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Fragmentation Process (fragmentation + process)
Selected AbstractsMatrix-assisted laser desorption/ionization collision-induced dissociation of linear single oligomers of nylon-6JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 10 2001Renata Murgasova Abstract Matrix-assisted laser desorption/ionization, collision induced-dissociation (MALDI-CID) has been used to obtain structural information for linear single oligomers of nylon-6. The effects of matrix and cationization agent in MALDI-CID analysis have been investigated. Fragmentation mechanisms are proposed for the series of ions that are observed in the MALDI-CID spectra of the hexamer, octamer and dodecamer. Fragmentation processes observed in the MALDI-CID spectra include cleavage of the end groups followed by dissociation of the m/z 113 unit. Cleavage of the oligamide chain occurs at the amide linkage, as well as at adjacent bonds. For the four matrices and three cationization agents investigated, 2,5-dihydroxybenzoic acid and sodium chloride showed the best performance for MALDI-CID analysis of the dodecamer. In addition, yields of the fragment ions in MALDI-CID spectra were found to be dependent on the chain length distribution. Copyright © 2001 John Wiley & Sons, Ltd. [source] Applying a continua landscape approach to evaluate plant response to fragmentation: Primula vulgaris in the Cantabrian mountainsAPPLIED VEGETATION SCIENCE, Issue 4 2009Alicia Valdés Abstract Question: Continua landscape approaches conceptualize the effects of habitat fragmentation on the biota by considering fragmented landscapes as continuous gradients, departing from the view of habitat as either suitable (fragment) or unsuitable (matrix). They also consider the ecological gradients or the ,Umwelt' (species-specific perception of the landscape) to represent the processes that ultimately limit organisms' ability to colonize and persist within habitat remnants. Are these approaches suitable for evaluating the response of plant species to fragmentation? Location: Fragmented mid-elevation temperate forests, Cantabrian range, Spain. Methods: The presence, abundance and demographic structure of populations of the perennial herb Primula vulgaris were sampled across a continuous extent of 100 ha, subdivided into 400 50 m × 50 m sampling units. These variables were related to forest availability, forest subdivision and edge density, topography and the spatial clumpiness of populations (a measure of plant dispersal constraints and, hence, a major surrogate of plant Umwelt). Results: Fragmentation processes, especially habitat loss, negatively affect P. vulgaris, with a stronger effect on presence than on abundance and demography. Despite the importance of habitat availability, P. vulgaris does not occupy all potentially suitable forest habitat, mostly owing to dispersal constraints. A positive effect of slope on plant presence also suggests some effect of habitat quality in determining establishment and occupancy of forest landscape. Conclusions: Within-habitat dispersal constraints are as important as forest fragmentation in determining the landscape-scale distribution of P. vulgaris. By assessing the relative role of the diverse fragmentation processes, and of the species' landscape perception, a continua landscape approach proves to be a valuable tool for predicting plant response to landscape change. [source] Dispersal ability and host-plant characteristics influence spatial population structure of monophagous beetlesECOLOGICAL ENTOMOLOGY, Issue 1 2005Matthew J. St Pierre Abstract., 1. Dispersal plays an integral role in determining spatial population structure and, consequently, the long-term survival of many species. Theoretical studies indicate that dispersal increases with population density and decreasing habitat stability. In the case of monophagous insect herbivores, the stability of host-plant populations may influence their spatial population structure. 2. The tallgrass prairie in Iowa, U.S.A. is highly fragmented and most prairie insects face a landscape with fewer habitat patches and smaller host-plant populations than 150 years ago, potentially making dispersal between patches difficult. Some herbivores, however, use native plant species with weedy characteristics that have increased in abundance because of disturbances. 3. Mark,recapture data and presence,absence surveys were used to examine dispersal and spatial population structure of two monophagous beetles with host plants that exhibit different population stability and have responded differently to fragmentation of tallgrass prairie. 