Heavy ion fragmentation experiments at the bevatron

NASA Technical Reports Server (NTRS)

Heckman, H. H.

1976-01-01

Collaborative research efforts to study the fragmentation processes of heavy nuclei in matter using heavy ion beams of the Bevatron/Bevalac are described. The goal of the program is to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Effects were also made to: (a) study processes of heavy nuclei in matter, (b) measure the total and partial production cross section for all isotopes, (c) test the applicability of high energy multiparticle interaction theory to nuclear fragmentation, (d) apply the cross section data and fragmentation probabilities to cosmic ray transport theory, and (e) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross-sections.

Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS.

PubMed

Lou, Xianwen; Li, Bao; de Waal, Bas F M; Schill, Jurgen; Baker, Matthew B; Bovee, Ralf A A; van Dongen, Joost L J; Milroy, Lech-Gustav; Meijer, E W

2018-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo-molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI-induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges. Copyright © 2017 John Wiley & Sons, Ltd.

Practical application of in silico fragmentation based residue screening with ion mobility high-resolution mass spectrometry.

PubMed

Kaufmann, Anton; Butcher, Patrick; Maden, Kathry; Walker, Stephan; Widmer, Mirjam

2017-07-15

A screening concept for residues in complex matrices based on liquid chromatography coupled to ion mobility high-resolution mass spectrometry LC/IMS-HRMS is presented. The comprehensive four-dimensional data (chromatographic retention time, drift time, mass-to-charge and ion abundance) obtained in data-independent acquisition (DIA) mode was used for data mining. An in silico fragmenter utilizing a molecular structure database was used for suspect screening, instead of targeted screening with reference substances. The utilized data-independent acquisition mode relies on the MS E concept; where two constantly alternating HRMS scans (low and high fragmentation energy) are acquired. Peak deconvolution and drift time alignment of ions from the low (precursor ion) and high (product ion) energy scan result in relatively clean product ion spectra. A bond dissociation in silico fragmenter (MassFragment) supplied with mol files of compounds of interest was used to explain the observed product ions of each extracted candidate component (chromatographic peak). Two complex matrices (fish and bovine liver extract) were fortified with 98 veterinary drugs. Out of 98 screened compounds 94 could be detected with the in silico based screening approach. The high correlation among drift time and m/z value of equally charged ions was utilized for an orthogonal filtration (ranking). Such an orthogonal ion mobility based filter removes multiply charged ions (e.g. peptides and proteins from the matrix) as well as noise and artefacts. Most significantly, this filtration dramatically reduces false positive findings but hardly increases false negative findings. The proposed screening approach may offer new possibilities for applications where reference compounds are hardly or not at all commercially available. Such areas may be the analysis of metabolites of drugs, pyrrolizidine alkaloids, marine toxins, derivatives of sildenafil or novel designer drugs (new psychoactive substances

Richness and Abundance of Ichneumonidae in a Fragmented Tropical Rain Forest.

PubMed

Ruiz-Guerra, B; Hanson, P; Guevara, R; Dirzo, R

2013-10-01

Because of the magnitude of land use currently occurring in tropical regions, the local loss of animal species due to habitat fragmentation has been widely studied, particularly in the case of vertebrates. Many invertebrate groups and the ichneumonid wasps in particular, however, have been poorly studied in this context, despite the fact that they are one of the most species-rich groups and play an important role as regulators of other insect populations. Here, we recorded the taxonomic composition of ichneumonid parasitoids and assessed their species richness, abundance, similarity, and dominance in the Los Tuxtlas tropical rain forest, Mexico. We compared two forest types: a continuous forest (640 ha) and a forest fragment (19 ha). We sampled ichneumonids using four malaise traps in both forest types during the dry (September-October) and rainy (March-April) seasons. A total of 104 individuals of Ichneumonidae belonging to 11 subfamilies, 18 genera, and 42 species were collected in the continuous forest and 11 subfamilies, 15 genera, and 24 species were collected in the forest fragment. Species richness, abundance, and diversity of ichneumonids were greater in the continuous forest than in the forest fragment. We did not detect differences between seasons. Species rank/abundance curves showed that the ichneumonid community between the forest types was different. Species similarity between forest types was low. The most dominant species in continuous forest was Neotheronia sp., whereas in the forest fragment, it was Orthocentrus sp. Changes in the ichneumonid wasp community may compromise important tropical ecosystem processes.

Negative Ion CID Fragmentation of O-linked Oligosaccharide Aldoses—Charge Induced and Charge Remote Fragmentation

NASA Astrophysics Data System (ADS)

Doohan, Roisin A.; Hayes, Catherine A.; Harhen, Brendan; Karlsson, Niclas Göran

2011-06-01

Collision induced dissociation (CID) fragmentation was compared between reducing and reduced sulfated, sialylated, and neutral O-linked oligosaccharides. It was found that fragmentation of the [M - H]- ions of aldoses with acidic residues gave unique Z-fragmentation of the reducing end GalNAc containing the acidic C-6 branch, where the entire C-3 branch was lost. This fragmentation pathway, which is not seen in the alditols, showed that the process involved charge remote fragmentation catalyzed by a reducing end acidic anomeric proton. With structures containing sialic acid on both the C-3 and C-6 branch, the [M - H]- ions were dominated by the loss of sialic acid. This fragmentation pathway was also pronounced in the [M - 2H]2- ions revealing both the C-6 Z-fragment plus its complementary C-3 C-fragment in addition to glycosidic and cross ring fragmentation. This generation of the Z/C-fragment pairs from GalNAc showed that the charges were not participating in their generation. Fragmentation of neutral aldoses showed pronounced Z-fragmentation believed to be generated by proton migration from the C-6 branch to the negatively charged GalNAc residue followed by charge remote fragmentation similar to the acidic oligosaccharides. In addition, A-type fragments generated by charge induced fragmentation of neutral oligosaccharides were observed when the charge migrated from C-1 of the GalNAc to the GlcNAc residue followed by rearrangement to accommodate the 0,2A-fragmentation. LC-MS also showed that O-linked aldoses existed as interchangeable α/β pyranose anomers, in addition to a third isomer (25% of the total free aldose) believed to be the furanose form.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

Analysis of multi-fragmentation reactions induced by relativistic heavy ions using the statistical multi-fragmentation model

NASA Astrophysics Data System (ADS)

Ogawa, T.; Sato, T.; Hashimoto, S.; Niita, K.

2013-09-01

The fragmentation cross-sections of relativistic energy nucleus-nucleus collisions were analyzed using the statistical multi-fragmentation model (SMM) incorporated with the Monte-Carlo radiation transport simulation code particle and heavy ion transport code system (PHITS). Comparison with the literature data showed that PHITS-SMM reproduces fragmentation cross-sections of heavy nuclei at relativistic energies better than the original PHITS by up to two orders of magnitude. It was also found that SMM does not degrade the neutron production cross-sections in heavy ion collisions or the fragmentation cross-sections of light nuclei, for which SMM has not been benchmarked. Therefore, SMM is a robust model that can supplement conventional nucleus-nucleus reaction models, enabling more accurate prediction of fragmentation cross-sections.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments.

PubMed

Harvey, David J; Seabright, Gemma E; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man 8 GlcNAc 2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments

NASA Astrophysics Data System (ADS)

Harvey, David J.; Seabright, Gemma E.; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B.

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. [Figure not available: see fulltext.

Multi-scale models of grassland passerine abundance in a fragmented system in Wisconsin

USGS Publications Warehouse

Renfrew, R.B.; Ribic, C.A.

2008-01-01

Fragmentation of grasslands has been implicated in grassland bird population declines. Multi-scale models are being increasingly used to assess potential factors that influence grassland bird presence, abundance, and productivity. However, studies rarely assess fragmentation metrics, and seldom evaluate more than two scales or interactions among scales. We evaluated the relative importance of characteristics at multiple scales to patterns in relative abundance of Savannah Sparrow (Passerculus sandwichensis), Grasshopper Sparrow (Ammodramus savannarum), Eastern Meadowlark (Sturnella magna), and Bobolink (Dolichonyx oryzivorus). We surveyed birds in 74 southwestern Wisconsin pastures from 1997 to 1999 and compared models with explanatory variables from multiple scales: within-patch vegetation structure (microhabitat), patch (macrohabitat), and three landscape extents. We also examined interactions between macrohabitat and landscape factors. Core area of pastures was an important predictor of relative abundance, and composition of the landscape was more important than configuration. Relative abundance was frequently higher in pastures with more core area and in landscapes with more grassland and less wooded area. The direction and strength of the effect of core pasture size on relative abundance changed depending on amount of wooded area in the landscape. Relative abundance of grassland birds was associated with landscape variables more frequently at the 1200-m scale than at smaller scales. To develop better predictive models, parameters at multiple scales and their interactive effects should be included, and results should be evaluated in the context of microhabitat variability, landscape composition, and fragmentation in the study area. ?? 2007 Springer Science+Business Media B.V.

Validation of Geant4 fragmentation for Heavy Ion Therapy

NASA Astrophysics Data System (ADS)

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo; Folger, Gunter; Incerti, Sebastien; Ivanchenko, Vladimir; Koi, Tatsumi; Mancusi, Davide; Pandola, Luciano; Romano, Francesco; Rosenfeld, Anatoly B.; Guatelli, Susanna

2017-10-01

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ∼ 70 % of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. This work investigates the accuracy of three different nuclear fragmentation models available in the Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ∼ 5 and ∼ 35 % with experimental measurements, the QMD using the "Frag" option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.

Validation of Geant4 fragmentation for Heavy Ion Therapy

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

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ~70% of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. Here, this work investigates the accuracy of three different nuclear fragmentation models available in themore » Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ~5 and ~35% with experimental measurements, the QMD using the “Frag” option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.« less

Validation of Geant4 fragmentation for Heavy Ion Therapy

DOE PAGES

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo; ...

2017-07-12

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ~70% of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. Here, this work investigates the accuracy of three different nuclear fragmentation models available in themore » Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ~5 and ~35% with experimental measurements, the QMD using the “Frag” option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.« less

Small-angle fragmentation of carbon ions at 0.6 GeV/n: A comparison with models of ion-ion interactions

DOE PAGES

Krutenkova, A. P.; Abramov, B. M.; Alekseev, P. N.; ...

2015-05-29

Momentum distributions of hydrogen and helium isotopes from ¹²C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. The differential cross sections cover six orders of magnitude. The distributions measured are compared tomore » the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

Small-angle fragmentation of carbon ions at 0.6 GeV/n. A comparison with models of ion-ion interactions

DOE PAGES

Krutenkova, Anna P.; Abramov, B. M.; Alekseev, P. N.; ...

2015-05-29

The momentum distributions of hydrogen and helium isotopes from 12C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. Moreover, the differential cross sections cover six orders of magnitude. The distributions measured aremore » compared to the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources

NASA Astrophysics Data System (ADS)

Newsome, G. Asher; Ackerman, Luke K.; Johnson, Kevin J.

2016-01-01

Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources.

PubMed

Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

2016-01-01

Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

Edge-interior differences in the species richness and abundance of drosophilids in a semideciduous forest fragment.

PubMed

Penariol, Leiza V; Madi-Ravazzi, Lilian

2013-12-01

Habitat fragmentation is the main cause of biodiversity loss, as remnant fragments are exposed to negative influences that include edge effects, prevention of migration, declines in effective population sizes, loss of genetic variability and invasion of exotic species. The Drosophilidae (Diptera), especially species of the genus Drosophila, which are highly sensitive to environmental variation, have been used as bioindicators. A twelve-month field study was conducted to evaluate the abundance and richness of drosophilids in an edge-interior transect in a fragment of semideciduous forest in São Paulo State, Brazil. One objective of the study was to evaluate the applied methodology with respect to its potential use in future studies addressing the monitoring and conservation of threatened areas. The species abundance along the transect showed a clear gradient, with species associated with disturbed environments, such as Drosophila simulans, Scaptodrosophila latifasciaeformis and Zaprionus indianus, being collected at the fragment edge and the species D. willistoni and D. mediostriata being found in the fragment's interior. Replacement of these species occurred at approximately 60 meters from the edge, which may be a reflection of edge effects on species abundance and richness because the species found within the habitat fragment are more sensitive to variations in temperature and humidity than those sampled near the edge. The results support the use of this methodology in studies on environmental impacts.

Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

NASA Astrophysics Data System (ADS)

Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

2015-12-01

In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

Fragmentation studies of relativistic iron ions using plastic nuclear track detectors.

PubMed

Scampoli, P; Durante, M; Grossi, G; Manti, L; Pugliese, M; Gialanella, G

2005-01-01

We measured fluence and fragmentation of high-energy (1 or 5 A GeV) 56Fe ions accelerated at the Alternating Gradient Synchrotron or at the NASA Space Radiation Laboratory (Brookhaven National Laboratory, NY, USA) using solid-state CR-39 nuclear track detectors. Different targets (polyethylene, PMMA, C, Al, Pb) were used to produce a large spectrum of charged fragments. CR-39 plastics were exposed both in front and behind the shielding block (thickness ranging from 5 to 30 g/cm2) at a normal incidence and low fluence. The radiation dose deposited by surviving Fe ions and charged fragments was measured behind the shield using an ionization chamber. The distribution of the measured track size was exploited to distinguish the primary 56Fe ions tracks from the lighter fragments. Measurements of projectile's fluence in front of the shield were used to determine the dose per incident particle behind the block. Simultaneous measurements of primary 56Fe ion tracks in front and behind the shield were used to evaluate the fraction of surviving iron projectiles and the total charge-changing fragmentation cross-section. These physical measurements will be used to characterize the beam used in parallel biological experiments. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Protons from carbon ion fragmentation at 0.3–2.0 GeV/nucleon: Comparison with models of ion-ion interactions

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

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.

2015-05-15

Yields of protons at 3.5° from carbon ion fragmentation at energies of T{sub 0} = 0.3, 0.6, 0.95, and 2.0 GeV/nucleon on a Be target were measured in the FRAGM experiment at TWA-ITEP heavy-ion facility. Proton momentum spectra cover both the region of the fragmentation maximum and the cumulative region. The differential cross sections span six orders of its magnitude. The spectra are compared with the predictions of four models of ion-ion interactions: LAQGSM03.03, SHIELD-HIT, QMD, and BC.

The impact of habitat fragmentation on tsetse abundance on the plateau of eastern Zambia.

PubMed

Ducheyne, E; Mweempwa, C; De Pus, C; Vernieuwe, H; De Deken, R; Hendrickx, G; Van den Bossche, P

2009-09-01

Tsetse-transmitted human or livestock trypanosomiasis is one of the major constraints to rural development in sub-Saharan Africa. The epidemiology of the disease is determined largely by tsetse fly density. A major factor, contributing to tsetse population density is the availability of suitable habitat. In large parts of Africa, encroachment of people and their livestock resulted in a destruction and fragmentation of such suitable habitat. To determine the effect of habitat change on tsetse density a study was initiated in a tsetse-infested zone of eastern Zambia. The study area represents a gradient of habitat change, starting from a zone with high levels of habitat destruction and ending in an area where livestock and people are almost absent. To determine the distribution and density of the fly, tsetse surveys were conducted throughout the study area in the dry and in the rainy season. Landsat ETM+ imagery covering the study area were classified into four land cover classes (munga, miombo, agriculture and settlements) and two auxiliary spectral classes (clouds and shadow) using a Gaussian Maximum Likelihood Classifier. The classes were regrouped into natural vegetation and agricultural zone. The binary images were overlaid with hexagons to obtain the spatial spectrum of spatial pattern. Hexagonal coverage was selected because of its compact and regular form. To identify scale-specific spatial patterns and associated entomological phenomena, the size of the hexagonal coverage was varied (250 and 500 m). Per coverage, total class area, mean patch size, number of patches and patch size standard deviation were used as fragmentation indices. Based on the fragmentation index values, the study zone was classified using a Partitioning Around Mediods (PAM) method. The number of classes was determined using the Wilks' lambda coefficient. To determine the impact of habitat fragmentation on tsetse abundance, the correlation between the fragmentation indices and the index

Angular distributions and mechanisms of fragmentation by relativistic heavy ions

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

Stoenner, R.W.; Haustein, P.E.; Cumming, J.B.

1984-07-23

Angular distributions of massive fragments from relativistic heavy-ion interactions are reported. Sideward peaking is observed for the light fragment /sup 37/Ar, from 25-GeV /sup 12/C+Au, while the distribution for /sup 127/Xe is strongly forward peaked. Conflicts of these observations and other existing data with predictions of models for the fragmentation process are discussed.

Edge disturbance drives liana abundance increase and alteration of liana-host tree interactions in tropical forest fragments.

PubMed

Campbell, Mason J; Edwards, Will; Magrach, Ainhoa; Alamgir, Mohammed; Porolak, Gabriel; Mohandass, D; Laurance, William F

2018-04-01

Closed-canopy forests are being rapidly fragmented across much of the tropical world. Determining the impacts of fragmentation on ecological processes enables better forest management and improves species-conservation outcomes. Lianas are an integral part of tropical forests but can have detrimental and potentially complex interactions with their host trees. These effects can include reduced tree growth and fecundity, elevated tree mortality, alterations in tree-species composition, degradation of forest succession, and a substantial decline in forest carbon storage. We examined the individual impacts of fragmentation and edge effects (0-100-m transect from edge to forest interior) on the liana community and liana-host tree interactions in rainforests of the Atherton Tableland in north Queensland, Australia. We compared the liana and tree community, the traits of liana-infested trees, and determinants of the rates of tree infestation within five forest fragments (23-58 ha in area) and five nearby intact-forest sites. Fragmented forests experienced considerable disturbance-induced degradation at their edges, resulting in a significant increase in liana abundance. This effect penetrated to significantly greater depths in forest fragments than in intact forests. The composition of the liana community in terms of climbing guilds was significantly different between fragmented and intact forests, likely because forest edges had more small-sized trees favoring particular liana guilds which preferentially use these for climbing trellises. Sites that had higher liana abundances also exhibited higher infestation rates of trees, as did sites with the largest lianas. However, large lianas were associated with low-disturbance forest sites. Our study shows that edge disturbance of forest fragments significantly altered the abundance and community composition of lianas and their ecological relationships with trees, with liana impacts on trees being elevated in fragments relative

Novel fragmentation pathways of anionic adducts of steroids formed by electrospray anion attachment involving regioselective attachment, regiospecific decompositions, charge-induced pathways, and ion-dipole complex intermediates.

PubMed

Rannulu, Nalaka S; Cole, Richard B

2012-09-01

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion](-) adducts of these steroids revealed that fluoride adduct [M + F](-) precursors first lose HF to produce [M - H](-) and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d(4)-pregnenolone, are also discussed.

Novel Fragmentation Pathways of Anionic Adducts of Steroids Formed by Electrospray Anion Attachment Involving Regioselective Attachment, Regiospecific Decompositions, Charge-Induced Pathways, and Ion-Dipole Complex Intermediates

NASA Astrophysics Data System (ADS)

Rannulu, Nalaka S.; Cole, Richard B.

2012-09-01

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion]- adducts of these steroids revealed that fluoride adduct [M + F]- precursors first lose HF to produce [M - H]- and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d4-pregnenolone, are also discussed.

Incorporation of the statistical multi-fragmentation model in PHITS and its application for simulation of fragmentation by heavy ions and protons

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

2014-06-01

The fragmentation reactions of relativistic-energy nucleus-nucleus and proton-nucleus collisions were simulated using the Statistical Multi-fragmentation Model (SMM) incorporated with the Particle and Heavy Ion Transport code System (PHITS). The comparisons of calculated cross-sections with literature data showed that PHITS-SMM predicts the fragmentation cross-sections of heavy nuclei up to two orders of magnitude more accurately than PHITS for heavy-ion-induced reactions. For proton-induced reactions, noticeable improvements are observed for interactions of the heavy target with protons at an energy greater than 1 GeV. Therefore, consideration for multi-fragmentation reactions is necessary for the accurate simulation of energetic fragmentation reactions of heavy nuclei.

Proposal for a common nomenclature for fragment ions in mass spectra of lipids

PubMed Central

Hartler, Jürgen; Christiansen, Klaus; Gallego, Sandra F.; Peng, Bing; Ahrends, Robert

2017-01-01

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines. PMID:29161304

Proposal for a common nomenclature for fragment ions in mass spectra of lipids.

PubMed

Pauling, Josch K; Hermansson, Martin; Hartler, Jürgen; Christiansen, Klaus; Gallego, Sandra F; Peng, Bing; Ahrends, Robert; Ejsing, Christer S

2017-01-01

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

Ion-polycyclic aromatic hydrocarbon collisions: kinetic energy releases for specific fragmentation channels

NASA Astrophysics Data System (ADS)

Reitsma, G.; Zettergren, H.; Boschman, L.; Bodewits, E.; Hoekstra, R.; Schlathölter, T.

2013-12-01

We report on 30 keV He2 + collisions with naphthalene (C10H8) molecules, which leads to very extensive fragmentation. To unravel such complex fragmentation patterns, we designed and constructed an experimental setup, which allows for the determination of the full momentum vector by measuring charged collision products in coincidence in a recoil ion momentum spectrometer type of detection scheme. The determination of fragment kinetic energies is found to be considerably more accurate than for the case of mere coincidence time-of-flight spectrometers. In fission reactions involving two cationic fragments, typically kinetic energy releases of 2-3 eV are observed. The results are interpreted by means of density functional theory calculations of the reverse barriers. It is concluded that naphthalene fragmentation by collisions with keV ions clearly is much more violent than the corresponding photofragmentation with energetic photons. The ion-induced naphthalene fragmentation provides a feedstock of various small hydrocarbonic species of different charge states and kinetic energy, which could influence several molecule formation processes in the cold interstellar medium and facilitates growth of small hydrocarbon species on pre-existing polycyclic aromatic hydrocarbons.

Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans

PubMed Central

Harvey, David J.; Scarff, Charlotte A.; Edgeworth, Matthew; Pagel, Kevin; Thalassinos, Konstantinos; Struwe, Weston B.; Crispin, Max; Scrivens, Jim

2016-01-01

Nitrogen cross sections of hybrid and complex glycans released from the glycoproteins IgG, gp120 (from human immunodeficiency virus), ovalbumin, α1-acid glycoprotein, thyroglobulin and fucosylated glycoproteins from the human parotid gland were measured with a travelling-wave ion mobility mass spectrometer using dextran as the calibrant. The utility of this instrument for isomer separation was also investigated. Some isomers, such as Man3GlcNAc3 from chicken ovalbumin and Man3GlcNAc3Fuc1 from thyroglobulin could be partially resolved and identified by their negative ion fragmentation spectra. Several other larger glycans, however, although existing as isomers, produced only asymmetric rather than separated arrival time distributions (ATDs). Nevertheless, in these cases, isomers could often be detected by plotting extracted fragment ATDs of diagnostic fragment ions from the negative ion spectra obtained in the transfer cell of the Waters Synapt mass spectrometer. Coincidence in the drift times of all fragment ions with an overall asymmetric ATD profile usually suggested that separations were due to conformers or anomers, whereas symmetrical ATDs of fragments showing differences in drift times indicated isomer separation. Although some significant differences in cross sections were found for the smaller isomeric glycans, the differences found for the larger compounds were usually too small to be analytically useful. Possible correlations between cross sections and structural types were also investigated and it was found that complex glycans tended to have slightly smaller cross sections than high-mannose glycans of comparable molecular weight. In addition, biantennary glycans containing a core fucose and/or a bisecting GlcNAc residue fell on different mobility-m/z trend lines to those glycans not so substituted with both of these substituents contributing to larger cross sections. PMID:27477117

Production of spin-polarized radioactive ion beams via projectile fragmentation reaction

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

Kameda, D.; Ueno, H.; Yoshimi, A.

2008-02-06

Spin-polarized radioactive ion beams are produced in the projectile fragmentation reaction induced by intermediate-energy heavy ion beams. The degree of spin polarization shows characteristic dependence on the outgoing momentum of the projectile fragment in the magnitude around 1{approx}10%. The qualitative behavior is well described by the kinematical model of the fragmentation process. Recently, we have successfully produced spin-polarized beams of aluminum isotopes in the mass A{approx}30 region via the fragmentation of 95 MeV/u {sup 40}Ar projectiles. The magnetic moments of {sup 30}Al and {sup 32}Al and the electric quadrupole moments of {sup 31}Al and {sup 32}Al have been measured usingmore » the {beta}-NMR technique with the polarized RI beams of the Al isotopes.« less

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

FIRST experiment: Fragmentation of Ions Relevant for Space and Therapy

NASA Astrophysics Data System (ADS)

Agodi, C.; Abou-Haidar, Z.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Bohlen, T. T.; Bondì, M.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cappuzzello, F.; Cavallaro, M.; Carbone, D.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; De Napoli, M.; Durante, M.; Fernandez-Garcia, J. P.; Finck, C.; Foti, A.; Gallardo, M. I.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kurz, N.; Labalme, M.; Lavagno, A.; Leifels, Y.; Le Fevre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Patera, V.; Piersanti, L.; Pleskac, R.; Quesada, J. M.; Randazzo, N.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Stuttge, L.; Tropea, S.; Younis, H.

2013-03-01

Nuclear fragmentation processes are relevant in different fields of basic research and applied physics and are of particular interest for tumor therapy and for space radiation protection applications. The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at SIS accelerator of GSI laboratory in Darmstadt, has been designed for the measurement of different ions fragmentation cross sections at different energies between 100 and 1000 MeV/nucleon. The experiment is performed by an international collaboration made of institutions from Germany, France, Italy and Spain. The experimental apparatus is partly based on an already existing setup made of the ALADIN magnet, the MUSIC IV TPC, the LAND2 neutron detector and the TOFWALL scintillator TOF system, integrated with newly designed detectors in the interaction Region (IR) around the carbon removable target: a scintillator Start Counter, a Beam Monitor drift chamber, a silicon Vertex Detector and a Proton Tagger for detection of light fragments emitted at large angles (KENTROS). The scientific program of the FIRST experiment started on summer 2011 with the study of the 400 MeV/nucleon 12C beam fragmentation on thin (8mm) carbon target.

A First Survey on the Abundance of Plastics Fragments and Particles on Two Sandy Beaches in Kuching, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Noik, V. James; Mohd Tuah, P.

2015-04-01

Plastic fragments and particles as an emerging environmental contaminant and pollutant are gaining scientific attention in the recent decades due to the potential threats on biota. This study aims to elucidate the presence, abundance and temporal change of plastic fragments and particles from two selected beaches, namely Santubong and Trombol in Kuching on two sampling times. Morphological and polymer identification assessment on the recovered plastics was also conducted. Overall comparison statistical analysis revealed that the abundance of plastic fragments/debris on both of sampling stations were insignificantly different (p>0.05). Likewise, statistical analysis on the temporal changes on the abundance yielded no significant difference for most of the sampling sites on each respective station, except STB-S2. Morphological studies revealed physical features of plastic fragments and debris were diverse in shapes, sizes, colors and surface fatigues. FTIR fingerprinting analysis shows that polypropylene and polyethylene were the dominant plastic polymers debris on both beaches.

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

On the gas phase fragmentation of protonated uracil: a statistical perspective.

PubMed

Rossich Molina, Estefanía; Salpin, Jean-Yves; Spezia, Riccardo; Martínez-Núñez, Emilio

2016-06-01

The potential energy surface of protonated uracil has been explored by an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us to determine the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role in this channel. Isocyanic acid (HNCOH(+)) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments.

Water cluster fragmentation probed by pickup experiments

NASA Astrophysics Data System (ADS)

Huang, Chuanfu; Kresin, Vitaly V.; Pysanenko, Andriy; Fárník, Michal

2016-09-01

Electron ionization is a common tool for the mass spectrometry of atomic and molecular clusters. Any cluster can be ionized efficiently by sufficiently energetic electrons, but concomitant fragmentation can seriously obstruct the goal of size-resolved detection. We present a new general method to assess the original neutral population of the cluster beam. Clusters undergo a sticking collision with a molecule from a crossed beam, and the velocities of neat and doped cluster ion peaks are measured and compared. By making use of longitudinal momentum conservation, one can reconstruct the sizes of the neutral precursors. Here this method is applied to H2O and D2O clusters in the detected ion size range of 3-10. It is found that water clusters do fragment significantly upon electron impact: the deduced neutral precursor size is ˜3-5 times larger than the observed cluster ions. This conclusion agrees with beam size characterization by another experimental technique: photoionization after Na-doping. Abundant post-ionization fragmentation of water clusters must therefore be an important factor in the interpretation of experimental data; interestingly, there is at present no detailed microscopic understanding of the underlying fragmentation dynamics.

Nuclear fragmentation of GCR-like ions: comparisons between data and PHITS

NASA Astrophysics Data System (ADS)

Zeitlin, Cary; Guetersloh, Stephen; Heilbronn, Lawrence; Miller, Jack; Sihver, Lembit; Mancusi, Davide; Fukumura, Aki; Iwata, Yoshi; Murakami, Takeshi

We present a summary of results from recent work in which we have compared nuclear fragmentation cross section data to predictions of the PHITS Monte Carlo simulation. The studies used beams of 12 C, 35 Cl, 40 Ar, 48 Ti, and 56 Fe at energies ranging from 290 MeV/nucleon to 1000 MeV/nucleon. Some of the data were obtained at the Brookhaven National Laboratory, others at the National Institute of Radiological Sciences in Japan. These energies and ion species are representative of the heavy ion component of the Galactic Cosmic Rays (GCR), which contribute significantly to the dose and dose equivalent that will be received by astronauts on deep-space missions. A critical need for NASA is the ability to accurately model the transport of GCR heavy ions through matter, including spacecraft walls, equipment racks, and other shielding materials, as well as through tissue. Nuclear interaction cross sections are of primary importance in the GCR transport problem. These interactions generally cause the incoming ion to break up (fragment) into one or more lighter ions, which continue approximately along the initial trajectory and with approximately the same velocity the incoming ion had prior to the interaction. Since the radiation dose delivered by a particle is proportional to the square of the quantity (charge/velocity), i.e., to (Z/β)2 , fragmentation reduces the dose (and, typically, dose equivalent) delivered by incident ions. The other mechanism by which dose can be reduced is ionization energy loss, which can lead to some particles stopping in the shielding. This is the conventional notion of shielding, but it is not applicable to human spaceflight, since the particles in the GCR tend to be highly energetic and because shielding must be relatively thin in order to keep overall mass as low as possible, keeping launch costs within reason. To support these goals, our group has systematically measured a large number of nuclear cross sections, intended to be used as either

Electron ionisation induced fragmentation of ethyl 5(1H)-oxo- and 7(1H)-oxo-1-aryl-2,3-dihydroimidazo[1,2-a]-pyrimidine-6-carboxylates: evidence for an unusually regioselective rearrangement of M(+*) ions.

PubMed

Ovcharenko, V V; Pihlaja, K; Matosiuk, D

2001-01-01

The 70-eV electron ionisation (EI) mass spectra of the title compounds show clear differences between the 5-oxo and 7-oxo isomers due to regioselective fragmentations involving the ester function. Exceptionally abundant metastable peaks due to molecular ions fragmenting to [M -CO2](+.) were observed exclusively for the 7-oxo isomers, suggesting that the sufficiently long-lived molecular ions undergo a slow rearrangement preceding this fragmentation reaction. The results are contrasted to the available literature data on the ester group fragmentations involving the loss of CO2 and the EI mass spectrometry of pyrimidone beta-oxo esters. A reaction mechanism is proposed for the elimination of CO2 following ethyl group migration to the pyrimidone carbonyl oxygen. Copyright 2001 John Wiley & Sons, Ltd.

Measurement of fragmentation cross sections of 12C ions on a thin gold target with the FIRST apparatus

NASA Astrophysics Data System (ADS)

Toppi, M.; Abou-Haidar, Z.; Agodi, C.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Böhlen, T. T.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cirio, R.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; de Napoli, M.; Durante, M.; Fernández-García, J. P.; Finck, Ch.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kummali, A. H.; Kurz, N.; Labalme, M.; Leifels, Y.; Le Fèvre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Piersanti, L.; Pleskac, R.; Randazzo, N.; Rescigno, R.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Salvador, S.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Tropea, S.; Vanstalle, M.; Younis, H.; Patera, V.; FIRST Collaboration

2016-06-01

A detailed knowledge of the light ions interaction processes with matter is of great interest in basic and applied physics. As an example, particle therapy and space radioprotection require highly accurate fragmentation cross-section measurements to develop shielding materials and estimate acute and late health risks for manned missions in space and for treatment planning in particle therapy. The Fragmentation of Ions Relevant for Space and Therapy experiment at the Helmholtz Center for Heavy Ion research (GSI) was designed and built by an international collaboration from France, Germany, Italy, and Spain for studying the collisions of a 12C ion beam with thin targets. The collaboration's main purpose is to provide the double-differential cross-section measurement of carbon-ion fragmentation at energies that are relevant for both tumor therapy and space radiation protection applications. Fragmentation cross sections of light ions impinging on a wide range of thin targets are also essential to validate the nuclear models implemented in MC simulations that, in such an energy range, fail to reproduce the data with the required accuracy. This paper presents the single differential carbon-ion fragmentation cross sections on a thin gold target, measured as a function of the fragment angle and kinetic energy in the forward angular region (θ ≲6° ), aiming to provide useful data for the benchmarking of the simulation softwares used in light ions fragmentation applications. The 12C ions used in the measurement were accelerated at the energy of 400 MeV/nucleon by the SIS (heavy ion synchrotron) GSI facility.

Anatomy of a cluster IDP. Part 2: Noble gas abundances, trace element geochemistry, isotopic abundances, and trace organic chemistry of several fragments from L2008#5

NASA Technical Reports Server (NTRS)

Thomas, K. L.; Clemett, S. J.; Flynn, G. J.; Keller, L. P.; Mckay, David S.; Messenger, S.; Nier, A. O.; Schlutter, D. J.; Sutton, S. R.; Walker, R. M.

1994-01-01

The topics discussed include the following: noble gas content and release temperatures; trace element abundances; heating summary of cluster fragments; isotopic measurements; and trace organic chemistry.

Predicting intensity ranks of peptide fragment ions.

PubMed

Frank, Ari M

2009-05-01

Accurate modeling of peptide fragmentation is necessary for the development of robust scoring functions for peptide-spectrum matches, which are the cornerstone of MS/MS-based identification algorithms. Unfortunately, peptide fragmentation is a complex process that can involve several competing chemical pathways, which makes it difficult to develop generative probabilistic models that describe it accurately. However, the vast amounts of MS/MS data being generated now make it possible to use data-driven machine learning methods to develop discriminative ranking-based models that predict the intensity ranks of a peptide's fragment ions. We use simple sequence-based features that get combined by a boosting algorithm into models that make peak rank predictions with high accuracy. In an accompanying manuscript, we demonstrate how these prediction models are used to significantly improve the performance of peptide identification algorithms. The models can also be useful in the design of optimal multiple reaction monitoring (MRM) transitions, in cases where there is insufficient experimental data to guide the peak selection process. The prediction algorithm can also be run independently through PepNovo+, which is available for download from http://bix.ucsd.edu/Software/PepNovo.html.

Predicting Intensity Ranks of Peptide Fragment Ions

PubMed Central

Frank, Ari M.

2009-01-01

Accurate modeling of peptide fragmentation is necessary for the development of robust scoring functions for peptide-spectrum matches, which are the cornerstone of MS/MS-based identification algorithms. Unfortunately, peptide fragmentation is a complex process that can involve several competing chemical pathways, which makes it difficult to develop generative probabilistic models that describe it accurately. However, the vast amounts of MS/MS data being generated now make it possible to use data-driven machine learning methods to develop discriminative ranking-based models that predict the intensity ranks of a peptide's fragment ions. We use simple sequence-based features that get combined by a boosting algorithm in to models that make peak rank predictions with high accuracy. In an accompanying manuscript, we demonstrate how these prediction models are used to significantly improve the performance of peptide identification algorithms. The models can also be useful in the design of optimal MRM transitions, in cases where there is insufficient experimental data to guide the peak selection process. The prediction algorithm can also be run independently through PepNovo+, which is available for download from http://bix.ucsd.edu/Software/PepNovo.html. PMID:19256476

Angular distributions and mechanisms for light fragment formation in relativistic heavy-ion collisions

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

Cumming, J.B.; Haustein, P.E.; Stoenner, R.W.

1986-03-01

Angular distributions are reported for /sup 37/Ar and /sup 127/Xe produced by the interaction of 8-GeV /sup 20/Ne and 25-GeV /sup 12/C ions with Au. A shift from a forward to a sideward peaked distribution is observed for /sup 37/Ar, similar to that known to occur for incident protons over the same energy interval. Analysis of these data and those for Z = 8 fragments indicate that reactions leading to heavy fragment emission become more peripheral as bombarding energies increase. A mechanistic analysis is presented which explores the ranges of applicability of several models and the reliability of their predictionsmore » to fragmentation reactions induced by both energetic heavy ions and protons.« less

Abundance and fragmentation patterns of the ecosystem engineer Lithophyllum byssoides (Lamarck) Foslie along the Iberian Peninsula Atlantic coast. Conservation and management implications

NASA Astrophysics Data System (ADS)

Veiga, Puri; Rubal, Marcos; Cacabelos, Eva; Moreira, Juan; Sousa-Pinto, Isabel

2013-10-01

The crustose calcareous red macroalgae Lithophyllum byssoides (Lamarck) Foslie is a common ecosystem engineer along the Atlantic and Mediterranean coast of the Iberian Peninsula. This species is threatened by several anthropogenic impacts acting at different spatial scales, such as pollution or global warming. The aim of this study is to identify scales of spatial variation in the abundance and fragmentation patterns of L. byssoides along the Atlantic coast of the Iberian Peninsula. For this aim we used a hierarchical sampling design considering four spatial scales (from metres to 100s of kilometres). Results of the present study indicated no significant variability among regions investigated whereas significant variability was found at the scales of shore and site in spatial patterns of abundance and fragmentation of L. byssoides. Variance components were higher at the spatial scale of shore for abundance and fragmentation of L. byssoides with the only exception of percentage cover and thus, processes acting at the scale of 10s of kilometres seem to be more relevant in shaping the spatial variability both in abundance and fragmentation of L. byssoides. These results provided quantitative estimates of abundance and fragmentation of L. byssoides at the Atlantic coast of the Iberian Peninsula establishing the observational basis for future assessment, monitoring and experimental investigations to identify the processes and anthropogenic impacts affecting L. byssoides populations. Finally we have also identified percentage cover and patch density as the best variables for long-term monitoring programs aimed to detect future anthropogenic impacts on L. byssoides. Therefore, our results have important implications for conservation and management of this valuable ecosystem engineer along the Atlantic coast of the Iberian Peninsula.

Fragmentation of negative ions from N-linked carbohydrates, part 4. Fragmentation of complex glycans lacking substitution on the 6-antenna.

PubMed

Harvey, David J; Jaeken, Jaak; Butler, Mike; Armitage, Alison J; Rudd, Pauline M; Dwek, Raymond A

2010-05-01

Negative ion CID spectra of N-linked glycans released from glycoproteins contain many ions that are diagnostic for specific structural features such as the detailed arrangement of antennae and the location of fucose residues. Identification of such ions requires reference glycans that are often difficult to acquire in a pure state. The recent acquisition of a sample of N-glycans from a patient lacking the enzyme N-acetylglucosaminyltransferase-2 provided an opportunity to investigate fragmentation of glycans lacking a 6-antenna. These glycans contained one or two galactose-N-acetylglucosamine-chains attached to the 3-linked mannose residue of the trimannosyl-chitobiose core with and without fucose substitution. The spectra from the patient sample clearly defined the antenna distribution and showed striking differences from the spectra of isomeric compounds obtained from normal subjects. Furthermore, they provided additional information on previously identified antenna-specific fragment ions and indicated the presence of additional ions that were diagnostic of fucose substitution. Glycans obtained from such enzyme-deficient patients can, thus, be a valuable way of obtaining spectra of specific isomers in a relatively pure state for interpretation of mass spectra. 2010 John Wiley & Sons, Ltd.

Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS

PubMed Central

Bilbao, Aivett; Zhang, Ying; Varesio, Emmanuel; Luban, Jeremy; Strambio-De-Castillia, Caterina; Lisacek, Frédérique; Hopfgartner, Gérard

2016-01-01

Data-independent acquisition LC-MS/MS techniques complement supervised methods for peptide quantification. However, due to the wide precursor isolation windows, these techniques are prone to interference at the fragment ion level, which in turn is detrimental for accurate quantification. The “non-outlier fragment ion” (NOFI) ranking algorithm has been developed to assign low priority to fragment ions affected by interference. By using the optimal subset of high priority fragment ions these interfered fragment ions are effectively excluded from quantification. NOFI represents each fragment ion as a vector of four dimensions related to chromatographic and MS fragmentation attributes and applies multivariate outlier detection techniques. Benchmarking conducted on a well-defined quantitative dataset (i.e. the SWATH Gold Standard), indicates that NOFI on average is able to accurately quantify 11-25% more peptides than the commonly used Top-N library intensity ranking method. The sum of the area of the Top3-5 NOFIs produces similar coefficients of variation as compared to the library intensity method but with more accurate quantification results. On a biologically relevant human dendritic cell digest dataset, NOFI properly assigns low priority ranks to 85% of annotated interferences, resulting in sensitivity values between 0.92 and 0.80 against 0.76 for the Spectronaut interference detection algorithm. PMID:26412574

The dehydroalanine effect in the fragmentation of ions derived from polypeptides

PubMed Central

Pilo, Alice L.; Peng, Zhou; McLuckey, Scott A.

2016-01-01

The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N—Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. PMID:27484024

Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

PubMed

Somogyi, Arpád

2008-12-01

The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia.

PubMed

Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

2010-10-01

Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures.

On the differences in element abundances of energetic ions from corotating events and from large solar events

NASA Technical Reports Server (NTRS)

Reames, D. V.; Richardson, I. G.; Barbier, L. M.

1991-01-01

The abundances of energetic ions accelerated from high-speed solar wind streams by shock waves formed at corotating interaction regions (CIRs) where high-speed streams overtake the lower-speed solar wind are examined. The observed element abundances appear to represent those of the high-speed solar wind, unmodified by the shock acceleration. These abundances, relative to those in the solar photosphere, are organized by the first ionization potential (FIP) of the ions in a way that is different from the FIP effect commonly used to describe differences between abundances in the solar photosphere and those in the solar corona, solar energetic particles (SEPs), and the low-speed solar wind. In contrast, the FIP effect of the ion abundances in the CIR events is characterized by a smaller amplitude of the differences between high-FIP and low-FIP ions and by elevated abundances of He, C, and S.

