS techniques. Both {M-H]- and M.- ions were obsd. in the DCI mass spectra. The collisonally activated dissocn. (CAD) spectra were characteristic of the str...

Suspected-target pesticide screening using gas chromatography-quadrupole time-of-flight mass spectrometry with high resolution deconvolution and retention index/mass spectrum library.

PubMed

Zhang, Fang; Wang, Haoyang; Zhang, Li; Zhang, Jing; Fan, Ruojing; Yu, Chongtian; Wang, Wenwen; Guo, Yinlong

2014-10-01

A strategy for suspected-target screening of pesticide residues in complicated matrices was exploited using gas chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS). The screening workflow followed three key steps of, initial detection, preliminary identification, and final confirmation. The initial detection of components in a matrix was done by a high resolution mass spectrum deconvolution; the preliminary identification of suspected pesticides was based on a special retention index/mass spectrum (RI/MS) library that contained both the first-stage mass spectra (MS(1) spectra) and retention indices; and the final confirmation was accomplished by accurate mass measurements of representative ions with their response ratios from the MS(1) spectra or representative product ions from the second-stage mass spectra (MS(2) spectra). To evaluate the applicability of the workflow in real samples, three matrices of apple, spinach, and scallion, each spiked with 165 test pesticides in a set of concentrations, were selected as the models. The results showed that the use of high-resolution TOF enabled effective extractions of spectra from noisy chromatograms, which was based on a narrow mass window (5 mDa) and suspected-target compounds identified by the similarity match of deconvoluted full mass spectra and filtering of linear RIs. On average, over 74% of pesticides at 50 ng/mL could be identified using deconvolution and the RI/MS library. Over 80% of pesticides at 5 ng/mL or lower concentrations could be confirmed in each matrix using at least two representative ions with their response ratios from the MS(1) spectra. In addition, the application of product ion spectra was capable of confirming suspected pesticides with specificity for some pesticides in complicated matrices. In conclusion, GC-QTOF MS combined with the RI/MS library seems to be one of the most efficient tools for the analysis of suspected-target pesticide residues

Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions

NASA Astrophysics Data System (ADS)

Solano, Eduardo A.; Mohamed, Sabria; Mayer, Paul M.

2016-10-01

The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions p M (" separators=" E , T char ) . The mean vibrational energy excess of the ions was characterized by the parameter Tchar ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below Tchar = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of Tchar as a function of Ecom (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dEvib/dEcom) changes with Ecom according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.

Modeling collision energy transfer in APCI/CID mass spectra of PAHs using thermal-like post-collision internal energy distributions.

PubMed

Solano, Eduardo A; Mohamed, Sabria; Mayer, Paul M

2016-10-28

The internal energy transferred when projectile molecular ions of naphthalene collide with argon gas atoms was extracted from the APCI-CID (atmospheric-pressure chemical ionization collision-induced dissociation) mass spectra acquired as a function of collision energy. Ion abundances were calculated by microcanonical integration of the differential rate equations using the Rice-Ramsperger-Kassel-Marcus rate constants derived from a UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) fragmentation mechanism and thermal-like vibrational energy distributions p M E,T char . The mean vibrational energy excess of the ions was characterized by the parameter T char ("characteristic temperature"), determined by fitting the theoretical ion abundances to the experimental breakdown graph (a plot of relative abundances of the ions as a function of kinetic energy) of activated naphthalene ions. According to these results, the APCI ion source produces species below T char = 1457 K, corresponding to 3.26 eV above the vibrational ground state. Subsequent collisions heat the ions up further, giving rise to a sigmoid curve of T char as a function of E com (center-of-mass-frame kinetic energy). The differential internal energy absorption per kinetic energy unit (dE vib /dE com ) changes with E com according to a symmetric bell-shaped function with a maximum at 6.38 ± 0.32 eV (corresponding to 6.51 ± 0.27 eV of vibrational energy excess), and a half-height full width of 6.30 ± 1.15 eV. This function imposes restrictions on the amount of energy that can be transferred by collisions, such that a maximum is reached as kinetic energy is increased. This behavior suggests that the collisional energy transfer exhibits a pronounced increase around some specific value of energy. Finally, the model is tested against the CID mass spectra of anthracene and pyrene ions and the corresponding results are discussed.

Protein Identification Using Top-Down Spectra*

PubMed Central

Liu, Xiaowen; Sirotkin, Yakov; Shen, Yufeng; Anderson, Gordon; Tsai, Yihsuan S.; Ting, Ying S.; Goodlett, David R.; Smith, Richard D.; Bafna, Vineet; Pevzner, Pavel A.

2012-01-01

In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set. PMID:22027200

Mass spectrometry of analytical derivatives. 2. “Ortho” and “Para” effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids1

PubMed Central

Todua, Nino G.; Mikaia, Anzor I.

2016-01-01

Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS1 spectra of unlabeled compounds to their 2H and 13C labeled analogs, and analysis of collision-induced dissociation data from MS2 spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested. PMID:27891187

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

NASA Astrophysics Data System (ADS)

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

2009-08-01

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

Effects of Reductions in Body Mass Index on Future Osteoarthritis Burden in Canada: A Population-Based Microsimulation Study

PubMed Central

Kopec, Jacek A.; Sayre, Eric C.; Fines, Philippe; Flanagan, William M.; Nadeau, Claude; Okhmatovskaia, Anya; Wolfson, Michael C.

2016-01-01

Background Osteoarthritis (OA) is the most common joint disease and a major cause of disability. Incidence and prevalence of OA are expected to increase due to population aging and increased levels of obesity. Objective The purpose of this study was to project the effect of hypothetical interventions that change the distribution of body mass index (BMI) on OA burden in Canada. Methods We used a microsimulation computer model of OA called POHEM-OA. The model used demographic predictions for Canada and population data from an administrative database in British Columbia and national Canadian surveys. Results Under the base-case scenario, between 2010 and 2030 OA prevalence is expected to increase from 11.5% to 15.6% in men and 16.3% to 21.1% in women. In scenarios assuming, on average, a 0.3, 0.5 or 1-unit drop in BMI/year, OA prevalence in 2030 would reach 14.9%, 14.6% and 14.2% in men and 20.3%, 19.7%, and 18.5%, in women, respectively. Under these scenarios, the proportion of new cases prevented would be 9.5%, 13.2% and 16.7%, respectively, in men, and 9.1%, 15.2% and 25.0% in women. Targeting only those aged 50 years or older for weight reduction would achieve about 70% of the impact of a full population strategy. Targeting only the obese (BMI>30) would likely result in a larger benefit for men than women. Conclusions Due to the aging of the population, OA will remain a major and growing health issue in Canada over the next two decades, regardless of the course of the obesity epidemic. PMID:26606744

Synovial tissue volume: a treatment target in knee osteoarthritis (OA).

PubMed

O'Neill, Terence W; Parkes, Matthew J; Maricar, Nasimah; Marjanovic, Elizabeth J; Hodgson, Richard; Gait, Andrew D; Cootes, Timothy F; Hutchinson, Charles E; Felson, David T

2016-01-01

Synovitis occurring frequently in osteoarthritis (OA) may be a targeted outcome. There are no data examining whether synovitis changes following intra-articular intervention. Persons aged 40 years and older with painful knee OA participated in an open label trial of intra-articular steroid therapy. At all time points they completed the Knee Injury and Osteoarthritis Outcome Score (KOOS) questionnaire. They had a contrast-enhanced (CE) MRI immediately prior to an intra-articular steroid injection with a repeat scan within 20 days. Response status was assessed using the Osteoarthritis Research Society International (OARSI) response criteria. OARSI responders were followed until their pain relapsed either within 20% of baseline or 6 months, shortly after which a third MRI was performed. Synovial tissue volume (STV) was measured on postcontrast knee images. We looked at changes in the STV and in pain, and their association. 120 subjects with preinjection and postinjection CE MRI were followed. Their mean age was 62.3 years (SD=10.3) and 62 (52%) were women. The median time between injection and follow-up scan was 8 days (IQR 7-14 days). 85/120 (71%) were OARSI responders. Pain decreased (mean change in KOOS=+23.9; 95% CI 20.1 to 27.8, p<0.001) following steroid injection, as did mean STV (mean change=-1071 mm(3); 95% CI -1839 mm(3) to -303 mm(3), p=0.01). Of the 80 who returned for a third MRI, pain relapsed in 57, and in the 48 of those with MRI data, STV increased between follow-up and final visit (+1220 mm(3); 95% CI 25 mm(3) to 2414 mm(3), p=0.05). 23 were persistent responders at 6 months and, in these, STV did not increase (mean change=-202 mm(3); 95% CI -2008 mm(3) to 1604 mm(3), p=0.83). Controlling for variation over time, there was a significant association between synovitis volume and KOOS pain (b coefficient-change in KOOS pain score per 1000 mm(3) change in STV=-1.13; 95% CI -1.87 to -0.39, p=0.003), although STV accounted for only a small proportion of

Organic aerosol evolution and transport observed at Mt. Cimone (2165 m a.s.l.), Italy, during the PEGASOS campaign

NASA Astrophysics Data System (ADS)

Rinaldi, M.; Gilardoni, S.; Paglione, M.; Sandrini, S.; Fuzzi, S.; Massoli, P.; Bonasoni, P.; Cristofanelli, P.; Marinoni, A.; Poluzzi, V.; Decesari, S.

2015-10-01

High-resolution aerosol mass spectrometer measurements were performed, for the first time, at the Mt. Cimone Global Atmosphere Watch (GAW) station between June and July 2012, within the EU project PEGASOS and the ARPA-Emilia-Romagna project SUPERSITO. Submicron aerosol was dominated by organics (63 %), with sulfate, ammonium and nitrate contributing the remaining 20, 9 and 7 %, respectively. Organic aerosol (OA) was in general highly oxygenated, consistent with the remote character of the site; our observations suggest that oxidation and secondary organic aerosol (SOA) formation processes occurred during aerosol transport to high altitudes. All of the aerosol component concentrations as well as the OA elemental ratios showed a clear daily trend, driven by the evolution of the planetary boundary layer (PBL) and by the mountain wind regime. Higher loadings and lower OA oxidation levels were observed during the day, when the site was within the PBL, and therefore affected by relatively fresh aerosol transported from lower altitudes. Conversely, lower loadings and higher OA oxidation levels were observed at night, when the top of Mt. Cimone resided in the free troposphere although affected by the transport of residual layers on several days of the campaign. Analysis of the elemental ratios in a Van Krevelen space shows that OA oxidation follows a slope comprised between -0.5 and -1, consistent with addition of carboxylic groups, with or without fragmentation of the parent molecules. The increase of carboxylic groups during OA ageing is confirmed by the increased contribution of organic fragments containing more than one oxygen atom in the free troposphere night-time mass spectra. Finally, positive matrix factorization was able to deconvolve the contributions of relatively fresh OA (OOAa) originating from the PBL, more aged OA (OOAb) present at high altitudes during periods of atmospheric stagnation, and very aged aerosols (OOAc) transported over long distances in the

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

NASA Technical Reports Server (NTRS)

Gloeckler, G.

1977-01-01

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

15 CFR 742.17 - Exports of firearms to OAS member countries.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATIONS CONTROL POLICY-CCL BASED CONTROLS § 742.17 Exports of firearms to OAS member countries. (a... not entered into force. (b) Licensing policy. Applications supported by an Import Certificate or... be approved, except there is a policy of denial for applications to export items linked to such...

Processing MALDI mass spectra to improve mass spectral direct tissue analysis

NASA Astrophysics Data System (ADS)

Norris, Jeremy L.; Cornett, Dale S.; Mobley, James A.; Andersson, Malin; Seeley, Erin H.; Chaurand, Pierre; Caprioli, Richard M.

2007-02-01

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.

41 CFR 102-85.65 - How does an OA obligate the customer agency?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL PROPERTY 85-PRICING POLICY FOR OCCUPANCY IN GSA SPACE Occupancy Agreement § 102-85.65 How does an OA obligate the customer...

Well-Being among Older Adults with OA: Direct and Mediated Patterns of Control Beliefs, Optimism and Pessimism

PubMed Central

Sherman, Aurora M.; Cotter, Kelly A.

2013-01-01

Objectives To assess the contribution of important psychological resources (i.e., optimism, pessimism, control beliefs) to the psychological well-being of older adults with Osteoarthritis (OA); to assess the direct and mediated association of these psychosocial resources to outcomes (depressive symptoms, life satisfaction, and self-esteem). These objectives are important because OA is a significant stressor, treatments are limited, and psychological functioning is at risk for those coping with the condition, even compared to other chronic illnesses. Method A cross-sectional survey of 160 community-dwelling older adults with OA (81% women). Participants were not randomly selected, but nonetheless reflected the demographic makeup of the selection area. Results Ordinary least squares regression analyses using the PROCESS macro (Hayes, 2012) revealed that optimism and pessimism were associated with higher depressive symptoms and lower self-esteem indirectly through constraints beliefs. The analysis of life satisfaction showed that optimism and pessimism were each partially mediated through mastery and constraints beliefs. Discussion These results suggest that prior research, which has assessed these psychological resources as having singular relationships to outcomes, may have underestimated the importance of the relationship between these variables. We discuss possible points of intervention for older adults with OA who may experience increasing constraints beliefs over time. PMID:23418813

41 CFR 102-85.205 - What happens if a customer agency continues occupancy after the expiration of an OA?

Code of Federal Regulations, 2010 CFR

2010-07-01

... assignments. However, provisions are necessary to cover the GSA and customer relationship if an OA expires... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What happens if a customer agency continues occupancy after the expiration of an OA? 102-85.205 Section 102-85.205 Public...

41 CFR 102-85.205 - What happens if a customer agency continues occupancy after the expiration of an OA?

Code of Federal Regulations, 2011 CFR

2011-01-01

... assignments. However, provisions are necessary to cover the GSA and customer relationship if an OA expires... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What happens if a customer agency continues occupancy after the expiration of an OA? 102-85.205 Section 102-85.205 Public...

Reassessing the Role of N-Hydroxytryptamine in Auxin Biosynthesis1[W][OA

PubMed Central

Tivendale, Nathan D.; Davies, Noel W.; Molesworth, Peter P.; Davidson, Sandra E.; Smith, Jason A.; Lowe, Edwin K.; Reid, James B.; Ross, John J.

2010-01-01

The tryptamine pathway is one of five proposed pathways for the biosynthesis of indole-3-acetic acid (IAA), the primary auxin in plants. The enzymes AtYUC1 (Arabidopsis thaliana), FZY (Solanum lycopersicum), and ZmYUC (Zea mays) are reported to catalyze the conversion of tryptamine to N-hydroxytryptamine, putatively a rate-limiting step of the tryptamine pathway for IAA biosynthesis. This conclusion was based on in vitro assays followed by mass spectrometry or HPLC analyses. However, there are major inconsistencies between the mass spectra reported for the reaction products. Here, we present mass spectral data for authentic N-hydroxytryptamine, 5-hydroxytryptamine (serotonin), and tryptamine to demonstrate that at least some of the published mass spectral data for the YUC in vitro product are not consistent with N-hydroxytryptamine. We also show that tryptamine is not metabolized to IAA in pea (Pisum sativum) seeds, even though a PsYUC-like gene is strongly expressed in these organs. Combining these findings, we propose that at present there is insufficient evidence to consider N-hydroxytryptamine an intermediate for IAA biosynthesis. PMID:20974893

Validation of the doubly labeled water method using off-axis integrated cavity output spectroscopy and isotope ratio mass spectrometry.

PubMed

Melanson, Edward L; Swibas, Tracy; Kohrt, Wendy M; Catenacci, Vicki A; Creasy, Seth A; Plasqui, Guy; Wouters, Loek; Speakman, John R; Berman, Elena S F

2018-02-01

When the doubly labeled water (DLW) method is used to measure total daily energy expenditure (TDEE), isotope measurements are typically performed using isotope ratio mass spectrometry (IRMS). New technologies, such as off-axis integrated cavity output spectroscopy (OA-ICOS) provide comparable isotopic measurements of standard waters and human urine samples, but the accuracy of carbon dioxide production (V̇co 2 ) determined with OA-ICOS has not been demonstrated. We compared simultaneous measurement V̇co 2 obtained using whole-room indirect calorimetry (IC) with DLW-based measurements from IRMS and OA-ICOS. Seventeen subjects (10 female; 22 to 63 yr) were studied for 7 consecutive days in the IC. Subjects consumed a dose of 0.25 g H 2 18 O (98% APE) and 0.14 g 2 H 2 O (99.8% APE) per kilogram of total body water, and urine samples were obtained on days 1 and 8 to measure average daily V̇co 2 using OA-ICOS and IRMS. V̇co 2 was calculated using both the plateau and intercept methods. There were no differences in V̇co 2 measured by OA-ICOS or IRMS compared with IC when the plateau method was used. When the intercept method was used, V̇co 2 using OA-ICOS did not differ from IC, but V̇co 2 measured using IRMS was significantly lower than IC. Accuracy (~1-5%), precision (~8%), intraclass correlation coefficients ( R = 0.87-90), and root mean squared error (30-40 liters/day) of V̇co 2 measured by OA-ICOS and IRMS were similar. Both OA-ICOS and IRMS produced measurements of V̇co 2 with comparable accuracy and precision compared with IC.

Martian neutron leakage spectra

NASA Astrophysics Data System (ADS)

Drake, D. M.; Feldman, W. C.; Jakosky, B. M.

1988-06-01

A high-energy nucleon-meson transport code is used to calculate energy spectra of Martian leakage neutrons. Four calculations are used to simulate a uniform surface layer containing various amounts of water, different burial depths of a 50 percent water layer underneath a 1 percent water layer, changing atmospheric pressure, and a thick carbon dioxide ice sheet overlying a "dirty" water ice sheet. Calculated spectra at energies less than about 1000 eV were fitted by a superposition of thermal and epithermal functions having four free parameters, two of which (thermal and epithermal amplitudes) were found to vary systematically and to specify uniquely the configuration in each of the series. Parameter variations depend on the composition of the assumed surface layers through the average atomic mass and the macroscopic scattering and absorption cross sections. It is concluded that measurements of leakage neutron spectra should allow determination of the hydrogen content of surface layers buried to depths up to about 100 g/sq. cm and determination of the thickness of a polar dry ice cap up to a thickness of about 250 g/sq. cm.

Cost analysis of flavocoxid compared to naproxen for management of mild to moderate OA.

PubMed

Walton, Surrey M; Schumock, Glen T; McLain, David Andrew

2010-09-01

Flavocoxid is a medical food used for the clinical dietary management of osteoarthritis (OA). The acquisition cost of flavocoxid is higher than most traditional, generic NSAIDs. However, flavocoxid may have more favorable gastrointestinal (GI) toxicity resulting in lower overall costs. These costs have not been previously examined. This study provides a decision analytic model to assess the net costs of using flavocoxid for OA from a Medicare perspective. A decision model was developed to estimate the total costs associated with flavocoxid versus naproxen for the management of Medicare patients with mild to moderate OA. Probabilities were obtained from literature and expert opinion, and costs were obtained from Medicare. Sensitivity analyses were conducted by varying probabilities and costs within clinically relevant ranges. The base case resulted in flavocoxid having lower total annual costs ($1482 per patient) compared to naproxen ($1592). Flavocoxid remained the lowest cost option when the cost inputs were varied by 25% (above and below the base case), and when the probability of GI events with flavocoxid were varied by 25%. However, when GI rates from the literature and implied relative risks from the expert panel were used, or if the cost of PPIs was $0, then naproxen was the less costly alternative, though saving less than the annual cost of flavocoxid. Key limitations were the limited outcomes in the model (only GI events), lack of consideration of adherence or combination therapy, and the reliance on expert opinion due to a lack of data for flavocoxid. In patients over 65 years of age who suffer from mild to moderate OA, flavocoxid may result in lower overall costs, despite a higher acquisition cost. Managed care organizations should consider total health care costs in the decision to include flavocoxid as a covered benefit.

