Yields Of Fragments Research Articles

Removal of 3-Epi-25-Hydroxyvitamin D3 Interference by Liquid Chromatography–Tandem Mass Spectrometry Is Not Required for the Measurement of 25-Hydroxyvitamin D3 in Patients Older than 2 Years

To the Editor: There is growing evidence that 3-epi-25-hydroxyvitamin D3 (3-epi-25OHD3)1 is present in sera from most patients, not just sera from children younger than 1 year as was first described (1). Extended chromatography has been performed with liquid chromatography–tandem mass spectrometry (LC-MS/MS) assays (2–4) to eliminate interference from 3-epi-25OHD3, although one report (5) found that 3-epi-25OHD3 had a negligible effect on an LC-MS/MS assay (5). We examined the importance of separating the C3 epimer from 25-hydroxyvitamin D3 (25OHD3) in a large population of patients. We used both a proprietary LC-MS/MS method that does not resolve 3-epi-25OHD3 and an in-house epimer-resolving assay (epiRA) to measure 25OHD3 in excess serum samples from 71 infants <1 year old and 1046 adults. These samples were analyzed in 11 batches over a 2-month period. Samples were prepared by protein precipitation. Analytes were detected with atmospheric pressure chemical ionization (APCI) in the positive ion mode (AB Sciex) by monitoring m / z transitions of 383→257 and 389→263 for 25OHD3 and deuterated 25OHD3, respectively. Under the APCI conditions used, 3-epi-25OHD3 gave slightly different fragment yields and thus could not be quantified. The nonresolving assay (NRA) method consisted of online solid-phase extraction and analytical separation with the MassChrom® 25-OH-Vitamin D3/D2 Reagent kit (Chromsystems). The …

Temperature determined by isobaric yield ratios in heavy-ion collisions

Background: Temperature ($T$) in heavy-ion collisions is an important parameter. Previously, many works have focused on the temperature of the hot emitting source. But there are few systematic studies of the temperature among heavy fragments in peripheral collisions with incident energies near the Fermi energy to a few $A$ GeV, though it is very important to study the property of neutron-rich nucleus in heavy-ion collisions.Purpose: This work focuses on the study of temperature associated with the final heavy fragments in reactions induced by both the neutron-proton symmetric and the neutron-rich projectiles, and with incident energy ranges from 60$A$ MeV to 1$A$ GeV.Methods: Isobaric yield ratio (IYR) is used to determine the temperature of heavy fragments. Cross sections of measured fragments in reactions are analyzed, and a modified statistical abrasion-ablation (SAA) model is used to calculate the yield of fragment in 140$A$ MeV ${}^{64}$Ni+${}^{9}$Be and 1$A$ GeV ${}^{136}$Xe+${}^{208}$Pb reactions.Results: Relatively low $T$ of heavy fragments are obtained in different reactions ($T$ ranges from 1 to 3 MeV). $T$ is also found to depend on the neutron richness of the projectile. The incident energy affects $T$ very little. $\ensuremath{\Delta}\ensuremath{\mu}/T$ (the ratio of the difference between the chemical potential of neutron and proton to temperature) is found to increase linearly as $N/Z$ of projectile increases. It is found that $T$ of the ${}^{48}$Ca reaction, for which IYRs are $A&lt;50$ isobars, is affected greatly by the temperature-corrected $\ensuremath{\Delta}B(T)$. But $T$ of reactions using IYRs of heavier fragments are only slightly affected by the temperature-corrected $\ensuremath{\Delta}B(T)$. The SAA model analysis gives a consistent overview of the results extracted in this work.Conclusions: $T$ from IYR, which is for secondary fragments, is different from that of the hot emitting source. $T$ and $\ensuremath{\Delta}\ensuremath{\mu}$ are essentially governed by the sequential decay process.