4. Chrysochus auratus Fabricius exhibits a patchy population structure and has relatively large dispersal distances and frequencies. Its host plant is variable locally in time and space, but is more abundant than 150 years ago. The other species, Anomoea laticlavia Forster, exhibits a metapopulation or non-equilibrium population structure and has relatively small dispersal distances and frequencies. Its host-plant populations are stable in time and space. 5. The results indicate that dispersal ability of monophagous beetles reflects the life-history dynamics of their host plants, but the spatial population structure exhibited today is strongly influenced by how the host plants have responded to the fragmentation process over both time and space. [source] Dynamic crack propagation with cohesive elements: a methodology to address mesh dependencyINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 1 2004F. Zhou Abstract In this paper, two brittle fracture problems are numerically simulated: the failure of a ceramic ring under centrifugal loading and crack branching in a PMMA strip. A three-dimensional finite element package in which cohesive elements are dynamically inserted has been developed. The cohesive elements' strength is chosen to follow a modified weakest link Weibull distribution. The probability of introducing a weak cohesive element is set to increase with the cohesive element size. This reflects the physically based effect according to which larger elements are more likely to contain defects. The calculations illustrate how the area dependence of the Weibull model can be used to effectively address mesh dependency. On the other hand, regular Weibull distributions have failed to reduce mesh dependency for the examples shown in this paper. The ceramic ring calculations revealed that two distinct phenomena appear depending on the magnitude of the Weibull modulus. For low Weibull modulus, the fragmentation of the ring is dominated by heterogeneities. Whereas many cracks were generated, few of them could propagate to the outer surface. Monte Carlo simulations revealed that for highly heterogeneous rings, the number of small fragments was large and that few large fragments were generated. For high Weibull modulus, signifying that the ring is close to being homogeneous, the fragmentation process was very different. Monte Carlo simulations highlighted that a larger number of large fragments are generated due to crack branching. Copyright © 2003 John Wiley & Sons, Ltd. [source] Estimating and eliminating redundant data transfers over the web: a fragment based approachINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 2 2005Christos Bouras Abstract Redundant data transfers over the Web, can be mainly attributed to the repeated transfers of unchanged data. Web caches and Web proxies are some of the solutions that have been proposed, to deal with the issue of redundant data transfers. In this paper we focus on the efficient estimation and reduction of redundant data transfers over the Web. We first prove that a vast amount of redundant data is transferred in Web pages that are considered to carry fresh data. We show this by following an approach based on Web page fragmentation and manipulation. Web pages are broken down to fragments, based on specific criteria. We then deal with these fragments as independent constructors of the Web page and study their change patterns independently and in the context of the whole Web page. After the fragmentation process, we propose solutions for dealing with redundant data transfers. This paper has been based on our previous work on ,Web Components' but also on related work by other researchers. It utilises a proxy based, client/server architecture, and imposes changes to the algorithms executed on the Proxy server and on clients. We show that our proposed solution can considerably reduce the amount of redundant data transferred on the Web. Copyright © 2004 John Wiley & Sons, Ltd. [source] Particle Characteristics of Trace High Explosives: RDX and PETN,JOURNAL OF FORENSIC SCIENCES, Issue 2 2007Jennifer R. Verkouteren M.S. ABSTRACT: The sizes of explosives particles in fingerprint residues produced from C-4 and Semtex-1A were investigated with respect to a fragmentation model. Particles produced by crushing crystals of RDX and PETN were sized by using scanning electron microscopy, combined with image analysis, and polarized light microscopy was used for imaging and identifying explosive particles in fingerprint residues. Crystals of RDX and PETN fragment in a manner that concentrates mass in the largest particles of the population, which is common for a fragmentation process. Based on the fingerprints studied, the particle size to target for improving mass detection in fingerprint residues by ion mobility