pinecone/core-2020-05-10-deduplication huggingface dataset:
Laser desorption ionization time-of-flight mass spectrometry of erbium-doped Ga-Ge-Sb-S glasses.

International audienceRATIONALE: Rare earth-doped sulphide glasses in the Ga-Ge-Sb-S system present radiative emissions from the visible to the middle infrared range (mid-IR) range, which are of interest for a variety of applications including (bio)-chemical optical sensing, light detection, and military counter-measures. The aim of this work was to reveal structural motifs present during the fabrication of thin films by plasma deposition techniques as such knowledge is important for the optimization of thin film growth. METHODS: The formation of clusters in plasma plume from different concentrations of erbium-doped Ga5 Ge20 Sb10 S65 glasses (0.05, 0.1, and 0.5 wt. % of erbium) using laser (337 nm) desorption ionization (LDI) was studied by time-of-flight mass spectrometry (TOF MS) in both positive and negative ion mode. The stoichiometry of the Gam Gen Sbo Sp (+/-) clusters was determined via isotopic envelope analysis and computer modelling. RESULTS: Several Gam Gen Sbo Sp (+/-) singly charged clusters were found but, surprisingly, only four species (Sb3 S4 (+/-) , GaSb2 Sp (+/-) (p = 4, 5), Ga3 Sb2 S7 (+/-) ) were common to both ion modes. For the first time, species containing rare earths (GaSb2 SEr(+) and GaS6 Er2 (+) ) were identified in the plasma formed from rare earth-doped chalcogenide glasses, directly confirming the importance of gallium presence for rare earth bonding within the glassy matrix. CONCLUSIONS: The local structure of Ga-Ge-Sb-S glasses is at least partly different from the structure of species identified in plasma by mass spectrometry, as deduced from Raman scattering spectroscopy analysis; these glasses are mainly formed by [GeS4/2 ]/[GaS4/2 ] tetrahedra and [SbS3/2 ] pyramids. Extended X-ray absorption fine structure measurements show that Er(3+) ions in Ga-Ge-Sb-S glasses are surrounded by 7 sulphur atoms. Copyright © 2014 John Wiley & Sons, Ltd
Internal Energy Distribution in Electrospray Ionization from the Multiple-Collision Model: The case of a Thermal-Like Distribution

In the presented study, the ion survival yields of the theoretical mass spectra simulated by the MassKinetic software are fitted with the experimental ion survival yield of substituted benzylpyridinium cations reported in a precedent paper (J. Mass Spectrom. 1999, 34, 1373-1379).  A partially elastic multiple collision model is considered for describing the ion behaviour into the desolation area of the ESI source. The adjusting parameters are not the shape and the position of the P(Eint) curve but rather parameters related to the source acting, such as the pressure and the kinetic energy of ions entering the desolvation zone. In the case of a PE SCIEX ESI source interfaced with a quadrupole mass spectrometer, the energy uptake can then be well-defined by considering the case of a thermal-like distribution an average number of “effective” collisions of 29. From this model, it’s possible to correlate the voltage values applied on the orifice of the desolvation area to initial kinetic energy of ions entering into the collision zone of the ESI source. In the present case, these theoretical initial kinetic energy values range from 5.5 to 9 eV and the results of calculations shown also that the mean internal energy <Eint> increases linearly with the orifice voltage. This modelling allows defining the internal energy distribution of ions in different part of the ESI source. The activation conditions occurring into the studied ESI source can be compared to a warm-up of ions. Indeed, the internal energy distributions resemble to thermal distribution of ions having a “characteristic temperature” (Tchar) parameter between 1020 to 1550 K. In addition, this study evidences a linear correlation between <Eint> and Tchar. The slope value of this curve can be related to a calorimetric parameter such as the heat capacity of the activated substituted benzytlpyridinium cations
Mass spectral characterisation of a polar, esterified fraction of an organic extract of an oil sands process water.

