pinecone/core-2020-05-10-deduplication huggingface dataset:
Importance of MS selectivity and chromatographic separation in LC-MS/MS-based methods when investigating pharmaceutical metabolites in water. Dipyrone as a case of study.

Pharmaceuticals are emerging contaminants of increasing concern because of their presence in the aquatic environment and potential to reach drinking-water sources. After human and/or veterinary consumption, pharmaceuticals can be excreted in unchanged form, as the parent compound, and/or as free or conjugated metabolites. Determination of most pharmaceuticals and metabolites in the environment is commonly made by liquid chromatography (LC) coupled to mass spectrometry (MS). LC coupled to tandem MS is the technique of choice nowadays in this field. The acquisition of two selected reaction monitoring (SRM) transitions together with the retention time is the most widely accepted criterion for a safe quantification and confirmation assay. However, scarce attention is normally paid to the selectivity of the selected transitions as well as to the chromatographic separation. In this work, the importance of full spectrum acquisition high-resolution MS data using a hybrid quadrupole time-of-flight analyser and/or a suitable chromatographic separation (to reduce the possibility of co-eluting interferences) is highlighted when investigating pharmaceutical metabolites that share common fragment ions. For this purpose, the analytical challenge associated to the determination of metabolites of the widely used analgesic dipyrone (also known as metamizol) in urban wastewater is discussed. Examples are given on the possibilities of reporting false positives of dypirone metabolites by LC-MS/MS under SRM mode due to a wrong assignment of identity of the compounds detected
Characterization of gas phase aggregates of\ud
bis(2-ethylhexyl)sulfosuccinate (AOT) and\ud
divalent metal ions. Elimination of radical\ud
species in the decomposition pathways of\ud
even-electron [AOTMIICl2]– anions

Structure and properties of even-electron anionic species formed by bis(2-ethylhexyl)sulfosuccinate (AOT) and divalentmetal ions\ud
(MII) with stoichiometry [AOTMIICl2]– have been investigated by using electrospray ionization and different mass spectrometry\ud
techniques, such as high resolution, accurate mass measurements, collision-induced dissociation (CID) multiple-stage mass\ud
spectrometry.Owing to CID, eliminations of neutrals,mainly consisting in hydrochloric acid, 2-ethyl-1-hexene and 2-ethylhexanol,\ud
and an unexpected loss of an alkyl radical have been observed. The radical anions [C4HO6SMIICl]–• so produced have been\ud
characterized by MS3 experiments. Density functional theory calculations have been carried out for investigating structure and\ud
stability of the ionic species formed in the decomposition pathways
Degrees of freedom effect on fragmentation in tandem mass spectrometry of singly charged supramolecular aggregates of sodium sulfonates

The characteristic collision energy (CCE) to obtain 50% fragmentation of positively and negatively single charged non-covalent clusters has been measured. CCE was found to increase linearly with the degrees of freedom (DoF) of the precursor ion, analogously to that observed for synthetic polymers. This suggests that fragmentation behavior (e.g. energy randomization) in covalent molecules and clusters are similar. Analysis of the slope of CCE with molecular size (DoF) indicates that activation energy of fragmentation of these clusters (loss of a monomer unit) is similar to that of the lowest energy fragmentation of protonated leucine-enkephalin. Positively and negatively charged aggregates behave similarly, but the slope of the CCE vs DoF plot is steeper for positive ions, suggesting that these are more stable than their negative counterparts
Molecular dynamics of electrosprayed\ud
water nanodroplets containing sodium\ud
bis(2-ethylhexyl)sulfosuccinate

