pinecone/core-2020-05-10-deduplication huggingface dataset:
Secreted proteome of the murine multipotent hematopoietic progenitor cell line DKmix

Administration of the multipotent hematopoietic progenitor cell (HPC) line DKmix improved cardiac function after myocardial infarction and accelerated dermal wound healing due to paracrine mechanisms. The aim of this study was to analyse the secreted proteins of DKmix cells in order to identify the responsible paracrine factors and assess their relevance to the wide spectrum of therapeutic effects. A mass spectrometry (MS)-based approach was used to identify secreted proteins of DKmix cells. Serum free culture supernatants of DKmix-conditioned medium were collected and the proteins present were separated, digested by trypsin and the resulting peptides were then analyzed by matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) MS. Overall 95 different proteins were identified. Among them, secretory proteins galectin-3 and gelsolin were identified. These proteins are known to stimulate cell migration and influence wound healing and cardiac remodelling. The remaining proteins originate from intracellular compartments like cytoplasm (69%), nucleus (12%), mitochondria (4%), and cytoplasmic membrane (3%) indicating permeable or leaky DKmix cells in the conditioned medium. Additionally, a sandwich immunoassay was used to detect and quantify cytokines and chemokines. Interleukin-6 (IL-6), interleukin-13 (IL-13), monocyte-chemoattractant protein-1 (MCP-1), monocyte-chemoattractant protein-3 (MCP-3), monocyte-chemoattractant protein-1alpha (MIP-1alpha) and monocyte-chemoattractant protein-1beta (MIP-1beta) were detected in low concentrations. This study identified a subset of proteins present in the DKmix-conditioned medium that act as paracrine modulators of tissue repair. Moreover, it suggests that DKmix-derived conditioned medium might have therapeutic potency by promoting tissue regeneration
Selective linkage detection of O-sialoglycan isomers by negative electrospray ionization ion trap tandem mass spectrometry

9 páginas, 6 figuras, 2 esquemas.-- El pdf del artículo es la versión de autor.Sialylated O-linked oligosaccharides are involved in many biological processes, such as cell-cell interactions, cell-substance adhesion, and virus-host interactions. These activities depend on their structure, which is frequently determined by tandem mass spectrometry. However, these spectra are frequently analyzer-dependent, which makes it difficult to develop widely applicable analytical methods. In order to deepen the origin of this behavior, two couples of isomers of sialylated O-linked oligosaccharides, NeuAcα2-3Galβ1-3GalNAc-ol/Galβ1-3(NeuAcα2-6)GalNAc-ol and NeuGcα2-3Galβ1-3GalNAc-ol/Galβ1-3(NeuGcα2-6)GalNAc-ol, were analyzed by liquid chromatography/negative electrospray ionization ion trap tandem mass spectrometry (LC/ESI(−)-MSn) using both an ion trap and a triple quadrupole mass spectrometer. Results clearly showed that while ions obtained in the triple quadrupole instrument fitted very well with the standard fragmentation routes, in the ion trap several intense ions could not be explained by these rules, specially a fragment at m/z 597. Furthermore, this ion was observed in the mass spectrum of those isomers that sialic acid binds to GalNAc by an α2-6 linkage. From the MS3 spectrum of this ion an unexpected structure was deduced, and it led to propose alternative fragmentation pathways. Molecular mechanics calculations suggested that the found atypical route could be promoted by a hydrogen bond located only in α2-6-linked oligosaccharides. It has also been demonstrated that this process follows a slow kinetic, explaining why it cannot be observed using an ion beam-type mass analyzer. In conclusion, ion traps seem to be more appropriate than triple quadrupoles to develop a reliable analytical method to distinguish between isomeric O-linked glycans.Financial\ud
support was obtained from projects ANALISYC S-0505/\ud
AGR/000312 from the Comunidad de Madrid, Consolider\ud
Ingenio 2010 (FUN-C-FOOD); CSD 2007-00063 from the\ud
Ministerio de Educación y Ciencia; and PIF-SIALOBIOTIC\ud
200870F010-1 and -2 from CSIC.Peer reviewe
Development of a targeted adductomic method for the determination of polycyclic aromatic hydrocarbon DNA adducts using online column-switching liquid chromatography/tandem mass spectrometry

