pinecone/core-2020-05-10-deduplication huggingface dataset:
Preventing false negatives with high-resolution mass spectrometry: the benzophenone case

Benzophenone (BP) is one of the many contaminants reported as present in foodstuff due to its migration from food packaging materials. Liquid chromatography tandem mass spectrometry (LC-MS/MS) is acknowledged in the literature as the method of choice for this analysis. However, cases have been reported where the use of this methodology was not enough to unambiguously confirm the presence of a contaminant. In previous work performed by the authors, the unequivocal identification of BP in packaged foods was not possible even when monitoring two m/z transitions, since ion ratio errors higher than 20% were obtained. In order to overcome this analytical problem a fast, sensitive and selective liquid chromatography-high resolution-mass spectrometry (LC-HRMS) methodology has been developed and applied to the analysis of BP in packaged foods. A direct comparison between liquid chromatography high resolution mass spectrometry (LC-HRMS) and LC-MS/MS data indicated better selectivity when working with LC-HRMS at a resolving power of 50,000 FWHM than when monitoring two m/z transitions by LC-MS/MS. The resolving power used enabled the detection and identification of Harman as the compound impeding the confirmation of BP by LC-MS/MS. Similar quantitative results were obtained by an Orbitrap mass analyser (Exactive ¿) and a triple quadrupole mass analyser (TSQ Quantum Ultra AM ¿)
MALDI-TOFMS for phycotoxins detection in microalgae whole cells

Rapid and sensitive methods for identification of several phycotoxins produced by\ud
microalgae species such as Yessotoxins (YTXs) for Protoceratium reticulatum, Okadaic\ud
acid (OA) and Pectenotoxins (PTXs) for Prorocentrum spp. and Dinophysis spp.,\ud
Palytoxins (PLTXs) for Ostreopsis spp., Ciguatoxins (CTXs) for Gambierdiscus spp. or\ud
Domoic acid (DA) for Pseudo-nitzschia spp. are of great importance to shellfish and\ud
fish industry. In this study, matrix-assisted laser desorption/ionization time-of-flight\ud
mass spectrometry (MALDI-TOFMS) was used to detect several phycotoxins in whole\ud
cells of some microalgae which are known as toxin producers. To achieve an\ud
appropriate MALDI matrix and a sample preparation method, several matrices and\ud
solvent mixtures were tested. The most appropriate matrix system for toxin detection\ud
was obtained with 10 μg μL-1 of DHB in 0.1 % TFA:ACN (3:7, v/v) by mixing the\ud
intact cells with the matrix solution directly on the MALDI target (dried-droplet\ud
technique). Toxin detection by this procedure is much faster than up-to-now procedures\ud
based on solvent extraction and chromatographic separation. This method allowed the\ud
rapid detection of main phycotoxins in some dinoflagellate cells of genus Ostreopsis,\ud
Prorocentrum, Protoceratium, Gambierdiscus, Dinophysis and diatoms from Pseudonitzschia\ud
genus.This work was finding by projects EBITOX (Study of the biological and toxicological\ud
aspects of benthic dinoflagellates associated with risks to human health) CTQ 2008-06754-C04-04 and CCVIEO (Culture Collection at the Instituto Español de\ud
Oceanografía in Vigo, Spain).Peer reviewe
Charge state dependent top-down characterisation using electron transfer dissociation

The dissociation of protein ions (5–30 kDa) as a function of charge state has been explored in order to suggest the optimal charge state range for top-down sequencing. Proteins were generated under denaturing conditions and their charge states were modified via ion/ion proton transfer reactions prior to dissociation. Electron transfer dissociation (ETD) data suggested optimal sequence coverage for charge states in the m/z range from 700 to 950 while limited sequence coverage was noted when the precursor m/z was above 1000. Sequence coverage from ETD data was found to be dependent on protein size, with smaller proteins having better sequence coverage. An observed depletion in sequence-related information was mainly attributed to limited instrument (ion trap) performance (m/z range and resolution). For a combined ETD/collision-induced dissociation (CID) approach it is difficult to propose an optimal m/z range since good sequence coverage for CID is at intermediate charge states and the optimal m/z range increases with protein size. When only one charge state can be analysed in a combined ETD/CID approach, a range around 950 m/z is suggested as a starting point. Alternatively, two charge states should be explored, each optimal for either ETD or CID. Overall, these suggestions should be useful to achieve enhanced characterisation of smaller proteins/ large protein fragments (generated from denaturing solutions) in minimal analysis times
Direct detection of additives and degradation products from polymers by liquid extraction surface analysis employing chip-based nanospray mass spectrometry