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) subject to electrospray ionization (ESI)\ud
has been investigated by molecular dynamics (MD) simulations at three temperatures (350, 500 and 800 K). We consider\ud
several types of water nanodroplets containing AOTNa molecules and composed of a fixed number of water molecules\ud
(1000), N0\ud
AOT AOT  anions (N0\ud
AOT = 0, 5, 10) and N0\ud
Na sodium ions (N0\ud
Na = 0, 5, 10, 15, 20): in a short time scale (less than 1 ns),\ud
the AOTNa molecules, initially forming direct micelles in the interior of the water nanodroplets, are observed in all cases\ud
to diffuse nearby the nanodroplet surface, so that the hydrophilic heads and sodium ions become surrounded by water\ud
molecules, whereas the alkyl chains lay at the droplet surface. Meanwhile, evaporation of water molecules and of solvated\ud
sodium ions occurs, leading to a decrease of the droplet size and charge. At 350 K, no ejection of neutral or charged surfactant\ud
molecules is observed, whereas at 500 K, some fragmentation occurs, and at 800 K, this event becomes more frequent. The\ud
interplay of all these processes, which depend on the values of temperature, N0\ud
AOT and N0\ud
Na eventually leads to anhydrous\ud
charged surfactant aggregates with prevalence of monocharged ones, in agreement with experimental results of ESI mass\ud
spectrometry. The quantitative analysis of theMD trajectories allows to evidencemolecular details potentially useful in designing\ud
future ESI experimental conditions
Study of solid/gas phase photocatalytic reactions by electron ionization mass spectrometry

This paper describes a novel methodology for the real-time study of solid-gas phase photocatalytic reactions in situ. A novel reaction chamber has been designed and developed to facilitate the investigation of photoactive materials under different gas compositions. UV irradiation in the wavelength of ranges 376-387 and 381-392 nm was provided using specially designed high efficiency light emitting diode arrays. The experiments used air containing 190 ppm NO in a moist environment with a relative humidity of 0.1%. Photocatalytic samples consisting of pressed pellets of rutile and anatase crystalline forms of TiO were monitored over a period of 150 min. An ultra-high vacuum right angled bleed valve allowed a controlled flow of gas from the main reaction chamber at atmospheric pressure to a residual gas analyser operating at a vacuum of 10 mbar. The apparatus and methodology have been demonstrated to provide high sensitivity (ppb). The rate of degradation of NO attributed to reaction at the TiO surface was sensitive to both crystal structures (anatase or rutile) and wavelength of irradiation
Specific rearrangement reactions of acetylated lysine containing peptide bn (n=4-7) ion series

Characterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAcYAGFLVG and YAKAcGFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n=4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n=4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions,which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n=4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment.Scientific and Technological Research Council of Turkey (113Z172); State Planning Organization, DPT; Reseau National de Spectrometrie de Masse FT - ICR a tres haut champ (FR3624
A critique on the structural analysis of lignins and application of novel tandem mass spectrometric strategies to determine lignin sequencing

This review is devoted to the application of MS using soft ionization methods with a special emphasis on electrospray ionization, atmospheric pressure photoionization and matrix‐assisted laser desorption/ionization MS and tandem MS (MS/MS) for the elucidation of the chemical structure of native and modified lignins. We describe and critically evaluate how these soft ionization methods have contributed to the present‐day knowledge of the structure of lignins. Herein, we will introduce new nomenclature concerning the chemical state of lignins, namely, virgin released lignins (VRLs) and processed modified lignins (PML). VRLs are obtained by liberation of lignins through degradation of vegetable matter by either chemical hydrolysis and/or enzymatic hydrolysis. PMLs are produced by subjecting the VRL to a series of further chemical transformations and purifications that are likely to alter their original chemical structures. We are proposing that native lignin polymers, present in the lignocellulosic biomass, are not made of macromolecules linked to cellulose fibres as has been frequently reported. Instead, we propose that the lignins are composed of vast series of linear related oligomers, having different lengths that are covalently linked in a criss‐cross pattern to cellulose and hemicellulose fibres forming the network of vegetal matter. Consequently, structural elucidation of VRLs, which presumably have not been purified and processed by any other type of additional chemical treatment and purification, may reflect the structure of the native lignin. In this review, we present an introduction to a MS/MS top–down concept of lignin sequencing and how this technique may be used to address the challenge of characterizing the structure of VRLs. Finally, we offer the case that although lignins have been reported to have very high or high molecular weights, they might not exist on the basis that such polymers have never been identified by the mild ionizing techniques used in modern MS. Copyright © 2015 John Wiley & Sons, Ltd
Simple correction improving long-term reproducibility of HPLC-MS