This is the pre-peer reviewed version of the following article: Rapid Communications in Mass Spectrometry, 2010, 24 (16), pp. 2329-2340, which has been published in final form at  www3.interscience.wiley.com, Doi: 10.1002/rcm.4645Human exposure to polycyclic aromatic hydrocarbons (PAHs) from sources such as industrial or urban air pollution, tobacco smoke and cooked food is not confined to a single compound, but instead to mixtures of different PAHs. The interaction of different PAHs may lead to additive, synergistic or antagonistic effects in terms of DNA adduct formation and carcinogenic activity resulting from changes in metabolic activation to reactive intermediates and DNA repair. The development of a targeted DNA adductomic approach using liquid chromatography/tandem mass spectrometry (LC/MS/MS) incorporating software-based peak picking and integration for the assessment of exposure to mixtures of PAHs is described. For method development PAH-modified DNA samples were obtained by reaction of the anti-dihydrodiol epoxide metabolites of benzo[a]pyrene, benzo[b]fluoranthene, dibenzo[a,l]pyrene (DB[a,l]P) and dibenz[a,h]anthracene with calf thymus DNA in vitro and enzymatically hydrolysed to 2 -deoxynucleosides. Positive LC/electrospray ionisation (ESI)-MS/MS collision-induced dissociation product ion spectra data showed that the majority of adducts displayed a common fragmentation for the neutral loss of 116 u (2 -deoxyribose) resulting in a major product ion derived from the adducted base. The exception was the DB[a,l]P dihydrodiol epoxide adduct of 2 -deoxyadenosine which resulted in major product ions derived from the PAH moiety being detected. Specific detection of mixtures of PAH-adducted 2 -deoxynucleosides was achieved using online column-switching LC/MS/MS in conjunction with selected reaction monitoring (SRM) of the [M+H]+ to [M+H-116]+ transition plus product ions derived from the PAH moiety for improved sensitivity of detection and a comparison was made to detection by constant neutral loss scanning. In conclusion, different PAH DNA adducts were detected by employing SRM [M+H-116]+ transitions or constant neutral loss scanning. However, for improved sensitivity of detection optimised SRM transitions relating to the PAH moiety product ions are required for certain PAH DNA adducts for the development of targeted DNA adductomic methods
Energetics of fragmentation for cationized poly(ethylene glycol) oligomers.

International audienceThere are various difficulties studying macromolecular systems. One on these is that the applicable theoretical and experimental methodologies often have significant limitations. A common solution is to use smaller "model" compounds; study them in detail; and extrapolate these results to the larger system. Although very useful, this raises the question, how accurate is the extrapolation? In the present Letter we want to give an example related to activation energies, which have large importance describing fragmentation processes. There are diverse methods determining activation energies in mass spectrometry; many values obtained this way can be found in the literature. However, most of these relate to small molecules. Available methods for studying compounds over ca. 200 Da size are less accurate; and there are few reliable values. "Common wisdom" suggests that, for the same reaction type, increasing the molecular size should decrease the barrier height (i.e. the critical energy, but not the internal energy needed for fragmentation!): Increasing size typically stabilizes the product ion (and product radical, if any) with respect to the parent compound. With the advance of experimental techniques to study macromolecules, it may become useful to be able to estimate, how molecular size influences the activation energy
Discrimination between charge-catalyzed and charge-independent fragmentation processes of cationized poly(n-butyl acrylate).