Determination of N-linked glycosylation in viral glycoproteins by negative ion mass spectrometry and ion mobility

PubMed Central

Bitto, David; Harvey, David J.; Halldorsson, Steinar; Doores, Katie J.; Pritchard, Laura K.; Huiskonen, Juha T.; Bowden, Thomas A.; Crispin, Max

2016-01-01

Summary Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans. PMID:26169737

Effect of land cover, habitat fragmentation and ant colonies on the distribution and abundance of shrews in southern California

USGS Publications Warehouse

Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

2001-01-01

Because effects of habitat fragmentation and anthropogenic disturbance on native animals have been relatively little studied in arid areas and in insectivores, we investigated the roles of different land covers, habitat fragmentation and ant colonies on the distribution and abundance of shrews, Notiosorex crawfordi and Sorex ornatus, in southern California.Notiosorex crawfordi was the numerically dominant species (trap-success rate 0·52) occurring in 21 of the 22 study sites in 85% of the 286 pitfall arrays used in this study.Sorex ornatus was captured in 14 of the sites, in 52% of the arrays with a total trap-success rate of 0·2. Neither of the species was found in one of the sites.The population dynamics of the two shrew species were relatively synchronous during the 4–5-year study; the peak densities usually occurred during the spring. Precipitation had a significant positive effect, and maximum temperature a significant negative effect on the trap-success rate of S. ornatus.Occurrence and abundance of shrews varied significantly between sites and years but the size of the landscape or the study site had no effect on the abundance of shrews. The amount of urban edge had no significant effect on the captures of shrews but increased edge allows invasion of the Argentine ants, which had a highly significant negative impact on the abundance of N. crawfordi.At the trap array level, the percentage of coastal sage scrub flora had a significant positive, and the percentage of other flora had a significant negative effect on the abundance of N. crawfordi. The mean canopy height and the abundance of N. crawfordi had a significant positive effect on the occurrence of S. ornatus.Our study suggests that the loss of native coastal sage scrub flora and increasing presence of Argentine ant colonies may significantly effect the distribution and abundance of N. crawfordi. The very low overall population densities of both shrew species in most study sites make both species

Optical model calculations of heavy-ion target fragmentation

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Wilson, J. W.; Cucinotta, F. A.; Norbury, J. W.

1986-01-01

The fragmentation of target nuclei by relativistic protons and heavy ions is described within the context of a simple abrasion-ablation-final-state interaction model. Abrasion is described by a quantum mechanical formalism utilizing an optical model potential approximation. Nuclear charge distributions of the excited prefragments are calculated by both a hypergeometric distribution and a method based upon the zero-point oscillations of the giant dipole resonance. Excitation energies are estimated from the excess surface energy resulting from the abrasion process and the additional energy deposited by frictional spectator interactions of the abraded nucleons. The ablation probabilities are obtained from the EVA-3 computer program. Isotope production cross sections for the spallation of copper targets by relativistic protons and for the fragmenting of carbon targets by relativistic carbon, neon, and iron projectiles are calculated and compared with available experimental data.

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil, E-mail: Anil.Shukla@pnnl.gov; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N{sub 2}). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi){sub n}Li{sup +}, (HCOOLi){sub n}Li{sub m}{sup m+}, (HCOOLi){sub n}HCOO{sup −}, and (HCOOLi){sub n}(HCOO){sub m}{sup m−}. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi){sub 3}Li{sup +} being the most abundant and stable cluster ion. Fragmentations ofmore » singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi){sub 2}) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi){sub 3}Li{sup +} as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Environmental drivers of Ixodes ricinus abundance in forest fragments of rural European landscapes.

PubMed

Ehrmann, Steffen; Liira, Jaan; Gärtner, Stefanie; Hansen, Karin; Brunet, Jörg; Cousins, Sara A O; Deconchat, Marc; Decocq, Guillaume; De Frenne, Pieter; De Smedt, Pallieter; Diekmann, Martin; Gallet-Moron, Emilie; Kolb, Annette; Lenoir, Jonathan; Lindgren, Jessica; Naaf, Tobias; Paal, Taavi; Valdés, Alicia; Verheyen, Kris; Wulf, Monika; Scherer-Lorenzen, Michael

2017-09-06

The castor bean tick (Ixodes ricinus) transmits infectious diseases such as Lyme borreliosis, which constitutes an important ecosystem disservice. Despite many local studies, a comprehensive understanding of the key drivers of tick abundance at the continental scale is still lacking. We analyze a large set of environmental factors as potential drivers of I. ricinus abundance. Our multi-scale study was carried out in deciduous forest fragments dispersed within two contrasting rural landscapes of eight regions, along a macroclimatic gradient stretching from southern France to central Sweden and Estonia. We surveyed the abundance of I. ricinus, plant community composition, forest structure and soil properties and compiled data on landscape structure, macroclimate and habitat properties. We used linear mixed models to analyze patterns and derived the relative importance of the significant drivers. Many drivers had, on their own, either a moderate or small explanatory value for the abundance of I. ricinus, but combined they explained a substantial part of variation. This emphasizes the complex ecology of I. ricinus and the relevance of environmental factors for tick abundance. Macroclimate only explained a small fraction of variation, while properties of macro- and microhabitat, which buffer macroclimate, had a considerable impact on tick abundance. The amount of forest and the composition of the surrounding rural landscape were additionally important drivers of tick abundance. Functional (dispersules) and structural (density of tree and shrub layers) properties of the habitat patch played an important role. Various diversity metrics had only a small relative importance. Ontogenetic tick stages showed pronounced differences in their response. The abundance of nymphs and adults is explained by the preceding stage with a positive relationship, indicating a cumulative effect of drivers. Our findings suggest that the ecosystem disservices of tick-borne diseases, via the

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

PubMed Central

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

2016-01-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

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

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

Liquid chromatography, in combination with a quadrupole time-of-flight instrument (LC QTOF), with sequential window acquisition of all theoretical fragment-ion spectra (SWATH) acquisition: systematic studies on its use for screenings in clinical and forensic toxicology and comparison with information-dependent acquisition (IDA).

PubMed

Roemmelt, Andreas T; Steuer, Andrea E; Poetzsch, Michael; Kraemer, Thomas

2014-12-02

Forensic and clinical toxicological screening procedures are employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques with information-dependent acquisition (IDA) approaches more and more often. It is known that the complexity of a sample and the IDA settings might prevent important compounds from being triggered. Therefore, data-independent acquisition (DIA) methods should be more suitable for systematic toxicological analysis (STA). The DIA method sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which uses Q1 windows of 20-35 Da for data-independent fragmentation, was systematically investigated for its suitability for STA. Quality of SWATH-generated mass spectra were evaluated with regard to mass error, relative abundance of the fragments, and library hits. With the Q1 window set to 20-25 Da, several precursors pass Q1 at the same time and are fragmented, thus impairing the library search algorithms to a different extent: forward fit was less affected than reverse fit and purity fit. Mass error was not affected. The relative abundance of the fragments was concentration dependent for some analytes and was influenced by cofragmentation, especially of deuterated analogues. Also, the detection rate of IDA compared to SWATH was investigated in a forced coelution experiment (up to 20 analytes coeluting). Even using several different IDA settings, it was observed that IDA failed to trigger relevant compounds. Screening results of 382 authentic forensic cases revealed that SWATH's detection rate was superior to IDA, which failed to trigger ∼10% of the analytes.

Reduction of the K* meson abundance in heavy ion collisions

NASA Astrophysics Data System (ADS)

Cho, Sungtae; Lee, Su Houng

2018-03-01

We study the K* meson reduction in heavy-ion collisions by focusing on the hadronic effects on the K* meson abundance. We evaluate the absorption cross sections of the K* and K meson by light mesons in the hadronic matter, and further investigate the variation in the meson abundances for both particles during the hadronic stage of heavy-ion collisions. We show how the interplay between the interaction of the K* meson and kaon with light mesons in the hadronic medium determines the final yield difference of the statistical hadronization model to the experimental measurements. For the central Au+Au collision at √{sN N}=200 GeV, we find that the K*/K yield ratio at chemical freeze-out decreases by 37 % during the expansion of the hadronic matter, resulting in the final ratio comparable to STAR measurements of 0.23 ±0.05 .

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.

Electron impact fragmentation of adenine: partial ionization cross sections for positive fragments

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Finnegan, Sinead; Eden, Samuel

2015-07-01

Using computer-controlled data acquisition we have measured mass spectra of positive ions for electron impact on adenine, with electron energies up to 100 eV. Ion yield curves for 50 ions have been obtained and normalized by comparing their sum to the average of calculated total ionization cross sections. Appearance energies have been determined for 37 ions; for 20 ions for the first time. All appearance energies are consistent with the fragmentation pathways identified in the literature. Second onset energies have been determined for 12 fragment ions (for 11 ions for the first time), indicating the occurrence of more than one fragmentation process e.g. for 39 u (C2HN+) and 70 u (C2H4N3+). Matching ion yield shapes (118-120 u, 107-108 u, 91-92 u, and 54-56 u) provide new evidence supporting closely related fragmentation pathways and are attributed to hydrogen rearrangement immediately preceding the fragmentation. We present the first measurement of the ion yield curve of the doubly charged parent ion (67.5 u), with an appearance energy of 23.5 ± 1.0 eV. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes*

PubMed Central

Michalski, Annette; Damoc, Eugen; Lange, Oliver; Denisov, Eduard; Nolting, Dirk; Müller, Mathias; Viner, Rosa; Schwartz, Jae; Remes, Philip; Belford, Michael; Dunyach, Jean-Jacques; Cox, Juergen; Horning, Stevan; Mann, Matthias; Makarov, Alexander

2012-01-01

Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides. PMID:22159718

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

PubMed

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

2015-11-01

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

Induced in-source fragmentation pattern of certain novel (1Z,2E)-N-(aryl)propanehydrazonoyl chlorides by electrospray mass spectrometry (ESI-MS/MS)

PubMed Central

2013-01-01

Background Collision induced dissociation (CID) in the triple quadrupole mass spectrometer system (QQQ) typically yields more abundant fragment ions than those produced with resonance excitation in the presence of helium gas in the ion trap mass spectrometer system (IT). Detailed product ion spectra can be obtained from one stage MS2 scan using the QQQ. In contrast, generating the same number of fragment ions in the ion trap requires multiple stages of fragmentation (MSn) using CID via in-trap resonance excitation with the associated time penalties and drop in sensitivity. Results The use of in-source fragmentation with electrospray ionization (ESI) followed by product ion scan (MS2) in a triple quadrupole mass spectrometer system, was demonstrated. This process enhances the qualitative power of tandem mass spectrometry to simulate the MS3 of ion trap for a comprehensive study of fragmentation mechanisms. A five pharmacologically significant (1Z, 2E)-N-arylpropanehydrazonoyl chlorides (3a-e) were chosen as model compounds for this study. In this work, detailed fragmentation pathways were elucidated by further dissociation of each fragment ion in the ion spectrum, essentially, by incorporating fragmentor voltage induced dissociation (in-source fragmentation) and isolation of fragments in a quadrupole cell Q1. Subsequently, CID occurs in cell, Q2, and fragment ions are analyzed in Q3 operated in product ion mode this process can be referred to as pseudo-MS3 scan mode. Conclusions This approach allowed unambiguous assignment of all fragment ions using tandem mass spectrometer and provided adequate sensitivity and selectivity. It is beneficial for structure determination of unknown trace components. The data presented in this paper provide useful information on the effect of different substituents on the ionization/fragmentation processes and can be used in the characterization of this important class of compounds. PMID:23351484

Fragmentation of amino acids induced by collisions with low-energy highly charged ions

NASA Astrophysics Data System (ADS)

Piekarski, D. G.; Maclot, S.; Domaracka, A.; Adoui, L.; Alcamí, M.; Rousseau, P.; Díaz-Tendero, S.; Huber, B. A.; Martín, F.

2014-04-01

Fragmentation of amino acids NH2-(CH2)n-COOH (n=1 glycine; n=2 β-alanine and n=3 γ-aminobutyric acid GABA) following collisions with slow highly charged ions has been studied in the gas phase by a combined experimental and theoretical approach. In the experiments, a multi-coincidence detection method was used to deduce the charge state of the molecules before fragmentation. Quantum chemistry calculations have been carried out in the basis of the density functional theory and ab initio molecular dynamics. The combination of both methodologies is essential to unambiguously unravel the different fragmentation pathways.

The anatomy of a cluster IDP. Part 1: Carbon abundance, bulk chemistry, and mineralogy of fragments from L2008#5

NASA Technical Reports Server (NTRS)

Thomas, K. L.; Keller, L. P.; Klock, W.; Warren, J.; Blanford, G. E.; Mckay, David S.

1994-01-01

The objective of this study was to determine whether or not cluster particles are sufficiently homogeneous to enable observations from one fragment of the cluster to be extrapolated to the entire cluster. We report on the results of a consortium study of the fragments of a large cluster particle. Multiple fragments from one large cluster were distributed to several research groups and were subjected to a variety of mineralogical and chemical analyses including: SEM, TEM, ion probe, SXRF, noble gas measurements, and microprobe laser mass spectrometry of individual fragments.

How enhanced molecular ions in Cold EI improve compound identification by the NIST library.

PubMed

Alon, Tal; Amirav, Aviv

2015-12-15

Library-based compound identification with electron ionization (EI) mass spectrometry (MS) is a well-established identification method which provides the names and structures of sample compounds up to the isomer level. The library (such as NIST) search algorithm compares different EI mass spectra in the library's database with the measured EI mass spectrum, assigning each of them a similarity score called 'Match' and an overall identification probability. Cold EI, electron ionization of vibrationally cold molecules in supersonic molecular beams, provides mass spectra with all the standard EI fragment ions combined with enhanced Molecular Ions and high-mass fragments. As a result, Cold EI mass spectra differ from those provided by standard EI and tend to yield lower matching scores. However, in most cases, library identification actually improves with Cold EI, as library identification probabilities for the correct library mass spectra increase, despite the lower matching factors. This research examined the way that enhanced molecular ion abundances affect library identification probability and the way that Cold EI mass spectra, which include enhanced molecular ions and high-mass fragment ions, typically improve library identification results. It involved several computer simulations, which incrementally modified the relative abundances of the various ions and analyzed the resulting mass spectra. The simulation results support previous measurements, showing that while enhanced molecular ion and high-mass fragment ions lower the matching factor of the correct library compound, the matching factors of the incorrect library candidates are lowered even more, resulting in a rise in the identification probability for the correct compound. This behavior which was previously observed by analyzing Cold EI mass spectra can be explained by the fact that high-mass ions, and especially the molecular ion, characterize a compound more than low-mass ions and therefore carries more

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices.

PubMed

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MS E mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. Graphical Abstract.

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices

NASA Astrophysics Data System (ADS)

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MSE mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. [Figure not available: see fulltext.

Effect of Ambipolar Diffusion on Ion Abundances in Contracting Protostellar Cores

NASA Astrophysics Data System (ADS)

Ciolek, Glenn E.; Mouschovias, Telemachos Ch.

1998-09-01

Numerical simulations and analytical solutions have established that ambipolar diffusion can reduce the dust-to-gas ratio in magnetically and thermally supercritical cores during the epoch of core formation. We study the effect that this has on the ion chemistry in contracting protostellar cores and present a simplified analytical method that allows one to calculate the ion power-law exponent k (≡d ln ni/d ln nn, where ni and nn are the ion and neutral densities, respectively) as a function of core density. We find that, as in earlier numerical simulations, no single value of k can adequately describe the ion abundance for nn <~ 109 cm-3, a result that is contrary to the ``canonical'' value of k = 1/2 found in previous static equilibrium chemistry calculations and often used to study the effect of ambipolar diffusion in interstellar clouds. For typical cloud and grain parameters, reduction of the abundance of grains results in k > 1/2 during the core formation epoch (densities <~105 cm-3). As a consequence, observations of the degree of ionization in cores could be used, in principle, to determine whether ambipolar diffusion is responsible for core formation in interstellar molecular clouds. For densities >>105 cm-3, k is generally <<1/2.

An (e, 2e+ ion) study of electron-impact ionization and fragmentation of tetrafluoromethane at low energies

NASA Astrophysics Data System (ADS)

Hossen, Khokon; Ren, Xueguang; Wang, Enliang; Kumar, S. V. K.; Dorn, Alexander

2018-03-01

We study ionization and fragmentation of tetrafluoromethane (CF4) molecule induced by electron impact at low energies ( E 0 = 38 and 67 eV). We use a reaction microscope combined with a pulsed photoemission electron beam for our experimental investigation. The momentum vectors of the two outgoing electrons (energies E 1, E 2) and one fragment ion are detected in triple coincidence (e, 2e+ ion). After dissociation, the fragment products observed are CF3 +, CF2 +, CF+, F+ and C+. For CF3 + and CF2 + channels, we measure the ionized orbitals binding energies, the kinetic energy (KE) of the charged fragments and the two-dimensional (2D) correlation map between binding energy (BE) and KE of the fragments. From the BE and KE spectra, we conclude which molecular orbitals contribute to particular fragmentation channels of CF4. We also measure the total ionization cross section for the formation of CF3 + and CF2 + ions as function of projectile energy. We compare our results with earlier experiments and calculations for electron-impact and photoionization. The major contribution to CF3 + formation originates from ionization of the 4t2 orbital while CF2 + is mainly formed after 3t2 orbital ionization. We also observe a weak contribution of the (4a1)-1 state for the channel CF3 +.

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry. Singly as well as multiply charged clusters were formed with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO- and (HCOOLi)n(HCOO)mm-. Several magic number cluster ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ions. Fragmentations of singly charged clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by sequential loss of monomer units (HCOOLi). In the case ofmore » positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ at higher collision energies which later fragments to dimer and monomer ions in lower abundance. Quantum mechanical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Product ion isotopologue pattern: A tool to improve the reliability of elemental composition elucidations of unknown compounds in complex matrices.

PubMed

Kaufmann, A; Walker, S; Mol, G

2016-04-15

Elucidation of the elemental compositions of unknown compounds (e.g., in metabolomics) generally relies on the availability of accurate masses and isotopic ratios. This study focuses on the information provided by the abundance ratio within a product ion pair (monoisotopic versus the first isotopic peak) when isolating and fragmenting the first isotopic ion (first isotopic mass spectrum) of the precursor. This process relies on the capability of the quadrupole within the Q Orbitrap instrument to isolate a very narrow mass window. Selecting only the first isotopic peak (first isotopic mass spectrum) leads to the observation of a unique product ion pair. The lighter ion within such an isotopologue pair is monoisotopic, while the heavier ion contains a single carbon isotope. The observed abundance ratio is governed by the percentage of carbon atoms lost during the fragmentation and can be described by a hypergeometric distribution. The observed carbon isotopologue abundance ratio (product ion isotopologue pattern) gives reliable information regarding the percentage of carbon atoms lost in the fragmentation process. It therefore facilitates the elucidation of the involved precursor and product ions. Unlike conventional isotopic abundances, the product ion isotopologue pattern is hardly affected by isobaric interferences. Furthermore, the appearance of these pairs greatly aids in cleaning up a 'matrix-contaminated' product ion spectrum. The product ion isotopologue pattern is a valuable tool for structural elucidation. It increases confidence in results and permits structural elucidations for heavier ions. This tool is also very useful in elucidating the elemental composition of product ions. Such information is highly valued in the field of multi-residue analysis, where the accurate mass of product ions is required for the confirmation process. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

In Situ Plasma Measurements of Fragmented Comet 73P Schwassmann-Wachmann 3

NASA Astrophysics Data System (ADS)

Gilbert, J. A.; Lepri, S. T.; Rubin, M.; Combi, M.; Zurbuchen, T. H.

2015-12-01

The interiors of comets contain some of the most pristine material in the solar system. Comet 73P/Schwassmann-Wachmann 3, discovered in 1930, is a Jupiter-family comet with a 5.34-year period. This comet split into 5 fragments in 1995 and disintegrated into nearly 70 major pieces in 2006. In 2006 May and June, recently ionized cometary particles originating from fragments including and surrounding some of these major objects were collected with the ACE/SWICS and Wind/STICS sensors. Due to a combination of the instrument characteristics and the close proximity of the fragments passing between those spacecraft and the Sun, unique measurements regarding the charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during that time. The cometary material released from some of these fragments can be identified by the concentrations of water-group pickup ions having a mass-per-charge ratio of 16-18 amu e-1, indicating that while these fragments are small, they are still actively sublimating. We present an analysis of cometary composition, spatial distribution, and heliospheric interactions, with a focus on helium, C+/O+, and water-group ions.

Application of stored waveform ion modulation 2D-FTICR MS/MS to the analysis of complex mixtures.

PubMed

Ross, Charles W; Simonsick, William J; Aaserud, David J

2002-09-15

Component identification of complex mixtures, whether they are from polymeric formulations or combinatorial synthesis, by conventional MS/MS techniques generally requires component separation by chromatography or mass spectrometry. An automated means of acquiring simultaneous MS/MS data from a complex mixture without prior separation is obtained from stored waveform ion modulation (SWIM) two-dimensional FTICR MS/MS. The technique applies a series of SWIFT excitation waveforms whose frequency domain magnitude spectrum is a sinusoid increasing in frequency from one waveform to the next. The controlled dissociation of the precursor ions produces an associated modulation of the product ion abundances. Fourier transformation of these abundances reveals the encoded modulation frequency from which connectivities of precursor and product ions are observed. The final result is total assignment of product ions for each precursor ion in a mixture from one automated experiment. We demonstrated the applicability of SWIM 2D-FTICR MS/MS to two diverse samples of industrial importance. We characterized structured polyester oligomers and products derived from combinatorial synthesis. Fragmentation pathways identified in standard serial ion isolation MS/MS experiments were observed for trimethylolpropane/methyl hexahydrophthalic anhydride. A 20-component sample derived from combinatorial synthesis was fragmented, and the template ion along with another key fragment ion was identified for each of the 20 components.

Fragmentation of molecular ions in differential mobility spectrometry as a method for identification of chemical warfare agents.

PubMed

Maziejuk, M; Puton, J; Szyposzyńska, M; Witkiewicz, Z

2015-11-01

The subject of the work is the use of differential mobility spectrometry (DMS) for the detection of chemical warfare agents (CWA). Studies were performed for mustard gas, i.e., bis(2-chloroethyl)sulfide (HD), sarin, i.e., O-isopropyl methylphosphonofluoridate (GB) and methyl salicylate (MS) used as test compounds. Measurements were conducted with two ceramic DMS analyzers of different constructions allowing the generation of an electric field with an intensity of more than 120 Td. Detector signals were measured for positive and negative modes of operation in a temperature range from 0 to 80 °C. Fragmentations of ions containing analyte molecules were observed for all tested compounds. The effective temperatures of fragmentation estimated on the basis of dispersion plots were equal from about 148 °C for GB to 178 °C for MS. It was found that values of separation voltage (SV) and compensation voltage (CV) at which the fragmentation of sample ions is observed may be the parameters improving the certainty of detection for different analytes. The DMS analyzers enabling the observation of ion fragmentation can be successfully used for effective CWA detection. Copyright © 2015. Published by Elsevier B.V.

Fragmentation of D- and L-enantiomers of amino acids through interaction with 3He2+ ions

NASA Astrophysics Data System (ADS)

Smirnov, O. V.; Basalaev, A. A.; Boitsov, V. M.; Vyaz'min, S. Yu.; Orbeli, A. L.; Dubina, M. V.

2014-11-01

The relative cross section of processes attendant on the capture of an electron by 12-keV 3He2+ ions are measured by time-of-flight mass spectrometry for leucine (C6H13NO2), methionine (C5H11NO2S), and glutmic acid (C5H9NO4) molecules. No differences between the formation relative cross sections of different fragment ions for the D- and L-enantiomeric forms of the amino acids are revealed. The spectrum of glutamic acid fragments taken at temperatures above 110°C is explained by decomposition of the acid with the formation of pyroglutamic acid (C5H7NO3) and water. The results are compared with published data on fragmentation of the same molecules via electron-impact ionization.

Factors Affecting the Production of Aromatic Immonium Ions in MALDI 157 nm Photodissociation Studies

NASA Astrophysics Data System (ADS)

DeGraan-Weber, Nick; Ashley, Daniel C.; Keijzer, Karlijn; Baik, Mu-Hyun; Reilly, James P.

2016-05-01

Immonium ions are commonly observed in the high energy fragmentation of peptide ions. In a MALDI-TOF/TOF mass spectrometer, singly charged peptides photofragmented with 157 nm VUV light yield a copious abundance of immonium ions, especially those from aromatic residues. However, their intensities may vary from one peptide to another. In this work, the effect of varying amino acid position, peptide length, and peptide composition on immonium ion yield is investigated. Internal immonium ions are found to have the strongest intensity, whereas immonium ions arising from C-terminal residues are the weakest. Peptide length and competition among residues also strongly influence the immonium ion production. Quantum calculations provide insights about immonium ion structures and the fragment ion conformations that promote or inhibit immonium ion formation.

Comprehensive Study On The Metastable Negative Ion Fragmentation Of Individual Dna Components And Larger Oligonucleotides

NASA Astrophysics Data System (ADS)

Ingolfsson, O.; Flosadottir, H. D.; Omarsson, B.; Ilko, B.

2010-07-01

Here we present a systematic study on the unimolecular decay pathways of the deprotonated building blocks of DNA and RNA to address the following questions: 1. Are the negative ion fragmentation patterns observed in the metastable decay of individual DNA components still evident when these are combined to larger oligonucleotides? 2. What is the significance of the charge location in determining the fragmentation pathways in the metastable decay process? 3. Are those metastable decay channels relevant in dissociative electron attachment to DNA components? To address these questions we have studied the fragmentation patterns of the deprotonated ribose and ribose 5'-monophosphate, the fragmentation patterns of the individual bases, all nucleosides and all 2'-deoxynucleosides as well as the individual nucleotides and several combinations of hexameric oligonucleotides. Furthermore, to understand the significance of the charge location in determining the fragmentation path in the metastable decay process of these deprotonated ions we have also studied modified uridine and guanosine. These have been modified to block different deprotonation sites and thus to control the initial step in the in the fragmentation process i.e. the site of deprotonation. In addition to our experimental approach we have also simulated the metastable fragmentation of the deprotonated uridine and 2'-deoxyguanosine to clarify the mechanisms and fragmentation patterns observed. Where data is available, the results are compared to dissociative electron attachment to DNA components and discussed in context to the underlying mechanism. Experiments on modified nucleosides where selected deprotonation sites have been blocked are used to verify the predicted reaction paths and imulations on uridine and 2'-deoxyguanosine are compared to the experimental results and used to shed light on the mechanisms involved.

Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Kerlin, Austin B.

2016-01-01

We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

PubMed

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

Fragmentation of DNA components by hyperthermal heavy ion (Ar+ and Xe+) impact in the condensed phase

NASA Astrophysics Data System (ADS)

Sarabipour, Sarvenaz; Sarvenaz Sarabipour, Ms; Michaud, Marc; Deng, Zongwu; Huels, Michael A.

The overriding environmental factor that presently limits human endeavors in space is exposure to heavy ion radiation. While knowledge of its damage to living tissue is essential for radiation protection and risk estimates for astronauts, very little data exists at the molecular level regarding the nascent DNA damage by the primary particle track, or by secondary species during subsequent reaction cascades. This persistent lack of a basic understanding of nascent damage induced by such low dose, high LET radiation, introduces unacceptable errors in radiation risk estimates (based mainly on extrapolation from high dose, low LET radiation), particularly for long term exposure. Mutagenic effects induced by heavy ion radiation to cells are largely due to DNA damage by secondary transient species, i.e. secondary ballistic ions, electrons and radicals generated along the ion tracks; the secondary ions have hyperthermal energies up to several 100 eV, which they will deposit within a few nm in the surrounding medium; thus their LET is very high, and yields lethal clustered DNA lesions. We present measurements of molecular damage induced in films of DNA components by ions with precisely such low energies (1-100 eV) and compare results to conventional electron impact measurements. Experiments are conducted in UHV using a mass selected low energy ion source, and a high-resolution quadrupole MS to monitor ion yields desorbing from molecular films. Among the major fragments, NH4 + is identified in the desorption mass spectra of irradiated films of Adenine, Guanine, Cytosine, indicating efficient deamination; in cells this results in pre-mutagenic lesions. Experiments with 5-amino-Uracil, and comparison to previous results on uracil and thymine show that deamination is a key step in the NH4 + fragment formation. For Adenine, we also observe formation of amine aducts in the films, viz. amination of Adenine, and global fragmentation in all ion impact mass spectra, attributed

Biophysical modeling of fragment length distributions of DNA plasmids after X and heavy-ion irradiation analyzed by atomic force microscopy.

PubMed

Elsässer, Thilo; Brons, Stephan; Psonka, Katarzyna; Scholz, Michael; Gudowska-Nowak, Ewa; Taucher-Scholz, Gisela

2008-06-01

The investigation of fragment length distributions of plasmid DNA gives insight into the influence of localized energy distribution on the induction of DNA damage, particularly the clustering of double-strand breaks. We present an approach that determines the fragment length distributions of plasmid DNA after heavy-ion irradiation by using the Local Effect Model. We find a good agreement of our simulations with experimental fragment distributions derived from atomic force microscopy (AFM) studies by including experimental constraints typical for AFM. Our calculations reveal that by comparing the fragmentation in terms of fluence, we can uniquely distinguish the effect of different radiation qualities. For very high-LET irradiation using nickel or uranium ions, no difference between their fragment distributions can be expected for the same dose level. However, for carbon ions with an intermediate LET, the fragmentation pattern differs from the distribution for very high-LET particles. The results of the model calculations can be used to determine the optimal experimental parameters for a demonstration of the influence of track structure on primary radiation damage. Additionally, we compare the results of our model for two different plasmid geometries.

Can collision-induced negative-ion fragmentations of [M-H](-) anions be used to identify phosphorylation sites in peptides?

PubMed

Tran, T T Nha; Wang, Tianfang; Hack, Sandra; Hoffmann, Peter; Bowie, John H

2011-12-15

A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers. Copyright © 2011 John Wiley & Sons, Ltd.

Precursor Ion Scan Mode-Based Strategy for Fast Screening of Polyether Ionophores by Copper-Induced Gas-Phase Radical Fragmentation Reactions.

PubMed

Crevelin, Eduardo J; Possato, Bruna; Lopes, João L C; Lopes, Norberto P; Crotti, Antônio E M

2017-04-04

The potential of copper(II) to induce gas-phase fragmentation reactions in macrotetrolides, a class of polyether ionophores produced by Streptomyces species, was investigated by accurate-mass electrospray tandem mass spectrometry (ESI-MS/MS). Copper(II)/copper(I) transition directly induced production of diagnostic acylium ions with m/z 199, 185, 181, and 167 from α-cleavages of [macrotetrolides + Cu] 2+ . A UPLC-ESI-MS/MS methodology based on the precursor ion scan of these acylium ions was developed and successfully used to identify isodinactin (1), trinactin (2), and tetranactin (3) in a crude extract of Streptomyces sp. AMC 23 in the precursor ion scan mode. In addition, copper(II) was also used to induce radical fragmentation reactions in the carboxylic acid polyether ionophore nigericin. The resulting product ions with m/z 755 and 585 helped to identify nigericin in a crude extract of Streptomyces sp. Eucal-26 by means of precursor ion scan experiments, demonstrating that copper-induced fragmentation reactions can potentially identify different classes of polyether ionophores rapidly and selectively.

Structural Studies of Fucosylated N-Glycans by Ion Mobility Mass Spectrometry and Collision-Induced Fragmentation of Negative Ions

NASA Astrophysics Data System (ADS)

Harvey, David J.; Struwe, Weston B.

2018-05-01

There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers. Specific information that could be obtained from the intact N-glycans by negative ion CID included the general topology of the glycan such as the presence or absence of a bisecting GlcNAc residue and the branching pattern of the triantennary glycans. Information on the location of the fucose residues was also readily obtainable from ions specific to each antenna. Some isobaric fragment ions produced prior to ion mobility could subsequently be separated and, in some cases, provided additional valuable structural information that was missing from the CID spectra alone.

Fast Biological Modeling for Voxel-based Heavy Ion Treatment Planning Using the Mechanistic Repair-Misrepair-Fixation Model and Nuclear Fragment Spectra.

PubMed

Kamp, Florian; Cabal, Gonzalo; Mairani, Andrea; Parodi, Katia; Wilkens, Jan J; Carlson, David J

2015-11-01

The physical and biological differences between heavy ions and photons have not been fully exploited and could improve treatment outcomes. In carbon ion therapy, treatment planning must account for physical properties, such as the absorbed dose and nuclear fragmentation, and for differences in the relative biological effectiveness (RBE) of ions compared with photons. We combined the mechanistic repair-misrepair-fixation (RMF) model with Monte Carlo-generated fragmentation spectra for biological optimization of carbon ion treatment plans. Relative changes in double-strand break yields and radiosensitivity parameters with particle type and energy were determined using the independently benchmarked Monte Carlo damage simulation and the RMF model to estimate the RBE values for primary carbon ions and secondary fragments. Depth-dependent energy spectra were generated with the Monte Carlo code FLUKA for clinically relevant initial carbon ion energies. The predicted trends in RBE were compared with the published experimental data. Biological optimization for carbon ions was implemented in a 3-dimensional research treatment planning tool. We compared the RBE and RBE-weighted dose (RWD) distributions of different carbon ion treatment scenarios with and without nuclear fragments. The inclusion of fragments in the simulations led to smaller RBE predictions. A validation of RMF against measured cell survival data reported in published studies showed reasonable agreement. We calculated and optimized the RWD distributions on patient data and compared the RMF predictions with those from other biological models. The RBE values in an astrocytoma tumor ranged from 2.2 to 4.9 (mean 2.8) for a RWD of 3 Gy(RBE) assuming (α/β)X = 2 Gy. These studies provide new information to quantify and assess uncertainties in the clinically relevant RBE values for carbon ion therapy based on biophysical mechanisms. We present results from the first biological optimization of carbon ion radiation

Fast Biological Modeling for Voxel-based Heavy Ion Treatment Planning Using the Mechanistic Repair-Misrepair-Fixation Model and Nuclear Fragment Spectra

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

Kamp, Florian; Department of Radiation Oncology, Technische Universität München, Klinikum Rechts der Isar, München; Physik-Department, Technische Universität München, Garching

2015-11-01

Purpose: The physical and biological differences between heavy ions and photons have not been fully exploited and could improve treatment outcomes. In carbon ion therapy, treatment planning must account for physical properties, such as the absorbed dose and nuclear fragmentation, and for differences in the relative biological effectiveness (RBE) of ions compared with photons. We combined the mechanistic repair-misrepair-fixation (RMF) model with Monte Carlo-generated fragmentation spectra for biological optimization of carbon ion treatment plans. Methods and Materials: Relative changes in double-strand break yields and radiosensitivity parameters with particle type and energy were determined using the independently benchmarked Monte Carlo damagemore » simulation and the RMF model to estimate the RBE values for primary carbon ions and secondary fragments. Depth-dependent energy spectra were generated with the Monte Carlo code FLUKA for clinically relevant initial carbon ion energies. The predicted trends in RBE were compared with the published experimental data. Biological optimization for carbon ions was implemented in a 3-dimensional research treatment planning tool. Results: We compared the RBE and RBE-weighted dose (RWD) distributions of different carbon ion treatment scenarios with and without nuclear fragments. The inclusion of fragments in the simulations led to smaller RBE predictions. A validation of RMF against measured cell survival data reported in published studies showed reasonable agreement. We calculated and optimized the RWD distributions on patient data and compared the RMF predictions with those from other biological models. The RBE values in an astrocytoma tumor ranged from 2.2 to 4.9 (mean 2.8) for a RWD of 3 Gy(RBE) assuming (α/β){sub X} = 2 Gy. Conclusions: These studies provide new information to quantify and assess uncertainties in the clinically relevant RBE values for carbon ion therapy based on biophysical mechanisms. We present

IN SITU PLASMA MEASUREMENTS OF FRAGMENTED COMET 73P SCHWASSMANN–WACHMANN 3

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

Gilbert, J. A.; Lepri, S. T.; Combi, M.

2015-12-10

The interiors of comets contain some of the most pristine material in the solar system. Comet 73P/Schwassmann–Wachmann 3, discovered in 1930, is a Jupiter-family comet with a 5.34-year period. This comet split into 5 fragments in 1995 and disintegrated into nearly 70 major pieces in 2006. In 2006 May and June, recently ionized cometary particles originating from fragments including and surrounding some of these major objects were collected with the ACE/SWICS and Wind/STICS sensors. Due to a combination of the instrument characteristics and the close proximity of the fragments passing between those spacecraft and the Sun, unique measurements regarding themore » charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during that time. The cometary material released from some of these fragments can be identified by the concentrations of water-group pickup ions having a mass-per-charge ratio of 16–18 amu e{sup −1}, indicating that while these fragments are small, they are still actively sublimating. We present an analysis of cometary composition, spatial distribution, and heliospheric interactions, with a focus on helium, C{sup +}/O{sup +}, and water-group ions.« less

Electron Transfer Ion/Ion Reactions in a Three-Dimensional Quadrupole Ion Trap: Reactions of Doubly and Triply Protonated Peptides with SO2·−

PubMed Central

Pitteri, Sharon J.; Chrisman, Paul A.; Hogan, Jason M.; McLuckey, Scott A.

2005-01-01

Ion–ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2·−. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2·− give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2·− shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide. PMID:15762593

Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics

PubMed Central

2014-01-01

Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native 12C- and uniformly 13C (U-13C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-13C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

Recent (2000-2015) developments in the analysis of minor unknown natural products based on characteristic fragment information using LC-MS.

PubMed

Cai, Tian; Guo, Ze-Qin; Xu, Xiao-Ying; Wu, Zhi-Jun

2018-03-01

Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MS n spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:202-216, 2018. © 2016 Wiley Periodicals, Inc.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

ACE-SWICS In Situ Plasma Composition of Fragmented Comet 73P/Schwassmann-Wachmann 3

NASA Astrophysics Data System (ADS)

Gilbert, J. A.; Lepri, S. T.; Rubin, M.; Zurbuchen, T.

2013-12-01

The interiors of comets contain some of the most pristine material in the solar system. Comet 73P/Schwassmann-Wachmann 3, discovered in 1930 with a double nucleus, is a Jupiter-family comet with a 5.34-year period. This comet split into 5 fragments in 1995 and disintegrated into nearly 70 pieces in 2006. In May and June of 2006, recently ionized cometary particles originating from some of these fragments were collected with the ACE-SWICS sensor. Due to a combination of the close proximity of the fragments passing between ACE-SWICS and the Sun, and the instrument characteristics, unique measurements regarding the charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during this time. The cometary material released from some of these fragments can be identified by the concentrations of water-group pick-up ions having a mass-per-charge of 16-18 amu/e. With a focus on Helium, Carbon, and water-group ions, we present an analysis of the cometary plasma. Charge state ratios of C+/O+ fall below 0.1 during detection of comet fragment plasma, and there is a clear increase in He+ during fragment crossings. The C/O ratio and He charge states are used to provide constraints on the activity of the cometary fragments and also the spatial distribution of the extended and ionized cometary tail.

CF3+ fragmentation by electron impact ionization of perfluoro-propyl-vinyl-ethers, C5F10O, in gas phase

NASA Astrophysics Data System (ADS)

Kondo, Yusuke; Ishikawa, Kenji; Hayashi, Toshio; Miyawaki, Yudai; Takeda, Keigo; Kondo, Hiroki; Sekine, Makoto; Hori, Masaru

2015-04-01

The gas phase fragmentations of perfluoro-propyl-vinyl ether (PPVE, C5F10O) are studied experimentally. Dominant fragmentations of PPVE are found to be the result of a dissociative ionization reaction, i.e., CF3+ via direct bond cleavage, and C2F3O- and C3F7O- via electron attachment. Regardless of the appearance energy of around 14.5 eV for the dissociative ionization of CF3+, the observed ion efficiency for the CF3+ ion was extremely large the order of 10-20 cm-2, compared with only 10-21 cm-2 for the other channels. PPVE characteristically generated CF3+ as the largest abundant ion are advantageous for use of feedstock gases in plasma etching processes.

Parasitic production of slow RI-beam from a projectile fragment separator by ion guide Laser Ion Source (PALIS)

NASA Astrophysics Data System (ADS)

Sonoda, Tetsu

2009-10-01

The projectile fragment separator BigRIPS of RIBF at RIKEN provides a wide variety of short-lived radioactive isotope (RI) ions without restrictions on their lifetime or chemical properties. A universal slow RI-beam facility (SLOWRI) to decelerate the beams from BigRIPS using an RF-carpet ion guide has been proposed as a principal facility of RIBF. However, beam time at such a modern accelerator facility is always limited and operational costs are high. We therefore propose an additional scheme as a complementary option to SLOWRI to drastically enhance the usability of such an expensive facility. In BigRIPS, a single primary beam produces thousands of isotopes but only one isotope is used for an experiment while the other >99.99% of isotopes are simply dumped in the slits or elsewhere in the fragment separator. We plan to locate a compact gas cell with 1 bar Ar at the slits. The thermalized ions in the cell will be quickly neutralized and transported to the exit by gas flow and resonantly re-ionized by lasers. Such low energy RI-beams will always be provided without any restriction to the main experiment. It will allow us to run parasitic experiments for precision atomic or decay spectroscopy, mass measurements. Furthermore, the resonance ionization in the cell itself can be used for high-sensitive laser spectroscopy, which will expand our knowledge of the ground state property of unstable nuclei.

Fragmentation pathways of 2-substituted pyrrole derivatives using electrospray ionization ion trap and electrospray ionization quadrupole time-of-flight mass spectrometry.

PubMed

Liang, Xianrui; Guo, Zili; Yu, Chuanming

2013-10-30

Pyrrole derivatives are of considerable importance and are present in a wide range of natural products and used extensively in drug discovery. Fragmentation pathway studies play an important role in the structural identification of pyrrole derivatives. As a part of our ongoing work on heterocycles, fragmentation pathways of 2-substituted pyrrole derivatives were investigated by mass spectrometry (MS). Twelve pyrrole derivatives were synthesized and analyzed. Low-resolution fragmentation ions of all the compounds were generated by ion trap mass spectrometry (ITMS(n) ) with an electrospray ionization (ESI) source in positive mode. Hybrid quadrupole time-of-flight mass spectrometry (QTOFMS) was used to determine the elemental compositions of the resultant product ions. The side-chain substituents at the 2-position influence the fragmentation pathways. Typical losses of H2 O, aldehydes and pyrrole moieties from the [M + H](+) ion are observed for the compounds with side chains bearing aromatic groups at the 2-position of the pyrrole. However, losses of H2 O, alcohols and C3 H6 are the main cleavage pathways for compounds 6 and 12 with nonphenyl-substituted side chains at the 2-position. Typical fragmentation mechanisms of 2-substituted pyrrole derivatives are proposed and elucidated based on the observations of ITMS(n) and QTOFMS spectra. The results showed that the fragmentation pathways were remarkably influenced by the side-chain substituents at the 2-position of pyrrole. This investigation should have value in the structural identification of this series of molecules or compounds with similar structures. Copyright © 2013 John Wiley & Sons, Ltd.