RATIONALE: Polymer-based surface coatings in outdoor applications experience accelerated degradation due to exposure to solar radiation, oxygen and atmospheric pollutants. These deleterious agents cause undesirable changes to the aesthetic and mechanical properties of the polymer, reducing its lifetime. The use of antioxidants such as hindered amine light stabilisers (HALS) retards these degradative processes; however, mechanisms for HALS action and polymer degradation are poorly understood. \ud
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METHODS: Detection of the HALS TINUVINW123 (bis(1-octyloxy-2,2,6,6-tetramethyl-4-piperidyl) sebacate) and the polymer degradation products directly from a polyester-based coil coating was achieved by liquid extraction surface analysis (LESA) coupled to a triple quadrupole QTRAPW 5500 mass spectrometer. The detection of TINUVINW123 and melamine was confirmed by the characteristic fragmentation pattern observed in LESA-MS/MS spectra that was identical to that reported for authentic samples. \ud
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RESULTS: Analysis of an unstabilised coil coating by LESA-MS after exposure to 4 years of outdoor field testing revealed the presence of melamine (1,3,5-triazine-2,4,6-triamine) as a polymer degradation product at elevated levels. Changes to the physical appearance of the coil coating, including powder-like deposits on the coating's surface, were observed to coincide with melamine deposits and are indicative of the phenomenon known as polymer ' blooming'. \ud
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CONCLUSIONS: For the first time, in situ detection of analytes from a thermoset polymer coating was accomplished without any sample preparation, providing advantages over traditional extraction-analysis approaches and some contemporary ambient MS methods. Detection of HALS and polymer degradation products such as melamine provides insight into the mechanisms by which degradation occurs and suggests LESA-MS is a powerful new tool for polymer analysis. Copyright (C) 2012 John Wiley & Sons, Ltd
Isotopic values of the Amazon headwaters in Peru: comparison of the wet upper Río Madre de Dios watershed with the dry Urubamba-Apurimac river system

RATIONALE: The Amazon River is a huge network of long tributaries, and little is known about the headwaters. Here we present a study of one wet tropical Amazon forest side, and one dry and cold Atiplano plateau, originating from the same cordillera. The aim is to see how this difference affects the water characteristics. METHODS: Different kind of water (spring, lake, river, rainfall) were sampled to determine their stable isotopes ratios (oxygen 18/16 and hydrogen 2/1) by continuous flow isotope ratio mass spectrometry (IRMS). These ratios coupled with chemical analysis enabled us to determine the origin of the water, the evaporation process and the water recycling over the Amazon plain forest and montane cloud forest. RESULTS: Our study shows that the water flowing in the upper Madre de Dios basin comes mainly from the foothill humid forest, with a characteristic water recycling process signature, and not from higher glacier melt. On the contrary, the water flowing in the Altiplano Rivers is mainly from glacier melts, with a high evaporation process. This snow and glacier are fed mainly by Atlantic moisture which transits over the large Amazon forest. CONCLUSIONS: The Atlantic moisture and its recycling over this huge tropical forest display a progressive isotopic gradient, as a function of distance from the ocean. At the level of the montane cloud forest and on the altiplano, respectively, additional water recycling and evaporation occur, but they are insignificant in the total water discharge
Stable isotope switching (SIS): a new stable isotope probing (SIP) approach to determine carbon flow in the soil food web and dynamics in organic matter pools