International audienceWhen performing structural investigation of macromolecular systems using tandem mass spectrometry, an important matter is the choice of the cation and how that does affect the tandem mass spectra. Moreover, when studying mechanistic aspects, the role of the adduct ions in the mechanism of the fragmentation processes is often discussed: Is the process charge-induced (more accurately described as charge-catalyzed) or charge-remote (more accurately described as charge-independent). In a previous study[1], we shed light on the catalytic effect of lithium in the case of cationized poly(ethylene glycols) (PEGs). The activation energy of the main fragmentation process for the trimer was shown, by means of Density Functional Theory calculations, to decrease by as much as 0.3 eV in the presence of lithium. To further sketch our picture of the role of cation adducts on the fragmentation of even electron ions, we present in this communication the results obtained on the fragmentation of poly (n-butyl acrylate), PBA, with different alkali ions and various degrees of polymerization. Thus, we present a method to clarify the role of the charge on the fragmentation processes
Olive oil or lard?  Distinguishing plant oils from animal fats in the archaeological record of the eastern Mediterranean using gas chromatography/combustion/isotope ratio mass spectrometry

YesDistinguishing animal fats from plant oils in archaeological residues is not straightforward. Characteristic plant sterols, such as ¿-sitosterol, are often missing in archaeological samples and specific biomarkers do not exist for most plant fats. Identification is usually based on a range of characteristics such as fatty acid ratios, all of which indicate that a plant oil may be present, none of which uniquely distinguish plant oils from other fats. Degradation and dissolution during burial alter fatty acid ratios and remove short chain fatty acids, resulting in degraded plant oils with similar fatty acid profiles to other degraded fats.
Compound specific stable isotope analysis of ¿13C18:0 and ¿13C16:0, carried out by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS), has provided a means of distinguishing fish oils, dairy fats, ruminant and non-ruminant adipose fats but plant oils are rarely included in these analyses. For modern plant oils where C18:1 is abundant, ¿13C18:1 and ¿13C16:0 are usually measured. These results cannot be compared with archaeological data or other modern reference fats where ¿13C18:0 and ¿13C16:0 are measured, as C18:0 and C18:1 are formed by different processes resulting in different isotopic values.

Eight samples of six modern plant oils were saponified releasing sufficient C18:0 to measure the isotopic values, which were plotted against ¿13C16:0. The isotopic values for these oils, with one exception, formed a tight cluster between ruminant and non-ruminant animal fats. This result complicates the interpretation of mixed fatty residues in geographical areas where both animal fats and plant oils were in use.AHR
Improving peptide fragmentation by N-terminal derivatization with high proton affinity.

Article first published online: 12 APR 2011An improved method of de novo peptide sequencing based on mass spectrometry using novel N-terminal derivatization reagents with high proton affinity has been developed. The introduction of a positively charged group into the N-terminal amino group of a peptide is known to enhance the relative intensity of b-ions in product ion spectra, allowing the easy interpretation of the spectra. However, the physicochemical properties of charge derivatization reagents required for efficient fragmentation remain unclear. In this study, we prepared several derivatization reagents with high proton affinity, which are thought to be appropriate for peptide fragmentation under low-energy collision-induced dissociation (CID) conditions, and examined their usefulness in de novo peptide sequencing. Comparison of the effects on fragmentation among three derivatization reagents having a guanidino or an amidino moiety, which differ in proton affinity, clearly indicated that there was an optimal proton affinity for efficient fragmentation of peptides. Among reagents tested in this study, derivatization with 4-amidinobenzoic acid brought about the most effective fragmentation. This derivatization approach will offer a novel de novo peptide sequencing method under low-energy CID conditions
Evidence for bias in measured [delta]15N values of terrestrial and aquatic organic materials due to pre-analysis acid treatment methods

We investigate the effect of acid treatment methods on δ15N values from a range of environmental organic materials in the context of the increased application of ‘dual-mode’ isotope analysis (the simultaneous measurement of δ13C and δ15N from the same acid-treated sample). Three common methods are compared; (i) untreated samples; (ii) acidification followed by sequential water rinse (rinse method); and (iii) acidification in silver capsules (capsule method). The influence of capsule type (silver and tin) on δ15N is also independently assessed (as the capsule and rinse methods combust samples in different capsules; silver and tin, respectively). We find significant differences in δ15N values between methods and the precision of any one method varies significantly between sample materials and above the instrument precision (>0.3‰). The δ15N values of untreated samples did not produce the most consistent data on all sample materials. In addition, the capsule type appears to influence the measured δ15N value of some materials, particularly those combusted only in silver capsules. We also compare the new δ15N data with previously published δ13C data on the same materials. The response of δ13C and δ15N within and between methods and sample materials to acidification appears to be relatively disproportionate, which can influence the environmental interpretation of the measured data. In addition, statistical methods used to estimate inorganic nitrogen are shown to be seriously flawed
Developing a methodology for carbon isotope analysis of lacustrine diatoms