The influence of dose, dose-rate and particle fragmentation on cataract induction by energetic iron ions

NASA Technical Reports Server (NTRS)

Medvedovsky, C.; Worgul, B. V.; Huang, Y.; Brenner, D. J.; Tao, F.; Miller, J.; Zeitlin, C.; Ainsworth, E. J.

1994-01-01

Because activities in space necessarily involve chronic exposure to a heterogeneous charged particle radiation field it is important to assess the influence of dose-rate and the possible modulating role of heavy particle fragmentation on biological systems. Using the well-studied cataract model, mice were exposed to plateau 600 MeV/amu Fe-56 ions either as acute or fractionated exposures at total doses of 5-504 cGy. Additional groups of mice received 20, 360 and 504 cGy behind 50 mm of polyethylene, which simulates body shielding. The reference radiation consisted of Co-60 gamma radiation. The animals were examined by slit lamp biomicroscopy over their three year life spans. In accordance with our previous observations with heavy particles, the cataractogenic potential of the 600 MeV/amu Fe-56 ions was greater than for low-Linear Energy Transfer (LET) radiation and increased with decreasing dose relative to gamma rays. Fractionation of a given dose of Fe-56 ions did not reduce the cataractogenicity of the radiation compared to the acute regimen. Fragmentation of the beam in the polyethylene did not alter the cataractotoxicity of the ions, either when administered singly or in fractions.

The influence of dose, dose-rate and particle fragmentation on cataract induction by energetic iron ions

NASA Astrophysics Data System (ADS)

Medvedovsky, C.; Worgul, B. V.; Huang, Y.; Brenner, D. J.; Tao, F.; Miller, J.; Zeitlin, C.; Ainsworth, E. J.

1994-10-01

Because activities in space necessarily involve chronic exposure to a heterogeneous charged particle radiation field it is important to assess the influence of dose-rate and the possible modulating role of heavy particle fragmentation on biological systems. Using the well-studied cataract model, mice were exposed to plateau 600 MeV/amu 56Fe ions either as acute or fractionated exposures at total doses of 5 - 504 cGy. Additional groups of mice received 20, 360 and 504 cGy behind 50 mm of polyethylene, which simulates body shielding. The reference radiation consisted of 60Co γ radiation. The animals were examined by slit lamp biomicroscopy over their three year life spans. In accordance with our previous observations with heavy particles, the cataractogenic potential of the 600 MeV/amu 56Fe ions was greater than for low-LET radiation and increased with decreasing dose relative to γ-rays. Fractionation of a given dose of 56Fe ions did not reduce the cataractogenicity of the radiation compared to the acute regimen. Fragmentation of the beam in the polyethylene did not alter the cataractotoxicity of the ions, either when administered singly or in fractions.

Dynamic of negative ions in potassium-D-ribose collisions.

PubMed

Almeida, D; Ferreira da Silva, F; García, G; Limão-Vieira, P

2013-09-21

We present negative ion formation from collisions of neutral potassium atoms with D-ribose (C5H10O5), the sugar unit in the DNA/RNA molecule. From the negative ion time-of-flight (TOF) mass spectra, OH(-) is the main fragment detected in the collision range 50-100 eV accounting on average for 50% of the total anion yield. Prominence is also given to the rich fragmentation pattern observed with special attention to O(-) (16 m/z) formation. These results are in sharp contrast to dissociative electron attachment experiments. The TOF mass spectra assignments show that these channels are also observed, albeit with a much lower relative intensity. Branching ratios of the most abundant fragment anions as a function of the collision energy are obtained, allowing to establish a rationale on the collision dynamics.

Hyperthermal (1-100 eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films.

PubMed

Deng, Zongwu; Bald, Ilko; Illenberger, Eugen; Huels, Michael A

2007-10-14

Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1-100 eV) scattering of one such fragment ion (N(+)) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N(+) ion scattering at kinetic energies down to 10 eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-(13)C D-ribose and 1-D D-ribose) partly reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN(-) anion at energies down to approximately 5 eV. N(+) ions also abstract hydrogen from hydroxyl groups of the molecules to form NH(-) and NH(2) (-) anions. A fraction of OO(-) fragments abstract hydrogen to form OH(-). The formation of H(3)O(+) ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes.

Differentiating chondroitin sulfate glycosaminoglycans using collision-induced dissociation; uronic acid cross-ring diagnostic fragments in a single stage of tandem mass spectrometry.

PubMed

Kailemia, Muchena J; Patel, Anish B; Johnson, Dane T; Li, Lingyun; Linhardt, Robert J; Amster, I Jonathan

2015-01-01

The stereochemistry of the hexuronic acid residues of the structure of glycosaminoglycans (GAGs) is a key feature that affects their interactions with proteins and other biological functions. Electron based tandem mass spectrometry methods, in particular electron detachment dissociation (EDD), have been able to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) residues in some heparan sulfate tetrasaccharides by producing epimer-specific fragments. Similarly, the relative abundance of glycosidic fragment ions produced by collision-induced dissociation (CID) or EDD has been shown to correlate with the type of hexuronic acid present in chondroitin sulfate GAGs. The present work examines the effect of charge state and degree of sodium cationization on the CID fragmentation products that can be used to distinguish GlcA and IdoA containing chondroitin sulfate A and dermatan sulfate chains. The cross-ring fragments (2,4)A(n) and (0,2)X(n) formed within the hexuronic acid residues are highly preferential for chains containing GlcA, distinguishing it from IdoA. The diagnostic capability of the fragments requires the selection of a molecular ion and fragment ions with specific ionization characteristics, namely charge state and number of ionizable protons. The ions with the appropriate characteristics display diagnostic properties for all the chondroitin sulfate and dermatan sulfate chains (degree of polymerization of 4-10) studied.

Impact of energetic cosmic-ray ions on astrophysical ice grains

NASA Astrophysics Data System (ADS)

Mainitz, Martin; Anders, Christian; Urbassek, Herbert M.

2017-02-01

Using molecular-dynamics simulation with REAX potentials, we study the consequences of cosmic-ray ion impact on ice grains. The grains are composed of a mixture of H2O, CO2, NH3, and CH3OH molecules. Due to the high energy deposition of the cosmic-ray ion, 5 keV/nm, a strong pressure wave runs through the grain, while the interior of the ion track gasifies. Abundant molecular dissociations occur; reactions of the fragments form a variety of novel molecular product species.

High Abundance of Ions in Cosmic Ices

NASA Technical Reports Server (NTRS)

Gudipati, Murthy S.; Allamandola, Louis J.; Fonda, Mark (Technical Monitor)

2002-01-01

Water-rich, mixed molecular ices and polycyclic aromatic hydrocarbons (PAHs) are common throughout interstellar molecular clouds and the Solar System. Vacuum ultraviolet (VUV) irradiation and particle bombardment of these abiotic ices produces complex organic species, including important biogenic molecules such as amino acids and functionalized PAHs which may have played a role in the origin of life. This ability of such water-rich, oxygen dominated ices to promote production of complex organic species is surprising and points to an important, unusual, but previously overlooked mechanism at play within the ice. Here we report the nature of this mechanism using electronic spectroscopy. VUV-irradiation of PAH/H2O ices leads to an unprecedented and efficient (greater than 70 %) conversion of the neutral PAHs to their cation form (PAH+). Further, these H2O/PAH+ ices are stabile at temperatures below 50 K, a temperature domain common throughout interstellar clouds and the Solar System. Between 50 and 125 K they react to form the complex organics. In view of this, we conclude that charged PAHs and other molecular ions should be common and abundant in many cosmic ices. The chemical, spectroscopic and physical properties of these ion-rich ices can be of fundamental importance for objects as diverse as comets, planets, and molecular clouds and may account for several poorly understood phenomena associated with each of these object classes.

Relative abundance of heavy ions in the inner zone of the radiation belts of the earth

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

Panasyuk, M.I.

1986-03-01

The energy dependences of the relative abundances of energetic (E > 1 MeV/nucleon) H, He, and O ions in the radiation belts are analyzed on the basis of experimental results obtained from measurement of their spectral characteristics on several satellites: Molniya-2, Kosmos-900, Prognoz-5, Explorer-45, ISEE-1, and OV1-19. It is shown that the formation of the energy dependence of He/H and O/H can be explained with a model providing for ion diffusion into the interior of the radiation belts with Coulomb losses taken into account under thecondition that the total-energy spectra at the boundary are more rigid for the heavy ionsmore » and are determined by such parameters of the quiet solar wind as the relative concentrations of the individual ion components and their charge states. It is shown that the fluxes of O and Fe ions with E > 1 MeV/nucleon measured on the orbital stations Salyut-6 and Skylab have an energy dependence of the relative abundances not inconsistent with above-noted mechanism for the formation of energetic ions of the inner radiation belt.« less

Mercury-induced fragmentation of n-decane and n-undecane in positive mode ion mobility spectrometry.

PubMed

Gunzer, F

2015-09-21

Ion mobility spectrometry is a well-known technique for trace gas analysis. Using soft ionization techniques, fragmentation of analytes is normally not observed, with the consequence that analyte spectra of single substances are quite simple, i.e. showing in general only one peak. If the concentration is high enough, an extra cluster peak involving two analyte molecules can often be observed. When investigating n-alkanes, different results regarding the number of peaks in the spectra have been obtained in the past using this spectrometric technique. Here we present results obtained when analyzing n-alkanes (n-hexane to n-undecane) with a pulsed electron source, which show no fragmentation or clustering at all. However, when investigating a mixture of mercury and an n-alkane, a situation quite typical in the oil and gas industry, a strong fragmentation and cluster formation involving these fragments has been observed exclusively for n-decane and n-undecane.

DEATH-STAR: Silicon and Photovoltaic Fission Fragment Detector Arrays for Light-Ion Induced Fission Correlation Studies

NASA Astrophysics Data System (ADS)

Koglin, J. D.; Burke, J. T.; Fisher, S. E.; Jovanovic, I.

2017-05-01

The Direct Excitation Angular Tracking pHotovoltaic-Silicon Telescope ARray (DEATH-STAR) combines a series of 12 silicon detectors in a ΔE - E configuration for charged particle identification with a large-area array of 56 photovoltaic (solar) cells for detection of fission fragments. The combination of many scattering angles and fission fragment detectors allows for an angular-resolved tool to study reaction cross sections using the surrogate method, anisotropic fission distributions, and angular momentum transfers through stripping, transfer, inelastic scattering, and other direct nuclear reactions. The unique photovoltaic detectors efficiently detect fission fragments while being insensitive to light ions and have a timing resolution of 15.63±0.37 ns. Alpha particles are detected with a resolution of 35.5 keV 1σ at 7.9 MeV. Measured fission fragment angular distributions are also presented.

Secondary radiation measurements for particle therapy applications: nuclear fragmentation produced by 4He ion beams in a PMMA target.

PubMed

Marafini, M; Paramatti, R; Pinci, D; Battistoni, G; Collamati, F; De Lucia, E; Faccini, R; Frallicciardi, P M; Mancini-Terracciano, C; Mattei, I; Muraro, S; Piersanti, L; Rovituso, M; Rucinski, A; Russomando, A; Sarti, A; Sciubba, A; Solfaroli Camillocci, E; Toppi, M; Traini, G; Voena, C; Patera, V

2017-02-21

Nowadays there is a growing interest in particle therapy treatments exploiting light ion beams against tumors due to their enhanced relative biological effectiveness and high space selectivity. In particular promising results are obtained by the use of 4 He projectiles. Unlike the treatments performed using protons, the beam ions can undergo a fragmentation process when interacting with the atomic nuclei in the patient body. In this paper the results of measurements performed at the Heidelberg Ion-Beam Therapy center are reported. For the first time the absolute fluxes and the energy spectra of the fragments-protons, deuterons, and tritons-produced by 4 He ion beams of 102, 125 and 145 MeV u -1 energies on a poly-methyl methacrylate target were evaluated at different angles. The obtained results are particularly relevant in view of the necessary optimization and review of the treatment planning software being developed for clinical use of 4 He beams in clinical routine and the relative bench-marking of Monte Carlo algorithm predictions.

Infrared Multiple-Photon Dissociation Action Spectroscopy of the b2 + Ion from PPG: Evidence of Third Residue Affecting b2 + Fragment Structure

NASA Astrophysics Data System (ADS)

Poutsma, John C.; Martens, Jonathan; Oomens, Jos; Maitre, Phillipe; Steinmetz, Vincent; Bernier, Matthew; Jia, Mengxuan; Wysocki, Vicki

2017-07-01

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2 + fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2 + ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2 + ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation.

Hyperthermal (1-100 eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films

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

Deng Zongwu; Bald, Ilko; Illenberger, Eugen

2007-10-14

Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1-100 eV) scattering of one such fragment ion (N{sup +}) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N{sup +} ion scattering at kinetic energies down to 10 eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-{sup 13}C D-ribose and 1-D D-ribose) partlymore » reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN{sup -} anion at energies down to {approx}5 eV. N{sup +} ions also abstract hydrogen from hydroxyl groups of the molecules to form NH{sup -} and NH{sub 2}{sup -} anions. A fraction of O/O{sup -} fragments abstract hydrogen to form OH{sup -}. The formation of H{sub 3}O{sup +} ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes.« less

DNA fragmentation induced by Fe ions in human cells: shielding influence on spatially correlated damage

NASA Technical Reports Server (NTRS)

Antonelli, F.; Belli, M.; Campa, A.; Chatterjee, A.; Dini, V.; Esposito, G.; Rydberg, B.; Simone, G.; Tabocchini, M. A.

2004-01-01

Outside the magnetic field of the Earth, high energy heavy ions constitute a relevant part of the biologically significant dose to astronauts during the very long travels through space. The typical pattern of energy deposition in the matter by heavy ions on the microscopic scale is believed to produce spatially correlated damage in the DNA which is critical for radiobiological effects. We have investigated the influence of a lucite shielding on the initial production of very small DNA fragments in human fibroblasts irradiated with 1 GeV/u iron (Fe) ions. We also used gamma rays as reference radiation. Our results show: (1) a lower effect per incident ion when the shielding is used; (2) an higher DNA Double Strand Breaks (DSB) induction by Fe ions than by gamma rays in the size range 1-23 kbp; (3) a non-random DNA DSB induction by Fe ions. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Fragmentation Pathways of Lithiated Hexose Monosaccharides

NASA Astrophysics Data System (ADS)

Abutokaikah, Maha T.; Frye, Joseph W.; Tschampel, John; Rabus, Jordan M.; Bythell, Benjamin J.

2018-05-01

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. [Figure not available: see fulltext.

DEATH-STAR: Silicon and photovoltaic fission fragment detector arrays for light-ion induced fission correlation studies

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

Koglin, J. D.; Burke, J. T.; Fisher, S. E.

Here, the Direct Excitation Angular Tracking pHotovoltaic-Silicon Telescope ARray (DEATH-STAR) combines a series of 12 silicon detectors in a ΔE–E configuration for charged particle identification with a large-area array of 56 photovoltaic (solar) cells for detection of fission fragments. The combination of many scattering angles and fission fragment detectors allows for an angular-resolved tool to study reaction cross sections using the surrogate method, anisotropic fission distributions, and angular momentum transfers through stripping, transfer, inelastic scattering, and other direct nuclear reactions. The unique photovoltaic detectors efficiently detect fission fragments while being insensitive to light ions and have a timing resolution ofmore » 15.63±0.37 ns. Alpha particles are detected with a resolution of 35.5 keV 1σ at 7.9 MeV. Measured fission fragment angular distributions are also presented.« less

DEATH-STAR: Silicon and photovoltaic fission fragment detector arrays for light-ion induced fission correlation studies

DOE PAGES

Koglin, J. D.; Burke, J. T.; Fisher, S. E.; ...

2017-02-20

Here, the Direct Excitation Angular Tracking pHotovoltaic-Silicon Telescope ARray (DEATH-STAR) combines a series of 12 silicon detectors in a ΔE–E configuration for charged particle identification with a large-area array of 56 photovoltaic (solar) cells for detection of fission fragments. The combination of many scattering angles and fission fragment detectors allows for an angular-resolved tool to study reaction cross sections using the surrogate method, anisotropic fission distributions, and angular momentum transfers through stripping, transfer, inelastic scattering, and other direct nuclear reactions. The unique photovoltaic detectors efficiently detect fission fragments while being insensitive to light ions and have a timing resolution ofmore » 15.63±0.37 ns. Alpha particles are detected with a resolution of 35.5 keV 1σ at 7.9 MeV. Measured fission fragment angular distributions are also presented.« less

Fragmentation of copper current collectors in Li-ion batteries during spherical indentation

NASA Astrophysics Data System (ADS)

Wang, Hsin; Watkins, Thomas R.; Simunovic, Srdjan; Bingham, Philip R.; Allu, Srikanth; Turner, John A.

2017-10-01

Large, areal, brittle fracture of copper current collector foils has been observed by 3D x-ray computed tomography (XCT) of a spherically indented Li-ion cell. This fracture is hidden and non-catastrophic to a degree because the graphite layers deform plastically, and hold the materials together so that the cracks in the foils cannot be seen under optical and electron microscopy. The cracking of copper foils could not be immediately confirmed when the cell is opened for post-mortem examination. However, 3D XCT on the indented cell reveals ;mud cracks; within the copper layer and an X-ray radiograph on a single foil of the Cu anode shows clearly that the copper foil has broken into multiple pieces. This failure mode of anodes in Li-ion cell has very important implications on the behavior of Li-ion cells under mechanical abuse conditions. The fragmentation of current collectors in the anode must be taken into consideration for the electrochemical responses which may lead to capacity loss and affect thermal runaway behavior of the cells.

Low-energy mass-selected ion beam production of fragments produced from hexamethyldisilane for SiC film formation

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

Yoshimura, Satoru, E-mail: yosimura@ppl.eng.osaka-u.ac.jp; Sugimoto, Satoshi; Kiuchi, Masato

2016-03-14

We have proposed an experimental methodology which makes it possible to deposit silicon carbide (SiC) films on Si substrates with a low-energy mass-selected ion beam system using hexamethyldisilane (HMD) as a gas source. In this study, one of the fragment ions produced from HMD, SiCH{sub 4}{sup +}, was mass-selected. The ion energy was approximately 100 eV. Then, the SiCH{sub 4}{sup +} ions were irradiated to a Si(100) substrate. When the temperature of the Si substrate was set at 800 °C during the ion irradiation, the X-ray diffraction and Raman spectroscopy of the substrate following the completion of ion irradiation experiment demonstrated themore » occurrence of 3C-SiC deposition.« less

The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. I. Fragment fluence spectra

NASA Technical Reports Server (NTRS)

Zeitlin, C.; Miller, J.; Heilbronn, L.; Frankel, K.; Gong, W.; Schimmerling, W.

1996-01-01

The fragmentation of 510 MeV/nucleon iron ions in several thicknesses of polyethylene has been measured. Non-interacting primary beam particles and fragments have been identified and their LETs calculated by measuring ionization energy loss in a stack of silicon detectors. Fluences, normalized to the incident beam intensity and corrected for detector effects, are presented for each fragment charge and target. Histograms of fluence as a function of LET are also presented. Some implications of these data for measurements of the biological effects of heavy ions are discussed.

Manifestation of quark clusters in the emission of cumulative protons in the experiment on the fragmentation of carbon ions

NASA Astrophysics Data System (ADS)

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Krutenkova, A. P.; Kulikov, V. V.; Martemyanov, M. A.; Matsyuk, M. A.; Turdakina, E. N.; Khanov, A. I.

2013-06-01

The proton yields at an angle of 3.5° have been measured in the FRAGM experiment on the fragmentation of carbon ions with the energies T 0 = 0.6, 0.95, and 2.0 GeV/nucleon on a beryllium target at the heavy-ion accelerator complex TWAC (terawatt accumulator, Institute for Theoretical and Experimental Physics). The data are represented in the form of the dependences of the invariant cross section for proton yield on the cumulative variable x in the range of 0.9 < x < 2.4. This invariant cross section varies within six orders of magnitude. The proton spectra have been analyzed within the theoretical approach of the fragmentation of quark clusters with the fragmentation functions obtained in the quark-gluon string model. The probabilities of the existence of six- and nine-quark clusters in the carbon nuclei are estimated as 8-12 and 0.2-0.6%, respectively. The results are compared to the estimated of quark effects obtained by other methods.

Isomer-dependent fragmentation dynamics of inner-shell photoionized difluoroiodobenzene

DOE PAGES

Ablikim, Utuq; Bomme, Cédric; Savelyev, Evgeny; ...

2017-05-11

The fragmentation dynamics of 2,6- and 3,5-difluoroiodobenzene after iodine 4d inner-shell photoionization with soft X-rays are studied using coincident electron and ion momentum imaging. By analyzing the momentum correlation between iodine and fluorine cations in three-fold ion coincidence events, we can distinguish the two isomers experimentally. Classical Coulomb explosion simulations are in overall agreement with the experimentally determined fragment ion kinetic energies and momentum correlations and point toward different fragmentation mechanisms and time scales. Finally, while most three-body fragmentation channels show clear evidence for sequential fragmentation on a time scale larger than the rotational period of the fragments, the breakupmore » into iodine and fluorine cations and a third charged co-fragment appears to occur within several hundred femtoseconds.« less

Nuclear fragmentation energy and momentum transfer distributions in relativistic heavy-ion collisions

NASA Technical Reports Server (NTRS)

Khandelwal, Govind S.; Khan, Ferdous

1989-01-01

An optical model description of energy and momentum transfer in relativistic heavy-ion collisions, based upon composite particle multiple scattering theory, is presented. Transverse and longitudinal momentum transfers to the projectile are shown to arise from the real and absorptive part of the optical potential, respectively. Comparisons of fragment momentum distribution observables with experiments are made and trends outlined based on our knowledge of the underlying nucleon-nucleon interaction. Corrections to the above calculations are discussed. Finally, use of the model as a tool for estimating collision impact parameters is indicated.

Absolute Infrared Intensities and Interstellar Ice Abundances- From Neutrals to Ions

NASA Astrophysics Data System (ADS)

Gerakines, Perry

Infrared (IR) telescopes, such as Spitzer and SOFIA, have revealed a rich variety of chemical species trapped in interstellar ices. However, quantifying the abundances of these species has been difficult because some molecules, such as formaldehyde (H2CO), and some ions, such as ammonium (NH4+), have poorly-known IR optical parameters, such as band strengths and optical constants. In the case of NH4+, the most widely used band-intensity values are from a mere two measurements published over a decade ago. Those two experiments cannot be repeated or checked as the original publication provided no information on reaction temperature, heating rate, spectral resolution, and so forth, and the two authors are no longer active in the field. Moreover, neither kinetic data nor statistics on the two measurements were provided, clearly an unsatisfactory situation. Exacerbating the problem is that NH4+ is sometimes used as a check on the IR spectral intensities of other ions, such as OCN- (cyanate), which has its own checkered past. We propose to correct these problems associated with abundance determinations of selected interstellar ices. We will combine two recent successful efforts from our laboratory and measure band intensities for NH4+ and OCN-, as well as HCOO- (formate). To unravel the interstellar formate band requires that we also properly determine its spectral baseline to distinguish from co-absorbing species, primarily formaldehyde (H2CO). Since the latter also has, at best, poorly-determined IR absolute intensities, we will measure them at multiple temperatures and ice phases for this project. This work will build on our recent success in deriving optical constants from IR spectra for interstellar hydrocarbon and nitrile ices (Hudson et al., 2014a, 2014b), and in generating NH4+ in situ for a study of Jupiter's atmosphere (Loeffler and Hudson, 2015). As a bonus, the proposed measurements also will enable the determination of band-strengths for such ions as CN-, NO

Fragmentation of copper current collectors in Li-ion batteries during spherical indentation

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

Wang, Hsin; Watkins, Thomas R.; Simunovic, Srdjan

Large, areal, brittle fracture of copper current collector foils was observed by 3D x-ray computed tomography (XCT) of a spherically indented Li-ion cell. This fracture was hidden and non-catastrophic to a degree because the graphite layers deformed plastically, and held the materials together so that the cracks in the foils could not be seen under optical and electron microscopy. 3D XCT on the indented cell showed “mud cracks” within the copper layer. The cracking of copper foils could not be immediately confirmed when the cell was opened for post-mortem examination. However, an X-ray radiograph on a single foil of themore » Cu anode showed clearly that the copper foil had broken into multiple pieces similar to the brittle cracking of a ceramic under indentation. This new failure mode of anodes on Li-ion cell has very important implications on the behavior of Li-ion cells under mechanical abuse conditions. Furthermore, the fragmentation of current collectors in the anode must be taken into consideration for the electrochemical responses which may lead to capacity loss and affect thermal runaway behavior of the cells.« less

Fragmentation of copper current collectors in Li-ion batteries during spherical indentation

DOE PAGES

Wang, Hsin; Watkins, Thomas R.; Simunovic, Srdjan; ...

2017-08-29

Large, areal, brittle fracture of copper current collector foils was observed by 3D x-ray computed tomography (XCT) of a spherically indented Li-ion cell. This fracture was hidden and non-catastrophic to a degree because the graphite layers deformed plastically, and held the materials together so that the cracks in the foils could not be seen under optical and electron microscopy. 3D XCT on the indented cell showed “mud cracks” within the copper layer. The cracking of copper foils could not be immediately confirmed when the cell was opened for post-mortem examination. However, an X-ray radiograph on a single foil of themore » Cu anode showed clearly that the copper foil had broken into multiple pieces similar to the brittle cracking of a ceramic under indentation. This new failure mode of anodes on Li-ion cell has very important implications on the behavior of Li-ion cells under mechanical abuse conditions. Furthermore, the fragmentation of current collectors in the anode must be taken into consideration for the electrochemical responses which may lead to capacity loss and affect thermal runaway behavior of the cells.« less

Structural characterization of arginine-vasopressin and lysine-vasopressin by Fourier- transform ion cyclotron resonance mass spectrometry and infrared multiphoton dissociation.

PubMed

Bianco, Giuliana; Battista, Fabio; Buchicchio, Alessandro; Amarena, Concetta G; Schmitt-Kopplin, Philippe; Guerrieri, Antonio

2015-01-01

Arginine-vasopressin (AVP) and lysine-vasopressin (LVP) were analyzed by reversed-phase liquid chromatography/mass spectrometry (LC-MS) using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) electrospray ionization (ESI) in the positive ion mode. LVP and AVP exhibited the protonated adduct [M+H](+) as the predominant ion at m/z 1056.43965 and at m/z 1084.44561, respectively. Infrared multiphoton dissociation (IRMPD), using a CO(2) laser source at a wavelength of 10.6 μm, was applied to protonated vasopressin molecules. The IRMPD mass spectra presented abundant mass fragments essential for a complete structural information. Several fragment ions, shared between two target molecules, are discussed in detail. Some previously unpublished fragments were identified unambiguously utilizing the high resolution and accurate mass information provided by the FT-ICR mass spectrometer. The opening of the disulfide loop and the cleavage of the peptide bonds within the ring were observed even under low-energy fragmentation conditions. Coupling the high-performance FT-ICR mass spectrometer with IRMPD as a contemporary fragmentation technique proved to be very promising for the structural characterization of vasopressin.

Surface-induced dissociation: a unique tool for studying energetics and kinetics of the gas-phase fragmentation of large ions

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

Laskin, Julia

2015-01-01

Surface-induced dissociation (SID) is valuable tool for investigating activation and dissociation of large ions in tandem mass spectrometry. This account summarizes key findings from studies of the energetics and mechanisms of complex ion dissociation, in which SID experiments were combined with Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data. These studies used time- and collision-energy-resolved SID experiments and SID combined with resonant ejection of selected fragment ions on a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Fast ion activation by collision with a surface combined with the long and variable timescale of a FT-ICR MS is perfectlymore » suited for studying the energetics and dynamics of complex ion dissociation in the gas phase. Modeling of time- and collision-energy-resolved SID enables accurate determination of energy and entropy effects in the dissociation process. It has been demonstrated that entropy effects play an important role in determining the dissociation rates of both covalent and non-covalent bonds in large gaseous ions. SID studies have provided important insights on the competition between charge-directed and charge-remote fragmentation in even-electron peptide ions and the role of charge and radical site on the energetics of the dissociation of odd-electron peptide ions. Furthermore, this work examined factors that affect the strength of non-covalent binding, as well as the competition between covalent and non-covalent bond cleavages and between proton and electron transfer in model systems. Finally, SID studies have been used to understand the factors affecting nucleation and growth of clusters in solution and the gas phase.« less

Non-thermal ion desorption from an acetonitrile (CH3CN) astrophysical ice analogue studied by electron stimulated ion desorption.

PubMed

Ribeiro, F de A; Almeida, G C; Garcia-Basabe, Y; Wolff, W; Boechat-Roberty, H M; Rocco, M L M

2015-11-07

The incidence of high-energy radiation onto icy surfaces constitutes an important route for leading new neutral or ionized molecular species back to the gas phase in interstellar and circumstellar environments, especially where thermal desorption is negligible. In order to simulate such processes, an acetonitrile ice (CH3CN) frozen at 120 K is bombarded by high energy electrons, and the desorbing positive ions are analyzed by time-of-flight mass spectrometry (TOF-MS). Several fragment and cluster ions were identified, including the Hn=1-3(+), CHn=0-3(+)/NHn=0-1(+); C2Hn=0-3(+)/CHn=0-3N(+), C2Hn=0-6N(+) ion series and the ion clusters (CH3CN)n=1-2(+) and (CH3CN)n=1-2H(+). The energy dependence on the positive ion desorption yield indicates that ion desorption is initiated by Coulomb explosion following Auger electronic decay. The results presented here suggest that non-thermal desorption processes, such as desorption induced by electronic transitions (DIET) may be responsible for delivering neutral and ionic fragments from simple nitrile-bearing ices to the gas-phase, contributing to the production of more complex molecules. The derived desorption yields per electron impact may contribute to chemical evolution models in different cold astrophysical objects, especially where the abundance of CH3CN is expected to be high.

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet*

PubMed Central

Keller, Andrew; Bader, Samuel L.; Shteynberg, David; Hood, Leroy; Moritz, Robert L.

2015-01-01

Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users. PMID:25713123

Fragment profiling of low molecular weight heparins using reversed phase ion pair liquid chromatography-electrospray mass spectrometry.

PubMed

Xu, Xiaohui; Li, Daoyuan; Chi, Lequan; Du, Xuzhao; Bai, Xue; Chi, Lianli

2015-04-30

Low molecular weight heparins (LMWHs) are linear and highly charged carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. Compared to unfractionated heparin (UFH), LMWHs are prevalently used as clinical anticoagulant drugs due to their lower side effects and better bioavailability. The work presented herein provides a rapid and powerful fragment mapping method for structural characterization of LMWHs. The chain fragments of two types of LMWHs, enoxaparin and nadroparin, were generated by controlled enzymatic digestion with each of heparinase I (Hep I, Enzyme Commission (EC) # 4.2.2.7), heparinase II (Hep II, no EC # assigned) and heparinase III (Hep III, EC # 4.2.2.8). Reversed phase ion pair high performance liquid chromatography (RPIP-HPLC) coupled with electrospray ion trap time-of-flight mass spectrometry (ESI-IT-TOF-MS) was used to profile the oligosaccharide chains ranging from disaccharides to decasaccharides. A database containing all theoretical structural compositions was established to assist the mass spectra interpretation. The six digests derived by three enzymes from two types of LMWHs exhibited distinguishable fingerprinting patterns. And a total of 94 enoxaparin fragments and 109 nadroparin fragments were detected and identified. Besides the common LMWH oligosaccharides, many components containing characteristic LMWH structures such as saturated L-idopyranosuronic acid, 2,5-anhydro-D-mannitol, 1,6-anhydro-D-aminopyranose, as well as odd number oligosaccharides were also revealed. Quantitative comparison of major components derived from innovator and generic nadroparin products was presented. This approach to profile LMWHs' fragments offers a highly reproducible, high resolution and information-rich tool for evaluating the quality of this category of anticoagulant drugs or comparing structural similarities among samples from various sources. Copyright © 2015 Elsevier Ltd. All rights reserved.

On moments of the multiplicity events of slow target fragments in relativistic Sulfur-ion collisions

NASA Astrophysics Data System (ADS)

Abdelsalam, A.; Kamel, S.; Rashed, N.; Sabry, N.

2014-07-01

A detailed study on the multiplicity characteristics of the slow target fragments emitted in relativistic heavy-ion collisions has been carried out at ELab = 3.7A and 200A GeV using 32S projectile. The beam energy dependence of the black particles produced in the full phase space of 32S-emulsion (32S-Em) interactions on the target size in terms of their moments (mean, variance, skewness and kurtosis) is investigated. The various order moments of target fragments emitted in the interactions of 32S beams with the heavy (AgBr) target nuclei are estimated in the forward (FHS) and backward (BHS) hemispheres. The investigated values of ratio of variance to mean at both energies show that the multiplicity distributions (MDs) are not Poissonian and the strongly correlated emission of target fragments are in the forward directions. The degree of anisotropic fragment emission and nature of correlation among the emitted fragments are investigated. The energy dependence of entropy is examined in both hemispheres. The entropy values normalized to average multiplicity are found to be energy independent. Scaling of MD of black particles produced in these interactions has been studied to verify the validity of scaling hypothesis via two scaling (Koba-Nielsen-Olesen (KNO)-scaling and Hegyi-scaling) functions. A simplified universal function has been used in each scaling to display the experimental data.

Space-based measurements of elemental abundances and their relation to solar abundances

NASA Technical Reports Server (NTRS)

Coplan, M. A.; Ogilvie, K. W.; Bochsler, P.; Geiss, J.

1990-01-01

The Ion Composition Instrument (ICI) aboard the ISEE-3/ICE spacecraft was in the solar wind continuously from August 1978 to December 1982. The results made it possible to establish long-term average solar wind abundance values for helium, oxygen, neon, silicon, and iron. The Charge-Energy-Mass instrument aboard the CCE spacecraft of the AMPTE mission has measured the abundance of these elements in the magnetosheath and has also added carbon, nitrogen, magnesium, and sulfur to the list. There is strong evidence that these magnetosheath abundances are representative of the solar wind. Other sources of solar wind abundances are Solar Energetic Particle experiments and Apollo lunar foils. When comparing the abundances from all of these sources with photospheric abundances, it is clear that helium is depleted in the solar wind while silicon and iron are enhanced. Solar wind abundances for carbon, nitrogen, oxygen, and neon correlate well with the photospheric values. The incorporation of minor ions into the solar wind appears to depend upon both the ionization times for the elements and the Coulomb drag exerted by the outflowing proton flux.

Light ion components of the galactic cosmic rays: Nuclear interactions and transport theory

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Townsend, L. W.; Wilson, J. W.; Shinn, J. L.; Badhwar, G. D.; Dubey, R. R.

1996-01-01

Light nuclei are present in the primary galactic cosmic rays (GCR) and are produced in thick targets due to projectile or target fragmentation from both nucleon and heavy induced reactions. In the primary GCR, He-4 is the most abundant nucleus after H-1. However, there are also a substantial fluxes of H-2 and He-3. In this paper we describe theoretical models based on quantum multiple scattering theory for the description of light ion nuclear interactions. The energy dependence of the light ion fragmentation cross section is considered with comparisons of inclusive yields and secondary momentum distributions to experiments described. We also analyze the importance of a fast component of lights ions from proton and neutron induced target fragementation. These theoretical models have been incorporated into the cosmic ray transport code HZETRN and will be used to analyze the role of shielding materials in modulating the production and the energy spectrum of light ions.

Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

NASA Astrophysics Data System (ADS)

Medzihradszky, Katalin F.; Bohlen, Christopher J.

2012-05-01

A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

The collision of a hypervelocity massive projectile with free-standing graphene: Investigation of secondary ion emission and projectile fragmentation.

PubMed

Geng, Sheng; Verkhoturov, Stanislav V; Eller, Michael J; Della-Negra, Serge; Schweikert, Emile A

2017-02-07

We present here the study of the individual hypervelocity massive projectiles (440-540 keV, 33-36 km/s Au 400 4+ cluster) impact on 1-layer free-standing graphene. The secondary ions were detected and recorded separately from each individual impact in the transmission direction using a time-of-flight mass spectrometer. We observed C 1-10 ± ions emitted from graphene, the projectiles which penetrated the graphene, and the Au 1-3 ± fragment ions in mass spectra. During the projectile-graphene interaction, the projectile loses ∼15% of its initial kinetic energy (∼0.18 keV/atom, 72 keV/projectile). The Au projectiles are neutralized when approaching the graphene and then partially ionized again via electron tunneling from the hot rims of the holes on graphene, obtaining positive and negative charges. The projectile reaches an internal energy of ∼450-500 eV (∼4400-4900 K) after the impact and then undergoes a ∼90-100 step fragmentation with the ejection of Au 1 atoms in the experimental time range of ∼0.1 μs.

The collision of a hypervelocity massive projectile with free-standing graphene: Investigation of secondary ion emission and projectile fragmentation

NASA Astrophysics Data System (ADS)

Geng, Sheng; Verkhoturov, Stanislav V.; Eller, Michael J.; Della-Negra, Serge; Schweikert, Emile A.

2017-02-01

We present here the study of the individual hypervelocity massive projectiles (440-540 keV, 33-36 km/s Au4004+ cluster) impact on 1-layer free-standing graphene. The secondary ions were detected and recorded separately from each individual impact in the transmission direction using a time-of-flight mass spectrometer. We observed C1-10± ions emitted from graphene, the projectiles which penetrated the graphene, and the Au1-3± fragment ions in mass spectra. During the projectile-graphene interaction, the projectile loses ˜15% of its initial kinetic energy (˜0.18 keV/atom, 72 keV/projectile). The Au projectiles are neutralized when approaching the graphene and then partially ionized again via electron tunneling from the hot rims of the holes on graphene, obtaining positive and negative charges. The projectile reaches an internal energy of ˜450-500 eV (˜4400-4900 K) after the impact and then undergoes a ˜90-100 step fragmentation with the ejection of Au1 atoms in the experimental time range of ˜0.1 μs.

Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry.

PubMed

Nikolskiy, Igor; Siuzdak, Gary; Patti, Gary J

2015-06-15

The goal of large-scale metabolite profiling is to compare the relative concentrations of as many metabolites extracted from biological samples as possible. This is typically accomplished by measuring the abundances of thousands of ions with high-resolution and high mass accuracy mass spectrometers. Although the data from these instruments provide a comprehensive fingerprint of each sample, identifying the structures of the thousands of detected ions is still challenging and time intensive. An alternative, less-comprehensive approach is to use triple quadrupole (QqQ) mass spectrometry to analyze predetermined sets of metabolites (typically fewer than several hundred). This is done using authentic standards to develop QqQ experiments that specifically detect only the targeted metabolites, with the advantage that the need for ion identification after profiling is eliminated. Here, we propose a framework to extend the application of QqQ mass spectrometers to large-scale metabolite profiling. We aim to provide a foundation for designing QqQ multiple reaction monitoring (MRM) experiments for each of the 82 696 metabolites in the METLIN metabolite database. First, we identify common fragmentation products from the experimental fragmentation data in METLIN. Then, we model the likelihoods of each precursor structure in METLIN producing each common fragmentation product. With these likelihood estimates, we select ensembles of common fragmentation products that minimize our uncertainty about metabolite identities. We demonstrate encouraging performance and, based on our results, we suggest how our method can be integrated with future work to develop large-scale MRM experiments. Our predictions, Supplementary results, and the code for estimating likelihoods and selecting ensembles of fragmentation reactions are made available on the lab website at http://pattilab.wustl.edu/FragPred. © The Author 2015. Published by Oxford University Press. All rights reserved. For

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Edelson-Averbukh, Marina; Shevchenko, Andrej; Pipkorn, Rüdiger; Lehmann, Wolf D.

2011-12-01

Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80]- and [M-H-98]- fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79](n-1)- and [M-nH-79-NL]( n-1)- ( n = 2, 3) fragment ions (NL = neutral loss).

Electron impact fragmentation of thymine: partial ionization cross sections for positive fragments

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Mahon, Francis; Barrett, Gerard; Gradziel, Marcin L.

2014-06-01

We have measured mass spectra for positive ions for low-energy electron impact on thymine using a reflectron time-of-flight mass spectrometer. Using computer controlled data acquisition, mass spectra have been acquired for electron impact energies up to 100 eV in steps of 0.5 eV. Ion yield curves for most of the fragment ions have been determined by fitting groups of adjacent peaks in the mass spectra with sequences of normalized Gaussians. The ion yield curves have been normalized by comparing the sum of the ion yields to the average of calculated total ionization cross sections. Appearance energies have been determined. The nearly equal appearance energies of 83 u and 55 u observed in the present work strongly indicate that near threshold the 55 u ion is formed directly by the breakage of two bonds in the ring, rather than from a successive loss of HNCO and CO from the parent ion. Likewise 54 u is not formed by CO loss from 82 u. The appearance energies are in a number of cases consistent with the loss of one or more hydrogen atoms from a heavier fragment, but 70 u is not formed by hydrogen loss from 71 u.

A modular solid state detector for measuring high energy heavy ion fragmentation near the beam axis

NASA Technical Reports Server (NTRS)

Zeitlin, C. J.; Frankel, K. A.; Gong, W.; Heilbronn, L.; Lampo, E. J.; Leres, R.; Miller, J.; Schimmerling, W.

1994-01-01

A multi-element solid state detector has been designed to measure fluences of fragments produced near the beam axis by high energy heavy ion beams in thick targets. The detector is compact and modular, so as to be readily reconfigured according to the range of fragment charges and energies to be measured. Preamplifier gain settings and detector calibrations are adjustable remotely under computer control. We describe the central detector, its associated detectors and electronics, triggering scheme, data acquisition and particle identification techniques, illustrated by data taken with 600 MeV/u 56Fe beams and thick polyethylene targets at the LBL Bevalac. The applications of this work to space radiation protection are discussed.

Fission fragment yields from heavy-ion-induced reactions measured with a fragment separator

NASA Astrophysics Data System (ADS)

Tarasov, O. B.; Delaune, O.; Farget, F.; Morrissey, D. J.; Amthor, A. M.; Bastin, B.; Bazin, D.; Blank, B.; Cacéres, L.; Chbihi, A.; Fernández-Dominguez, B.; Grévy, S.; Kamalou, O.; Lukyanov, S. M.; Mittig, W.; Pereira, J.; Perrot, L.; Saint-Laurent, M.-G.; Savajols, H.; Sherrill, B. M.; Stodel, C.; Thomas, J. C.; Villari, A. C.