5-Amino-1-naphthol, a novel 1,5-naphthalene derivative matrix suitable for matrix-assisted laser desorption/ionization in-source decay of phosphorylated peptides

Although matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is an important method for post-translational modification (PTM) analysis, the conventional matrices, 2,5-dihydroxybenzoic acid (2,5-DHB) and 1,5-diaminonaphthalene (1,5-DAN), are poor in terms of the fragment ion yields of the phosphorylated peptides. The use of 5-amino-1-naphthol (5,1-ANL) as a novel matrix for ISD of phosphorylated peptides in MALDI time-of-flight mass spectrometry (TOFMS) is described here. We have evaluated the ion yields of ISD fragments obtained from phosphorylated peptides using three 1,5-naphthalene derivatives as MALDI-ISD matrices, i.e., 5,1-ANL, 1,5-DAN and 1,5-dihydroxynaphthalene (1,5-DHN). The signal-to-noise ratio (S/N) of c'-series ions obtained from these matrices was used to estimate their suitability for MALDI-ISD of non-modified and phosphorylated peptides. The order of the S/N values of the ISD fragments for non-modified and phosphorylated peptides were 1,5-DAN > 5,1-ANL > 1,5-DHN and 5,1-ANL > 1,5-DHN > 1,5-DAN, respectively. The newly introduced matrix 5,1-ANL gave highest ion yields of ISD fragments from mono-, di-, and tetraphosphorylated peptides, while 1,5-DAN was poor in the ISD ion yields for phosphorylated peptides.

Discrimination of cyclic and linear oligosaccharides by tandem mass spectrometry using collision‐induced dissociation (CID), pulsed‐Q‐dissociation (PQD) and the higher‐energy C‐trap dissociation modes

Carbohydrates have essential functions in living organisms and cells, but, due to the presence of numerous linkage combinations, substituent sites and possible conformations, they are the class of biomolecules which exhibits the huge structural diversity found in nature. Thereby, due to such diversity and poor ionization, their structural deciphering by mass spectrometry is still a very challenging task. Here, we studied a series of linear and cyclic neutral oligosaccharides using electrospray with collision-induced dissociation (CID), pulsed-Q-dissociation (PQD) and the higher-energy C-trap dissociation (HCD) feature of a linear ion trap Orbitrap hybrid mass spectrometer (LTQ-Orbitrap). The collision energy necessary to obtain 50% fragmentation (CE(50) values) in CID, PQD and HCD was used to correlate both size and structures. The default settings for activation time and/or activation Q are the most appropriate, except for HCD, where 100 ms instead of 30 ms gave more intense fragment ions. PQD exhibits a 2-8-fold lower sensitivity than CID. HCD provides signals closer or slightly superior by 1.5-fold than PQD, and offers a more balanced ion distribution through the spectrum. Furthermore, HCD offers the possibility to make fine adjustments of the energy via the eV scale to further increase the yield of low-mass fragments. The complementarity of CID, PQD and HCD was clearly demonstrated by obtaining structural information on hexa-, hepta- and octasaccharides. Together, these results clearly indicate the usefulness of the CID/HCD pair for further structural deciphering, and analysis of more complex structures such as multi-antennary carbohydrates or glycoconjuguates alone or in mixture.

Ionization of uracil in collisions with fast bare ions

We study the atomic collisions with large molecules and simple atoms. The ionization and fragmentation spectra are investigated for uracil, a RNA base molecule, under the impact of fast bare C, O and F-ions. The experiments are conducted using a recoil-ion time-of-flight spectrometer. The energy dependence of the total ionization cross sections (TCS) and fragmentation yields are measured for MeV/u energies. In addition, the angular distribution of the electron double differential cross sections (DDCS) are also shown in some cases. The total cross sections of ionization and also the DDCS data are compared with the CDW-EIS calculations. The qualitative agreement is good but, in general, the theory tends to overestimate the data by a factor of 2.2. The angular distribution of electrons clearly indicates a good qualitative agreement except for the lowest energy electrons.

Isotopic yields and symmetry energy in nuclear multifragmentation reactions

Isotopic yields of light intermediate mass fragments (Z ⩽ 8) were studied with data from the MSU experiments for central collisions of 124Sn + 124Sn and 112Sn + 112Sn at E/A = 50 MeV. Within the statistical multifragmentation model, microcanonical Markov-chain calculations were performed with the aim to reproduce experimental elemental and isotopic distributions. The effects of varying liquid-drop parameters of hot fragments formed inside the freeze-out volume on charge and isotopic distributions are demonstrated. It is seen that the isotopic distributions of these fragments are very sensitive to the variation of the symmetry energy of fragments. Comparing our results with the experimental data, it is seen that a significant reduction of the symmetry term coefficient leads to better reproduction of the isotopic distributions. Comparison with other statistical calculations has been made. This is in agreement with previous conclusions obtained from the interpretation of both central and peripheral heavy ion collisions.