RATIONALE: Characterising complex mixtures of organic compounds in polar fractions of heavy petroleum is challenging, but is important for pollution studies and for exploration and production geochemistry. Oil sands process-affected water (OSPW) stored in large tailings ponds by Canadian oil sands industries contains such mixtures. METHODS: A polar OSPW fraction was obtained by silver ion solid-phase extraction with methanol elution. This was examined by numerous methods, including electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) and ultra-high-pressure liquid chromatography (uHPLC)/Orbitrap MS, in multiple ionisation and MS/MS modes. Compounds were also synthesised for comparison. RESULTS: The major ESI ionisable compounds detected (+ion mode) were C15-28 SO3 species with 3-7 double bond equivalents (DBE) and C27-28 SO5 species with 5 DBE. ESI-MS/MS collision-induced losses were due to water, methanol, water plus methanol and water plus methyl formate, typical of methyl esters of hydroxy acids. Once the fraction was re-saponified, species originally detected by positive ion MS, could be detected only by negative ion MS, consistent with their assignment as sulphur-containing hydroxy carboxylic acids. The free acid of a keto dibenzothiophene alkanoic acid was added to an unesterified acid extract of OSPW in known concentrations as a putative internal standard, but attempted quantification in this way proved unreliable. CONCLUSIONS: The results suggest the more polar acidic organic SO3 constituents of OSPW include C15-28  S-containing, alicyclic and aromatic hydroxy carboxylic acids. SO5 species are possibly sulphone analogues of these. The origin of such compounds is probably via further biotransformation (hydroxylation) of the related S-containing carboxylic acids identified previously in a less polar OSPW fraction. The environmental risks, corrosivity and oil flow assurance effects should be easier to assess, given that partial structures are now known, although further identification is still needed
Identification of plasma protease derived metabolites of glucagon and their formation under typical laboratory sample handling conditions

This is the peer reviewed version of the following article: HOWARD, J.W. ...et al., 2015. Identification of plasma protease derived metabolites of glucagon and their formation under typical laboratory sample handling conditions. Rapid Communications in Mass Spectrometry, 29(2), pp. 171-181., which has been published in final form at http://dx.doi.org/10.1002/rcm.7090. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingCopyright © 2014 John Wiley & Sons, Ltd. RATIONALE Glucagon modulates glucose production, and it is also a biomarker for several pathologies. It is known to be unstable in human plasma, and consequently stabilisers are often added to samples, although these are not particularly effective. Despite this, there have not been any studies to identify in vitro plasma protease derived metabolites; such a study is described here. Knowledge of metabolism should allow the development of more effective sample stabilisation strategies. METHODS Several novel metabolites resulting from the incubation of glucagon in human plasma were identified using high-resolution mass spectrometry with positive electrospray ionisation. Tandem mass spectrometric (MS/MS) scans were acquired for additional confirmation using a QTRAP. Separation was performed using reversed-phase ultra-high-performance liquid chromatography. The formation of these metabolites was investigated during a time-course experiment and under specific stress conditions representative of typical laboratory handling conditions. Clinical samples were also screened for metabolites. RESULTS Glucagon < inf > 3-29 < /inf > and [pGlu] < sup > 3 < /sup > glucagon < inf > 3-29 < /inf > were the major metabolites detected, both of which were also present in clinical samples. We also identified two oxidised forms of [pGlu] < sup > 3 < /sup > glucagon < inf > 3-29 < /inf > as well as glucagon < inf > 19-29 < /inf > , or 'miniglucagon', along with the novel metabolites glucagon < inf > 20-29 < /inf > and glucagon < inf > 21-29 < /inf > . The relative levels of these metabolites varied throughout the time-course experiment, and under the application of the different sample handling conditions. Aprotinin stabilisation of samples had negligible effect on metabolite formation. CONCLUSIONS Novel plasma protease metabolites of glucagon have been confirmed, and their formation characterised over a time-course experiment and under typical laboratory handling conditions. These metabolites could be monitored to assess the effectiveness of new sample stabilisation strategies, and further investigations into their formation could suggest specific enzyme inhibitors to use to increase sample stability. In addition the potential of the metabolites to affect immunochemistry-based assays as a result of cross-reactivity could be investigated
Isotope fractionation factors controlling isotopocule signatures of soil-emitted N2O produced by denitrification processes of various rates

RATIONALEThis study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously. METHODSSoil incubations were performed under a He/O-2 atmosphere and the denitrification product ratio [N2O/(N-2+N2O)] was determined by direct measurement of N-2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine O-18, N-15 and N-15 site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects () of both N2O production and reduction, taking into account emissions from two distinct soil pools. RESULTSA clear relationship was observed between N-15 and O-18 isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller. CONCLUSIONSThe fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the O-18/N-15 ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions. Copyright (c) 2014 John Wiley & Sons, Ltd
Archaeological bone lipids as palaeodietary markers