Stable isotope analysis of sedimentary carbon in lakes can help reveal changes in terrestrial and aquatic carbon cycles. A method based on a single, photosynthetic organism, where host effects are minimised, should offer more precision than carbon isotope studies of bulk lake sediments. Here we report the development of a systematic method for use on fossil lacustrine diatom frustules, adapted from previous studies in marine environments. A step-wise cleaning experiment on diatomaceous lake sediments from Lake Challa, near Mount Kilimanjaro, was made to demonstrate the necessary treatment stages to remove external sedimentary carbon. Changes in soluble carbon compounds during these cleaning experiments were measured using gas chromatography/mass spectrometry (GC/MS). The mass spectrometry methods were refined to measure the small percentage of carbon in these samples and details of these methods are presented. Samples of cleaned diatoms containing <1% carbon yielded robust results. Carbon isotope analyses of diatom samples containing different species mixtures were performed and suggested that differences existed, although the effects lay within current experimental error and require further work. Unlike what was found in work on oxygen and silicon isotopes from diatom frustules, mineral contamination had no discernible impact on the diatom carbon isotope ratios from these sediments. The range of values found in the lakes investigated thus far can be interpreted with reference to the supply and nature of carbon from the catchment as well as to the demand generated from lake primary productivit
Use of  soft and hard MS ionization techniques for unknown compounds elucidation by GC

Investigation of trace-level non-target compounds by gas chromatography/mass spectrometry (GC/MS) often is a challenging task that requires powerful software tools to detect the unknown components, to obtain the deconvoluted mass spectra, and to interpret the data if no acceptable library match is obtained. In this paper, the complementary use of electron ionization (EI) and chemical ionization (CI) is investigated in combination with GC/time-of-flight (TOF) MS for the elucidation of organic non-target (micro)contaminants in water samples. Based on accurate mass measurement of the molecular and fragment ions from the TOF MS, empirical formulae were calculated. Isotopic patterns, carbon number prediction filter and nitrogen rule were used to reduce the number of possible formulae. The candidate formulae were searched in databases to find possible chemical structures. Selection from possible structure candidates was achieved using information on substructures and observed neutral losses derived from the fragment ions. Four typical examples (bifenazate, boscalid, epoxiconazole, and fenhexamid) are used to illustrate the methodology applied and the various difficulties encountered in this process. Our results indicate that elucidation of unknowns cannot be achieved by following a standardized procedure, as both expertise and creativity are necessary in the proces
Sap flow measurements of Ceriops tagal and Rhizophora mucronata mangrove trees by deuterium tracing and lysimetry

Mangrove forest trees grow in severe conditions such as diurnal submersion and high salinity surface and subsurface waters. This study focuses on two species on Mayotte Island, i.e. Ceriops tagal and Rhizophora mucronata, living in the middle range of the coastal mangrove. The seedlings of these trees were planted in a tropical greenhouse with an original pump system built to reproduce the natural tidal effect. The water used by these saplings, in two contrasted salinity conditions, was measured by lysimetry. For adult species, the trees’ water consumption was measured on the field side after being injected with heavy water (D2O). Our work shows that this isotopic technique also works in saline conditions, and a water consumption of around 1 ± 0.2 L per day and per centimeter of diameter was found. These values are discussed as follows: the techniques used, the distinctive features of the mangrove trees, and other factors affecting the water absorption
Tracing the sources of water using stable isotopes: first results along the Mangalore-Udupi region, south-west coast of India