RATIONALE: Recent advances in stable isotope probing (SIP) have allowed direct linkage of microbial population structure and function. This paper details a new development of SIP, Stable Isotope Switching (SIS), which allows the simultaneous assessment of carbon (C) uptake, turnover and decay, and the elucidation of soil food webs within complex soils or sedimentary matrices.\ud
METHODS: SIS utilises a stable isotope labelling approach whereby the 13C-labelled substrate is switched part way through the incubation to a natural abundance substrate. A 13CH4 SIS study of landfill cover soils from Odcombe (Somerset, UK) was conducted. Carbon assimilation and dissimilation processes were monitored through bulk elemental analysis isotope ratio mass spectrometry and compound-specific gas chromatography/combustion/isotope ratio mass spectrometry, targeting a wide range of biomolecular components including: lipids, proteins and carbohydrates.\ud
RESULTS: Carbon assimilation by primary consumers (methanotrophs) and sequential assimilation into secondary (Gram-negative and -positive bacteria) and tertiary consumers (Eukaryotes) was observed. Up to 45% of the bacterial membrane lipid C was determined to be directly derived from CH4 and at the conclusion of the experiment ca. 50% of the bulk soil C derived directly from CH4 was retained within the soil.\ud
CONCLUSIONS: This is the first estimate of soil organic carbon derived from CH4 and it is comparable with levels observed in lakes that have high levels of benthic methanogenesis. SIS opens the way for a new generation of SIP studies aimed at elucidating total C dynamics (incorporation, turnover and decay) at the molecular level in a wide range of complex environmental and biological matrices
Carbon isotopic (C-13 and C-14) composition of synthetic estrogens and progestogens

RATIONALE:

Steroids are potent hormones that are found in many environments. Yet, contributions from synthetic and endogenous sources are largely uncharacterized. The goal of this study was to evaluate whether carbon isotopes could be used to distinguish between synthetic and endogenous steroids in wastewater and other environmental matrices.
METHODS:

Estrogens and progestogens were isolated from oral contraceptive pills using semi-preparative liquid chromatography/diode array detection (LC/DAD). Compound purity was confirmed by gas chromatography/flame ionization detection (GC/FID), gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS) and liquid chromatography/mass spectrometry using negative electrospray ionization (LC/ESI-MS). The 13C content was determined by gas chromatography/isotope ratio mass spectrometry (GC/IRMS) and 14C was measured by accelerator mass spectrometry (AMS).
RESULTS:

Synthetic estrogens and progestogens are 13C-depleted (δ13Cestrogen = –30.0 ± 0.9 ‰; δ13Cprogestogen = –30.3 ± 2.6 ‰) compared with endogenous hormones (δ13C ~ –16 to –26 ‰). The 14C content of the majority of synthetic hormones is consistent with synthesis from C3 plant-based precursors, amended with 'fossil' carbon in the case of EE2 and norethindrone acetate. Exceptions are progestogens that contain an ethyl group at carbon position 13 and have entirely 'fossil' 14C signatures.
CONCLUSIONS:

Carbon isotope measurements have the potential to distinguish between synthetic and endogenous hormones in the environment. Our results suggest that 13C could be used to discriminate endogenous from synthetic estrogens in animal waste, wastewater effluent, and natural waters. In contrast, 13C and 14C together may prove useful for tracking synthetic progestogens. Copyright © 2012 John Wiley & Sons, Ltd.Martin Family Society of Fellows for SustainabilityUnited States. Environmental Protection Agency (STAR Graduate Fellowship FP-91713401
Precision and long-term stability of clumped-isotope analysis of CO2 using a small-sector isotope ratio mass spectrometer

RATIONALE The ratio of the measured abundance of 13C18O bonding CO2 to its stochastic abundance, prescribed by the delta 13C and delta 18O values from a carbonate mineral, is sensitive to its growth temperature. Recently, clumped-isotope thermometry, which uses this ratio, has been adopted as a new tool to elucidate paleotemperatures quantitatively. METHODS Clumped isotopes in CO2 were measured with a small-sector isotope ratio mass spectrometer. CO2 samples digested from several kinds of calcium carbonates by phosphoric acid at 25 degrees C were purified using both cryogenic and gas-chromatographic separations, and their isotopic composition (delta 13C, delta 18O, Delta 47, Delta 48 and Delta 49 values) were then determined using a dual-inlet Delta XP mass spectrometer. RESULTS The internal precisions of the single gas Delta 47 measurements were 0.005 and 0.02 parts per thousand (1 SE) for the optimum and the routine analytical conditions, respectively, which are comparable with those obtained using a MAT 253 mass spectrometer. The long-term variations in the Delta 47 values for the in-house working standard and the heated CO2 gases since 2007 were close to the routine, single gas uncertainty while showing seasonal-like periodicities with a decreasing trend. Unlike the MAT 253, the Delta XP did not show any significant relationship between the Delta 47 and delta 47 values. CONCLUSIONS The Delta XP gave results that were approximately as precise as those of the MAT 253 for clumped-isotope analysis. The temporal stability of the Delta XP seemed to be lower, although an advantage of the Delta XP was that no dependency of delta 47 on Delta 47 was found. Copyright (c) 2012 John Wiley & Sons, Ltd
Novel laser spectroscopic technique for continuous analysis of N2O isotopomers - application and intercomparison with isotope ratio mass spectrometry

