pinecone/core-2020-05-10-deduplication huggingface dataset:
Simultaneous detection of five different 2-hydroxyethyl-DNA adducts formed by ethylene oxide exposure, using a high-performance liquid chromatography/electrospray ionisation tandem mass spectrometry assay

This is the author's final draft of the version published as Rapid Communications in Mass Spectrometry, 2008, 22 (1),pp.19-28. The definitive version is available at www3.interscience.wiley.com, Doi: 10.1002/rcm.3328.A method has been developed for the simultaneous detection and quantitation of five different (2-hydroxyethyl)-DNA adducts (HE-DNA adducts) that could be formed as a result of exposure to ethylene oxide (EO). In addition to the major N7-HE-guanine (N7-HEG) adducts this assay can also measure the less prevalent but potentially more biologically significant N1-HE-2’-deoxyadenosine (N1-HEdA), O6-HE-2’-deoxyguanosine (O6-HEdG), N6-HE-2’-deoxyadenosine (N6-HEdA) and N3-HE-2’-deoxyuridine adducts (N3-HEdU). The method involves the isolation of HE-adducts from the unmodified nucleosides by either neutral thermal hydrolysis or enzymatic digestion, followed by HPLC purification, before detection and quantification by liquid-chromatography tandem mass spectrometry (LC-MS/MS) using selective reaction monitoring (SRM). The limits of detection were in the range 0.5 – 25 fmoles for each individual adduct, making this one of the most sensitive assays available for the detection of N7-HEG. To illustrate the possible applications of the assay, it has been employed in the measurement of endogenous/background and EO-induced HE-adducts in a variety of DNA samples
Rapid screening of anthocyanins in berry samples by\ud
surfactant-mediated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Surfactant-mediated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry\ud
(MALDI-TOF-MS) has been used for the identification of flavonoids from three berry extracts:\ud
lowbush blueberry (Vaccinium angustifolium), lingonberry (Vaccinium vitis-idaea), and blackberry\ud
(Rubus armeniacus). The addition of the surfactant led to suppression of matrix ions from both\ud
a-cyano-4-hydroxycinnamic acid (CHCA) and 2(,4(,6(-trihydroxyacetophenone (THAP). This is the\ud
first case of this method being successfully employed with a matrix other than CHCA. It was observed\ud
that CHCA led to a great deal of fragmentation of the sugar moiety from glycosides, whereas THAP\ud
produced more intact glycoside molecules, and thus leads to better characterization of the flavonoids\ud
in a berry sample. The flavonoids were characterized and quantified by liquid chromatography/\ud
electrospray ionization mass spectrometry (LC/ESI-MS) with UV detection. Although MALDITOF-\ud
MS did not lead to the identification of as many flavonoids, it did enable us to identify many\ud
anthocyanin glycosides. Quantification was achieved and demonstrated that use of the THAP matrix\ud
can enable quantification of the intact glycosides with relative standard deviation (RSD) values of\ud
less than 10% with surfactant addition. These results are comparable with LC results. MALDITOF-\ud
MS with THAP matrix thus provided a rapid method for the qualitative screening of these\ud
compounds. It took only a few minutes, greatly reducing the analysis time from that in traditional LC/\ud
MS methods. Copyright # 2007 John Wiley & Sons, Ltd
The gas-phase interactions of TEMPO radicals with Fe+ ions

The gas phase ligation of 2, 2, 6, 6-tetramethyl-piperidyl-1-oxide (TEMPO) radical (1) and its 4- hydroxy- derivative (2) with Fe+ ions in a 3T FT ICR mass spectrometer was investigated. Triple ligation may occur: the first ligation produces a transient species prone to either charge exchange or a stable second ligation ; the third ligand adds slowly, with fragmentation. 1 and 2 differ in that 1 binds exclusively at the nitroxyl oxygen while 2 also binds at the OH site after the loss of a H-radical. Calculations combined with steric considerations support such a mechanism for 2. The site and the mechanism of the important side reaction of 1 that involves OH addition from a water impurity to yield an FeR2+ species remain unexplained
Mangrove trees growing in a very saline condition but\ud
not using seawater