The Mangalore and Udupi region on the south‐west coast of India is characterized by small west‐flowing rivers (150–250km in length) originating in the Western Ghats (up to 1940 meters above sea level (m asl)) and joining the Arabian Sea. The area experiences a humid tropical climate with frequent, high‐intensity rainfall (4000mm annual average). Nevertheless, there is a shortage of water during the peak dry season immediately before the onset of monsoon because of a rapid fall in the groundwater level. From the humid high‐altitude forests to the intense agriculture in the coastal area, there is an urgent need to understand the movement of water between evapotranspiration, rainfall, river systems and the groundwater compartments in order to achieve better water resource management. Demographic pressure on the area with over half a million inhabitants and industrial activity strongly influence this fragile ecosystem. The coastal area is characterized by shallow open wells, which are particularly sensitive to pollution and eutrophication. Stable water isotopes (18O and deuterium) were used for the first time in this region to determine the isotopic characteristics of the different waters. There is a clear seasonal difference in the isotopic ratios and d‐excess values between the summer and winter monsoon periods, with a predominance of lighter isotopes in the latter period. No significant variations in isotopic ratios were observed in relation to altitude because of the possible role of mist formation at high altitude. Greater d‐excess values were observed in the west‐flowing streams than in rivers flowing east on account of the moist westerly oceanic winds and water vapour recycling
Tracing sewage water by 15N in a mangrove ecosystem to test its bioremediation ability

Mangrove forests could be a simple and effective alternative to conventional sewage treatment, particularly for island communities given its low cost and low maintenance. Due to their high adaptation capacity, these plants are able to tolerate and bioremediate the high levels of nutrients and pollutants found in sewage water. This solution could be applied to small tropical islands with high population density such as Mayotte in the Indian Ocean. This paper reports on a trial by stable isotopic 15N tracing of such a bioremediation process on pre-treated wastewater near the village of Malamani, in the middle of the large coastal mangrove in the bay near Chirongui. The first results show a boost in the mangrove growth, but a longer period of observation is needed to confirm the beneficial effects, and also to clarify the role of the local crab population, whose engineering activities play an important part in the ecosystem. The exact denitrification process is not yet understood, and the mass balance equation also reveals loss of nitrogen-containing compounds, which needs to be analyzed more closely
Use of quadrupole time-of-flight mass spectrometry for proposal of transformation products of the herbicide bromacil after water chlorination

The herbicide bromacil has been extensively used in the Spanish Mediterranean region, and although plant protection products containing bromacil have been withdrawn by the European Union, this compound is still frequently detected in surface and ground water of this area. However, the fast and complete disappearance of this compound has been observed in water intended for human consumption, after it has been subjected to chlorination. There is a concern about the possible degradation products formed, since they might be present in drinking water and might be hazardous. In this work, the sensitive full-spectrum acquisition, high resolution and exact mass capabilities of hybrid quadrupole time-of-flight (QTOF) mass spectrometry have allowed the discovery and proposal of structures of transformation products (TPs) of bromacil in water subjected to chlorination. Different ground water samples spiked at 0.5 µg/mL were subjected to the conventional chlorination procedure applied to drinking waters, sampling 2-mL aliquots at different time intervals (1, 10 and 30 min). The corresponding non-spiked water was used as control sample in each experiment. Afterwards, 50 μL of the water was directly injected into an ultra-high-pressure liquid chromatography (UHPLC)/electrospray ionization (ESI)-(Q)TOF system. The QTOF instrument enabled the simultaneous recording of two acquisition functions at different collision energies (MSE approach): the low-energy (LE) function, fixed at 4 eV, and the high-energy (HE) function, with a collision energy ramp from 15 to 40 eV. This approach enables the simultaneous acquisition of both parent (deprotonated and protonated molecules) and fragment ions in a single injection. The low mass errors observed for the deprotonated and protonated molecules (detected in LE function) allowed the assignment of a highly probable molecular formula. Fragment ions and neutral losses were investigated in both LE and HE spectra to elucidate the structures of the TPs found. For those compounds that displayed poor fragmentation, product ion scan (MS/MS) experiments were also performed. On processing the data with specialized software (MetaboLynx), four bromacil TPs were detected and their structures were elucidated. To our knowledge, two of them had not previously been reported