Characterization and source apportionment of organic aerosol at 260 m on a meteorological tower in Beijing, China

NASA Astrophysics Data System (ADS)

Zhou, Wei; Wang, Qingqing; Zhao, Xiujuan; Xu, Weiqi; Chen, Chen; Du, Wei; Zhao, Jian; Canonaco, Francesco; Prévôt, André S. H.; Fu, Pingqing; Wang, Zifa; Worsnop, Douglas R.; Sun, Yele

2018-03-01

Despite extensive efforts toward the characterization of submicron aerosols at ground level in the megacity of Beijing, our understanding of aerosol sources and processes at high altitudes remains low. Here we conducted a 3-month real-time measurement of non-refractory submicron aerosol (NR-PM1) species at a height of 260 m from 10 October 2014 to 18 January 2015 using an aerosol chemical speciation monitor. Our results showed a significant change in aerosol composition from the non-heating period (NHP) to the heating period (HP). Organics and chloride showed clear increases during HP due to coal combustion emissions, while nitrate showed substantial decreases from 28 to 15-18 %. We also found that NR-PM1 species in the heating season can have average mass differences of 30-44 % under similar emission sources yet different meteorological conditions. Multi-linear engine 2 (ME-2) using three primary organic aerosol (OA) factors as constraints, i.e., fossil-fuel-related OA (FFOA) dominantly from coal combustion emissions, cooking OA (COA), and biomass burning OA (BBOA) resolved from ground high-resolution aerosol mass spectrometer measurements, was applied to OA mass spectra of ACSM. Two types of secondary OA (SOA) that were well correlated with nitrate and chloride-CO, respectively, were identified. SOA played a dominant role in OA during all periods at 260 m although the contributions were decreased from 72 % during NHP to 58-64 % during HP. The SOA composition also changed significantly from NHP to HP. While the contribution of oxygenated OA (OOA) was decreased from 56-63 to 32-40 %, less oxidized OOA (LO-OOA) showed a large increase from 9-16 to 24-26 %. COA contributed a considerable fraction of OA at high altitude, and the contribution was relatively similar across different periods (10-13 %). In contrast, FFOA showed a large increase during HP due to the influences of coal combustion emissions. We also observed very different OA composition between ground level

EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra*

PubMed Central

Yuan, Zuo-Fei; Lin, Shu; Molden, Rosalynn C.; Cao, Xing-Jun; Bhanu, Natarajan V.; Wang, Xiaoshi; Sidoli, Simone; Liu, Shichong; Garcia, Benjamin A.

2015-01-01

Histone post-translational modifications contribute to chromatin function through their chemical properties which influence chromatin structure and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis because of the high sensitivity and the high mass accuracy of this approach that provides confident identification. However, analysis of histones with this method is even more challenging because of the large number and variety of isobaric histone peptides and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to label-free quantification of histone peptides, EpiProfile is flexible and can quantify different types of isotopically labeled histone peptides. EpiProfile is unique in generating layouts (i.e. relative retention time) of histone peptides when compared with manual quantification of the data and other programs (such as Skyline), filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. PMID:25805797

Organics in comet 67P - a first comparative analysis of mass spectra from ROSINA-DFMS, COSAC and Ptolemy

NASA Astrophysics Data System (ADS)

Altwegg, Kathrin; Balsiger, H.; Berthelier, J. J.; Bieler, A.; Calmonte, U.; Fuselier, S. A.; Goesmann, F.; Gasc, S.; Gombosi, T. I.; Le Roy, L.; de Keyser, J.; Morse, A.; Rubin, M.; Schuhmann, M.; Taylor, M. G. G. T.; Tzou, C.-Y.; Wright, I.

2017-07-01

The ESA Rosetta spacecraft followed comet 67P at a close distance for more than 2 yr. In addition, it deployed the lander Philae on to the surface of the comet. The (surface) composition of the comet is of great interest to understand the origin and evolution of comets. By combining measurements made on the comet itself and in the coma, we probe the nature of this surface material and compare it to remote sensing observations. We compare data from the double focusing mass spectrometer (DFMS) of the ROSINA experiment on ESA's Rosetta mission and previously published data from the two mass spectrometers COSAC (COmetary Sampling And Composition) and Ptolemy on the lander. The mass spectra of all three instruments show very similar patterns of mainly CHO-bearing molecules that sublimate at temperatures of 275 K. The DFMS data also show a great variety of CH-, CHN-, CHS-, CHO2- and CHNO-bearing saturated and unsaturated species. Methyl isocyanate, propanal and glycol aldehyde suggested by the earlier analysis of the measured COSAC spectrum could not be confirmed. The presence of polyoxymethylene in the Ptolemy spectrum was found to be unlikely. However, the signature of the aromatic compound toluene was identified in DFMS and Ptolemy data. Comparison with remote sensing instruments confirms the complex nature of the organics on the surface of 67P, which is much more diverse than anticipated.

OA-7 Service Module Arrival, Uncrating, Move from Airlock to Highbay inside SSPF

NASA Image and Video Library

2017-02-01

The Orbital ATK OA-7 Cygnus spacecraft's service module arrives inside the Space Station Processing Facility of NASA's Kennedy Space Center in Florida, sealed in an environmentally controlled shipping container, pulled in by truck on a low-boy flatbed trailer. The service module is uncrate from the shipping container, lifted and positioned on a work stand, and moved from the airlock to the highbay for processing. Scheduled to launch on March 19, 2017, the Orbital ATK OA-7 mission will lift off atop a United Launch Alliance Atlas V rocket from Space launch Complex 41 at Cape Canaveral Air Force Station. The commercial resupply services mission to the International Space Station will deliver thousands of pounds of supplies, equipment and scientific research materials that improve life on Earth and drive progress toward future space exploration.

Mass spectrometry of aerospace materials

NASA Technical Reports Server (NTRS)

Colony, J. A.

1976-01-01

Mass spectrometry is used for chemical analysis of aerospace materials and contaminants. Years of analytical aerospace experience have resulted in the development of specialized techniques of sampling and analysis which are required in order to optimize results. This work has resulted in the evolution of a hybrid method of indexing mass spectra which include both the largest peaks and the structurally significant peaks in a concise format. With this system, a library of mass spectra of aerospace materials was assembled, including the materials responsible for 80 to 90 percent of the contamination problems at Goddard Space Flight Center during the past several years.

Heat capacities and entropies of Mg2SiOa, Mn2SiOa, and Co2SiOa between 5 and 380 K

USGS Publications Warehouse

Robie, Richard A.; Hemingway, Bruch S.; Takei, Humihiko

1982-01-01

whereas the shoulder near 12 K corresponds to the change from the collinear to a canted spin structure. Our calorimetric values for the antiferromagnetic-paramagnetictr ansition temperature (N6el Temperature) are in excellent agreement with those obtained by powder magnetic susceptibility measurements, 49t2 K and 5015 K for co2Sioa and Mn2Sioa respectively. The thermal Debye temperature, 0$, of Mg2Sioa calculated from our c$ measurements between 6.3 and 13.8 K is 768+15 K and agrees well with the elastic vaiue ofi of 758 K based on the mean sound velocity calculated from the room temperature elastic stiffness constants (ci:) of Graham and Barsch. At 298.15K (25"c) the molar heat capacitiesa re 118.6,1 28.7, and 133.4J /(mol . K) and the molar entropiesa re 94.11-r0.101, 55.910.4a nd,1 42.6-+0.J2l (mol . K) respectivelyf or Mg2SiO4M, n2SiOaa, nd Co2SiOa.

Primary and secondary aerosols in Beijing in winter: sources, variations and processes

NASA Astrophysics Data System (ADS)

Sun, Yele; Du, Wei; Fu, Pingqing; Wang, Qingqing; Li, Jie; Ge, Xinlei; Zhang, Qi; Zhu, Chunmao; Ren, Lujie; Xu, Weiqi; Zhao, Jian; Han, Tingting; Worsnop, Douglas R.; Wang, Zifa

2016-07-01

Winter has the worst air pollution of the year in the megacity of Beijing. Despite extensive winter studies in recent years, our knowledge of the sources, formation mechanisms and evolution of aerosol particles is not complete. Here we have a comprehensive characterization of the sources, variations and processes of submicron aerosols that were measured by an Aerodyne high-resolution aerosol mass spectrometer from 17 December 2013 to 17 January 2014 along with offline filter analysis by gas chromatography/mass spectrometry. Our results suggest that submicron aerosols composition was generally similar across the winter of different years and was mainly composed of organics (60 %), sulfate (15 %) and nitrate (11 %). Positive matrix factorization of high- and unit-mass resolution spectra identified four primary organic aerosol (POA) factors from traffic, cooking, biomass burning (BBOA) and coal combustion (CCOA) emissions as well as two secondary OA (SOA) factors. POA dominated OA, on average accounting for 56 %, with CCOA being the largest contributor (20 %). Both CCOA and BBOA showed distinct polycyclic aromatic hydrocarbons (PAHs) spectral signatures, indicating that PAHs in winter were mainly from coal combustion (66 %) and biomass burning emissions (18 %). BBOA was highly correlated with levoglucosan, a tracer compound for biomass burning (r2 = 0.93), and made a considerable contribution to OA in winter (9 %). An aqueous-phase-processed SOA (aq-OOA) that was strongly correlated with particle liquid water content, sulfate and S-containing ions (e.g. CH2SO2+) was identified. On average aq-OOA contributed 12 % to the total OA and played a dominant role in increasing oxidation degrees of OA at high RH levels (> 50 %). Our results illustrate that aqueous-phase processing can enhance SOA production and oxidation states of OA as well in winter. Further episode analyses highlighted the significant impacts of meteorological parameters on aerosol composition, size

Search for electroweak production of supersymmetric states in scenarios with compressed mass spectra at √{s }=13 TeV with the ATLAS detector

NASA Astrophysics Data System (ADS)