Mangrove trees, which develop along tropical coasts, are known to use saline water uptake. In French Guiana, the high salinity condition is the result of seawater evaporation on mud banks formed from the Amazon sediment flumes. In the back mangrove a few kilometres inland, groundwater, soil water and the xylem sap uptake in the trees remain highly salty, and only very tolerant plants like Avicennia germinans can flourish, whereas the less salt-tolerant Rhizophora mangle is more difficult to find.\ud
Curiously, the same Avicennia trees propagate on the seafront. However, stable isotope ratio mass spectrometry (IRMS) measurements and ion analysis (high-performance liquid chromatography (HPLC) and inductively coupled plasma atomic emission (ICP-AES) spectroscopy reveal that the\ud
origin of the water in the back mangrove is not seawater. It is freshwater percolating into the sand bars from the inland marshes and rainwater during the wet season that redissolves a marine evaporite and gives a saline groundwater. The absence of barren saltine areas (‘tanne’) in French Guiana could be explained by this freshwater inflow, the aquifer being no longer linked with the ocean
Availability of 15N from pioneer herbaceous plants to pine seedlings in reclaimed burnt soils.

A pot experiment was used to assess the N uptake by pine seedlings\ud
during two years on a burnt soil added with 15N-labelled ryegrass, obtained from\ud
 a 15N-enriched sample of this soil after the fire. Nitrogen concentration in needles,\ud
stems and roots of seedlings decreased significantly from the first to the second\ud
 growing period (from 2.55, 1.30 and 2.19% to 1.19, 0.47 and 1.00%, respectively),\ud
 needles accounting for 53-58% of pine-N. At the end of the experiment, 98.87 ±\ud
 1.12% of the added ryegrass-15N was recovered: two thirds in the soil organic N\ud
 pool and one third in the pine seedlings. Therefore, the post fire pulse of\ud
 inorganic N, which was successfully kept in the burnt soil-plant system through\ud
 its uptake by the pioneer species, is available for trees at the medium term. Pine\ud
 seedlings assimilated 16.4% and 16.9% of  of added N uptake by plants; a possible explanation is the transient increase of\ud
 available N in burnt soils that would have modified the mineralization pattern\ud
 of the 15N-labelled phytomass. The pine N derived from the ryegrass-N decreased\ud
 from 4.05% in the first year to 2.53% in the second one, being 3.10% the two-years\ud
 weighed average. Besides the direct contribution of ryegrass to pine N nutrition reflected by these figures, the rapid post fire establishment of a herbaceous cover\ud
on the burnt soil also provides important indirect benefits for tree nutrition by\ud
 reducing organic- and inorganic-N losses.This research was supported by the Comisión Interministerial de Ciencia y Tecnología (CICYT, Spain) and by the Consellería de Educación e Ordenación Universitaria (Xunta de Galicia, Spain). The isotopic ratio mass spectrometer was partly financed by the European Regional Development Fund (EU).Peer reviewe
Can we use the CO2 concentrations determined by continuous-flow isotope ratio mass spectrometry from small samples for the Keeling plot approach?

A common method to estimate the carbon isotopic composition of soil-respired air is to use Keeling plots (d13C versus 1/CO2 concentration). This approach requires the precise determination of both CO2 concentration ([CO2]), usually measured with an infrared gas analyser (IRGA) in the \ud
field, and the analysis of d13C by isotope ratio mass spectrometry (IRMS) in the laboratory. We measured [CO2] with an IRGA in the field (n 637) and simultaneously collected air samples in 12 mL vials for analysis of the 13C values and the [CO2] using a continuous-flow isotope ratio mass spectrometer. In this study we tested if measurements by the IRGA and IRMS yielded the same results for [CO2], and also investigated the effects of different sample vial preparation methods on the [CO2] measurement and the thereby obtained Keeling plot results. Our results show that IRMS \ud
measurements of the [CO2] (during the isotope analysis) were lower than when the [CO2] was measured in the field with the IRGA. This is especially evident when the sample vials were not treated in the same way as the standard vials. From the three different vial preparation methods, the one using N2-filled and overpressurised vials resulted in the best agreement between the IRGA and IRMS [CO2] values. There was no effect on the 13C-values from the different methods. The Keeling plot results confirmed that the overpressurised vials performed best. We conclude that in the cases where the ranges of [CO2] are large (>300 ppm; in our case it ranged between 70 and 1500 ppm) reliable estimation of the [CO2] with small samples using IRMS is possible for Keeling plot application. We also suggest some guidelines for sample handling in order to achieve proper results
Comprehensive inter-laboratory calibration of reference materials for δ18O versus VSMOW using various on-line high-temperature conversion techniques