2018-04-01

The systematic study of fission fragment yields under different initial conditions has provided valuable experimental data for benchmarking models of fission product yields. Nuclear reactions using inverse kinematics coupled to the use of a high-resolution spectrometer with good fragment identification are shown here to be a powerful tool to measure the inclusive isotopic yields of fission fragments. In-flight fusion-fission was used in this work to produce secondary beams of neutron-rich isotopes in the collisions of a 238U beam at 24 MeV/u with 9Be and 12C targets at GANIL using the LISE3 fragment separator. Unique identification of the A, Z, and atomic charge state, q, of fission products was attained with the Δ E- TKE-B ρ- ToF measurement technique. Mass, and atomic number distributions are reported for the two reactions. The results show the importance of different reaction mechanisms in the two cases. The optimal target material for higher yields of neutron-rich high- Z isotopes produced in fusion-fission reactions as a function of projectile energy is discussed.

Fragmentation of endohedral fullerene H o 3 N @ C 80 in an intense femtosecond near-infrared laser field

DOE PAGES

Xiong, Hui; Fang, Li; Osipov, Timur; ...

2018-02-22

The fragmentation of gas phase endohedral fullerene, Ho 3N@C 80, was investigated using femtosecond near-infrared laser pulses with an ion velocity map imaging spectrometer. Here, we observed that Ho + abundance associated with carbon cage opening dominates at an intensity of 1.1 x 10 14 W/cm 2. As the intensity increases, the Ho + yield associated with multifragmentation of the carbon cage exceeds the prominence of Ho + associated with the gentler carbon cage opening. Moreover, the power law dependence of Ho + on laser intensity indicates that the transition of the most likely fragmentation mechanisms occurs around 2.0 xmore » 10 14 W/cn 2.« less

Fragmentation of endohedral fullerene H o 3 N @ C 80 in an intense femtosecond near-infrared laser field

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

Xiong, Hui; Fang, Li; Osipov, Timur

The fragmentation of gas phase endohedral fullerene, Ho 3N@C 80, was investigated using femtosecond near-infrared laser pulses with an ion velocity map imaging spectrometer. Here, we observed that Ho + abundance associated with carbon cage opening dominates at an intensity of 1.1 x 10 14 W/cm 2. As the intensity increases, the Ho + yield associated with multifragmentation of the carbon cage exceeds the prominence of Ho + associated with the gentler carbon cage opening. Moreover, the power law dependence of Ho + on laser intensity indicates that the transition of the most likely fragmentation mechanisms occurs around 2.0 xmore » 10 14 W/cn 2.« less

Hydrogen rearrangements in the fragmentation of anthracene by low-energy electron impact

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Dunne, Melissa; Gradziel, Marcin L.

2018-02-01

We have measured mass spectra for positive ions produced by low-energy electron impact on anthracene using a reflectron time-of-flight mass spectrometer. The electron impact energy has been varied from 0 to 100 eV in steps of 0.5 eV. Ion yield curves of most of the fragment ions have been determined by fitting groups of adjacent peaks in the mass spectra with sequences of normalized Gaussians. Appearance energies for all these ions have been determined, and we report the first direct measurement of the triple ionization energy of anthracene at 45.5±0.5 eV. The groups of fragments containing 8-13 carbon atoms provide evidence for hydrogen rearrangements during the fragmentation, involving retention or loss of one or two additional hydrogen atoms. Groups of fragments with 6 and 7 carbon atoms clearly show the presence of doubly-charged fragments. The smaller fragments with 1-4 carbon atoms all show broadened peaks, and these fragments may be partly or mostly due to energetic charge-separation fragmentations of doubly-charged anthracene.

Evidence of diketopiperazine and oxazolone structures for HA b2+ ion.

PubMed

Perkins, Brittany R; Chamot-Rooke, Julia; Yoon, Sung Hwan; Gucinski, Ashley C; Somogyi, Arpád; Wysocki, Vicki H

2009-12-09

Peptide fragmentation can lead to an oxazolone or diketopiperazine b(2)(+) ion structure. IRMPD spectroscopy combined with computational modeling and gas-phase H/D exchange was used to study the structure of the b(2)(+) ion from protonated HAAAA. The experimental spectrum of the b(2)(+) ion matches both the experimental spectrum for the protonated cyclic dipeptide HA (a commercial diketopiperazine) and the theoretical spectrum for a diketopiperazine protonated at the imidazole pi nitrogen. A characteristic band at 1875 cm(-1) and increased abundance of the peaks at 1619 and 1683 cm(-1) indicate a second population corresponding to an oxazolone species. H/D exchange also shows a mixture of two populations consistent with a mixture of b(2)(+) ion diketopiperazine and oxazolone structures.

Complementary b/y fragment ion pairs from post-source decay of metastable YahO for calibration of MALDI-TOF-TOF-MS/MS

USDA-ARS?s Scientific Manuscript database

Complementary b/y fragment ion pairs from post-source decay (PSD) of metastable YahO protein ion were evaluated for use in the calibration of MALDI-TOF-TOF for tandem mass spectrometry (MS/MS). The yahO gene from pathogenic Escherichia coli O157:H7 strain EDL933 was cloned into a pBAD18 plasmid vect...

The identification of disulfides in ricin D using proteolytic cleavage followed by negative-ion nano-electrospray ionization mass spectrometry of the peptide fragments.

PubMed

Tran, T T Nha; Brinkworth, Craig S; Bowie, John H

2015-01-30

To use negative-ion nano-electrospray ionization mass spectrometry of peptides from the tryptic digest of ricin D, to provide sequence information; in particular, to identify disulfide position and connectivity. Negative-ion fragmentations of peptides from the tryptic digest of ricin D was studied using a Waters QTOF2 mass spectrometer operating in MS and MS(2) modes. Twenty-three peptides were obtained following high-performance liquid chromatography and studied by negative-ion mass spectrometry covering 73% of the amino-acid residues of ricin D. Five disulfide-containing peptides were identified, three intermolecular and two intramolecular disulfide-containing peptides. The [M-H](-) anions of the intermolecular disulfides undergo facile cleavage of the disulfide units to produce fragment peptides. In negative-ion collision-induced dissociation (CID) these source-formed anions undergo backbone cleavages, which provide sequencing information. The two intramolecular disulfides were converted proteolytically into intermolecular disulfides, which were identified as outlined above. The positions of the five disulfide groups in ricin D may be determined by characteristic negative-ion cleavage of the disulfide groups, while sequence information may be determined using the standard negative-ion backbone cleavages of the resulting cleaved peptides. Negative-ion mass spectrometry can also be used to provide partial sequencing information for other peptides (i.e. those not containing Cys) using the standard negative-ion backbone cleavages of these peptides. Copyright © 2014 John Wiley & Sons, Ltd.

Separation and characterization of unknown impurities and isomers in flomoxef sodium by LC-IT-TOF MS and study of their negative-ion fragmentation regularities.

PubMed

Yu, Xu; Wang, Fan; Li, Jiani; Shan, Weiguang; Zhu, Bingqi; Wang, Jian

2017-06-05

Thirteen unknown impurities in flomoxef sodium were separated and characterized by liquid chromatography coupled with high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF MS)with positive and negative modes of electrospray ionization method for further improvement of official monographs in pharmacopoeias. The fragmentation patterns of impurities in flomoxef in the negative ion mode were studied in detail, and new negative-ion fragmentation regularities were discovered. Chromatographic separation was performed on a Kromasil C18 column (250mm×4.6mm, 5μm). The mobile phase consisted of (A) ammonium formate aqueous solution (10mM)-methanol (84:16, v/v) and (B) ammonium formate aqueous solution (10mM)-methanol (47:53, v/v). In order to determine the m/z values of the molecular ions and formulas of all detected impurities, full scan LC-MS in both positive and negative ion modes was firstly executed to obtain the m/z value of the molecules. Then LC-MS 2 and LC-MS 3 were carried out on target compounds to obtain as much structural information as possible. Complete fragmentation patterns of impurities were studied and used to obtain information about the structures of these impurities. Structures of thirteen unknown degradation products in flomoxef sodium were deduced based on the high resolution MS n data with both positive and negative modes. The forming mechanisms of degradation products in flomoxef sodium were also studied. Copyright © 2017. Published by Elsevier B.V.

Experimental determination of particle range and dose distribution in thick targets through fragmentation reactions of stable heavy ions.

PubMed

Inaniwa, Taku; Kohno, Toshiyuki; Tomitani, Takehiro; Urakabe, Eriko; Sato, Shinji; Kanazawa, Mitsutaka; Kanai, Tatsuaki

2006-09-07

In radiation therapy with highly energetic heavy ions, the conformal irradiation of a tumour can be achieved by using their advantageous features such as the good dose localization and the high relative biological effectiveness around their mean range. For effective utilization of such properties, it is necessary to evaluate the range of incident ions and the deposited dose distribution in a patient's body. Several methods have been proposed to derive such physical quantities; one of them uses positron emitters generated through projectile fragmentation reactions of incident ions with target nuclei. We have proposed the application of the maximum likelihood estimation (MLE) method to a detected annihilation gamma-ray distribution for determination of the range of incident ions in a target and we have demonstrated the effectiveness of the method with computer simulations. In this paper, a water, a polyethylene and a polymethyl methacrylate target were each irradiated with stable (12)C, (14)N, (16)O and (20)Ne beams. Except for a few combinations of incident beams and targets, the MLE method could determine the range of incident ions R(MLE) with a difference between R(MLE) and the experimental range of less than 2.0 mm under the circumstance that the measurement of annihilation gamma rays was started just after the irradiation of 61.4 s and lasted for 500 s. In the process of evaluating the range of incident ions with the MLE method, we must calculate many physical quantities such as the fluence and the energy of both primary ions and fragments as a function of depth in a target. Consequently, by using them we can obtain the dose distribution. Thus, when the mean range of incident ions is determined with the MLE method, the annihilation gamma-ray distribution and the deposited dose distribution can be derived simultaneously. The derived dose distributions in water for the mono-energetic heavy-ion beams of four species were compared with those measured with an

Secondary ion emission from phosphatidic acid sandwich films under atomic and molecular primary ion bombardment

NASA Astrophysics Data System (ADS)

Stapel, D.; Benninghoven, A.

2001-11-01

Secondary ion yields increase considerably when changing from atomic to molecular primary ions. Since secondary ion emission from deeper layers could result in a pronounced yield increase, the secondary ion emission depth of molecular fragments was investigated. A phosphatidic acid Langmuir-Blodgett (LB) sandwich system was applied. The well-defined layer structure of the applied sample allows the assignment of different depths of origin to the selected fragment ions. At least 93% of the detected characteristic molecular fragment ions originate from the first and second layers. This holds true for all applied atomic and molecular primary ions.

Season-modulated responses of Neotropical bats to forest fragmentation.

PubMed

Ferreira, Diogo F; Rocha, Ricardo; López-Baucells, Adrià; Farneda, Fábio Z; Carreiras, João M B; Palmeirim, Jorge M; Meyer, Christoph F J

2017-06-01

Seasonality causes fluctuations in resource availability, affecting the presence and abundance of animal species. The impacts of these oscillations on wildlife populations can be exacerbated by habitat fragmentation. We assessed differences in bat species abundance between the wet and dry season in a fragmented landscape in the Central Amazon characterized by primary forest fragments embedded in a secondary forest matrix. We also evaluated whether the relative importance of local vegetation structure versus landscape characteristics (composition and configuration) in shaping bat abundance patterns varied between seasons. Our working hypotheses were that abundance responses are species as well as season specific, and that in the wet season, local vegetation structure is a stronger determinant of bat abundance than landscape-scale attributes. Generalized linear mixed-effects models in combination with hierarchical partitioning revealed that relationships between species abundances and local vegetation structure and landscape characteristics were both season specific and scale dependent. Overall, landscape characteristics were more important than local vegetation characteristics, suggesting that landscape structure is likely to play an even more important role in landscapes with higher fragment-matrix contrast. Responses varied between frugivores and animalivores. In the dry season, frugivores responded more to compositional metrics, whereas during the wet season, local and configurational metrics were more important. Animalivores showed similar patterns in both seasons, responding to the same group of metrics in both seasons. Differences in responses likely reflect seasonal differences in the phenology of flowering and fruiting between primary and secondary forests, which affected the foraging behavior and habitat use of bats. Management actions should encompass multiscale approaches to account for the idiosyncratic responses of species to seasonal variation in

Collision-induced dissociation of aminophospholipids (PE, MMPE, DMPE, PS): an apparently known fragmentation process revisited.

PubMed

Pittenauer, Ernst; Rehulka, Pavel; Winkler, Wolfgang; Allmaier, Günter

2015-07-01

A new type of low-mass substituted 4-oxazolin product ions of [M + H](+) precursor ions of aminophospholipids (glycerophosphatidylethanolamine, glycerophosphatidyl-N-methylethanolamine, glycerophosphatidyl-N,N-dimethylethanolamine, glycerophosphatidylserine) resulting from high-energy collision-induced dissociation (matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry) and low-energy collision-induced dissociation (e.g., electrospray ionization quadrupole reflectron time-of-flight mass spectrometry) with accurate mass determination is described; these were previously misidentified as CHO-containing radical cationic product ions. The mechanism for the formation of these ions is proposed to be via rapid loss of water followed by cyclization to an 11-membered-ring transition state for the sn-1 fatty acid substituent and to a ten-membered-ring transition state for the sn-2 fatty acid substituent, and via final loss of monoacylglycerol phosphate, leading to substituted 4-oxazolin product ions. The minimum structural requirement for this interesting skeletal rearrangement fragmentation is an amino group linked to at least one hydrogen atom (i.e., ethanolamine, N-methylethanolamine, serine). Therefore, N,N-dimethylethanolamine derivates do not exhibit this type of fragmentation. The analytical value of these product ions is given by the fact that by post source decay and particularly high-energy collision-induced dissociation achieved via matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry, the sn-2-related substituted 4-oxazolin product ion is always significantly more abundant than the sn-1-related one, which is quite helpful for detailed structural analysis of complex lipids. All other important product ions found are described in detail (following our previously published glycerophospholipid product ion nomenclature; Pittenauer and Allmaier, Int. J. Mass. Spectrom

Seasonal Blowfly Distribution and Abundance in Fragmented Landscapes. Is It Useful in Forensic Inference about Where a Corpse Has Been Decaying?

PubMed Central

Zabala, Jabi; Díaz, Beatriz; Saloña-Bordas, Marta I.

2014-01-01

Blowflies are insects of forensic interest as they may indicate characteristics of the environment where a body has been laying prior to the discovery. In order to estimate changes in community related to landscape and to assess if blowfly species can be used as indicators of the landscape where a corpse has been decaying, we studied the blowfly community and how it is affected by landscape in a 7,000 km2 region during a whole year. Using baited traps deployed monthly we collected 28,507 individuals of 10 calliphorid species, 7 of them well represented and distributed in the study area. Multiple Analysis of Variance found changes in abundance between seasons in the 7 analyzed species, and changes related to land use in 4 of them (Calliphora vomitoria, Lucilia ampullacea, L. caesar and L. illustris). Generalised Linear Model analyses of abundance of these species compared with landscape descriptors at different scales found only a clear significant relationship between summer abundance of C. vomitoria and distance to urban areas and degree of urbanisation. This relationship explained more deviance when considering the landscape composition at larger geographical scales (up to 2,500 m around sampling site). For the other species, no clear relationship between land uses and abundance was found, and therefore observed changes in their abundance patterns could be the result of other variables, probably small changes in temperature. Our results suggest that blowfly community composition cannot be used to infer in what kind of landscape a corpse has decayed, at least in highly fragmented habitats, the only exception being the summer abundance of C. vomitoria. PMID:24918607

Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance.

PubMed

Johnson, Kenneth L; Mason, Christopher J; Muddiman, David C; Eckel, Jeanette E

2004-09-01

This study quantifies the experimental uncertainty for LC retention time, mass measurement precision, and ion abundance obtained from replicate nLC-dual ESI-FT-ICR analyses of the low molecular weight fraction of serum. We used ultrafiltration to enrich the < 10-kDa fraction of components from the high-abundance proteins in a pooled serum sample derived from ovarian cancer patients. The THRASH algorithm for isotope cluster detection was applied to five replicate nLC-dual ESI-FT-ICR chromatograms. A simple two-level grouping algorithm was applied to the more than 7000 isotope clusters found in each replicate and identified 497 molecular species that appeared in at least four of the replicates. In addition, a representative set of 231 isotope clusters, corresponding to 188 unique molecular species, were manually interpreted to verify the automated algorithm and to set its tolerances. For nLC retention time reproducibility, 95% of the 497 species had a 95% confidence interval of the mean of +/- 0.9 min or less without the use of chromatographic alignment procedures. Furthermore, 95% of the 497 species had a mass measurement precision of < or = 3.2 and < or = 6.3 ppm for internally and externally calibrated spectra, respectively. Moreover, 95% of replicate ion abundance measurements, covering an ion abundance range of approximately 3 orders of magnitude, had a coefficient of variation of less than 62% without using any normalization functions. The variability of ion abundance was independent of LC retention time, mass, and ion abundance quartile. These measures of analytical reproducibility establish a statistical rationale for differentiating healthy and disease patient populations for the elucidation of biomarkers in the low molecular fraction of serum. Copyright 2004 American Chemical Society

Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Marto, J A; White, F M; Seldomridge, S; Marshall, A G

1995-11-01

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode.

Does Tropical Forest Fragmentation Increase Long-Term Variability of Butterfly Communities?

PubMed Central

Leidner, Allison K.; Haddad, Nick M.; Lovejoy, Thomas E.

2010-01-01

Habitat fragmentation is a major driver of biodiversity loss. Yet, the overall effects of fragmentation on biodiversity may be obscured by differences in responses among species. These opposing responses to fragmentation may be manifest in higher variability in species richness and abundance (termed hyperdynamism), and in predictable changes in community composition. We tested whether forest fragmentation causes long-term hyperdynamism in butterfly communities, a taxon that naturally displays large variations in species richness and community composition. Using a dataset from an experimentally fragmented landscape in the central Amazon that spanned 11 years, we evaluated the effect of fragmentation on changes in species richness and community composition through time. Overall, adjusted species richness (adjusted for survey duration) did not differ between fragmented forest and intact forest. However, spatial and temporal variation of adjusted species richness was significantly higher in fragmented forests relative to intact forest. This variation was associated with changes in butterfly community composition, specifically lower proportions of understory shade species and higher proportions of edge species in fragmented forest. Analysis of rarefied species richness, estimated using indices of butterfly abundance, showed no differences between fragmented and intact forest plots in spatial or temporal variation. These results do not contradict the results from adjusted species richness, but rather suggest that higher variability in butterfly adjusted species richness may be explained by changes in butterfly abundance. Combined, these results indicate that butterfly communities in fragmented tropical forests are more variable than in intact forest, and that the natural variability of butterflies was not a buffer against the effects of fragmentation on community dynamics. PMID:20224772

Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kuchibhotla, Bhanuramanand; Kola, Sankara Rao; Medicherla, Jagannadham V.; Cherukuvada, Swamy V.; Dhople, Vishnu M.; Nalam, Madhusudhana Rao

2017-06-01

Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. [Figure not available: see fulltext.

Would protecting tropical forest fragments provide carbon and biodiversity cobenefits under REDD+?

PubMed

Magnago, Luiz Fernando S; Magrach, Ainhoa; Laurance, William F; Martins, Sebastião V; Meira-Neto, João Augusto A; Simonelli, Marcelo; Edwards, David P

2015-09-01

Tropical forests store vast amounts of carbon and are the most biodiverse terrestrial habitats, yet they are being converted and degraded at alarming rates. Given global shortfalls in the budgets required to prevent carbon and biodiversity loss, we need to seek solutions that simultaneously address both issues. Of particular interest are carbon-based payments under the Reducing Emissions from Deforestation and Forest Degradation (REDD+) mechanism to also conserve biodiversity at no additional cost. One potential is for REDD+ to protect forest fragments, especially within biomes where contiguous forest cover has diminished dramatically, but we require empirical tests of the strength of any carbon and biodiversity cobenefits in such fragmented systems. Using the globally threatened Atlantic Forest landscape, we measured above-ground carbon stocks within forest fragments spanning 13 to 23 442 ha in area and with different degrees of isolation. We related these stocks to tree community structure and to the richness and abundance of endemic and IUCN Red-listed species. We found that increasing fragment size has a positive relationship with above-ground carbon stock and with abundance of IUCN Red-listed species and tree community structure. We also found negative relationships between distance from large forest block and tree community structure, endemic species richness and abundance, and IUCN Red-listed species abundance. These resulted in positive congruence between carbon stocks and Red-listed species, and the abundance and richness of endemic species, demonstrating vital cobenefits. As such, protecting forest fragments in hotspots of biodiversity, particularly larger fragments and those closest to sources, offers important carbon and biodiversity cobenefits. More generally, our results suggest that macroscale models of cobenefits under REDD+ have likely overlooked key benefits at small scales, indicating the necessity to apply models that include finer

Observation of shape isomers states in fission fragments

NASA Astrophysics Data System (ADS)

Kamanin, D. V.; Pyatkov, Yu V.; Alexandrov, A. A.; Alexandrova, I. A.; Mkaza, N.; Malaza, V.; Kuznetsova, E. A.; Strekalovsky, A. O.; Strekalovsky, O. V.; Zhuchko, V. E.

2017-06-01

We discuss the manifestations of a new original effect appeared at crossing of the metal foils by fission fragments. We have observed significant mass deficit in the total mass Ms of the fission fragments detected in coincidence with ions knocked out from the foil. It was shown that at the large angles of scattering of the knocked-out ions from the foil predominantly conventional elastic Rutherford scattering takes place. As the result Ms corresponds to the mean mass of the mother system after emission of fission neutrons (no missing mass). In contrast, in near frontal impacts fission fragment misses essential part of its mass. Residual nuclei at least for the fragments from the heavy mass peak show magic nucleon composition.

DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. II. Probing individual notI fragments by hybridization.

PubMed

Löbrich, M; Rydberg, B; Cooper, P K

1994-08-01

The initial yields of DNA double-strand breaks induced by energetic heavy ions (425 MeV/u neon and 250, 400 and 600 MeV/u iron) in comparison to X rays were measured in normal human diploid fibroblast cells within three small areas of the genome, defined by NotI fragments of 3.2, 2.0 and 1.2 Mbp. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated cells, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with probes recognizing single-copy sequences within the three NotI fragments. The gradual disappearance of the full-size NotI fragment with dose and the appearance of a smear of broken DNA molecules are quantified. Assuming Poisson statistics for the number of double-strand breaks induced per NotI fragment of known size, absolute yields of DNA double-strand breaks were calculated and determined to be linear with dose in all cases, with the neon ion (LET 32 keV/microns) producing 4.4 x 10(-3) breaks/Mbp/Gy and all three iron-ion beams (LETs from 190 to 350 keV/microns) producing 2.8 x 10(-3) breaks/Mbp/Gy, giving RBE values for production of double-strand breaks of 0.76 for neon and 0.48 for iron in comparison to our previously determined X-ray induction rate of 5.8 x 10(-3) breaks/Mbp/Gy. These RBE values are in good agreement with results of measurements over the whole genome as reported in the accompanying paper (B. Rydberg, M. Löbrich and P. Cooper, Radiat. Res. 139, 133-141, 1994). The distribution of broken DNA molecules was similar for the various radiations, supporting a random distribution of double-strand breaks induced by the heavy ions over Mbp distances; however, correlated breaks (clusters) over much smaller distances are not ruled out. Reconstitution of the 3.2 Mbp NotI fragment was studied during postirradiation incubation of the cells as a measure of rejoining of correct DNA ends. The proportion of breaks repaired decreased with increasing LET.

Rain forest fragmentation and the proliferation of successional trees.

PubMed

Laurance, William F; Nascimento, Henrique E M; Laurance, Susan G; Andrade, Ana C; Fearnside, Philip M; Ribeiro, José E L; Capretz, Robson L

2006-02-01

The effects of habitat fragmentation on diverse tropical tree communities are poorly understood. Over a 20-year period we monitored the density of 52 tree species in nine predominantly successional genera (Annona, Bellucia, Cecropia, Croton, Goupia, Jacaranda, Miconia, Pourouma, Vismia) in fragmented and continuous Amazonian forests. We also evaluated the relative importance of soil, topographic, forest dynamic, and landscape variables in explaining the abundance and species composition of successional trees. Data were collected within 66 permanent 1-ha plots within a large (approximately 1000 km2) experimental landscape, with forest fragments ranging from 1 to 100 ha in area. Prior to forest fragmentation, successional trees were uncommon, typically comprising 2-3% of all trees (> or =10 cm diameter at breast height [1.3 m above the ground surface]) in each plot. Following fragmentation, the density and basal area of successional trees increased rapidly. By 13-17 years after fragmentation, successional trees had tripled in abundance in fragment and edge plots and constituted more than a quarter of all trees in some plots. Fragment age had strong, positive effects on the density and basal area of successional trees, with no indication of a plateau in these variables, suggesting that successional species could become even more abundant in fragments over time. Nonetheless, the 52 species differed greatly in their responses to fragmentation and forest edges. Some disturbance-favoring pioneers (e.g., Cecropia sciadophylla, Vismia guianensis, V. amazonica, V. bemerguii, Miconia cf. crassinervia) increased by >1000% in density on edge plots, whereas over a third (19 of 52) of all species remained constant or declined in numbers. Species responses to fragmentation were effectively predicted by their median growth rate in nearby intact forest, suggesting that faster-growing species have a strong advantage in forest fragments. An ordination analysis revealed three main

Fragmentations of [M-H]- anions of peptides containing tyrosine sulfate. Does the sulfate group rearrange? A joint experimental and theoretical study.

PubMed

Tran, T T Nha; Wang, Tianfang; Hack, Sandra; Bowie, John H

2013-05-30

To investigate the fragmentations in the negative-ion electrospray mass spectra of peptides containing tyrosine sulfate. Possible fragmentation mechanisms were explored using a Waters QTOF2 tandem mass spectrometer in concert with calculations at the CAM-B3LYP/6-311++g(d,p) level of theory. The major negative ion formed in the ESI-MS of peptides containing tyrosine sulfate is [(M-H)-SO3](-) and this process normally yields the base peak of the spectrum. The basic backbone cleavages of [(M-H)-SO3](-) allowed the sequence of the peptide to be determined. Rearrangement reactions involving the formation of HOSO3(-) and [(M-H)-H2SO4](-) yielded minor peaks with relative abundances ≤ 10% and ≤ 2%, respectively. The mass spectra of the [M-H](-) and [(M-H)-SO3](-) anions of peptides containing tyrosine sulfate allowed the position of the tyrosine sulfate group to be determined, together with the amino acid sequence of the peptide. Copyright © 2013 John Wiley & Sons, Ltd.

[An ultra-high-pressure liquid chromatography/linear ion trap-Orbitrap mass spectrometry method coupled with a diagnostic fragment ions-searching-based strategy for rapid identification and characterization of chemical components in Polygonum cuspidatum].

PubMed

Pan, Zhiran; Liang, Hailong; Liang, Chabhufi; Xu, Wen

2015-01-01

A method for qualitative analysis of constituents in Polygonum cuspidatum by ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MS) has been established. The methanol extract of Polygonum cuspidatumrn was separated on a Waters UPLC C18 column using acetonitrile-water (containing formic acid) eluting system and detected by LTQ-Orbitrap hybrid mass spectrometer in negative mode. The targeted components were further fragmented in LTQ and high accuracy data were acquired by Orbitrap MS. The summarized fragmentation pathways of typical reference components and a diagnostic fragment ions-searching-based strategy were used for detection and identification of the main phenolic components in Polygonum cuspidatum. Other clues such as nitrogen rule, even electron rule, degree of unsaturation rule and isotopic peak data were included for the structural elucidation as well. The whole analytical procedure was within 10 min and more than 30 components were identified or tentatively identified. This method is helpful for further phytochemical research and quality control on Polygonum cuspidatum and related preparations.

Effects of landscape composition and wetland fragmentation on frog and toad abundance and species richness in Iowa and Wisconsin, USA [abstract

USGS Publications Warehouse

Knutson, M.G.; Sauer, J.R.; Olsen, D.A.; Mossman, M.J.; Hemesath, L.M.; Lannoo, M.J.

1998-01-01

We examined the relationships between anuran diversity and landscape features in the Upper Midwestern United States. Anuran relative abundance and species richness were measured using data collected by Wisconsin and Iowa state calling surveys conducted from 1990-1995. Landscape features surrounding survey points were determined using National Wetland Inventory and Wisconsin Wetland Inventory maps. We tested several hypotheses suggested by the literature. We hypothesized that the relative abundance and species richness of anurans that breed in ephemeral wetlands is positively correlated with the surrounding area of temporary wetlands and emergent wetlands. We hypothesized that the relative abundance and species richness of anurans is positively correlated with patch diversity and wetland edges, in the absence of local fragmentation effects. We hypothesized that the relative abundance and species richness of anurans is positively associated with forests but negatively associated with agriculture and urban areas. Our results show that the interspersion of different wetland types and the concomitant increase in wetland edge habitats were generally positive for frogs and toads and anuran abundance and diversity were generally higher in association with forests, especially forested wetlands. The presence of agriculture did not always depress frog and toad populations or diversity; some species were associated with agricultural landscapes. The two states differed in how anurans were associated with landscape features like lakes and permanent wetlands. We found that frog and toad relative abundance and diversity were lower when urban areas were present. Managers can use models like ours, generated from landscape analyses, along with range maps and population trend analyses to get a comprehensive picture of the health of individual species and groups of species. Our models could be applied to the landscape as a whole, and used to predict species relative abundance and

Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

DOE PAGES

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; ...

2016-05-01

We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

Comparison of habitat quality and diet of Colobus vellerosus in forest fragments in Ghana.

PubMed

Wong, Sarah N P; Saj, Tania L; Sicotte, Pascale

2006-10-01

The forest fragments surrounding the Boabeng-Fiema Monkey Sanctuary (BFMS) in central Ghana shelter small populations of Colobus vellerosus. Little is known about these populations or the ability of the fragments to support them, despite the fact that these fragments represent potentially important habitat for the colobus in this region. We compared the diet of three groups of C. vellerosus in the fragments to two groups in BFMS. We also examined the differences in plant species composition and food abundance among fragments. The study took place from June to November 2003. Dietary data were collected using scan sampling. Plant species composition and food abundance were evaluated using tree plots and large tree surveys. As in BFMS groups, leaves constituted the highest proportion of the diet of fragment groups, yet the colobus in fragments fed on more lianas than did those in BFMS. Over 50% of all species observed eaten by colobus in the fragments were not consumed in BFMS groups during the same season. Food abundance was similar between fragments and BFMS, although species composition differed. There was no relationship between the density of colobus and the density of food trees or percentage of food species, suggesting that other factors may be influencing the number of colobus present. This study highlights the broad dietary range of C. vellerosus, which may be a factor allowing its survival in these fragments.

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

DOE PAGES

Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

2013-03-07

In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

NASA Astrophysics Data System (ADS)

Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

2006-07-01

Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

DNA fragmentation by charged particle tracks.

PubMed

Stenerlow, B; Hoglund, E; Carlsson, J

2002-01-01

High-LET (linear energy transfer) charged particles induce DNA double-strand breaks (DSB) in a non-random fashion in mammalian cells. The clustering of DSB, probably determined by track structure as well as chromatin conformation, results in an excess of small- and intermediate-sized DNA fragments. DNA fragmentation in normal human fibroblasts (GM5758) was analyzed by pulsed-field gel electrophoresis after irradiation with photons (60Co) or 125 keV/micrometers nitrogen ions. Compared to conventional DSB analysis, i.e. assays only measuring the fraction of DNA smaller than a single threshold, the relative biological effectiveness (RBE) for DSB induction increased with 100%. Further, the size distribution of DNA fragments showed a significant dependence on radiation quality, with an excess of fragments up to 1 Mbp. Irradiation of naked genomic DNA without histone proteins increased the DSB yields 25 and 13 times for photons and nitrogen ions, respectively. The results suggest possible roles of both track structure and chromatin organization in the distribution of DNA double-strand breaks along the chromosome. c2002 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

PubMed Central

Zhang, Liangyi; Reilly, James P.

2009-01-01

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v- and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds. PMID:19113943

Geographic variation in cowbird distribution, abundance, and parasitism

USGS Publications Warehouse

Morrison, M.L.; Hahn, D.C.; George, T. Luke; Dobkin, David S.

2002-01-01

We evaluated geographical patterns in the abundance and distribution of Brown-headed Cowbirds (Molothrus ater), and in the frequency of cowbird parasitism, across North America in relation to habitat fragmentation. We found no distinctive parasitism patterns at the national or even regional scales, but the species is most abundant in the Great Plains, the heart of their original range, and least common in the southeastern U.S. This situation is dynamic, because both the Brown-headed and two other cowbird species are actively expanding their ranges in the southern U.S. We focused almost entirely in this paper on the Brown-headed Cowbird, because it is the only endemic North American cowbird, its distribution is much wider, and it has been much more intensively studied. We determined that landscape is the most meaningful unit of scale for comparing cowbird parasitism patterns as, for example, in comparisons of northeastern and central hardwood forests within agricultural matrices, and suburbanized areas versus western coniferous forests. We concluded that cowbird parasitism patterns were broadly similar within all landscapes. Even comparisons between prominently dissimilar landscapes, such as hardwoods in agriculture and suburbia versus coniferous forest, display a striking similarity in the responses of cowbirds. Our review clearly indicated that proximity of feeding areas is the key factor influencing presence and parasitism patterns within the landscape. We considered intensity of landscape fragmentation from forest-dominated landscapes altered in a forest management context to fragmentation characterized by mixed suburbanization or agricultural development. Our review consistently identified an inverse relationship between extent of forest cover across the landscape and cowbird presence. Invariably, the variation seen in parasitism frequencies within a region was at least partially explained as a response to changes in forest cover. The most salient geographic

Analysis of Bacterial Lipooligosaccharides by MALDI-TOF MS with Traveling Wave Ion Mobility

NASA Astrophysics Data System (ADS)

Phillips, Nancy J.; John, Constance M.; Jarvis, Gary A.

2016-07-01

Lipooligosaccharides (LOS) are major microbial virulence factors displayed on the outer membrane of rough-type Gram-negative bacteria. These amphipathic glycolipids are comprised of two domains, a core oligosaccharide linked to a lipid A moiety. Isolated LOS samples are generally heterogeneous mixtures of glycoforms, with structural variability in both domains. Traditionally, the oligosaccharide and lipid A components of LOS have been analyzed separately following mild acid hydrolysis, although important acid-labile moieties can be cleaved. Recently, an improved method was introduced for analysis of intact LOS by MALDI-TOF MS using a thin layer matrix composed of 2,4,6-trihydroxyacetophenone (THAP) and nitrocellulose. In addition to molecular ions, the spectra show in-source "prompt" fragments arising from regiospecific cleavage between the lipid A and oligosaccharide domains. Here, we demonstrate the use of traveling wave ion mobility spectrometry (TWIMS) for IMS-MS and IMS-MS/MS analyses of intact LOS from Neisseria spp. ionized by MALDI. Using IMS, the singly charged prompt fragments for the oligosaccharide and lipid A domains of LOS were readily separated into resolved ion plumes, permitting the extraction of specific subspectra, which led to increased confidence in assigning compositions and improved detection of less abundant ions. Moreover, IMS separation of precursor ions prior to collision-induced dissociation (CID) generated time-aligned, clean MS/MS spectra devoid of fragments from interfering species. Incorporating IMS into the profiling of intact LOS by MALDI-TOF MS exploits the unique domain structure of the molecule and offers a new means of extracting more detailed information from the analysis.

Laser ion source for isobaric heavy ion collider experiment.

PubMed

Kanesue, T; Kumaki, M; Ikeda, S; Okamura, M

2016-02-01

Heavy-ion collider experiment in isobaric system is under investigation at Relativistic Heavy Ion Collider. For this experiment, ion source is required to maximize the abundance of the intended isotope. The candidate of the experiment is (96)Ru + (96)Zr. Since the natural abundance of particular isotope is low and composition of isotope from ion source depends on the composites of the target, an isotope enriched material may be needed as a target. We studied the performance of the laser ion source required for the experiment for Zr ions.

The Zero-Degree Detector System for Fragmentation Studies

NASA Technical Reports Server (NTRS)

Adams, J. H., Jr.; Christl, M. J.; Howell, L. W.; Kuznetsov, E.

2006-01-01

The measurement of nuclear fragmentation cross sections requires the detection and identification of individual projectile fragments. If light and heavy fragments are recorded in 'ne same detector, it may be impossible distinguish the signal from the light fragment. To overcome this problem, we have developed the Zero-Degree Detector System. The ZDDS enables the measurement of cross sections for light fragment production by using pixelated detectors to separately measure the signals of each fragment. The system has been used to measure the fragmentation of beams as heavy as Fe at the NASA Space Radiation Laboratory at Brookhaven National Laboratory and the Heavy Ion Medical Accelerator in Chiba, Japan.

Secondary radiation measurements for particle therapy applications: nuclear fragmentation produced by 4He ion beams in a PMMA target

NASA Astrophysics Data System (ADS)

Marafini, M.; Paramatti, R.; Pinci, D.; Battistoni, G.; Collamati, F.; De Lucia, E.; Faccini, R.; Frallicciardi, P. M.; Mancini-Terracciano, C.; Mattei, I.; Muraro, S.; Piersanti, L.; Rovituso, M.; Rucinski, A.; Russomando, A.; Sarti, A.; Sciubba, A.; Solfaroli Camillocci, E.; Toppi, M.; Traini, G.; Voena, C.; Patera, V.

2017-02-01

Nowadays there is a growing interest in particle therapy treatments exploiting light ion beams against tumors due to their enhanced relative biological effectiveness and high space selectivity. In particular promising results are obtained by the use of 4He projectiles. Unlike the treatments performed using protons, the beam ions can undergo a fragmentation process when interacting with the atomic nuclei in the patient body. In this paper the results of measurements performed at the Heidelberg Ion-Beam Therapy center are reported. For the first time the absolute fluxes and the energy spectra of the fragments—protons, deuterons, and tritons—produced by 4He ion beams of 102, 125 and 145 MeV u-1 energies on a poly-methyl methacrylate target were evaluated at different angles. The obtained results are particularly relevant in view of the necessary optimization and review of the treatment planning software being developed for clinical use of 4He beams in clinical routine and the relative bench-marking of Monte Carlo algorithm predictions.

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

PubMed Central

de la Fuente, Gabriel; Belanche, Alejandro; Girwood, Susan E.; Pinloche, Eric; Wilkinson, Toby; Newbold, C. Jamie

2014-01-01

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population. PMID:25051490

Binning of shallowly sampled metagenomic sequence fragments reveals that low abundance bacteria play important roles in sulfur cycling and degradation of complex organic polymers in an acid mine drainage community

NASA Astrophysics Data System (ADS)

Dick, G. J.; Andersson, A.; Banfield, J. F.

2007-12-01

Our understanding of environmental microbiology has been greatly enhanced by community genome sequencing of DNA recovered directly the environment. Community genomics provides insights into the diversity, community structure, metabolic function, and evolution of natural populations of uncultivated microbes, thereby revealing dynamics of how microorganisms interact with each other and their environment. Recent studies have demonstrated the potential for reconstructing near-complete genomes from natural environments while highlighting the challenges of analyzing community genomic sequence, especially from diverse environments. A major challenge of shotgun community genome sequencing is identification of DNA fragments from minor community members for which only low coverage of genomic sequence is present. We analyzed community genome sequence retrieved from biofilms in an acid mine drainage (AMD) system in the Richmond Mine at Iron Mountain, CA, with an emphasis on identification and assembly of DNA fragments from low-abundance community members. The Richmond mine hosts an extensive, relatively low diversity subterranean chemolithoautotrophic community that is sustained entirely by oxidative dissolution of pyrite. The activity of these microorganisms greatly accelerates the generation of AMD. Previous and ongoing work in our laboratory has focused on reconstrucing genomes of dominant community members, including several bacteria and archaea. We binned contigs from several samples (including one new sample and two that had been previously analyzed) by tetranucleotide frequency with clustering by Self-Organizing Maps (SOM). The binning, evaluated by comparison with information from the manually curated assembly of the dominant organisms, was found to be very effective: fragments were correctly assigned with 95% accuracy. Improperly assigned fragments often contained sequences that are either evolutionarily constrained (e.g. 16S rRNA genes) or mobile elements that are

Ion Trap Collisional Activation of c and z• Ions Formed via Gas-Phase Ion/Ion Electron Transfer Dissociation

PubMed Central

Han, Hongling; Xia, Yu; McLuckey, Scott A.

2008-01-01

A series of c- and z•-type product ions formed via gas-phase electron transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z• species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-and z-type ions. Most of the fragmentation pathways of z• species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z• species are different from the small losses observed from the charge-reduced peptide molecular species in electron transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues. PMID:17608403

Effects of habitat fragmentation on wild mammal infection by Trypanosoma cruzi.

PubMed

Vaz, V C; D'Andrea, P S; Jansen, A M

2007-11-01

Expansion of human activities frequently results in habitat fragmentation, a phenomenon that has been widely recognized in the last decades as one of the major threats to world's biodiversity. The transformation of a continuous forest into a fragmented area results in a hyper-dynamic landscape with unpredictable consequences to overall ecosystem health. The effect of the fragmentation process on Trypanosoma cruzi infection among small wild mammals was studied in an Atlantic Rain Forest landscape. Comparing continous forest to fragmented habitat, marsupials were less abundant than rodents in the continuous landscape. An overall decrease in small wild mammal richness was observed in the smaller fragments. An anti-T. cruzi seroprevalence of 18% (82/440) was deteced by immunofluorescence assay. Moreover, this seroprevalence was higher in the fragmented habitat than in the continuous forest. According to the collected data, 3 main factors seem to modulate infection by T. cruzi in small wild mammals: (i) habitat fragmentation; (ii) biodiversity loss; (iii) increase of marsupial abundance in mammal communities. Furthermore, an extremely mild controlled infection by T. cruzi was detected since no patent parasitaemia could be detected in fresh blood samples, and no parasites were isolated by haemoculture.

Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups

PubMed Central

Braschler, Brigitte; Baur, Bruno

2016-01-01

Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species’ preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related

Habitat fragmentation effects on the orchid bee communities in remnant forests of southeastern Brazil.