RATIONALE Nitrous oxide (N2O), a highly climate-relevant trace gas, is mainly derived from microbial denitrification and nitrification processes in soils. Apportioning N2O to these source processes is a challenging task, but better understanding of the processes is required to improve mitigation strategies. The N2O site-specific 15?N signatures from denitrification and nitrification have been shown to be clearly different, making this signature a potential tool for N2O source identification. We have applied for the first time quantum cascade laser absorption spectroscopy (QCLAS) for the continuous analysis of the intramolecular 15?N distribution of soil-derived N2O and compared this with state-of-the-art isotope ratio mass spectrometry (IRMS). METHODS Soil was amended with nitrate and sucrose and incubated in a laboratory setup. The N2O release was quantified by FTIR spectroscopy, while the N2O intramolecular 15?N distribution was continuously analyzed by online QCLAS at 1?Hz resolution. The QCLAS results on time-integrating flask samples were compared with those from the IRMS analysis. RESULTS The analytical precision (2 sigma) of QCLAS was around 0.3 parts per thousand for the delta 15Nbulk and the 15?N site preference (SP) for 1-min average values. Comparing the two techniques on flask samples, excellent agreement (R2?=?0.99; offset of 1.2 parts per thousand) was observed for the delta 15Nbulk values while for the SP values the correlation was less good (R2?=?0.76; offset of 0.9 parts per thousand), presumably due to the lower precision of the IRMS SP measurements. CONCLUSIONS These findings validate QCLAS as a viable alternative technique with even higher precision than state-of-the-art IRMS. Thus, laser spectroscopy has the potential to contribute significantly to a better understanding of N turnover in soils, which is crucial for advancing strategies to mitigate emissions of this efficient greenhouse gas. Copyright (c) 2012 John Wiley & Sons, Ltd
Rapid differentiation of isomeric lipids by photodissociation mass spectrometry of fatty acid derivatives

RATIONALE Both traditional electron ionization and electrospray ionization tandem mass spectrometry have demonstrated limitations in the unambiguous identification of fatty acids. In the former case, high electron energies lead to extensive dissociation of the radical cations from which little specific structural information can be obtained. In the latter, conventional collision-induced dissociation (CID) of even-electron ions provides little intra-chain fragmentation and thus few structural diagnostics. New approaches that harness the desirable features of both methods, namely radical-driven dissociation with discrete energy deposition, are thus required. METHODS Herein we describe the derivatization of a structurally diverse suite of fatty acids as 4-iodobenzyl esters (FAIBE). Electrospray ionization of these derivatives in the presence of sodium acetate yields abundant [M+Na]+ ions that can be mass-selected and subjected to laser irradiation (=266nm) on a modified linear ion-trap mass spectrometer. RESULTS Photodissociation (PD) of the FAIBE derivatives yields abundant radical cations by loss of atomic iodine and in several cases selective dissociation of activated carboncarbon bonds (e.g., at allylic positions) are also observed. Subsequent CID of the [M+NaI]center dot+ radical cations yields radical-directed dissociation (RDD) mass spectra that reveal extensive carboncarbon bond dissociation without scrambling of molecular information. CONCLUSIONS Both PD and RDD spectra obtained from derivatized fatty acids provide a wealth of structural information including the position(s) of unsaturation, chain-branching and hydroxylation. The structural information obtained by this approach, in particular the ability to rapidly differentiate isomeric lipids, represents a useful addition to the lipidomics tool box. Copyright (c) 2013 John Wiley & Sons, Ltd
Isotopic evidence of limited exchange between Mediterranean and eastern North Atlantic fin whales