Internationally distributed organic and inorganic oxygen isotopic reference materials have been calibrated by six laboratories carrying out more than 5300 measurements using a variety of high-temperature conversion techniques (HTC) in an evaluation sponsored by the International Union of Pure and Applied Chemistry (IUPAC). To aid in the calibration of these reference materials, which span more than 125‰, an artificially enriched reference water (δ18O of +78.91‰) and two barium sulfates (one depleted and one enriched in 18O) were prepared and calibrated relative to VSMOW2 and SLAP reference waters. These materials were used to calibrate the other isotopic reference materials in this study.
The seemingly large estimated combined uncertainties arise from differences in instrumentation and methodology and difficulty in accounting for all measurement bias. They are composed of the 3-fold standard errors directly calculated from the measurements and provision for systematic errors discussed in this paper. A primary conclusion of this study is that nitrate samples analyzed for δ18O should be analyzed with internationally distributed isotopic nitrates, and likewise for sulfates and organics. Authors reporting relative differences of oxygen-isotope ratios (δ18O) of nitrates, sulfates, or organic material should explicitly state in their reports the δ18O values of two or more internationally distributed nitrates (USGS34, IAEA-NO-3, and USGS35), sulfates (IAEA-SO-5, IAEA-SO-6, and NBS 127), or organic material (IAEA-601 benzoic acid, IAEA-602 benzoic acid, and IAEA-600 caffeine), as appropriate to the material being analyzed, had these reference materials been analyzed with unknowns. This procedure ensures that readers will be able to normalize the δ18O values at a later time should it become necessary.
The high-temperature reduction technique for analyzing δ18O and δ2H is not as widely applicable as the well-established combustion technique for carbon and nitrogen stable isotope determination. To obtain the most reliable stable isotope data, materials should be treated in an identical fashion; within the same sequence of analyses, samples should be compared with working reference materials that are as similar in nature and in isotopic composition as feasible.
Determination of sub-ppb epichlorohydrin levels in water by on-line solid-phase extraction liquid chromatography/tandem mass spectrometry

A new sensitive and selective method based on on-line solid-phase extraction (SPE) coupled to liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) using a triple quadrupole mass spectrometer has been developed for the determination of epichlorohydrin (ECH) in different types of water samples. ECH is not easily determined directly by ESI-MS as it is not readily ionized, and it has a low molecular mass and high polarity. Thus, prior derivatization of ECH was necessary, employing 3,5-difluorobenzylamine as a derivatizing agent with Fe(III) as a catalyst. In order to achieve accurate quantification, correcting for matrix effects, losses in the derivatization process and instrumental deviations, isotope labelled ECH (ECH-d(5)) was added as an internal standard (IS) to the water samples. The method was validated based on European SANCO guidelines using drinking and other types of treated water spiked at two concentration levels (0.1 and 1.0 microg/L), the lower level having been established as the limit of quantification (LOQ) of the method. Satisfactory accuracy (recoveries between 70 and 103%), precision (RSD <20%) and linearity (from 0.05 to 50 microg/L, r >0.99) were obtained. The limit of detection (LOD) was set up at 0.03 microg/L. The method was applied to different water samples (drinking water and water samples collected from a municipal treatment water plant). In order to enhance confidence, five selected reaction monitoring (SRM) transitions were acquired, thus obtaining a simultaneous reliable quantification and identification of ECH in water, even at sub-ppb level
Isotopic characteristics of the Garonne River and its\ud
tributaries