spectrometry (IMS) is ,10 ,m in diameter. Although particles smaller than 10 ,m in diameter have a higher frequency, they constitute <20% of the total mass. Efforts to improve collection efficiency of explosives particles for detection by IMS, or other techniques, must take into consideration that the mass may be concentrated in a relatively few particles that may not be homogeneously distributed over the fingerprint area. These results are based on plastic-bonded explosives such as C-4 that contain relatively large crystals of explosive, where fragmentation is the main process leading to the presence of particles in the fingerprint residues. [source] Substituent effect and multisite protonation in the fragmentation of alkyl benzoatesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2002Chagit Denekamp Abstract The dissociation of protonated alkyl benzoates (para H, CN, OMe and NO2) into protonated benzoic acids and alkyl cations was studied in the gas phase. It was found that the product ratio depends on the substituent at the para position of the phenyl ring. The substituent effect is probably the result of the formation of an ion,neutral complex intermediate that decomposes to an ion and a neutral, according to the relative proton affinities of the two moieties. The experimental results and theoretical calculations indicate that the favored protonation site in these compounds is the ester's carbonyl and that proton transfer from the phenyl ring to the ester group is very likely to occur under chemical ionization conditions. It is most probable that the carbonyl protonated form is a common intermediate in the fragmentation process, regardless of the protonation site. Copyright © 2002 John Wiley & Sons, Ltd. [source] Organic cyclic difluoramino-nitramines: infrared and Raman spectroscopy of 3,3,7,7-tetrakis(difluoramino)octahydro 1,5-dinitro-1,5-diazocine (HNFX)JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Philippe F. Weck Abstract We present the first vibrational structure investigation of 3,3,7,7-tetrakis(difluoramino)octahydro-1,5-dinitro- 1,5-diazocine (HNFX),and, more generally, of a member of the new class of gem -bis(difluoramino)-substituted heterocyclic nitramine energetic materials,using combined theoretical and experimental approaches. Optimized molecular structure and vibrational spectra of the Ci, symmetry conformer constituting the HNFX crystal were computed using density functional theory methods. Fourier transform infrared and Raman spectra of HNFX crystalline samples were also collected at ambient temperature and pressure. The average deviation of calculated structural parameters from X-ray diffraction data is ,1% at the B3LYP/6-311 + + G(d,p) level of theory, suggesting the absence of significant molecular distortion induced by the crystal field. Very good agreement was found between simulated and measured spectra, allowing reliable assignment of the fundamental normal modes of vibration of the HNFX crystal. Detailed analysis of the normal modes of the C,(NF2)2 and N,NO2 moieties was performed due to their critical importance in the initial steps of the molecular homolytic fragmentation process. Copyright © 2009 John Wiley & Sons, Ltd. [source] Fragmentation model of meteoroid motion, mass loss, and radiation in the atmosphereMETEORITICS & PLANETARY SCIENCE, Issue 1 2005k CEPLECHA We solve them numerically including two possible types of fragmentation: into large pieces and into a cluster of small fragments. We have written a Fortran code that computes the motion, ablation and light intensity of a meteoroid at chosen heights, and allows for the ablation and shape density coefficients , and K, as well as the luminous efficiency ,, to be variable with height/time. We calibrated our fragmentation model (FM) by the best fit to observational values for the motion, ablation, radiation, fragmentation and the terminal masses (recovered meteorites) for the Lost City bolide. The FM can also handle multiple and overlapping meteor flares. We separately define both the apparent and intrinsic values of ,, K, and ,. We present in this paper values of the intrinsic luminous efficiency as function of velocity, mass, and normalized air density. Detailed results from the successful application of the FM to the Lost City, Innisfree, and Benesov bolides are also presented. Results of applying the FM to 15 bolides with very precise observational data are presented in a survey mode (Table 7). Standard deviations of applying our FM to all these events correspond to the precision of the observed values. Typical values of the intrinsic ablation coefficient are low, mostly in the range from 0.004 to 0.008 s2 km,2, and do not depend on the bolide type. The apparent ablation