PubMed

Knoll, Fátima do Rosário Naschenveng; Penatti, N C

2012-10-01

The effect of habitat fragmentation on the structure of orchid bee communities was analyzed by the investigation of the existence of a spatial structure in the richness and abundance of Euglossini species and by determining the relationship between these data and environmental factors. The surveys were carried out in four different forest fragments and one university campus. Richness, abundance, and diversity of species were analyzed in relation to abiotic (size of the area, extent of the perimeter, perimeter/area ratio, and shape index) and biotic characteristics (vegetation index of the fragment and of the matrix of each of the locations studied). We observed a highly significant positive correlation between the diversity index and the vegetation index of the fragment, landscape and shape index. Our analysis demonstrated that the observed variation could be explained mainly by the vegetation index and the size of the fragment. Variations in relative abundance showed a tendency toward an aggregated spatial distribution between the fragments studied, as well as between the sampling stations within the same habitat, demonstrating the existence of a spatial structure on a small scale in the populations of Euglossini. This distribution will determine the composition of species that coexist in the area after fragmentation. These data help in understanding the differences and similarities in the structure of communities of Euglossini resulting from forest fragmentation.

A DNA logic gate based on strand displacement reaction and rolling circle amplification, responding to multiple low-abundance DNA fragment input signals, and its application in detecting miRNAs.

PubMed

Chen, Yuqi; Song, Yanyan; Wu, Fan; Liu, Wenting; Fu, Boshi; Feng, Bingkun; Zhou, Xiang

2015-04-25

A conveniently amplified DNA AND logic gate platform was designed for the highly sensitive detection of low-abundance DNA fragment inputs based on strand displacement reaction and rolling circle amplification strategy. Compared with others, this system can detect miRNAs in biological samples. The success of this strategy demonstrates the potential of DNA logic gates in disease diagnosis.

Landscape responses of bats to habitat fragmentation in Atlantic forest of paraguay

USGS Publications Warehouse

Gorresen, P.M.; Willig, M.R.

2004-01-01

Understanding effects of habitat loss and fragmentation on populations or communities is critical to effective conservation and restoration. This is particularly important for bats because they provide vital services to ecosystems via pollination and seed dispersal, especially in tropical and subtropical habitats. Based on more than 1,000 h of survey during a 15-month period, we quantified species abundances and community structure of phyllostomid bats at 14 sites in a 3,000-km2 region of eastern Paraguay. Abundance was highest for Artibeus lituratus in deforested landscapes and for Chrotopterus auritus in forested habitats. In contrast, Artibeus fimbriatus, Carollia perspicillata, Glossophaga soricina, Platyrrhinus lineatus, Pygoderma bilabiatum, and Sturnira lilium attained highest abundance in moderately fragmented forest landscapes. Forest cover, patch size, and patch density frequently were associated with abundance of species. At the community level, species richness was highest in partly deforested landscapes, whereas evenness was greatest in forested habitat. In general, the highest diversity of bats occurred in landscapes comprising moderately fragmented forest habitat. This underscores the importance of remnant habitat patches to conservation strategies.

Transport of Light Ions in Matter

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Cucinotta, F. A.; Tai, H.; Shinn, J. L.; Chun, S. Y.; Tripathi, R. K.; Sihver, L.

1998-01-01

A recent set of light ion experiments are analyzed using the Green's function method of solving the Boltzmann equation for ions of high charge and energy (the GRNTRN transport code) and the NUCFRG2 fragmentation database generator code. Although the NUCFRG2 code reasonably represents the fragmentation of heavy ions, the effects of light ion fragmentation requires a more detailed nuclear model including shell structure and short range correlations appearing as tightly bound clusters in the light ion nucleus. The most recent NTJCFRG2 code is augmented with a quasielastic alpha knockout model and semiempirical adjustments (up to 30 percent in charge removal) in the fragmentation process allowing reasonable agreement with the experiments to be obtained. A final resolution of the appropriate cross sections must await the full development of a coupled channel reaction model in which shell structure and clustering can be accurately evaluated.

Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

NASA Astrophysics Data System (ADS)

Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

Electromagnetic Dissociation Cross Sections for High LET Fragments

NASA Technical Reports Server (NTRS)

Norbury, John

2016-01-01

Nuclear interaction cross sections are used in space radiation transport codes to calculate the probability of fragment emission in high energy nucleus-nucleus collisions. Strong interactions usually dominate in these collisions, but electromagnetic (EM) interactions can also sometimes be important. Strong interactions typically occur when the projectile nucleus hits a target nucleus, with a small impact parameter. For impact parameters larger than the sum of the nuclear radii, EM reactions dominate and the process is called electromagnetic dissociation (EMD) if one of the nuclei undergo fragmentation. Previous models of EMD have been used to calculate single proton (p) production, single neutron (n) production or light ion production, where a light ion is defined as an isotope of hydrogen (H) or helium (He), such as a deuteron (2H), a triton (3H), a helion (3He) or an alpha particle (4He). A new model is described which can also account for multiple nucleon production, such as 2p, 2n, 1p1n, 2p1n, 2p2n, etc. in addition to light ion production. Such processes are important to include for the following reasons. Consider, for example, the EMD reaction 56Fe + Al --> 52Cr + X + Al, for a 56Fe projectile impacting Al, which produces the high linear energy transfer (LET) fragment 52Cr. In this reaction, the most probable particles representing X are either 2p2n or 4He. Therefore, production of the high LET fragment 52Cr, must include the multiple nucleon production of 2p2n in addition to the light ion production of 4He. Previous models, such as the NUCFRG3 model, could only account for the 4He production process in this reaction and could not account for 2p2n. The new EMD model presented in this work accounts for both the light ion and multiple nucleon processes, and is therefore able to correctly account for the production of high LET products such as 52Cr. The model will be described and calculations will be presented that show the importance of light ion and multiple

Ion abundances and implications for photochemistry in Comets Halley (1986 III) and Bradfield (1987 XXIX)

NASA Astrophysics Data System (ADS)

Lutz, B. L.; Womack, M.; Wagner, R. M.

1993-04-01

The Ohio State University Image Dissector Scanner on the Perkins 1.8-m telescope at the Lowell Observatory was used to record spectra of the plasma tails of Comets P/Halley (1986 III) and P/Bradfield (1987 XXIX, also 1987s). The ionic species CO(+), N2(+), CH(+), and H2O(+) were identified in these spectra, and column densities for them were calculated from measured fluxes. The observed N2(+)/H2O(+) ratios are at least an order of magnitude lower and the observed CH(+)/H2O(+) ratios are a factor of 100 higher than theoretical results. The abundance ratio N2/CO was derived in the plasma tail of Bradfield from N2(+) and CO(+) data, and found to be an order of magnitude higher than a value measured in Halley. The relative ion abundances of CH(+), N2(+), CO(+), and H2O(+) in Halley are consistent with in situ measurements obtained from the Giotto spacecraft.

Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

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

Chugh, Rajiv, E-mail: rajivchug@gmail.com; Kumar, Rohit, E-mail: rohitksharma.pu@gmail.com; Vinayak, Karan Singh, E-mail: drksvinayak@gmail.com

2016-05-06

Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetrymore » energy.« less

Computer Model Of Fragmentation Of Atomic Nuclei

NASA Technical Reports Server (NTRS)

Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.

1995-01-01

High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.

MS/MS analysis and imaging of lipids across Drosophila brain using secondary ion mass spectrometry.

PubMed

Phan, Nhu T N; Munem, Marwa; Ewing, Andrew G; Fletcher, John S

2017-06-01

Lipids are abundant biomolecules performing central roles to maintain proper functioning of cells and biological bodies. Due to their highly complex composition, it is critical to obtain information of lipid structures in order to identify particular lipids which are relevant for a biological process or metabolic pathway under study. Among currently available molecular identification techniques, MS/MS in secondary ion mass spectrometry (SIMS) imaging has been of high interest in the bioanalytical community as it allows visualization of intact molecules in biological samples as well as elucidation of their chemical structures. However, there have been few applications using SIMS and MS/MS owing to instrumental challenges for this capability. We performed MS and MS/MS imaging to study the lipid structures of Drosophila brain using the J105 and 40-keV Ar 4000 + gas cluster ion source, with the novelty being the use of MS/MS SIMS analysis of intact lipids in the fly brain. Glycerophospholipids were identified by MS/MS profiling. MS/MS was also used to characterize diglyceride fragment ions and to identify them as triacylglyceride fragments. Moreover, MS/MS imaging offers a unique possibility for detailed elucidation of biomolecular distribution with high accuracy based on the ion images of its fragments. This is particularly useful in the presence of interferences which disturb the interpretation of biomolecular localization. Graphical abstract MS/MS was performed during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of Drosophila melongaster (fruit fly) to elucidate the structure and origin of different chemical species in the brain including a range of different phospholipid classes (PC, PI, PE) and di- and triacylglycerides (DAG & TAG) species where reference MS/MS spectra provided a potential means of discriminating between the isobaric [M-OH] + ion of DAGs and the [M-RCO] + ion of TAGs.

The effects of forest fragmentation on biodiversity under post-drought conditions

NASA Astrophysics Data System (ADS)

Lawrence, A.; Swei, A.

2016-12-01

Habitat fragmentation is the greatest threat to wildlife worldwide. Understanding the impact of habitat fragmentation on biodiversity can benefit from theories established in island biogeography. Landscapes surrounded by human development are analogous to oceanic islands in that the size of habitat fragment can determine biodiversity. For terrestrial ecosystems, species traits can influence how they respond to the disturbance of habitat fragmentation. We tested how habitat patch size correlates to species richness and abundance of mammals in northern California in a post-drought environment. Using GIS and Fragstat we established nine forest fragments of varying size, differing minimally in location, topography, climate, and vegetation cover. This allows us to minimize site differences to test the effects of patch size on biodiversity. We used wildlife cameras to estimate richness of medium and large mammals and mark-and-recapture analysis to estimate species richness and abundance of small mammals. We also collected ticks with standard dragging and flagging techniques to determine the relationship between habitat patch size and species richness on Lyme disease risk. Our preliminary results indicate that meso-and-large mammal richness increases significantly with patch area (P=0.024) as well as larval tick density (P=0.035). At the same time, small mammal richness, abundance and diversity peaks in intermediate sized fragments. Further we found invasive species such as house mouse, Norway rat, and black rat only in patches smaller than 50 ha. Our results support the theory that invasive species are better adapted to disturbed areas versus native habitat. The ways in which habitat destruction and fragmentation are acting upon species and communities has critical consequences for conservation, ecosystem services, landscape planning, and many fields of environmental change research.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

PubMed

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

Fragmentation mechanisms for methane induced by 55 eV, 75 eV, and 100 eV electron impact

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

Wei, B.; Zhang, Y.; Wang, X., E-mail: xinchengwang@fudan.edu.cn

2014-03-28

The fragmentation of CH{sub 4}{sup 2+} dications following 55 eV, 75 eV, and 100 eV electron impact double ionization of methane was studied using a cold target recoil-ion momentum spectroscopy. From the measured momentum of each recoil ion, the momentum of the neutral particles has been deduced and the kinetic energy release distribution for the different fragmentation channels has been obtained. The doubly charged molecular ions break up into three or more fragments in one or two-step processes, resulting in different signatures in the data. We observed the fragmentation of CH{sub 4}{sup 2+} dications through different mechanisms according to themore » momentum of the neutral particles. For example, our result shows that there are three reaction channels to form CH{sub 2}{sup +}, H{sup +}, and H, one synchronous concerted reaction channel and two two-step reaction channels. For even more complicated fragmentation processes of CH{sub 4}{sup 2+} dications, the fragmentation mechanism can still be identified in the present measurements. The slopes of the peak in the ion-ion coincidence spectra were also estimated here, as they are also related to the fragmentation mechanism.« less

Fragmentation mechanisms for methane induced by 55 eV, 75 eV, and 100 eV electron impact.

PubMed

Wei, B; Zhang, Y; Wang, X; Lu, D; Lu, G C; Zhang, B H; Tang, Y J; Hutton, R; Zou, Y

2014-03-28

The fragmentation of CH4 (2+) dications following 55 eV, 75 eV, and 100 eV electron impact double ionization of methane was studied using a cold target recoil-ion momentum spectroscopy. From the measured momentum of each recoil ion, the momentum of the neutral particles has been deduced and the kinetic energy release distribution for the different fragmentation channels has been obtained. The doubly charged molecular ions break up into three or more fragments in one or two-step processes, resulting in different signatures in the data. We observed the fragmentation of CH4 (2+) dications through different mechanisms according to the momentum of the neutral particles. For example, our result shows that there are three reaction channels to form CH2 (+), H(+), and H, one synchronous concerted reaction channel and two two-step reaction channels. For even more complicated fragmentation processes of CH4 (2+) dications, the fragmentation mechanism can still be identified in the present measurements. The slopes of the peak in the ion-ion coincidence spectra were also estimated here, as they are also related to the fragmentation mechanism.

Comparison of Data Acquisition Strategies on Quadrupole Ion Trap Instrumentation for Shotgun Proteomics

PubMed Central

Canterbury, Jesse D.; Merrihew, Gennifer E.; Goodlett, David R.; MacCoss, Michael J.; Shaffer, Scott A.

2015-01-01

A common strategy in mass spectrometry analyses of complex protein mixtures is to digest the proteins to peptides, separate the peptides by microcapillary liquid chromatography and collect tandem mass spectra (MS/MS) on the eluting, complex peptide mixtures, a process commonly termed “shotgun proteomics”. For years, the most common way of data collection was via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest, a process often leaving lower abundant signals unanalyzed and therefore unidentified in the experiment. Advances in both instrumentation duty cycle and sensitivity allow DDA to probe to lower peptide abundance and therefore enable mapping proteomes to a more significant depth. An alternative to acquiring data by DDA is by data-independent acquisition (DIA), in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum. As a consequence, DIA acquisition potentially offers more comprehensive analysis of peptides than DDA and in principle can yield tandem mass spectra of all ionized molecules following their conversion to the gas-phase. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified in-house with an electrodynamic ion funnel, and an LTQ-Velos. These instruments were chosen as they are representative of both older (LTQ) and newer (LTQ-Velos) ion trap designs i.e., linear ion trap and dual ion traps, respectively, and allow direct comparison of peptide identification using both DDA and DIA analysis. Further, as the LTQ-Velos has an improved “S-lens” ion guide in the high-pressure region to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different

Decomposition of cyclohexane ion induced by intense femtosecond laser fields by ion-trap time-of-flight mass spectrometry

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

Yamazaki, Takao; Watanabe, Yusuke; Kanya, Reika

2016-01-14

Decomposition of cyclohexane cations induced by intense femtosecond laser fields at the wavelength of 800 nm is investigated by ion-trap time-of-flight mass spectrometry in which cyclohexane cations C{sub 6}H{sub 12}{sup +} stored in an ion trap are irradiated with intense femtosecond laser pulses and the generated fragment ions are recorded by time-of-flight mass spectrometry. The various fragment ion species, C{sub 5}H{sub n}{sup +} (n = 7, 9), C{sub 4}H{sub n}{sup +} (n = 5–8), C{sub 3}H{sub n}{sup +} (n = 3–7), C{sub 2}H{sub n}{sup +} (n = 2–6), and CH{sub 3}{sup +}, identified in the mass spectra show that decompositionmore » of C{sub 6}H{sub 12}{sup +} proceeds efficiently by the photo-irradiation. From the laser intensity dependences of the yields of the fragment ion species, the numbers of photons required for producing the respective fragment ions are estimated.« less

Fragmentation in the branching coral Acropora palmata (Lamarck): growth, survivorship, and reproduction of colonies and fragments.

PubMed

Lirman

2000-08-23

Acropora palmata, a branching coral abundant on shallow reef environments throughout the Caribbean, is susceptible to physical disturbance caused by storms. Accordingly, the survivorship and propagation of this species are tied to its capability to recover after fragmentation. Fragments of A. palmata comprised 40% of ramets within populations that had experienced recent storms. While the survivorship of A. palmata fragments was not directly related to the size of fragments, removal of fragments from areas where they settled was influenced by size. Survivorship of fragments was also affected by type of substratum; the greatest mortality (58% loss within the first month) was observed on sand, whereas fragments placed on top of live colonies of A. palmata fused to the underlying tissue and did not experience any losses. Fragments created by Hurricane Andrew on a Florida reef in August 1992 began developing new growth (proto-branches) 7 months after the storm. The number of proto-branches on fragments was dependent on size, but growth was not affected by the size of fragments. Growth-rates of proto-branches increased exponentially with time (1.7 cm year(-1) for 1993-1994, 2.7 cm year(-1) for 1994-1995, 4.2 cm year(-1) for 1995-1996, and 6.5 cm year(-1) for 1996-1997), taking over 4 years for proto-branches to achieve rates comparable to those of adult colonies on the same reef (6.9 cm year(-1)). In addition to the initial mortality and reduced growth-rates, fragmentation resulted in a loss of reproductive potential. Neither colonies that experienced severe fragmentation nor fragments contained gametes until 4 years after the initial damage. Although A. palmata may survive periodic fragmentation, the long-term effects of this process will depend ultimately on the balance between the benefits and costs of this process.

Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4.

PubMed

Pesavento, James J; Mizzen, Craig A; Kelleher, Neil L

2006-07-01

Here we show that fragment ion abundances from dissociation of ions created from mixtures of multiply modified histone H4 (11 kDa) or of N-terminal synthetic peptides (2 kDa) correspond to their respective intact ion abundances measured by Fourier transform mass spectrometry. Isomeric mixtures of modified forms of the same protein are resolved and quantitated with a precision of fragment ions, with intact protein ions created by electrospray greatly easing many of the systematic biases that more strongly affect small peptides (e.g., differences in ionization efficiency and ion m/z values). The ion fragmentation methods validated here are directly extensible to intact human proteins to derive quantitative information on the highly related and often isomeric protein forms created by combinatorial arrays of posttranslational modifications.

Quantum control of molecular fragmentation in strong laser fields

NASA Astrophysics Data System (ADS)

Zohrabi, Mohammad

Present advances in laser technology allow the production of ultrashort (<˜5 fs, approaching single cycle at 800 nm), intense tabletop laser pulses. At these high intensities laser-matter interactions cannot be described with perturbation theory since multiphoton processes are involved. This is in contrast to photodissociation by the absorption of a single photon, which is well described by perturbation theory. For example, at high intensities (<˜5x1013 W/cm2) the fragmentation of molecular hydrogen ions has been observed via the absorption of three or more photons. In another example, an intriguing dissociation mechanism has been observed where molecular hydrogen ions seem to fragment by apparently absorbing no photons. This is actually a two photon process, photoabsorption followed by stimulated emission, resulting in low energy fragments. We are interested in exploring these kinds of multiphoton processes. Our research group has studied the dynamics and control of fragmentation induced by strong laser fields in a variety of molecular targets. The main goal is to provide a basic understanding of fragmentation mechanisms and possible control schemes of benchmark systems such as H2+. This knowledge is further extended to more complex systems like the benchmark H3+ polyatomic and other molecules. In this dissertation, we report research based on two types of experiments. In the first part, we describe laser-induced fragmentation of molecular ion-beam targets. In the latter part, we discuss the formation of highly-excited neutral fragments from hydrogen molecules using ultrashort laser pulses. In carrying out these experiments, we have also extended experimental techniques beyond their previous capabilities. We have performed a few experiments to advance our understanding of laser-induced fragmentation of molecular-ion beams. For instance, we explored vibrationally resolved spectra of O2+ dissociation using various wavelengths. We observed a vibrational suppression

Fragmentation of ionized doped helium nanodroplets: theoretical evidence for a dopant ejection mechanism.

PubMed

Bonhommeau, D; Lewerenz, M; Halberstadt, N

2008-02-07

We report a theoretical study of the effect induced by a helium nanodroplet environment on the fragmentation dynamics of a dopant. The dopant is an ionized neon cluster Ne(n) (+) (n=4-6) surrounded by a helium nanodroplet composed of 100 atoms. A newly designed mixed quantum/classical approach is used to take into account both the large helium cluster zero-point energy due to the light mass of the helium atoms and all the nonadiabatic couplings between the Ne(n) (+) potential-energy surfaces. The results reveal that the intermediate ionic dopant can be ejected from the droplet, possibly with some helium atoms still attached, thereby reducing the cooling power of the droplet. Energy relaxation by helium atom evaporation and dissociation, the other mechanism which has been used in most interpretations of doped helium cluster dynamics, also exhibits new features. The kinetic energy distribution of the neutral monomer fragments can be fitted to the sum of two Boltzmann distributions, one with a low kinetic energy and the other with a higher kinetic energy. This indicates that cooling by helium atom evaporation is more efficient than was believed so far, as suggested by recent experiments. The results also reveal the predominance of Ne(2) (+) and He(q)Ne(2) (+) fragments and the absence of bare Ne(+) fragments, in agreement with available experimental data (obtained for larger helium nanodroplets). Moreover, the abundance in fragments with a trimeric neon core is found to increase with the increase in dopant size. Most of the fragmentation is achieved within 10 ps and the only subsequent dynamical process is the relaxation of hot intermediate He(q)Ne(2) (+) species to Ne(2) (+) by helium atom evaporation. The dependence of the ionic fragment distribution on the parent ion electronic state reached by ionization is also investigated. It reveals that He(q)Ne(+) fragments are produced only from the highest electronic state, whereas He(q)Ne(2) (+) fragments originate from

WITHDRAWN: Fragmentation of charged aqueous nanodroplets

NASA Astrophysics Data System (ADS)

Ichiki, Kengo

2005-11-01

The whole evaporating process of charged aqueous nanodroplets is studied by systematic molecular dynamics simulations until most of the solvent molecules are evaporated. % The solvent evaporation makes the droplet smaller and smaller, and at a certain point the repulsive force among ions causes an instability, where typically single ion and 10 to 20 water molecules are disintegrated from the main droplet. % This ion fragmentation occurs around 70 to 80% of the charge predicted by the Rayleigh theory [Lord Rayleigh, Phil. Mag. 14, 184 (1882)]. % The numerical results are summarized in the function R(z) which is the fragmentation radius at the charge z. From the fitting by the power law Rz^β, we find that at lower temperature T=350 and 370 K the result is close to the Rayleigh theory β= 2/3, while at higher temperature T=400 and 450 K it is like β= 1/2. % Another fitting on R(z) by the extended ion evaporation mechanism [M. Gamero-Castaño and J. Fern'andez de la Mora, Anal. Chim. Acta 406, 67 (2000)] works well for both cases. % The final state of the evaporation process is typically a single ion with several water molecules. If we put an alanine dipeptide in zwitterionic form at the beginning, two charges remain in some cases.

Analysis of the theory of high energy ion transport

NASA Technical Reports Server (NTRS)

Wilson, J. W.

1977-01-01

Procedures for the approximation of the transport of high-energy ions are discussed on the basis of available data on ion nuclear reactions. A straightahead approximation appears appropriate for space applications. The assumption that the secondary-ion-fragment velocity is equal to that of the fragmenting nucleus is inferior to straightahead theory but is of sufficient accuracy if the primary ions display a broad energy spectrum. An iterative scheme for the solution of the inhomogenous integral transport equations holds promise for practical calculation. A model calculation shows that multiple charged ion fragments penetrate to greater depths in comparison with the free path of a primary heavy ion.

Low-energy collision-induced fragmentation of negative ions derived from ortho-, meta-, and para-hydroxyphenyl carbaldehydes, ketones, and related compounds.

PubMed

Attygalle, Athula B; Ruzicka, Josef; Varughese, Deepu; Bialecki, Jason B; Jafri, Sayed

2007-09-01

Collision-induced dissociation (CID) mass spectra of anions derived from several hydroxyphenyl carbaldehydes and ketones were recorded and mechanistically rationalized. For example, the spectrum of m/z 121 ion of deprotonated ortho-hydroxybenzaldehyde shows an intense peak at m/z 93 for a loss of carbon monoxide attributable to an ortho-effect mediated by a charge-directed heterolytic fragmentation mechanism. In contrast, the m/z 121 ion derived from meta and para isomers undergoes a charge-remote homolytic cleavage to eliminate an *H and form a distonic anion radical, which eventually loses CO to produce a peak at m/z 92. In fact, for the para isomer, this two-step homolytic mechanism is the most dominant fragmentation pathway. The spectrum of the meta isomer on the other hand, shows two predominant peaks at m/z 92 and 93 representing both homolytic and heterolytic fragmentations, respectively. (18)O-isotope-labeling studies confirmed that the oxygen in the CO molecule that is eliminated from the anion of meta-hydroxybenzaldehyde originates from either the aldehydic or the phenolic group. In contrast, anions of ortho-hydroxybenzaldehyde and 2-hydroxy-1-naphthaldehyde, both of which show two consecutive CO eliminations, specifically lose the carbonyl oxygen first, followed by that of the phenolic group. Anions from 2-hydroxyphenyl alkyl ketones lose a ketene by a hydrogen transfer predominantly from the alpha position. Interestingly, a very significant charge-remote 1,4-elimination of a H(2) molecule was observed from the anion derived from 2,4-dihydroxybenzaldehyde. For this mechanism to operate, a labile hydrogen atom should be available on the hydroxyl group adjacent to the carbaldehyde functionality.

Photoionization and Photofragmentation of Carbon Fullerene Molecular Ions

NASA Astrophysics Data System (ADS)

Baral, Kiran Kumar

Cross sections are reported for single and double photoionization accompanied by the loss of as many as seven pairs of C atoms of C60 + and C70+ fullerene molecular ions in the photon energy range 18 eV to 150 eV. These measurements were performed at the Advanced Light Source (ALS) by merging a mass-selected ion beam with a beam of monochromatized synchrotron radiation. Threshold energies were determined for the formation of doubly and triply charged fragment ions from parent ions C60+ and C70+. The energy dependences of cross-sections for direct photoionization yielding C60 2+ and C702+ are compared with those for forming different doubly and triply charged fullerene fragment ions. Two-dimensional product ion scans were measured and quantified at four discrete photon energies: 35 eV, 65 eV, 105 eV and 140 eV, in the vacuum ultraviolet region, providing a comprehensive mapping of the product channels involving single ionization of fullerene ions C60+ and C 70+ accompanied by fragmentation. Since fullerenes are composed of even numbers of carbon atoms, the fragmentation occurs by the loss of differing numbers of carbon atom pairs. In addition to pure ionization, fragmentation product channels become relatively more important at higher photon energies.

Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

PubMed

Dáttilo, Wesley; Aguirre, Armando; Quesada, Mauricio; Dirzo, Rodolfo

2015-01-01

Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.

Isomerization and fragmentation reactions of gaseous phenylarsane radical cations and phenylarsanyl cations. A study by tandem mass spectrometry and theoretical calculations.

PubMed

Letzel, Matthias; Kirchhoff, Dirk; Grützmacher, Hans-Friedrich; Stein, Daniel; Grützmacher, Hansjörg

2006-04-28

The unimolecular reactions of radical cations and cations derived from phenylarsane, C6H5AsH2 (1) and dideutero phenylarsane, C6H5AsD2 (1-d2), were investigated by methods of tandem mass spectrometry and theoretical calculations. The mass spectrometric experiments reveal that the molecular ion of phenylarsane, 1*+, exhibits different reactivity at low and high internal excess energy. Only at low internal energy the observed fragmentations are as expected, that is the molecular ion 1*+ decomposes almost exclusively by loss of an H atom. The deuterated derivative 1-d2 with an AsD2 group eliminates selectively a D atom under these conditions. The resulting phenylarsenium ion [C6H5AsH]+, 2+, decomposes rather easily by loss of the As atom to give the benzene radical cation [C6H6]*+ and is therefore of low abundance in the 70 eV EI mass spectrum. At high internal excess energy, the ion 1*+ decomposes very differently either by elimination of an H2 molecule, or by release of the As atom, or by loss of an AsH fragment. Final products of these reactions are either the benzoarsenium ion 4*+, or the benzonium ion [C6H7]+, or the benzene radical cation, [C6H6]*+. As key-steps, these fragmentations contain reductive eliminations from the central As atom under H-H or C-H bond formation. Labeling experiments show that H/D exchange reactions precede these fragmentations and, specifically, that complete positional exchange of the H atoms in 1*+ occurs. Computations at the UMP2/6-311+G(d)//UHF/6-311+G(d) level agree best with the experimental results and suggest: (i) 1*+ rearranges (activation enthalpy of 93 kJ mol(-1)) to a distinctly more stable (DeltaH(r)(298) = -64 kJ mol(-1)) isomer 1 sigma*+ with a structure best represented as a distonic radical cation sigma complex between AsH and benzene. (ii) The six H atoms of the benzene moiety of 1 sigma*+ become equivalent by a fast ring walk of the AsH group. (iii) A reversible isomerization 1+<==>1 sigma*+ scrambles eventually all H

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants.

PubMed

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages.

Atmospheric-pressure ionization and fragmentation of peptides by solution-cathode glow discharge

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

Schwartz, Andrew J.; Shelley, Jacob T.; Walton, Courtney L.

Modern “-omics” (e.g., proteomics, glycomics, metabolomics, etc.) analyses rely heavily on electrospray ionization and tandem mass spectrometry to determine the structural identity of target species. Unfortunately, these methods are limited to specialized mass spectrometry instrumentation. Here in this paper, a novel approach is described that enables ionization and controlled, tunable fragmentation of peptides at atmospheric pressure. In the new source, a direct-current plasma is sustained between a tapered metal rod and a flowing sample-containing solution. As the liquid stream contacts the electrical discharge, peptides from the solution are volatilized, ionized, and fragmented. At high discharge currents (e.g., 70 mA), electrospray-likemore » spectra are observed, dominated by singly and doubly protonated molecular ions. At lower currents (35 mA), many peptides exhibit extensive fragmentation, with a-, b-, c-, x-, and y-type ion series present as well as complex fragments, such as d-type ions, not previously observed with atmospheric-pressure dissociation. Though the mechanism of fragmentation is currently unclear, observations indicate it could result from the interaction of peptides with gas-phase radicals or ultraviolet radiation generated within the plasma.« less

Atmospheric-pressure ionization and fragmentation of peptides by solution-cathode glow discharge

DOE PAGES

Schwartz, Andrew J.; Shelley, Jacob T.; Walton, Courtney L.; ...

2016-06-27

Modern “-omics” (e.g., proteomics, glycomics, metabolomics, etc.) analyses rely heavily on electrospray ionization and tandem mass spectrometry to determine the structural identity of target species. Unfortunately, these methods are limited to specialized mass spectrometry instrumentation. Here in this paper, a novel approach is described that enables ionization and controlled, tunable fragmentation of peptides at atmospheric pressure. In the new source, a direct-current plasma is sustained between a tapered metal rod and a flowing sample-containing solution. As the liquid stream contacts the electrical discharge, peptides from the solution are volatilized, ionized, and fragmented. At high discharge currents (e.g., 70 mA), electrospray-likemore » spectra are observed, dominated by singly and doubly protonated molecular ions. At lower currents (35 mA), many peptides exhibit extensive fragmentation, with a-, b-, c-, x-, and y-type ion series present as well as complex fragments, such as d-type ions, not previously observed with atmospheric-pressure dissociation. Though the mechanism of fragmentation is currently unclear, observations indicate it could result from the interaction of peptides with gas-phase radicals or ultraviolet radiation generated within the plasma.« less

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches

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

Zheng, Xueyun; Smith, Richard D.; Baker, Erin S.

Lipids are a vital class of molecules that play important and varied roles in biological processes. Fully understanding lipid roles, however, is extremely difficult since the number and diversity of lipid species is immense, with cells expressing hundreds of enzymes that synthesize tens of thousands of different lipids. While recent advances in chromatography and high resolution mass spectrometry have greatly progressed the understanding of lipid species and functions, effectively separating many lipids still remains problematic. Isomeric lipids have made lipid characterization especially difficult and occur due to subclasses having the same chemical composition, or species having multiple acyl chains connectivitiesmore » (sn-1, sn-2, or sn-3), double bond positions and orientations (cis or trans), and functional group stereochemistry (R versus S). Fully understanding the roles of lipids in biological processes therefore requires separating and evaluating how isomers change in biological and environmental samples. To address this challenge, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows to improve identifications. In this manuscript, we review the current state of these approaches and their capabilities for improving the identification of specific lipid species.« less

Angular distribution measurement of fragment ions from a molecule using a new beamline consisting of a Grasshopper monochromator

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

Saito, N.; Suzuki, I. H.; Onuki, H.

1989-07-01

Optical characteristics of a new beamline consisting of a premirror, a Grasshopper monochromator, and a refocusing mirror have been investigated. The intensity of the monochromatic soft x-ray was estimated to be about 10/sup 8/ photons/(s 100 mA) at 500 eV with the storage electron energy of 600 MeV and the minimum slit width. This slit width provides a resolution of about 500. Angular distributions of fragment ions from an inner-shell excited nitrogen molecule have been measured with a rotatable time-of-flight mass spectrometer by using this beamline.

New Approach for Studying Slow Fragmentation Kinetics in FT-ICR: Surface-Induced Dissociation Combined with Resonant Ejection

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

Laskin, Julia; Futrell, Jean H.

2015-02-01

We introduce a new approach for studying the kinetics of large ion fragmentation in the gas phase by coupling surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer with resonant ejection of selected fragment ions using a relatively short (5 ms) ejection pulse. The approach is demonstrated for singly protonated angiotensin III ions excited by collisions with a self-assembled monolayer of alkylthiol on gold (HSAM). The overall decomposition rate and rate constants of individual reaction channels are controlled by varying the kinetic energy of the precursor ion in a range of 65–95 eV. The kinetics of peptidemore » fragmentation are probed by varying the delay time between resonant ejection and fragment ion detection at a constant total reaction time. RRKM modeling indicates that the shape of the kinetics plots is strongly affected by the shape and position of the energy deposition function (EDF) describing the internal energy distribution of the ion following ion-surface collision. Modeling of the kinetics data provides detailed information on the shape of the EDF and energy and entropy effects of individual reaction channels.« less

Source abundances of ultra heavy elements derived from UHCRE measurements.

PubMed

Domingo, C; Font, J; Baixeras, C; Fernandez, F

1996-11-01

A total of 205 tracks have been located, measured, and positively identified as originating from Ultra Heavy (Z > or = 65) cosmic ray ions with energies over 2 GeV/amu in the 10 UHCRE plastic track detector (mainly Lexan polycarbonate) stacks studied by our Group. About 40 values of reduced etch rate S have been obtained along each of these tracks. A method based on determining the gradient of S, together with calibration in accelerators, is used to determine the charge of each ion resulting in one of such tracks to obtain the charge spectrum of the recorded Ultra Heavy ions. The abundance ratio of ions with 87 < or = Z < or = 100 to those with 74 < or = Z < or = 86 as well as that of ions with 81 < or = Z < or = 86 to those with 74 < or = Z < or = 80 are calculated at 0.016 and 0.32, respectively, which agree with the values obtained from measurements in the HEAO-3 and Ariel-6 experiments. The abundance ratio of ions with 70 < or = Z < or = 73 to those with 74 < or = Z < or = 86 is also calculated, but its value (0.074) did not seem to be significant because of our detectors' low registration efficiency in the charge range 70 < or = Z < or = 73. A computer program developed by our Group, based on the Leaky Box cosmic ray propagation model, has been used to determine the source abundances of cosmic ray nuclei with Z > or = 65 inferred from the abundances measured in the UHCRE. It appeared that r-process synthesized elements were overabundant compared to the Solar System abundances, as predicted by other authors.

Effects of Charge State on Fragmentation Pathways, Dynamics, and Activation Energies of Ubiquitin Ions Measured by Blackbody Infrared Radiative Dissociation

PubMed Central

Jockusch, Rebecca A.; Schnier, Paul D.; Price, William D.; Strittmatter, Eric. F.; Demirev, Plamen A.; Williams*, Evan R.

2005-01-01

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 1012 s−1, respectively. These values for the 6+ and 7+ ions are 0.9–1.0 eV and 109 s−1, and those for the 10+ and 11+ ions are 1.6 eV and 1016–1017 s−1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed. PMID:9075403

Effects of charge state on fragmentation pathways, dynamics, and activation energies of ubiquitin ions measured by blackbody infrared radiative dissociation.

PubMed

Jockusch, R A; Schnier, P D; Price, W D; Strittmatter, E F; Demirev, P A; Williams, E R

1997-03-15

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 10(12) s-1, respectively. These values for the 6+ and 7+ ions are 0.9-1.0 eV and 10(9) s-1, and those for the 10+ and 11+ ions are 1.6 eV and 10(16)-10(17) s-1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed.

Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters

NASA Astrophysics Data System (ADS)

Neustetter, Michael; Mahmoodi-Darian, Masoomeh; Denifl, Stephan

2017-05-01

Mass spectroscopic investigations on tetrahydrofuran (THF, C4H8O), a common model molecule of the DNA-backbone, have been carried out. We irradiated isolated THF and (hydrated) THF clusters with low energy electrons (electron energy 70 eV) in order to study electron ionization and ionic fragmentation. For elucidation of fragmentation pathways, deuterated TDF (C4D8O) was investigated as well. One major observation is that the cluster environment shows overall a protective behavior on THF. However, also new fragmentation channels open in the cluster. In this context, we were able to solve a discrepancy in the literature about the fragment ion peak at mass 55 u in the electron ionization mass spectrum of THF. We ascribe this ion yield to the fragmentation of ionized THF clusters.

Unusual Fragmentation of Pro-Ser/Thr-Containing Peptides Detected in Collision-Induced Dissociation Spectra

NASA Astrophysics Data System (ADS)

Medzihradszky, Katalin F.; Trinidad, Jonathan C.

2012-04-01

During collision-induced dissociation (CID)-, phosphoserine- and phosphothreonine-containing peptides frequently undergo neutral loss of phosphoric acid. Subsequent amide bond cleavage N-terminal to the site of phosphorylation results in a y ion with a mass 18 Da lower than the corresponding unmodified y fragment. We report here that when the phosphoserine or phosphothreonine is directly preceded by a proline, an unusual fragment with a mass 10 Da higher than the corresponding unmodified y ion is frequently observed. Accurate mass measurements are consistent with elimination of the phosphoric acid followed by fragmentation between the α carbon and the carbonyl group of the proline residue. We propose a cyclic oxazoline structure for this fragment. Our observation may be explained by the charge-directed SN2 neighboring group participation reaction proposed for the phosphoric acid elimination by Palumbo et al. [Palumbo, A. M., Tepe, J. J., Reid, G. E. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides. J. Protein Res. 7(2), 771-779 (2008)]. Considering such specific fragment ions for confirmation purposes after regular database searches may boost the confidence of peptide identifications as well as phosphorylation site assignments.

Secondary forest regeneration benefits old-growth specialist bats in a fragmented tropical landscape.

PubMed

Rocha, Ricardo; Ovaskainen, Otso; López-Baucells, Adrià; Farneda, Fábio Z; Sampaio, Erica M; Bobrowiec, Paulo E D; Cabeza, Mar; Palmeirim, Jorge M; Meyer, Christoph F J

2018-02-28

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.

Fragmentation of molecular tributyltin chloride

NASA Astrophysics Data System (ADS)

Osmekhin, S.; Caló, A.; Kisand, V.; Nõmmiste, E.; Kotilainen, H.; Aksela, H.; Aksela, S.

2008-06-01

Fragmentation of tributyltin chloride (TBTCl) vapour has been studied experimentally by means of time-of-flight mass spectrometry at the photon energy range of 9-25 eV of synchrotron radiation, at 21.22 eV of HeI as well as with 500 eV electron beam excitation. Branching ratios of the tributyltin chloride fragments taken with HeI and synchrotron radiation have been presented first time. Calculations based on density functional theory (DFT) were carried out for TBTCl and the ionization energies obtained were used to predict the dissociation pathways creating the observed ions.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization.

PubMed

Neustetter, M; Jabbour Al Maalouf, E; Limão-Vieira, P; Denifl, S

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n (+) (0 ≤ n ≤ 6) and W2(CO)n (+) (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n (+) (0 ≤ n ≤ 3) and W2C(CO)n (+) (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

Penning ionization and ion fragmentation of formamide HCONH2 by He∗, Ne∗, and Ar∗ in molecular beams

NASA Astrophysics Data System (ADS)

Madison, Tamika A.; Siska, P. E.

2009-10-01

Mass spectra from Penning ionization by metastable atom bombardment (MAB) in the title system at kinetic energies near 1 kcal/mol are reported. The experiments employ a supersonic excited noble gas beam crossing an effusive beam of formamide vapor. Product ions are extracted perpendicular to the plane of the beams, analyzed by a quadrupole mass filter, and counted by a scintillation-type ion counter. Relative to 70 eV electron impact, the He∗ and Ne∗ spectra show more extensive breakage of C-N and C-H bonds despite the smaller available energy, while the Ar∗ spectrum shows only the molecular ion (m /z 45), H atom elimination (44), and the decarbonylation products CO+NH3+ (17). Fragmentation in the latter system has been analyzed using a combination of ab initio calculations and Rice-Ramsperger-Kassel-Marcus theory with tunneling correction; good agreement with the experimental 45/44/17 intensity ratio 100/6.8±0.7/6.2±1.7 is obtained. 15% of m/z 17 and 50% of m /z 44 is attributed to tunneling. The ab initio decarbonylation reaction path yields a hydrogen bonded H2N-HCO+ transition state, which transfers a proton while proceeding downhill to the observed products, while both the path and the energetics support the earlier conclusion that the lowest lying electronically excited state of the ion (2π or 2a″) crosses the ground state early along the reaction path, thereby dominating the dynamics of decarbonylation.

Selective enhancement of carbohydrate ion abundances by diamond nanoparticles for mass spectrometric analysis.

PubMed

Wu, Chieh-Lin; Wang, Chia-Chen; Lai, Yin-Hung; Lee, Hsun; Lin, Jia-Der; Lee, Yuan Tseh; Wang, Yi-Sheng

2013-04-16

Diamond nanoparticles (DNPs) were incorporated into matrix-assisted laser desorption/ionization (MALDI) samples to enhance the sensitivity of the mass spectrometer to carbohydrates. The DNPs optimize the MALDI sample morphology and thermalize the samples for thermally labile compounds because they have a high thermal conductivity, a low extinction coefficient in UV-vis spectral range, and stable chemical properties. The best enhancement effect was achieved when matrix, DNP, and carbohydrate solutions were deposited and vacuum-dried consecutively to form a trilayer sample morphology. It allows the direct identification of underivatized carbohydrates mixed with equal amount of proteins because no increase in the ion abundance of proteins was achieved. For dextran with an average molecular weight of 1500, the trilayer method typically improves the sensitivity by 79- and 7-fold in comparison to the conventional dried-droplet and thin-layer methods, respectively.