Rationale Stable isotope analysis of archaeological and fossil bone samples can provide important insights into past environments, ecologies and diets. Previous studies have focused on stable carbon and nitrogen isotopes in bone collagen, or carbon isotopes in bone mineral (bioapatite). Carbon isotope analysis of lipids from archaeological bone has received much less attention, partly due to the lack of suitable methodologies allowing sufficient recovery of compounds for structural and isotopic characterisation. Here we show that lipids can be easily and reliably recovered from archaeological bone using a modified protocol, and that these provide complementary dietary information to other bone components. Methods Human and animal bones were obtained from a variety of archaeological contexts. Lipids were sequentially extracted using solvent extraction (dichloromethane/methanol), followed by acidified methanol extraction (methanol/H2SO4). The lipids were then analysed by gas chromatography/mass spectrometry (GC/MS) and gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). Results Appreciable amounts of endogenous lipid were recovered from archaeological bone. Importantly, a comparison between compound-specific and bulk collagen isotopic data shows that archaeological bone lipids reflect dietary input and can be used to distinguish between marine and terrestrial consumers, as well as between C3 and C4 plant consumers. Furthermore, the presence of essential fatty acids directly incorporated from diet to bone may provide additional palaeodietary information. Conclusions Our findings suggest that archaeological bone lipids are a hitherto untapped resource of dietary information that offer additional insights to those gained from other isotopic analyses of bone
Methods of lipid-normalization for multi-tissue stable isotope analyses in tropical tuna

International audienceRATIONALE: The bias associated with lipid contents in fish tissues is a recalcitrant topic for trophic studies using stableisotopes. Lipids are depleted in the heavy carbon isotope (13C) and the lipid content varies considerably among species,tissues and in both time and space. We have applied and assessed different correction methods for tropical tuna tissues.METHODS:We tested two types of normalization methods to deal with variable lipid content in liver, gonads, and whiteand red muscles of yellowfin, bigeye and skipjack tuna: a chemical extraction using dichloromethane and a mathematicalcorrection based on three modeling approaches (linear, non-linear and mass balance models). We measured isotopicratios of bulk and lipid-free tissues and assessed the predictive ability of the correction models with the lipid-freemeasurements. The parameters of the models were estimated from our dataset and from results from published studieson other species.RESULTS: Comparison between bulk, lipid-free and lipid-corrected isotopic ratios demonstrated that (1) chemicalextraction using dichloromethane did not affect δ15N values; (2) the change in δ13C values after extraction was tissuespecific;(3) lipid-normalization models using published parameter estimates failed to predict lipid-corrected δ13C values;and (4) linear and non-linear models using parameters estimated for each tissue from our dataset provided accurate δ13Cpredictions for all tissues, and mass balance model for white muscle only.CONCLUSIONS: Models using published estimates for parameters from other species cannot be used. Based on a rangeof lipid content that do not exceed 45%, we recommend the linear model to correct the bulk δ13C values in theinvestigated tissues but the parameters have to be estimated from a proportion of the original data for which chemicalextraction is required and the isotopic values of bulk and lipid-free tissues are measured
Analysis of stable isotope ratios in blood of tracked wandering albatrosses fails to distinguish a δ13C gradient within their winter foraging areas in the southwest Atlantic Ocean

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The main limitation of isotopic tracking for inferring distribution is the lack of detailed reference maps of the isotopic landscape (i.e. isoscapes) in the marine environment. Here, we attempt to map the marine δ13C isoscape for the southwestern sector of the Atlantic Ocean, and assess any temporal variation using the wandering albatross as a model species.\ud
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Methods\ud
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Tracking data and blood and diet samples were collected monthly from wandering albatrosses rearing chicks at Bird Island, South Georgia, during the austral winter between May and October 2009. The δ13C and δ15N values were measured by mass spectrometry in plasma and blood cells, and related to highly accurate data on individual movements and feeding activity obtained using three types of device: GPS, activity (immersion) loggers and stomach temperature probes.\ud
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Results\ud
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The tracked birds foraged in waters to the north or northwest of South Georgia, including the Patagonian shelf-break, as far as 2000 km from the colony. The foraging region encompassed the two main fronts in the Southern Ocean (Polar and Subantarctic fronts). The δ13C values varied by only 2.1 ‰ in plasma and 2.5 ‰ in blood cells, and no relationships were found between the δ13C values in plasma and the mean latitude or longitude of landings or feeding events of each individual.\ud
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Conclusions\ud
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The failure to distinguish a major biogeographic gradient in δ13C values suggest that these values in the south Atlantic Ocean are fairly homogeneous. There was no substantial variation among months in either the δ13C or the δ15N values of plasma or blood cells of tracked birds. As birds did not show a significant change in diet composition or foraging areas during the study period, these results provide no evidence for major temporal variation in stable isotope ratios in consumer tissues, or in the regional marine isoscape in the austral winter of 2009
An improved 15N tracer approach to study denitrification and nitrogen turnover in soil incubations