coefficients reflect the process of fragmentation. The bolide types indicate severity of the fragmentation process. The large differences of the "dynamic" and "photometric" mass from numerous earlier studies are completely explained by our FM. The fragmentation processes cannot be modeled simply by large values of the apparent ablation coefficient and of the apparent luminous efficiency. Moreover, our new FM can also well explain the radiation and full dynamics of very fast meteoroids at heights from 200 km to 130 km. [source] Ionization-induced star formation , I. The collect-and-collapse modelMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2007J. E. Dale ABSTRACT We conduct smoothed particle hydrodynamics simulations of the ,collect-and-collapse' scenario for star formation triggered by an expanding H ii region. We simulate the evolution of a spherical uniform molecular cloud with an ionizing source at its centre. The gas in the cloud is self-gravitating, although the cloud is prevented from globally collapsing. We find that the shell driven by the H ii region fragments to form numerous self-gravitating objects. We repeat our calculations at four numerical resolutions to ensure that they are converged. We compare our results to the analytical model of Whitworth et al. and show that our simulations and the predictions of Whitworth et al. are in good agreement in the sense that the shell fragments at the time and radius predicted by Whitworth et al. to within 20 and 25 per cent, respectively. Most of the fragments produced in our two highest resolution calculations are approximately half the mass of those predicted by Whitworth et al., but this conclusion is robust against both numerical resolution and the presence of random noise (local fluctuations in density of a factor of ,2) in the initial gas distribution. We conclude that such noise has little impact on the fragmentation process. [source] The origin of the initial mass function and its dependence on the mean Jeans mass in molecular cloudsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2005Matthew R. Bate ABSTRACT We investigate the dependence of stellar properties on the mean thermal Jeans mass in molecular clouds. We compare the results from the two largest hydrodynamical simulations of star formation to resolve the fragmentation process down to the opacity limit, the first of which was reported by Bate, Bonnell & Bromm. The initial conditions of the two calculations are identical except for the radii of the clouds, which are chosen so that the mean densities and mean thermal Jeans masses of the clouds differ by factors of 9 and 3, respectively. We find that the denser cloud, with the lower mean thermal Jeans mass, produces a higher proportion of brown dwarfs and has a lower characteristic (median) mass of the stars and brown dwarfs. This dependence of the initial mass function (IMF) on the density of the cloud may explain the observation that the Taurus star-forming region appears to be deficient in brown dwarfs when compared with the Orion Trapezium cluster. The new calculation also produces wide binaries (separations >20 au), one of which is a wide binary brown dwarf system. Based on the hydrodynamical calculations, we develop a simple accretion/ejection model for the origin of the IMF. In the model, all stars and brown dwarfs begin with the same mass (set by the opacity limit for fragmentation) and grow in mass until their accretion is terminated stochastically by their ejection from the cloud through dynamically interactions. The model predicts that the main variation of the IMF in different star-forming environments should be in the location of the peak (due to variations in the mean thermal Jeans mass of the cloud) and in the substellar regime. However, the slope of the IMF at high masses may depend on the dispersion in the accretion rates of protostars. [source] Determination of N-glycosylation sites and site heterogeneity in a monoclonal antibody by electrospray quadrupole ion-mobility time-of-flight mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 1 2008Petra Olivova This paper presents an improved analytical method for glycosylation structural characterizations of a monoclonal antibody (mAb) using a newly developed quadrupole ion-mobility time-of-flight (ESI-Q-IM-TOF) mass spectrometer. Using this method, high-resolution mass spectra were acquired to produce the overall glycosylation profile of the mAb. Additionally, the light and heavy chains from the reduced antibody were separated in the gas phase by the ion mobility functionality of the instrument, allowing accurate mass measurement of each subunit. Furthermore, the glycan sequences, as well as the glycosylation site, were determined by a two-step sequential fragmentation process using the unique dual-collision-cell design of the instrument, thus providing detailed characterizations of the glycan structures. Copyright © 2007 John Wiley & Sons, Ltd. [source] Electron ionization mass spectra of phosphorus-containing heterocycles.