Fragmentation of Electrospray-produced Deprotonated Ions of Oligodeoxyribonucleotides Containing an Alkylated or Oxidized Thymidine

PubMed Central

Wang, Pengcheng; Williams, Renee T.; Guerrero, Candace R.; Ji, Debin; Wang, Yinsheng

2014-01-01

Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O2, N3 and O4) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3′-O3′ bond, the incorporation of an alkyl group to the O2 position and, to a much lesser extent, the O4 position, but not the N3 position of thymine, led to facile cleavage of the C3′-O3′ bond on the 3′ side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation. PMID:24664806

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants

PubMed Central

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages. PMID:26731271

Fragmentation of nitrogen-14 nuclei at 2.1 Gev per nucleon.

NASA Technical Reports Server (NTRS)

Heckman, H. H.; Greiner, D. E.; Lindstrom, P. J.; Bieser, F. S.

1971-01-01

An experiment has been carried out at the bevatron on the nuclear fragmentation of nitrogen-14 ions at an energy of 2.1 billion electron volts (Gev) per nucleon. Because of the near equality of the velocities of the nitrogen-14 beam and the fragmentation products at an angle of 0 deg, we find it possible to identify the nuclear fragments isotopically.

Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers.

PubMed

Sherwood, Carly A; Eastham, Ashley; Lee, Lik Wee; Risler, Jenni; Vitek, Olga; Martin, Daniel B

2009-09-01

Multiple reaction monitoring mass spectrometry (MRM-MS) is a technique for high-sensitivity targeted analysis. In proteomics, MRM-MS can be used to monitor and quantify a peptide based on the production of expected fragment peaks from the selected peptide precursor ion. The choice of which fragment ions to monitor in order to achieve maximum sensitivity in MRM-MS can potentially be guided by existing MS/MS spectra. However, because the majority of discovery experiments are performed on ion trap platforms, there is concern in the field regarding the generalizability of these spectra to MRM-MS on a triple quadrupole instrument. In light of this concern, many operators perform an optimization step to determine the most intense fragments for a target peptide on a triple quadrupole mass spectrometer. We have addressed this issue by targeting, on a triple quadrupole, the top six y-ion peaks from ion trap-derived consensus library spectra for 258 doubly charged peptides from three different sample sets and quantifying the observed elution curves. This analysis revealed a strong correlation between the y-ion peak rank order and relative intensity across platforms. This suggests that y-type ions obtained from ion trap-based library spectra are well-suited for generating MRM-MS assays for triple quadrupoles and that optimization is not required for each target peptide.

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

PubMed Central

Dalmay, Tamas

2018-01-01

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues. PMID:29474379

Formation of a1 Ions Directly from Oxazolone b2 Ions: an Energy-Resolved and Computational Study

NASA Astrophysics Data System (ADS)

Bythell, Benjamin J.; Harrison, Alex G.

2015-05-01

It is well-known that oxazolone b2 ions fragment extensively by elimination of CO to form a2 ions, which often fragment further to form a1 ions. Less well-known is that some oxazolone b2 ions may fragment directly to form a1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b2→a1 fragmentation reaction. The experimental results show that the direct b2→a1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a2 product in the b2→a2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b2→a2 reaction compared with those for the b2→a1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar = N-methylglycine) oxazolone b2 ions, a1 ions are not formed but rather neutral imine elimination from the N-terminus of the b2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these SN2-like b2→a1 reaction. The difference between the two methods of barrier calculation are highly significant ( P < 0.001) for the b2→a1 reaction, but only marginally significant ( P = 0.05) for the b2→a2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing SN2-like reactions.

New Development on Modelling Fluctuations and Fragmentation in Heavy-Ion Collisions

NASA Astrophysics Data System (ADS)

Lin, Hao; Danielewicz, Pawel

2017-09-01

During heavy-ion collisions (HIC), colliding nuclei form an excited composite system. Instabilities present in the system may deform the shape of the system exotically, leading to a break-up into fragments. Many experimental efforts have been devoted to the nuclear multifragmentation phenomenon, while traditional HIC models, lacking in proper treatment of fluctuations, fall short in explaining it. In view of this, we are developing a new model to implement realistic fluctuations into transport simulation. The new model is motivated by the Brownian motion description of colliding particles. The effects of two-body collisions are recast in one-body diffusion processes. Vastly different dynamical paths are sampled by solving Langevin equations in momentum space. It is the stochastic sampling of dynamical paths that leads to a wide spread of exit channels. In addition, the nucleon degree of freedom is used to enhance the fluctuations. The model has been tested in reactions such as 112Sn + 112Sn and 58Ni + 58Ni, where reasonable results are yielded. An exploratory comparison on the 112Sn + 112Sn reaction at 50 MeV/nucleon with two other models, the stochastic mean-field (SMF) and the antisymmetrized molecular dynamics (AMD) models, has also been conducted. Work supported by the NSF Grant No. PHY-1403906.

A novel method for assessment of fragmentation and beam-material interactions in helium ion radiotherapy with a miniaturized setup.

PubMed

Gallas, Raya R; Arico, Giulia; Burigo, Lucas N; Gehrke, Tim; Jakůbek, Jan; Granja, Carlos; Tureček, Daniel; Martišíková, Maria

2017-10-01

Radiotherapy with protons and carbon ions enables to deliver dose distributions of high conformation to the target. Treatment with helium ions has been suggested due to their physical and biological advantages. A reliable benchmarking of the employed physics models with experimental data is required for treatment planning. However, experimental data for helium interactions is limited, in part due to the complexity and large size of conventional experimental setups. We present a novel method for the investigation of helium interactions with matter using miniaturized instrumentation based on highly integrated pixel detectors. The versatile setup consisted of a monitoring detector in front of the PMMA phantom of varying thickness and a detector stack for investigation of outgoing particles. The ion type downstream from the phantom was determined by high-resolution pattern recognition analysis of the single particle signals in the pixelated detectors. The fractions of helium and hydrogen ions behind the used targets were determined. As expected for the stable helium nucleus, only a minor decrease of the primary ion fluence along the target depth was found. E.g. the detected fraction of hydrogen ions on axis of a 220MeV/u 4 He beam was below 6% behind 24.5cm of PMMA. Monte-Carlo simulations using Geant4 reproduce the experimental data on helium attenuation and yield of helium fragments qualitatively, but significant deviations were found for some combinations of target thickness and beam energy. The presented method is promising to contribute to the reduction of the uncertainty of treatment planning for helium ion radiotherapy. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Solar abundances as derived from solar energetic particles

NASA Technical Reports Server (NTRS)

Stone, E. C.

1989-01-01

Recent studies have shown that there are well defined average abundances of heavy (Z above 2) solar energetic particles (SEPs), with variations in the acceleration and propagation producing a systematic flare-to-flare fractionation that depends on the charge per unit mass of the ion. Correcting the average SEP abundances for this fractionation yields SEP-derived coronal abundances for 20 elements. High-resolution SEP studies have also provided isotopic abundances for five elements. SEP-derived abundances indicate that elements with high first ionization potentials (greater than 10 eV) are depleted in the corona relative to the photosphere and provide new information on the solar abundance of C and Ne-22.

A small mammal community in a forest fragment, vegetation corridor and coffee matrix system in the Brazilian Atlantic forest.

PubMed

Rocha, Mariana Ferreira; Passamani, Marcelo; Louzada, Júlio

2011-01-01

The objective of our work was to verify the value of the vegetation corridor in the conservation of small mammals in fragmented tropical landscapes, using a model system in the southeastern Minas Gerais. We evaluated and compared the composition and structure of small mammals in a vegetation corridor, forest fragments and a coffee matrix. A total of 15 species were recorded, and the highest species richness was observed in the vegetation corridor (13 species), followed by the forest fragments (10) and the coffee matrix (6). The absolute abundance was similar between the vegetation corridor and fragments (F = 22.94; p = 0.064), and the greatest differences occurred between the vegetation corridor and the matrix (F = 22.94; p = 0.001) and the forest fragments and the matrix (F = 22.94; p = 0.007). Six species showed significant habitat preference possibly related to the sensitivity of the species to the forest disturbance. Marmosops incanus was the species most sensitive to disturbance; Akodon montensis, Cerradomys subflavus, Gracilinanus microtarsus and Rhipidomys sp. displayed little sensitivity to disturbance, with a high relative abundance in the vegetation corridor. Calomys sp. was the species least affected by habitat disturbance, displaying a high relative abundance in the coffee matrix. Although the vegetation corridors are narrow (4 m width), our results support the hypothesis in which they work as a forest extension, share most species with the forest fragment and support species richness and abundance closer to forest fragments than to the coffee matrix. Our work highlights the importance and cost-effectiveness of these corridors to biodiversity management in the fragmented Atlantic Forest landscapes and at the regional level.

A Small Mammal Community in a Forest Fragment, Vegetation Corridor and Coffee Matrix System in the Brazilian Atlantic Forest

PubMed Central

Rocha, Mariana Ferreira; Passamani, Marcelo; Louzada, Júlio

2011-01-01

The objective of our work was to verify the value of the vegetation corridor in the conservation of small mammals in fragmented tropical landscapes, using a model system in the southeastern Minas Gerais. We evaluated and compared the composition and structure of small mammals in a vegetation corridor, forest fragments and a coffee matrix. A total of 15 species were recorded, and the highest species richness was observed in the vegetation corridor (13 species), followed by the forest fragments (10) and the coffee matrix (6). The absolute abundance was similar between the vegetation corridor and fragments (F = 22.94; p = 0.064), and the greatest differences occurred between the vegetation corridor and the matrix (F = 22.94; p = 0.001) and the forest fragments and the matrix (F = 22.94; p = 0.007). Six species showed significant habitat preference possibly related to the sensitivity of the species to the forest disturbance. Marmosops incanus was the species most sensitive to disturbance; Akodon montensis, Cerradomys subflavus, Gracilinanus microtarsus and Rhipidomys sp. displayed little sensitivity to disturbance, with a high relative abundance in the vegetation corridor. Calomys sp. was the species least affected by habitat disturbance, displaying a high relative abundance in the coffee matrix. Although the vegetation corridors are narrow (4 m width), our results support the hypothesis in which they work as a forest extension, share most species with the forest fragment and support species richness and abundance closer to forest fragments than to the coffee matrix. Our work highlights the importance and cost-effectiveness of these corridors to biodiversity management in the fragmented Atlantic Forest landscapes and at the regional level. PMID:21912591

Characterization of limonin glucoside metabolites from human prostate cell culture medium using high-performance liquid chromatography/electrospray ionization mass spectrometry and tandem mass spectrometry.

PubMed

Tian, Qingguo; Kent, Kyle D; Bomser, Joshua A; Schwartz, Steven J

2004-01-01

The metabolism of limonin 17-beta-D-glucopyranoside (LG) by non-cancerous (RWPE-1) and cancerous (PC-3) human prostate epithelial cells was investigated using high-performance liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) with in-source fragmentation and tandem mass spectrometry (MS/MS). During positive ion LC/ESI-MS, LG formed an abundant sodiated species ([M+Na]+) while the protonated molecule was barely observable. [M+Na]+ further fragmented into the less abundant [LARL+H]+ and a predominantly protonated aglycone molecule (limonin) due to in-source fragmentation. The major metabolite, limonin A-ring lactone (LARL), formed an abundant protonated molecule that was fragmented into a protonated molecule of limonin by loss of one molecule of water. In MS/MS by collisionally activated dissociation (CAD), LG produced the sodiated aglycone, [aglycone+Na]+, while LARL fragmented into [M+H]+ of limonin and fragment ions resulted by further loss of water, carbon monoxide and carbon dioxide, indicating the presence of oxygenated-ring structures. The limits of detection of LG were 0.4 and 20 fmol in selected-ion monitoring (SIM) and selected-reaction monitoring (SRM) detection, respectively. Copyright 2004 John Wiley & Sons, Ltd.

Distribution and abundance of anadromous Sea Lamprey Spawners in a fragmented stream: Current status and potential range expansion following barrier removal

USGS Publications Warehouse

Zydlewski, Joseph D.; Gardner, Cory; Coghlan, Stephen M.

2012-01-01

Dams fragment watersheds and prevent anadromous fishes from reaching historic spawning habitat. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine), has been the focus of efforts to reestablish marine-freshwater connectivity and restore anadromous fishes via the removal of two barriers to fish migration. Currently, Petromyzon marinus (Sea Lamprey) is the only anadromous fish known to spawn successfully in the stream downstream of the lowermost dam. Here, we describe the distribution and abundance of a spawning population of Sea Lamprey in Sedgeunkedunk Stream, prior to and in anticipation of habitat increase after the completion of one barrier removal. In 2008, we estimated the abundance of Sea Lamprey and its nests using daily stream surveys and an open-population mark-recapture model. We captured 47 Sea Lamprey and implanted each with a PIT tag so that we could track movements and nest associations of individual fish. The spawning migration began on 18 June, and the last living individual was observed on 27 June. We located 31 nests, distributed from head-of-tide to the lowermost dam; no spawners or nests were observed in the tidally influenced zone or upstream of this dam. Mean longevity in the stream and the number of nests attended were correlated with arrival date; early migrants were alive longer and attended more nests than later migrants. Males were more likely to be observed away from a nest, or attending three or more nests, than were females, which attended usually one or two nests. We observed a negative association between nest abundance and substrate cover by fine sediment. Based on their observed movements in the system, and the extent of their habitat use, we anticipate that spawning Sea Lamprey will recolonize formerly inaccessible habitat after dam removals.

Red-shouldered Hawk (Buteo lineatus) abundance and habitat in a reclaimed mine landscape

USGS Publications Warehouse

Balcerzak, M.J.; Wood, P.B.

2003-01-01

Fragmentation of the landscape by large-scale mining may affect Red-shouldered Hawk (Buteo lineatus) populations by reducing the amount of forested habitat available in a landscape and by creating fragmented forest parches surrounded by reclaimed mine lands. We examined habitat characteristics and relative abundance of Red-shouldered Hawks in reclaimed mine landscapes within four treatments: early-successional grassland habitat, mid-successional shrub/pole habitat, late-successional fragmented forest habitat, and late-successional intact forest habitat. We quantified microhabitat characteristics within an 11.3-m-radius plot centered on 156 vegetation plots throughout the four treatments. We surveyed 48 stations on and adjacent to three mines for Red-shouldered Hawks using standardized broadcast call techniques during February 2000-January 2001 and measured landscape characteristics within 1000-m buffer zones centered on each station from digitized aerial photographs. Mean abundance of Red-shouldered Hawks was significantly higher in the intact forest (x?? = 0.07 detections/ point, SE = 0.03) than the grassland (x?? = 0.01, SE = 0.01) treatment, but did not differ from the fragmented forest (x?? = 0.03, SE = 0.01) or shrub/pole (x?? = 0.03, SE = 0.01) treatments. Most microhabitat characteristics in both fragmented and intact forest differed from shrub/pole and grasslands. Amount of wetland was the most important characteristic determining presence of Red-shouldered Hawks in a forest-dominated landscape. More wetlands in the landscape may provide abundant amphibians and reptiles, which are important in the diet of Red-shouldered Hawks. ?? 2003 The Raptor Research Foundation, Inc.

Imaging mass spectrometry reveals direct albumin fragmentation within the diabetic kidney.

PubMed

Grove, Kerri J; Lareau, Nichole M; Voziyan, Paul A; Zeng, Fenghua; Harris, Raymond C; Hudson, Billy G; Caprioli, Richard M

2018-05-17

Albumin degradation in the renal tubules is impaired in diabetic nephropathy such that levels of the resulting albumin fragments increase with the degree of renal injury. However, the mechanism of albumin degradation is unknown. In particular, fragmentation of the endogenous native albumin has not been demonstrated in the kidney and the enzymes that may contribute to fragmentation have not been identified. To explore this we utilized matrix-assisted laser desorption/ionization imaging mass spectrometry for molecular profiling of specific renal regions without disturbing distinct tissue morphology. Changes in protein expression were measured in kidney sections of eNOS -/- db/db mice, a model of diabetic nephropathy, by high spatial resolution imaging allowing molecular localizations at the level of single glomeruli and tubules. Significant increases were found in the relative abundances of several albumin fragments in the kidney of the mice with diabetic nephropathy compared with control nondiabetic mice. The relative abundance of fragments detected correlated positively with the degree of nephropathy. Furthermore, specific albumin fragments accumulating in the lumen of diabetic renal tubules were identified and predicted the enzymatic action of cathepsin D based on cleavage specificity and in vitro digestions. Importantly, this was demonstrated directly in the renal tissue with the endogenous nonlabeled murine albumin. Thus, our results provide molecular insights into the mechanism of albumin degradation in diabetic nephropathy. Copyright © 2018 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Energetics and Dynamics of Dissociation of Deprotonated Peptides: Fragmentation of Angiotensin Analogs

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

Laskin, Julia; Yang, Zhibo

2011-12-01

We present a first study of the energetics and dynamics of dissociation of deprotonated peptides using time- and collision-energy resolved surface-induced dissociation (SID) experiments. SID of four model peptides: RVYIHPF, HVYIHPF, DRVYIHPF, and DHVYIHPF was studied using a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for studying ion-surface collisions. Energy and entropy effects for the overall decomposition of the precursor ion were deduced by modeling the time- and collision energy-resolved survival curves using an RRKM based approach developed in our laboratory. The results were compared to the energetics and dynamics of dissociation of the correspondingmore » protonated species. We demonstrate that acidic peptides are less stable in the negative mode because of the low threshold associated with the kinetically hindered loss of H2O from [M-H]- ions. Comparison between the two basic peptides indicates that the lower stability of the [M-H]- ion of RVYIHPF as compared to HVYIHPF towards fragmentation is attributed to the differences in fragmentation mechanisms. Specifically, threshold energy associated with losses of NH3 and NHCNH from RVYIHPF is lower than the barrier for backbone fragmentation that dominates gas-phase decomposition of HVYIHPF. The results provide a first quantitative comparison between the energetics and dynamics of dissociation of [M+H]+ and [M-H]- ions of acidic and basic peptides.« less

Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

PubMed

Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

2013-01-30

A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. Copyright © 2012 Elsevier B.V. All rights reserved.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

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

Neustetter, M.; Jabbour Al Maalouf, E.; Denifl, S., E-mail: Stephan.Denifl@uibk.ac.at, E-mail: plimaovieira@fct.unl.pt

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO){sub 6}) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO){sub 6} clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO){sub n}{sup +} (0 ≤ n ≤ 6) and W{sub 2}(CO){sub n}{sup +} (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO){sub n}{sup +} (0 ≤more » n ≤ 3) and W{sub 2}C(CO){sub n}{sup +} (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.« less

Measurement of the velocity of neutral fragments by the "correlated ion and neutral time of flight" method combined with "velocity-map imaging"

NASA Astrophysics Data System (ADS)

Berthias, F.; Feketeová, L.; Della Negra, R.; Dupasquier, T.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Märk, T. D.

2017-08-01

In the challenging field of imaging molecular dynamics, a novel method has been developed and implemented that allows the measurement of the velocity of neutral fragments produced in collision induced dissociation experiments on an event-by-event basis. This has been made possible by combining a correlated ion and neutral time of flight method with a velocity map imaging technique. This new method relies on a multiparametric correlated detection of the neutral and charged fragments from collision induced dissociation on one single detector. Its implementation on the DIAM device (Device for irradiation of biomolecular clusters) (Dispositif d'Irradiation d'Agrégats bioMoléculaires) allowed us to measure the velocity distribution of water molecules evaporated from collision induced dissociation of mass- and energy-selected protonated water clusters.

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Dupré, Mathieu; Cantel, Sonia; Martinez, Jean; Enjalbal, Christine

2012-02-01

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (bn-1 + H2O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H2O and NH3) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Target fragmentation in radiobiology

NASA Technical Reports Server (NTRS)

Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.; Townsend, Lawrence W.

1993-01-01

Nuclear reactions in biological systems produce low-energy fragments of the target nuclei seen as local high events of linear energy transfer (LET). A nuclear-reaction formalism is used to evaluate the nuclear-induced fields within biosystems and their effects within several biological models. On the basis of direct ionization interaction, one anticipates high-energy protons to have a quality factor and relative biological effectiveness (RBE) of unity. Target fragmentation contributions raise the effective quality factor of 10 GeV protons to 3.3 in reasonable agreement with RBE values for induced micronuclei in bean sprouts. Application of the Katz model indicates that the relative increase in RBE with decreasing exposure observed in cell survival experiments with 160 MeV protons is related solely to target fragmentation events. Target fragment contributions to lens opacity given an RBE of 1.4 for 2 GeV protons in agreement with the work of Lett and Cox. Predictions are made for the effective RBE for Harderian gland tumors induced by high-energy protons. An exposure model for lifetime cancer risk is derived from NCRP 98 risk tables, and protraction effects are examined for proton and helium ion exposures. The implications of dose rate enhancement effects on space radiation protection are considered.

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

NASA Astrophysics Data System (ADS)

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

Distinguishing aspartic and isoaspartic acids in peptides by several mass spectrometric fragmentation methods

PubMed Central

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

2016-01-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post source decay (PSD), MALDI 157 nm photodissociation, TMPP charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. PMID:27613306

Characterization of compounds by time-of-flight measurement utilizing random fast ions

DOEpatents

Conzemius, R.J.

1989-04-04

An apparatus is described for characterizing the mass of sample and daughter particles, comprising a source for providing sample ions; a fragmentation region wherein a fraction of the sample ions may fragment to produce daughter ion particles; an electrostatic field region held at a voltage level sufficient to effect ion-neutral separation and ion-ion separation of fragments from the same sample ion and to separate ions of different kinetic energy; a detector system for measuring the relative arrival times of particles; and processing means operatively connected to the detector system to receive and store the relative arrival times and operable to compare the arrival times with times detected at the detector when the electrostatic field region is held at a different voltage level and to thereafter characterize the particles. Sample and daughter particles are characterized with respect to mass and other characteristics by detecting at a particle detector the relative time of arrival for fragments of a sample ion at two different electrostatic voltage levels. The two sets of particle arrival times are used in conjunction with the known altered voltage levels to mathematically characterize the sample and daughter fragments. In an alternative embodiment the present invention may be used as a detector for a conventional mass spectrometer. In this embodiment, conventional mass spectrometry analysis is enhanced due to further mass resolving of the detected ions. 8 figs.

Characterization of compounds by time-of-flight measurement utilizing random fast ions

DOEpatents

Conzemius, Robert J.

1989-01-01

An apparatus for characterizing the mass of sample and daughter particles, comprising a source for providing sample ions; a fragmentation region wherein a fraction of the sample ions may fragment to produce daughter ion particles; an electrostatic field region held at a voltage level sufficient to effect ion-neutral separation and ion-ion separation of fragments from the same sample ion and to separate ions of different kinetic energy; a detector system for measuring the relative arrival times of particles; and processing means operatively connected to the detector system to receive and store the relative arrival times and operable to compare the arrival times with times detected at the detector when the electrostatic field region is held at a different voltage level and to thereafter characterize the particles. Sample and daughter particles are characterized with respect to mass and other characteristics by detecting at a particle detector the relative time of arrival for fragments of a sample ion at two different electrostatic voltage levels. The two sets of particle arrival times are used in conjunction with the known altered voltage levels to mathematically characterize the sample and daughter fragments. In an alternative embodiment the present invention may be used as a detector for a conventional mass spectrometer. In this embodiment, conventional mass spectrometry analysis is enhanced due to further mass resolving of the detected ions.

Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

PubMed

Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

2014-04-04

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

PubMed Central

2015-01-01

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

Electron molecular ion recombination: product excitation and fragmentation.

PubMed

Adams, Nigel G; Poterya, Viktoriya; Babcock, Lucia M

2006-01-01

Electron-ion dissociative recombination is an important ionization loss process in any ionized gas containing molecular ions. This includes the interstellar medium, circumstellar shells, cometary comae, planetary ionospheres, fusion plasma boundaries, combustion flames, laser plasmas and chemical deposition and etching plasmas. In addition to controlling the ionization density, the process generates many radical species, which can contribute to a parallel neutral chemistry. Techniques used to obtain rate data and product information (flowing afterglows and storage rings) are discussed and recent data are reviewed including diatomic to polyatomic ions and cluster ions. The data are divided into rate coefficients and cross sections, including their temperature/energy dependencies, and quantitative identification of neutral reaction products. The latter involve both ground and electronically excited states and including vibrational excitation. The data from the different techniques are compared and trends in the data are examined. The reactions are considered in terms of the basic mechanisms (direct and indirect processes including tunneling) and recent theoretical developments are discussed. Finally, new techniques are mentioned (for product identification; electrostatic storage rings, including single and double rings; Coulomb explosion) and new ways forward are suggested.

Titan's Topside Ionospheric Composition: Cassini Plasma Spectrometer Ion Mass Spectrometer Measurements

NASA Astrophysics Data System (ADS)

Sittler, Edward; Hartle, Richard; Ali, Ashraf; Cooper, John; Lipatov, Alexander; Simpson, David; Sarantos, Menelaos; Chornay, Dennis; Smith, Todd

2017-01-01

We present ion composition measurements of Titan's topside ionosphere using both T9 and T15 Cassini Plasma Spectrometer (CAPS) Ion Mass Spectrometer (IMS) measurements. The IMS is able to make measurements of Titan's ionosphere due to ionospheric outflows as originally reported for the T9 flyby. This allows one to take advantage of the unique capabilities of the CAPS IMS which measures both the mass-per-charge (M/Q) of the ions and the fragments of the ions produced inside the sensor such as carbon, nitrogen and oxygen fragments. Specific attention will be given to such ions as NH4 +, N +, O +, CH4 +, CxHy +, and HCNH + ions as examples. The CAPS IMS uses a time-of-flight (TOF) technique which accelerates ions up to 14.6 kV, so they can pass through ultra-thin carbon foils. Neutral fragments are used to measure the ion M/Q and positive fragments to measure the atomic components. We preliminarily find, by using IMS measurements of T9 and T15 ionospheric outflows, evidence for methane group ions, nitrogen ions, ammonium ions, water group ions and CnHm + ions with n = 2, 3, and 4 within Titan's topside ionosphere. E.C. Sittler acknowledges support at Goddard Space Flight Center by the CAPS Cassini Project from JPL funds under contract # NAS703001TONMO711123/1405851.

Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

NASA Astrophysics Data System (ADS)

Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

2017-04-01

We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms . Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

Targeted Identification of SUMOylation Sites in Human Proteins Using Affinity Enrichment and Paralog-specific Reporter Ions*

PubMed Central

Lamoliatte, Frederic; Bonneil, Eric; Durette, Chantal; Caron-Lizotte, Olivier; Wildemann, Dirk; Zerweck, Johannes; Wenshuk, Holger; Thibault, Pierre

2013-01-01

Protein modification by small ubiquitin-like modifier (SUMO) modulates the activities of numerous proteins involved in different cellular functions such as gene transcription, cell cycle, and DNA repair. Comprehensive identification of SUMOylated sites is a prerequisite to determine how SUMOylation regulates protein function. However, mapping SUMOylated Lys residues by mass spectrometry (MS) is challenging because of the dynamic nature of this modification, the existence of three functionally distinct human SUMO paralogs, and the large SUMO chain remnant that remains attached to tryptic peptides. To overcome these problems, we created HEK293 cell lines that stably express functional SUMO paralogs with an N-terminal His6-tag and an Arg residue near the C terminus that leave a short five amino acid SUMO remnant upon tryptic digestion. We determined the fragmentation patterns of our short SUMO remnant peptides by collisional activation and electron transfer dissociation using synthetic peptide libraries. Activation using higher energy collisional dissociation on the LTQ-Orbitrap Elite identified SUMO paralog-specific fragment ions and neutral losses of the SUMO remnant with high mass accuracy (< 5 ppm). We exploited these features to detect SUMO modified tryptic peptides in complex cell extracts by correlating mass measurements of precursor and fragment ions using a data independent acquisition method. We also generated bioinformatics tools to retrieve MS/MS spectra containing characteristic fragment ions to the identification of SUMOylated peptide by conventional Mascot database searches. In HEK293 cell extracts, this MS approach uncovered low abundance SUMOylated peptides and 37 SUMO3-modified Lys residues in target proteins, most of which were previously unknown. Interestingly, we identified mixed SUMO-ubiquitin chains with ubiquitylated SUMO proteins (K20 and K32) and SUMOylated ubiquitin (K63), suggesting a complex crosstalk between these two modifications. PMID

Changes in Tree Reproductive Traits Reduce Functional Diversity in a Fragmented Atlantic Forest Landscape

PubMed Central

Girão, Luciana Coe; Lopes, Ariadna Valentina; Tabarelli, Marcelo; Bruna, Emilio M.

2007-01-01

Functional diversity has been postulated to be critical for the maintenance of ecosystem functioning, but the way it can be disrupted by human-related disturbances remains poorly investigated. Here we test the hypothesis that habitat fragmentation changes the relative contribution of tree species within categories of reproductive traits (frequency of traits) and reduces the functional diversity of tree assemblages. The study was carried out in an old and severely fragmented landscape of the Brazilian Atlantic forest. We used published information and field observations to obtain the frequency of tree species and individuals within 50 categories of reproductive traits (distributed in four major classes: pollination systems, floral biology, sexual systems, and reproductive systems) in 10 fragments and 10 tracts of forest interior (control plots). As hypothesized, populations in fragments and control plots differed substantially in the representation of the four major classes of reproductive traits (more than 50% of the categories investigated). The most conspicuous differences were the lack of three pollination systems in fragments-pollination by birds, flies and non-flying mammals-and that fragments had a higher frequency of both species and individuals pollinated by generalist vectors. Hermaphroditic species predominate in both habitats, although their relative abundances were higher in fragments. On the contrary, self-incompatible species were underrepresented in fragments. Moreover, fragments showed lower functional diversity (H' scores) for pollination systems (−30.3%), floral types (−23.6%), and floral sizes (−20.8%) in comparison to control plots. In contrast to the overwhelming effect of fragmentation, patch and landscape metrics such as patch size and forest cover played a minor role on the frequency of traits. Our results suggest that habitat fragmentation promotes a marked shift in the relative abundance of tree reproductive traits and greatly

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods.

PubMed

DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P

2016-12-01

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H 2 O, are present in PSD, photodissociation, and charge tagging. c • +57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.

Structure characterization of lipocyclopeptide antibiotics, aspartocins A, B & C, by ESI-MSMS and ESI-nozzle-skimmer-MSMS.

PubMed

Siegel, Marshall M; Kong, Fangming; Feng, Xidong; Carter, Guy T

2009-12-01

Three lipocyclopeptide antibiotics, aspartocins A (1), B (2), and C (3), were obtained from the aspartocin complex by HPLC separation methodology. Their structures were elucidated using previously published chemical degradation results coupled with spectroscopic studies including ESI-MS, ESI-Nozzle Skimmer-MSMS and NMR. All three aspartocin compounds share the same cyclic decapeptide core of cyclo [Dab2 (Asp1-FA)-Pip3-MeAsp4-Asp5-Gly6-Asp7-Gly8-Dab9-Val10-Pro11]. They differ only in the fatty acid side chain moiety (FA) corresponding to (Z)-13-methyltetradec-3-ene-carbonyl, (+,Z)-12-methyltetradec-3-ene-carbonyl and (Z)-12-methyltridec-3-ene-carbonyl for aspartocins A (1), B (2), and C (3), respectively. All of the sequence ions were observed by ESI-MSMS of the doubly charged parent ions. However, a number of the sequence ions observed were of low abundance. To fully sequence the lipocyclopeptide antibiotic structures, these low abundance sequence ions together with complementary sequence ions were confirmed by ESI-Nozzle-Skimmer-MSMS of the singly charged linear peptide parent fragment ions H-Asp5-Gly6-Asp7-Gly8-Dab9-Val10-Pro11-Dab2(1+)-Asp1-FA. Cyclization of the aspartocins was demonstrated to occur via the beta-amino group of Dab2 from ions of moderate intensity in the ESI-MSMS spectra. As the fatty acid moieties do not undergo internal fragmentations under the experimental ESI mass spectral conditions used, the 14 Da mass difference between the fatty acid moieties of aspartocins A (1) and B (2) versus aspartocin C (3) was used as an internal mass tag to differentiate fragment ions containing fatty acid moieties and those not containing the fatty acid moieties. The most numerous and abundant fragment ions observed in the tandem mass spectra are due to the cleavage of the tertiary nitrogen amide of the pipecolic acid residue-3 (16 fragment ions) and the proline residue-11 (7 fragment ions). In addition, the neutral loss of ethanimine from alpha

Mass spectrometric study of the negative and positive secondary ions emitted from ethanol microdroplets by MeV-energy heavy ion impact

NASA Astrophysics Data System (ADS)

Kitajima, Kensei; Majima, Takuya; Nishio, Tatsuya; Oonishi, Yoshiki; Mizutani, Shiori; Kohno, Jun-ya; Saito, Manabu; Tsuchida, Hidetsugu

2018-06-01

We have investigated the negative and positive secondary ions emitted from ethanol droplets by 4.0-MeV C3+ impact to reveal the characteristic features of the reaction processes induced by fast heavy ions at the liquid ethanol surface. Analysis of the secondary ions was performed by time-of-flight mass spectrometry for microdroplet targets in a high vacuum environment. Fragment ions, deprotonated cluster ions, and trace amounts of the reaction product ions are observed in the negative secondary ions. The main fragment anions are C2HmO- (m = 1, 3, and 5) and C2H- generated by loss of hydrogen and oxygen atoms. The reaction product anions include deprotonated glycols, larger alcohols, and their dehydrated and dehydrogenated forms generated by secondary reactions between fragments and radicals. Furthermore, C3Hm- (m = 0-2) and C4Hm- (m = 0 and 1) are observed, which could be produced through a plasma state generated in the heavy ion track. Deprotonated ethanol cluster ions, [(EtOH)n - H]-, are observed up to about n = 25. [(EtOH)n - H]- have smaller kinetic energies than the protonated cluster ions (EtOH)nH+. This probably represents the effect of the positive Coulomb potential transiently formed in the ion track. We also discuss the size distributions and structures of the water- and CH2OH-radical-attached ethanol cluster ions.

MS/MS Automated Selected Ion Chromatograms

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

Monroe, Matthew

2005-12-12

This program can be used to read a LC-MS/MS data file from either a Finnigan ion trap mass spectrometer (.Raw file) or an Agilent Ion Trap mass spectrometer (.MGF and .CDF files) and create a selected ion chromatogram (SIC) for each of the parent ion masses chosen for fragmentation. The largest peak in each SIC is also identified, with reported statistics including peak elution time, height, area, and signal to noise ratio. It creates several output files, including a base peak intensity (BPI) chromatogram for the survey scan, a BPI for the fragmentation scans, an XML file containing the SICmore » data for each parent ion, and a "flat file" (ready for import into a database) containing summaries of the SIC data statistics.« less

A Multi-Scale Perspective of the Effects of Forest Fragmentation on Birds in Eastern Forests

Treesearch

Frank R. Thompson; Therese M. Donovan; Richard M. DeGraff; John Faaborg; Scott K. Robinson

2002-01-01

We propose a model that considers forest fragmentation within a spatial hierarchy that includes regional or biogeographic effects, landscape-level fragmentation effects, and local habitat effects. We hypothesize that effects operate "top down" in that larger scale effects provide constraints or context for smaller scale effects. Bird species' abundance...

EUV emission spectra in collisions of highly charged tantalum ions with nitrogen and oxygen molecules

NASA Astrophysics Data System (ADS)

Tanuma, Hajime; Numadate, Naoki; Uchikura, Yoshiyuki; Shimada, Kento; Akutsu, Takuto; Long, Elaine; O'Sullivan, Gerry

2017-10-01

We have performed ion beam collision experiments using multiply charged tantalum ions and observed EUV (extreme ultra-violet) emission spectra in collisions of ions with molecular targets, N2 and O2. Broad UTAs (un-resolved transition arrays) from multiply charged Ta ions were observed, and the mean wavelengths of the UTAs shifted and became shorter at higher charge statea of Ta ions. These UTAs may be attributed to the 4f-5d and 4f-5g transitions. Not only the UTA emission from incident ions, but also the sharp emission lines from multiply charged fragment atomic ions were observed. Production of temporary highly charged molecular ions, their kinetic energy and fragmentation processes have been investigated with coincident detection technique. However, the observation of emission from the fragments might be for the first time. The formation mechanisms of the multiply charged fragment atomic ions from target molecules are discussed.

Absolute quantitation of low abundance plasma APL1β peptides at sub-fmol/mL Level by SRM/MRM without immunoaffinity enrichment.

PubMed

Sano, Shozo; Tagami, Shinji; Hashimoto, Yuuki; Yoshizawa-Kumagaye, Kumiko; Tsunemi, Masahiko; Okochi, Masayasu; Tomonaga, Takeshi

2014-02-07

Selected/multiple reaction monitoring (SRM/MRM) has been widely used for the quantification of specific proteins/peptides, although it is still challenging to quantitate low abundant proteins/peptides in complex samples such as plasma/serum. To overcome this problem, enrichment of target proteins/peptides is needed, such as immunoprecipitation; however, this is labor-intense and generation of antibodies is highly expensive. In this study, we attempted to quantify plasma low abundant APLP1-derived Aβ-like peptides (APL1β), a surrogate marker for Alzheimer's disease, by SRM/MRM using stable isotope-labeled reference peptides without immunoaffinity enrichment. A combination of Cibacron Blue dye mediated albumin removal and acetonitrile extraction followed by C18-strong cation exchange multi-StageTip purification was used to deplete plasma proteins and unnecessary peptides. Optimal and validated precursor ions to fragment ion transitions of APL1β were developed on a triple quadruple mass spectrometer, and the nanoliquid chromatography gradient for peptide separation was optimized to minimize the biological interference of plasma. Using the stable isotope-labeled (SI) peptide as an internal control, absolute concentrations of plasma APL1β peptide could be quantified as several hundred amol/mL. To our knowledge, this is the lowest detection level of endogenous plasma peptide quantified by SRM/MRM.

Re-investigation of the fragmentation of protonated carotenoids by electrospray ionization and nanospray tandem mass spectrometry.

PubMed

Neto, Fausto Carnevale; Guaratini, Thais; Costa-Lotufo, Letícia; Colepicolo, Pio; Gates, Paul J; Lopes, Norberto Peporine

2016-07-15

Carotenoids are polyene isoprenoids with an important role in photosynthesis and photoprotection. Their characterization in biological matrices is a crucial subject for biochemical research. In this work we report the full fragmentation of 16 polyenes (carotenes and xanthophylls) by electrospray ionization tandem mass spectrometry (ESI-CID-MS/MS) and nanospray tandem mass spectrometry (nanoESI-CID-MS/MS). Analyses were carried out on a quadrupole time-of-flight (QTOF) mass spectrometer coupled with a nanoESI source and on a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer with an ESI source. The formulae of the product ions were determined by accurate-mass measurements. It is demonstrated that the fragmentation routes observed for the protonated carotenoids derive essentially from charge-remote fragmentations and pericyclic rearrangements, such as electrocyclic and retro-ene eliminations (assisted or not by a sigmatropic hydrogen shift). All mechanisms are dependent on cis-trans isomerization through the formation of several conjugated polyene carbocation intermediates. Some specific ions for the carotenoid epoxides were justified through formation of cyclic oxonium ions. Complete fragmentation pathways of protonated carotenoids by ESI- and nanoESI-CID-MS/MS provided structural information about functional groups, polyene chain and double bonds, and contribute to identification of carotenoids based on MS/MS fragmentation patterns. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

DOE PAGES

Chen, Tsung-Chi; Ibrahim, Yehia M.; Webb, Ian K.; ...

2016-01-11

The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in a more reliable and cost-effective manner, while opening opportunities for much more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolationmore » and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. Lastly, we observed a linear increase in ion intensity with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.« less

Interstellar abundances - Gas and dust

NASA Technical Reports Server (NTRS)

Field, G. B.

1974-01-01

Data on abundances of interstellar atoms, ions and molecules in front of zeta Oph are assembled and analyzed. The gas-phase abundances of at least 11 heavy elements are significantly lower, relative to hydrogen, than in the solar system. The abundance deficiencies of certain elements correlate with the temperatures derived theoretically for particle condensation in stellar atmospheres or nebulae, suggesting that these elements have condensed into dust grains near stars. There is evidence that other elements have accreted onto such grains after their arrival in interstellar space. The extinction spectrum of zeta Oph can be explained qualitatively and, to a degree, quantitatively by dust grains composed of silicates, graphite, silicon carbide, and iron, with mantles composed of complex molecules of H, C, N, and O. This composition is consistent with the observed gas-phase deficiencies.

Time-resolved ion imaging at free-electron lasers using TimepixCam.

PubMed

Fisher-Levine, Merlin; Boll, Rebecca; Ziaee, Farzaneh; Bomme, Cédric; Erk, Benjamin; Rompotis, Dimitrios; Marchenko, Tatiana; Nomerotski, Andrei; Rolles, Daniel

2018-03-01

The application of a novel fast optical-imaging camera, TimepixCam, to molecular photoionization experiments using the velocity-map imaging technique at a free-electron laser is described. TimepixCam is a 256 × 256 pixel CMOS camera that is able to detect and time-stamp ion hits with 20 ns timing resolution, thus making it possible to record ion momentum images for all fragment ions simultaneously and avoiding the need to gate the detector on a single fragment. This allows the recording of significantly more data within a given amount of beam time and is particularly useful for pump-probe experiments, where drifts, for example, in the timing and pulse energy of the free-electron laser, severely limit the comparability of pump-probe scans for different fragments taken consecutively. In principle, this also allows ion-ion covariance or coincidence techniques to be applied to determine angular correlations between fragments.

Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

NASA Astrophysics Data System (ADS)

Martens, Sabrina M.; Marta, Rick A.; Martens, Jonathan K.; McMahon, Terry B.

2012-10-01

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm-1. The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

Effects of habitat fragmentation on passerine birds breeding in Intermountain shrubsteppe

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.