Rationale: Denitrification (the reduction of oxidized forms of inorganic N to N2O and N2) from upland soils is considered to be the least well understood process in the global N cycleDenitrification from upland soils is considered to be the least well understood process in the global N cycle due to methodical constraints of existing methods. . The main reason for this lack of understanding is that the terminal product (N2) of denitrification is extremely difficult to measure against the hugelarge atmospheric background.\ud
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Methods: Here wWe describe a system that combines the 15N-tracer technique with a 40-fold reduced N2 (2 % v/v) atmosphere in a fully automated incubation set up for direct quantification of N2 and N2O emissions. The system was tested on a pasture soil from sub-tropical Australia under different soil moisture conditions and combined with 15N tracing in extractable soil N pools to establish a full N balance. \ud
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Results: The method proved to be highly sensitive for detecting N2 (1.12 µg N h-1 kg-1ds1 dry soil (ds)) and N2O (0.36 µg N h-1 kg 1 ds) emissions. The main end-product of denitrification in the investigated soil was N2O for both water contents with N2 accounting for only 3% to13% of the total denitrification losses. Between 90-95% of the added 15N fertiliser could be recovered in N gases and extractable soil N pools. \ud
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Conclusions: These high and N2O-dominated denitrification rates found in this study are pointing at both a high ecological and agronomic importance of denitrification in subtropical pasture soils. The new system allows for a direct and highly sensitive detection of N2 and N2O fluxes from soils and may help to significantly improve our mechanistic understanding of N cycling and denitrification in terrestrial agro-ecosystems
Characterization of 2,3-diarylxanthones by electrospray mass spectrometry: gas-phase chemistry versus known antioxidant activity properties

Xanthones (XH) are a class of heterocyclic compounds widely distributed in nature that hold numerous noteworthy biological and antioxidant activities. Therefore, it is of utmost importance to achieve relevant detailed structural information to understand and assist prediction of their biological properties. The potential relationship between radical-mediated xanthone chemistry in the gas phase and their promising antioxidant activities has not been previously explored.Thanks are due to Fundação para a Ciência e Tecnologia (FCT,
Portugal), European Union, QREN, FEDER and COMPETE,
for funding the QOPNA research unit (project PEst-C/QUI/UI0062/2013; FCOMP-01-0124-FEDER-037296), and the Portuguese National Mass Spectrometry Network, RNEM (REDE/1504/REM/2005). E. M. P. Silva is also grateful to FCT (ref SFRH/BPD/66961/2009) for a Post-Doc grant.info:eu-repo/semantics/publishedVersio
Characterisation of phosphorylated nucleotides by collisional and electron-based tandem mass spectrometry.

Rationale:\ud
Tandem mass spectrometry of phosphorylated ions can often yield a limited number of product ions owing to the labile nature of phosphate groups. Developing techniques to improve dissociation for this type of ion has implications for the structural characterisation of many different phosphorylated ions, such as those from nucleotides, pharmaceutical compounds, peptides and polymers.\ud
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Methods:\ud
Solutions of adenosine monophosphate, diphosphate and triphosphate (AMP, ADP and ATP) were studied in a hybrid linear ion trap–Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Precursor ions with an overall single positive charge, including protonated nucleotides or nucleotide cations containing one, two or three sodium atoms, were isolated for tandem mass spectrometry. Collision-induced dissociation (CID) was performed in the linear ion trap, with electron-induced dissociation (EID) being conducted in the FTICR cell.\ud
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Results:\ud
EID resulted in many product ions not seen in CID. EID product ion spectra were seen to vary for AMP, ADP and ATP when the nucleotide cation contained zero, one, two or three sodiums. Precursor cations that contain two or three sodiums mainly formed product ions derived from the phosphate group. Conversely, when a precursor ion containing no sodium underwent EID, product ions mainly relating to the non-phosphate end of the ion were observed. The number of phosphate groups was not seen to greatly affect either CID or EID product ion spectra.\ud
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Conclusions:\ud
The presence of sodium in a precursor ion directs electron-induced bond dissociation, thus enabling targeted, and therefore tuneable, fragmentation of groups within that precursor ion. For all precursor ions, the most useful product ion spectra were obtained by EID for a precursor ion containing one sodium, with bond dissociation occurring across the entire nucleotide cation. The findings of this study can be used to improve the structural elucidation of many phosphorylated molecules by broadening the range of product ions achievable