Superexcited states in the vacuum-ultraviolet photofragmentation of isoxazole molecules

The photofragmentation of isoxazole molecules producing excited atomic and molecular fragments has been investigated over the energy range 16–50 eV, using photon-induced fluorescence spectroscopy. The following fragments have been identified by their fluorescence: the excited hydrogen atoms H(n), n = 3–7 and the diatomic CH(A2Δ, B2Σ−), CN(B2Σ+) and C2(d3Πg) fragments. The diatomic fragments are vibrationally and highly rotationally excited. The fragmentation yield curves for the CH(A2Δ), CN(B2Σ+), C2(d3Πg) and the H(n), n = 3–7 deduced from their emission yields, were obtained in the photon energy ranges from their appearance energies up to 50 eV. It is found that the fragmentation occurs via excitation into higher lying superexcited states of isoxazole. The vertical excitation energies of these states were determined and their possible fragmentation processes are discussed.

Projectile structure effects in multi-nucleon and cluster transfers in 16,18O+164Dy, 208Pb reactions

The yield of projectile like fragments (PLFs) has been measured in the reactions of 16,18O with 164Dy and 208Pb targets at energies above the Coulomb barrier. The experimental data are analyzed to ascertain the role of projectile structure on the multi-nucleon and cluster correlations in transfer reactions. The variation of transfer probability with the number of nucleons transferred from the projectile to the target nucleus at the grazing angle has been investigated for both the systems. In the case of 18O induced reactions the cross sections of the two neutron (2n) stripping as well as the 2n- correlated cluster transfer are strongly enhanced as compared to the 16O induced reactions. These results have been discussed on the basis of the possible influence of the valence di-neutrons in the 18O nucleus on multi-particle transfer reactions.

Spectator fragmentation in nucleus-nucleus collisions: Phase space approach

Dynamics of spectator matter break-up in non-central collisions of 197Au+ 197Au at 1000 MeV/A are explored within the framework of a quantum molecular dynamics (QMD) model. The phase space of nucleons bound in intermediate mass fragments are studied using two clustering subroutines. Backtracking the origin of fragments to the time of the initial contact between the colliding nuclei and applying the simulated annealing clusterization algorithm (SACA) indicates a significant yield of projectile-like and target-like fragments. The simplest clusterization approach based on the spatial correlation technique, however, predicted a much lesser production probability of fragments in the spectator zone.

Ion interaction with biomolecular systems and the effect of the environment

To fully understand the mechanisms of radiation damage in living tissues, a detailed knowledge of the processes occurring at the molecular level is needed. In the gas phase, most of the investigations concerning the ionization and fragmentation of biologically relevant molecular systems are performed with isolated molecules. The importance of such studies is limited to the intrinsic properties of these molecules because of the lack of a chemical environment. To probe the effect of such an environment on the behavior of small biomolecules under irradiation, the molecules (α-amino acids, adenine) were embedded into clusters. The present results, obtained with multiply charged ions, clearly indicate the protective role of the clusters since the total fragmentation yield is reduced for all systems. The surrounding molecules allow for a redistribution of the excess energy and of the charge within the cluster. In the case of adenine clusters, a new fragmentation channel is identified. Moreover, for hydrated adenine clusters, low-energy ion induced chemical reactions are observed, namely the proton transfer from the water cluster to the adenine molecule.

Low energy electron induced dissociation in condensed diallyl disulfide

Using a high sensitivity Time of Flight mass analyser we have measured the electron stimulated desorption (ESD) of anions and cations from multilayer thin films of diallyl disulfide (DADS) formed by condensation onto Pt and Kr substrates. Measurements were performed as a function of incident electron energy (Ei), film thickness and effective incident current. For Ei ≲ 15 eV the desorption yields of anions are the result of dissociative electron attachment (DEA) via several transient negative ions often associated with electron capture into C-S and S-S σ* bonds. The minimum incident energies observed for desorption of the anionic fragments H−, S−, CH2CHCH-2, and CH2CHCH2S− are compared to theoretical bond dissociation energies calculated using DFT methods. In comparison to gas-phase electron impact mass spectra, the yield of cationic fragments are dominated by desorption of low mass fragments although similar species are observed in both cases. Electron impact at higher electron energies on thicker films of DADS enhances desorption of larger fragment ions, including those formed by the scission and formation of multiple bonds.