2002-01-01

Habitat fragmentation and loss strongly influence the distribution and abundance of passerine birds breeding in Intermountain shrubsteppe. Wildfires, human activities, and change in vegetation communities often are synergistic in these systems and can result in radical conversion from shrubland to grasslands dominated by exotic annuals at large temporal and spatial scales from which recovery to native conditions is unlikely. As a result, populations of 5 of the 12 species in our review of Intermountain shrubsteppe birds are undergoing significant declines; 5 species are listed as at-risk or as candidates for protection in at least one state. The process by which fragmentation affects bird distributions in these habitats remains unknown because most research has emphasized the detection of population trends and patterns of habitat associations at relatively large spatial scales. Our research indicates that the distribution of shrubland-obligate species, such as Brewer's Sparrows (Spizella breweri), Sage Sparrows (Amphispiza belli), and Sage Thrashers (Oreoscoptes montanus), was highly sensitive to fragmentation of shrublands at spatial scales larger than individual home ranges. In contrast, the underlying mechanisms for both habitat change and bird population dynamics may operate independently of habitat boundaries. We propose alternative, but not necessarily exclusive, mechanisms to explain the relationship between habitat fragmentation and bird distribution and abundance. Fragmentation might influence productivity through differences in breeding density, nesting success, or predation. However, local and landscape variables were not significant determinants either of success, number fledged, or probability of predation or parasitism (although our tests had relatively low statistical power). Alternatively, relative absence of natal philopatry and redistribution by individuals among habitats following fledging or post-migration could account for the pattern of

Collisions of slow ions C3Hn+ and C3Dn+ (n = 2-8) with room temperature carbon surfaces: mass spectra of product ions and the ion survival probability.

PubMed

Pysanenko, Andriy; Zabka, Jan; Feketeová, Linda; Märk, Tilmann D; Herman, Zdenek

2008-01-01

Collisions of C3Hn+ (n = 2-8) ions and some of their per- deuterated analogs with room temperature carbon (HOPG) surfaces (hydrocarbon-covered) were investigated over the incident energy range 13-45 eV in beam scattering experiments. The mass spectra of product ions were measured and main fragmentation paths of the incident projectile ions, energized in the surface collision, were determined. The extent of fragmentation increased with increasing incident energy. Mass spectra of even-electron ions C3H7+ and C3H5+ showed only fragmentations, mass spectra of radical cations C3H8*+ and C3H6*+ showed both simple fragmentations of the projectile ion and formation of products of its surface chemical reaction (H-atom transfer between the projectile ion and hydrocarbons on the surface). No carbon-chain build-up reaction (formation of C4 hydrocarbons) was detected. The survival probability of the incident ions, S(a), was usually found to be about 1-2% for the radical cation projectile ions C3H8*+, C3H6*+, C3H4*+ and C3H2*+ and several percent up to about 20% for the even-electron projectile ions C3H7+, C3H5+, C3H3+. A plot of S(a) values of C1, C2, C3, some C7 hydrocarbon ions, Ar+ and CO2+ on hydrocarbon-covered carbon surfaces as a function of the ionization energies (IE) of the projectile species showed a drop from about 10% to about 1% and less at IE 8.5-9.5 eV and further decrease with increasing IE. A strong correlation was found between log S(a) and IE, a linear decrease over the entire range of IE investigated (7-16 eV), described by log S(a) = (3.9 +/- 0.5)-(0.39 +/- 0.04) IE.

Gas chromatography-mass spectrometric studies of O-alkyl O-2-(N,N-dialkylamino) ethyl alkylphosphonites(phosphonates) for chemical weapons convention verification.

PubMed

Saeidian, Hamid; Babri, Mehran; Ramezani, Atefeh; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-01-01

The electron ionization (EI) mass spectra of a series of O-alkyl O-2-(N,N-dialkylaminolethyl alkylphosphonites(phosphonates), which are precursors of nerve agents, were studied for Chemical Weapons Convention (CWC) verification. General El fragmentation pathways were constructed and discussed. Proposed fragment structures were confirmed through analyzing fragment ions of deuterated analogs and density functional theory (DFT) calculations. The observed fragment ions are due to different fragmentation pathways such as hydrogen and McLafferty+1 rearrangements, alkene, amine and alkoxy elimination by alpha- or beta-cleavage process. Fragment ions distinctly allow unequivocal identification of the interested compounds including those of isomeric compounds. The presence and abundance of fragment ions were found to depend on the size and structure of the alkyl group attached to nitrogen, phosphorus and oxygen atoms.

Aggregation-fragmentation-diffusion model for trail dynamics

DOE PAGES

Kawagoe, Kyle; Huber, Greg; Pradas, Marc; ...

2017-07-21

We investigate statistical properties of trails formed by a random process incorporating aggregation, fragmentation, and diffusion. In this stochastic process, which takes place in one spatial dimension, two neighboring trails may combine to form a larger one, and also one trail may split into two. In addition, trails move diffusively. The model is defined by two parameters which quantify the fragmentation rate and the fragment size. In the long-time limit, the system reaches a steady state, and our focus is the limiting distribution of trail weights. We find that the density of trail weight has power-law tail P(w)~w –γ formore » small weight w. We obtain the exponent γ analytically and find that it varies continuously with the two model parameters. In conclusion, the exponent γ can be positive or negative, so that in one range of parameters small-weight trails are abundant and in the complementary range they are rare.« less

Comprehensive and accurate tracking of carbon origin of LC-tandem mass spectrometry collisional fragments for 13C-MFA.

PubMed

Kappelmann, Jannick; Klein, Bianca; Geilenkirchen, Petra; Noack, Stephan

2017-03-01

In recent years the benefit of measuring positionally resolved 13 C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of 13 C-Metabolic Flux Analysis ( 13 C-MFA) has become evident. However, the usage of positional labeling information for 13 C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known. The present contribution addresses the latter challenge by deducing the maximal positional labeling information contained in LC-ESI-MS/MS spectra of product anions of central metabolism as well as product cations of amino acids. For this purpose, we draw on accurate mass spectrometry, selectively labeled standards, and published fragmentation pathways to structurally annotate all dominant mass peaks of a large collection of metabolites, some of which with a complete fragmentation pathway. Compiling all available information, we arrive at the most detailed map of carbon atom fate of LC-ESI-MS/MS collisional fragments yet, comprising 170 intense and structurally annotated product ions with unique carbon origin from 76 precursor ions of 72 metabolites. Our 13 C-data proof that heuristic fragmentation rules often fail to yield correct fragment structures and we expose common pitfalls in the structural annotation of product ions. We show that the positionally resolved 13 C-label information contained in the product ions that we structurally annotated allows to infer the entire isotopomer distribution of several central metabolism intermediates, which is experimentally demonstrated for malate using quadrupole-time-of-flight MS technology. Finally, the inclusion of the label information from a subset of these fragments improves flux precision in a Corynebacterium glutamicum model of the central carbon metabolism.

Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes

PubMed Central

Marion, Scott R.; Lombana, Alfonso V.; Orth, Robert J.

2016-01-01

Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4–400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities. PMID:27244652

Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes.

PubMed

Lefcheck, Jonathan S; Marion, Scott R; Lombana, Alfonso V; Orth, Robert J

2016-01-01

Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities.

Isotopic Effects in Nuclear Fragmentation and GCR Transport Problems

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.

2002-01-01

Improving the accuracy of the galactic cosmic ray (GCR) environment and transport models is an important goal in preparing for studies of the projected risks and the efficiency of potential mitigations methods for space exploration. In this paper we consider the effects of the isotopic composition of the primary cosmic rays and the isotopic dependence of nuclear fragmentation cross sections on GCR transport models. Measurements are used to describe the isotopic composition of the GCR including their modulation throughout the solar cycle. The quantum multiple-scattering approach to nuclear fragmentation (QMSFRG) is used as the data base generator in order to accurately describe the odd-even effect in fragment production. Using the Badhwar and O'Neill GCR model, the QMSFRG model and the HZETRN transport code, the effects of the isotopic dependence of the primary GCR composition and on fragment production for transport problems is described for a complete GCR isotopic-grid. The principle finding of this study is that large errors ( 100%) will occur in the mass-flux spectra when comparing the complete isotopic-grid (141 ions) to a reduced isotopic-grid (59 ions), however less significant errors 30%) occur in the elemental-flux spectra. Because the full isotopic-grid is readily handled on small computer work-stations, it is recommended that they be used for future GCR studies.

UV photodissociation of proline-containing peptide ions: insights from molecular dynamics.

PubMed

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

NASA Astrophysics Data System (ADS)

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S2 and S3, lie close to 213 nm. Non-adiabatic MD simulation starting from S2 and S3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

Fragmentation characteristics of hydroxycinnamic acids in ESI-MSn by density functional theory.

PubMed

Yin, Zhi-Hui; Sun, Chang-Hai; Fang, Hong-Zhuang

2017-07-01

This work aims to analyze the electrospray ionization multistage mass spectrometry (ESI-MS n ) fragmentation characteristics of hydroxycinnamic acids (HCAs) in negative ion mode. The geometric parameters, energies, natural bond orbitals and frontier orbitals of fragments were calculated by density functional theory (DFT) to investigate mass spectral fragmentation mechanisms. The results showed that proton transfer always occurred during fragmentation of HCAs; their quasi-molecular ions ([M - H] - ) existed in more than one form and were mainly with the lowest energy. The fragmentation characteristics included the followings: (1) according to the different substitution position of phenolic hydroxyl group, the ring contraction reaction by CO elimination from benzene was in an increasingly difficult order: m-phenolic hydroxyl > p-phenolic hydroxyl > o-phenolic hydroxyl; and (2) ortho effect always occurred in o-dihydroxycinnamic acids (o-diHCAs), i.e. one phenolic hydroxyl group offered H + , which combined with the other one to lose H 2 O. In addition, there was a nucleophilic reaction during ring contraction in diHCAs that oxygen atom attacked the carbon atom binding with the other phenolic hydroxyl to lose CO 2 . The fragmentation characteristics and mechanism of HCAs could be used for analysis and identification of such compounds quickly and effectively, and as reference for structural analogues by ESI-MS. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Molecular resolution and fragmentation of fulvic acid by electrospray ionization/multistage tandem mass spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Gates, Paul M.; Furlong, E.T.; Ferrer, I.

2001-01-01

Molecular weight distributions of fulvic acid from the Suwannee River, Georgia, were investigated by electrospray ionization/quadrupole mass spectrometry (ESI/QMS), and fragmentation pathways of specific fulvic acid masses were investigated by electrospray ionization/ion trap multistage tandem mass spectrometry (ESI/MST/MS). ESI/QMS studies of the free acid form of low molecular weight poly(carboxylic acid) standards in 75% methanol/25% water mobile phase found that negative ion detection gave the optimum generation of parent ions that can be used for molecular weight determinations. However, experiments with poly(acrylic acid) mixtures and specific high molecular weight standards found multiply charged negative ions that gave a low bias to molecular mass distributions. The number of negative charges on a molecule is dependent on the distance between charges. ESI/MST/MS of model compounds found characteristic water loss from alcohol dehydration and anhydride formation, as well as CO2 loss from decarboxylation, and CO loss from ester structures. Application of these fragmentation pathways to specific masses of fulvic acid isolated and fragmented by ESI/MST/MS is indicative of specific structures that can serve as a basis for future structural confirmation after these hypothesized structures are synthesized.

HZEFRG1 - SEMIEMPIRICAL NUCLEAR FRAGMENTATION MODEL

NASA Technical Reports Server (NTRS)

Townsend, L. W.

1994-01-01

The high charge and energy (HZE), Semiempirical Nuclear Fragmentation Model, HZEFRG1, was developed to provide a computationally efficient, user-friendly, physics-based program package for generating nuclear fragmentation databases. These databases can then be used in radiation transport applications such as space radiation shielding and dosimetry, cancer therapy with laboratory heavy ion beams, and simulation studies of detector design in nuclear physics experiments. The program provides individual element and isotope production cross sections for the breakup of high energy heavy ions by the combined nuclear and Coulomb fields of the interacting nuclei. The nuclear breakup contributions are estimated using an energy-dependent abrasion-ablation model of heavy ion fragmentation. The abrasion step involves removal of nucleons by direct knockout in the overlap region of the colliding nuclei. The abrasions are treated on a geometric basis and uniform spherical nuclear density distributions are assumed. Actual experimental nuclear radii obtained from tabulations of electron scattering data are incorporated. Nuclear transparency effects are included by using an energy-dependent, impact-parameter-dependent average transmission factor for the projectile and target nuclei, which accounts for the finite mean free path of nucleons in nuclear matter. The ablation step, as implemented by Bowman, Swiatecki, and Tsang (LBL report no. LBL-2908, July 1973), was treated as a single-nucleon emission for every 10 MeV of excitation energy. Fragmentation contributions from electromagnetic dissociation (EMD) processes, arising from the interacting Coulomb fields, are estimated by using the Weiszacker-Williams theory, extended to include electric dipole and electric quadrupole contributions to one-nucleon removal cross sections. HZEFRG1 consists of a main program, seven function subprograms, and thirteen subroutines. Each is fully commented and begins with a brief description of its

How Hot are Your Ions in TWAVE Ion Mobility Spectrometry?

PubMed Central

Merenbloom, Samuel I.; Flick, Tawnya G.; Williams, Evan R.

2012-01-01

Effective temperatures of ions during traveling wave ion mobility spectrometry (TWIMS) analysis were measured using singly protonated leucine enkephalin dimer as a chemical thermometer by monitoring dissociation of the dimer into monomer, as well as the subsequent dissociation of monomer into a-, b-, and y-ions, as a function of instrumental parameters. At fixed helium cell and TWIMS cell gas flow rates, the extent of dissociation does not vary significantly with either the wave velocity or wave height, except at low (<500 m/s) wave velocities that are not commonly used. Increasing the flow rate of nitrogen gas into the TWIMS cell and decreasing the flow rate of helium gas into the helium cell resulted in greater dissociation. However, the mobility distributions of the fragment ions formed by dissociation of the dimer upon injection into the TWIMS cell are nearly indistinguishable from those of fragment ions formed in the collision cell prior to TWIMS analysis for all TWIMS experiments. These results indicate that heating and dissociation occur when ions are injected into the TWIMS cell, and that the effective temperature subsequently decreases to a point at which no further dissociation is observed during the TWIMS analysis. An upper limit to the effective ion temperature of 449 K during TWIMS analysis is obtained at a helium flow rate of 180 mL/min, TWIMS flow rate of 80 mL/min and traveling wave height of 40 V, which is well below previously reported values. Effects of ion heating in TWIMS on gas-phase protein conformation are presented. PMID:22203576

Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

PubMed

Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

2013-09-24

Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale. Copyright © 2013 Elsevier B.V. All rights reserved.

Dependence on radiation quality of DNA fragmentation spectra

NASA Astrophysics Data System (ADS)

Campa, Alessandro; Ottolenghi, Andrea; Alloni, Daniele; Ballarini, Francesca; Belli, Mauro; Esposito, Giuseppe; Facoetti, Angelica; Friedland, Werner; Liotta, Marco; Paretzke, Herwig

Energy deposition by radiation initially gives rise to cellular critical lesions such as DNA doublestrand breaks (DSB), that later lead to the formation of relevant biological endpoints. Studies on fragment size distributions induced by radiations of various qualities can be of great help in linking the characteristics of radiation to cellular endpoints, providing information for understanding the main mechanisms of cell damage. Here we are concerned with the damage induced by heavy charged particles; this issue is very important in the field of radioprotection of astronauts participating in long term space missions, besides being relevant also in other fields, like hadrontherapy. Galactic Cosmic Rays contain a large component of high-LET particles (HZE), e.g. helium and carbon ions, as well as highcharge particles such as iron ions. These particles are characterized by complex track structures with energy depositions not only along the path of the primary particle, but also at relatively large distance form the path, due to the presence of high energy secondary electrons. In this work we have simulated the irradiation of human fibroblasts with γ-rays, protons, helium, carbon and iron ions at a fixed dose with the biophysical Monte Carlo code PARTRAC,and calculated the induction of DSB. The PARTRAC code includes accurate representation of the chromatin geometry and of the physical and physico-chemical processes associated with the energy deposition by radiation. The results of a first validation of the code have been reported in A. Campa et al. (2005) and D. Alloni et al. (2007a, 2007b). DNA fragment spectra were calculated based on the DSB induction patterns and compared in particular for particles of the same specific energy and for particles of the same LET. Special emphasis has been directed to the calculation of very small fragments (< 1 kbp) that are not detectable by the most common experimental techniques and that can significantly influence the RBE

Importance of riparian remnants for frog species diversity in a highly fragmented rainforest.

PubMed

Rodríguez-Mendoza, Clara; Pineda, Eduardo

2010-12-23

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.

Distinctive and Complementary MS2 Fragmentation Characteristics for Identification of Sulfated Sialylated N-Glycopeptides by nanoLC-MS/MS Workflow

NASA Astrophysics Data System (ADS)

Kuo, Chu-Wei; Guu, Shih-Yun; Khoo, Kay-Hooi

2018-04-01

High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS2 fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS2 fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS2 analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics. [Figure not available: see fulltext.

The impact of edge effect on termite community (Blattodea: Isoptera) in fragments of Brazilian Atlantic Rainforest.

PubMed

Almeida, C S; Cristaldo, P F; Florencio, D F; Ribeiro, E J M; Cruz, N G; Silva, E A; Costa, D A; Araújo, A P A

2017-01-01

Habitat fragmentation is considered to be one of the biggest threats to tropical ecosystem functioning. In this region, termites perform an important ecological role as decomposers and ecosystem engineers. In the present study, we tested whether termite community is negatively affected by edge effects on three fragments of Brazilian Atlantic Rainforest. Termite abundance and vegetation structure were sampled in 10 transects (15 × 2 m), while termite richness, activity, and soil litter biomass were measured in 16 quadrants (5 × 2 m) at forest edge and interior of each fragment. Habitat structure (i.e. number of tree, diameter at breast height and soil litter biomass) did not differ between forest edge and interior of fragments. Termite richness, abundance and activity were not affected by edge effect. However, differences were observed in the β diversity between forest edge and interior as well as in the fragments sampled. The β diversity partitioning indicates that species turnover is the determinant process of termite community composition under edge effect. Our results suggest that conservation strategies should be based on the selection of several distinct sites instead of few rich sites (e.g. nesting).

Bat-Fruit Interactions Are More Specialized in Shaded-Coffee Plantations than in Tropical Mountain Cloud Forest Fragments

PubMed Central

Hernández-Montero, Jesús R.; Saldaña-Vázquez, Romeo A.; Galindo-González, Jorge; Sosa, Vinicio J.

2015-01-01

Forest disturbance causes specialization of plant-frugivore networks and jeopardizes mutualistic interactions through reduction of ecological redundancy. To evaluate how simplification of a forest into an agroecosystem affects plant-disperser mutualistic interactions, we compared bat-fruit interaction indexes of specialization in tropical montane cloud forest fragments (TMCF) and shaded-coffee plantations (SCP). Bat-fruit interactions were surveyed by collection of bat fecal samples. Bat-fruit interactions were more specialized in SCP (mean H2 ' = 0.55) compared to TMCF fragments (mean H2 ' = 0.27), and were negatively correlated to bat abundance in SCP (R = -0.35). The number of shared plant species was higher in the TMCF fragments (mean = 1) compared to the SCP (mean = 0.51) and this was positively correlated to the abundance of frugivorous bats (R= 0.79). The higher specialization in SCP could be explained by lower bat abundance and lower diet overlap among bats. Coffee farmers and conservation policy makers must increase the proportion of land assigned to TMCF within agroecosystem landscapes in order to conserve frugivorous bats and their invaluable seed dispersal service. PMID:25992550

Bat-fruit interactions are more specialized in shaded-coffee plantations than in tropical mountain cloud forest fragments.

PubMed

Hernández-Montero, Jesús R; Saldaña-Vázquez, Romeo A; Galindo-González, Jorge; Sosa, Vinicio J

2015-01-01

Forest disturbance causes specialization of plant-frugivore networks and jeopardizes mutualistic interactions through reduction of ecological redundancy. To evaluate how simplification of a forest into an agroecosystem affects plant-disperser mutualistic interactions, we compared bat-fruit interaction indexes of specialization in tropical montane cloud forest fragments (TMCF) and shaded-coffee plantations (SCP). Bat-fruit interactions were surveyed by collection of bat fecal samples. Bat-fruit interactions were more specialized in SCP (mean H2 ' = 0.55) compared to TMCF fragments (mean H2 ' = 0.27), and were negatively correlated to bat abundance in SCP (R = -0.35). The number of shared plant species was higher in the TMCF fragments (mean = 1) compared to the SCP (mean = 0.51) and this was positively correlated to the abundance of frugivorous bats (R= 0.79). The higher specialization in SCP could be explained by lower bat abundance and lower diet overlap among bats. Coffee farmers and conservation policy makers must increase the proportion of land assigned to TMCF within agroecosystem landscapes in order to conserve frugivorous bats and their invaluable seed dispersal service.

Astrochemistry in TSR and CSR Ion Storage Rings

NASA Astrophysics Data System (ADS)

Novotny, Oldrich

2017-04-01

Dissociative recombination (DR) of molecular ions plays a key role in controlling the charge density and composition of the cold interstellar medium (ISM). Experimental data on DR are required in order to understand the chemical network in the ISM and related processes such as star formation from molecular clouds. Needed data include not only total reaction cross sections, but also the chemical composition and excitation states of the neutral products. Utilizing the TSR storage ring in Heidelberg, Germany, we have carried out DR measurements for astrophysically important molecular ions. We use a merged electron-ion beams technique combined with event-by-event fragment counting and fragment imaging. The count rate of detected neutral DR products yields the absolute DR rate coefficient. Imaging the distribution of fragment distances provides information on the kinetic energy released including the states of both the initial molecule and the final products. Additional kinetic energy sensitivity of the employed detector allows for identification of fragmentation channels by fragment-mass combination within each dissociation event. Such combined information is essential for studies on DR of polyatomic ions with multi-channel breakup. The recently commissioned Cryogenic Storage Ring (CSR) in Heidelberg, Germany, extends the experimental capabilities of TSR by operation at cryogenic temperatures down to 6 K. At these conditions residual gas densities down to 100 cm-3 can be reached resulting in beam storage times of several hours. Long storage in the cold environment allows the ions to relax down to their rotational ground state, thus mimicking well the conditions in the cold ISM. A variety of astrophysically relevant reactions will be investigated at these conditions, such as DR, electron impact excitation, ion-neutral collisions, etc. We report our TSR results on DR of HCl+ and D2Cl+. We also present first results from the CSR commissioning experiments.

Explosive volcanism may not be an inevitable consequence of magma fragmentation.

PubMed

Gonnermann, Helge M; Manga, Michael

2003-11-27

The fragmentation of magma, containing abundant gas bubbles, is thought to be the defining characteristic of explosive eruptions. When viscous stresses associated with the growth of bubbles and the flow of the ascending magma exceed the strength of the melt, the magma breaks into disconnected fragments suspended within an expanding gas phase. Although repeated effusive and explosive eruptions for individual volcanoes are common, the dynamics governing the transition between explosive and effusive eruptions remain unclear. Magmas for both types of eruptions originate from sources with similar volatile content, yet effusive lavas erupt considerably more degassed than their explosive counterparts. One mechanism for degassing during magma ascent, consistent with observations, is the generation of intermittent permeable fracture networks generated by non-explosive fragmentation near the conduit walls. Here we show that such fragmentation can occur by viscous shear in both effusive and explosive eruptions. Moreover, we suggest that such fragmentation may be important for magma degassing and the inhibition of explosive behaviour. This implies that, contrary to conventional views, explosive volcanism is not an inevitable consequence of magma fragmentation.

The Complex Stratigraphy of the Highland Crust in the Serenitatis Region of the Moon Inferred from Mineral Fragment Chemistry

NASA Technical Reports Server (NTRS)

Ryder, Graham; Norman, Marc D.; Taylor, G. Jeffrey

1997-01-01

Large impact basins are natural drill holes into the Moon, and their ejecta carries unique information about the rock types and stratigraphy of the lunar crust. We have conducted an electron microprobe study of mineral fragments in the poikilitic melt breccias collected from the Taurus Mountains at the Apollo 17 landing site. These breccias are virtually unanimously agreed to be impact melt produced in the Serenitatis impact event. They contain lithic fragments and much more abundant mineral fragments of crustal origin. We have made precise microprobe analyses of minor element abundances in fragments of olivine, pyroxene, and plagioclase to provide new information on the possible source rocks and the crustal stratigraphy in the Serenitatis region. These data were also intended to elucidate the nature of the cryptic geochemical component in breccias such as these with low-K Fra Mauro basalt compositions. We chose the finest-grained (i.e., most rapidly quenched) breccias for study, to avoid reacted and partly assimilated fragments as much as possible. Most of the mineral fragments appear to have been derived from rocks that would fall into the pristine igneous Mg-suite as represented by lithic fragments in the Apollo collection, or reasonable extensions of it. Gabbroic rocks were more abundant in the target stratigraphy than is apparent from the Apollo sample collection. Some pyroxene and plagiociase, but probably not much olivine, could be derived from feldspathic granulites, which are metamorphosed polymict breccias. Some mineral fragments are from previously unknown rocks. These include highly magnesian olivines (up to Fo(sub 94)), possibly volcanic in origin, that exacerbate the difficulty in explaining highly magnesian rocks in the lunar crust. It appears that some part of the lunar interior has an mg*(= 100 x Mg/(Mg/Fe) atomic) greater than the conventional bulk Moon value of 80-84. Other volcanic rocks, including mare basalts, and rapidly- cooled impact melt

Scalable Synthesis of Defect Abundant Si Nanorods for High-Performance Li-Ion Battery Anodes.

PubMed

Wang, Jing; Meng, Xiangcai; Fan, Xiulin; Zhang, Wenbo; Zhang, Hongyong; Wang, Chunsheng

2015-06-23

Microsized nanostructured silicon-carbon composite is a promising anode material for high energy Li-ion batteries. However, large-scale synthesis of high-performance nano-Si materials at a low cost still remains a significant challenge. We report a scalable low cost method to synthesize Al/Na-doped and defect-abundant Si nanorods that have excellent electrochemical performance with high first-cycle Coulombic efficiency (90%). The unique Si nanorods are synthesized by acid etching the refined and rapidly solidified eutectic Al-Si ingot. To maintain the high electronic conductivity, a thin layer of carbon is then coated on the Si nanorods by carbonization of self-polymerized polydopamine (PDA) at 800 °C. The carbon coated Si nanorods (Si@C) electrode at 0.9 mg cm(-2) loading (corresponding to area-specific-capacity of ∼2.0 mAh cm(-2)) exhibits a reversible capacity of ∼2200 mAh g(-1) at 100 mA g(-1) current, and maintains ∼700 mAh g(-1) over 1000 cycles at 1000 mA g(-1) with a capacity decay rate of 0.02% per cycle. High Coulombic efficiencies of 87% in the first cycle and ∼99.7% after 5 cycles are achieved due to the formation of an artificial Al2O3 solid electrolyte interphase (SEI) on the Si surface, and the low surface area (31 m(2) g(-1)), which has never been reported before for nano-Si anodes. The excellent electrochemical performance results from the massive defects (twins, stacking faults, dislocations) and Al/Na doping in Si nanorods induced by rapid solidification and Na salt modifications; this greatly enhances the robustness of Si from the volume changes and alleviates the mechanical stress/strain of the Si nanorods during the lithium insertion/extraction process. Introducing massive defects and Al/Na doping in eutectic Si nanorods for Li-ion battery anodes is unexplored territory. We venture this uncharted territory to commercialize this nanostructured Si anode for the next generation of Li-ion batteries.

Time-resolved ion imaging at free-electron lasers using TimepixCam

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

Fisher-Levine, Merlin; Boll, Rebecca; Ziaee, Farzaneh

In this paper, the application of a novel fast optical-imaging camera, TimepixCam, to molecular photoionization experiments using the velocity-map imaging technique at a free-electron laser is described. TimepixCam is a 256 × 256 pixel CMOS camera that is able to detect and time-stamp ion hits with 20 ns timing resolution, thus making it possible to record ion momentum images for all fragment ions simultaneously and avoiding the need to gate the detector on a single fragment. This allows the recording of significantly more data within a given amount of beam time and is particularly useful for pump–probe experiments, where drifts,more » for example, in the timing and pulse energy of the free-electron laser, severely limit the comparability of pump–probe scans for different fragments taken consecutively. Finally, in principle, this also allows ion–ion covariance or coincidence techniques to be applied to determine angular correlations between fragments.« less

Time-resolved ion imaging at free-electron lasers using TimepixCam

DOE PAGES

Fisher-Levine, Merlin; Boll, Rebecca; Ziaee, Farzaneh; ...

2018-02-20

In this paper, the application of a novel fast optical-imaging camera, TimepixCam, to molecular photoionization experiments using the velocity-map imaging technique at a free-electron laser is described. TimepixCam is a 256 × 256 pixel CMOS camera that is able to detect and time-stamp ion hits with 20 ns timing resolution, thus making it possible to record ion momentum images for all fragment ions simultaneously and avoiding the need to gate the detector on a single fragment. This allows the recording of significantly more data within a given amount of beam time and is particularly useful for pump–probe experiments, where drifts,more » for example, in the timing and pulse energy of the free-electron laser, severely limit the comparability of pump–probe scans for different fragments taken consecutively. Finally, in principle, this also allows ion–ion covariance or coincidence techniques to be applied to determine angular correlations between fragments.« less

Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

PubMed Central

Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

2009-01-01

A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

Human impacts affect tree community features of 20 forest fragments of a vanishing neotropical hotspot.

PubMed

Pereira, José Aldo Alves; de Oliveira-Filho, Ary Teixeira; Eisenlohr, Pedro V; Miranda, Pedro L S; de Lemos Filho, José Pires

2015-02-01

The loss in forest area due to human occupancy is not the only threat to the remaining biodiversity: forest fragments are susceptible to additional human impact. Our aim was to investigate the effect of human impact on tree community features (species composition and abundance, and structural descriptors) and check if there was a decrease in the number of slender trees, an increase in the amount of large trees, and also a reduction in the number of tree species that occur in 20 fragments of Atlantic montane semideciduous forest in southeastern Brazil. We produced digital maps of each forest fragment using Landsat 7 satellite images and processed the maps to obtain morphometric variables. We used investigative questionnaires and field observations to survey the history of human impact. We then converted the information into scores given to the extent, severity, and duration of each impact, including proportional border area, fire, trails, coppicing, logging, and cattle, and converted these scores into categorical levels. We used linear models to assess the effect of impacts on tree species abundance distribution and stand structural descriptors. Part of the variation in floristic patterns was significantly correlated to the impacts of fire, logging, and proportional border area. Structural descriptors were influenced by cattle and outer roads. Our results provided, for the first time, strong evidence that tree species occurrence and abundance, and forest structure of Atlantic seasonal forest fragments respond differently to various modes of disturbance by humans.

Diversity and abundance of nitrate assimilation genes in the northern South china sea.

PubMed

Cai, Haiyuan; Jiao, Nianzhi

2008-11-01

Marine heterotrophic microorganisms that assimilate nitrate play an important role in nitrogen and carbon cycling in the water column. The nasA gene, encoding the nitrate assimilation enzyme, was selected as a functional marker to examine the nitrate assimilation community in the South China Sea (SCS). PCR amplification, restriction fragment length polymorphism (RFLP) screening, and phylogenetic analysis of nasA gene sequences were performed to characterize in situ nitrate assimilatory bacteria. Furthermore, the effects of nutrients and other environmental factors on the genetic heterogeneity of nasA fragments from the SCS were evaluated at the surface in three stations, and at two other depths in one of these stations. The diversity indices and rarefaction curves indicated that the nasA gene was more diverse in offshore waters than in the Pearl River estuary. The phylotype rank abundance curve showed an abundant and unique RFLP pattern in all five libraries, indicating that a high diversity but low abundance of nasA existed in the study areas. Phylogenetic analysis of environmental nasA gene sequences further revealed that the nasA gene fragments came from several common aquatic microbial groups, including the Proteobacteria, Cytophaga-Flavobacteria (CF), and Cyanobacteria. In addition to the direct PCR/sequence analysis of environmental samples, we also cultured a number of nitrate assimilatory bacteria isolated from the field. Comparison of nasA genes from these isolates and from the field samples indicated the existence of horizontal nasA gene transfer. Application of real-time quantitative PCR to these nasA genes revealed a great variation in their abundance at different investigation sites and water depths.

Reproduction of Amorpha canescens (Fabaceae) and diversity of its bee community in a fragmented landscape.

PubMed

Slagle, Malinda W; Hendrix, Stephen D

2009-10-01

Loss of insect pollinators due to habitat fragmentation often results in negative effects on plant reproduction, but few studies have simultaneously examined variation in the bee community, site characteristics and plant community characteristics to evaluate their relative effects on plant reproduction in a fragmented habitat. We examined the reproduction of a common tallgrass prairie forb, Amorpha canescens (Fabaceae), in large (>40 ha) and small (<2 ha) prairie remnants in Iowa and Minnesota in relation to the diversity and abundance of its bee visitors, plant population size, and species density of the forb flowering community. We found significant positive effects of the diversity of bees visiting A. canescens on percent fruit set at a site in both years of the study and in 2002 an additional significant positive effect of plant species density. Abundance of bees visiting A. canescens had a significant positive effect on percent fruit set in 2002, but was only marginally significant in 2003. In 2003 but not 2002, the plant species density at the sites had a significant negative effect on the diversity and abundance of bees visiting A. canescens, indicating community-level characteristics can influence the bee community visiting any one species. Site size, a common predictor of plant reproduction in fragmented habitats did not contribute to any models of fruit set and was only marginally related to bee diversity one year. Andrena quintilis, one of the three oligolectic bee species associated with A. canescens, was abundant at all sites, suggesting it has not been significantly affected by fragmentation. Our results show that the diversity of bees visiting A. canescens is important for maintaining fruit set and that bee visitation is still sufficient for at least some fruit set in all populations, suggesting these small remnants act as floral resource oases for bees in landscapes often dominated by agriculture.

Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

PubMed Central

Lloyd, John R.; Hess, Sonja

2010-01-01

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

Extracellular matrix fragmentation in young, healthy cartilaginous tissues.

PubMed

Craddock, R J; Hodson, N W; Ozols, M; Shearer, T; Hoyland, J A; Sherratt, M J

2018-02-09

Although the composition and structure of cartilaginous tissues is complex, collagen II fibrils and aggrecan are the most abundant assemblies in both articular cartilage (AC) and the nucleus pulposus (NP) of the intervertebral disc (IVD). Whilst structural heterogeneity of intact aggrecan ( containing three globular domains) is well characterised, the extent of aggrecan fragmentation in healthy tissues is poorly defined. Using young, yet skeletally mature (18-30 months), bovine AC and NP tissues, it was shown that, whilst the ultrastructure of intact aggrecan was tissue-dependent, most molecules (AC: 95 %; NP: 99.5 %) were fragmented (lacking one or more globular domains). Fragments were significantly smaller and more structurally heterogeneous in the NP compared with the AC (molecular area; AC: 8543 nm2; NP: 4625 nm2; p < 0.0001). In contrast, fibrillar collagen appeared structurally intact and tissue-invariant. Molecular fragmentation is considered indicative of a pathology; however, these young, skeletally mature tissues were histologically and mechanically (reduced modulus: AC: ≈ 500 kPa; NP: ≈ 80 kPa) comparable to healthy tissues and devoid of notable gelatinase activity (compared with rat dermis). As aggrecan fragmentation was prevalent in neonatal bovine AC (99.5 % fragmented, molecular area: 5137 nm2) as compared with mature AC (95.0 % fragmented, molecular area: 8667 nm2), it was hypothesised that targeted proteolysis might be an adaptive process that modified aggrecan packing (as simulated computationally) and, hence, tissue charge density, mechanical properties and porosity. These observations provided a baseline against which pathological and/or age-related fragmentation of aggrecan could be assessed and suggested that new strategies might be required to engineer constructs that mimic the mechanical properties of native cartilaginous tissues.

Feedback between intracellular flow, signaling and active stresses in Physarum plasmodial fragments

NASA Astrophysics Data System (ADS)

Zhang, Shun; Guy, Robert; Del Alamo, Juan Carlos

2016-11-01

Physarum polycephalum is a multinucleated slime mold whose endoplasm flows periodically driven by the contraction of its ectoplasm, a dense shell of F-actin cross-linked by myosin molecular motors and attached to the cell membrane. Ectoplasm contractions are regulated by calcium ions whose propagation is in turn governed by the flow. We study experimentally how this feedback leads to auto-oscillation by simultaneously measuring endoplasmic flow speed and rheological properties, the traction stresses between the ectoplasm and its substratum and the distribution of endoplasmic free calcium ions. We find that physarum fragments smaller than 100 microns remain round and stay in place. However, larger fragments break symmetry leading to sustained forward locomotion, in process that is reminiscent of an interfacial instability that seems to settle around two different limit cycles (traveling waves and standing waves). By using different adhesive coatings in the substratum we investigate the role of substratum friction in the emergence of coherent endoplasmic flow patterns and overall physarum fragment locomotion.

Fragment quality and matrix affect epiphytic performance in a Mediterranean forest landscape.

PubMed

Belinchón, Rocío; Martínez, Isabel; Otálora, Mónica A G; Aragón, Gregorio; Dimas, Jesús; Escudero, Adrián

2009-11-01

Destruction and fragmentation of habitats represent one of the most important threats for biodiversity. Here, we examined the effects of fragmentation in Mediterranean forests on the epiphytic lichen Lobaria pulmonaria (Lobariaceae). We tested the hypothesis that not only the level of fragmentation affects L. pulmonaria populations, but also the quality of the habitat and the nature of the surrounding matrix affect them. The presence and abundance of the lichen was recorded on 2039 trees in a total of 31 stands. We recorded habitat quality and landscape variables at three hierarchical levels: tree, plot, and patch. We found that L. pulmonaria tends to occur in trees with larger diameters in two types of surveyed forests. In Quercus pyrenaica patches, the mean diameter of colonized trees was smaller, suggesting the importance of bark roughness. Factors affecting the presence and cover of the lichen in each type of forest were different. There was a strong positive influence of distance from a river in beech forests, whereas proximity to forest edge positively affected in oak forests. The influence of the surrounding matrix was also an important factor explaining the epiphytic lichen abundance.

Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations.

PubMed

Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Żmudzińska, Wioletta; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

2016-09-01

Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process. Copyright © 2016 Elsevier B.V. All rights reserved.

Technical Report: Algorithm and Implementation for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

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

McLoughlin, Kevin

2016-01-11

This report describes the design and implementation of an algorithm for estimating relative microbial abundances, together with confidence limits, using data from metagenomic DNA sequencing. For the background behind this project and a detailed discussion of our modeling approach for metagenomic data, we refer the reader to our earlier technical report, dated March 4, 2014. Briefly, we described a fully Bayesian generative model for paired-end sequence read data, incorporating the effects of the relative abundances, the distribution of sequence fragment lengths, fragment position bias, sequencing errors and variations between the sampled genomes and the nearest reference genomes. A distinctive featuremore » of our modeling approach is the use of a Chinese restaurant process (CRP) to describe the selection of genomes to be sampled, and thus the relative abundances. The CRP component is desirable for fitting abundances to reads that may map ambiguously to multiple targets, because it naturally leads to sparse solutions that select the best representative from each set of nearly equivalent genomes.« less

Fragmentation dynamics of meso-tetraphenyl iron (III) porphyrin chloride dication under energy control

NASA Astrophysics Data System (ADS)

Li, B.; Allouche, A. R.; Bernard, J.; Brédy, R.; Qian, D. B.; Ma, X.; Martin, S.; Chen, L.

2017-03-01

Meso-tetraphenyl iron (III) porphyrin chloride dications (FeTPPCl2+)* were prepared in collisions with F+ and H+ at 3 keV. The dominant fragmentation channels were observed to involve the loss of the Cl atom and the successive loss of neutral phenyl groups for both collisional systems. The mass spectra in correlation with the deposited excitation energy distributions of the parent ions for the main fragmentation channels were measured by using the collision induced dissociation under energy control method. The global excitation energy distribution was found to be shifted to lower energies in collisions with H+ compared to collisions with F+ showing a noteworthy change of the excitation energy window using different projectile ions. Partial excitation energy distributions of the parent ions FeTPPCl2+ were obtained for each fragmentation group. In a theoretical work, we have calculated the dissociation energies for the loss of one and two phenyl groups, including phenyl and (phenyl ± H). The energy barrier for the hydrogen atom transfer during the loss of (phenyl-H) has been also calculated. The measured energy difference for the successive loss of two phenyl groups was compared with the theoretical values.

Neutrons produced by known energies of ions abundant in space

NASA Technical Reports Server (NTRS)

Wadman, W. W., III

1972-01-01

Particle accelerator radiation measurements are applied to the problem of calculating biological dose from radiation produced in the walls of a spacecraft by various ions in space. Neutrons, one of the products of the interactions of energetic ions with matter, are usually quite penetrating and have large values of Q.F. or R.B.E. Ions of helium, boron, carbon, nitrogen, and oxygen were accelerated and directed onto target materials of copper or tantalum. The secondary neutron production was determined. Studies were made of the angular distribution and an inferred neutron spectrum was calculated from activities of threshold reaction detectors.

Rapid profiling of polymeric phenolic acids in Salvia miltiorrhiza by hybrid data-dependent/targeted multistage mass spectrometry acquisition based on expected compounds prediction and fragment ion searching.

PubMed

Shen, Yao; Feng, Zijin; Yang, Min; Zhou, Zhe; Han, Sumei; Hou, Jinjun; Li, Zhenwei; Wu, Wanying; Guo, De-An

2018-04-01

Phenolic acids are the major water-soluble components in Salvia miltiorrhiza (>5%). According to previous studies, many of them contribute to the cardiovascular effects and antioxidant effects of S. miltiorrhiza. Polymeric phenolic acids can be considered as the tanshinol derived metabolites, e.g., dimmers, trimers, and tetramers. A strategy combined with tanshinol-based expected compounds prediction, total ion chromatogram filtering, fragment ion searching, and parent list-based multistage mass spectrometry acquisition by linear trap quadropole-orbitrap Velos mass spectrometry was proposed to rapid profile polymeric phenolic acids in S. miltiorrhiza. More than 480 potential polymeric phenolic acids could be screened out by this strategy. Based on the fragment information obtained by parent list-activated data dependent multistage mass spectrometry acquisition, 190 polymeric phenolic acids were characterized by comparing their mass information with literature data, and 18 of them were firstly detected from S. miltiorrhiza. Seven potential compounds were tentatively characterized as new polymeric phenolic acids from S. miltiorrhiza. This strategy facilitates identification of polymeric phenolic acids in complex matrix with both selectivity and sensitivity, which could be expanded for rapid discovery and identification of compounds from complex matrix. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relative abundance of mesopredators and size of oak patches in the cross-timbers ecoregion

USGS Publications Warehouse

Disney, M.R.; Hellgren, E.C.; Davis, C.A.; Leslie, David M.; Engle, David M.