The Garonne is the largest river in the south-west of France, and its drainage basin stretches between\ud
the Pyrenees and the Massif Central mountains. Until now, no water stable isotope study has been\ud
performed on the whole Garonne river basin which is composed of different geological substrata,\ud
and where the water resources are limited during the dry summer period. This study focuses on the\ud
Garonne river and its tributaries from the Pyre´ne´es foothill upstream to its confluence with the Lot\ud
River downstream. The aim of the study is to determine the origins of the surface waters using their\ud
chemical and stable isotopic compositions (18O, D and 13C), to better understand their circulation\ud
within the drainage basin and to assess the anthropogenic influences. The Garonne displays a\ud
specific 18O seasonal effect, and keeps its Pyre´nean characteristics until its confluence with the Tarn\ud
River. The difference in the dissolved inorganic carbon (DIC) comes mainly from the change in\ud
lithology between the Pyre´ne´es and the Massif Central mountains. Agriculture activity is only\ud
detected in the small tributaries
A reliable analytical approach based on gas chromatography coupled to triple quadrupole and time-of-flight mass analyzers for the determination and confirmation of polycyclic aromatic hydrocarbons in complex matrices from aquaculture activities

The potential of gas chromatography coupled to tandem mass spectrometry (GC/MS/MS) with a triple quadrupole analyzer (QqQ) has been investigated for the quantification and reliable identi- fication of sixteen polycyclic aromatic hydrocarbons (PAHs) from the EPA priority list in animal and vegetable samples from aquaculture activities, whose fat content ranged from 5 to 100%. Matrices analyzed included fish fillet, fish feed, fish oil and linseed oil. Combining optimized saponification and solid-phase extraction led to high efficiency in the elimination of interfering compounds, mainly fat, from the extracts. The developed procedure minimized the presence of these interfering compounds in the extracts and provided satisfactory recoveries of PAHs. The excellent sensitivity and selectivity of GC/(QqQ)MS/MS in selected reaction monitoring (SRM) allowed to reach limits of detection at pg/g levels. Two SRM transitions were acquired for each analyte to ensure reliable identification of compounds detected in samples. Confirmation of positive findings was performed by GC coupled to high-resolution time-of-flight mass spectrometry (GC/TOFMS). The accurate mass information provided by GC/TOFMS in full acquisition mode together with its high mass resolution makes it a powerful analytical tool for the unequivocal confirmation of PAHs in the matrices tested. The method developed was applied to the analysis of real-world samples of each matrix studied with the result of detecting and confirming the majority of analytes at the mg/kg level by both QqQ and TOF mass spectrometer
Fragmentation pathways of 2,3-dimethyl-2,3-dinitrobutane cations in the gas phase

2,3-Dimethyl-2,3-dinitrobutane (DMNB) is an explosive taggant added to plastic explosives during manufacture making them more susceptible to vapour-phase detection systems. In this study, the formation and detection of gas-phase \[M+H](+), \[M+Li](+), \[M+NH(4)](+) and \[M+Na](+) adducts of DMNB was achieved using electrospray ionisation on a triple quadrupole mass spectrometer. The \[M+H](+) ion abundance was found to have a strong dependence on ion source temperature, decreasing markedly at source temperatures above 50 degrees C. In contrast, the \[M+Na](+) ion demonstrated increasing ion abundance at source temperatures up to 105 degrees C. The relative susceptibility of DMNB adduct ions toward dissociation was investigated by collision-induced dissociation. Probable structures of product ions and mechanisms for unimolecular dissociation have been inferred based on fragmentation patterns from tandem mass (MS/MS) spectra of source-formed ions of normal and isotopically labelled DMNB, and quantum chemical calculations. Both thermal and collisional activation studies suggest that the \[M+Na](+) adduct ions are significantly more stable toward dissociation than their protonated analogues and, as a consequence, the former provide attractive targets for detection by contemporary rapid screening methods such as desorption electrospray ionisation mass spectrometry. Copyright (C) 2009 Commonwealth of Australia. Published by John Wiley & Sons, Ltd
Development of an advanced on-line position-specific stable carbon isotope system and application to methyl tert-butyl ether