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2006The electron ionization mass spectra of 27 cis - and trans -annelated 1,4,4a,5,6,7,8,8a-octahydro-2H -3,1,2-benzoxazaphosphinine 2-oxides were recorded to clarify the effects of the ring heteroatom (O or N), ring annelation, the P configuration and the substituents attached to the ring or to the N and P atoms. For compounds 1,12 different alkyl radical and alkene losses and the cleavage of the P,heteroatom bonds, instead of the P,C bonds, were representative and dependent mainly on the substitution on the N and P atoms. The replacement of Ph and OPh by N(CH2CH2Cl)2 on the P atom had a dramatic influence on the fragmentation process: new fragment ions were obtained and very little M+. (1,3%) was formed. Only slight differences were found between some of the corresponding isomers, but interestingly the compounds formed clear groups on the basis of the differences in their fragmentation, depending on the ring-N and ring-P substituents. Copyright © 2006 John Wiley & Sons, Ltd. [source] On the use of breakdown graphs combined with energy-dependent mass spectrometry to provide a complete picture of fragmentation processesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2002Colin P. G. Butcher Both breakdown graphs and energy-dependent (ED) maps provide a means of visually representing the fragmentation processes resulting from collision-induced dissociation at different energies. The two presentation methods may be combined for a complete picture of the appearance, disappearance and maximum abundance collision potentials of each of the ions involved in the fragmentation process. A demonstration of this approach is presented using two very different classes of compound, an amino acid and a transition metal carbonyl cluster. Copyright © 2002 John Wiley & Sons, Ltd. [source] Susceptibility of Common and Rare Plant Species to the Genetic Consequences of Habitat FragmentationCONSERVATION BIOLOGY, Issue 3 2007OLIVIER HONNAY diversidad genética; endogamia; fragmentación de hábitat; sistema reproductivo; tamaño poblacional Abstract:,Small plant populations are more prone to extinction due to the loss of genetic variation through random genetic drift, increased selfing, and mating among related individuals. To date, most researchers dealing with genetic erosion in fragmented plant populations have focused on threatened or rare species. We raise the question whether common plant species are as susceptible to habitat fragmentation as rare species. We conducted a formal meta-analysis of habitat fragmentation studies that reported both population size and population genetic diversity. We estimated the overall weighted mean and variance of the correlation coefficients among four different measures of genetic diversity and plant population size. We then tested whether rarity, mating system, and plant longevity are potential moderators of the relationship between population size and genetic diversity. Mean gene diversity, percent polymorphic loci, and allelic richness across studies were positively and highly significantly correlated with population size, whereas no significant relationship was found between population size and the inbreeding coefficient. Genetic diversity of self-compatible species was less affected by decreasing population size than that of obligate outcrossing and self-compatible but mainly outcrossing species. Longevity did not affect the population genetic response to fragmentation. Our most important finding, however, was that common species were as, or more, susceptible to the population genetic consequences of habitat fragmentation than rare species, even when historically or naturally rare species were excluded from the analysis. These results are dramatic in that many more plant species than previously assumed may be vulnerable to genetic erosion and loss of genetic diversity as a result of ongoing fragmentation processes. This implies that many fragmented habitats have become unable to support plant populations that are large enough to maintain a mutation-drift balance and that occupied habitat fragments have become too isolated to allow sufficient gene flow to enable replenishment of lost alleles. Resumen:,Las poblaciones pequeñas de plantas son más propensas a la extinción debido a la pérdida de variación genética por medio de la deriva génica aleatoria, el incremento de autogamia y la reproducción