Aaboud, M.; Aad, G.; Abbott, B.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; Abouzeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Afik, Y.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Åkesson, T. P. A.; Akilli, E.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Alderweireldt, S. C.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allaire, C.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M. I.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Ambroz, L.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amoroso, S.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Araujo Pereira, R.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkin, R. J.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Avramidou, R.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Bagnaia, P.; Bahmani, M.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Bakker, P. J.; Bakshi Gupta, D.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Bandyopadhyay, A.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barkeloo, J. T.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bauer, K. T.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Beck, H. C.; Becker, K.; Becker, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behera, A.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Bergsten, L. J.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertram, I. A.; Bertsche, C.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Bethani, A.; Bethke, S.; Betti, A.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Bierwagen, K.; Biesuz, N. V.; Biglietti, M.; Billoud, T. R. V.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blumenschein, U.; Blunier, Dr.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boerner, D.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bolz, A. E.; Bomben, M.; Bona, M.; Bonilla, J. S.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossio Sola, J. D.; Boudreau, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozson, A. J.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Braren, F.; Bratzler, U.; Brau, B.; Brau, J. E.; Breaden Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Briglin, D. L.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brost, E.; Broughton, J. H.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruni, A.; Bruni, G.; Bruni, L. S.; Bruno, S.; Brunt, Bh; Bruschi, M.; Bruscino, N.; Bryant, P.; Bryngemark, L.; Buanes, T.; Buat, Q.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Buehrer, F.; Bugge, M. K.; Bulekov, O.; Bullock, D.; Burch, T. J.; Burdin, S.; Burgard, C. D.; Burger, A. M.; Burghgrave, B.; Burka, K.; Burke, S.; Burmeister, I.; Burr, J. T. P.; Büscher, D.; Büscher, V.; Buschmann, E.; Bussey, P.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Buzykaev, A. R.; C.-Q., Changqiao; Cabras, G.; Cabrera Urbán, S.; Caforio, D.; Cai, H.; Cairo, V. M. M.; Cakir, O.; Calace, N.; Calafiura, P.; Calandri, A.; Calderini, G.; Calfayan, P.; Callea, G.; Caloba, L. P.; Calvente Lopez, S.; Calvet, D.; Calvet, S.; Calvet, T. P.; Camacho Toro, R.; Camarda, S.; Camarri, P.; Cameron, D.; Caminal Armadans, R.; Camincher, C.; Campana, S.; Campanelli, M.; Camplani, A.; Campoverde, A.; Canale, V.; Cano Bret, M.; Cantero, J.; Cao, T.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Carbone, R. M.; Cardarelli, R.; Cardillo, F.; Carli, I.; Carli, T.; Carlino, G.; Carlson, B. T.; Carminati, L.; Carney, R. M. D.; Caron, S.; Carquin, E.; Carrá, S.; Carrillo-Montoya, G. D.; Casadei, D.; Casado, M. P.; Casha, A. F.; Casolino, M.; Casper, D. W.; Castelijn, R.; Castillo Gimenez, V.; Castro, N. F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavallaro, E.; Cavalli-Sforza, M.; Cavasinni, V.; Celebi, E.; Ceradini, F.; Cerda Alberich, L.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chan, S. K.; Chan, W. S.; Chan, Y. L.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Che, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, C.; Chen, H.; Chen, J.; Chen, J.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, H. J.; Cheplakov, A.; Cheremushkina, E.; Cherkaoui El Moursli, R.; Cheu, E.; Cheung, K.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chitan, A.; Chiu, I.; Chiu, Y. H.; Chizhov, M. V.; Choi, K.; Chomont, A. R.; Chouridou, S.; Chow, Y. S.; Christodoulou, V.; Chu, M. C.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Cinca, D.; Cindro, V.; Cioarǎ, I. A.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Citterio, M.; Clark, A.; Clark, M. R.; Clark, P. J.; Clarke, R. N.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Colasurdo, L.; Cole, B.; Colijn, A. P.; Collot, J.; Conde Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Constantinescu, S.; Conti, G.; Conventi, F.; Cooper-Sarkar, A. M.; Cormier, F.; Cormier, K. J. R.; Corradi, M.; Corrigan, E. E.; Corriveau, F.; Cortes-Gonzalez, A.; Costa, M. J.; Costanzo, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Crawley, S. J.; Creager, R. A.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Cristinziani, M.; Croft, V.; Crosetti, G.; Cueto, A.; Cuhadar Donszelmann, T.; Cukierman, A. R.; Cummings, J.; Curatolo, M.; Cúth, J.; Czekierda, S.; Czodrowski, P.; D'Amen, G.; D'Auria, S.; D'Eramo, L.; D'Onofrio, M.; da Cunha Sargedas de Sousa, M. J.; da Via, C.; Dabrowski, W.; Dado, T.; Dahbi, S.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Dandoy, J. R.; Daneri, M. F.; Dang, N. P.; Dann, N. S.; Danninger, M.; Dano Hoffmann, M.; Dao, V.; Darbo, G.; Darmora, S.; Dattagupta, A.; Daubney, T.; Davey, W.; David, C.; Davidek, T.; Davis, D. R.; Davison, P.; Dawe, E.; Dawson, I.; de, K.; de Asmundis, R.; de Benedetti, A.; de Castro, S.; de Cecco, S.; de Groot, N.; de Jong, P.; de la Torre, H.; de Lorenzi, F.; de Maria, A.; de Pedis, D.; de Salvo, A.; de Sanctis, U.; de Santo, A.; de Vasconcelos Corga, K.; de Vivie de Regie, J. B.; Debenedetti, C.; Dedovich, D. V.; Dehghanian, N.; Deigaard, I.; Del Gaudio, M.; Del Peso, J.; Delgove, D.; Deliot, F.; Delitzsch, C. M.; Dell'Acqua, A.; Dell'Asta, L.; Della Pietra, M.; Della Volpe, D.; Delmastro, M.; Delporte, C.; Delsart, P. A.; Demarco, D. A.; Demers, S.; Demichev, M.; Denisov, S. P.; Denysiuk, D.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Dette, K.; Devesa, M. R.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; di Bello, F. A.; di Ciaccio, A.; di Ciaccio, L.; di Clemente, W. K.; di Donato, C.; di Girolamo, A.; di Micco, B.; di Nardo, R.; di Petrillo, K. F.; di Simone, A.; di Sipio, R.; di Valentino, D.; Diaconu, C.; Diamond, M.; Dias, F. A.; Diaz, M. A.; Dickinson, J.; Diehl, E. B.; Dietrich, J.; Díez Cornell, S.; Dimitrievska, A.; Dingfelder, J.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Djuvsland, J. I.; Do Vale, M. A. B.; Dobre, M.; Dodsworth, D.; Doglioni, C.; Dolejsi, J.; Dolezal, Z.; Donadelli, M.; Donini, J.; Dopke, J.; Doria, A.; Dova, M. T.; Doyle, A. T.; Drechsler, E.; Dreyer, E.; Dris, M.; Du, Y.; Duarte-Campderros, J.; Dubinin, F.; Dubreuil, A.; Duchovni, E.; Duckeck, G.; Ducourthial, A.; Ducu, O. A.; Duda, D.; Dudarev, A.; Dudder, A. Chr.; Duffield, E. M.; Duflot, L.; Dührssen, M.; Dulsen, C.; Dumancic, M.; Dumitriu, A. E.; Duncan, A. K.; Dunford, M.; Duperrin, A.; Duran Yildiz, H.; Düren, M.; Durglishvili, A.; Duschinger, D.; Dutta, B.; Duvnjak, D.; Dyndal, M.; Dziedzic, B. S.; Eckardt, C.; Ecker, K. M.; Edgar, R. C.; Eifert, T.; Eigen, G.; Einsweiler, K.; Ekelof, T.; El Kacimi, M.; El Kosseifi, R.; Ellajosyula, V.; Ellert, M.; Ellinghaus, F.; Elliot, A. A.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Enari, Y.; Ennis, J. S.; Epland, M. B.; Erdmann, J.; Ereditato, A.; Errede, S.; Escalier, M.; Escobar, C.; Esposito, B.; Estrada Pastor, O.; Etienvre, A. I.; Etzion, E.; Evans, H.; Ezhilov, A.; Ezzi, M.; Fabbri, F.; Fabbri, L.; Fabiani, V.; Facini, G.; Fakhrutdinov, R. M.; Falciano, S.; Faltova, J.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farina, E. M.; Farooque, T.; Farrell, S.; Farrington, S. M.; Farthouat, P.; Fassi, F.; Fassnacht, P.; Fassouliotis, D.; Faucci Giannelli, M.; Favareto, A.; Fawcett, W. J.; Fayard, L.; Fedin, O. L.; Fedorko, W.; Feickert, M.; Feigl, S.; Feligioni, L.; Feng, C.; Feng, E. J.; Feng, M.; Fenton, M. J.; Fenyuk, A. B.; Feremenga, L.; Fernandez Martinez, P.; Ferrando, J.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferreira de Lima, D. E.; Ferrer, A.; Ferrere, D.; Ferretti, C.; Fiedler, F.; Filipčič, A.; Filthaut, F.; Fincke-Keeler, M.; Finelli, K. D.; Fiolhais, M. C. N.; Fiorini, L.; Fischer, C.; Fischer, J.; Fisher, W. C.; Flaschel, N.; Fleck, I.; Fleischmann, P.; Fletcher, R. R. M.; Flick, T.; Flierl, B. M.; Flores Castillo, L. R.; Fomin, N.; Forcolin, G. T.; Formica, A.; Förster, F. 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B.; Nicolaidou, R.; Nielsen, J.; Nikiforou, N.; Nikolaenko, V.; Nikolic-Audit, I.; Nikolopoulos, K.; Nilsson, P.; Ninomiya, Y.; Nisati, A.; Nishu, N.; Nisius, R.; Nitsche, I.; Nitta, T.; Nobe, T.; Noguchi, Y.; Nomachi, M.; Nomidis, I.; Nomura, M. A.; Nooney, T.; Nordberg, M.; Norjoharuddeen, N.; Novak, T.; Novgorodova, O.; Novotny, R.; Nozaki, M.; Nozka, L.; Ntekas, K.; Nurse, E.; Nuti, F.; O'Connor, K.; O'Neil, D. C.; O'Rourke, A. A.; O'Shea, V.; Oakham, F. G.; Oberlack, H.; Obermann, T.; Ocariz, J.; Ochi, A.; Ochoa, I.; Ochoa-Ricoux, J. P.; Oda, S.; Odaka, S.; Oh, A.; Oh, S. H.; Ohm, C. C.; Ohman, H.; Oide, H.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olariu, A.; Oleiro Seabra, L. F.; Olivares Pino, S. A.; Oliveira Damazio, D.; Oliver, J. L.; Olsson, M. J. R.; Olszewski, A.; Olszowska, J.; Onofre, A.; Onogi, K.; Onyisi, P. U. E.; Oppen, H.; Oreglia, M. J.; Oren, Y.; Orestano, D.; Orgill, E. C.; Orlando, N.; Orr, R. S.; Osculati, B.; Ospanov, R.; Otero Y Garzon, G.; Otono, H.; Ouchrif, M.; Ould-Saada, F.; Ouraou, A.; Oussoren, K. P.; Ouyang, Q.; Owen, M.; Owen, R. E.; Ozcan, V. E.; Ozturk, N.; Pachal, K.; Pacheco Pages, A.; Pacheco Rodriguez, L.; Padilla Aranda, C.; Pagan Griso, S.; Paganini, M.; Paige, F.; Palacino, G.; Palazzo, S.; Palestini, S.; Palka, M.; Pallin, D.; Panagiotopoulou, E. St.; Panagoulias, I.; Pandini, C. E.; Panduro Vazquez, J. G.; Pani, P.; Pantea, D.; Paolozzi, L.; Papadopoulou, Th. D.; Papageorgiou, K.; Paramonov, A.; Paredes Hernandez, D.; Parida, B.; Parker, A. J.; Parker, M. A.; Parker, K. A.; Parodi, F.; Parsons, J. A.; Parzefall, U.; Pascuzzi, V. R.; Pasner, J. M.; Pasqualucci, E.; Passaggio, S.; Pastore, Fr.; Pataraia, S.; Pater, J. R.; Pauly, T.; Pearson, B.; Pedraza Lopez, S.; Pedro, R.; Peleganchuk, S. V.; Penc, O.; Peng, C.; Peng, H.; Penwell, J.; Peralva, B. S.; Perego, M. M.; Perepelitsa, D. V.; Peri, F.; Perini, L.; Pernegger, H.; Perrella, S.; Peshekhonov, V. D.; Peters, K.; Peters, R. F. Y.; Petersen, B. A.; Petersen, T. C.; Petit, E.; Petridis, A.; Petridou, C.; Petroff, P.; Petrolo, E.; Petrov, M.; Petrucci, F.; Pettersson, N. E.; Peyaud, A.; Pezoa, R.; Pham, T.; Phillips, F. H.; Phillips, P. W.; Piacquadio, G.; Pianori, E.; Picazio, A.; Pickering, M. A.; Piegaia, R.; Pilcher, J. E.; Pilkington, A. D.; Pinamonti, M.; Pinfold, J. L.; Pitt, M.; Pleier, M.-A.; Pleskot, V.; Plotnikova, E.; Pluth, D.; Podberezko, P.; Poettgen, R.; Poggi, R.; Poggioli, L.; Pogrebnyak, I.; Pohl, D.; Pokharel, I.; Polesello, G.; Poley, A.; Policicchio, A.; Polifka, R.; Polini, A.; Pollard, C. S.; Polychronakos, V.; Ponomarenko, D.; Pontecorvo, L.; Popeneciu, G. A.; Portillo Quintero, D. M.; Pospisil, S.; Potamianos, K.; Potrap, I. N.; Potter, C. J.; Potti, H.; Poulsen, T.; Poveda, J.; Pozo Astigarraga, M. E.; Pralavorio, P.; Prell, S.; Price, D.; Primavera, M.; Prince, S.; Proklova, N.; Prokofiev, K.; Prokoshin, F.; Protopopescu, S.; Proudfoot, J.; Przybycien, M.; Puri, A.; Puzo, P.; Qian, J.; Qin, Y.; Quadt, A.; Queitsch-Maitland, M.; Qureshi, A.; Radeka, V.; Radhakrishnan, S. K.; Rados, P.; Ragusa, F.; Rahal, G.; Raine, J. A.; Rajagopalan, S.; Rashid, T.; Raspopov, S.; Ratti, M. G.; Rauch, D. M.; Rauscher, F.; Rave, S.; Ravinovich, I.; Rawling, J. H.; Raymond, M.; Read, A. L.; Readioff, N. P.; Reale, M.; Rebuzzi, D. M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reed, R. G.; Reeves, K.; Rehnisch, L.; Reichert, J.; Reiss, A.; Rembser, C.; Ren, H.; Rescigno, M.; Resconi, S.; Resseguie, E. D.; Rettie, S.; Reynolds, E.; Rezanova, O. L.; Reznicek, P.; Richter, R.; Richter, S.; Richter-Was, E.; Ricken, O.; Ridel, M.; Rieck, P.; Riegel, C. J.; Rifki, O.; Rijssenbeek, M.; Rimoldi, A.; Rimoldi, M.; Rinaldi, L.; Ripellino, G.; Ristić, B.; Ritsch, E.; Riu, I.; Rivera Vergara, J. C.; Rizatdinova, F.; Rizvi, E.; Rizzi, C.; Roberts, R. T.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robson, A.; Rocco, E.; Roda, C.; Rodina, Y.; Rodriguez Bosca, S.; Rodriguez Perez, A.; Rodriguez Rodriguez, D.; Rodríguez Vera, A. M.; Roe, S.; Rogan, C. S.; Røhne, O.; Röhrig, R.; Roloff, J.; Romaniouk, A.; Romano, M.; Romano Saez, S. M.; Romero Adam, E.; Rompotis, N.; Ronzani, M.; Roos, L.; Rosati, S.; Rosbach, K.; Rose, P.; Rosien, N.-A.; Rossi, E.; Rossi, L. P.; Rossini, L.; Rosten, J. H. N.; Rosten, R.; Rotaru, M.; Rothberg, J.; Rousseau, D.; Roy, D.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubbo, F.; Rühr, F.; Ruiz-Martinez, A.; Rurikova, Z.; Rusakovich, N. A.; Russell, H. L.; Rutherfoord, J. P.; Ruthmann, N.; Rüttinger, E. M.; Ryabov, Y. F.; Rybar, M.; Rybkin, G.; Ryu, S.; Ryzhov, A.; Rzehorz, G. F.; Saavedra, A. F.; Sabato, G.; Sacerdoti, S.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Saha, P.; Sahinsoy, M.; Saimpert, M.; Saito, M.; Saito, T.; Sakamoto, H.; Salamanna, G.; Salazar Loyola, J. E.; Salek, D.; Sales de Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sammel, D.; Sampsonidis, D.; Sampsonidou, D.; Sánchez, J.; Sanchez Pineda, A.; Sandaker, H.; Sander, C. O.; Sandhoff, M.; Sandoval, C.; Sankey, D. P. C.; Sannino, M.; Sano, Y.; Sansoni, A.; Santoni, C.; Santos, H.; Santoyo Castillo, I.; Sapronov, A.; Saraiva, J. G.; Sasaki, O.; Sato, K.; Sauvan, E.; Savard, P.; Savic, N.; Sawada, R.; Sawyer, C.; Sawyer, L.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Schaarschmidt, J.; Schacht, P.; Schachtner, B. M.; Schaefer, D.; Schaefer, L.; Schaeffer, J.; Schaepe, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Schegelsky, V. A.; Scheirich, D.; Schenck, F.; Schernau, M.; Schiavi, C.; Schier, S.; Schildgen, L. K.; Schillaci, Z. M.; Schillo, C.; Schioppa, E. J.; Schioppa, M.; Schleicher, K. E.; Schlenker, S.; Schmidt-Sommerfeld, K. R.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, S.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schopf, E.; Schott, M.; Schouwenberg, J. F. P.; Schovancova, J.; Schramm, S.; Schuh, N.; Schulte, A.; Schultz-Coulon, H.-C.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwartzman, A.; Schwarz, T. A.; Schweiger, H.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Sciandra, A.; Sciolla, G.; Scornajenghi, M.; Scuri, F.; Scutti, F.; Scyboz, L. M.; Searcy, J.; Seema, P.; Seidel, S. C.; Seiden, A.; Seixas, J. M.; Sekhniaidze, G.; Sekhon, K.; Sekula, S. J.; Semprini-Cesari, N.; Senkin, S.; Serfon, C.; Serin, L.; Serkin, L.; Sessa, M.; Severini, H.; Šfiligoj, T.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shahinian, J. D.; Shaikh, N. W.; Shan, L. Y.; Shang, R.; Shank, J. T.; Shapiro, M.; Sharma, A. S.; Shatalov, P. B.; Shaw, K.; Shaw, S. M.; Shcherbakova, A.; Shehu, C. Y.; Shen, Y.; Sherafati, N.; Sherman, A. D.; Sherwood, P.; Shi, L.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shipsey, I. P. J.; Shirabe, S.; Shiyakova, M.; Shlomi, J.; Shmeleva, A.; Shoaleh Saadi, D.; Shochet, M. J.; Shojaii, S.; Shope, D. R.; Shrestha, S.; Shulga, E.; Sicho, P.; Sickles, A. M.; Sidebo, P. E.; Sideras Haddad, E.; Sidiropoulou, O.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silva, J.; Silva, M.; Silverstein, S. B.; Simic, L.; Simion, S.; Simioni, E.; Simmons, B.; Simon, M.; Sinervo, P.; Sinev, N. B.; Sioli, M.; Siragusa, G.; Siral, I.; Sivoklokov, S. Yu.; Sjölin, J.; Skinner, M. B.; Skubic, P.; Slater, M.; Slavicek, T.; Slawinska, M.; Sliwa, K.; Slovak, R.; Smakhtin, V.; Smart, B. H.; Smiesko, J.; Smirnov, N.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, J. W.; Smith, M. N. K.; Smith, R. W.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snyder, I. M.; Snyder, S.; Sobie, R.; Socher, F.; Soffa, A. M.; Soffer, A.; Søgaard, A.; Soh, D. A.; Sokhrannyi, G.; Solans Sanchez, C. A.; Solar, M.; Soldatov, E. Yu.; Soldevila, U.; Solodkov, A. A.; Soloshenko, A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Son, H.; Song, W.; Sopczak, A.; Sopkova, F.; Sosa, D.; Sotiropoulou, C. L.; Sottocornola, S.; Soualah, R.; Soukharev, A. M.; South, D.; Sowden, B. C.; Spagnolo, S.; Spalla, M.; Spangenberg, M.; Spanò, F.; Sperlich, D.; Spettel, F.; Spieker, T. M.; Spighi, R.; Spigo, G.; Spiller, L. A.; Spousta, M.; St. Denis, R. D.; Stabile, A.; Stamen, R.; Stamm, S.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stanitzki, M. M.; Stapf, B. S.; Stapnes, S.; Starchenko, E. A.; Stark, G. H.; Stark, J.; Stark, S. H.; Staroba, P.; Starovoitov, P.; Stärz, S.; Staszewski, R.; Stegler, M.; Steinberg, P.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stevenson, T. J.; Stewart, G. A.; Stockton, M. C.; Stoicea, G.; Stolte, P.; Stonjek, S.; Straessner, A.; Stramaglia, M. E.; Strandberg, J.; Strandberg, S.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Suchek, S.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultan, Dms; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Suruliz, K.; Suster, C. J. E.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Swift, S. P.; Sydorenko, A.; Sykora, I.; Sykora, T.; Ta, D.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Tahirovic, E.; Taiblum, N.; Takai, H.; Takashima, R.; Takasugi, E. H.; Takeda, K.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanioka, R.; Tannenwald, B. B.; Tapia Araya, S.; Tapprogge, S.; Tarek Abouelfadl Mohamed, A. T.; Tarem, S.; Tarna, G.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, A. J.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teixeira-Dias, P.; Temple, D.; Ten Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Thais, S. J.; Theveneaux-Pelzer, T.; Thiele, F.; Thomas, J. P.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Tian, Y.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorova-Nova, S.; Todt, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Tornambe, P.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Treado, C. J.; Trefzger, T.; Tresoldi, F.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsang, K. W.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tulbure, T. T.; Tuna, A. N.; Turchikhin, S.; Turgeman, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Uno, K.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usui, J.; Vacavant, L.; Vacek, V.; Vachon, B.; Vadla, K. O. H.; Vaidya, A.; Valderanis, C.; Valdes Santurio, E.; Valente, M.; Valentinetti, S.; Valero, A.; Valéry, L.; Vallier, A.; Valls Ferrer, J. A.; van den Wollenberg, W.; van der Graaf, H.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vari, R.; Varnes, E. W.; Varni, C.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquez Furelos, D.; Vazquez Schroeder, T.; Veatch, J.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vogel, M.; Vokac, P.; Volpi, G.; von Buddenbrock, S. E.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Wakamiya, K.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, A. M.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.-J.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. M.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Weston, T. D.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, A.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Woods, N. L.; Worm, S. D.; Wosiek, B. K.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Xu, T.; Xu, W.; Yabsley, B.; Yacoob, S.; Yajima, K.; Yallup, D. P.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamanaka, T.; Yamane, F.; Yamatani, M.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, S.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemaityte, G.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; Zhou, M.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zhulanov, V.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zorbas, T. G.; Zou, R.; Zur Nedden, M.; Zwalinski, L.; Atlas Collaboration

2018-03-01

A search for electroweak production of supersymmetric particles in scenarios with compressed mass spectra in final states with two low-momentum leptons and missing transverse momentum is presented. This search uses proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015-2016, corresponding to 36.1 fb-1 of integrated luminosity at √{s }=13 TeV . Events with same-flavor pairs of electrons or muons with opposite electric charge are selected. The data are found to be consistent with the Standard Model prediction. Results are interpreted using simplified models of R -parity-conserving supersymmetry in which there is a small mass difference between the masses of the produced supersymmetric particles and the lightest neutralino. Exclusion limits at 95% confidence level are set on next-to-lightest neutralino masses of up to 145 GeV for Higgsino production and 175 GeV for wino production, and slepton masses of up to 190 GeV for pair production of sleptons. In the compressed mass regime, the exclusion limits extend down to mass splittings of 2.5 GeV for Higgsino production, 2 GeV for wino production, and 1 GeV for slepton production. The results are also interpreted in the context of a radiatively-driven natural supersymmetry model with nonuniversal Higgs boson masses.

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.

Theoretical Near-IR Spectra for Surface Abundance Studies of Massive Stars

NASA Technical Reports Server (NTRS)

Sonneborn, George; Bouret, J.

2011-01-01

We present initial results of a study of abundance and mass loss properties of O-type stars based on theoretical near-IR spectra computed with state-of-the-art stellar atmosphere models. The James Webb Space Telescope (JWST) will be a powerful tool to obtain high signal-to-noise ratio near-IR (1-5 micron) spectra of massive stars in different environments of local galaxies. Our goal is to analyze model near-IR spectra corresponding to those expected from NIRspec on JWST in order to map the wind properties and surface composition across the parameter range of 0 stars and to determine projected rotational velocities. As a massive star evolves, internal coupling, related mixing, and mass loss impact its intrinsic rotation rate. These three parameters form an intricate loop, where enhanced rotation leads to more mixing which in turn changes the mass loss rate, the latter thus affecting the rotation rate. Since the effects of rotation are expected to be much more pronounced at low metallicity, we pay special attention to models for massive stars in the the Small Magellanic Cloud. This galaxy provides a unique opportunity to probe stellar evolution, and the feedback of massive stars on galactic evol.ution in conditions similar to the epoch of maximal star formation. Plain-Language Abstract: We present initial results of a study of abundance and mass loss properties of massive stars based on theoretical near-infrared (1-5 micron) spectra computed with state-of-the-art stellar atmosphere models. This study is to prepare for observations by the James Webb Space Telescope.

Evaluation of the performance of a tandem mass spectral library with mass spectral data extracted from literature.

PubMed

Würtinger, Philipp; Oberacher, Herbert

2012-01-01

MSforID represents a database of tandem mass spectral data obtained from (quasi-)molecular ions produced by atmospheric pressure ionization methods. At the current stage of development the library contains 12 122 spectra of 1208 small (bio-)organic molecules. The present work was aimed to evaluate the performance of the MSforID library in terms of accuracy and transferability with a collection of fragment ion mass spectra from various compounds acquired on multiple instruments. A literature survey was conducted to collect the set of sample spectra. A total number of 554 spectra covering 291 compounds were extracted from 109 publications. The majority of spectra originated from publications on applications of LC/MS/MS in drug monitoring, pharmacokinetics, environmental analysis, forensic analysis as well as food analysis. Almost all types of tandem mass spectrometric instruments distributed by the five most important instrument vendors were included in the study. The overall sensitivity of library search was found to be 96.4%, which clearly proves that the MSforID library can successfully handle data from a huge variety of mass spectrometric instruments to allow accurate compound identification. Only for spectra containing three or more fragment ions, however, the rate of classified matches (= matches with a relative average match probability (ramp) score > 40.0) was 95%. Ambiguous or unclassified results were mainly obtained for searches with single precursor-to-fragment ion transitions due to the insufficient specificity of such a low amount of structural information to unequivocally define a single compound. Copyright © 2011 John Wiley & Sons, Ltd.

MALDI Mass Spectrometry of Fullero[C60]tetrahydropyridines

NASA Astrophysics Data System (ADS)

Fatkullina, A. F.; Yanybin, V. M.; Asfandiarov, N. L.; Tuktarov, A. R.; Khalilov, L. M.

2018-07-01

Mass spectra of positive and negative MALDI ions of the series of fullero[C60] tetrahydropyridines with different substituents in a heterocycle are systematically studied for the first time. All mass spectra contain C60 fullerene peaks as a result of the reduction of fullero[C60]tetrahydropyridines. The intensities of the protonated molecular ions' [M + H]+ peaks are highest in the mass spectra of positive ions of the studied compounds, while molecular radical ion [M]+ is less intense. The intensities of the peaks of molecular radical ion [M]- are highest in the mass spectra of the negative ions. The [C60C2H5] ions formed during the decay of the molecular ions with the detachment of neutral nitrile molecules is characteristic of all compounds. Using DFT quantum-chemical calculations (PBE/3z), the energies of the highest (HOMO) and lowest unoccupied molecular orbitals (LUMO) are determined for fullero[C60]tetrahydropyridines with substituents in the heterocycle.

Chemical characterization and source apportionment of fine particulate matter in Yangzhou, China, using offline aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Li, L.; Ge, X.; Xu, J.; Ye, Z.