RATIONALE The relationship between stocks of fin whales inhabiting the temperate eastern North Atlantic and the Mediterranean Sea is subject to controversy. The use of chemical markers facilitates an alternative insight into population structure and potential borders between stocks because the two areas present dissimilar isotopic baselines. METHODS Baleen plates, composed of inert tissue that keeps a permanent chronological record of the isotopic value of body circulating fluids, were used to investigate connectivity and boundaries between the stocks. Values were determined by continuous flow isotope ratio mass spectrometry. RESULTS Stable isotopes confirm that, while the two subpopulations generally forage in well-differentiated grounds, some individuals with characteristic Atlantic values do penetrate into the Mediterranean Sea up to the northernmost latitudes of the region. As a consequence, the border between the two putative subpopulations may be not as definite as previous acoustic investigations suggested. The discriminant function obtained in this study may assist researchers to use baleen plate isotopic data to assign the origin of fin whales of uncertain provenance. CONCLUSIONS This study strengthens the stock subdivision currently accepted for management and conservation while recognizes a low level of exchange between the Mediterranean and temperate eastern North Atlantic subdivisions. Copyright © 2013 John Wiley & Sons, Ltd.Peer Reviewe
The quantitative surface analysis of an antioxidant additive in a lubricant oil matrix by desorption electrospray ionization mass spectrometry

This is an Open Access Article. It is published by John Wiley and Sons under the Creative Commons Attribution 3.0 Unported Licence (CC BY). Full details of this licence are available at: http://creativecommons.org/licenses/by/3.0/Rationale Chemical additives are incorporated into commercial lubricant oils to modify the physical and chemical properties of the lubricant. The quantitative analysis of additives in oil-based lubricants deposited on a surface without extraction of the sample from the surface presents a challenge. The potential of desorption electrospray ionization mass spectrometry (DESI-MS) for the quantitative surface analysis of an oil additive in a complex oil lubricant matrix without sample extraction has been evaluated. Methods The quantitative surface analysis of the antioxidant additive octyl (4-hydroxy-3,5-di-tert-butylphenyl)propionate in an oil lubricant matrix was carried out by DESI-MS in the presence of 2-(pentyloxy)ethyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate as an internal standard. A quadrupole/time-of-flight mass spectrometer fitted with an in-house modified ion source enabling non-proximal DESI-MS was used for the analyses. RESULTS An eight-point calibration curve ranging from 1 to 80 μg/spot of octyl (4-hydroxy-3,5-di-tert-butylphenyl)propionate in an oil lubricant matrix and in the presence of the internal standard was used to determine the quantitative response of the DESI-MS method. The sensitivity and repeatability of the technique were assessed by conducting replicate analyses at each concentration. The limit of detection was determined to be 11 ng/mm additive on spot with relative standard deviations in the range 3-14%. CONCLUSIONS The application of DESI-MS to the direct, quantitative surface analysis of a commercial lubricant additive in a native oil lubricant matrix is demonstrated
Diamondoid diacids ('O4' species) in oil sands process-affected water.

RATIONALE: As a by-product of oil sands extraction, large volumes of oil sands process water (OSPW) are generated, which are contaminated with a large range of water-soluble organic compounds. The acids are thought to be derived from hydrocarbons via natural biodegradation pathways such as α- and β-oxidation of alkyl substituents, which could produce mono- and diacids, for example. However, while several monoacids ('O2' species) have been identified, the presence of diacids (i.e. 'O4' species) has only been deduced from results obtained via Fourier transform infrared (FTIR) spectroscopy, Fourier transform ion cyclotron resonance high-resolution mass spectrometry (FTICR-HRMS) and nuclear magnetic resonance ((1)H-NMR) spectroscopy and the structures have never been confirmed. METHODS: An extract of an OSPW from a Canadian tailings pond was analysed and the retention times and the electron ionization mass spectra of some analytes were compared with those of bis-methyl esters of authentic diacids by gas chromatography × gas chromatography/time-of-flight mass spectrometry (GCxGC/TOFMS) in nominal and accurate mass configurations. RESULTS: Two diamondoid diacids (3-carboxymethyladamantane-1-carboxylic acid and adamantane-1,3-dicarboxylic acid) were firmly identified as their bis-methyl esters by retention time and mass spectral matching and several other structural isomers were more tentatively assigned. Diacids have substantially increased polarity over the hydrocarbon and monoacid species from which they probably derive: as late members of biodegradation processes they may be useful indicators of weathering and ageing, not only of OSPW, but potentially of crude oil residues more generally. CONCLUSIONS: Structures of O4 species in OSPW have been identified. This confirms pathways of microbial biodegradation, which were only postulated previously, and may be a further indication that remediation of OSPW toxicity can occur by natural microbial action. The presence and abundance of these diacids might therefore be useful as a measure of biodegradation and weathering