entre individuos emparentados. A la fecha, la mayoría de los investigadores que trabajan con erosión genética en poblaciones fragmentadas de plantas se han enfocado en las especies amenazadas o raras. Cuestionamos si las especies de plantas comunes son tan susceptibles a la fragmentación del hábitat como las especies raras. Realizamos un meta análisis formal de estudios de fragmentación que reportaron tanto tamaño poblacional como diversidad genética. Estimamos la media general ponderada y la varianza de los coeficientes de correlación entre cuatro medidas de diversidad genética y de tamaño poblacional de las plantas. Posteriormente probamos si la rareza, el sistema reproductivo y la longevidad de la planta son moderadores potenciales de la relación entre el tamaño poblacional y la diversidad genética. La diversidad genética promedio, el porcentaje de loci polimórficos y la riqueza alélica en los estudios tuvieron una correlación positiva y altamente significativa con el tamaño poblacional, mientras que no encontramos relación significativa entre el tamaño poblacional y el coeficiente de endogamia. La diversidad genética de especies auto compatibles fue menos afectada por la reducción en el tamaño poblacional que la de especies exogámicas obligadas y especies auto compatibles, pero principalmente exogámicas. La longevidad no afectó la respuesta genética de la población a la fragmentación. Sin embargo, nuestro hallazgo más importante fue que las especies comunes fueron tan, o más, susceptibles a las consecuencias genéticas de la fragmentación del hábitat que las especies raras, aun cuando las especies histórica o naturalmente raras fueron excluidas del análisis. Estos resultados son dramáticos porque muchas especies más pueden ser vulnerables a la erosión genética y a la pérdida de diversidad genética como consecuencia de los procesos de fragmentación que lo se asumía previamente. Esto implica que muchos hábitats fragmentados han perdido la capacidad para soportar poblaciones de plantas lo suficientemente grandes para mantener un equilibrio mutación-deriva y que los fragmentos de hábitat ocupados están tan aislados que el flujo génico es insuficiente para permitir la reposición de alelos perdidos. [source] Do collisions inside the collision cell play a relevant role in CID-LIFT experiments?,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2007Gloriano Moneti Abstract Collision experiments are a valid approach to characterize the ionic species generated by matrix assisted laser desorption ionization (MALDI). When a time-of-flight analyzer is employed, three different approaches are available for these experiments: the postsource decay (PSD), the LIFT and the MALDI-TOF/TOF. The last two are of particular interest because of the overcoming of the PSD problems related to mass calibration of the product ion spectra. Experiments performed by LIFT on linear or cyclic peptides, in presence or in absence of collision gas in the collision cell, gave evidence of an unexpected behavior: the two spectra were practically superimposable, and in the former case only a few new fragmentation channels were activated with low yield. These results mean that the selected ion exhibits a large amount of internal energy, capable of promoting fragmentation processes in the time window corresponding to the flight time between ion source and the acceleration electrode placed after the collision cell. Experiments performed by varying the plume density show that this internal energy uptake occurs in the expanding plume, through multiple collisions. The LIFT data have been compared with those achieved by collisions of ESI-generated [MH]+ ions of angotensin II performed under ,in-source' conditions and by triple-quadrupole experiments. The obtained results show a strong similarity among the spectra, indicating that the internal energy uptake in a MALDI source is comparable with that of 40-eV ions colliding with Ar in a triple-quadrupole instrument. Copyright © 2006 John Wiley & Sons, Ltd. [source] Reversible coagulation,fragmentation processes and random combinatorial structures: Asymptotics for the number of groupsRANDOM STRUCTURES AND ALGORITHMS, Issue 2 2004Michael M. Erlihson Abstract The equilibrium distribution of a reversible coagulation-fragmentation process (CFP) and the joint distribution of components of a random combinatorial structure (RCS) are given by the same probability measure on the set of partitions. We establish a central limit theorem for the number of groups (= components) in the case a(k) = qkp,1, k , 1, q, p > 0, where a(k), k , 1, is the parameter function that induces the invariant measure. The result obtained is compared with the ones for logarithmic RCS's and for