2016-12-01

In recent years, Aerodyne Aerosol Mass Spectrometer (AMS) has been widely used for online and real-time monitoring of fine aerosol particles all over the world. However, due to the high cost and complex maintenance, the AMS was typically deployed for short-term intense field measurements, limiting its ability in elucidating the long-term behaviors and dominant sources of regional fine particles (PM2.5). In this study, we collected daily PM2.5 filter samples across a relatively long period (November 2015 to April 2016, in total >100 samples) using a high-volume sampler, in urban Yangzhou - a city in the Yangtze River Delta region, China. These samples were analyzed by using a suite of analytical techniques, for the water-soluble inorganic ions (WSIs), organic carbon (OC), elemental carbon (EC), water-soluble organic carbon (WSOC) and total nitrogen (TN), trace metal elements, etc. More importantly, an Aerodyne soot particle aerosol mass spectrometer (SP-AMS) was for the first time introduced for the offline characterization of the PM2.5 samples collected in this region. In particular, Positive matrix factorization was conducted on the SP-AMS determined water-soluble fraction of organic aerosols (WSOA), and three distinct sources were separated, including a primary OA (POA), a less oxygenated OA (LOOA), and a more oxygenated OA (MOOA). Chemical characteristics and evolution processes of these OA subcomponents were further discussed. Our results are useful for the air pollution management in the YRD region, and the technique developed can be applied elsewhere as well.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

NASA Astrophysics Data System (ADS)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

Synovial fluid progenitors expressing CD90+ from normal but not osteoarthritic joints undergo chondrogenic differentiation without micro-mass culture.

PubMed

Krawetz, Roman J; Wu, Yiru Elizabeth; Martin, Liam; Rattner, Jerome B; Matyas, John R; Hart, David A

2012-01-01

Mesenchymal progenitor cells (MPCs) can differentiate into osteoblasts, adipocytes, and chondrocytes, and are in part responsible for maintaining tissue integrity. Recently, a progenitor cell population has been found within the synovial fluid that shares many similarities with bone marrow MPCs. These synovial fluid MPCs (sfMPCs) share the ability to differentiate into bone and fat, with a bias for cartilage differentiation. In this study, sfMPCs were isolated from human and canine synovial fluid collected from normal individuals and those with osteoarthritis (human: clinician-diagnosed, canine: experimental) to compare the differentiation potential of CD90+ vs. CD90- sfMPCs, and to determine if CD90 (Thy-1) is a predictive marker of synovial fluid progenitors with chondrogenic capacity in vitro. sfMPCs were derived from synovial fluid from normal and OA knee joints. These cells were induced to differentiate into chondrocytes and analyzed using quantitative PCR, immunofluorescence, and electron microscopy. The CD90+ subpopulation of sfMPCs had increased chondrogenic potential compared to the CD90- population. Furthermore, sfMPCs derived from healthy joints did not require a micro-mass step for efficient chondrogenesis. Whereas sfMPCs from OA synovial fluid retain the ability to undergo chondrogenic differentiation, they require micro-mass culture conditions. Overall, this study has demonstrated an increased chondrogenic potential within the CD90+ fraction of human and canine sfMPCs and that this population of cells derived from healthy normal joints do not require a micro-mass step for efficient chondrogenesis, while sfMPCs obtained from OA knee joints do not differentiate efficiently into chondrocytes without the micro-mass procedure. These results reveal a fundamental shift in the chondrogenic ability of cells isolated from arthritic joint fluids, and we speculate that the mechanism behind this change of cell behavior is exposure to the altered milieu of the OA

BOREAS TF-1 SSA-OA Tower Flux, Meteorological, and Soil Temperature Data

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Huemmrich, Karl (Editor); Black, T. Andrew; Chen, Z.; Nesic, Zoran

2000-01-01

The BOREAS TF-1 team collected energy, carbon dioxide, and momentum flux data above the canopy along with meteorological and soils data at the BOREAS SSA-OA site from mid-April to the end of the year for 1996. The data are available in tabular ASCII files.

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.

PubMed

Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry

PubMed Central

Yao, Jingwen; Utsunomiya, Shin-ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/). PMID:26819872

Search for resonances and quantum black holes using dijet mass spectra in proton-proton collisions at $$\\sqrt{s} =$$ 8 TeV

DOE PAGES

Khachatryan, Vardan

2015-03-12

Our search for resonances and quantum black holes is performed using the dijet mass spectra measured in proton-proton collisions at √s=8 TeV with the CMS detector at the LHC. The data set corresponds to an integrated luminosity of 19.7 fb -1. In a search for narrow resonances that couple to quark-quark, quark-gluon, or gluon-gluon pairs, model-independent upper limits, at 95% confidence level, are obtained on the production cross section of resonances, with masses above 1.2 TeV. When interpreted in the context of specific models the limits exclude string resonances with masses below 5.0 TeV; excited quarks below 3.5 TeV; scalarmore » diquarks below 4.7 TeV; W' bosons below 1.9 TeV or between 2.0 and 2.2 TeV; Z' bosons below 1.7 TeV; and Randall-Sundrum gravitons below 1.6 TeV. A separate search is conducted for narrow resonances that decay to final states including b quarks. Furthermore, the first exclusion limit is set for excited b quarks, with a lower mass limit between 1.2 and 1.6 TeV depending on their decay properties. Searches are also carried out for wide resonances, assuming for the first time width-to-mass ratios up to 30%, and for quantum black holes with a range of model parameters. The wide resonance search excludes axigluons and colorons with mass below 3.6 TeV, and color-octet scalars with mass below 2.5 TeV. Lower bounds between 5.0 and 6.3 TeV are set on the masses of quantum black holes.« less

Sources, Properties, Aging, and Anthropogenic Influences on OA and SOA over the Southeast US and the Amazon duing SOAS, DC3, SEAC4RS, and GoAmazon

EPA Science Inventory

The SE US and the Amazon have large sources of biogenic VOCs, varying anthropogenic pollution impacts, and often poor organic aerosol (OA) model performance. Recent results on the sources, properties, aging, and impact of anthropogenic pollution on OA and secondary OA (SOA) over ...

Utility operational experience on the NASA/DOE Mod-OA 200 kW Wind Turbine

NASA Technical Reports Server (NTRS)

Glasgow, J. C.; Robbins, W. H.

1979-01-01

The Mod-OA 200 kW Wind Turbine was designed and fabricated by the Lewis Research Center of the NASA under the direction of the U.S. Department of Energy. The project is a part of the Federal Wind Energy Program and is designed to obtain early wind turbine operation and performance data while gaining initial experience in the operation of large, horizontal axis wind turbines in typical utility environments. On March 6, 1978, the Mod-OA wind turbine was turned over to the Town of Clayton Light and Water Plant, Clayton, NM, for utility operation and on December 31, 1978 the machine had completed ten months of utility operation. This paper describes the machine and documents the recent operational experience at Clayton, NM.

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

PubMed

The, Matthew; Käll, Lukas

2016-03-04

Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

PubMed

Levander, Fredrik; James, Peter

2005-01-01

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

PubMed

Bandeira, Nuno; Clauser, Karl R; Pevzner, Pavel A

2007-07-01

Despite significant advances in the identification of known proteins, the analysis of unknown proteins by MS/MS still remains a challenging open problem. Although Klaus Biemann recognized the potential of MS/MS for sequencing of unknown proteins in the 1980s, low throughput Edman degradation followed by cloning still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed the powerful shotgun DNA sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated shotgun protein sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that shotgun protein sequencing has the potential to overcome the limitations of current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins.

On the Controls of Leaf-Water Oxygen Isotope Ratios in the Atmospheric Crassulacean Acid Metabolism Epiphyte Tillandsia usneoides1[W][OA

PubMed Central

Helliker, Brent R.

2011-01-01

Previous theoretical work showed that leaf-water isotope ratio (δ18OL) of Crassulacean acid metabolism epiphytes was controlled by the δ18O of atmospheric water vapor (δ18Oa), and observed δ18OL could be explained by both a non-steady-state model and a “maximum enrichment” steady-state model (δ18OL-M), the latter requiring only δ18Oa and relative humidity (h) as inputs. δ18OL, therefore, should contain an extractable record of δ18Oa. Previous empirical work supported this hypothesis but raised many questions. How does changing δ18Oa and h affect δ18OL? Do hygroscopic trichomes affect observed δ18OL? Are observations of changes in water content required for the prediction of δ18OL? Does the leaf need to be at full isotopic steady state for observed δ18OL to equal δ18OL-M? These questions were examined with a climate-controlled experimental system capable of holding δ18Oa constant for several weeks. Water adsorbed to trichomes required a correction ranging from 0.5‰ to 1‰. δ18OL could be predicted using constant values of water content and even total conductance. Tissue rehydration caused a transitory change in δ18OL, but the consequent increase in total conductance led to a tighter coupling with δ18Oa. The non-steady-state leaf water models explained observed δ18OL (y = 0.93*x − 0.07; r2 = 0.98) over a wide range of δ18Oa and h. Predictions of δ18OL-M agreed with observations of δ18OL (y = 0.87*x − 0.99; r2 = 0.92), and when h > 0.9, the leaf did not need to be at isotopic steady state for the δ18OL-M model to predict δ18OL in the Crassulacean acid metabolism epiphyte Tillandsia usneoides. PMID:21300917

41 CFR 102-85.20 - What does an Occupancy Agreement (OA) do?

Code of Federal Regulations, 2010 CFR

2010-07-01

... defines GSA's relationship with each customer agency and: (a) Establishes specific financial terms... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What does an Occupancy Agreement (OA) do? 102-85.20 Section 102-85.20 Public Contracts and Property Management Federal Property...

BOREAS TF-1 SSA-OA Understory Flux, Meteorological, and Soil Temperature Data

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Huemmrich, Karl (Editor); Black, T. Andrew; Chen, Z.; Nesic, Zoran

2000-01-01

The BOREAS TF-1 team collected energy, carbon dioxide, and momentum flux data under the canopy along with meteorological and soils data at the BOREAS SSA-OA site from mid-October to mid-November of 1993 and throughout all of 1994. The data are available in tabular ASCII files.

41 CFR 102-85.20 - What does an Occupancy Agreement (OA) do?

Code of Federal Regulations, 2014 CFR

2014-01-01

... defines GSA's relationship with each customer agency and: (a) Establishes specific financial terms... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What does an Occupancy Agreement (OA) do? 102-85.20 Section 102-85.20 Public Contracts and Property Management Federal Property...

41 CFR 102-85.20 - What does an Occupancy Agreement (OA) do?

Code of Federal Regulations, 2011 CFR

2011-01-01

... defines GSA's relationship with each customer agency and: (a) Establishes specific financial terms... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What does an Occupancy Agreement (OA) do? 102-85.20 Section 102-85.20 Public Contracts and Property Management Federal Property...

41 CFR 102-85.20 - What does an Occupancy Agreement (OA) do?

Code of Federal Regulations, 2012 CFR

2012-01-01

... defines GSA's relationship with each customer agency and: (a) Establishes specific financial terms... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What does an Occupancy Agreement (OA) do? 102-85.20 Section 102-85.20 Public Contracts and Property Management Federal Property...

41 CFR 102-85.20 - What does an Occupancy Agreement (OA) do?

Code of Federal Regulations, 2013 CFR

2013-07-01

... defines GSA's relationship with each customer agency and: (a) Establishes specific financial terms... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false What does an Occupancy Agreement (OA) do? 102-85.20 Section 102-85.20 Public Contracts and Property Management Federal Property...

Leptin enhances MMP-1, MMP-3 and MMP-13 production in human osteoarthritic cartilage and correlates with MMP-1 and MMP-3 in synovial fluid from OA patients.

PubMed

Koskinen, Anna; Vuolteenaho, Katriina; Nieminen, Riina; Moilanen, Teemu; Moilanen, Eeva

2011-01-01

In the present study, we investigated the role of adipocytokine leptin in the pathogenesis of osteoarthritis (OA) by measuring its effects on matrix metalloproteinase (MMP) production in human OA cartilage. In addition, the correlations between leptin and MMP concentrations in synovial fluid from OA patients were studied. Cartilage tissue obtained from leftover pieces of total knee replacement surgery from patients with OA was used in the experiments. Production of collagenases MMP-1, MMP-8 and MMP-13, and stromelysin-1 (MMP-3) in the cartilage was measured by immunoassay and the signalling pathways were explored by pharmacological means. In addition, synovial fluid samples were collected from 84 OA patients undergoing knee replacement surgery. The concentrations of leptin and MMPs in synovial fluid were measured by immunoassay. Leptin alone and in combination with IL-1β enhanced production of MMP-1, MMP-3, and MMP-13 in human OA cartilage, while MMP-8 concentrations remained undetectable. The effects of leptin on MMP-1, MMP-3 and MMP-13 production were mediated through transcription factor NF-κβ, and through protein kinase C and MAP kinase pathways. Interestingly, leptin concentrations in synovial fluid from OA patients correlated positively with MMP-3 (r=0.51, p<0.001) and MMP-1 (r=0.41, p<0.001) levels. To our knowledge, this is the first study to show that leptin up-regulates MMP-1 and MMP-3 production in human OA cartilage and correlates positively to MMP-1 and MMP-3 in synovial fluid from OA patients. The findings suggest that leptin has catabolic effects in OA joints by increasing MMP production in cartilage.

Mass spectrometry.

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Johanson, G. A.

1972-01-01

Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

Chemical characterization of fine particulate matter in Changzhou, China, and source apportionment with offline aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Ye, Zhaolian; Liu, Jiashu; Gu, Aijun; Feng, Feifei; Liu, Yuhai; Bi, Chenglu; Xu, Jianzhong; Li, Ling; Chen, Hui; Chen, Yanfang; Dai, Liang; Zhou, Quanfa; Ge, Xinlei

2017-02-01

Knowledge of aerosol chemistry in densely populated regions is critical for effective reduction of air pollution, while such studies have not been conducted in Changzhou, an important manufacturing base and populated city in the Yangtze River Delta (YRD), China. This work, for the first time, performed a thorough chemical characterization on the fine particulate matter (PM2.5) samples, collected during July 2015 to April 2016 across four seasons in this city. A suite of analytical techniques was employed to measure the organic carbon (OC), elemental carbon (EC), water-soluble organic carbon (WSOC), water-soluble inorganic ions (WSIIs), trace elements, and polycyclic aromatic hydrocarbons (PAHs) in PM2.5; in particular, an Aerodyne soot particle aerosol mass spectrometer (SP-AMS) was deployed to probe the chemical properties of water-soluble organic aerosol (WSOA). The average PM2.5 concentration was found to be 108.3 µg m-3, and all identified species were able to reconstruct ˜ 80 % of the PM2.5 mass. The WSIIs occupied about half of the PM2.5 mass (˜ 52.1 %), with SO42-, NO3-, and NH4+ as the major ions. On average, nitrate concentrations dominated over sulfate (mass ratio of 1.21), indicating that traffic emissions were more important than stationary sources. OC and EC correlated well with each other and the highest OC / EC ratio (5.16) occurred in winter, suggesting complex OC sources likely including both secondary and primary ones. Concentrations of eight trace elements (Mn, Zn, Al, B, Cr, Cu, Fe, Pb) can contribute up to ˜ 5.0 % of PM2.5 during winter. PAH concentrations were also high in winter (140.25 ng m-3), which were predominated by median/high molecular weight PAHs with five and six rings. The organic matter including both water-soluble and water-insoluble species occupied ˜ 21.5 % of the PM2.5 mass. SP-AMS determined that the WSOA had average atomic oxygen-to-carbon (O / C), hydrogen-to-carbon (H / C), nitrogen-to-carbon (N / C), and organic

Nuclear Neutrino Spectra in Late Stellar Evolution

NASA Astrophysics Data System (ADS)

Misch, G. Wendell; Sun, Yang; Fuller, George

2018-05-01

Neutrinos are the principle carriers of energy in massive stars, beginning from core carbon burning and continuing through core collapse and after the core bounce. In fact, it may be possible to detect neutrinos from nearby pre-supernova stars. Therefore, it is of great interest to understand the neutrino energy spectra from these stars. Leading up to core collapse, beginning around core silicon burning, nuclei become dominant producers of neutrinos, particularly at high neutrino energy, so a systematic study of nuclear neutrino spectra is desirable. We have done such a study, and we present our sd-shell model calculations of nuclear neutrino energy spectra for nuclei in the mass number range A = 21 - 35. Our study includes neutrinos produced by charged lepton capture, charged lepton emission, and neutral current nuclear deexcitation. Previous authors have tabulated the rates of charged current nuclear weak interactions in astrophysical conditions, but the present work expands on this not only by providing neutrino energy spectra, but also by including the heretofore untabulated neutral current de-excitation neutrino pairs.

Quality evaluation of tandem mass spectral libraries.

PubMed

Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

2011-06-01

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

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.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

PubMed Central

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L.; Dianes, José A.; del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W.; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-01-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra. PMID:27493588

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

PubMed

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L; Dianes, José A; Del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-08-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.

Development and preliminary evaluation of the OsteoArthritis Questionnaire (OA-Quest): a psychometric study.

PubMed

Busija, L; Buchbinder, R; Osborne, R H

2016-08-01

This study reports the development of the OsteoArthritis Questionnaire (OA-Quest) - a new measure designed to comprehensively capture the potentially modifiable burden of osteoarthritis. Item development was guided by the a priori conceptual framework of the Personal Burden of Osteoarthritis (PBO) which captures 8 dimensions of osteoarthritis burden (Physical distress, Fatigue, Physical limitations, Psychosocial distress, Physical de-conditioning, Financial hardship, Sleep disturbances, Lost productivity). One hundred and twenty three candidate items were pretested in a clinical sample of 18 osteoarthritis patients. The measurement properties of the OA-Quest were assessed with exploratory factor analysis (EFA), Rasch modelling, and confirmatory factor analysis (CFA) in a community-based sample (n = 792). EFA replicated 7 of the 8 PBO domains. An exception was PBO Fatigue domain, with items merging into the Physical distress subscale in the OA-Quest. Following item analysis, a 42-item 7-subscale questionnaire was constructed, measuring Physical distress (seven items, Cronbach's α = 0.93), Physical limitations (11 items, α = 0.95), Psychosocial distress (seven items, α = 0.93), Physical de-conditioning (four items, α = 0.87), Financial hardship (four items, α = 0.93), Sleep disturbances (five items, α = 0.96), and Lost productivity (four items α = 0.90). A highly restricted 7-factor CFA model had excellent fit with the data (χ(2)(113) = 316.36, P < 0.001; chi-square/degrees of freedom = 2.8; comparative fit index [CFI] = 0.97; root mean square error of approximation [RMSEA] = 0.07), supporting construct validity of the new measure. The OA-Quest is a new measure of osteoarthritis burden that is founded on a comprehensive conceptual model. It has strong evidence of construct validity and provides reliable measurement across a broad range of osteoarthritis burden. Copyright © 2016 Osteoarthritis Research Society International

In silico analysis of miRNA-mediated gene regulation in OCA and OA genes.

PubMed

Kamaraj, Balu; Gopalakrishnan, Chandrasekhar; Purohit, Rituraj

2014-12-01

Albinism is an autosomal recessive genetic disorder due to low secretion of melanin. The oculocutaneous albinism (OCA) and ocular albinism (OA) genes are responsible for melanin production and also act as a potential targets for miRNAs. The role of miRNA is to inhibit the protein synthesis partially or completely by binding with the 3'UTR of the mRNA thus regulating gene expression. In this analysis, we predicted the genetic variation that occurred in 3'UTR of the transcript which can be a reason for low melanin production thus causing albinism. The single nucleotide polymorphisms (SNPs) in 3'UTR cause more new binding sites for miRNA which binds with mRNA which leads to inhibit the translation process either partially or completely. The SNPs in the mRNA of OCA and OA genes can create new binding sites for miRNA which may control the gene expression and lead to hypopigmentation. We have developed a computational procedure to determine the SNPs in the 3'UTR region of mRNA of OCA (TYR, OCA2, TYRP1 and SLC45A2) and OA (GPR143) genes which will be a potential cause for albinism. We identified 37 SNPs in five genes that are predicted to create 87 new binding sites on mRNA, which may lead to abrogation of the translation process. Expression analysis confirms that these genes are highly expressed in skin and eye regions. It is well supported by enrichment analysis that these genes are mainly involved in eye pigmentation and melanin biosynthesis process. The network analysis also shows how the genes are interacting and expressing in a complex network. This insight provides clue to wet-lab researches to understand the expression pattern of OCA and OA genes and binding phenomenon of mRNA and miRNA upon mutation, which is responsible for inhibition of translation process at genomic levels.