The contribution of medium-modified color flow to jet quenching

Abstract Multiple interactions between parton showers and the surrounding QCD matter are expected to underlie the strong medium-modifications of jet observables in ultra- relativistic heavy ion collisions at RHIC and at the LHC. Here, we note that such jet- medium interactions alter generically and characteristically the color correlations in the parton shower. We characterize these effects in a color-differential calculation of the medium-induced gluon radiation spectrum to first and second order in opacity. By interfacing simple branching histories of medium-modified color flow with the Lund hadronization model, we analyze how the medium modification of color correlations can affect the distribution of hadronic fragments in jets. Importantly, we observe that jet-medium interactions give rise to the medium-induced color decoherence of gluons from the parton shower. Since hadronization respects color flow and since each color singlet in a parton shower is hadronized separately, this medium-induced color decoherence leaves characteristic signatures in the jet fragmentation pattern. In particular, it can contribute to the quenching of leading hadron spectra. Moreover, it can increase strongly the yield of soft hadronic fragments from a jet, while the distribution of more energetic hadrons follows naturally the shape of a vacuum-like fragmentation pattern of lower total energy.

Evaluation of nuclear reaction cross-sections and fragment yields in carbon beams using the SHIELD-HIT Monte Carlo code. Comparison with experiments

In light ion therapy, the knowledge of the spectra of both primary and secondary particles in the target volume is needed in order to accurately describe the treatment. The transport of ions in matter is complex and comprises both atomic and nuclear processes involving primary and secondary ions produced in the cascade of events. One of the critical issues in the simulation of ion transport is the modeling of inelastic nuclear reaction processes, in which projectile nuclei interact with target nuclei and give rise to nuclear fragments. In the Monte Carlo code SHIELD-HIT, inelastic nuclear reactions are described by the Many Stage Dynamical Model (MSDM), which includes models for the different stages of the interaction process. In this work, the capability of SHIELD-HIT to simulate the nuclear fragmentation of carbon ions in tissue-like materials was studied. The value of the parameter κ, which determines the so-called freeze-out volume in the Fermi break-up stage of the nuclear interaction process, was adjusted in order to achieve better agreement with experimental data. In this paper, results are shown both with the default value κ = 1 and the modified value κ = 10 which resulted in the best overall agreement. Comparisons with published experimental data were made in terms of total and partial charge-changing cross-sections generated by the MSDM, as well as integral and differential fragment yields simulated by SHIELD-HIT in intermediate and thick water targets irradiated with a beam of 400 MeV u−1 12C ions. Better agreement with the experimental data was in general obtained with the modified parameter value (κ = 10), both on the level of partial charge-changing cross-sections and fragment yields.

Effect of isospin-dependent cluster recognition on the observables in heavy ion collisions

We introduce isospin dependence in the cluster recognition algorithms used in the quantum molecular dynamics model to describe fragment formation in heavy ion collisions. This change reduces the yields of emitted nucleons and enhances the yields of fragments, especially heavier fragments. The enhancement of neutron-rich lighter fragments mainly occurs at midrapidity. Consequently, isospin-dependent observables, such as isotope distributions, yield ratios of $n/p$, $t{/}^{3}\text{He}$, and isoscaling parameters are affected. We also investigate how equilibration in heavy ion collisions is affected by this change.

Single and multiple electron removal processes in proton–water-molecule collisions

Charge-state correlated cross sections for single- and multiple-electron removal processes (capture and ionization) in proton-H${}_{2}$O collisions are calculated by using the nonperturbative basis generator method adapted for ion-molecule collisions [Phys. Rev. A 80, 060702(R) (2009)]. The results are compared with experimental data for a wide range of impact energies spanning from 20 keV to several MeV. Single-electron removal probabilities in each molecular orbital are evaluated using the inclusive-probability formalism to predict the yields of charged fragments (H${}_{2}$O${}^{+}$, OH${}^{+}$, H${}^{+}$, O${}^{+}$) according to branching ratios that are valid at high impact energies. At intermediate and low energies, we calculate improved fragmentation cross sections that include the effects of multiple-electron removal processes. The resulting fragmentation yields agree with experiments at the 20$%$--30$%$ level even below 100 keV impact energy.