2008-01-01

Mesopredators (e.g., raccoon Procyon lotor, Virginia opossum Didelphis virginiana, striped skunk Mephitis mephitis) have received considerable attention because of links to population declines in birds via increased nest predation, especially in landscapes fragmented by anthropogenic forces. Relationships of abundance of mesopredators to size of habitat patches have received less attention than relationships to other metrics of fragmentation, particularly edge characteristics. We tested the hypothesis that relative abundance of mesopredators (e.g., raccoons and Virginia opossums) was related negatively to size of forest patch. We delineated 15 patches of oak (Quercus) forest ranging from 0.2 to 55.3 ha within a grassland-woodland mosaic in the cross-timbers ecoregion of Oklahoma. Scent stations and live traps within these patches were used to index relative abundance of mesopredators in summers 2003 and 2004. Both indices of relative abundance were related weakly and negatively to area of forest patch. However, rate of capture and visitation to scent station were not correlated consistently throughout the study. Our results suggested that the two methods to index abundance provided separate information on functional and numerical responses to size of patch. Our evidence that mesopredators within the cross timbers were more likely to be in smaller patches of oak forest may have implications to success of avian nesting in these patches.

Consequences of Landscape Fragmentation on Lyme Disease Risk: A Cellular Automata Approach

PubMed Central

Li, Sen; Hartemink, Nienke; Speybroeck, Niko; Vanwambeke, Sophie O.

2012-01-01

The abundance of infected Ixodid ticks is an important component of human risk of Lyme disease, and various empirical studies have shown that this is associated, at least in part, to landscape fragmentation. In this study, we aimed at exploring how varying woodland fragmentation patterns affect the risk of Lyme disease, through infected tick abundance. A cellular automata model was developed, incorporating a heterogeneous landscape with three interactive components: an age-structured tick population, a classical disease transmission function, and hosts. A set of simplifying assumptions were adopted with respect to the study objective and field data limitations. In the model, the landscape influences both tick survival and host movement. The validation of the model was performed with an empirical study. Scenarios of various landscape configurations (focusing on woodland fragmentation) were simulated and compared. Lyme disease risk indices (density and infection prevalence of nymphs) differed considerably between scenarios: (i) the risk could be higher in highly fragmented woodlands, which is supported by a number of recently published empirical studies, and (ii) grassland could reduce the risk in adjacent woodland, which suggests landscape fragmentation studies of zoonotic diseases should not focus on the patch-level woodland patterns only, but also on landscape-level adjacent land cover patterns. Further analysis of the simulation results indicated strong correlations between Lyme disease risk indices and the density, shape and aggregation level of woodland patches. These findings highlight the strong effect of the spatial patterns of local host population and movement on the spatial dynamics of Lyme disease risks, which can be shaped by woodland fragmentation. In conclusion, using a cellular automata approach is beneficial for modelling complex zoonotic transmission systems as it can be combined with either real world landscapes for exploring direct spatial

Optical model analyses of galactic cosmic ray fragmentation in hydrogen targets

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.

1993-01-01

Quantum-mechanical optical model methods for calculating cross sections for the fragmentation of galactic cosmic ray nuclei by hydrogen targets are presented. The fragmentation cross sections are calculated with an abrasion-ablation collision formalism. Elemental and isotopic cross sections are estimated and compared with measured values for neon, sulfur, and calcium ions at incident energies between 400A MeV and 910A MeV. Good agreement between theory and experiment is obtained.

Spatial fragment distribution from a therapeutic pencil-like carbon beam in water.

PubMed

Matsufuji, Naruhiro; Komori, Masataka; Sasaki, Hitomi; Akiu, Kengo; Ogawa, Masako; Fukumura, Akifumi; Urakabe, Eriko; Inaniwa, Taku; Nishio, Teiji; Kohno, Toshiyuki; Kanai, Tatsuaki

2005-07-21

The latest heavy ion therapy tends to require information about the spatial distribution of the quality of radiation in a patient's body in order to make the best use of any potential advantage of swift heavy ions for the therapeutic treatment of a tumour. The deflection of incident particles is described well by Molière's multiple-scattering theory of primary particles; however, the deflection of projectile fragments is not yet thoroughly understood. This paper reports on our investigation of the spatial distribution of fragments produced from a therapeutic carbon beam through nuclear reactions in thick water. A DeltaE-E counter telescope system, composed of a plastic scintillator, a gas-flow proportional counter and a BGO scintillator, was rotated around a water target in order to measure the spatial distribution of the radiation quality. The results revealed that the observed deflection of fragment particles exceeded the multiple scattering effect estimated by Molière's theory. However, the difference can be sufficiently accounted for by considering one term involved in the multiple-scattering formula; this term corresponds to a lateral 'kick' at the point of production of the fragment. This kick is successfully explained as a transfer of the intra-nucleus Fermi momentum of a projectile to the fragment; the extent of the kick obeys the expectation derived from the Goldhaber model.

Hypochlorite and superoxide radicals can act synergistically to induce fragmentation of hyaluronan and chondroitin sulphates

PubMed Central

2004-01-01

Activated phagocytes release the haem enzyme MPO (myeloperoxidase) and also generate superoxide radicals (O2•−), and hence H2O2, via an oxidative burst. Reaction of MPO with H2O2 in the presence of chloride ions generates HOCl (the physiological mixture of hypochlorous acid and its anion present at pH 7.4). Exposure of glycosaminoglycans to a MPO–H2O2–Cl− system or reagent HOCl generates long-lived chloramides [R-NCl-C(O)-R′] derived from the glycosamine N-acetyl functions. Decomposition of these species by transition metal ions gives polymer-derived amidyl (nitrogen-centred) radicals [R-N•-C(O)-R′], polymer-derived carbon-centred radicals and site-specific strand scission. In the present study, we have shown that exposure of glycosaminoglycan chloramides to O2•− also promotes chloramide decomposition and glycosaminoglycan fragmentation. These processes are inhibited by superoxide dismutase, metal ion chelators and the metal ion-binding protein BSA, consistent with chloramide decomposition and polymer fragmentation occurring via O2•−-dependent one-electron reduction, possibly catalysed by trace metal ions. Polymer fragmentation induced by O2•− [generated by the superoxide thermal source 1, di-(4-carboxybenzyl)hyponitrite] was demonstrated to be entirely chloramide dependent as no fragmentation occurred with the native polymers or when the chloramides were quenched by prior treatment with methionine. EPR spin-trapping experiments using 5,5-dimethyl1-pyrroline-N-oxide and 2-methyl-2-nitrosopropane have provided evidence for both O2•− and polymer-derived carbon-centred radicals as intermediates. The results obtained are consistent with a mechanism involving one-electron reduction of the chloramides to yield polymer-derived amidyl radicals, which subsequently undergo intramolecular hydrogen atom abstraction reactions to give carbon-centred radicals. The latter undergo fragmentation reactions in a site-specific manner. This synergistic

The Competitive Influence of Li+, Na+, K+, Ag+, and H+ on the Fragmentation of a PEGylated Polymeric Excipient

NASA Astrophysics Data System (ADS)

Wei, Juan; Bristow, Anthony W. T.; O'Connor, Peter B.

2015-01-01

The collisionally activated dissociation (CAD) and electron capture dissociation (ECD) of doubly charged tocopheryl polyethylene glycol succinate (TPGS) have been examined. Li+, Na+, K+, Ag+, and H+ were selected in the study, and the competitive influence of each ion was investigated by fragmenting TPGS attached with two different cations, [M + X1 + X2]2+ (X1 and X2 refer to Li+, Na+, K+, Ag+, H+). For metallic adducts, CAD results show that the dissociation of ionic adducts from the precursor is most likely depending on the binding strength, where the affinity of each ion to the TPGS is in the order of Ag+ ≈ Li+ ˃ Na+ ˃ K+. Introducing more strongly bound adducts increases fragmentation. During ECD, however, the silver cation is lost most easily compared with the other alkali metal ions, but silver also shows a dominant role in producing fragmentations. Moreover, the charge carriers are lost in an order (Ag+ ˃ Na+ ˃ K+ ≥ Li+ where the loss of Ag is most easily) that appears to correlate with the standard reduction potential of the metallic ions (Ag+ ˃ Na+ ˃ K+ ˃ Li+). The ECD results suggest that the reduction potential of the charge carrier could be an important factor influencing the fragmentation, where the ion with a high reduction potential is more effective in capturing electrons, but may also be lost easily before leading to any fragmentation. Finally, a proton has the weakest binding with the TPGS according to the CAD results, and its dissociation in ECD follows the order of the reduction potential (Ag+ ˃ H+ ˃ Na+ ˃ K+ > Li+).

Tuning Li2MO3 phase abundance and suppressing migration of transition metal ions to improve the overall performance of Li- and Mn-rich layered oxide cathode

NASA Astrophysics Data System (ADS)

Zhang, Shiming; Tang, Tian; Ma, Zhihua; Gu, Haitao; Du, Wubing; Gao, Mingxia; Liu, Yongfeng; Jian, Dechao; Pan, Hongge

2018-03-01

The poor cycling stability of Li- and Mn-rich layered oxide cathodes used in lithium-ion batteries (LIBs) has severely limited their practical application. Unfortunately, current strategies to improve their lifecycle sacrifice initial capacity. In this paper, we firstly report the synergistic improvement of the electrochemical performance of a Li1.2Ni0.13Co0.13Mn0.54O2 (LNCMO) cathode material, including gains for capacity, cycling stability, and rate capability, by the partial substitution of Li+ ions by Mg2+ ions. Electrochemical performance is evaluated by a galvanostatic charge and discharge test and electrochemical impedance spectroscopy (EIS). Structure and morphology are characterized by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). Compared with the substitution of transition metal (TM) ions with Mg2+ ions reported previously, the substitution of Li+ ions by Mg2+ ions not only drastically ameliorates the capacity retention and rate performance challenges of LNCMO cathodes but also markedly suppresses their voltage fading, due to the inhibition of the migration of TM ions during cycling, while also increasing the capacity of the cathode due to an increased abundance of the Li2MO3 phase.

DETERMINATION OF ION AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF PRODUCT ION MASS SPECTRA USING AN ORTHOGONAL ACCELERATION, TIME-OF-FLIGHT MASS SPECTROMETER AND AN ION CORRELATION PROGRAM

EPA Science Inventory

Exact masses of monoisotopic ions and the relative isotopic abundances (RIAs) of ions greater in mass by 1 and 2 Da than the monoisotopic ion are independent and complementary physical properties useful for istinguishing among ion compositions possible for a given nominal mass. U...

Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry.

PubMed

Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

2017-02-01

Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C-C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

Rapid decay of tree-community composition in Amazonian forest fragments

PubMed Central

Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

2006-01-01

Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

Projectile fragmentation of 500 A MeV 56Fe in nuclear emulsion

NASA Astrophysics Data System (ADS)

Li, Jun-Sheng; Zhang, Dong-Hai; Li, Hui-Ling; Yasuda, N.

2013-07-01

N-4 stacks of nuclear emulsion were exposed to 500 A MeV 56Fe ions at the HIMAC NIRS. Particle production was investigated in 56Fe-Em interactions. The multiplicity distribution of projectile fragments was done in this paper and compared with interactions induced by 56Fe and other heavy ions in nuclear emulsion at other energies. The variation of characteristics of the heavy ion interactions with the mass and energy of the projectile is studied.

ORTHO-TO-PARA ABUNDANCE RATIO OF WATER ION IN COMET C/2001 Q4 (NEAT): IMPLICATION FOR ORTHO-TO-PARA ABUNDANCE RATIO OF WATER

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

Shinnaka, Yoshiharu; Kawakita, Hideyo; Kobayashi, Hitomi

2012-04-20

The ortho-to-para abundance ratio (OPR) of cometary molecules is considered to be one of the primordial characteristics of cometary ices, and contains information concerning their formation. Water is the most abundant species in cometary ices, and OPRs of water in comets have been determined from infrared spectroscopic observations of H{sub 2}O rovibrational transitions so far. In this paper, we present a new method to derive OPR of water in comets from the high-dispersion spectrum of the rovibronic emission of H{sub 2}O{sup +} in the optical wavelength region. The rovibronic emission lines of H{sub 2}O{sup +} are sometimes contaminated by othermore » molecular emission lines but they are not affected seriously by telluric absorption compared with near-infrared observations. Since H{sub 2}O{sup +} ions are mainly produced from H{sub 2}O by photoionization in the coma, the OPR of H{sub 2}O{sup +} is considered to be equal to that of water based on the nuclear spin conservation through the reaction. We have developed a fluorescence excitation model of H{sub 2}O{sup +} and applied it to the spectrum of comet C/2001 Q4 (NEAT). The derived OPR of water is 2.54{sup +0.32}{sub -0.25}, which corresponds to a nuclear spin temperature (T{sub spin}) of 30{sup +10}{sub -4} K. This is consistent with the previous value determined in the near-infrared for the same comet (OPR = 2.6 {+-} 0.3, T{sub spin} = 31{sup +11}{sub -5} K).« less

ION COMPOSITION ELUCIDATION (ICE)

EPA Science Inventory

Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer to simultaneously determine exact masses and relative isotopic abundances from mass peak profiles. These can be determined more accurately and at higher sensitivity ...

The potential of combining ion trap/MS/MS and TOF/MS for identification of emerging contaminants

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.; Heine, C.E.; Thurman, E.M.

2002-01-01

The use of a method combining ion trap tandem mass spectrometry (MS/MS) and time of flight mass spectrometry (TOF/MS) for identification of emerging contaminates was discussed. The two tools together complemented each other in sensitivity, fragmentation and accurate mass determination. Liquid chromatography/electrospray ionization/ion-trap tandem mass spectrometry (LC/ESI/MS/MS), in positive ion mode of operation, was used to separate and identify specific compounds. Diagnostic fragment ions were obtained for a polyethyleneglycol(PEG) homolog by ion trap MS/MS, and fragments were measured by TOF/MS. It was observed that the combined method gave an exact mass measurement that differed from the calculated mass.

Nanosheets of earth-abundant jarosite as novel anodes for high-rate and long-life lithium-ion batteries.

PubMed

Ding, Yuan-Li; Wen, Yuren; Chen, Chia-Chin; van Aken, Peter A; Maier, Joachim; Yu, Yan

2015-05-20

Nanosheets of earth-abundant jarosite were fabricated via a facile template-engaged redox coprecipitation strategy at room temperature and employed as novel anode materials for lithium-ion batteries (LIBs) for the first time. These 2D materials exhibit high capacities, excellent rate capability, and prolonged cycling performance. As for KFe3(SO4)2(OH)6 jarosite nanosheets (KNSs), the reversible capacities of above 1300 mAh g(-1) at 100 mA g(-1) and 620 mAh g(-1) after 4000 cycles at a very high current density of 10 A g(-1) were achieved, respectively. Moreover, the resulting 2D nanomaterials retain good structural integrity upon cycling. These results reveal great potential of jarosite nanosheets as low-cost and high-performance anode materials for next-generation LIBs.

Inner-shell excitation and ionic fragmentation of molecules

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

Hitchcock, A.P.; Tyliszczak, T.; Cavell, R.G.

1997-04-01

Inner-shell excitation and associated decay spectroscopies are site specific probes of electronic and geometrical structure and photoionization dynamics. X-ray absorption probes the geometric and electronic structure, while time-of-flight mass spectrometry with multi-coincidence detection provides information on the photofragmentation dynamics of the initially produced inner-shell state. Auger decay of inner-shell excited and ionised states is an efficient source of multiply charged ions. The charge separation and fragmentation of these species, studied by photoelectron-photoion-photoion coincidence (also called charge separation mass spectrometry) gives insights into bonding and electronic structure. In molecules, the dependence of the fragmentation process on the X-ray energy can revealmore » cases of site and/or state selective fragmentation. At the ALS the authors have examined the soft X-ray spectroscopy and ionic fragmentation of a number of molecules, including carboranes, silylenes, phosphorus halides, SF{sub 6} and CO{sub 2}. Their work is illustrated using results from the carborane and PF{sub 3} studies.« less

Fragment generation, survival, and attachment of Dictyota spp. at Conch Reef in the Florida Keys, USA

NASA Astrophysics Data System (ADS)

Herren, L. W.; Walters, L. J.; Beach, K. S.

2006-05-01

During the past decade, the relative abundance of the brown macroalgae Dictyota spp. has been high in the Florida Keys. Recent studies have shown that members of this genus successfully reproduce via vegetative fragmentation. To investigate the importance of fragmentation on the reef community, this study examined: (1) the degree of epiphytism on benthic organisms, (2) the rate of fragment production through fish foraging activities, (3) the likelihood of fragment entanglement, and (4) the fragment attachment and success rate. It was found that reef fish contributed substantially to the fragment pool; furthermore, most fish-produced fragments produced rhizoids and attached to sand grains within 24 h in the field. Fragments of Dictyota spp. most commonly became entangled around and then attached themselves to the green alga Halimeda tuna, and other Dictyota spp. These results suggest that vegetative fragmentation of Dictyota spp. plays an important role in the changing community structure on the Florida Keys reef tract.

Communication: Identification of daughter ions through their electronic spectroscopy at low temperature

NASA Astrophysics Data System (ADS)

Dedonder, Claude; Féraud, Géraldine; Jouvet, Christophe

2014-10-01

We present experimental results on photofragmentation of cooled fragments issued from the photofragmentation of cold parent ions. The cooling of the daughter ions at a few K allows its characterization not only through its fragmentation pattern but also through its well resolved electronic spectroscopy. The proof of principle of the method is demonstrated on the photofragment resulting from Cα-Cβ bond rupture in protonated tyrosine (TyrH+). The analysis of the daughter ion (m/z 108) photofragmentation spectrum is in agreement with the proposed mechanism implying a proton transfer to the phenyl ring as the first step of the fragmentation mechanism of TyrH+.

Ion-ion coincidence imaging at high event rate using an in-vacuum pixel detector.

PubMed

Long, Jingming; Furch, Federico J; Durá, Judith; Tremsin, Anton S; Vallerga, John; Schulz, Claus Peter; Rouzée, Arnaud; Vrakking, Marc J J

2017-07-07

A new ion-ion coincidence imaging spectrometer based on a pixelated complementary metal-oxide-semiconductor detector has been developed for the investigation of molecular ionization and fragmentation processes in strong laser fields. Used as a part of a velocity map imaging spectrometer, the detection system is comprised of a set of microchannel plates and a Timepix detector. A fast time-to-digital converter (TDC) is used to enhance the ion time-of-flight resolution by correlating timestamps registered separately by the Timepix detector and the TDC. In addition, sub-pixel spatial resolution (<6 μm) is achieved by the use of a center-of-mass centroiding algorithm. This performance is achieved while retaining a high event rate (10 4 per s). The spectrometer was characterized and used in a proof-of-principle experiment on strong field dissociative double ionization of carbon dioxide molecules (CO 2 ), using a 400 kHz repetition rate laser system. The experimental results demonstrate that the spectrometer can detect multiple ions in coincidence, making it a valuable tool for studying the fragmentation dynamics of molecules in strong laser fields.

Ion-ion coincidence imaging at high event rate using an in-vacuum pixel detector

NASA Astrophysics Data System (ADS)

Long, Jingming; Furch, Federico J.; Durá, Judith; Tremsin, Anton S.; Vallerga, John; Schulz, Claus Peter; Rouzée, Arnaud; Vrakking, Marc J. J.

2017-07-01

A new ion-ion coincidence imaging spectrometer based on a pixelated complementary metal-oxide-semiconductor detector has been developed for the investigation of molecular ionization and fragmentation processes in strong laser fields. Used as a part of a velocity map imaging spectrometer, the detection system is comprised of a set of microchannel plates and a Timepix detector. A fast time-to-digital converter (TDC) is used to enhance the ion time-of-flight resolution by correlating timestamps registered separately by the Timepix detector and the TDC. In addition, sub-pixel spatial resolution (<6 μm) is achieved by the use of a center-of-mass centroiding algorithm. This performance is achieved while retaining a high event rate (104 per s). The spectrometer was characterized and used in a proof-of-principle experiment on strong field dissociative double ionization of carbon dioxide molecules (CO2), using a 400 kHz repetition rate laser system. The experimental results demonstrate that the spectrometer can detect multiple ions in coincidence, making it a valuable tool for studying the fragmentation dynamics of molecules in strong laser fields.

Initial measurements of O-ion and He-ion decay rates observed from the Van Allen probes RBSPICE instrument

PubMed Central

Gerrard, Andrew; Lanzerotti, Louis; Gkioulidou, Matina; Mitchell, Donald; Manweiler, Jerry; Bortnik, Jacob; Keika, Kunihiro

2014-01-01

H-ion (∼45 keV to ∼600 keV), He-ion (∼65 keV to ∼520 keV), and O-ion (∼140 keV to ∼1130 keV) integral flux measurements, from the Radiation Belt Storm Probe Ion Composition Experiment (RBSPICE) instrument aboard the Van Allan Probes spacecraft B, are reported. These abundance data form a cohesive picture of ring current ions during the first 9 months of measurements. Furthermore, the data presented herein are used to show injection characteristics via the He-ion/H-ion abundance ratio and the O-ion/H-ion abundance ratio. Of unique interest to ring current dynamics are the spatial-temporal decay characteristics of the two injected populations. We observe that He-ions decay more quickly at lower L shells, on the order of ∼0.8 day at L shells of 3–4, and decay more slowly with higher L shell, on the order of ∼1.7 days at L shells of 5–6. Conversely, O-ions decay very rapidly (∼1.5 h) across all L shells. The He-ion decay time are consistent with previously measured and calculated lifetimes associated with charge exchange. The O-ion decay time is much faster than predicted and is attributed to the inclusion of higher-energy (> 500 keV) O-ions in our decay rate estimation. We note that these measurements demonstrate a compelling need for calculation of high-energy O-ion loss rates, which have not been adequately studied in the literature to date. Key Points We report initial observations of ring current ions We show that He-ion decay rates are consistent with theory We show that O-ions with energies greater than 500 keV decay very rapidly PMID:26167435

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

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

Transitions from functionalization to fragmentation reactions of laboratory secondary organic aerosol (SOA) generated from the OH oxidation of alkane precursors.

PubMed

Lambe, Andrew T; Onasch, Timothy B; Croasdale, David R; Wright, Justin P; Martin, Alexander T; Franklin, Jonathan P; Massoli, Paola; Kroll, Jesse H; Canagaratna, Manjula R; Brune, William H; Worsnop, Douglas R; Davidovits, Paul

2012-05-15

Functionalization (oxygen addition) and fragmentation (carbon loss) reactions governing secondary organic aerosol (SOA) formation from the OH oxidation of alkane precursors were studied in a flow reactor in the absence of NO(x). SOA precursors were n-decane (n-C10), n-pentadecane (n-C15), n-heptadecane (n-C17), tricyclo[5.2.1.0(2,6)]decane (JP-10), and vapors of diesel fuel and Southern Louisiana crude oil. Aerosol mass spectra were measured with a high-resolution time-of-flight aerosol mass spectrometer, from which normalized SOA yields, hydrogen-to-carbon (H/C) and oxygen-to-carbon (O/C) ratios, and C(x)H(y)+, C(x)H(y)O+, and C(x)H(y)O(2)+ ion abundances were extracted as a function of OH exposure. Normalized SOA yield curves exhibited an increase followed by a decrease as a function of OH exposure, with maximum yields at O/C ratios ranging from 0.29 to 0.74. The decrease in SOA yield correlates with an increase in oxygen content and decrease in carbon content, consistent with transitions from functionalization to fragmentation. For a subset of alkane precursors (n-C10, n-C15, and JP-10), maximum SOA yields were estimated to be 0.39, 0.69, and 1.1. In addition, maximum SOA yields correspond with a maximum in the C(x)H(y)O+ relative abundance. Measured correlations between OH exposure, O/C ratio, and H/C ratio may enable identification of alkane precursor contributions to ambient SOA.

Mechanism of Formation of the Major Estradiol Product Ions Following Collisional Activation of the Molecular Anion in a Tandem Quadrupole Mass Spectrometer

NASA Astrophysics Data System (ADS)

Wooding, Kerry M.; Barkley, Robert M.; Hankin, Joseph A.; Johnson, Christopher A.; Bradford, Andrew P.; Santoro, Nanette; Murphy, Robert C.

2013-10-01

The importance of the mass spectral product ion structure is highlighted in quantitative assays, which typically use multiple reaction monitoring (MRM), and in the discovery of novel metabolites. Estradiol is an important sex steroid whose quantitation and metabolite identification using tandem mass spectrometry has been widely employed in numerous clinical studies. Negative electrospray ionization tandem mass spectrometry of estradiol (E2) results in several product ions, including the abundant m/z 183 and 169. Although m/z 183 is one of the most abundant product ions used in many quantitative assays, the structure of m/z 183 has not been rigorously examined. We suggest a structure for m/z 183 and a mechanism of formation consistent with collision induced dissociation (CID) of E2 and several stable isotopes ([D4]-E2, [13C6]-E2, and [D1]-E2). An additional product ion from E2, namely m/z 169, has also been examined. MS3 experiments indicated that both m/z 183 and m/z 169 originate from only E2 [M - H]- m/z 271. These ions, m/z 183 and m/z 169, were also present in the collision induced decomposition mass spectra of other prominent estrogens, estrone (E1) and estriol (E3), indicating that these two product ions could be used to elucidate the estrogenic origin of novel metabolites. We propose two fragmentation schemes to explain the CID data and suggest a structure of m/z 183 and m/z 169 consistent with several isotopic variants and high resolution mass spectrometric measurements.

Impacts of macro - and microplastic on macrozoobenthos abundance in intertidal zone

NASA Astrophysics Data System (ADS)

Bangun, A. P.; Wahyuningsih, H.; Muhtadi, A.

2018-02-01

Plastics pollution in coastal areas is one of the topics that have received more attention over the past few years. The intertidal zone is a waters area that is directly affected by contamination of plastic waste from land and sea. The purpose of this study was to analyze the types and abundance of plastic waste in the intertidal zone and its impact on macrozoobenthos abundance. This research was conducted at Pesisir Desa Jaring Halus in February-April 2017. Macrozoobenthos and macro - micro plastic were collected by using quadratic transect. Sediments were collected with a core, to a depth of 30 cm. Microplastic and macroplastic abundances were analyzed using separation of sediment density and hand sorting. The dominant micro plastic types were film (52.30%), fiber (24.88%), fragments (22.74%), followed by pellets (0.1%). The total number of microplastics were 326,33 items and macro plastic were 308 items. Macroplastic abundance is positively correlated with microplastic (0.765). The abundance of macrozoobenthos is negatively correlated with microplastic abundance (-0.368) and with macro plastic abundance (-0.633). The management strategies were suggested clean up marine debris, decrease plastic using and built up the station of debris processing.

Analytical Utility of Mass Spectral Binning in Proteomic Experiments by SPectral Immonium Ion Detection (SPIID)*

PubMed Central

Kelstrup, Christian D.; Frese, Christian; Heck, Albert J. R.; Olsen, Jesper V.; Nielsen, Michael L.

2014-01-01

Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids. PMID:24895383

Terrestrial salamander abundance on reclaimed mountaintop removal mines

USGS Publications Warehouse

Wood, Petra Bohall; Williams, Jennifer M.

2013-01-01

Mountaintop removal mining, a large-scale disturbance affecting vegetation, soil structure, and topography, converts landscapes from mature forests to extensive grassland and shrubland habitats. We sampled salamanders using drift-fence arrays and coverboard transects on and near mountaintop removal mines in southern West Virginia, USA, during 2000–2002. We compared terrestrial salamander relative abundance and species richness of un-mined, intact forest with habitats on reclaimed mountaintop removal mines (reclaimed grassland, reclaimed shrubland, and fragmented forest). Salamanders within forests increased in relative abundance with increasing distance from reclaimed mine edge. Reclaimed grassland and shrubland habitats had lower relative abundance and species richness than forests. Characteristics of reclaimed habitats that likely contributed to lower salamander abundance included poor soils (dry, compacted, little organic matter, high rock content), reduced vertical structure of vegetation and little tree cover, and low litter and woody debris cover. Past research has shown that salamander populations reduced by clearcutting may rebound in 15–24 years. Time since disturbance was 7–28 years in reclaimed habitats on our study areas and salamander populations had not reached levels found in adjacent mature forests.

Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

PubMed

Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

2009-10-07

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

Fragmentation and hydration of tektites and microtektites

USGS Publications Warehouse

Glass, B.P.; Muenow, D.W.; Bohor, B.F.; Meeker, G.P.

1997-01-01

An examination of data collected over the last 30 years indicates that the percent of glass fragments vs. whole splash forms in the Cenozoic microtektite strewn fields increases towards the source crater (or source region). We propose that this is due to thermal stress produced when tektites and larger microtektites fall into water near the source crater while still relatively hot (>1150 ??C). We also find evidence (low major oxide totals, frothing when melted) for hydration of most of the North American tektite fragments and microtektites found in marine sediments. High-temperature mass spectrometry indicates that these tektite fragments and microtektites contain up to 3.8 wt% H2O. The H2O-release behavior during the high-temperature mass-spectrometric analysis, plus high Cl abundances (???0.05 wt%), indicate that the North. American tektite fragments and microtektites were hydrated in the marine environment (i.e., the H2O was not trapped solely on quenching from a melt). The younger Ivory Coast and Australasian microtektites do not exhibit much evidence of hydration (at least not in excess of 0.5 wt% H2O); this suggests that the degree of hydration increases with age. In addition, we find that some glass spherules (with 65 wt% SiO2 can undergo simple hydration in the marine environment, while impact glasses (with <65 wt% SiO2) can also undergo palagonitization.

Statistical prescission point model of fission fragment angular distributions

NASA Astrophysics Data System (ADS)

John, Bency; Kataria, S. K.

1998-03-01

In light of recent developments in fission studies such as slow saddle to scission motion and spin equilibration near the scission point, the theory of fission fragment angular distribution is examined and a new statistical prescission point model is developed. The conditional equilibrium of the collective angular bearing modes at the prescission point, which is guided mainly by their relaxation times and population probabilities, is taken into account in the present model. The present model gives a consistent description of the fragment angular and spin distributions for a wide variety of heavy and light ion induced fission reactions.

A fragmentation study of dihydroquercetin using triple quadrupole mass spectrometry and its application for identification of dihydroflavonols in Citrus juices.

PubMed

Abad-García, Beatriz; Garmón-Lobato, Sergio; Berrueta, Luis A; Gallo, Blanca; Vicente, Francisca

2009-09-01

A mass spectrometric method using electrospray ionization with triple quadrupole and quadrupole time-of-flight hybrid (Q-Tof) mass spectrometry has been applied to the structural characterization of dihydroflavonols. This family of compounds has been studied by liquid chromatography/tandem mass spectrometry (LC/MS/MS) for the first time in this work. A comprehensive study of the product ion MS spectra of the [M+H](+) ion of a commercially available standard has been performed. The most useful fragmentations in terms of structural identification are those that involve cleavage of the C-ring, resulting in diagnostic ions of dihydroflavonol family: (1,3)A(0) (+), (1,2)B(0) (+), (1,2)B(0) (+)-CO, (0,2)A(0) (+), (0,2)A(0) (+)-H(2)O, (0,2)A(0) (+)-CO, and (0,2)A(0) (+)-H(2)O-CO, that allow the characterization of the substituents in the A- and B-rings. In addition to those ions, other product ions due to losses of H(2)O and CO molecules from the Y(0) (+) ion were observed. Their fragmentation mechanisms and ion structures have been proposed. The established fragmentation patterns have been used to successfully identity three dihydroflavonols found in tangerine juices for the first time. Copyright (c) 2009 John Wiley & Sons, Ltd.

Primary fragmentation pathways of gas phase [M(uracil-H)(uracil)]+ complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): loss of uracil versus HNCO.

PubMed

Ali, Osama Y; Randell, Nicholas M; Fridgen, Travis D

2012-04-23

Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive-ion electrospray spectra show that [M(Ura-H)(Ura)](+) (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI-CID experiments show that the main primary decomposition pathway for all [M(Ura-H)(Ura)](+) , except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI-CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura-H)(Ura)](+) are shown to lose a molecule of uracil. Similar results were observed under infrared multiple-photon dissociation excitation conditions, except that [Ca(Ura-H)(Ura)](+) was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura-H)](+) (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic-structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura-H)](+) is ion-dipole complexation and the experimental evidence presented supports this. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bulk plasma fragmentation in a C4F8 inductively coupled plasma: A hybrid modeling study

NASA Astrophysics Data System (ADS)

Zhao, Shu-Xia; Zhang, Yu-Ru; Gao, Fei; Wang, You-Nian; Bogaerts, Annemie

2015-06-01

A hybrid model is used to investigate the fragmentation of C4F8 inductive discharges. Indeed, the resulting reactive species are crucial for the optimization of the Si-based etching process, since they determine the mechanisms of fluorination, polymerization, and sputtering. In this paper, we present the dissociation degree, the density ratio of F vs. CxFy (i.e., fluorocarbon (fc) neutrals), the neutral vs. positive ion density ratio, details on the neutral and ion components, and fractions of various fc neutrals (or ions) in the total fc neutral (or ion) density in a C4F8 inductively coupled plasma source, as well as the effect of pressure and power on these results. To analyze the fragmentation behavior, the electron density and temperature and electron energy probability function (EEPF) are investigated. Moreover, the main electron-impact generation sources for all considered neutrals and ions are determined from the complicated C4F8 reaction set used in the model. The C4F8 plasma fragmentation is explained, taking into account many factors, such as the EEPF characteristics, the dominance of primary and secondary processes, and the thresholds of dissociation and ionization. The simulation results are compared with experiments from literature, and reasonable agreement is obtained. Some discrepancies are observed, which can probably be attributed to the simplified polymer surface kinetics assumed in the model.

Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

NASA Astrophysics Data System (ADS)

Anders, Christian; Urbassek, Herbert M.

2017-01-01

Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

A 3.8-V earth-abundant sodium battery electrode

PubMed Central

Barpanda, Prabeer; Oyama, Gosuke; Nishimura, Shin-ichi; Chung, Sai-Cheong; Yamada, Atsuo

2014-01-01

Rechargeable lithium batteries have ushered the wireless revolution over last two decades and are now matured to enable green automobiles. However, the growing concern on scarcity and large-scale applications of lithium resources have steered effort to realize sustainable sodium-ion batteries, Na and Fe being abundant and low-cost charge carrier and redox centre, respectively. However, their performance is limited owing to low operating voltage and sluggish kinetics. Here we report a hitherto-unknown material with entirely new composition and structure with the first alluaudite-type sulphate framework, Na2Fe2(SO4)3, registering the highest-ever Fe3+/Fe2+ redox potential at 3.8 V (versus Na, and hence 4.1 V versus Li) along with fast rate kinetics. Rare-metal-free Na-ion rechargeable battery system compatible with the present Li-ion battery is now in realistic scope without sacrificing high energy density and high power, and paves way for discovery of new earth-abundant sustainable cathodes for large-scale batteries. PMID:25030272

Tandem mass spectrometry of large biomolecule ions by blackbody infrared radiative dissociation.

PubMed

Price, W D; Schnier, P D; Williams, E R

1996-03-01

A new method for the dissociation of large ions formed by electrospray ionization is demonstrated. Ions trapped in a Fourier transform mass spectrometer at pressures below 10(-)(8) Torr are dissociated by elevating the vacuum chamber to temperatures up to 215 °C. Rate constants for dissociation are measured and found to be independent of pressure below 10(-)(7) Torr. This indicates that the ions are activated by absorption of blackbody radiation emitted from the chamber walls. Dissociation efficiencies as high as 100% are obtained. There is no apparent mass limit to this method; ions as large as ubiquitin (8.6 kDa) are readily dissociated. Thermally stable ions, such as melittin 3+ (2.8 kDa), did not dissociate at temperatures up to 200 °C. This method is highly selective for low-energy fragmentation, from which limited sequence information can be obtained. From the temperature dependence of the dissociation rate constants, Arrhenius activation energies in the low-pressure limit are obtained. The lowest energy dissociation processes for the singly and doubly protonated ions of bradykinin are loss of NH(3) and formation of the b(2)/y(7) complementary pair, with activation energies of 1.3 and 0.8 eV, respectively. No loss of NH(3) is observed for the doubly protonated ion; some loss of H(2)O occurs. These results show that charge-charge interactions not only lower the activation energy for dissociation but also can dramatically change the fragmentation, most likely through changes in the gas-phase conformation of the ion. Dissociation of ubiquitin ions produces fragmentation similar to that obtained by IRMPD and SORI-CAD. Higher charge state ions dissociate to produce y and b ions; the primary fragmentation process for low charge state ions is loss of H(2)O.

Scale-dependent effects of nonnative plant invasion on host-seeking tick abundance

PubMed Central

Adalsteinsson, Solny A.; D’Amico, Vincent; Shriver, W. Gregory; Brisson, Dustin; Buler, Jeffrey J.

2016-01-01

Nonnative, invasive shrubs can affect human disease risk through direct and indirect effects on vector populations. Multiflora rose (Rosa multiflora) is a common invader within eastern deciduous forests where tick-borne disease (e.g. Lyme disease) rates are high. We tested whether R. multiflora invasion affects blacklegged tick (Ixodes scapularis) abundance, and at what scale. We sampled host-seeking ticks at two spatial scales: fine-scale, within R. multiflora-invaded forest fragments; and patch scale, among R. multiflora-invaded and R. multiflora-free forest fragments. At a fine scale, we trapped 2.3 times more ticks under R. multiflora compared to paired traps 25 m away from R. multiflora. At the patch scale, we trapped 3.2 times as many ticks in R. multiflora-free forests compared to R. multiflora-invaded forests. Thus, ticks are concentrated beneath R. multiflora within invaded forests, but uninvaded forests support significantly more ticks. Among all covariates tested, leaf litter volume was the best predictor of tick abundance; at the patch scale, R. multiflora-invaded forests had less leaf litter than uninvaded forests. We suggest that leaf litter availability at the patch-scale plays a greater role in constraining tick abundance than the fine-scale, positive effect of invasive shrubs. PMID:27088044

Anisotropy of the angular distribution of fission fragments in heavy-ion fusion-fission reactions: The influence of the level-density parameter and the neck thickness

NASA Astrophysics Data System (ADS)

Naderi, D.; Pahlavani, M. R.; Alavi, S. A.

2013-05-01

Using the Langevin dynamical approach, the neutron multiplicity and the anisotropy of angular distribution of fission fragments in heavy ion fusion-fission reactions were calculated. We applied one- and two-dimensional Langevin equations to study the decay of a hot excited compound nucleus. The influence of the level-density parameter on neutron multiplicity and anisotropy of angular distribution of fission fragments was investigated. We used the level-density parameter based on the liquid drop model with two different values of the Bartel approach and Pomorska approach. Our calculations show that the anisotropy and neutron multiplicity are affected by level-density parameter and neck thickness. The calculations were performed on the 16O+208Pb and 20Ne+209Bi reactions. Obtained results in the case of the two-dimensional Langevin with a level-density parameter based on Bartel and co-workers approach are in better agreement with experimental data.

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.

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

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

McLoughlin, K.

2016-01-11

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from itsmore » nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.« less

Quantification and micron-scale imaging of spatial distribution of trace beryllium in shrapnel fragments and metallurgic samples with correlative fluorescence detection method and secondary ion mass spectrometry (SIMS).

PubMed

Abraham, J L; Chandra, S; Agrawal, A

2014-11-01

Recently, a report raised the possibility of shrapnel-induced chronic beryllium disease from long-term exposure to the surface of retained aluminum shrapnel fragments in the body. Since the shrapnel fragments contained trace beryllium, methodological developments were needed for beryllium quantification and to study its spatial distribution in relation to other matrix elements, such as aluminum and iron, in metallurgic samples. In this work, we developed methodology for quantification of trace beryllium in samples of shrapnel fragments and other metallurgic sample-types with main matrix of aluminum (aluminum cans from soda, beer, carbonated water and aluminum foil). Sample preparation procedures were developed for dissolving beryllium for its quantification with the fluorescence detection method for homogenized measurements. The spatial distribution of trace beryllium on the sample surface and in 3D was imaged with a dynamic secondary ion mass spectrometry instrument, CAMECA IMS 3f secondary ion mass spectrometry ion microscope. The beryllium content of shrapnel (∼100 ppb) was the same as the trace quantities of beryllium found in aluminum cans. The beryllium content of aluminum foil (∼25 ppb) was significantly lower than cans. SIMS imaging analysis revealed beryllium to be distributed in the form of low micron-sized particles and clusters distributed randomly in X-Y- and Z dimensions, and often in association with iron, in the main aluminum matrix of cans. These observations indicate a plausible formation of Be-Fe or Al-Be alloy in the matrix of cans. Further observations were made on fluids (carbonated water) for understanding if trace beryllium in cans leached out and contaminated the food product. A direct comparison of carbonated water in aluminum cans and plastic bottles revealed that beryllium was below the detection limits of the fluorescence detection method (∼0.01 ppb). These observations indicate that beryllium present in aluminum matrix was either

Rare earth element abundances in presolar SiC

NASA Astrophysics Data System (ADS)

Ireland, T. R.; Ávila, J. N.; Lugaro, M.; Cristallo, S.; Holden, P.; Lanc, P.; Nittler, L.; Alexander, C. M. O'D.; Gyngard, F.; Amari, S.

2018-01-01

Individual isotope abundances of Ba, lanthanides of the rare earth element (REE) group, and Hf have been determined in bulk samples of fine-grained silicon carbide (SiC) from the Murchison CM2 chondrite. The analytical protocol involved secondary ion mass spectrometry with combined high mass resolution and energy filtering to exclude REE oxide isobars and Si-C-O clusters from the peaks of interest. Relative sensitivity factors were determined through analysis of NIST SRM reference glasses (610 and 612) as well as a trace-element enriched SiC ceramic. When normalised to chondrite abundances, the presolar SiC REE pattern shows significant deficits at Eu and Yb, which are the most volatile of the REE. The pattern is very similar to that observed for Group III refractory inclusions. The SiC abundances were also normalised to s-process model predictions for the envelope compositions of low-mass (1.5-3 M⊙) AGB stars with close-to-solar metallicities (Z = 0.014 and 0.02). The overall trace element abundances (excluding Eu and Yb) appear consistent with the predicted s-process patterns. The depletions of Eu and Yb suggest that these elements remained in the gas phase during the condensation of SiC. The lack of depletion in some other moderately refractory elements (like Ba), and the presence of volatile elements (e.g. Xe) indicates that these elements were incorporated into SiC by other mechanisms, most likely ion implantation.

Characteristic fragment size distributions in dynamic fragmentation

NASA Astrophysics Data System (ADS)

Zhou, Fenghua; Molinari, Jean-François; Ramesh, K. T.

2006-06-01

The one-dimensional fragmentation of a dynamically expanding ring (Mott's problem) is studied numerically to obtain the fragment signatures under different strain rates. An empirical formula is proposed to calculate an average fragment size. Rayleigh distribution is found to describe the statistical properties of the fragment populations.