We present an advanced system for on-line position-specific carbon isotope analysis. The main limitation of on-line intramolecular isotope ratio measurements has been that optimal pyrolytic fragments are obtained mostly at temperatures where the analyte has not completely reacted. As a result of undetermined isotopic fractionation, the isotopic signatures of the pyrolysis products are not strictly equal to these of the equivalent moieties in the parent molecule. We designed a pyrolytic unit in which both temperature and reaction time are variable parameters, enabling determination of the enrichment factor of the pyrolysis at optimal temperature by construction of a Rayleigh plot. In the case of methyl tert-butyl ether (MTBE) presented here, a 'pre-pyrolysis' fractionation of MTBE leading to a depletion of 0.9 parts per thousand was discovered and the enrichment factor of the optimal pyrolysis reaction was determined at -1.7 parts per thousand. Absolute delta C-13 values of two functional groups of MTBE - the methoxy group and the 2-methylpropane group - could be determined with 95% confidence intervals of 0.4 parts per thousand and 0.5 parts per thousand, respectively
Simultaneous δ15N, δ13C and δ34S measurements of low-biomass samples using a technically advanced high sensitivity elemental analyzer connected to an isoptope ratio mass spectrometer

Conventional simultaneous CNS stable isotope abundance measurements of solid samples usually require high sample amounts, up to 1 mg carbon, to achieve exact analytical results. This rarely used application is often impaired by high C:S element ratios when organic samples are analyzed and problems such as incomplete conversion into sulphur dioxide occur during analysis. We introduce, as a technical innovation, a high sensitivity elemental analyzer coupled to a conventional isotope ratio mass spectrometer, with which CNS-stable isotope ratios can be determined simultaneously in samples with low carbon content (&lt;40 mu g C corresponding to similar to 100 mu g dry weight). The system includes downsized reactors, a temperature program-controlled gas chromatography (GC) column and a cryogenic trap to collect small amounts of sulphur dioxide. This modified application allows for highly sensitive measurements in a fully automated operation with standard deviations better than +/-0.47 parts per thousand for delta N-15 and delta S-34 and +/-0.12 parts per thousand for delta C-13 (n=127). Samples collected from one sampling site in a Baltic fjord within a short time period were measured with the new system to get a first impression of triple stable isotope signatures. The results confirm the potential of using delta S-34 as a stable isotope tracer in combination with delta N-15 and delta C-13 measurements to improve discrimination of food sources in aquatic food webs. Copyright (C) 2009 John Wiley &amp; Sons, Lt
Stable isotope analysis of dissolved organic carbon in soil solutions using a catalytic combustion TOC analyzer – IRMS with cryofocusing interface

Stable carbon isotopes are a powerful tool to assess the origin and dynamics of carbon in soils. However, direct analysis of the 13C/12C ratio in the dissolved organic carbon (DOC) pool has proved to be difficult. Recently, several systems have been developed to measure isotope ratios in DOC by coupling a total organic carbon (TOC) analyzer with an isotope ratio mass spectrometer. However these systems were designed for the analysis of fresh and marine water and no results for soil solutions or 13C-enriched samples have been reported. Because we mainly deal with soil solutions in which the difficult to oxidize humic and fulvic acids are the predominant carbon-containing components, we preferred to use thermal catalytic oxidation to convert DOC into CO2. We therefore coupled a high-temperature combustion TOC analyzer with an isotope ratio mass spectrometer, by trapping and focusing the CO2 cryogenically between the instruments. The analytical performance was tested by measuring solutions of compounds varying in the ease with which they can be oxidized. Samples with DOC concentrations between 1 and 100 mg C/L could be analyzed with good precision (standard deviation (SD) 0.6), acceptable accuracy, good linearity (overall SD = 1) and without significant memory effects. In a 13C-tracer experiment, we observed that mixing plant residues with soil caused a release of plant-derived DOC, which was degraded or sorbed during incubation. Based on these results, we are confident that this approach can become a relatively simple alternative method for the measurement of the 13C/12C ratio of DOC in soil solutions.status: publishe