Search for electroweak production of supersymmetric states in scenarios with compressed mass spectra at s = 13     TeV with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2018-03-27

A search for electroweak production of supersymmetric particles in scenarios with compressed mass spectra in final states with two low-momentum leptons and missing transverse momentum is presented. This search uses proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015–2016, corresponding to 36.1 fb –1 of integrated luminosity at √s=13 TeV. Events with same-flavor pairs of electrons or muons with opposite electric charge are selected. The data are found to be consistent with the Standard Model prediction. Results are interpreted using simplified models of R-parity-conserving supersymmetry in which there is a small mass difference betweenmore » the masses of the produced supersymmetric particles and the lightest neutralino. Exclusion limits at 95% confidence level are set on next-to-lightest neutralino masses of up to 145 GeV for Higgsino production and 175 GeV for wino production, and slepton masses of up to 190 GeV for pair production of sleptons. In the compressed mass regime, the exclusion limits extend down to mass splittings of 2.5 GeV for Higgsino production, 2 GeV for wino production, and 1 GeV for slepton production. Here, the results are also interpreted in the context of a radiatively-driven natural supersymmetry model with nonuniversal Higgs boson masses.« less

Search for electroweak production of supersymmetric states in scenarios with compressed mass spectra at s = 13     TeV with the ATLAS detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaboud, M.; Aad, G.; Abbott, B.

A search for electroweak production of supersymmetric particles in scenarios with compressed mass spectra in final states with two low-momentum leptons and missing transverse momentum is presented. This search uses proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015–2016, corresponding to 36.1 fb –1 of integrated luminosity at √s=13 TeV. Events with same-flavor pairs of electrons or muons with opposite electric charge are selected. The data are found to be consistent with the Standard Model prediction. Results are interpreted using simplified models of R-parity-conserving supersymmetry in which there is a small mass difference betweenmore » the masses of the produced supersymmetric particles and the lightest neutralino. Exclusion limits at 95% confidence level are set on next-to-lightest neutralino masses of up to 145 GeV for Higgsino production and 175 GeV for wino production, and slepton masses of up to 190 GeV for pair production of sleptons. In the compressed mass regime, the exclusion limits extend down to mass splittings of 2.5 GeV for Higgsino production, 2 GeV for wino production, and 1 GeV for slepton production. Here, the results are also interpreted in the context of a radiatively-driven natural supersymmetry model with nonuniversal Higgs boson masses.« less

Chemometric and multivariate statistical analysis of time-of-flight secondary ion mass spectrometry spectra from complex Cu-Fe sulfides.

PubMed

Kalegowda, Yogesh; Harmer, Sarah L

2012-03-20

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra of mineral samples are complex, comprised of large mass ranges and many peaks. Consequently, characterization and classification analysis of these systems is challenging. In this study, different chemometric and statistical data evaluation methods, based on monolayer sensitive TOF-SIMS data, have been tested for the characterization and classification of copper-iron sulfide minerals (chalcopyrite, chalcocite, bornite, and pyrite) at different flotation pulp conditions (feed, conditioned feed, and Eh modified). The complex mass spectral data sets were analyzed using the following chemometric and statistical techniques: principal component analysis (PCA); principal component-discriminant functional analysis (PC-DFA); soft independent modeling of class analogy (SIMCA); and k-Nearest Neighbor (k-NN) classification. PCA was found to be an important first step in multivariate analysis, providing insight into both the relative grouping of samples and the elemental/molecular basis for those groupings. For samples exposed to oxidative conditions (at Eh ~430 mV), each technique (PCA, PC-DFA, SIMCA, and k-NN) was found to produce excellent classification. For samples at reductive conditions (at Eh ~ -200 mV SHE), k-NN and SIMCA produced the most accurate classification. Phase identification of particles that contain the same elements but a different crystal structure in a mixed multimetal mineral system has been achieved.

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

NASA Astrophysics Data System (ADS)

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

2009-03-01

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

Overexpression of the Transcription Factor Sp1 Activates the OAS-RNAse L-RIG-I Pathway

PubMed Central

Dupuis-Maurin, Valéryane; Brinza, Lilia; Baguet, Joël; Plantamura, Emilie; Schicklin, Stéphane; Chambion, Solène; Macari, Claire; Tomkowiak, Martine; Deniaud, Emmanuelle; Leverrier, Yann

2015-01-01

Deregulated expression of oncogenes or transcription factors such as specificity protein 1 (Sp1) is observed in many human cancers and plays a role in tumor maintenance. Paradoxically in untransformed cells, Sp1 overexpression induces late apoptosis but the early intrinsic response is poorly characterized. In the present work, we studied increased Sp1 level consequences in untransformed cells and showed that it turns on an early innate immune transcriptome. Sp1 overexpression does not activate known cellular stress pathways such as DNA damage response or endoplasmic reticulum stress, but induces the activation of the OAS-RNase L pathway and the generation of small self-RNAs, leading to the upregulation of genes of the antiviral RIG-I pathway at the transcriptional and translational levels. Finally, Sp1-induced intrinsic innate immune response leads to the production of the chemokine CXCL4 and to the recruitment of inflammatory cells in vitro and in vivo. Altogether our results showed that increased Sp1 level in untransformed cells constitutes a novel danger signal sensed by the OAS-RNase L axis leading to the activation of the RIG-I pathway. These results suggested that the OAS-RNase L-RIG-I pathway may be activated in sterile condition in absence of pathogen. PMID:25738304

Low Masses and High Redshifts: The Evolution of the Mass-Metallicity Relation

NASA Technical Reports Server (NTRS)

Henry, Alaina; Scarlata, Claudia; Dominguez, Alberto; Malkan, Matthew; Martin, Crystal L.; Siana, Brian; Atek, Hakim; Bedregal, Alejandro G.; Colbert, James W.; Rafelski, Marc;

OAS and PKR are not Required for the Anti-viral Effect of Ad:IFN-γ Against Acute HSV-1 in Primary Trigeminal Ganglia Cultures

PubMed Central

Austin, Bobbie Ann; Halford, William; Silverman, Robert H.; Williams, Bryan R. G.; Carr, Daniel J. J.

2005-01-01

Three interferon-gamma (IFNG) induced anti-viral pathways have been reported. Involved anti-viral proteins include: Mx, RNaseL/2'-5'-OAS, and PKR. Involvement of OAS and PKR in IFNG-induced anti-HSV-1 pathways has not been previously reported, but IFNG induces OAS and PKR when other viruses invade the nervous system. The aim of the current study was to determine whether the absence of intact OAS and PKR anti-viral pathways affect the anti-viral activity of IFNG during acute HSV-1 infection within trigeminal ganglia (TG). To investigate this, primary TG cultures were established using TGs removed from C57BL/6 (Wt), RNase L knockout, and RNase L/PKR double knockout mice. Each dissociated TG was transduced with an adenoviral vector containing an IFNG transgene or vector alone. Viral titers following HSV-1 infection of primary TG cell cultures were determined. Significant differences in viral titer for Ad:Null versus Ad:IFNG tranduced TGs were found in each genotype. However, the effectiveness of Ad:IFNG was not reduced in the absence of both OAS and PKR pathways or OAS alone. Recombinant IFNG also exhibited anti-HSV-1 activity. The effectiveness of the IFNG transgene was lost in primary TG cells from IFNG receptor knockout mice. The data suggest that novel anti-HSV-1 mechanisms are induced by IFNG. PMID:16704298

Production and Characterization of an Extracellular Acid Protease from Thermophilic Brevibacillus sp. OA30 Isolated from an Algerian Hot Spring.

PubMed

Gomri, Mohamed Amine; Rico-Díaz, Agustín; Escuder-Rodríguez, Juan-José; El Moulouk Khaldi, Tedj; González-Siso, María-Isabel; Kharroub, Karima

2018-04-12

Proteases have numerous biotechnological applications and the bioprospection for newly-thermostable proteases from the great biodiversity of thermophilic microorganisms inhabiting hot environments, such as geothermal sources, aims to discover more effective enzymes for processes at higher temperatures. We report in this paper the production and the characterization of a purified acid protease from strain OA30, a moderate thermophilic bacterium isolated from an Algerian hot spring. Phenotypic and genotypic study of strain OA30 was followed by the production of the extracellular protease in a physiologically-optimized medium. Strain OA30 showed multiple extracellular proteolytic enzymes and protease 32-F38 was purified by chromatographic methods and its biochemical characteristics were studied. Strain OA30 was affiliated with Brevibacillus thermoruber species. Protease 32-F38 had an estimated molecular weight of 64.6 kDa and was optimally active at 50 °C. It showed a great thermostability after 240 min and its optimum pH was 6.0. Protease 32-F38 was highly stable in the presence of different detergents and solvents and was inhibited by metalloprotease inhibitors. The results of this work suggest that protease 32-F38 might have interesting biotechnological applications.

Individual patient data meta-analysis of trials investigating the effectiveness of intra-articular glucocorticoid injections in patients with knee or hip osteoarthritis: an OA Trial Bank protocol for a systematic review

PubMed Central

2013-01-01

Background Based on small to moderate effect sizes for the wide range of symptomatic treatments in osteoarthritis (OA), and on the heterogeneity of OA patients, treatment guidelines for OA have stressed the need for research on clinical predictors of response to different treatments. A meta-analysis to quantify the effect modified by the predictors using individual patient data (IPD) is suggested. The initiative to collect and analyze IPD in OA research is commenced by the OA Trial Bank. The study aims are therefore: to evaluate the efficacy of intra-articular glucocorticoids for knee or hip OA in specific subgroups of patients with severe pain and (mild) inflammatory signs, over both short-term and long-term follow-up, using IPD from existing studies; to reach consensus on the rules for cooperation in a consortium; and to develop and explore the methodological issues of meta-analysis with individual OA patient data. Methods/Design For the current IPD analysis we will collect and synthesize IPD from randomized trials studying the effect of intra-articular glucocorticoid injections in patients with hip or knee OA. Subgroup analyses will be performed for the primary outcome of pain at both short-term and long-term follow-up, in the subgroups of patients with and without severe pain and with and without inflammatory signs. Discussion This study protocol includes the first study of the OA Trial Bank, an international collaboration that initiates meta-analyses on predefined subgroups of OA patients from existing literature. This approach ensures a widely supported initiative and is therefore likely to be successful in data collection of existing trials. The collaboration developed (that is, the OA Trial Bank) may also lead to future IPD analyses on subgroups of patients with several intervention strategies applied in OA patients. PMID:23830482

Individual patient data meta-analysis of trials investigating the effectiveness of intra-articular glucocorticoid injections in patients with knee or hip osteoarthritis: an OA Trial Bank protocol for a systematic review.

PubMed

van Middelkoop, Marienke; Dziedzic, Krysia S; Doherty, Michael; Zhang, Weiya; Bijlsma, Johannes W; McAlindon, Timothy E; Lohmander, Stefan L; Bierma-Zeinstra, Sita M A

2013-07-05

Based on small to moderate effect sizes for the wide range of symptomatic treatments in osteoarthritis (OA), and on the heterogeneity of OA patients, treatment guidelines for OA have stressed the need for research on clinical predictors of response to different treatments. A meta-analysis to quantify the effect modified by the predictors using individual patient data (IPD) is suggested. The initiative to collect and analyze IPD in OA research is commenced by the OA Trial Bank. The study aims are therefore: to evaluate the efficacy of intra-articular glucocorticoids for knee or hip OA in specific subgroups of patients with severe pain and (mild) inflammatory signs, over both short-term and long-term follow-up, using IPD from existing studies; to reach consensus on the rules for cooperation in a consortium; and to develop and explore the methodological issues of meta-analysis with individual OA patient data. For the current IPD analysis we will collect and synthesize IPD from randomized trials studying the effect of intra-articular glucocorticoid injections in patients with hip or knee OA. Subgroup analyses will be performed for the primary outcome of pain at both short-term and long-term follow-up, in the subgroups of patients with and without severe pain and with and without inflammatory signs. This study protocol includes the first study of the OA Trial Bank, an international collaboration that initiates meta-analyses on predefined subgroups of OA patients from existing literature. This approach ensures a widely supported initiative and is therefore likely to be successful in data collection of existing trials. The collaboration developed (that is, the OA Trial Bank) may also lead to future IPD analyses on subgroups of patients with several intervention strategies applied in OA patients.

NITPICK: peak identification for mass spectrometry data.

PubMed

Renard, Bernhard Y; Kirchner, Marc; Steen, Hanno; Steen, Judith A J; Hamprecht, Fred A

2008-08-28

The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments. This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra. NITPICK is based on fractional averaging, a novel extension to Senko's well-known averaging model, and on a modified version of sparse, non-negative least angle regression, for which a suitable, statistically motivated early stopping criterion has been derived. The strength of NITPICK is the deconvolution of overlapping mixture mass spectra. Extensive comparative evaluation has been carried out and results are provided for simulated and real-world data sets. NITPICK outperforms pepex, to date the only alternate, publicly available, non-greedy feature extraction routine. NITPICK is available as software package for the R programming language and can be downloaded from (http://hci.iwr.uni-heidelberg.de/mip/proteomics/).

NITPICK: peak identification for mass spectrometry data

PubMed Central

Renard, Bernhard Y; Kirchner, Marc; Steen , Hanno; Steen, Judith AJ; Hamprecht , Fred A

2008-01-01

Background The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments. Results This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra. NITPICK is based on fractional averagine, a novel extension to Senko's well-known averagine model, and on a modified version of sparse, non-negative least angle regression, for which a suitable, statistically motivated early stopping criterion has been derived. The strength of NITPICK is the deconvolution of overlapping mixture mass spectra. Conclusion Extensive comparative evaluation has been carried out and results are provided for simulated and real-world data sets. NITPICK outperforms pepex, to date the only alternate, publicly available, non-greedy feature extraction routine. NITPICK is available as software package for the R programming language and can be downloaded from . PMID:18755032

BOREAS TF-2 SSA-OA Tethersonde Meteorological and Ozone Data

NASA Technical Reports Server (NTRS)

Arnold, A. James; Mickle, Robert E.; Hall, Forrest G. (Editor); Huemmrich, Karl (Editor)

2000-01-01

The BOReal Ecosystem-Atmosphere Study Tower Flux-2 (BOREAS TF-2) team collected meteorological and ozone measurements from instruments mounted below a tethered balloon. These data were collected at the Southern Study Area Old Aspen (SSA-OA) site to extend meteorological and ozone measurements made from the flux tower to heights of 300 m. The tethersonde operated during the fall of 1993 and the spring, summer, and fall of 1994. The data are available in tabular ASCII files.

Demonstration of Laser Induced Acoustic Desoprtion - Chemical Ionization Mass Spectrometry (LIAD-CIMS) for Fragment-Free Measurements of Organic Aerosol Molecular Composition

NASA Astrophysics Data System (ADS)

Browne, E. C.; Abdelhamid, A.; Berry, J.; Alton, M.

2017-12-01

Organic compounds account for a significant portion of fine atmospheric aerosol. Current analytical techniques have provided insights on organic aerosol (OA) sources, composition, and chemical modification pathways. Despite this knowledge, large uncertainties remain and hinder our understanding of aerosol impacts on climate, air quality, and health. Measuring OA composition is challenging due to the complex chemical composition and the wide variation in the properties (e.g., vapor pressure, solubility, reactivity) of organic compounds. In many current measurement techniques, the ability to chemically resolve and quantify OA components is complicated by molecular decomposition, matrix effects, and/or preferential ionization mechanisms. Here, we utilize a novel desorption technique, laser induced acoustic desorption (LIAD), that generates fragment-free, neutral gas-phase molecules. We couple LIAD with a high-resolution chemical ionization mass spectrometer (CIMS) to provide molecular composition OA measurements. Through a series of laboratory experiments, we demonstrate the ability of this technique to measure large, thermally labile species without fragmentation/thermal decomposition. We discuss quantification and detection limits of this technique. We compare LIAD-CIMS measurements with thermal desorption-CIMS measurements using off-line measurements of ambient aerosol collected in Boulder, CO. Lastly, we discuss future development for on-line measurements of OA using LIAD-CIMS.

Mass Spectral Library with Search Program, Data Version: NIST v17

National Institute of Standards and Technology Data Gateway

SRD 1A NIST/EPA/NIH Mass Spectral Library with Search Program, Data Version: NIST v17 (PC database for purchase)   Available with full-featured NIST MS Search Program for Windows integrated tools, the NIST '98 is a fully evaluated collection of electron-ionization mass spectra. (147,198 Compounds with Spectra; 147,194 Chemical Structures; 174,948 Spectra )

Association of Oral Fat Sensitivity with Body Mass Index, Taste Preference, and Eating Habits in Healthy Japanese Young Adults.

PubMed

Asano, Masanobu; Hong, Guang; Matsuyama, Yusuke; Wang, Weiqi; Izumi, Satoshi; Izumi, Masayuki; Toda, Takashi; Kudo, Tada-Aki

2016-02-01

Oral fat sensitivity (OFS, the ability to detect fat) may be related to overeating-induced obesity. However, it is largely unknown whether OFS affects taste preference and eating habits. Therefore, we aimed to evaluate (1) the association between body mass index (BMI) and OFS and (2) the relationship of OFS with four types of taste preference (sweet, sour, salty, and bitter) and eating habits using serial concentrations of oleic acid (OA) homogenized in non-fat milk and a self-reported questionnaire. Participants were 25 healthy Japanese individuals (mean age: 27.0 ± 5.6 years), among whom the OA detection threshold was significantly associated with BMI. Participants were divided into two subgroups based on oral sensitivity to 2.8 mM OA: hypersensitive (able to detect 2.8 mM OA, n = 16) and hyposensitive (unable to detect 2.8 mM OA, n = 9). The degree of sweet taste preference of the hypersensitive group was significantly higher than that of the hyposensitive group. Furthermore, there was significantly higher degree of preference for high-fat sweet foods than low-fat sweet foods in the hypersensitive group. There was also a significant inverse correlation between the OA detection threshold and the degree of both spare eating and postprandial satiety. Thus, OFS is associated not only with BMI, but also with the preference for high-fat sweet foods and eating habits. The present study provides novel insights that measuring OFS may be useful for assessing the risk of obesity associated with overeating in countries, including Japan, where BMI is increasing in the population.

Single-protein nanomechanical mass spectrometry in real time

PubMed Central

Hanay, M.S.; Kelber, S.; Naik, A.K.; Chi, D.; Hentz, S.; Bullard, E.C.; Colinet, E.; Duraffourg, L.; Roukes, M.L.

2012-01-01

Nanoelectromechanical systems (NEMS) resonators can detect mass with exceptional sensitivity. Previously, mass spectra from several hundred adsorption events were assembled in NEMS-based mass spectrometry using statistical analysis. Here, we report the first realization of single-molecule NEMS-based mass spectrometry in real time. As each molecule in the sample adsorbs upon the NEMS resonator, its mass and the position-of-adsorption are determined by continuously tracking two driven vibrational modes of the device. We demonstrate the potential of multimode NEMS-based mass spectrometry by analyzing IgM antibody complexes in real-time. NEMS-MS is a unique and promising new form of mass spectrometry: it can resolve neutral species, provides resolving power that increases markedly for very large masses, and allows acquisition of spectra, molecule-by-molecule, in real-time. PMID:22922541

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

NASA Technical Reports Server (NTRS)

Harper, Graham M.