Chromatographic peak areas in long series of high-performance liquid chromatography-MS experiments often vary, which decrease reproducibility and may cause bias in the results. It was found that the sensitivity of various components change differently; in our case, variability is in the order of 20-40%, and it is most likely due to changing conditions in electrospray ionization (ESI). The most often used peak area correction methods do not take this effect into account. The change in peak areas can be well described by a polynomial function; we found that a fourth-order polynomial is most often suitable. We suggest a simple correction algorithm based on polynomial fitting. When the experiments were inherently well reproducible, this correction improved reproducibility from 12% to 3% (on average for various components). When random errors were larger, this improvement was less significant (15% to 12% in nano-ESI) but nevertheless essential in order to avoid possible bias in the results. Copyright © 2015 John Wiley & Sons, Ltd
Travelling-wave ion mobility and negative ion fragmentation of high-mannoseN-glycans

The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed
Mapping #Dicorynia guianensis# Amsh. wood constituents by submicron resolution cluster-TOF-SIMS imaging

The preparation of tropical wood surface sections for time-of-flight secondary ion mass spectrometry imaging is described, and the use of delayed extraction of secondary ions and its interest for the analysis of vegetal surface are shown. The method has been applied to the study by time-of-flight secondary ion mass spectrometry imaging with a resolution of less than one micron of a tropical wood species, Dicorynia guianensis, which is one of the most exploited wood in French Guiana for its durable heartwood. The heartwood of this species exhibits an economical importance, but its production is not controlled in forestry. Results show an increase of tryptamine from the transition zone and a concomitant decrease of inorganic ions and starch fragment ions. These experiments lead to a better understanding of the heartwood formation and the origin of the natural durability of D. guianensis. (Résumé d'auteur
Development and application of an UHPLC-MS/MS method for the simultaneous determination of 17 steroidal hormones in equine serum

A new, fast and simple analytical method that is able to identify and quantify simultaneously 17 steroid hormones and metabolites (Pregnenolone, 17-OH-Pregnenolone, Progesterone, 17-OH Progesterone, Androsterone, Androstenedione, DHEA, DHEAS, Testosterone, Cortisol, Corticosterone, Aldosterone, 11-Deoxycortisol, 11-Deoxycorticosterone, Dihydrotestosterone, Estrone, Estradiol) has been developed in equine serum using the UHPLC-MS/MS technique. 400 μL of sample were deproteinized with 1000 µl of acetonitrile, evaporated, restored with 50 µl of a solution of 25% methanol and injected in UHPLC-MS/MS triple quadrupole. The recovery percentage obtained by spiking the matrix at two different concentrations with a standard mixture of steroid hormones was in all cases higher than 85.60 % and with the percentage of coefficient of variation (CV) lower than 8.37%. The range of the correlation coefficients of the calibration curves of the analyzed compounds was 0.9922–0.9986, and the limits of detection (LODs) and limits of quantification (LOQs) were in the range of 0.002–2 ng ml-1 and 0.0055-5.5 ng ml-1, respectively. The detected LOQ for testosterone (i.e. 50 pg ml-1) is two-fold lower with respect to its threshold admitted in geldings plasma (100 pg ml-1 free testosterone). The high sensitivity and the quantitative aspect of the method permitted to detect most of steroids in equine serum. Once validated, the method was used to quantify 17 steroid hormones in mare, stallion and gelding serum samples. The main steroids detected were corticosterone (range 37.25-51.26 ng ml-1) and cortisol (range 32.57-52.24 ng ml-1), followed by 17-OH-pregnenolone, dihydrotestosterone and pregnenolone
Tailoring the volatility and stability of oligopeptides

Amino acids are essential building blocks of life, and fluorinated derivatives have gained interest in chemistry andmedicine. Modern mass spectrometry has enabled the study of oligo- and polypeptides as isolated entities in the gas phase, but predominantly as singly or even multiply charged species. While laser desorption of neutral peptides into adiabatically expanding supersonic noble gas jets is possible, UV-VIS spectroscopy, electric or magnetic deflectometry as well as quantum interferometry would profit from the possibility to prepare thermally slow molecular beams. This has typically been precluded by the fragility of the peptide bond and the fact that a peptide would rather 'fry', i.e. denature and fragment than 'fly'. Here, we explore how tailored perfluoroalkyl functionalization can reduce the intermolecular binding and thus increase the volatility of peptides and compare it to previously explored methylation, acylation and amidation of peptides. We show that this strategy is essential and enables the formation of thermal beams of intact neutral tripeptides, whereas only fragments were observed for an extensively fluoroalkyl-decorated nonapeptide
Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments

Themost stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theorymethods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistentwith the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by ∼ 8 kJmol− 1, it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations
ショウカカン オヨビ ジュウジツセイ ゾウキ ゲンパツ ノ ジョウヒセイ シュヨウ ノ ナカ デワ オモニ リンパ ジョウヒシュ ヨウ ソシキゾウ オ テイスル イガン ガ EB ウイルス ニ カンレン スル

To demonstrate the association of Epstein-Barr virus (EBV) with primary epithelial neoplasms in the south part of Kyushu, Japan, 761 carcinomas consisting of 75 lung, 61 breast, 107 esophagus, 102 colon, 58 pancreas, 45 thyroid, and 313 gastric cancers were examined by EBER-1 in situ hybridization. EBER-1 was detected in 23 cases (7.3%) out of 313 gastric carcinomas, while none of the other carcinomas was positive for EBER-1. Twenty-eight (9.4%) out of 313 gastric carcinomas were differentiated poorly to moderately carcinomas with prominent lymphoid cell infiltration, similar to so-called lymphoepithelioma-like carcinoma, and 19 cases (67.9%) were positive for EBER-1. Although two (2.6%) and 11(10.3%) out of 75 lung and 107 esophagus carcinomas were so-called lymphoepithelioma-like carcinomas, respectively, but EBER-1 was not detected in other epithelial neoplasms that originated from the lung, esophagus, breast, colon, pancreas, and thyroid in the south of Kyushu, Japan. As a result, EBV was associated with only some gastric carcinomas but not with other epithelial neoplasms originating from the lung, esophagus, breast, colon, pancreas, and thyroid in southern Japan.喜島祐子　医歯学総合研究科博士論文(医学) ; 学位取得日: 平成13年3月23
Occurrence of cytomegalovirus hepatitis in liver transplant patients

The differential diagnosis of liver dysfunction after orthotopic liver transplantation can be difficult. Cytomegalovirus (CMV) hepatitis is one possibility. This report reviews our experience with 17 cases of pathologically proven CMV hepatitis following liver transplantation and demonstrates the need for percutaneous liver biopsies to establish the diagnosis. There were seven pediatric patients (ages 2–11 years, five males, two females) and ten adult patients (ages 17–53 years, eight males, two females). The most common symptoms were prolonged fever (15 patients, with a mean duration of 22 ± 5.5 days), elevation in total bilirubin (14 patients), and elevation in liver enzymes (15 patients); all symptoms were also found in rejection. Leukopenia and thrombocytopenia, reported to frequently occur with CMV infection, were found in only three and five patients, respectively. Twelve patients with the above symptoms underwent percutaneous biopsy on one or more occasions to differentiate CMV hepatitis from rejection. The diagnosis was made at retransplantation in five patients. CMV hepatitis followed treatment for acute rejection in 14 patients and occurred without additional immunosuppression in three patients. All patients were maintained on cyclosporine and prednisone. Acute rejection episodes were treated with a 5‐day tapering dose of steroids (17 courses in 12 patients), OKT3 monoclonal antibody [Ortho (4 patients)] antithymocyte globulin [Upjohn (2 patients)], and azathioprine (1 patient). CMV was isolated from urine (nine patients), blood (nine patients), throat (seven patients), lungs (two patients), and other organs (two patients). CMV was cultured from the liver biopsy specimens in five of the seven attempts in pediatric patients. When the diangosis was confirmed in the absence of rejection, immunosuppression was routinely lowered. When rejection occurred concomitantly with CMV hepatitis, therapy had to be individualized. Retrospectively, three patients treated for rejection were noted at retransplantation to have only CMV hepatitis, and all three paients died. A high index of suspicion and the judicioususe of liver bopsies is essential in order to differentiate CMV hepatitis from other causes of posttransplant liver dysfunction. Copyright © 1988 Wiley‐Liss, Inc., A Wiley Compan