Use of procaine and procainamide as derivatizing co-matrices for the analysis of oligosaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Analysis of oligosaccharides by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry often yields only alkali metal cation adducts, which results in lower fragmentation yields and difficulty to retrieve sequence information. Derivatization by reductive amination may be used to promote Y-type glycosidic cleavages. However, this involves time-consuming preparations and purifications with sample loss. Here, procaine and procainamide were used directly as co-matrices with 2,5-dihydroxybenzoic acid (DHB). Acidified 10 g/L procaine hydrochloride or procainamide hydrochloride solutions in water/acetonitrile were added to the oligosaccharide solution one minute before preparing our MALDI targets using DHB with the dried-droplet method. This simple protocol resulted in deposits of very fine homogeneous crystals. Positive ion mass spectra, easily acquired in an automated mode, presented a high percentage of oligosaccharides derivatized as Schiff base or glycosylamine notably detected as protonated molecules [M + H](+). The high abundance of procaine or procainamide on the target did not impede the ionization process, improved the signal-to-noise ratio and eliminated the need to search for 'sweet spots'. Fragmentation of the protonated precursor ions of the derivatives largely favored Y-type glycosidic cleavages. This easy and fast sample preparation, involving low toxicity and easily accessible chemicals, allowed the selection of protonated molecules as precursor ions for post-source decay analyses. This opened the possibility of simplifying sequence retrieval in routine oligosaccharide analyses.

Optimizing SHIELD-HIT for carbon ion treatment

The SHIELD-HIT Monte Carlo transport code has been widely used in particle therapy, but has previously shown some discrepancies, when compared with experimental data. In this work, the inelastic nuclear cross sections of SHIELD-HIT are calibrated to experimental data for carbon ions. In addition, the models for nuclear fragmentation were adjusted to experiments, for the partial charge-changing cross section of carbon ions in water. Comparison with fragmentation yield experiments for carbon and neon primaries were made for validation. For carbon primaries, excellent agreement between simulation and experiment was observed, with only minor discrepancies. For neon primaries, the agreement was also good, but larger discrepancies were observed, which require further investigation. In conclusion, the current version SHIELD-HIT10A is well suited for simulating problems arising in particle therapy for clinical ion beams.

Constraining the symmetry term in the nuclear equation of state at subsaturation densities and finite temperatures

Methods of extraction of the symmetry energy (or enthalpy) coefficient to temperature ratio from isobaric and isotopic yields of fragments produced in Fermi-energy heavy-ion collisions are discussed. We show that the methods are consistent when the hot fragmenting source is well characterized and its excitation energy and isotopic composition are properly taken into account. The results are independent of the mass number of the detected fragments, which suggests that their fate is decided very early in the reaction.

Mechanisms of the electron-impact-induced methionine molecule fragmentation

The fragmentation of a methionine (C5H11NO2S) molecule by a low-energy electron impact has been studied both experimentally and theoretically. A series of doubly-charged fragment ions have been observed for the first time. The main emphasis has been given to the mechanisms of the initial molecule fragment production. A special attention has been paid to the energy characteristics of the ionic fragment yield. The geometrical parameters of the initial molecule rearrangement have also been analyzed.

ROLE OF QUASIPROJECTILE ISOSPIN ASYMMETRY IN NUCLEAR FRAGMENTATION

Fragment yield data, selected with different values of the isospin asymmetry of the quasiprojectile from 78, 86 Kr +58, 64 Ni reactions at E lab = 35 MeV/nucleon, have been analyzed within the framework of Landau free energy approach. Fits to the free energy data indicated the system to be in the regime of a first-order phase transition. The plot of free energy versus isospin asymmetry of the fragments showed a systematic change with increasing isospin asymmetry of the fragmenting source. This observation demonstrated the role of quasiprojectile isospin asymmetry as an external field which governed the minima positions in the free energy plot. The position of the central minimum was found to be in close agreement with the average isospin asymmetry of the fragments calculated excluding neutrons and protons. Significant deviations from the free energy plot were observed for N = Z fragments, particularly for the lighter ones, which could be corrected after inclusion of odd–even effects in the analysis. Analysis of yield data of N = Z nuclei gave a reasonable estimate of temperature. Analysis of free energy data gated with excitation energy of the fragmenting source showed a dependence of fit parameters of Landau free energy equation on the excitation energy as well as isospin asymmetry of the source.