2005-01-01

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

41 CFR 102-85.140 - How are changes in Rent reflected in OAs?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false How are changes in Rent reflected in OAs? 102-85.140 Section 102-85.140 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT REGULATION REAL PROPERTY 85-PRICING POLICY FOR...

Olive Tree Branches Burning: A major pollution source in the Mediterranean

NASA Astrophysics Data System (ADS)

Kostenidou, Evangelia; Kaltsonoudis, Christos; Tsiflikiotou, Maria; Louvaris, Evangelos; Russell, Lynn; Pandis, Spyros

2013-04-01

Olive tree branches burning is a common agricultural waste management practice after the annual pruning of olive trees from November to February. Almost 1 billion (90%) of the olive trees in our planet are located around the Mediterranean, so the corresponding emissions of olive tree branches burning can be a significant source of fine aerosols during the cold months. Organic aerosol produced during the burning of olive tree branches (otBB-OA) was characterized with both direct source-sampling (using a mobile smog chamber) and ambient measurements during the burning season in the area of Patras, Greece. The aerosol emitted consists of organics, black carbon (BC), potassium, chloride, nitrate and sulfate. In addition to NOx, O3, CO and CO2, Volatile Organic Compounds (VOCs) such as methanol, acetonitrile, benzene and toluene were also produced. The Aerosol Mass Spectrometry (AMS) mass spectrum of otBB-OA is characterized by the m-z's27, 29, 39, 41, 43, 44, 55, 57, 67, 69 and 91 and changes as the emissions react with OH and O3. Fourier Transform Infrared Spectroscopy (FTIR) analysis showed that otBB-OA was composed of 48% alkane groups, 27% organic hydroxyl groups, 11% carboxylic acid groups, 11% primary amine groups and 4% carbonyl groups. The oxygen to carbon (O:C) ratio is 0.29±0.04. The otBB-OA AMS mass spectrum differs from the other published biomass burning spectra. The m-z60, used as levoglucosan tracer, is lower than in most biomass burning sources. This is confirmed by Gas Chromatography Mass Spectroscopy (GC-MS) analysis on filters where the levoglucosan to OC mass ratio was between 0.034 and 0.043, close to the lower limit of the reported values for most fuel types. This may lead to an underestimation of the otBB-OA contribution in Southern Europe if levoglucosan is being used as a wood burning tracer. During the olive tree branches burning season, 20 days of ambient measurements were performed. Applying positive matrix factorization (PMF) to the

Microprocessor control system for 200-kilowatt Mod-OA wind turbines

NASA Technical Reports Server (NTRS)

Nyland, T. W.; Birchenough, A. G.

1982-01-01

The microprocessor system and program used to control the operation of the 200-kW Mod-OA wind turbines is described. The system is programmed to begin startup and shutdown sequences automatically and to control yaw motion. Rotor speed and power output are controlled with integral and proportional control of the blade pitch angle. Included in the report are a description of the hardware and a discussion of the software programming technique. A listing of the PL/M software program is given.

Chemical composition and characteristics of ambient aerosols and rainwater residues during Indian summer monsoon: Insight from aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Chakraborty, Abhishek; Gupta, Tarun; Tripathi, Sachchida N.

2016-07-01

Real time composition of non-refractory submicron aerosol (NR-PM1) is measured via Aerosol mass spectrometer (AMS) for the first time during Indian summer monsoon at Kanpur, a polluted urban location located at the heart of Indo Gangetic Plain (IGP). Submicron aerosols are found to be dominated by organics followed by nitrate. Source apportionment of organic aerosols (OA) via positive matrix factorization (PMF) revealed several types of secondary/oxidized and primary organic aerosols. On average, OA are completely dominated by oxidized OA with a very little contribution from biomass burning OA. During rain events, PM1 concentration is decreased almost by 60%, but its composition remains nearly the same. Oxidized OA showed slightly more decrease than primary OAs, probably due to their higher hygroscopicity. The presence of organo nitrates (ON) is also detected in ambient aerosols. Apart from real-time sampling, collected fog and rainwater samples were also analyzed via AMS in offline mode and in the ICP-OES (Inductively coupled plasma - Optical emission spectrometry) for elements. The presence of sea salt, organo nitrates and sulfates has been observed. Rainwater residues are also dominated by organics but their O/C ratios are 15-20% lower than the observed values for ambient OA. Alkali metals such as Ca, Na, K are found to be most abundant in the rainwater followed by Zn. Rainwater residues are also found to be much less oxidized than the aerosols present inside the fog water, indicating presence of less oxidized organics. These findings indicate that rain can act as an effective scavenger of different types of pollutants even for submicron particle range. Rainwater residues also contain organo sulfates which indicate that some portion of the dissolved aerosols has undergone aqueous processing, possibly inside the cloud. Highly oxidized and possibly hygroscopic OA during monsoon period compared to other seasons (winter, post monsoon), indicates that they can act

Ion Mobility Separation of Isomeric Carbohydrate Precursor Ions and Acquisition of their Independent Tandem Mass Spectra

PubMed Central

Zhu, Maolei; Bendiak, Brad; Clowers, Brian; Hill, Herbert H.

2010-01-01

The rapid separation of isomeric precursor ions of oligosaccharides prior to their analysis by MSn was demonstrated using an ambient pressure ion mobility spectrometer (IMS) interfaced with a quadrupole ion trap. Separations were not limited to specific types of isomers; representative isomers differing solely in the stereochemistry of sugars, in their anomeric configurations, and in their overall branching patterns and linkage positions could be resolved in the millisecond time frame. Physical separation of precursor ions permitted independent mass spectra of individual oligosaccharide isomers to be acquired to at least MS3, the number of stages of dissociation limited only practically by the abundance of specific product ions. IMS-MSn analysis was particularly valuable in the evaluation of isomeric oligosaccharides that yielded identical sets of product ions in MS/MS experiments, revealing pairs of isomers that would otherwise not be known to be present in a mixture if evaluated solely by MS dissociation methods alone. A practical example of IMS-MSn analysis of a set of isomers included within a single HPLC fraction of oligosaccharides released from bovine submaxillary mucin is described. PMID:19562326

Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

NASA Astrophysics Data System (ADS)

El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

2018-05-01

We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

Challenges to Constraining Exoplanet Masses via Transmission Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batalha, Natasha E.; Kempton, Eliza M.-R.; Mbarek, Rostom, E-mail: neb149@psu.edu

MassSpec , a method for determining the mass of a transiting exoplanet from its transmission spectrum alone, was proposed by de Wit and Seager. The premise of this method relies on the planet’s surface gravity being extracted from the transmission spectrum via its effect on the atmospheric scale height, which in turn determines the strength of absorption features. Here, we further explore the applicability of MassSpec to low-mass exoplanets—specifically those in the super-Earth size range for which radial velocity determinations of the planetary mass can be extremely challenging and resource intensive. Determining the masses of these planets is of themore » utmost importance because their nature is otherwise highly unconstrained. Without knowledge of the mass, these planets could be rocky, icy, or gas-dominated. To investigate the effects of planetary mass on transmission spectra, we present simulated observations of super-Earths with atmospheres made up of mixtures of H{sub 2}O and H{sub 2}, both with and without clouds. We model their transmission spectra and run simulations of each planet as it would be observed with James Webb Space Telescope using the NIRISS, NIRSpec, and MIRI instruments. We find that significant degeneracies exist between transmission spectra of planets with different masses and compositions, making it impossible to unambiguously determine the planet’s mass in many cases.« less

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

NASA Astrophysics Data System (ADS)

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

2010-02-01

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

Mass measurement using energy spectra in three-body decays

DOE PAGES

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

2016-05-24

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

First light: exploring the spectra of high-redshift galaxies in the Renaissance Simulations

NASA Astrophysics Data System (ADS)

Barrow, Kirk S. S.; Wise, John H.; Norman, Michael L.; O'Shea, Brian W.; Xu, Hao

2017-08-01

We present synthetic observations for the first generations of galaxies in the Universe and make predictions for future deep field observations for redshifts greater than 6. Due to the strong impact of nebular emission lines and the relatively compact scale of H II regions, high-resolution cosmological simulations and a robust suite of analysis tools are required to properly simulate spectra. We created a software pipeline consisting of fsps, hyperion, cloudy and our own tools to generate synthetic IR observations from a fully three-dimensional arrangement of gas, dust, and stars. Our prescription allows us to include emission lines for a complete chemical network and tackle the effect of dust extinction and scattering in the various lines of sight. We provide spectra, 2D binned photon imagery for both HST and JWST IR filters, luminosity relationships, and emission-line strengths for a large sample of high-redshift galaxies in the Renaissance Simulations. Our resulting synthetic spectra show high variability between galactic haloes with a strong dependence on stellar mass, metallicity, gas mass fraction, and formation history. Haloes with the lowest stellar mass have the greatest variability in [O III]/Hβ, [O III], and C III], while haloes with higher masses are seen to show consistency in their spectra and [O III] equivalent widths between 1 and 10 Å. Viewing angle accounted for threefold difference in flux due to the presence of ionized gas channels in a halo. Furthermore, JWST colour plots show a discernible relationship between redshift, colour, and mean stellar age.

Rapid and Sensitive Quantification of Ursolic Acid and Oleanolic Acid in Human Plasma Using Ultra-performance Liquid Chromatography-Mass Spectrometry.

PubMed

Stebounova, Larissa; Ebert, Scott M; Murry, Logan T; Adams, Christopher M; Murry, Daryl J

2018-04-26

Ultra-performance liquid chromatography (UPLC) interfaced with atmospheric pressure chemical ionization mass-spectrometry was used to separate and quantify ursolic acid (UA) and oleanolic acid (OA) in human plasma. UA and OA were extracted from 0.5 mL human plasma using supported liquid extraction and separated utilizing an Acquity UPLC HSS column. The method has been validated for both UA and OA quantitation with a limit of detection of 0.5 ng/mL. The UPLC separations are carried out with isocratic elution with methanol and 5 mM ammonium acetate in water (85:15) as a mobile phase at a flow rate of 0.4 mL/min. The assay was linear from 1 ng/mL to 100 ng/mL for both analytes. The total analysis time was 7 min with the retention times of 3.25 (internal standard), 3.65 (UA) and 3.85 min (OA). Recovery of drug from plasma ranged from 70% to 115%. Analysis of quality control samples at 3, 30 and 80 ng/mL (n = 14) had an intra-day coefficient of variation of 9.9%, 4.3% and 5.5%, respectively. A proof-of-concept study in human patients who consumed apple peels indicates that this analytical method could be applied to clinical studies of UA and/or OA in human subjects.

A cost-effectiveness analysis of celecoxib compared with diclofenac in the treatment of pain in osteoarthritis (OA) within the Swedish health system using an adaptation of the NICE OA model.

PubMed

Brereton, Nicholas; Pennington, Becky; Ekelund, Mats; Akehurst, Ronald

2014-09-01

Celecoxib for the treatment of pain resulting from osteoarthritis (OA) was reviewed by the Tandvårds- och läkemedelsförmånsverket-Dental and Pharmaceutical Benefits Board (TLV) in Sweden in late 2010. This study aimed to evaluate the incremental cost-effectiveness ratio (ICER) of celecoxib plus a proton pump inhibitor (PPI) compared to diclofenac plus a PPI in a Swedish setting. The National Institute for Health and Care Excellence (NICE) in the UK developed a health economic model as part of their 2008 assessment of treatments for OA. In this analysis, the model was reconstructed and adapted to a Swedish perspective. Drug costs were updated using the TLV database. Adverse event costs were calculated using the regional price list of Southern Sweden and the standard treatment guidelines from the county council of Stockholm. Costs for treating cardiovascular (CV) events were taken from the Swedish DRG codes and the literature. Over a patient's lifetime treatment with celecoxib plus a PPI was associated with a quality-adjusted life year (QALY) gain of 0.006 per patient when compared to diclofenac plus a PPI. There was an increase in discounted costs of 529 kr per patient, which resulted in an incremental cost-effectiveness ratio (ICER) of 82,313 kr ($12,141). Sensitivity analysis showed that treatment was more cost effective in patients with an increased risk of bleeding or gastrointestinal (GI) complications. The results suggest that celecoxib plus a PPI is a cost effective treatment for OA when compared to diclofenac plus a PPI. Treatment is shown to be more cost effective in Sweden for patients with a high risk of bleeding or GI complications. It was in this population that the TLV gave a positive recommendation. There are known limitations on efficacy in the original NICE model.

Evaluation of an operating MOD-OA 200 kW wind turbine blade

NASA Technical Reports Server (NTRS)

Donham, R. E.

1979-01-01

Operating loads and structural damage were monitored during operation of the MOD-OA electric generating system. The turbine was damaged locally between stations 48 and 125 after 2.8 million rotations. Loads due to degraded yaw stiffness and fretting at rib station 48 were identified as primary to this distress. The repaired blades operated an additional 4.8 million rotations without problems.

High-Speed Tandem Mass Spectrometric in Situ Imaging by Nanospray Desorption Electrospray Ionization Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew

Nanospray desorption electrospray ionization (nano-DESI) combined with tandem mass spectrometry (MS/MS), high-resolution mass analysis (m/m=17,500 at m/z 200), and rapid spectral acquisition enabled simultaneous imaging and identification of more than 300 molecules from 92 selected m/z windows (± 1 Da) with a spatial resolution of better than 150 um. Uterine sections of implantation sites on day 6 of pregnancy were analyzed in the ambient environment without any sample pre-treatment. MS/MS imaging was performed by scanning the sample under the nano-DESI probe at 10 um/s while acquiring higher-energy collision-induced dissociation (HCD) spectra for a targeted inclusion list of 92 m/z valuesmore » at a rate of ~6.3 spectra/s. Molecular ions and their corresponding fragments, separated using high-resolution mass analysis, were assigned based on accurate mass measurement. Using this approach, we were able to identify and image both abundant and low-abundance isobaric species within each m/z window. MS/MS analysis enabled efficient separation and identification of isobaric sodium and potassium adducts of phospholipids. Furthermore, we identified several metabolites associated with early pregnancy and obtained the first 2D images of these molecules.« less

Predicting ambient aerosol Thermal Optical Reflectance (TOR) measurements from infrared spectra: organic carbon

NASA Astrophysics Data System (ADS)

Dillner, A. M.; Takahama, S.

2014-11-01

Organic carbon (OC) can constitute 50% or more of the mass of atmospheric particulate matter. Typically, the organic carbon concentration is measured using thermal methods such as Thermal-Optical Reflectance (TOR) from quartz fiber filters. Here, methods are presented whereby Fourier Transform Infrared (FT-IR) absorbance spectra from polytetrafluoroethylene (PTFE or Teflon) filters are used to accurately predict TOR OC. Transmittance FT-IR analysis is rapid, inexpensive, and non-destructive to the PTFE filters. To develop and test the method, FT-IR absorbance spectra are obtained from 794 samples from seven Interagency Monitoring of PROtected Visual Environment (IMPROVE) sites sampled during 2011. Partial least squares regression is used to calibrate sample FT-IR absorbance spectra to artifact-corrected TOR OC. The FTIR spectra are divided into calibration and test sets by sampling site and date which leads to precise and accurate OC predictions by FT-IR as indicated by high coefficient of determination (R2; 0.96), low bias (0.02 μg m-3, all μg m-3 values based on the nominal IMPROVE sample volume of 32.8 m-3), low error (0.08 μg m-3) and low normalized error (11%). These performance metrics can be achieved with various degrees of spectral pretreatment (e.g., including or excluding substrate contributions to the absorbances) and are comparable in precision and accuracy to collocated TOR measurements. FT-IR spectra are also divided into calibration and test sets by OC mass and by OM / OC which reflects the organic composition of the particulate matter and is obtained from organic functional group composition; this division also leads to precise and accurate OC predictions. Low OC concentrations have higher bias and normalized error due to TOR analytical errors and artifact correction errors, not due to the range of OC mass of the samples in the calibration set. However, samples with low OC mass can be used to predict samples with high OC mass indicating that the

Rebamipide Attenuates Mandibular Condylar Degeneration in a Murine Model of TMJ-OA by Mediating a Chondroprotective Effect and by Downregulating RANKL-Mediated Osteoclastogenesis

PubMed Central

Izawa, Takashi; Mori, Hiroki; Shinohara, Tekehiro; Mino-Oka, Akiko; Hutami, Islamy Rahma; Iwasa, Akihiko; Tanaka, Eiji

2016-01-01

Temporomandibular joint osteoarthritis (TMJ-OA) is characterized by progressive degradation of cartilage and changes in subchondral bone. It is also one of the most serious subgroups of temporomandibular disorders. Rebamipide is a gastroprotective agent that is currently used for the treatment of gastritis and gastric ulcers. It scavenges reactive oxygen radicals and has exhibited anti-inflammatory potential. The aim of this study was to investigate the impact of rebamipide both in vivo and in vitro on the development of cartilage degeneration and osteoclast activity in an experimental murine model of TMJ-OA, and to explore its mode of action. Oral administration of rebamipide (0.6 mg/kg and 6 mg/kg) was initiated 24 h after TMJ-OA was induced, and was maintained daily for four weeks. Rebamipide treatment was found to attenuate cartilage degeneration, to reduce the number of apoptotic cells, and to decrease the expression levels of matrix metalloproteinase-13 (MMP-13) and inducible nitric oxide synthase (iNOS) in TMJ-OA cartilage in a dose-dependent manner. Rebamipide also suppressed the activation of transcription factors (e.g., NF-κB, NFATc1) and mitogen-activated protein kinases (MAPK) by receptor activator of nuclear factor kappa-B ligand (RANKL) to inhibit the differentiation of osteoclastic precursors, and disrupted the formation of actin rings in mature osteoclasts. Together, these results demonstrate the inhibitory effects of rebamipide on cartilage degradation in experimentally induced TMJ-OA. Furthermore, suppression of oxidative damage, restoration of extracellular matrix homeostasis of articular chondrocytes, and reduced subchondral bone loss as a result of blocked osteoclast activation suggest that rebamipide is a potential therapeutic strategy for TMJ-OA. PMID:27123995

Rebamipide Attenuates Mandibular Condylar Degeneration in a Murine Model of TMJ-OA by Mediating a Chondroprotective Effect and by Downregulating RANKL-Mediated Osteoclastogenesis.

PubMed

Izawa, Takashi; Mori, Hiroki; Shinohara, Tekehiro; Mino-Oka, Akiko; Hutami, Islamy Rahma; Iwasa, Akihiko; Tanaka, Eiji

2016-01-01

Temporomandibular joint osteoarthritis (TMJ-OA) is characterized by progressive degradation of cartilage and changes in subchondral bone. It is also one of the most serious subgroups of temporomandibular disorders. Rebamipide is a gastroprotective agent that is currently used for the treatment of gastritis and gastric ulcers. It scavenges reactive oxygen radicals and has exhibited anti-inflammatory potential. The aim of this study was to investigate the impact of rebamipide both in vivo and in vitro on the development of cartilage degeneration and osteoclast activity in an experimental murine model of TMJ-OA, and to explore its mode of action. Oral administration of rebamipide (0.6 mg/kg and 6 mg/kg) was initiated 24 h after TMJ-OA was induced, and was maintained daily for four weeks. Rebamipide treatment was found to attenuate cartilage degeneration, to reduce the number of apoptotic cells, and to decrease the expression levels of matrix metalloproteinase-13 (MMP-13) and inducible nitric oxide synthase (iNOS) in TMJ-OA cartilage in a dose-dependent manner. Rebamipide also suppressed the activation of transcription factors (e.g., NF-κB, NFATc1) and mitogen-activated protein kinases (MAPK) by receptor activator of nuclear factor kappa-B ligand (RANKL) to inhibit the differentiation of osteoclastic precursors, and disrupted the formation of actin rings in mature osteoclasts. Together, these results demonstrate the inhibitory effects of rebamipide on cartilage degradation in experimentally induced TMJ-OA. Furthermore, suppression of oxidative damage, restoration of extracellular matrix homeostasis of articular chondrocytes, and reduced subchondral bone loss as a result of blocked osteoclast activation suggest that rebamipide is a potential therapeutic strategy for TMJ-OA.