RCS's, corresponding to the case p < 0. © 2004 Wiley Periodicals, Inc. Random Struct. Alg. 2004 [source] Stereochemical effects in fragmentation of diastereoisomers of protected diethyl 1,2-diamino-alkylphosphonatesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2010Ewelina Drabik Diastereoisomers of diethyl 5-substituted (2-thioxo-imidazolidin-4-yl)phosphonates, which can be regarded as protected diethyl 1,2-diaminoalkylphosphonates, have been analyzed by electron ionization mass spectrometry. Significant differences in the fragmentation of cis - and trans -diastereoisomers were found. The stereospecificity of the elimination of diethyl phosphonate and the loss of the diethoxyphosphoryl group were studied using specific labeled compounds and collision-induced dissociation. The relative abundances of ions formed via these fragmentation processes can be used for differentiation of both diastereoisomers. Copyright © 2010 John Wiley & Sons, Ltd. [source] Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 10 2009King Wai Lau Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument-specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole-time-of-flight and quadrupole ion trap instruments. Specifically, quadrupole-time-of-flight tandem mass spectra show a significant under-representation of N-terminal b-type fragments in comparison to quadrupole ion trap product ion spectra. Energy-resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b-type ions are significantly less stable than their y-type N-terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole-time-of-flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. Copyright © 2009 John Wiley & Sons, Ltd. [source] Characterisation via electrospray ionisation multistage mass spectrometry of three related series of nitrido technetium complexes containing phosphinothiolate and dithiocarbamate ligandsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2005Michela Tubaro Nine nitrido technetium compounds comprising bis-substituted Tc(N)(PS)2 (1,4) (PS,=,bidentate phosphinothiolate ligands) and Tc(N)(dtc)2 (5, 6) derivatives (dtc,=,bidentate dithiocarbamate), and mixed-ligand Tc(N)(PS)(dtc) (7,9) species, were subjected to electrospray ionisation mass spectrometry and MSn experiments. Bis-substituted phosphinothiolato complexes 1,4 lead to the straightforward formation of dinuclear species reasonably originating from proton bound dimers. These dinuclear species do not show, under collisionally induced fragmentation processes, the formation of monomeric units but cleavages related to the ligand framework, thereby proving the high stability of the [TcH+Tc] bond. Bis-dithiocarbamate compounds 5 and 6 show, instead, abundant [M+H]+, [M+Na]+ and [2M+Na]+ ions, and their collisionally induced fragmentations are highly favoured with cleavages related to the CN and CS bonds. During these processes, the coordination of a water molecule to [MH,L]+ product ions is observed, as proved by the collisionally induced H2O loss detected for this species. Mixed-ligand compounds 7 and 8 show the protonated molecules and Na+ -cationised ions with fragmentation processes related to the dithiocarbamate moiety. This behaviour indicates that coordination of ether- and ester-substituted dithiocarbamates to the [Tc,,N] group is weaker than that of phosphinothiolates. Conversely, diethyldithiocarbamate inserted in mixed complex 9 enhances both CN and TcS bonds, and fragmentation processes suggest that metal-phosphinothiolate and metal-dithiocarbamate show comparable strength. Copyright © 2005 John Wiley & Sons, Ltd. [source] On the use of breakdown graphs combined with energy-dependent mass spectrometry to provide a complete picture of fragmentation processesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2002Colin P. G. Butcher Both breakdown graphs and energy-dependent (ED) maps provide a means of visually representing the fragmentation processes resulting from collision-induced dissociation at different energies. The two presentation methods may be combined for a complete picture of the appearance, disappearance and maximum abundance collision potentials of each of the ions involved in the fragmentation process. A demonstration of this approach is presented using two very different classes of compound, an amino acid and a transition metal carbonyl cluster. Copyright © 2002 John Wiley & Sons, Ltd. [source] Study of the mass spectrometric behaviour of phthalocyanine and azo dyes using electrospray ionisation and matrix-assisted laser desorption/ionisationRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2001A. Conneely The negative ion MALDI-MS and ESI-MS behaviour of sulphonated copper phthalocyanine dyes has shown the presence of both