Approach to calculation of mass spectra and two-photon decays of c c¯ mesons in the framework of Bethe-Salpeter equation

NASA Astrophysics Data System (ADS)

Bhatnagar, Shashank; Alemu, Lmenew

2018-02-01

In this work we calculate the mass spectra of charmonium for 1 P ,…,4 P states of 0++ and 1++, for 1 S ,…,5 S states of 0-+, and for 1 S ,…,4 D states of 1- along with the two-photon decay widths of the ground and first excited states of 0++ quarkonia for the process O++→γ γ in the framework of a QCD-motivated Bethe-Salpeter equation (BSE). In this 4 ×4 BSE framework, the coupled Salpeter equations are first shown to decouple for the confining part of the interaction (under the heavy-quark approximation) and are analytically solved, and later the one-gluon-exchange interaction is perturbatively incorporated, leading to mass spectral equations for various quarkonia. The analytic forms of wave functions obtained are used for the calculation of the two-photon decay widths of χc 0. Our results are in reasonable agreement with data (where available) and other models.

Reference intervals for orotic acid in urine, plasma and dried blood spot using hydrophilic interaction liquid chromatography-tandem mass spectrometry.

PubMed

D'Apolito, Oceania; Garofalo, Daniela; la Marca, Giancarlo; Dello Russo, Antonio; Corso, Gaetano

2012-02-01

Orotic acid (OA), a marker of hereditary orotic aciduria, is usually used for the differential diagnosis of some hyperammonemic inherited defects of urea cycle and of basic amino acid transporters. This study was aimed to establish age related reference intervals of OA in urine, and for the first time in plasma, and dried blood spot (DBS) from 229 apparently healthy subjects aged from three days to 40 years. The quantification of OA was performed by a previously implemented method, using a stable isotope dilution with 1,3-[(15)N(2)]-orotic acid and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS). The method has proved to be sensitive and accurate for a quantitative analysis of OA also in DBS and plasma. According to previous studies, urinary OA levels (mmol/mol of creatinine) decrease significantly with age. The upper limits (as 99th %ile) were of 3.44 and 1.30 in groups aged from three days to 1 year (group 1) and from 1 year to 12 years (group 2), respectively; in teenagers (from 13 to 19 years; group 3) and adults (from 20 to 40 years; group 4) urinary levels became more stable and the upper limits were of 0.64 and 1.21, respectively. Furthermore, OA levels in DBS (μM) also resulted significantly higher in subjects of group 1 (upper limit of 0.89) than in subjects of groups 2, 3 and 4 (upper limits of 0.24, 0.21, and 0.29, respectively). OA levels in plasma (μM) were significantly lower in subjects of group 3 (upper limit of 0.30) than in subjects of groups 1, 2, and 4 (upper limits of 0.59, 0.48, and 0.77, respectively). This method was also employed for OA quantification in plasma and DBS of 17 newborns affected by urea cycle defects, resulting sensitive and specific enough to screen these disorders. Copyright © 2011 Elsevier B.V. All rights reserved.

Characterization of aerosol composition and sources in the greater Atlanta area by aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Ng, N. L.; Xu, L.; Suresh, S.; Weber, R. J. J.; Baumann, K.; Edgerton, E. S.

2014-12-01

An important and uncertain aspect of biogenic secondary organic aerosol (SOA) formation is that it is often associated with anthropogenic pollution tracers. Prior studies in Atlanta suggested that 70-80% of the carbon in water-soluble organic carbon (WSOC) is modern, yet it is well-correlated with the anthropogenic CO. In this study, we deployed a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and an Aerosol Chemical Speciation Monitor (ACSM) at multiple sites in different seasons (May 2012-February 2013) to characterize the sources and chemical composition of aerosols in the greater Atlanta area. This area in the SE US is ideal to investigate anthropogenic-biogenic interactions due to high natural and anthropogenic emissions. These extensive field studies are part of the Southeastern Center for Air Pollution and Epidemiology study (SCAPE). The HR-ToF-AMS is deployed at four sites (~ 3 weeks each) in rotation: Jefferson Street (urban), Yorkville (rural), roadside site (near Highway 75/85), and Georgia Tech site (campus), with the urban and rural sites being part of the SEARCH network. We obtained seven HR-ToF-AMS datasets in total. During the entire measurement period, the ACSM is stationary at the GIT site and samples continuously. We perform positive matrix factorization (PMF) analysis on the HR-ToF-AMS and ACSM data to deconvolve the OA into different components. While the diurnal cycle of the total OA is flat as what have been previously observed, the OA factors resolved by PMF analysis show distinctively different diurnal trends. We find that the "more-oxidized oxygenated OA" (MO-OOA) constitutes a major fraction of OA at all sites. In summer, OA is dominated by SOA, e.g., isoprene-OA and OOA with different degrees of oxidation. In contrary, biomass burning OA is more prominent in winter data. By comparing HR-ToF-AMS and ACSM data during the same sampling periods, we find that the aerosol time series are highly correlated, indicating the

Features in the spectra of gamma-ray bursts

NASA Technical Reports Server (NTRS)

Stanek, Krzysztof Z.; Paczynski, Bohdan; Goodman, Jeremy

1993-01-01

Gravitational lensing of cosmological gamma-ray bursts by objects in the mass range about 10 exp 17 to 10 exp 20 g (femtolensing) may introduce complicated interference patterns that might be interpreted as absorption or emission lines in the bursts' spectra. This phenomenon, if detected, may be used as a unique probe of dark matter in the universe. The BATSE spectral data should allow one to detect such spectral features or to put significant upper limits on the cosmic density of a dark matter component that may be in the femtolensing range. Software to generate theoretical spectra has been developed, and it is accessible over the computer network with anonymous ftp.

Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry

PubMed Central

Polanski, Andrzej; Marczyk, Michal; Pietrowska, Monika; Widlak, Piotr; Polanska, Joanna

2015-01-01

Mixture - modeling of mass spectra is an approach with many potential applications including peak detection and quantification, smoothing, de-noising, feature extraction and spectral signal compression. However, existing algorithms do not allow for automated analyses of whole spectra. Therefore, despite highlighting potential advantages of mixture modeling of mass spectra of peptide/protein mixtures and some preliminary results presented in several papers, the mixture modeling approach was so far not developed to the stage enabling systematic comparisons with existing software packages for proteomic mass spectra analyses. In this paper we present an efficient algorithm for Gaussian mixture modeling of proteomic mass spectra of different types (e.g., MALDI-ToF profiling, MALDI-IMS). The main idea is automated partitioning of protein mass spectral signal into fragments. The obtained fragments are separately decomposed into Gaussian mixture models. The parameters of the mixture models of fragments are then aggregated to form the mixture model of the whole spectrum. We compare the elaborated algorithm to existing algorithms for peak detection and we demonstrate improvements of peak detection efficiency obtained by using Gaussian mixture modeling. We also show applications of the elaborated algorithm to real proteomic datasets of low and high resolution. PMID:26230717

High Pressure Oxygen A-Band Spectra

NASA Astrophysics Data System (ADS)

Drouin, Brian; Sung, Keeyoon; Yu, Shanshan; Lunny, Elizabeth M.; Bui, Thinh Quoc; Okumura, Mitchio; Rupasinghe, Priyanka; Bray, Caitlin; Long, David A.; Hodges, Joseph; Robichaud, David; Benner, D. Chris; Devi, V. Malathy; Hoo, Jiajun

2015-06-01

Composition measurements from remote sensing platforms require knowledge of air mass to better than the desired precision of the composition. Oxygen spectra allow determination of air mass since the mixing ratio of oxygen is fixed. The OCO-2 mission is currently retrieving carbon dioxide concentration using the oxygen A-band for air mass normalization. The 0.25% accuracy desired for the carbon dioxide concentration has pushed the state-of-the-art for oxygen spectroscopy. To produce atmospheric pressure A-band cross-sections with this accuracy requires a sophisticated line-shape model (Galatry or Speed-Dependent) with line mixing (LM) and collision induced absorption (CIA). Models of each of these phenomena exist, but an integrated self-consistent model must be developed to ensure accuracy. This presentation will describe the ongoing effort to parameterize these phenomena on a representative data set created from complementary experimental techniques. The techniques include Fourier transform spectroscopy (FTS), photo-acoustic spectroscopy (PAS) and cavity ring-down spectroscopy (CRDS). CRDS data allow long-pathlength measurements with absolute intensities, providing lineshape information as well as LM and CIA, however the subtleties of the lineshape are diminished in the saturated line-centers. Conversely, the short paths and large dynamic range of the PAS data allow the full lineshape to be discerned, but with an arbitrary intensity axis. Finally, the FTS data provides intermediate paths and consistency across a broad pressure range. These spectra are all modeled with the Labfit software using first the spectral line database HITRAN, and then model values are adjusted and fitted for better agreement with the data.

Raman study of the Hg0.7Cr0.3Sr2CuO4+δ superconductors

NASA Astrophysics Data System (ADS)

Lee, S.-Y.; Chang, B.-Y.; Yang, I.-S.; Gwak, J.-H.; Kim, S.-J.; Choi, J.-H.; Lee, S.-I.; Yakhmi, J. V.; Mandal, J. B.; Bandyopadhyay, B.; Ghosh, B.

1997-08-01

The local environment of the apical oxygens (OA) in the Sr-substituted mercury-based superconductor Hg0.7Cr0.3Sr2CuO4+δ is investigated using Raman spectroscopy. Raman spectra from the Sr-substituted Hg-1201 samples show broad OA A1g double peaks at 553 and 583 cm-l, which are 10 - 20 cm-1 lower than the pristine Hg-1201. The existence of, and lower shift of, the double peaks in the Raman spectra of the Sr-substituted Hg-1201 superconductors indicate changes in the environment of OA in the Sr-substituted mercury-based superconductors.

High mass resolution time of flight mass spectrometer for measuring products in heterogeneous catalysis in highly sensitive microreactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, T.; Jensen, R.; Christensen, M. K.

2012-07-15

We demonstrate a combined microreactor and time of flight system for testing and characterization of heterogeneous catalysts with high resolution mass spectrometry and high sensitivity. Catalyst testing is performed in silicon-based microreactors which have high sensitivity and fast thermal response. Gas analysis is performed with a time of flight mass spectrometer with a modified nude Bayard-Alpert ionization gauge as gas ionization source. The mass resolution of the time of flight mass spectrometer using the ion gauge as ionization source is estimated to m/{Delta}m > 2500. The system design is superior to conventional batch and flow reactors with accompanying product detectionmore » by quadrupole mass spectrometry or gas chromatography not only due to the high sensitivity, fast temperature response, high mass resolution, and fast acquisition time of mass spectra but it also allows wide mass range (0-5000 amu in the current configuration). As a demonstration of the system performance we present data from ammonia oxidation on a Pt thin film showing resolved spectra of OH and NH{sub 3}.« less

High mass resolution time of flight mass spectrometer for measuring products in heterogeneous catalysis in highly sensitive microreactors

NASA Astrophysics Data System (ADS)

Andersen, T.; Jensen, R.; Christensen, M. K.; Pedersen, T.; Hansen, O.; Chorkendorff, I.

2012-07-01

We demonstrate a combined microreactor and time of flight system for testing and characterization of heterogeneous catalysts with high resolution mass spectrometry and high sensitivity. Catalyst testing is performed in silicon-based microreactors which have high sensitivity and fast thermal response. Gas analysis is performed with a time of flight mass spectrometer with a modified nude Bayard-Alpert ionization gauge as gas ionization source. The mass resolution of the time of flight mass spectrometer using the ion gauge as ionization source is estimated to m/Δm > 2500. The system design is superior to conventional batch and flow reactors with accompanying product detection by quadrupole mass spectrometry or gas chromatography not only due to the high sensitivity, fast temperature response, high mass resolution, and fast acquisition time of mass spectra but it also allows wide mass range (0-5000 amu in the current configuration). As a demonstration of the system performance we present data from ammonia oxidation on a Pt thin film showing resolved spectra of OH and NH3.

High mass resolution time of flight mass spectrometer for measuring products in heterogeneous catalysis in highly sensitive microreactors.

PubMed

Andersen, T; Jensen, R; Christensen, M K; Pedersen, T; Hansen, O; Chorkendorff, I

2012-07-01

We demonstrate a combined microreactor and time of flight system for testing and characterization of heterogeneous catalysts with high resolution mass spectrometry and high sensitivity. Catalyst testing is performed in silicon-based microreactors which have high sensitivity and fast thermal response. Gas analysis is performed with a time of flight mass spectrometer with a modified nude Bayard-Alpert ionization gauge as gas ionization source. The mass resolution of the time of flight mass spectrometer using the ion gauge as ionization source is estimated to m/Δm > 2500. The system design is superior to conventional batch and flow reactors with accompanying product detection by quadrupole mass spectrometry or gas chromatography not only due to the high sensitivity, fast temperature response, high mass resolution, and fast acquisition time of mass spectra but it also allows wide mass range (0-5000 amu in the current configuration). As a demonstration of the system performance we present data from ammonia oxidation on a Pt thin film showing resolved spectra of OH and NH(3).

Light curves and spectra from a thermonuclear explosion of a white dwarf merger

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Rossum, Daniel R.; Kashyap, Rahul; Fisher, Robert

Double-degenerate (DD) mergers of carbon–oxygen white dwarfs have recently emerged as a leading candidate for normal Type Ia supernovae (SNe Ia). But, many outstanding questions surround DD mergers, including the characteristics of their light curves and spectra. We have recently identified a spiral instability in the post-merger phase of DD mergers and demonstrated that this instability self-consistently leads to detonation in some cases. We call this the spiral merger SN Ia model. We utilize the SuperNu radiative transfer software to calculate three-dimensional synthetic light curves and spectra of the spiral merger simulation with a system mass of 2.1more » $${M}_{\\odot }$$ from Kashyap et al. Because of their large system masses, both violent and spiral merger light curves are slowly declining. The spiral merger resembles very slowly declining SNe Ia, including SN 2001ay, and provides a more natural explanation for its observed properties than other SN Ia explosion models. Previous synthetic light curves and spectra of violent DD mergers demonstrate a strong dependence on viewing angle, which is in conflict with observations. Here, we demonstrate that the light curves and spectra of the spiral merger are less sensitive to the viewing angle than violent mergers, in closer agreement with observation. We find that the spatial distribution of 56Ni and IMEs follows a characteristic hourglass shape. Finally, we discuss the implications of the asymmetric distribution of 56Ni for the early-time gamma-ray observations of 56Ni from SN 2014J. We suggest that DD mergers that agree with the light curves and spectra of normal SNe Ia will likely require a lower system mass.« less

Light curves and spectra from a thermonuclear explosion of a white dwarf merger

DOE PAGES

van Rossum, Daniel R.; Kashyap, Rahul; Fisher, Robert; ...

2016-08-15

Double-degenerate (DD) mergers of carbon–oxygen white dwarfs have recently emerged as a leading candidate for normal Type Ia supernovae (SNe Ia). But, many outstanding questions surround DD mergers, including the characteristics of their light curves and spectra. We have recently identified a spiral instability in the post-merger phase of DD mergers and demonstrated that this instability self-consistently leads to detonation in some cases. We call this the spiral merger SN Ia model. We utilize the SuperNu radiative transfer software to calculate three-dimensional synthetic light curves and spectra of the spiral merger simulation with a system mass of 2.1more » $${M}_{\\odot }$$ from Kashyap et al. Because of their large system masses, both violent and spiral merger light curves are slowly declining. The spiral merger resembles very slowly declining SNe Ia, including SN 2001ay, and provides a more natural explanation for its observed properties than other SN Ia explosion models. Previous synthetic light curves and spectra of violent DD mergers demonstrate a strong dependence on viewing angle, which is in conflict with observations. Here, we demonstrate that the light curves and spectra of the spiral merger are less sensitive to the viewing angle than violent mergers, in closer agreement with observation. We find that the spatial distribution of 56Ni and IMEs follows a characteristic hourglass shape. Finally, we discuss the implications of the asymmetric distribution of 56Ni for the early-time gamma-ray observations of 56Ni from SN 2014J. We suggest that DD mergers that agree with the light curves and spectra of normal SNe Ia will likely require a lower system mass.« less

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

NASA Astrophysics Data System (ADS)

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.; Day, D. A.; Ortega, A. M.; Hayes, P. L.; Krechmer, J. E.; Chen, Q.; Kuwata, M.; Liu, Y. J.; de Sá, S. S.; McKinney, K.; Martin, S. T.; Hu, M.; Budisulistiorini, S. H.; Riva, M.; Surratt, J. D.; St. Clair, J. M.; Isaacman-Van Wertz, G.; Yee, L. D.; Goldstein, A. H.; Carbone, S.; Brito, J.; Artaxo, P.; de Gouw, J. A.; Koss, A.; Wisthaler, A.; Mikoviny, T.; Karl, T.; Kaser, L.; Jud, W.; Hansel, A.; Docherty, K. S.; Alexander, M. L.; Robinson, N. H.; Coe, H.; Allan, J. D.; Canagaratna, M. R.; Paulot, F.; Jimenez, J. L.

2015-10-01

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accounted by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C5H6O+ (m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine fC5H6O (fC5H6O= C5H6O+/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher fC5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. fC5H6O in IEPOX-SOA is always elevated (12-40 ‰) but varies substantially between locations, which is shown to reflect

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accountedmore » by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C 5H 6O + ( m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine f C5H6O ( f C5H6O= C 5H 6O +/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher f C5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. f C5H6O in IEPOX-SOA is always elevated (12–40 ‰) but varies substantially between locations

Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements

DOE PAGES

Hu, W. W.; Campuzano-Jost, P.; Palm, B. B.; ...

2015-10-23

Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accountedmore » by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C 5H 6O + ( m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine f C5H6O ( f C5H6O= C 5H 6O +/OA) across multiple field, chamber, and source data sets. A background of ~ 1.7 ± 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 ± 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 ± 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 ± 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher f C5H6O (~ 6.5 ± 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. f C5H6O in IEPOX-SOA is always elevated (12–40 ‰) but varies substantially between locations

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

PubMed Central

Wolski, Witold E; Lalowski, Maciej; Jungblut, Peter; Reinert, Knut

2005-01-01

Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. Results We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from . Conclusion The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%. PMID:16102175

A wogonin-rich-fraction of Scutellaria baicalensis root extract exerts chondroprotective effects by suppressing IL-1β-induced activation of AP-1 in human OA chondrocytes

PubMed Central

Khan, Nazir M.; Haseeb, Abdul; Ansari, Mohammad Y.; Haqqi, Tariq M.