anionic and radical anionic species. Substituent groups such as sulphonates and linker arms, as are present in commercial dyes such as Remazol TB and Everzol TB, are found to be labile and the dyes undergo in-source fragmentation in both MALDI-MS and ESI-MS. Ions corresponding to sodium salts can be formed. It appears that Cu is firmly bound in the phthalocyanine structure, unlike the corresponding Mg and Al chelates that can undergo demetallation. The application of ESI-MSn confirmed that these labile groups can be fragmented from the dye molecules and, in addition, SO2 losses are observed as for EI-MS. Hydrolysed commercial azo dyes such as Remazol Black B (I) and Remazol Red RB (III) showed both singly and doubly charged molecular anion species as well as sodium salts using negative ion ESI-MS, but did not desulphonate like the copper phthalocyanine dyes. The application of ESI-MSn revealed fragmentation of the dye molecules with the loss of entities such as HOCH2CH2SO2C6H4N2 (for both dyes) and SO2 (for Remazol Black B). MALDI-MS, ESI-MS and ESI-MSn can therefore be used for the characterisation of such dyes by exploiting these fragmentation processes, and some structural information can be obtained for the dyes whose structures are not in the public domain. Copyright© 2001 John Wiley & Sons, Ltd. [source] Applying a continua landscape approach to evaluate plant response to fragmentation: Primula vulgaris in the Cantabrian mountainsAPPLIED VEGETATION SCIENCE, Issue 4 2009Alicia Valdés Abstract Question: Continua landscape approaches conceptualize the effects of habitat fragmentation on the biota by considering fragmented landscapes as continuous gradients, departing from the view of habitat as either suitable (fragment) or unsuitable (matrix). They also consider the ecological gradients or the ,Umwelt' (species-specific perception of the landscape) to represent the processes that ultimately limit organisms' ability to colonize and persist within habitat remnants. Are these approaches suitable for evaluating the response of plant species to fragmentation? Location: Fragmented mid-elevation temperate forests, Cantabrian range, Spain. Methods: The presence, abundance and demographic structure of populations of the perennial herb Primula vulgaris were sampled across a continuous extent of 100 ha, subdivided into 400 50 m × 50 m sampling units. These variables were related to forest availability, forest subdivision and edge density, topography and the spatial clumpiness of populations (a measure of plant dispersal constraints and, hence, a major surrogate of plant Umwelt). Results: Fragmentation processes, especially habitat loss, negatively affect P. vulgaris, with a stronger effect on presence than on abundance and demography. Despite the importance of habitat availability, P. vulgaris does not occupy all potentially suitable forest habitat, mostly owing to dispersal constraints. A positive effect of slope on plant presence also suggests some effect of habitat quality in determining establishment and occupancy of forest landscape. Conclusions: Within-habitat dispersal constraints are as important as forest fragmentation in determining the landscape-scale distribution of P. vulgaris. By assessing the relative role of the diverse fragmentation processes, and of the species' landscape perception, a continua landscape approach proves to be a valuable tool for predicting plant response to landscape change. [source] An Experimental and Theoretical Investigation of Gas-Phase Reactions of Ca2+ with GlycineCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2006Inés Corral Dr. Abstract The gas-phase reactions between Ca2+ and glycine ([Ca(gly)]2+) have been investigated through the use of mass spectrometry techniques and B3-LYP/cc-pWCVTZ density functional theory computations. The major peaks observed in the electrospray MS/MS spectrum of [Ca(gly)]2+ correspond to the formation of the [Ca,C,O2,H]+, NH2CH2+, CaOH+, and NH2CH2CO+ fragment ions, which are produced in Coulomb explosion processes. The computed potential energy surface (PES) shows that not only are these species the most stable product ions from a thermodynamic point of view, but they may be produced with barriers lower than for competing processes. Carbon monoxide is a secondary product, derived from the unimolecular decomposition of some of the primary ions formed in the Coulomb explosions. In contrast to what is found for the reactions of Ca2+ with urea ([Ca(urea)]2+), minimal unimolecular losses of neutral fragments are observed for the gas-phase fragmentation processes of [Ca(gly)]2+, which is readily explained in terms of the topological differences between their respective PESs. [source] | |||||||||||||||||||