2017-01-01

Osteoarthritis (OA) is a common joint disorder with varying degrees of inflammation and sustained oxidative stress. The root extract of Scutellaria baicalensis (SBE) has been used for the treatment of inflammatory and other diseases. Here, we performed activity-guided HPLC-fractionation of SBE, identified the active ingredient(s) and investigated its chondroprotective potential. We found that the Wogonin containing fraction-4 (F4) was the most potent fraction based on its ability to inhibit ROS production and the suppression of catabolic markers including IL-6, COX-2, iNOS, MMP-3, MMP-9, MMP-13 and ADAMTS-4 in IL-1β-treated OA chondrocytes. OA chondrocytes treated with F4 in the presence of IL-1β showed significantly enhanced expression of anabolic genes ACAN and COL2A1. In an in vitro model of cartilage degradation treatment with F4 inhibited s-GAG release from IL-1β-treated human cartilage explants. The inhibitory effect of F4 was not mediated through the inhibition of MAPKs and NF-κB activation but was mediated through the suppression of c-Fos/AP-1 activity at transcriptional and post transcriptional levels in OA chondrocytes. Purified Wogonin mimicked the effects of F4 in IL-1β-stimulated OA chondrocytes. Our data demonstrates that a Wogonin-rich fraction of SBE exert chondroprotective effects through the suppression of c-Fos/AP-1 expression and activity in OA chondrocytes under pathological conditions. PMID:28256567

Reconstructing the δ(18) O of atmospheric water vapour via the CAM epiphyte Tillandsia usneoides: seasonal controls on δ(18) O in the field and large-scale reconstruction of δ(18) Oa.

PubMed

Helliker, Brent R

2014-03-01

Using both oxygen isotope ratios of leaf water (δ(18) OL ) and cellulose (δ(18) OC ) of Tillandsia usneoides in situ, this paper examined how short- and long-term responses to environmental variation and model parameterization affected the reconstruction of the atmospheric water vapour (δ(18) Oa ). During sample-intensive field campaigns, predictions of δ(18) OL matched observations well using a non-steady-state model, but the model required data-rich parameterization. Predictions from the more easily parameterized maximum enrichment model (δ(18) OL-M ) matched observed δ(18) OL and observed δ(18) Oa when leaf water turnover was less than 3.5 d. Using the δ(18) OL-M model and weekly samples of δ(18) OL across two growing seasons in Florida, USA, reconstructed δ(18) Oa was -12.6 ± 0.3‰. This is compared with δ(18) Oa of -12.4 ± 0.2‰ resolved from the growing-season-weighted δ(18) OC . Both of these values were similar to δ(18) Oa in equilibrium with precipitation, -12.9‰. δ(18) Oa was also reconstructed through a large-scale transect with δ(18) OL and the growing-season-integrated δ(18) OC across the southeastern United States. There was considerable large-scale variation, but there was regional, weather-induced coherence in δ(18) Oa when using δ(18) OL . The reconstruction of δ(18) Oa with δ(18) OC generally supported the assumption of δ(18) Oa being in equilibrium with precipitation δ(18) O (δ(18) Oppt ), but the pool of δ(18) Oppt with which δ(18) Oa was in equilibrium - growing season versus annual δ(18) Oppt - changed with latitude. © 2013 John Wiley & Sons Ltd.

Observational and theoretical spectra of supernovae

NASA Astrophysics Data System (ADS)

Wheeler, J. Craig; Swartz, Douglas A.; Harkness, Robert P.

1993-05-01

Progress in nuclear astrophysics by means of quantitative supernova spectroscopy is discussed with special concentration on type Ia, Ib and Ic and on SN 1987A. Spectral calculations continue to support an exploding C/O white dwarf as the best model of a SN Ia. Deflagration model W7 produces good maximum light spectra of SN Ia and seems to have a better composition distribution compared to delayed detonation models, but proper treatment of opacity remains a problem and the physical basis of SN Ia explosions is still not completely understood. All models for SN Ia predict large quantities of 56Co in the ejecta, but it is not clear that observations confirm this. Although the evolutionary origin of SN Ia remains uncertain, there is recent evidence that transfer of hydrogen in a binary system may be involved, as long suspected. There has been progress in comparing dynamical models with the optical/IR spectra of SN 1987A. The evolution of the [OI] λλ6300, 6364 feature and the presence of strong persistent HeI λ10 830 indicate that both the envelope and core material contribute substantially to the formation of emission lines in the nebular phase and that neither the core nor the envelope can be neglected. Blending with nearby hydrogen lines may affect both of these spectral features, thereby complicating the analysis of the lines. The effects of continuum transfer and photoionization have been included and are under study. The discrepancies between theoretical and observed spectra are due primarily to the one-dimensional hydrodynamic models. The spectral data are not consistent with the high density ``spike'' (in radial coordinate) of the core material that is predicted by all such models. Analysis of the light curves of SN Ib and SN Ic supernovae implies that there are significant differences in their physical properties. Some SN Ib have considerably more ejecta mass than SN Ic events. SN Ib require He-rich atmospheres to produce the observed strong optical lines of

Observational and theoretical spectra of supernovae

NASA Astrophysics Data System (ADS)

Craig Wheeler, J.; Swartz, Douglas A.; Harkness, Robert P.

1993-05-01

Progress in nuclear astrophysics by means of quantitative supernova spectroscopy is discussed with special concentration on type Ia, Ib and Ic and on SN 1987A. Spectral calculations continue to support an exploding C/O white dwarf as the best model of a SN Ia. Deflagration model W7 produces good maximum light spectra of SN Ia and seems to have a better composition distribution compared to delayed detonation models, but proper treatment of opacity remains a problem and the physical basis of SN Ia explosions is still not completely understood. All models for SN Ia predict large quantities of 56Co in the ejecta, but it is not clear that observations confirm this. Although the evolutionary origin of SN Ia remains uncertain, there is recent evidence that transfer of hydrogen in a binary system may be involved, as long suspected. There has been progress in comparing dynamical models with the optical/IR spectra of SN 1987A. The evolution of the [OI] λλ6300, 6364 feature and the presence of strong persistent HeI λ10 830 indicate that both the envelope and core material contribute substantially to the formation of emission lines in the nebular phase and that neither the core nor the envelope can be neglected. Blending with nearby hydrogen lines may affect both of these spectral features, thereby complicating the analysis of the lines. The effects of continuum transfer and photoionization have been included and are under study. The discrepancies between theoretical and observed spectra are due primarily to the one-dimensional hydrodynamic models. The spectral data are not consistent with the high density “spike” (in radial coordinate) of the core material that is predicted by all such models. Analysis of the light curves of SN Ib and SN Ic supernovae implies that there are significant differences in their physical properties. Some SN Ib have considerably more ejecta mass than SN Ic events. SN Ib require He-rich atmospheres to produce the observed strong optical lines

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kou, Qiang; Wu, Si; Tolić, Nikola

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result inmore » billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.« less

Mutual information optimization for mass spectra data alignment.

PubMed

Zoppis, Italo; Gianazza, Erica; Borsani, Massimiliano; Chinello, Clizia; Mainini, Veronica; Galbusera, Carmen; Ferrarese, Carlo; Galimberti, Gloria; Sorbi, Sandro; Borroni, Barbara; Magni, Fulvio; Antoniotti, Marco; Mauri, Giancarlo

2012-01-01

"Signal" alignments play critical roles in many clinical setting. This is the case of mass spectrometry data, an important component of many types of proteomic analysis. A central problem occurs when one needs to integrate (mass spectrometry) data produced by different sources, e.g., different equipment and/or laboratories. In these cases some form of "data integration'" or "data fusion'" may be necessary in order to discard some source specific aspects and improve the ability to perform a classification task such as inferring the "disease classes'" of patients. The need for new high performance data alignments methods is therefore particularly important in these contexts. In this paper we propose an approach based both on an information theory perspective, generally used in a feature construction problem, and on the application of a mathematical programming task (i.e. the weighted bipartite matching problem). We present the results of a competitive analysis of our method against other approaches. The analysis was conducted on data from plasma/ethylenediaminetetraacetic acid (EDTA) of "control" and Alzheimer patients collected from three different hospitals. The results point to a significant performance advantage of our method with respect to the competing ones tested.

Copernicus ultraviolet observations of mass-loss effects in O and B stars

NASA Technical Reports Server (NTRS)

Snow, T. P., Jr.; Morton, D. C.

1976-01-01

Far-UV spectra of 47 O, B, and A stars obtained with the Copernicus satellite are examined for P Cygni profiles. For all 40 stars with displaced absorption lines, values are given for the velocities of the short-wavelength edge, the line center, and the emission peak (if present). Parts of the spectra of 42 stars are reproduced, evidence for mass motions in ground-based spectra is discussed, and the best available data are summarized on the wavelengths and oscillator strengths of most lines likely to show mass-loss effects in either visual or UV spectra. The main conclusions are that: (1) the far-UV transitions, especially resonance lines, show that mass flow is present over a much wider group of stars than revealed by visible data on subordinate lines; (2) most of the line shifts imply mass motion away from the stars; (3) mass flow occurs in all but one star brighter than a bolometric magnitude of -6.0; and (4) the observed terminal velocities generally exhibit no significant correlation with temperature, luminosity, gravity, rotational velocity, or line strength.

AN ONLINE CATALOG OF CATACLYSMIC VARIABLE SPECTRA FROM THE FAR-ULTRAVIOLET SPECTROSCOPIC EXPLORER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godon, Patrick; Sion, Edward M.; Levay, Karen

2012-12-15

We present an online catalog containing spectra and supporting information for cataclysmic variables that have been observed with the Far-Ultraviolet Spectroscopic Explorer (FUSE). For each object in the catalog we list some of the basic system parameters such as (R.A., decl.), period, inclination, and white dwarf mass, as well as information on the available FUSE spectra: data ID, observation date and time, and exposure time. In addition, we provide parameters needed for the analysis of the FUSE spectra such as the reddening E(B - V), distance, and state (high, low, intermediate) of the system at the time it was observed.more » For some of these spectra we have carried out model fits to the continuum with synthetic stellar and/or disk spectra using the codes TLUSTY and SYNSPEC. We provide the parameters obtained from these model fits; this includes the white dwarf temperature, gravity, projected rotational velocity, and elemental abundances of C, Si, S, and N, together with the disk mass accretion rate, the resulting inclination, and model-derived distance (when unknown). For each object one or more figures are provided (as gif files) with line identification and model fit(s) when available. The FUSE spectra and the synthetic spectra are directly available for download as ASCII tables. References are provided for each object, as well as for the model fits. In this article we present 36 objects, and additional ones will be added to the online catalog in the future. In addition to cataclysmic variables, we also include a few related objects, such as a wind-accreting white dwarf, a pre-cataclysmic variable, and some symbiotics.« less

Identifying microbially mediated transformations of DOC across season and tide from simultaneous changes in whole community gene expression and in mass spectra generated by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS)

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Medeiros, P. M.; Moran, M. A.; Song, C.; Whitman, W. B.; Washington, B.; Yu, M.; Lee, J.

2017-12-01

Despite the advent of methods enabling high resolution characterization of metabolic activity and of organic matter, linking microbial metabolism to organic matter transformations remains a challenge. By sequencing metatranscriptomes and using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) to characterize organic matter (OM) at the beginning and at the end of incubations of estuarine water across tide and season, we sought to link observed a changes in OM composition to microbial metabolism. We used linear models and K means clustering to identify clusters of genes that responded coherently across season, which accounted for most of the variability in gene expression, over tidal regime, which explained the majority of the remaining variation, and over time during the 24 hour incubations. We used an approach from the field of signal processing, that to our knowledge has not been used to analyze FTICR-MS data, to identify formulae of compounds that changed in concentration during the incubations. This approach, based on the discrete wavelet transform (DWT), allowed us to overcome some of the challenges associated with analyzing FTICR-MS data: variable ionization of organic compounds, signal suppression by high concentration compounds, and uncertainty about how to normalize changes across spectra. We were able to link clusters of metabolic and transporter genes to changes in OM composition, and uniquely identify genes based on their cross correlation with changes in FTICR mass spectra. Our approach for analyzing FTICR- MS data enables more robust inference about OM transformations, and linking high resolution changes in gene expression and in OM data during incubations represents an important step toward formulating models of microbial metabolism relevant for predicting biogeochemically relevant C fluxes.

The 2nd order focusing sector field type TOF mass analyzer with an orthogonal ion acceleration for LC-IMS-MS.

PubMed

Poteshin, S S; Zarakovsky, A I

2017-03-15

Original orthogonal acceleration (OA) electrostatic sector time of flight (TOF) mass analyzer is proposed those allows the second order focusing of time of flight by initial ions position. Resolving power aberration limit exceeding 80,000 FW (full width mass peak) was shown to be obtainable for mass analyzer with the total length of flight L=133.2cm, the average ion energy 3700V and the ion energy spread of 2.5% on the entrance of sector field. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition.

PubMed

Bruderer, Tobias; Varesio, Emmanuel; Hidasi, Anita O; Duchoslav, Eva; Burton, Lyle; Bonner, Ron; Hopfgartner, Gérard

2018-03-01

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H] + and 483 in negative mode [M-H] - . MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously

Modeling the chemistry of plasma polymerization using mass spectrometry.

PubMed

Ihrig, D F; Stockhaus, J; Scheide, F; Winkelhake, Oliver; Streuber, Oliver

2003-04-01

The goal of the project is a solvent free painting shop. The environmental technologies laboratory is developing processes of plasma etching and polymerization. Polymerized thin films are first-order corrosion protection and primer for painting. Using pure acetylene we get very nice thin films which were not bonded very well. By using air as bulk gas it is possible to polymerize, in an acetylene plasma, well bonded thin films which are stable first-order corrosion protections and good primers. UV/Vis spectroscopy shows nitrogen oxide radicals in the emission spectra of pure nitrogen and air. But nitrogen oxide is fully suppressed in the presence of acetylene. IR spectroscopy shows only C=O, CH(2) and CH(3) groups but no nitrogen species. With the aid of UV/Vis spectra and the chemistry of ozone formation it is possible to define reactive traps and steps, molecule depletion and processes of proton scavenging and proton loss. Using a numerical model it is possible to evaluate these processes and to calculate theoretical mass spectra. Adjustment of theoretical mass spectra to real measurements leads to specific channels of polymerization which are driven by radicals especially the acetyl radical. The estimated theoretical mass spectra show the specific channels of these chemical processes. It is possible to quantify these channels. This quantification represents the mass flow through this chemical system. With respect to these chemical processes it is possible to have an idea of pollutant production processes.

Ion Mobility Mass Spectrometry for Extracting Spectra of N-Glycans Directly from Incubation Mixtures Following Glycan Release: Application to Glycans from Engineered Glycoforms of Intact, Folded HIV gp120

NASA Astrophysics Data System (ADS)

Harvey, David J.; Sobott, Frank; Crispin, Max; Wrobel, Antoni; Bonomelli, Camille; Vasiljevic, Snezana; Scanlan, Christopher N.; Scarff, Charlotte A.; Thalassinos, Konstantinos; Scrivens, James H.

2011-03-01

The analysis of glycosylation from native biological sources is often frustrated by the low abundances of available material. Here, ion mobility combined with electrospray ionization mass spectrometry have been used to extract the spectra of N-glycans released with PNGase F from a serial titration of recombinantly expressed envelope glycoprotein, gp120, from the human immunodeficiency virus (HIV). Analysis was also performed on gp120 expressed in the α-mannosidase inhibitor, and in a matched mammalian cell line deficient in GlcNAc transferase I. Without ion mobility separation, ESI spectra frequently contained no observable ions from the glycans whereas ions from other compounds such as detergents and residual buffer salts were abundant. After ion mobility separation on a Waters T-wave ion mobility mass spectrometer, the N-glycans fell into a unique region of the ion mobility/ m/z plot allowing their profiles to be extracted with good signal:noise ratios. This method allowed N-glycan profiles to be extracted from crude incubation mixtures with no clean-up even in the presence of surfactants such as NP40. Furthermore, this technique allowed clear profiles to be obtained from sub-microgram amounts of glycoprotein. Glycan profiles were similar to those generated by MALDI-TOF MS although they were more susceptible to double charging and fragmentation. Structural analysis could be accomplished by MS/MS experiments in either positive or negative ion mode but negative ion mode gave the most informative spectra and provided a reliable approach to the analysis of glycans from small amounts of glycoprotein.

Radio synchrotron spectra of star-forming galaxies

NASA Astrophysics Data System (ADS)

Klein, U.; Lisenfeld, U.; Verley, S.

2018-03-01

We investigated the radio continuum spectra of 14 star-forming galaxies by fitting nonthermal (synchrotron) and thermal (free-free) radiation laws. The underlying radio continuum measurements cover a frequency range of 325 MHz to 24.5 GHz (32 GHz in case of M 82). It turns out that most of these synchrotron spectra are not simple power-laws, but are best represented by a low-frequency spectrum with a mean slope αnth = 0.59 ± 0.20 (Sν ∝ ν-α), and by a break or an exponential decline in the frequency range of 1-12 GHz. Simple power-laws or mildly curved synchrotron spectra lead to unrealistically low thermal flux densities, and/or to strong deviations from the expected optically thin free-free spectra with slope αth = 0.10 in the fits. The break or cutoff energies are in the range of 1.5-7 GeV. We briefly discuss the possible origin of such a cutoff or break. If the low-frequency spectra obtained here reflect the injection spectrum of cosmic-ray electrons, they comply with the mean spectral index of Galactic supernova remnants. A comparison of the fitted thermal flux densities with the (foreground-corrected) Hα fluxes yields the extinction, which increases with metallicity. The fraction of thermal emission is higher than believed hitherto, especially at high frequencies, and is highest in the dwarf galaxies of our sample, which we interpret in terms of a lack of containment in these low-mass systems, or a time effect caused by a very young starburst.

Predicting charmonium and bottomonium spectra with a quark harmonic oscillator

NASA Technical Reports Server (NTRS)

Norbury, J. W.; Badavi, F. F.; Townsend, L. W.

1986-01-01

The nonrelativistic quark model is applied to heavy (nonrelativistic) meson (two-body) systems to obtain sufficiently accurate predictions of the spin-averaged mass levels of the charmonium and bottomonium spectra as an example of the three-dimensional harmonic oscillator. The present calculations do not include any spin dependence, but rather, mass values are averaged for different spins. Results for a charmed quark mass value of 1500 MeV/c-squared show that the simple harmonic oscillator model provides good agreement with experimental values for 3P states, and adequate agreement for the 3S1 states.

SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes.

PubMed

David, Matthieu; Fertin, Guillaume; Rogniaux, Hélène; Tessier, Dominique

2017-08-04

The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.

Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques.

PubMed

Peng, Wen-Ping; Chou, Szu-Wei; Patil, Avinash A

2014-07-21

Large biomolecules and bioparticles play a vital role in biology, chemistry, biomedical science and physics. Mass is a critical parameter for the characterization of large biomolecules and bioparticles. To achieve mass analysis, choosing a suitable ion source is the first step and the instruments for detecting ions, mass analyzers and detectors should also be considered. Abundant mass spectrometric techniques have been proposed to determine the masses of large biomolecules and bioparticles and these techniques can be divided into two categories. The first category measures the mass (or size) of intact particles, including single particle quadrupole ion trap mass spectrometry, cell mass spectrometry, charge detection mass spectrometry and differential mobility mass analysis; the second category aims to measure the mass and tandem mass of biomolecular ions, including quadrupole ion trap mass spectrometry, time-of-flight mass spectrometry, quadrupole orthogonal time-of-flight mass spectrometry and orbitrap mass spectrometry. Moreover, algorithms for the mass and stoichiometry assignment of electrospray mass spectra are developed to obtain accurate structure information and subunit combinations.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

PubMed

Kou, Qiang; Wu, Si; Tolic, Nikola; Paša-Tolic, Ljiljana; Liu, Yunlong; Liu, Xiaowen

2017-05-01

Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. http://proteomics.informatics.iupui.edu/software/topmg/. xwliu@iupui.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Characterization of a real-time tracer for Isoprene Epoxydiols-derived Secondary Organic Aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements