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Sample records for collision-induced dissociation product

  1. Collision-induced dissociation products of the protonated dipeptide carnosine: structural elucidation, fragmentation pathways and potential energy surface analysis.

    PubMed

    Moustafa, Eslam M; Ritacco, Ida; Sicilia, Emilia; Russo, Nino; Shoeib, Tamer

    2015-05-21

    Collision-induced dissociation (CID) experiments on protonated carnosine, [carnosine + H](+), with several collision energies were shown to yield eleven different fragment ions with the generation of product ions [carnosine-H2O + H](+) and [carnosine-NH3 + H](+) being the lowest energy processes. Energy-resolved CID showed that at slightly higher collision energies the ions [histidine + H](+) and [histidine-H2O-CO + H](+) are formed. At even higher energies four other product ions were observed, however, attained relatively lower abundances. Quantum chemistry calculations, carried out at different levels of theory, were employed to probe fragmentation mechanisms that account for all the experimental data. All the adopted computational protocols give similar energetic trends, and the range of the calculated free energy barrier values for the generation of all the observed product ions is in agreement with the fragmentation mechanisms offered here.

  2. DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Neumann, Elizabeth K.; Solouki, Touradj

    2015-08-01

    Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine]- fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine]- and complementary y-B type product ions.

  3. Comprehensive comparison of collision induced dissociation and electron transfer dissociation.

    PubMed

    Molina, Henrik; Matthiesen, Rune; Kandasamy, Kumaran; Pandey, Akhilesh

    2008-07-01

    Electron transfer dissociation (ETD) is a recently introduced mass spectrometric technique which has proven to be an excellent tool for the elucidation of labile post-translational modifications such as phosphorylation and O-GlcNAcylation of serine and threonine residues. However, unlike collision induced dissociation (CID), which has been studied for decades, the intricacies of ETD-based fragmentation have not yet been firmly established or systematically addressed. In this analysis, we have systematically compared the CID and ETD fragmentation patterns for the large majority of the peptides that do not contain such labile modifications. Using a standard 48 protein mix, we were able to measure false-positive rates for the experiments and also assess a large number of peptides for a detailed comparison of CID and ETD fragmentation pattern. Analysis of approximately 19,000 peptides derived from both standard proteins and complex protein samples revealed that (i) CID identified 50% more peptides than ETD; (ii) ETD resulted in approximately 20% increase in amino acid sequence coverage over CID; and (iii) combining CID and ETD fragmentation increased the sequence coverage for an average tryptic peptide to 92%. Interestingly, our analysis revealed that nearly 60% of all ETD-identified peptides carried two positive charges, which is in sharp contrast to what has been generally accepted. We also present a novel strategy for automatic validation of peptide assignments based on identification of a peptide by consecutive CID and ETD fragmentation in an alternating mode.

  4. Collision-induced dissociation with Fourier transform mass spectrometry

    SciTech Connect

    Cody, R.B.; Burnier, R.C.; Freiser, B.S.

    1982-01-01

    Collision-induced dissociations (CID) is demonstrated on a number of primary and secondary ions using a Nicolet prototype Fourier transform mass spectrometer (FT-MS). Like the triple quadrupole technique, CID using FT-MS is a relatively low energy and efficient process. The ability to study a wide range of ion-molecule reaction products is exemplified by results on proton-bound dimers and transition metal containing ionic species. Variation of collision energy by varying the RF irradiation level can provide information about product distributions as a function of energy as well as yield ion structural information. Like the triple quadrupole technique, no slits are employed and virtually all of the fragment ions formed by the CID process may be detected. Unlike all previous mass spectrometric techniques for studying CID, a tandem instrument is not required, and different experiments are performed by making software modifications rather than hardware modifications.

  5. Combined electron transfer dissociation-collision-induced dissociation fragmentation in the mass spectrometric distinction of leucine, isoleucine, and hydroxyproline residues in Peptide natural products.

    PubMed

    Gupta, Kallol; Kumar, Mukesh; Chandrashekara, Krishnappa; Krishnan, Kozhalmannom S; Balaram, Padmanabhan

    2012-02-03

    Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(•) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm = 43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z(•) ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MS(n)) method has been successfully implemented in a liquid chromatography-MS(n) platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

  6. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification.

    PubMed

    Zinnel, Nathanael F; Russell, David H

    2014-05-20

    Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

  7. Collision-induced gas phase dissociation rates

    NASA Technical Reports Server (NTRS)

    Hansen, C. Frederick

    1990-01-01

    The Landau-Zener theory of reactive cross sections was applied to diatomic molecules dissociating from a ladder of vibrational states. The result predicts a dissociation rate that is quite well duplicated by an Arrhenius function having a preexponential temperature dependence of about T(sub -1/2), at least for inert collision partners. This relation fits experimental data reasonably well. The theory is then used to calculate the effect of vibrational nonequilibrium on dissociation rate. For Morse oscillators, the results are about the same as given by Hammerling, Kivel, and Teare in their analytic approximation for harmonic oscillators, though at very high temperature a correction for the partition function limit is included. The empirical correction for vibration nonequilibrium proposed by Park, which is a convenient algorithm for CFD calculations, is modified to prevent a drastic underestimation of dissociation rates that occurs with this method when vibrational temperature is much smaller than the kinetic temperature of the gas.

  8. Collision-induced dissociation of protonated water clusters

    NASA Astrophysics Data System (ADS)

    Berthias, F.; Buridon, V.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.; Märk, T. D.

    2014-06-01

    Collision-induced dissociation (CID) has been studied for protonated water clusters H+(H2O)n, with n = 2-8, colliding with argon atoms at a laboratory energy of 8 keV. The experimental data have been taken with an apparatus (Device for Irradiation of Molecular Clusters, `Dispositif d'Irradiation d'Agrégats Moléculaire,' DIAM) that has been recently constructed at the Institut de Physique Nucléaire de Lyon. It includes an event-by-event mass spectrometry detection technique, COINTOF (correlated ion and neutral fragment time of flight). The latter device allows, for each collision event, to detect and identify in a correlated manner all produced neutral and charged fragments. For all the studied cluster ions, it has allowed us to identify branching ratios for the loss of i = 1 to i = n water molecules, leading to fragment ions ranging from H+(H2O)i=n-1 all the way down to the production of protons. Using a corresponding calibration technique we determine total charged fragment production cross sections for incident protonated water clusters H+(H2O)n, with n = 2-7. Observed trends for branching ratios and cross sections, and a comparison with earlier data on measured attenuation cross sections for water clusters colliding with other noble gases (He and Xe), give insight into the underlying dissociation mechanisms.

  9. Algorithm for thorough background subtraction of high-resolution LC/MS data: application to obtain clean product ion spectra from nonselective collision-induced dissociation experiments.

    PubMed

    Zhang, Haiying; Grubb, Mary; Wu, Wei; Josephs, Jonathan; Humphreys, William G

    2009-04-01

    Nonselective collision-induced dissociation (CID) is a technique for producing fragmentation products for all ions generated in an ion source. It is typical of liquid chromatography/mass spectrometry (LC/MS) analysis of complex samples that matrix-related components may contribute to the resulting product ion spectra and confound the usefulness of this technique for structure interpretation. In this proof-of-principle study, a high-resolution LC/MS-based background subtraction algorithm was used to process the nonselective CID data to obtain clean product ion spectra for metabolites in human plasma samples. With buspirone and clozapine metabolites in human plasma as examples, this approach allowed for not only facile detection of metabolites of interest but also generation of their respective product ion spectra that were clean and free of matrix-related interferences. This was demonstrated with both an MS(E) technique (where E represents collision energy) with a quadrupole time-of-flight (QTOF) instrument and an in-source fragmentation technique with an LTQ Orbitrap instrument. The combined nonselective CID and background subtraction approach should allow for detection and structural interpretation of other types of sample analyses where control samples are obtained.

  10. Simultaneous collision induced dissociation of the charge reduced parent ion during electron capture dissociation.

    PubMed

    Bushey, Jared M; Baba, Takashi; Glish, Gary L

    2009-08-01

    A method of performing collision induced dissociation (CID) on the charge-reduced parent ion as it is formed during electron capture dissociation (ECD), called ECD+CID, is described. In ECD+CID, the charge-reduced parent ion is selectively activated using resonant excitation and collisions with the helium bath gas inside a linear quadrupole ion trap ECD device (ECD(LIT)). It has been observed that ECD+CID can improve the sequence coverage for beta-endorphin over performing ECD alone (i.e., from 72 to 97%). Perhaps just as important, ECD+CID can be used to reduce the extent of multiple electron capture events observed when performing ECD in the ECD(LIT). Consequently, the abundance of mass-to-charge ratios corresponding to ECD product ions that contain neutralized protons is decreased, simplifying the interpretation of the product ion spectrum.

  11. Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments.

    PubMed

    Molina, Estefanía Rossich; Ortiz, Daniel; Salpin, Jean-Yves; Spezia, Riccardo

    2015-12-01

    In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

  12. Threshold collision induced dissociation experiment for azobenzene and its derivatives

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    In this study we investigated protonated azobenzene cation and properties of trans 2,2',6,6'-tetrafluoroazobenzene anion using the collision induced dissociation method and the results are compared with the results from ab initio electronic structure calculations. We measured the bond dissociation energies experimentally and found which theoretical quantum chemistry methods yield best results. Several high accuracy multi-level calculations such as CBS-QB3, G3 and G4 had been carried out to obtain reliable thermochemical information for azobenzene and several of its derivatives and their anion or cation. We also performed other experiments such as Raman spectroscopy to study these light sensitive molecules with promising applications such as photo-switching.

  13. Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ions.

    PubMed

    Bowers, Jeremiah J; Liu, Jian; Gunawardena, Harsha P; McLuckey, Scott A

    2008-01-01

    A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion.

  14. Collision-induced dissociation (CID) of peptides and proteins.

    PubMed

    Wells, J Mitchell; McLuckey, Scott A

    2005-01-01

    The most commonly used activation method in the tandem mass spectrometry (MS) of peptides and proteins is energetic collisions with a neutral target gas. The overall process of collisional activation followed by fragmentation of the ion is commonly referred to as collision-induced dissociation (CID). The structural information that results from CID of a peptide or protein ion is highly dependent on the conditions used to effect CID. These include, for example, the relative translational energy of the ion and target, the nature of the target, the number of collisions that is likely to take place, and the observation window of the apparatus. This chapter summarizes the key experimental parameters in the CID of peptide and protein ions, as well as the conditions that tend to prevail in the most commonly employed tandem mass spectrometers.

  15. Collision induced dissociation study of ester-based polyurethane fragmentation reactions.

    PubMed

    Gies, Anthony P; Hercules, David M

    2014-01-15

    A combination of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) collision induced dissociation (CID) and ion mobility separations (IMS) was used to study a complex mixture composed of unreacted polyester starting material (polybutylene adipate) and polyurethane (PUR) end products. Collision induced dissociation fragmentation identified two primary fragmentation mechanisms of PURs, which were used to generate a general fragmentation model. Predicted fragment ions were used to distinguish: (1) linear and cyclic PURs, (2) hard-block and soft-block PURS, (3) the degree of "blockiness" within hard- and soft-block PURs, (4) the location of the MDI linkages within each PUR chain, and (5) the relative intensities of various isobars intermingled within a precursor mass peak. These results were consistent with the observed IMS separations.

  16. Identifying drug metallation sites on peptides using electron transfer dissociation (ETD), collision induced dissociation (CID) and ion mobility-mass spectrometry (IM-MS).

    PubMed

    Williams, Jonathan P; Brown, Jeffery M; Campuzano, Iain; Sadler, Peter J

    2010-08-14

    Electron transfer dissociation (ETD) and collision induced dissociation (CID) have been used to locate the precise binding sites for platinum and ruthenium anticancer complexes on the peptide Substance P. We show that ETD combined with ion mobility-mass spectrometry significantly reduces mass spectral complexity and improves the S/N of the product-ions formed.

  17. Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps.

    PubMed

    Madsen, James A; Brodbelt, Jennifer S

    2009-03-01

    The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.

  18. On the dynamics of fragment isomerization in collision-induced dissociation of peptides.

    PubMed

    Polfer, Nick C; Bohrer, Brian C; Plasencia, Manolo D; Paizs, Béla; Clemmer, David E

    2008-02-14

    The structures of peptide collision-induced dissociation (CID) product ions are investigated using ion mobility/mass spectrometry techniques combined with theoretical methods. The cross-section results are consistent with a mixture of linear and cyclic structures for both b4 and a4 fragment ions. Direct evidence for cyclic structures is essential in rationalizing the appearance of fragments with scrambled (i.e., permutated) primary structures, as the cycle may not open up where it was initially formed. It is demonstrated here that cyclic and linear a4 structures can interconvert freely as a result of collisional activation, implying that isomerization takes place prior to dissociation.

  19. Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Hutchins, Patrick M.; Murphy, Robert C.

    2011-05-01

    Oxidative modification of polyunsaturated fatty acids, which occurs through enzymatic and nonenzymatic processes, is typically initiated by the attachment of molecular oxygen to an unsaturated fatty acyl chain forming a lipid hydroperoxide (LOOH). Enzymatic pathways are critical for cellular homeostasis but aberrant lipid peroxidation has been implicated in important pathologies. Analysis of primary oxidation products such as hydroperoxides has proven to be challenging for a variety of reasons. While negative ion electrospray ionization has been used for the specific detection of some LOOH species, hydroperoxide dehydration in the ion source has been a significant drawback. Here we describe positive ion electrospray ionization of ammoniated 13-hydroperoxy-9Z, 11E-octadecadienoyl cholesterol and 9-hydroperoxy-10E, 12Z-octadecadienoyl cholesterol, [M + NH4]+, following normal phase high-pressure liquid-chromatography. Dehydration in the ion source was not prevalent and the ammoniated molecular ion was the major species observed. Collisionally induced dissociation of the two positional isomers yielded unique product ion spectra resulting from carbon-carbon cleavages along their acyl chains. Further investigation of this behavior revealed that complex collision induced dissociations were initiated by scission of the hydroperoxide bond that drove subsequent acyl chain cleavages. Interestingly, some of the product ions retained the ammonium nitrogen through the formation of covalent carbon-nitrogen or oxygen-nitrogen bonds. These studies were carried out using hydroperoxy-octadecadienoate cholesteryl esters as model compounds, however the observed mechanisms of [LOOH + NH4]+ ionization and dissociation are likely applicable to the analysis of other lipid hydroperoxides and may serve as the basis for selective LOOH detection as well as aid in the identification of unknown lipid hydroperoxides.

  20. A tandem mass spectrometer for collision-induced dissociation

    NASA Astrophysics Data System (ADS)

    1982-02-01

    A tandem mass spectrometer is described for studies of collision-induced dissociation. This instrument is especially suited for investigations on organic molecules, e.g., biochemical substances, for m/z values up to 1000. The first stage is formed by a conventional EI source and a sector magnet, and has a mass resolution of about 600. The first stage is provided with a collision gas cell at the site of the detector slit. In the second stage the fragment ions are post-accelerated in order to reduce the relative energy-spread and to increase the resolution and transmission. The fragment spectrum is analyzed by a second magnet (R = 750 mm, deflection angle = 15 deg) and simultaneously recorded. Quadrupoles are added in order to vary the dispersion and to aid focussing. The ratio between the highest and lowest masses in a simultaneously detected spectrum may vary from 4 : 1 to 1.06 : 1. The resolution can be as high as 600, and the transmission from the collision cell to the CEMA ranges from 60 to 100%; the detection sensitivity can be as high as 1 ion per 10 s.

  1. Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization

    NASA Astrophysics Data System (ADS)

    Ropartz, David; Li, Pengfei; Fanuel, Mathieu; Giuliani, Alexandre; Rogniaux, Hélène; Jackson, Glen P.

    2016-10-01

    The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting.

  2. 4-HNE adduct stability characterized by collision-induced dissociation and electron transfer dissociation mass spectrometry.

    PubMed

    Fritz, Kristofer S; Kellersberger, Katherine A; Gomez, Jose D; Petersen, Dennis R

    2012-04-16

    4-Hydroxynonenal (4-HNE) alters numerous proteomic and genomic processes. Understanding chemical mechanisms of 4-HNE interactions with biomolecules and their respective stabilities may lead to new discoveries in biomarkers for numerous diseases of oxidative stress. Collision-induced dissociation (CID) and electron transfer dissociation (ETD) MS/MS were utilized to examine the stability of a 4-HNE-Cys Michael adduct. CID conditions resulted in the neutral loss of 4-HNE, also known as a retro-Michael addition reaction (RMA). Consequently, performing ETD fragmentation on this same adduct did not result in RMA. Interestingly, 4-HNE adduct reduction via sodium borohydride (NaBH₄) treatment stabilized against the CID induced RMA. In a direct comparison of three forms of 4-HNE adducts, computational modeling revealed sizable shifts in the shape and orientation of the lowest unoccupied molecular orbital (LUMO) density around the 4-HNE-Cys moiety. These findings demonstrate that ETD MS/MS analysis can be used to improve the detection of 4-HNE-protein modifications by preventing RMA reactions from occurring.

  3. Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation.

    PubMed

    Hayakawa, Eisuke; Menschaert, Gerben; De Bock, Pieter-Jan; Luyten, Walter; Gevaert, Kris; Baggerman, Geert; Schoofs, Liliane

    2013-12-06

    Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom peptides, and antimicrobial peptides. Since these peptides are processed at sites that are difficult to predict reliably, the search of their MS/MS spectra in sequence databases needs to be done without any protease setting. In addition, many endogenous peptides carry various post-translational modifications, making it essential to take these into account in the database search. These characteristics of endogenous peptides result in a huge search space, frequently leading to poor confidence of the peptide characterizations in peptidomics studies. We have developed a new MS/MS spectrum search tool for highly accurate and confident identification of endogenous peptides by combining two different fragmentation methods. Our approach takes advantage of the combination of two independent fragmentation methods (collision-induced dissociation and electron transfer dissociation). Their peptide spectral matching is carried out separately in both methods, and the final score is built as a combination of the two separate scores. We demonstrate that this approach is very effective in discriminating correct peptide identifications from false hits. We applied this approach to a spectral data set of neuropeptides extracted from mouse pituitary tumor cells. Compared to conventional MS-based identification, i.e., using a single fragmentation method, our approach significantly increased the peptide identification rate. It proved also highly effective for scanning spectra against a very large search space, enabling more accurate genome-wide searches and searches including multiple potential post-translational modifications.

  4. Collision Induced Dissociation and Energy Transfer in Molecular Hydroge

    NASA Astrophysics Data System (ADS)

    Mandy, Margot E.

    2006-06-01

    Molecular hydrogen is a significant constituent in giant molecular clouds in the interstellar medium. Shocks in these clouds are associated with star formation. The cooling of the shocks is governed by competition of collisional energy transfer and dissociation with radiative cooling by quadrupole emission. Thus a detailed understanding of collisional behaviour of molecular hydrogen is needed. Work in this group has examined energy transfer and dissociation in molecular energy transfer as the result of collisions with H, D, He, and H2. Using quasiclassical trajectories and chemically accurate ab initio potentials state-to-state rate coefficients have been determined. The uncertainties of the cross sections are propagated rigourously to give uncertainties of the rate coefficients and the rate coefficients are parameterized as a function of temperature. Comparisons with quantum calculations are discussed and the proposed website is described.This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada. The calculations were carried out using the high performance computing facility jointly supported by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, and Silicon Graphics at the University of Northern British Columbia.

  5. Multigenerational Broadband Collision-Induced Dissociation of Precursor Ions in a Linear Quadrupole Ion Trap

    NASA Astrophysics Data System (ADS)

    Snyder, Dalton T.; Cooks, R. Graham

    2016-12-01

    A method of fragmenting ions over a wide range of m/ z values while balancing energy deposition into the precursor ion and available product ion mass range is demonstrated. In the method, which we refer to as "multigenerational collision-induced dissociation", the radiofrequency (rf) amplitude is first increased to bring the lowest m/ z of the precursor ion of interest to just below the boundary of the Mathieu stability diagram (q = 0.908). A supplementary AC signal at a fixed Mathieu q in the range 0.2-0.35 (chosen to balance precursor ion potential well depth with available product ion mass range) is then used for ion excitation as the rf amplitude is scanned downward, thus fragmenting the precursor ion population from high to low m/ z. The method is shown to generate high intensities of product ions compared with other broadband CID methods while retaining low mass ions during the fragmentation step, resulting in extensive fragment ion coverage for various components of complex mixtures. Because ions are fragmented from high to low m/ z, space charge effects are minimized and multiple discrete generations of product ions are produced, thereby giving rise to "multigenerational" product ion mass spectra.

  6. Multigenerational Broadband Collision-Induced Dissociation of Precursor Ions in a Linear Quadrupole Ion Trap.

    PubMed

    Snyder, Dalton T; Cooks, R Graham

    2016-12-01

    A method of fragmenting ions over a wide range of m/z values while balancing energy deposition into the precursor ion and available product ion mass range is demonstrated. In the method, which we refer to as "multigenerational collision-induced dissociation", the radiofrequency (rf) amplitude is first increased to bring the lowest m/z of the precursor ion of interest to just below the boundary of the Mathieu stability diagram (q = 0.908). A supplementary AC signal at a fixed Mathieu q in the range 0.2-0.35 (chosen to balance precursor ion potential well depth with available product ion mass range) is then used for ion excitation as the rf amplitude is scanned downward, thus fragmenting the precursor ion population from high to low m/z. The method is shown to generate high intensities of product ions compared with other broadband CID methods while retaining low mass ions during the fragmentation step, resulting in extensive fragment ion coverage for various components of complex mixtures. Because ions are fragmented from high to low m/z, space charge effects are minimized and multiple discrete generations of product ions are produced, thereby giving rise to "multigenerational" product ion mass spectra. Graphical Abstract ᅟ.

  7. Collision-induced dissociation reactions and pulsed field ionization photoelectron

    SciTech Connect

    Stimson, Stephanie

    1999-02-12

    This report summarized the four parts of the research study and describes the general conclusions. Individual chapters have been removed for separate processing. The chapter titles are: A study of the dissociation of CH3SH+ by collisional activation: Observation of non-statistical behavior; High resolution vacuum ultraviolet pulsed field ionization photoelectron band for OCS+(X2π): An experimental and theoretical study; Rotationally resolved pulsed field ionization photoelectron bands of H2+2Σ+g, v+ = 0--18); and Rotationally resolved pulsed field ionization photoelectron bands of HD+2Σ+, v+ = 0--21).

  8. Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation.

    PubMed

    Guan, Ziqiang; Yates, Nathan A; Bakhtiar, Ray

    2003-06-01

    Electron capture dissociation (ECD) and collision-induced dissociation (CID), the two complementary fragmentation techniques, are demonstrated to be effective in the detection and localization of the methionine sulfoxide [Met(O)] residues in peptides using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The presence of Met(O) can be easily recognized in the low-energy CID spectrum showing the characteristic loss of methanesulfenic acid (CH(3)SOH, 64 Da) from the side chain of Met(O). The position of Met(O) can then be localized by ECD which is capable of providing extensive peptide backbone fragmentation without detaching the labile Met(O) side chain. We studied CID and ECD of several Met(O)-containing peptides that included the 44-residue human growth hormone-releasing factor (GRF) and the human atrial natriuretic peptide (ANP). The distinction and complementarity of the two fragmentation techniques were particularly remarkable in their effects on ANP, a disulfide bond-containing peptide. While the predominant fragmentation pathway in CID of ANP was the loss of CH(3)SOH (64 Da) from the molecular ion, ECD of ANP resulted in many sequence-informative products, including those from cleavages within the disulfide-bonded cyclic structure, to allow for the direct localization of Met(O) without the typical procedures for disulfide bond reduction followed by [bond]SH alkylation.

  9. Effects of electron-transfer coupled with collision-induced dissociation (ET/CID) on doubly charged peptides and phosphopeptides.

    PubMed

    Liu, Chih-Wei; Lai, Chien-Chen

    2011-01-01

    Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c- and z(·)-type product ions by randomly cleaving the N-Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in "bottom-up" proteomic analysis.

  10. Effects of Electron-Transfer Coupled with Collision-Induced Dissociation (ET/CID) on Doubly Charged Peptides and Phosphopeptides

    NASA Astrophysics Data System (ADS)

    Liu, Chih-Wei; Lai, Chien-Chen

    2011-01-01

    Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c- and z·-type product ions by randomly cleaving the N-Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in "bottom-up" proteomic analysis.

  11. Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology.

    PubMed

    Liu, Fan; Goshe, Michael B

    2010-07-15

    To ascertain more information on protein domain orientation and complex structure associations using chemical cross-linking, we have developed a combination of electrostatic collision-induced dissociative cross-linking reagents that differentially react with protein surfaces which are effectively analyzed by liquid chromatography-tandem mass spectrometry using ion trap multistage collision-induced dissociation. Implementing our original design and methodology based on disuccinimidyl-succinamyl-aspartyl-proline (SuDP) (Soderblom, E. J.; Goshe, M. B. Anal. Chem 2006, 78, 8059-8068. Soderblom, E. J.; Bobay, B. G.; Cavanagh, J.; Goshe, M. B. Rapid Commun Mass Spectrom 2007, 21, 3395-3408.), disuccinimidyl-succinamyl-valyl-proline (SuVP) was synthesized. The SuDP and SuVP reagents are the same except for the valyl and aspartyl groups which provide a distinctive chemical feature to each reagent. When performing labeling reactions using various protein-to-cross-linker ratios at pH 7.5, the negatively charged SuDP and neutral SuVP were used to label bovine serum albumin and hemoglobin. After protein digestion, the resulting peptides were analyzed using four different ion trap LC/MS(3) acquisition methods incorporating multistage CID. The more polar BSA surface resulted in a number of unique interpeptide and intrapeptide cross-links for each reagent whereas the less polarized surface of hemoglobin produced similar results for both reagents. Based on the identification of dead-end products (i.e., a cross-link modification containing a hydrolyzed end) for each protein, the aminolysis reactivity of each modified lysyl side chain revealed a preference for reacting with each reagent according to its local electrostatic surface environment. Overall, combinatorial application of SuDP and SuVP chemical labeling produces a set of unique interpeptide, intrapeptide, and dead-end cross-linked products that provides protein structural information according to its electrostatic surface

  12. Dynamic collision-induced dissociation of peptides in a quadrupole ion trap mass spectrometer.

    PubMed

    Collin, Olivier L; Beier, Matthias; Jackson, Glen P

    2007-07-15

    The fragmentation of natural peptides using dynamic collision-induced dissociation (DCID), a novel fragmentation method for quadrupole ion traps, is demonstrated. Using leucine enkephalin as a diagnostic molecule, the fragmentation efficiencies and energetics of DCID are compared with other methods of collisional activation in ion traps such as conventional on-resonance excitation and high-amplitude short-time excitation (HASTE). A typical fragmentation efficiency of approximately 20% is achieved for DCID, which is significantly lower than conventional CID (maximum near 80%). Tandem mass spectra of two other peptides, substance P and oxidized insulin alpha-chain, demonstrate that product ion spectra for DCID are comparable to conventional or HASTE CID. Because DCID achieves fragmentation during the standard mass acquisition scan, no extra time is necessary for on-resonance excitation or product ion collection, so analysis times are reduced by a minimum of 10-15% depending on the scanning conditions. DCID therefore offers more tandem mass spectra per second than conventional methods of collisional activation, which could be highly advantageous for bottom-up proteomics separations.

  13. Implementation of Dipolar Resonant Excitation Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS

    SciTech Connect

    Webb, Ian K.; Chen, Tsung-Chi; Danielson, William F.; Ibrahim, Yehia M.; Tang, Keqi; Anderson, Gordon A.; Smith, Richard D.

    2014-01-28

    Under and overfragmentation are significant hurdles to the data independent “bottom-up” approach to proteomics. Another challenge to the data independent approach is the convolution of fragments from different peptides that coelute in reverse-phase liquid chromatography/mass spectrometry (RPLC/MS). The ion mobility/collision induced dissociation/time-of flight mass spectrometry (IMS/CID/TOF MS) approach gives drift-time aligned fragment ions that have the same arrival time distributions as precursor ions, greatly aiding in fragment and peptide ion identification. We have modified an IMS/TOF MS platform to allow for resonant excitation CID experiments. Resonant excitation CID leads to highly efficient, mass-resolved fragmentation without additional excitation of product ions, alleviating the overfragmentation problem. The ability to apply resonant waveforms in mobility-resolved windows has been demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS separation experiment.

  14. Peptide scrambling during collision-induced dissociation is influenced by N-terminal residue basicity.

    PubMed

    Chawner, Ross; Holman, Stephen W; Gaskell, Simon J; Eyers, Claire E

    2014-11-01

    'Bottom up' proteomic studies typically use tandem mass spectrometry data to infer peptide ion sequence, enabling identification of the protein whence they derive. The majority of such studies employ collision-induced dissociation (CID) to induce fragmentation of the peptide structure giving diagnostic b-, y-, and a- ions. Recently, rearrangement processes that result in scrambling of the original peptide sequence during CID have been reported for these ions. Such processes have the potential to adversely affect ion accounting (and thus scores from automated search algorithms) in tandem mass spectra, and in extreme cases could lead to false peptide identification. Here, analysis of peptide species produced by Lys-N proteolysis of standard proteins is performed and sequences that exhibit such rearrangement processes identified. The effect of increasing the gas-phase basicity of the N-terminal lysine residue through derivatization to homoarginine toward such sequence scrambling is then assessed. The presence of a highly basic homoarginine (or arginine) residue at the N-terminus is found to disfavor/inhibit sequence scrambling with a coincident increase in the formation of b(n-1)+H(2)O product ions. Finally, further analysis of a sequence produced by Lys-C proteolysis provides evidence toward a potential mechanism for the apparent inhibition of sequence scrambling during resonance excitation CID.

  15. Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides

    NASA Astrophysics Data System (ADS)

    Robotham, Scott A.; Brodbelt, Jennifer S.

    2015-09-01

    In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types ( a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.

  16. Competitive threshold collision-induced dissociation: Gas-phase acidities and bond dissociation energies for a series of alcohols

    SciTech Connect

    DeTuri, V.F.; Ervin, K.M.

    1999-09-02

    Energy-resolved competitive collision-induced dissociation methods are used to measure the gas-phase acidities of a series of alcohols (methanol, ethanol, 2-propanol, and 2-methyl-2-propanol). The competitive dissociation reactions of fluoride-alcohol, [F{sup {minus}}{center{underscore}dot}HOR], alkoxide-water, [RO{sup {minus}}{center{underscore}dot}HOH], and alkoxide-methanol [RO{+-}{center{underscore}dot}HOCH{sub 3}] proton-bound complexes are studied using a guided ion beam tandem mass spectrometer. The reaction cross sections and product branching fractions to the two proton transfer channels are measured as a function of collision energy. The enthalpy difference between the two product channels is found by modeling the reaction cross sections near threshold using RRKM theory to account for the energy-dependent product branching ratio and kinetic shift. From the enthalpy difference, the alcohol gas-phase acidities are determined relative to the well-known values of HF and H{sub 2}O. The measured gas-phase acidities are {Delta}{sub acid}H{sub 298}(CH{sub 3}OH) = 1599 {+-} 3 kJ/mol, {Delta}{sub acid}H{sub 298}(CH{sub 3}CH{sub 2}OH) = 1586 {+-} 5 kJ/mol, {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 2}CHOH) = 1576 {+-} 4 kJ/mol, and {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 3}COH) = 1573 {+-} 3 kJ/mol.

  17. Low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides.

    PubMed

    Borisov, Oleg V; Goshe, Michael B; Conrads, Thomas P; Rakov, V Sergey; Veenstra, Timothy D; Smith, Richard D

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue-containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of Deinococcus radiodurans, the presence of these label-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys residue, and to differentiate identical Cys-peptides labeled with either ICAT-d0 or ICAT-d8.

  18. Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides

    SciTech Connect

    Borisov, Oleg V.; Goshe, Michael B. ); Conrads, Thomas P. ); Rakov, Vsevolod S. ); Veenstra, Timothy D. ); Smith, Richard D. )

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of D. radiodurans, the presence of these labeled-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys-residue, and to differentiate identical Cys-peptides labeled with either ICAT-D0 or ICAT-D8.

  19. Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions

    NASA Astrophysics Data System (ADS)

    Neta, Pedatsur; Stein, Stephen E.

    2011-05-01

    Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative intensities of charge states of product y- and b-ions depend on the final location of that proton. This study examines y-ion charge distributions for dissociation of doubly charged peptide ions, using a large reference library of peptide ion fragmentation generated from ion-trap CID of peptide ions from tryptic digests. Trends in relative intensities of y2+ and y1+ ions are examined as a function of bond cleavage position, peptide length (n), residues on either side of the bond and effects of residues remote from the bond. It is found that yn-2/b2 dissociation is the most sensitive to adjacent amino acids, that y2+/y1+ steadily increase with increasing peptide length, that the N-terminal amino acid can have a major influence in all dissociations, and in some cases other residues remote from the bond cleavage exert significant effects. Good correlation is found between the values of y2+/y1+ for the peptide and the proton affinities of the amino acids present at the dissociating peptide bond. A few deviations from this correlation are rationalized by specific effects of the amino acid residues. These correlations can be used to estimate trends in y2+/y1+ ratios for peptide ions from amino acid proton affinities.

  20. Collision-induced dissociation of glycero phospholipids using electrospray ion-trap mass spectrometry.

    PubMed

    Larsen, A; Uran, S; Jacobsen, P B; Skotland, T

    2001-01-01

    Characterisation of phospholipids was achieved using collision-induced dissociation (CID) with an ion-trap mass spectrometer. The product ions were compared with those obtained with a triple quadrupole mass spectrometer. In the negative ion mode the product ions were mainly sn-1 and sn-2 lyso-phospholipids with neutral loss of ketene in combination with neutral loss of the polar head group. Less abundant product ions were sn-1 and sn-2 carboxylate anions. CID using a triple quadrupole mass spectrometer, however, gave primarily the sn-1 and sn-2 carboxylate anions together with lyso-phosphatidic acid with neutral loss of water. For the ion trap a charge-remote-type mechanism is proposed for formation of the lyso-phospholipid product ions by loss of alpha-hydrogen on the fatty acid moiety, electron rearrangement and neutral loss of ketene. A second mechanism involves nucleophilic attack of the phosphate oxygen on the sn-1 and sn-2 glycerol backbone to form carboxylate anions with neutral loss of cyclo lyso-phospholipids. CID (MS(3) and MS(4)) of the lyso-phospholipids using the ion-trap gave the same carboxylate anions as those obtained with a triple quadrupole instrument where multiple collisions in the collision cell are expected to occur. The data demonstrate that phospholipid species determination can be performed by using LC/MS(n) with an ion-trap mass spectrometer with detection of the lyso-phospholipid anions. The ion-trap showed no loss in sensitivity in full scan MS(n) compared to multiple reaction monitoring data acquisition. In combination with on-line liquid chromatography this feature makes the ion-trap useful in the scanning modes for rapid screening of low concentrations of phospholipid species in biological samples as recently described (Uran S, Larsen A, Jacobsen PB, Skotland T. J. Chromatogr. B 2001; 758: 265).

  1. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer.

    PubMed

    Purvine, Samuel; Eppel, Jason-Thomas; Yi, Eugene C; Goodlett, David R

    2003-06-01

    Parallel collision-induced dissociation (CID) of peptides rather than serial, as is customary, results in loss of the obvious parent-fragment ion lineage available from CID on a single ion. We report proof-of-principle results suggesting the feasibility of parallel peptide CID, referred to here as shotgun CID, for protein identification when using the measured mass accuracies available from a time of flight mass analyzer and currently available search routines such as SEQUEST. Additionally, we report that parent-fragment ion lineage may be reconstructed from information encoded in the chromatographic single ion current traces of peptides.

  2. β-Methylphenylethylamines: common fragmentation pathways with amphetamines in electrospray ionization collision-induced dissociation.

    PubMed

    Brown, David H; Hansson, Robert; Oosthuizen, Francois; Sumner, Nathan

    2016-01-01

    β-Methylphenylethylamines are positional isomers of amphetamines and have been discovered in sporting supplements. Although the fragmentation of the β-methylphenylethylamine and N-methyl-β-methylphenylethylamine in gas chromatography-electron ionization-mass spectrometry (GC-EI-MS) systems is significantly different to their amphetamine and methylamphetamine isomers, under electrospray ionization commonly used in liquid chromatography-mass spectrometry (LC-MS) systems, the fragmentation of each of the isomeric pairs is almost identical. The similarities in fragmentation make it possible for the misidentification of the β-methylphenylethylamines as the illicit amphetamines. It is proposed that the similarities are due to a fragmentation pathway involving a common phenonium ion intermediate. By careful control of fragmentation energies in liquid chromatography-tandem mass spectrometry (LC-MS/MS) systems and/or close examination of the relative abundances of product ions formed by collision-induced dissociation (qualifier ratios), it is possible to distinguish the β-methylphenylethylamines from the amphetamines, even if significant retention time separation is not achieved. In liquid chromatography-electrospray ionization-quadrupole time of flight (LC-ESI-QTOF) systems the mass spectra of the β-methylphenylethylamines are identical to their amphetamine isomers. In such systems, retention time separation of the isomers is critical to avoid misidentification. During this study β-methylphenylethylamine and N-methyl-β-methylphenylethylamine have been identified in commercially available sporting supplements and oral fluid samples taken during the course of road-side drugs-in-drivers and workplace testing programmes. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Collision induced dissociation of protonated N-nitrosodimethylamine by ion trap mass spectrometry: Ultimate carcinogens in gas phase

    NASA Astrophysics Data System (ADS)

    Kulikova, Natalia; Baker, Michael; Gabryelski, Wojciech

    2009-12-01

    Collision induced dissociation of protonated N-nitrosodimethylamine (NDMA) and isotopically labeled N-nitrosodimethyl-d6-amine (NDMA-d6) was investigated by sequential ion trap mass spectrometry to establish mechanisms of gas phase reactions leading to intriguing products of this potent carcinogen. The fragmentation of (NDMA + H+) occurs via two dissociation pathways. In the alkylation pathway, homolytic cleavage of the N-O bond of N-dimethyl, N'-hydroxydiazenium ion generates N-dimethyldiazenium distonic ion which reacts further by a CH3 radical loss to form methanediazonium ion. Both methanediazonium ion and its precursor are involved in ion/molecule reactions. Methanediazonium ion showed to be capable of methylating water and methanol molecules in the gas phase of the ion trap and N-dimethyldiazenium distonic ion showed to abstract a hydrogen atom from a solvent molecule. In the denitrosation pathway, a tautomerization of N-dimethyl, N'-hydroxydiazenium ion to N-nitrosodimethylammonium intermediate ion results in radical cleavage of the N-N bond of the intermediate ion to form N-dimethylaminium radical cation which reacts further through [alpha]-cleavage to generate N-methylmethylenimmonium ion. Although the reactions of NDMA in the gas phase are different to those for enzymatic conversion of NDMA in biological systems, each activation method generates the same products. We will show that collision induced dissociation of N-nitrosodiethylamine (NDEA) and N-nitrosodipropylamine (NDPA) is also a feasible approach to gain information on formation, stability, and reactivity of alkylating agents originating from NDEA and NDPA. Investigating such biologically relevant, but highly reactive intermediates in the condensed phase is hampered by the short life-times of these transient species.

  4. Enhanced performance of pulsed Q collision induced dissociation-based peptide identification on a dual-pressure linear ion trap.

    PubMed

    Lössner, Christopher; Blackstock, Walter; Gunaratne, Jayantha

    2012-01-01

    Pulsed Q collision induced dissociation (PQD) was introduced for isobaric tag quantification on linear ion traps to circumvent the problem of the low-mass cut-off for collision induced dissociation (CID). Unfortunately, fragmentation efficiency is compromised and PQD has found limited use for identification as well as quantification. We demonstrate that PQD has a comparable peptide identification performance to CID on dual-pressure linear ion traps, opening the potential for wider use of isobaric tag quantification on this new generation of linear ion traps.

  5. Prediction of collision-induced dissociation spectra of common N-glycopeptides for glycoform identification.

    PubMed

    Zhang, Zhongqi; Shah, Bhavana

    2010-12-15

    Confident identification of the glycan moieties in glycopeptides by collision-induced dissociation (CID) requires accurate prediction of the CID spectrum of the glycopeptides. In this Article, the kinetic model for the prediction of peptide CID spectra is extended to predict the CID spectra of N-glycopeptides. The model was trained with 1831 ion-trap CID spectra of N-glycopeptides and is able to predict ion-trap CID spectra with excellent accuracy in ion intensities for N-glycopeptides up to 8000 u in mass. A total of 524 common glycoforms including complex N-glycans with 2-4 antennas, plus high-mannose type and hybrid type, can be predicted.

  6. A novel approach to collision-induced dissociation (CID) for ion mobility-mass spectrometry experiments.

    PubMed

    Becker, Christopher; Fernandez-Lima, Francisco A; Gillig, Kent J; Russell, William K; Cologna, Stephanie M; Russell, David H

    2009-06-01

    Collision induced dissociation (CID) combined with matrix assisted laser desorption ionization-ion mobility-mass spectrometry (MALDI-IM-MS) is described. In this approach, peptide ions are separated on the basis of mobility in a 15 cm drift cell. Following mobility separation, the ions exit the drift cell and enter a 5 cm vacuum interface with a high field region (up to 1000 V/cm) to undergo collisional activation. Ion transmission and ion kinetic energies in the interface are theoretically evaluated accounting for the pressure gradient, interface dimensions, and electric fields. Using this CID technique, we have successfully fragmented and sequenced a number of model peptide ions as well as peptide ions obtained by a tryptic digest. This instrument configuration allows for the simultaneous determination of peptide mass, peptide-ion sequence, and collision-cross section of MALDI-generated ions, providing information critical to the identification of unknown components in complex proteomic samples.

  7. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Webb, Ian K.; Garimella, Sandilya V. B.; Norheim, Randolph V.; Baker, Erin S.; Ibrahim, Yehia M.; Smith, Richard D.

    2016-07-01

    A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.

  8. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

    SciTech Connect

    Webb, Ian K.; Garimella, Sandilya V. B.; Norheim, Randolph V.; Baker, Erin S.; Ibrahim, Yehia M.; Smith, Richard D.

    2016-04-20

    A collision induced dissociation (CID) structures for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer (MS). The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably to other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of 9 peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.

  9. Identification of Proteins and Phosphoproteins Using Pulsed Q Collision Induced Dissociation (PQD)

    NASA Astrophysics Data System (ADS)

    Wu, Wells W.; Wang, Guanghui; Insel, Paul A.; Hsiao, Cheng-Te; Zou, Sige; Maudsley, Stuart; Martin, Bronwen; Shen, Rong-Fong

    2011-10-01

    Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.

  10. Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD).

    PubMed

    Wu, Wells W; Wang, Guanghui; Insel, Paul A; Hsiao, Cheng-Te; Zou, Sige; Maudsley, Stuart; Martin, Bronwen; Shen, Rong-Fong

    2011-10-01

    Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.

  11. Threshold collision-induced dissociation of protonated hydrazine and dimethylhydrazine clustered with water

    NASA Astrophysics Data System (ADS)

    McNary, Christopher P.; Armentrout, P. B.

    2016-12-01

    Threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer is performed on (N2H4)H+(H2O)n, where n = 1 and 2, and on the protonated unsymmetrical 1,1-dimethylhydrazine one-water complex. The primary dissociation pathway for all clusters is a loss of a single water molecule, which for n = 2 is followed by the sequential loss of an additional water molecule at higher collision energies. The data are analyzed using a statistical model after accounting for internal and kinetic energy distributions, multiple collisions, and kinetic shifts to obtain 0 K bond dissociation energies (BDEs). These are also converted using a rigid rotor/harmonic oscillator approximation to yield thermodynamic values at room temperature. Experimental BDEs compare favorably to theoretical BDEs determined at the B3LYP, M06, mPW1PW91, PBE0, MP2(full), and CCSD(T) levels of theory with a 6-311+G(2d,2p) basis set both with and without empirical dispersion. These calculations also allow visualization of the structures of these complexes, which are simple hydrogen-bonded donor-acceptors.

  12. Threshold Collision-Induced Dissociation of Proton-Bound Hydrazine and Dimethylhydrazine Clusters.

    PubMed

    McNary, Christopher P; Armentrout, P B

    2016-12-15

    Threshold collision-induced dissociation (TCID) using a guided ion beam tandem mass spectrometer is performed on (N2H4)nH(+) where n = 2-4 and on the proton-bound unsymmetrical 1,1-dimethylhydrazine (UDMH) dimer complex. The primary dissociation pathway for all reactants consists of loss of a single hydrazine (or UDMH) molecule followed by the sequential loss of additional hydrazine molecules at higher collision energies for n = 3 and 4. The data were analyzed using a statistical model after accounting for internal and kinetic energy distributions, multiple collisions, and kinetic shifts to obtain 0 K bond dissociation energies (BDEs). These are also converted to values at room temperature by using a rigid rotor/harmonic oscillator approximation and theoretical molecular constants. Experimental BDEs are compared to theoretical BDEs determined at the B3LYP, M06, mPW1PW91, PBE0, MP2(full), and CCSD(T) levels of theory with and without empirical dispersion with a 6-311+G(2d,2p) basis set. The structures of all clusters are explored and exhibit extensive hydrogen bonding.

  13. Bonding energetics in clusters formed by cesium salts: a study by collision-induced dissociation and density functional theory.

    PubMed

    Maria, Pierre-Charles; Massi, Lionel; Box, Natzaret Sindreu; Gal, Jean-François; Burk, Peeter; Tammiku-Taul, Jaana; Kutsar, Martin

    2006-01-01

    In relation to the interaction between (137)Cs and soil organic matter, electrospray mass spectrometry experiments and density functional theory (DFT) calculations were carried out on the dissociation of positively charged adducts formed by cesium nitrate and cesium organic salts attached to a cesium cation [Cs(CsNO(3))(CsA)](+) (A = benzoate, salicylate, hydrogen phthalate, hydrogen maleate, hydrogen fumarate, hydrogen oxalate, and hydrogen malonate ion). These mixed clusters were generated by electrospray from methanol solutions containing cesium nitrate and an organic acid. Collision-induced dissociation of [Cs(CsNO(3))(CsA)](+) in a quadrupole ion trap gave [Cs(CsNO(3))](+) and [Cs(CsA)](+) as major product ions. Loss of HNO(3) was observed, and also CO(2) loss in the case of A = hydrogen malonate. Branching ratios for the dissociation into [Cs(CsNO(3))](+) and [Cs(CsA)](+) were treated by the Cooks' kinetic method to obtain a quantitative order of bonding energetics (enthalpies and Gibbs free energies) between Cs(+) and the molecular salt (ion pair) CsA, and were correlated with the corresponding values calculated using DFT. The kinetic method leads to relative scales of Cs(+) affinities and basicities that are consistent with the DFT-calculated values. This study brings new data on the strong interaction between the cesium cation and molecular salts CsA.

  14. Bond dissociation energies of solvated silver(I)-amide complexes: competitive threshold collision-induced dissociations and calculations.

    PubMed

    Romanov, Vladimir; Siu, Chi-Kit; Verkerk, Udo H; Hopkinson, Alan C; Siu, K W Michael

    2010-07-08

    Using competitive threshold collision-induced dissociation (TCID) measurements, experimental bond dissociation energies have been evaluated for the water, methanol, and acetonitrile adducts of silver(I)-amide complexes. The influence of the solvent molecules on the binding energy of silver(I) to acetamide, N-methylacetamide, and N,N-dimethylacetamide was investigated. Experimental results show that solvents decrease the amide binding energy by 4-6 kcal mol(-1). Using density functional theory (DFT), binding energies were evaluated using nine functionals, after full geometry optimizations with the ECP28MWB basis set for silver and the 6-311++G(2df,2pd) basis set for the other atomic constituents of the ligands. In addition, calculations employing the DZVP basis set for Ag and DZVP2 for C, H, N, and O atoms at the B3LYP and MP2 levels of theory were used to investigate the influence of the basis set on the theoretical bond energies. A comparison of the experimental and theoretical silver(I)-ligand bond dissociation energies enables an assessment of the limitations in the basis sets and functionals in describing the energetics of the metal-solvent interaction and the metal-amide interaction. No single functional/basis set combination was found capable of predicting binding energies with a sufficiently high level of accuracy for the silver(I)-amide solvent complexes.

  15. Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions.

    PubMed

    Miladi, Mahsan; Harper, Brett; Solouki, Touradj

    2013-11-01

    Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where "A" denotes carbon thirteen ((13)C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic "b-type" ions.

  16. Comparison between Source-induced Dissociation and Collision-induced Dissociation of Ampicillin, Chloramphenicol, Ciprofloxacin, and Oxytetracycline via Mass Spectrometry.

    PubMed

    Lee, Seung Ha; Choi, Dal Woong

    2013-06-01

    Mass spectrometry (MS) is a very powerful instrument that can be used to analyze a wide range of materials such as proteins, peptides, DNA, drugs, and polymers. The process typically involves either chemical or electron (impact) ionization of the analyte. The resulting charged species or fragment is subsequently identified by the detector. Usually, single mass uses source-induced dissociation (SID), whereas mass/mass uses collision-induced dissociation (CID) to analyze the chemical fragmentations Each technique has its own advantages and disadvantages. While CID is most effective for the analysis of pure substances, multiple- step MS is a powerful technique to get structural data. Analysis of veterinary drugs ampicillin, chloramphenicol, ciprofloxacin, and oxytetracycline serves to highlight the slight differences between SID and CID. For example, minor differences were observed between ciprofloxacin and oxytetracycline via SID or CID. However, distinct fragmentation patterns were observed for ampicllin depending on the analysis method. Both SID and CID showed similar fragmentation spectra but different signal intensities for chloramphenicol. There are several factors that can influence the fragmentation spectra, such as the collision energy, major precursor ion, electrospray mode (positive or negative), and sample homogeneity. Therefore, one must select a fragmentation method on an empirical and case-by-case basis.

  17. Characterization of glycopeptides by combining collision-induced dissociation and electron-transfer dissociation mass spectrometry data.

    PubMed

    Alley, William R; Mechref, Yehia; Novotny, Milos V

    2009-01-01

    Structural characterization of a glycopeptide is not easily attained through collision-induced dissociation (CID), due to the extensive fragmentation of glycan moieties and minimal fragmentation of peptide backbones. In this study, we have exploited the potential of electron-transfer dissociation (ETD) as a complementary approach for peptide fragmentation. Model glycoproteins, including ribonuclease B, fetuin, horseradish peroxidase, and haptoglobin, were used here. In ETD, radical anions transfer an electron to the peptide backbone and induce cleavage of the N-Calpha bond. The glycan moiety is retained on the peptide backbone, being largely unaffected by the ETD process. Accordingly, ETD allows not only the identification of the amino acid sequence of a glycopeptide, but also the unambiguous assignment of its glycosylation site. When data acquired from both fragmentation techniques are combined, it is possible to characterize comprehensively the entire glycopeptide. This is being achieved with a mass spectrometer capable of alternating between CID and ETD on-the-fly during an LC/MS/MS analysis. This is demonstrated here with several tryptic glycopeptides.

  18. Tetrapositive plutonium, neptunium, uranium, and thorium coordination complexes: chemistry revealed by electron transfer and collision induced dissociation.

    PubMed

    Gong, Yu; Tian, Guoxin; Rao, Linfeng; Gibson, John K

    2014-04-17

    The Pu(4+), Np(4+), and U(4+) ions, which have large electron affinities of ∼34.6, ∼33.6, and ∼32.6 eV, respectively, were stabilized from solution to the gas phase upon coordination by three neutral tetramethyl-3-oxa-glutaramide ligands (TMOGA). Both collision induced dissociation (CID) and electron transfer dissociation (ETD) of Pu(TMOGA)3(4+) reveal the propensity for reduction of Pu(IV) to Pu(III), by loss of TMOGA(+) in CID and by simple electron transfer in ETD. The reduction of Pu(IV) is in distinct contrast to retention of Th(IV) in both CID and ETD of Th(TMOGA)3(4+), where only the C-Oether bond cleavage product was observed. U(TMOGA)3(4+) behaves similarly to Th(TMOGA)3(4+) upon CID and ETD, while the fragmentation patterns of Np(TMOGA)3(4+) lie between those of Pu(TMOGA)3(4+) and U(TMOGA)3(4+). It is notable that the gas-phase fragmentation behaviors of these exceptional tetrapositive complexes parallel fundamental differences in condensed phase chemistry within the actinide series, specifically the tendency for reduction from the IV to III oxidation states.

  19. Characterization of smokeless powders using multiplexed collision-induced dissociation mass spectrometry and chemometric procedures.

    PubMed

    Reese, Kristen L; Jones, A Daniel; Smith, Ruth Waddell

    2017-03-01

    This work demonstrates a non-targeted mass spectrometry approach for identification of organic compounds in smokeless powders. Unburned powders were removed from various commercial ammunitions of different brand, primer composition, caliber, and age. The unburned powders and corresponding fired residues were analyzed by liquid chromatography-atmospheric pressure chemical ionization-time-of-flight mass spectrometry (LC-APCI-TOFMS). Multiplexed collision-induced dissociation was performed at increasing collision potentials resulting in successive fragmentation that provided structural information for compound identification in a non-targeted manner. Nine compounds were identified in the powders, including akardite II, ethyl centralite, diphenylamine, N-nitrosodiphenylamine, and dibutyl phthalate. Multivariate statistical procedures were performed to first investigate association and discrimination of the unburned powders. Principal components analysis (PCA) of the chemical profiles suggested nine distinct groups of powders, according to the dominant organic compounds present. The clusters formed in hierarchical cluster analysis (HCA) were mostly in agreement with PCA groupings although HCA provided a metric to quantify the similarity. Finally, association of the fired residue to the corresponding unburned powder was possible although the success was highly dependent on the composition of the unburned powder and the extent of compound depletion as a result of firing.

  20. Detection of tyrosine phosphorylated peptides via skimmer collision-induced dissociation/ion trap mass spectrometry.

    PubMed

    Zolodz, Melissa D; Wood, Karl V

    2003-03-01

    Phosphorylation of proteins is an important post-translational protein modification in cellular response to environmental change and occurs in both prokaryotes and eukaryotes. Identification of the amino acid on individual proteins that become phosphorylated in response to extracellular stimulus is essential for understanding the mechanisms involved in the intracellular signals that these modifications facilitate. Most protein kinases catalyze the phosphorylation of proteins on serine, threonine or tyrosine. Although tyrosine phosphorylation is often the least abundant of the three major phosphorylation sites, it is important owing to its role in signal pathways. Currently available methods for the identification of phosphorylation sites can often miss low levels of tyrosine phosphorylations. This paper describes a method for the identification of phosphotyrosine-containing peptides using electrospray ionization on an ion trap mass spectrometer. Skimmer-activated collision-induced dissociation (CID) was used to generate the phosphotyrosine immonium ion at m/z 216. This method is gentle enough that the protonated molecule of the intact peptide is still observed. In-trap CID was employed for the verification of the phosphotyrosine immonium ion. Using this technique, low levels of phosphotyrosine-containing peptides can be identified from peptide mixtures separated by nanoflow micro liquid chromatography/mass spectrometry.

  1. The fate of b-ions in the two worlds of collision-induced dissociation.

    PubMed

    Waldera-Lupa, Daniel M; Stefanski, Anja; Meyer, Helmut E; Stühler, Kai

    2013-12-01

    Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss.

  2. Unusual Fragmentation of Pro-Ser/Thr-Containing Peptides Detected in Collision-Induced Dissociation Spectra

    NASA Astrophysics Data System (ADS)

    Medzihradszky, Katalin F.; Trinidad, Jonathan C.

    2012-04-01

    During collision-induced dissociation (CID)-, phosphoserine- and phosphothreonine-containing peptides frequently undergo neutral loss of phosphoric acid. Subsequent amide bond cleavage N-terminal to the site of phosphorylation results in a y ion with a mass 18 Da lower than the corresponding unmodified y fragment. We report here that when the phosphoserine or phosphothreonine is directly preceded by a proline, an unusual fragment with a mass 10 Da higher than the corresponding unmodified y ion is frequently observed. Accurate mass measurements are consistent with elimination of the phosphoric acid followed by fragmentation between the α carbon and the carbonyl group of the proline residue. We propose a cyclic oxazoline structure for this fragment. Our observation may be explained by the charge-directed SN2 neighboring group participation reaction proposed for the phosphoric acid elimination by Palumbo et al. [Palumbo, A. M., Tepe, J. J., Reid, G. E. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides. J. Protein Res. 7(2), 771-779 (2008)]. Considering such specific fragment ions for confirmation purposes after regular database searches may boost the confidence of peptide identifications as well as phosphorylation site assignments.

  3. Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology

    NASA Astrophysics Data System (ADS)

    Xu, Fuxing; Dang, Qiankun; Dai, Xinhua; Fang, Xiang; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2016-08-01

    Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry.

  4. Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation.

    PubMed

    Pak, Alireza; Lesage, Denis; Gimbert, Yves; Vékey, Károly; Tabet, Jean-Claude

    2008-04-01

    The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values () carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy () versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).

  5. Hydration Energies of Zinc(II): Threshold Collision-Induced Dissociation Experiments and Theoretical Studies

    NASA Astrophysics Data System (ADS)

    Cooper, Theresa E.; Carl, D. R.; Armentrout, P. B.

    2009-11-01

    The first experimentally determined sequential bond dissociation energies of Zn2+(H2O)n complexes, where n = 6-10, are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer coupled with an electrospray ionization source. Kinetic energy dependent cross sections are obtained and analyzed to yield 0 K threshold measurements for the loss of one and two water ligands after accounting for multiple collisions, kinetic shifts, and energy distributions. The threshold measurements are then converted from 0 to 298 K values to give the hydration energies for sequentially losing one water from each parent complex. Theoretical geometry optimizations and single-point energy calculations are performed using several levels of theory for comparison to experiment. Although different levels of theory disagree on the ground-state conformation of most complexes examined here leading to potential ambiguities in the final thermochemical values, calculations at the MP2(full) level provide the best agreement with experiment. On this basis, the present experiments are most consistent with the inner solvent shell of Zn2+ being five waters, except for Zn2+(H2O)6 where all waters bind directly to the metal ion. The charge separation process, Zn2+(H2O)n → ZnOH+(H2O)m + H+(H2O)n-m-1, which is in competition with the loss of water from the parent complex, is also observed for n = 6-8. These processes are analyzed in detail in the following paper.

  6. Selective cleavage of protonated penetratin and its substitutes under low-energy collision-induced dissociation condition.

    PubMed

    Peng, Juan; Zu, Lily; Fang, Weihai; Huang, Lingyun; Wang, Yaru; He, Dacheng

    2010-06-01

    An understanding of the dissociation of penetratin is important for improving its metabolic stability and cargo-delivery efficiency. In this study, we describe the selective cleavage of the K15-K16 amide bond of penetratin under the low-energy collision-induced dissociation condition in mass spectrometry. A variety of penetratin substitutes have been studied in which key basic amino acids have been substituted within the sequence. The calculated structure indicates that an alpha-helix structure prevents the fragmentation of the central peptide domain and the side chain of lysine is involved in the proton translocation process.

  7. Characterization of γ-carboxylated tryptic peptides by collision-induced dissociation and electron transfer dissociation mass spectrometry.

    PubMed

    Ramström, Margareta; Sandberg, Helena

    2011-01-01

    Vitamin K-dependent carboxylation of glutamic acid (Glu) residues into γ-carboxyglutamic acid (Gla) is a post-translational modification essential for normal protein activity of, for example, proteins involved in the blood coagulation system. These proteins may contain as many as 12 sites for γ-carboxylation within a protein sequence of 45 amino acid residues. In the biopharmaceutical industry, powerful analytical techniques are required for identification and localization of modified sites. We here present comparatively easy and rapid methods for studies of Gla-containing proteins using recent technology. The performances of two mass spectrometric fragmentation techniques, collision-induced dissociation (CID) and electron transfer dissociation (ETD), were evaluated with respect to γ-carboxylated peptides, applying on-line LC-ion trap MS. ETD MS has so far not been reported for Gla-containing peptides and the applicability of CID for heavily γ-carboxylated proteins has not been evaluated. The anticoagulant protein, protein C, containing nine Gla-sites, was chosen as a model protein. After tryptic digestion, three peptides containing Gla-residues were detected by MS; a 1.2 kDa fragment containing two Gla-residues, a 4.5 kDa peptide containing seven residues and also the 5.6 kDa tryptic peptides containing all nine Gla-residues. Regarding the shortest peptide, both CID and ETD provided extensive peptide sequencing. For the larger peptides, fragmentation by CID resulted in loss of the 44 Da CO(2)-group, while little additional fragmentation of the peptide chain was observed. In contrast, ETD resulted in comprehensive fragmentation of the peptide backbone. The study demonstrates that the combination of both techniques would be beneficial and complementary for investigation of γ-carboxylated proteins and peptides.

  8. Generation of peptide radical dications via low-energy collision-induced dissociation of [CuII(terpy)(M + H)].3+ .

    PubMed

    Chu, Ivan K; Lam, Corey N W

    2005-11-01

    The first example of the formation of hydrogen-deficient radical cations of the type [M + H](.2+) is demonstrated to occur through a one-electron-transfer mechanism upon low-energy collision-induced dissociation (CID) of gas-phase triply charged [Cu(II)(terpy)(M + H)](.3+) complex ions (where M is an angiotensin III or enkephalin derivative; terpy = 2,2':6',2''-terpyridine). The collision-induced dissociation of doubly charged [M + H](.2+) radical cations generates similar product ions to those prepared through hot electron capture dissociation (HECD). Isomeric isoleucine and leucine residues were distinguished by observing the mass differences between [z(n) + H](.+) and w(n)(+) ions (having the same residue number, n) of the Xle residues. The product ion spectrum of [z(n) + H](.+) reveals that the w(n)(+) ions are formed possibly from consecutive fragmentations of [z(n) + H](.+) ions. Although only the first few [M + H](.2+) species have been observed using this approach, these hydrogen-deficient radical cations produce fragment ions that have more structure-informative patterns and are very different from those formed during the low-energy tandem mass spectrometry of protonated peptides.

  9. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides.

    PubMed

    Giese, Sven H; Fischer, Lutz; Rappsilber, Juri

    2016-03-01

    Cross-linking/mass spectrometry resolves protein-protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers.

  10. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

    2016-04-01

    Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

  11. Identification of five pyrrolidinyl substituted cathinones and the collision-induced dissociation of electrospray-generated pyrrolidinyl substituted cathinones.

    PubMed

    Qian, Zhenhua; Jia, Wei; Li, Tao; Hua, Zhendong; Liu, Cuimei

    2016-07-01

    This article reports on the analytical properties of five pyrrolidinyl substituted cathinones: α-pyrrolidinononaphenone (α-PNP, 1), 4-chloro-α-pyrrolidinopropiophenone (4-Cl-α-PPP, 2), 4-chloro-α-pyrrolidinovalerophenone (4-Cl-α-PVP, 3), 5-dihydrobenzofuranpyrovalerone (5-DBFPV, 4), and 2-(pyrrolidin-1-yl)-1-(5,6,7,8-tetrahydronaphthalen-2-yl)hexan-1-one (β-THNPH, 5). These identifications were based on liquid chromatography-quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). To our knowledge, no analytical data about α-PNP, 4-Cl-α-PPP, 4-Cl-α-PVP, and β-THNPH have appeared until now, making this the first report on these compounds. Moreover, in order to study the collision-induced dissociation (CID) characteristic fragmentation routes of pyrrolidinyl substituted cathinones, a total number of 13 pyrrolidinyl substituted cathinones were selected and discussed. The major fragmentation pathways under CID mode are produced, leading to the formation of characteristic ions. Product ions of [M-C4 H9 N](+) and Cn H2n N(+) indicate the presence of pyrrolidinyl substitution. Characteristic fragments are also produced via the cleavages of the CH-N(CH2 )4 bond and the CO-CHN bond. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Appropriate choice of collision-induced dissociation energy for qualitative analysis of notoginsenosides based on liquid chromatography hybrid ion trap time-of-flight mass spectrometry.

    PubMed

    Wang, Guang-Ji; Fu, Han-Xu; Xiao, Jing-Cheng; Ye, Wei; Rao, Tai; Shao, Yu-Hao; Kang, Dian; Xie, Lin; Liang, Yan

    2016-04-01

    Liquid chromatography hybrid ion trap/time-of-flight mass spectrometry possessesd both the MS(n) ability of ion trap and the excellent resolution of a time-of-flight, and has been widely used to identify drug metabolites and determine trace multi-components for in natural products. Collision energy, one of the most important factors in acquiring MS(n) information, could be set freely in the range of 10%-400%. Herein, notoginsenosides were chosen as model compounds to build a novel methodology for the collision energy optimization. Firstly, the fragmental patterns of the representatives for the authentic standards of protopanaxadiol-type and protopanaxatriol-type notoginsenosides authentic standards were obtained based on accurate MS(2) and MS(3) measurements via liquid chromatography hybrid ion trap/time-of-flight mass spectrometry. Then the extracted ion chromatograms of characteristic product ions of notoginsenosides in Panax Notoginseng Extract, which were produced under a series of collision energies and, were compared to screen out the optimum collision energies values for MS(2) and MS(3). The results demonstrated that the qualitative capability of liquid chromatography hybrid ion trap/time-of-flight mass spectrometry was greatly influenced by collision energies, and 50% of MS(2) collision energy was found to produce the highest collision-induced dissociation efficiency for notoginsenosides. BesidesAddtionally, the highest collision-induced dissociation efficiency appeared when the collision energy was set at 75% in the MS(3) stage.

  13. Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z(+•) -type.

    PubMed

    Nguyen, Huong T H; Shaffer, Christopher J; Ledvina, Aaron R; Coon, Joshua J; Tureček, František

    2015-02-15

    The serine residue displays specific effects on the dissociations of peptide fragment cation-radicals of the z(+•) type which are produced by electron transfer dissociation. Energy-resolved collision-induced dissociation (ER-CID), time-resolved infrared multiphoton dissociation (TR-IRMPD), and single-photon UV photodissociation at 355 nm revealed several competitive dissociation pathways consisting of loss of OH radical, water, and backbone cleavages occurring at N-terminal and C-terminal positions relative to the serine residue. The activation modes using slow-heating and UV photon absorption resulted in different relative intensities of fragment ions. This indicated that the dissociations proceeded through several channels with different energy-dependent kinetics. The experimental data were interpreted with the help of electron structure calculations that provided fully optimized structures and relative energies for cis and trans amide isomers of the z4(+•) ions as well as isomerization, dissociation, and transition state energies. UV photon absorption by the z4(+•) ions was due to Cα-radical amide groups created by ETD that provided a new chromophore absorbing at 355 nm.

  14. Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z+•-type

    PubMed Central

    Nguyen, Huong T. H.; Shaffer, Christopher J.; Ledvina, Aaron R.; Coon, Joshua J.

    2014-01-01

    The serine residue displays specific effects on the dissociations of peptide fragment cation-radicals of the z+• type which are produced by electron transfer dissociation. Energy-resolved collision-induced dissociation (ER-CID), time-resolved infrared multiphoton dissociation (TR-IRMPD), and single-photon UV photodissociation at 355 nm revealed several competitive dissociation pathways consisting of loss of OH radical, water, and backbone cleavages occurring at N-terminal and C-terminal positions relative to the serine residue. The activation modes using slow-heating and UV photon absorption resulted in different relative intensities of fragment ions. This indicated that the dissociations proceeded through several channels with different energy-dependent kinetics. The experimental data were interpreted with the help of electron structure calculations that provided fully optimized structures and relative energies for cis and trans amide isomers of the z4+• ions as well as isomerization, dissociation, and transition state energies. UV photon absorption by the z4+• ions was due to Cα-radical amide groups created by ETD that provided a new chromophore absorbing at 355 nm. PMID:26005367

  15. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    PubMed

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

  16. Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents.

    PubMed

    Soderblom, Erik J; Bobay, Benjamin G; Cavanagh, John; Goshe, Michael B

    2007-01-01

    Chemical crosslinking combined with mass spectrometry is a useful tool for studying the topological organization of multiprotein interactions, but it is technically challenging to identify peptides involved in a crosslink using tandem mass spectrometry (MS/MS) due to the presence of product ions originating from both peptides within the same crosslink. We have previously developed a novel set of collision-induced dissociative chemical crosslinking reagents (CID-CXL reagents) that incorporate a labile bond within the linker which readily dissociates at a single site under low-energy collision-induced dissociation (CID) to enable independent isolation and sequencing of the crosslinked peptides by traditional MS/MS and database searching. Alternative low-energy CID events were developed within the in-source region by increasing the multipole DC offset voltage (ISCID) or within the ion trap by increasing the collisional excitation (ITCID). Both dissociation events, each having their unique advantages, occur without significant backbone fragmentation to the peptides, thus permitting subsequent CID to be applied to these distinct peptide ions for generation of suitable product ion spectra for database searching. Each approach was developed and applied to a chemical crosslinking study involving the N-terminal DNA-binding domain of AbrB (AbrBN), a transition-state regulator in Bacillus subtilis. A total of thirteen unique crosslinks were identified using the ITCID approach which represented a significant improvement over the eight unique crosslinks identified using the ISCID approach. The ability to segregate intrapeptide and interpeptide crosslinks using ITCID represents the first step towards high-throughput analysis of protein-protein crosslinks using our CID-CXL reagents.

  17. DART-MS in-source collision induced dissociation and high mass accuracy for new psychoactive substance determinations.

    PubMed

    Musah, Rabi A; Cody, Robert B; Domin, Marek A; Lesiak, Ashton D; Dane, A John; Shepard, Jason R E

    2014-11-01

    The influx of new psychoactive substances is a problem that is challenging the analytical capabilities of enforcement agencies. Cathinone designer drugs are less likely to be included in routine drug screens and typical drug formulations are commonly mixtures with continually shifting components. Ambient ionization mass spectrometry employs relatively mild conditions to desorb and ionize solid samples, imparting much less energy than that associated with conventional mass spectrometry methods. Direct analysis in real time mass spectrometry (DART-MS) is an ambient ionization method that was employed to rapidly screen cathinones, alone and in mixtures, readily enabling differentiation of the active drug(s) from various cutting agents. Accurate mass determinations provided preliminary identification of the various components of drug mixtures. The data generated in forensic mass spectrometry can be used for both elemental composition formulations and isotope abundance calculations for determination of unknown psychoactive substances, and we demonstrate how this data could be applied to the presence of new drugs as the active components shift in response to regulations. Isotope abundance calculations were used to develop a candidate pool of possible molecular formulas associated with cathinones as a specific class of designer drugs. Together, the combination of a time-of-flight (TOF) mass analyzer along with in-source collision-induced dissociation (CID) spectra were used to drastically narrow the pool of candidates to a single molecular formula. The [M+H](+) and product ion peaks provided data for presumptive analysis of various substituted synthetic cathinones in a manner that is complementary to conventional GC-MS analysis of new psychoactive substances.

  18. Mechanistic study of the collision-induced dissociation of sodium-cationized polylactide oligomers: a joint experimental and theoretical investigation.

    PubMed

    De Winter, Julien; Lemaur, Vincent; Marsal, Philippe; Coulembier, Olivier; Cornil, Jérôme; Dubois, Philippe; Gerbaux, Pascal

    2010-07-01

    The low-kinetic energy collision-induced dissociation (CID) behavior of different sodium-cationized polylactide (PLA) oligomers was thoroughly investigated to shed some light on the analytical potentialities of CID experiments in the context of polymer characterization. Indeed, investigation of several end-groups modified PLA reveals that, in addition to the expected end-group specific dissociations, collisionally-excited PLA.Na(+) suffer from a backbone cleavage. The so-obtained sodium-bound dimer cations consecutively undergo the loss of a monomeric residue that corresponds to neutral acrylic acid. The experimental observations, performed on a hybrid Q-ToF instrument, were totally corroborated by a theoretical study involving DFT calculations, molecular mechanics, and molecular dynamics calculations.

  19. Gas-phase dissociation of ionic liquid aggregates studied by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation.

    PubMed

    Fernandes, Ana M; Coutinho, João A P; Marrucho, Isabel M

    2009-01-01

    Positive singly charged ionic liquid aggregates [(C(n)mim)(m+1)(BF(4))(m)](+) (mim = 3-methylimidazolium; n = 2, 4, 8 and 10) and [(C(4)mim)(m+1)(A)(m)](+) (A = Cl(-), BF(4) (-), PF(6) (-), CF(3)SO(3) (-) and (CF(3)SO(2))(2)N(-)) were investigated by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation. The electrospray ionisation mass spectra (ESI-MS) showed the formation of an aggregate with extra stability for m = 4 for all the ionic liquids with the exception of [C(4)mim][CF(3)SO(3)]. ESI-MS-MS and breakdown curves of aggregate ions showed that their dissociation occurred by loss of neutral species ([C(n)mim][A])(a) with a >or= 1. Variable-energy collision induced dissociation of each aggregate from m = 1 to m = 8 for all the ionic liquids studied enabled the determination of E(cm, 1/2) values, whose variation with m showed that the monomers were always kinetically much more stable than the larger aggregates, independently of the nature of cation and anion. The centre-of-mass energy values correlate well with literature data on ionic volumes and interaction and hydrogen bond energies.

  20. Identification and relative quantification of proteins in Escherichia coli proteome by "up-front" collision-induced dissociation.

    PubMed

    Arike, Liisa; Nahku, Ranno; Borrisova, Maria; Adamberg, Kaarel; Vilu, Raivu

    2010-01-01

    A method for identifying and quantifying proteins with relatively low-cost orthogonal acceleration time-of- flight mass spectrometry (oa-ToF-MS) was tested. Escherichia coli (E. coli) K12 MG1655 cell lysate was separated by 1D gel-electrophoresis; fractions were digested and separated fast and reproducibly by ultra-performance liquid chromatography (UPLC). Peptides were identified using oa-ToF-MS to measure exact masses of parent ions and the fragment ions generated by up-front collision-induced dissociation. Fragmentation of all compounds was achieved by rapidly cycling between high- and low values of energy applied to ions. More than 100 proteins from E. coli K12 proteome were identified and relatively quantified. Results were found to correlate with transcriptome data determined by DNA microarrays.

  1. Top-down proteomics with a quadrupole time-of-flight mass spectrometer and collision-induced dissociation.

    PubMed

    Armirotti, Andrea; Benatti, Umberto; Damonte, Gianluca

    2009-03-01

    With slight modifications of the instrumental parameters, we demonstrate that satisfactory top-down data can be obtained with collision-induced dissociation (CID) tandem mass spectrometry on a quadrupole time-of-flight (qTOF) instrument not originally designed for this purpose. Protein identification is achieved with both N- and C-terminal sequence tags and BLAST database searches. The accurate mass measurement of multiply charged fragment ions (mostly y and b-type) supplements the limited set of cleavage sites and provides a high degree of sequence coverage (90-100%). Post-translational modification issues can be addressed too. This approach might help those mass spectrometry (MS) core facilities that are not able to afford very high-resolution instruments, thus expanding the benefits of top-down protein analysis over the worldwide MS community.

  2. High-energy collision induced dissociation fragmentation pathways of peptides, probed using a multiturn tandem time-of-flight mass spectrometer 'MULTUM-TOF/TOF'

    SciTech Connect

    Toyoda, Michisato; Giannakopulos, Anastassios E.; Colburn, Alex W.; Derrick, Peter J.

    2007-07-15

    A new multiturn tandem time-of-flight (TOF) mass spectrometer 'MULTUM-TOF/TOF' has been designed and constructed. It consists of a matrix-assisted laser desorption/ionization ion source, a multiturn TOF mass spectrometer, a collision cell, and a quadratic-field ion mirror. The multiturn TOF mass spectrometer can overcome the problem of precursor ion selection in TOF, due to insufficient time separation between two adjacent TOF peaks, by increasing the number of cycles. As a result, the total TOF increases with the increase in resolving power. The quadratic-field ion mirror allows temporal focusing for fragment ions with different kinetic energies. Product ion spectra from monoisotopically selected precursor ions of angiotensin I, substance P, and bradykinin have been obtained. The fragment ions observed are mainly the result of high-energy collision induced dissociation.

  3. Efficient Polyatomic Interference Reduction in Plasma-Source Mass Spectrometry Via Collision Induced Dissociation

    SciTech Connect

    Jackson, Glen P.; King, Fred L; Duckworth, Douglas {Doug} C

    2003-02-01

    Evidence is provided that illustrates quadrupole ion traps can be used to selectively attenuate strongly bound diatomic ions occurring at the same nominal mass as an analyte ion of interest. Dissociation rates for TaO{sup +} (D{sub 0} {approx} 750 kJ mol{sup -1}) are found to be at least an order of magnitude larger than the loss rate of Au{sup +} due to scattering under 'slow heating' resonance excitation conditions at q{sub z} {approx} 0.67 and using neon as the bath gas. This rate difference is sufficient for the selective removal of this strongly-bound diatomic ion over the loss of the Au{sup +} at the same mass-to-charge ratio. Other examples of quadrupole ion trap CID for the selective reduction of common plasma-generated species are also evaluated by examining the dissociation of GdO{sup +} in the presence of Yb{sup +}, and Cu{sub 2}{sup +} in the presence of Te{sup +}. In each case, a different method of applying the excitation signals is presented, and the attenuation rates for the diatomic species due to CID are substantially larger than scattering losses for the bare metal ions. Evidence is also presented that demonstrates CID can be accomplished in concert with a slow mass analysis scan, thereby providing a means of (1) eliminating polyatomic ions (formed in the plasma or reaction cell) over an extended mass range, (2) recovering metal ion signal from the metal-containing polyatomic ions, and (3) minimizing deleterious secondary reactions of product ions.

  4. Exploring salt bridge structures of gas-phase protein ions using multiple stages of electron transfer and collision induced dissociation.

    PubMed

    Zhang, Zhe; Browne, Shaynah J; Vachet, Richard W

    2014-04-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting noncovalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas-phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase.

  5. Effect of structural parameters on the electron capture dissociation and collision-induced dissociation pathways of copper(II)-peptide complexes.

    PubMed

    Chen, Xiangfeng; Wang, Ze; Li, Wan; Wong, Y L Elaine; Chan, T-W Dominic

    2015-01-01

    The gas-phase dissociation pathways of proteins/peptides are usually affected by the nature of the charge carrier and the sequence of amino acid residues. The effects of peptide structural parameters, including peptide composition, chain length and amide hydrogen, on the gas-phase dissociation of Cu(II)-model peptide complexes were explored in this study. Polyglycine peptides with flexible frames were used as probes to reduce the complexity of the system and illustrate the mechanism. Results revealed that the types of fragment ions generated in the electron capture dissociation (ECD) of Cu(II)-adducted peptides changed according to the basic amino acid residue composition. Charged or neutral tryptophan side-chain losses were observed in the collision-induced dissociation (CID) of Cu(II)-peptide complexes. Internal electron transfer between tryptophan and metal ion within the complex occurred during the CID reaction, leaving the charge-reduced Cu(+) as a closed d-shell stable electron configuration. The choice of the reaction channel was then determined by the gas-phase basicity of the peptide. Amide hydrogen was critical in the formation of metalated b-/y-ions in the ECD process as determined through mutation of the backbone amide group. Increasing the chain length suppressed the ECD of Cu-metalated peptide species. Our results indicate that the structural parameters of peptides play important roles in the gas-phase dissociation processes of Cu-peptide complexes.

  6. Quasiclassical trajectory study of the collision-induced dissociation dynamics of Ar + CH3SH+ using an ab initio interpolated potential energy surface.

    PubMed

    Martínez-Núñez, Emilio; Vázquez, Saulo A; Aoiz, F Javier; Castillo, Jesús F

    2006-02-02

    Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential energy surface includes seven accessible dissociation channels of the cation. The present QCT calculations show that migration of hydrogen atoms, leading to the rearrangement CH(3)SH(+) <--> CH(2)SH(2)(+), is significant at the collision energies considered (6.5-34.7 eV) and that the formation of CH(3)(+), CH(3)S(+), and CH(2)(+) cations takes place primarily by a "shattering" mechanism in which the products are formed just after the collision. The theoretical product abundances are found to be in qualitative agreement with the experimental data. However, at high collision energies, the calculated total cross sections for the formation of CH(3)(+) and CH(2)SH(+) cations are noticeably larger than the experimental determinations. Several features of the dynamics of the CID processes are discussed.

  7. Low-Energy Collision-Induced Dissociation Mass Spectra of Protonated p-Toluenesulfonamides Derived from Aliphatic Amines

    NASA Astrophysics Data System (ADS)

    Bialecki, Jason B.; Weisbecker, Carl S.; Attygalle, Athula B.

    2014-06-01

    Collision-induced fragmentation of protonated N-alkyl- p-toluenesulfonamides primarily undergo either an elimination of the amine to form CH3-(C6H4)-SO2 + cation ( m/z 155) or an alkene to form a cation for the protonated p-toluenesulfonamide ( m/z 172). To comprehend the fragmentation pathways, several deuterated analogs of N-decyl- p-toluenesulfonamides were prepared and evaluated. Hypothetically, two mechanisms, both of which involve ion-neutral complexes, can be envisaged. In one mechanism, the S-N bond fragments to produce an intermediate [sulfonyl cation/amine] complex, which dissociates to afford the m/z 155 cation (Pathway A). In the other mechanism, the C-N bond dissociates to produce a different intermediate complex. The fragmentation of this [ p-toluenesulfonamide/carbocation] complex eliminates p-toluenesulfonamide and releases the carbocation (Pathway B). Computations carried out by the Hartree-Fock method suggested that the Pathway B is more favorable. However, a peak for the carbocation is observed only when the carbocation formed is relatively stable. For example, the spectrum of N-phenylethyl- p-toluenesulfonamide is dominated by the peak at m/z 105 for the incipient phenylethyl cation, which rapidly isomerizes to the remarkably stable methylbenzyl cation. The peaks for the carbocations are weak or absent in the spectra of most of N-alkyl- p-toluenesulfonamides because alkyl carbocations, such as the decyl cation, rearrange to more stable secondary cations by 1,2-hydride and alkyl shifts. The energy freed is not dissipated, but gets internalized, causing the carbocation to dissociate either by transferring a proton to the sulfonamide or by releasing smaller alkenes to form smaller carbocations. The loss of the positional integrity in this way was proven by deuterium labeling experiments.

  8. Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach

    SciTech Connect

    Ibrahim, Yehia M.; Prior, David C.; Baker, Erin Shammel; Smith, Richard D.; Belov, Mikhail E.

    2010-06-01

    The confidence in peptide (and protein) identifications with ion mobility spectrometry time-of-flight mass spectrometry (IMS-TOFMS) is expected to drastically improve with the addition of information from an efficient ion dissociation step prior to MS detection. High throughput IMS-TOFMS analysis imposes a strong need for multiplexed ion dissociation approaches where multiple precursor ions yield complex sets of fragment ions that are often intermingled with each other in both the drift time and m/z domains. We have developed and evaluated a novel approach for collision-induced dissociation (CID) with an IMS-TOFMS instrument. It has been shown that precursor ions activated inside an rf-device with an axial dc-electric field produce abundant fragment ions which are radially confined with the rf-field and collisionally cooled at an elevated pressure, resulting in high CID efficiencies comparable or higher than those measured in triple-quadrupole instruments We have also developed an algorithm for deconvoluting these complex multiplexed tandem MS spectra by clustering both the precursor and fragment ions into the matching drift time profiles and by effectively utilizing high mass measurement accuracy of the TOFMS. In a single IMS separation with a tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using multiplexed CID approach downstream of the IMS separation. Peptides were identified based upon the correlation between the precursor and fragment drift time profiles and by matching the profile representative masses to those of in silico BSA tryptic peptides and their fragments. The false discovery rate (FDR) of peptide identifications from multiplexed MS/MS spectra was less than 1%.

  9. Linkage determination of linear oligosaccharides by MS(n) (n > 2) collision-induced dissociation of Z₁ ions in the negative ion mode.

    PubMed

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2014-02-01

    Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MS(n), n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides (18)O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS(3) CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MS(n) CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

  10. Collision-induced dissociation of sulfur-containing imidazolium ionic liquids.

    PubMed

    Lesimple, Alain; He, Xun; Chan, Tak-Hang; Mamer, Orval

    2008-01-01

    A number of 1,2-dimethylimidazole ionic liquids substituted on N(II) with alkyl chains of varying lengths terminated with sulfur-containing groups were investigated by electrospray high-resolution tandem Fourier-transform mass spectrometry. Fragmentation pathways are strongly dependent on the oxidation state of the sulfur and the alkyl chain length. The dissociations detected are rationalized by deuterium labeling, comparisons between homologous compounds and accurate mass data. Several homolytic processes are reported, leading to distonic ions and loss of hydrogen, methyl and other free radicals.

  11. High-Energy Collision-Induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

    2014-08-01

    A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

  12. Collision-induced dissociation fragmentation inside disulfide C-terminal loops of natural non-tryptic peptides.

    PubMed

    Samgina, Tatiana Y; Vorontsov, Egor A; Gorshkov, Vladimir A; Artemenko, Konstantin A; Zubarev, Roman A; Ytterberg, Jimmy A; Lebedev, Albert T

    2013-07-01

    Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.

  13. Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues.

    PubMed

    Leitner, Alexander; Foettinger, Alexandra; Lindner, Wolfgang

    2007-07-01

    Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.

  14. Differentiation of lisinopril and its RSS diastereomer by liquid chromatography combined with collision-induced dissociation mass spectrometry.

    PubMed

    Sun, Cuirong; Zhu, Peixi; Hu, Nan; Wang, Danhua; Pan, Yuanjiang

    2010-01-01

    A simple and sensitive liquid chromatography tandem multiple-stage mass spectrometry (HPLC/MS/MS) method suitable for bulk lisinopril analysis was developed, by which lisinopril and its RSS isomer were separated and differentiated. In the collision-induced dissociation (CID) mass spectra of the [M + H](+) ions, the abundance of the fragment ion of m/z 246 for lisinopril was about two times higher than the ion of m/z 245; however, the former fragment ion was noted to be a little lower than the latter for RSS isomer at all collision energies. In the CID mass spectra of the [M + Li](+) ion, the abundance of the rearrangement ion of m/z 315 for the RSS isomer was about three times higher than that for lisinopril. Furthermore, the difference was supported by the results of energy-resolved mass spectrometry (ERMS) in the test range of collision energies. Similar differences were also observed between the CID mass spectra of lisinopril and RSS isomer methylester, which indicated that the RSS isomer could be rapidly characterized by the CID mass spectra of both the protonated and lithium adduct ion. Elemental compositions of all the ions were confirmed by Fourier Transform ion cyclotron resonance ESI mass spectrometry (FT-ICR-ESI/MS). In addition, theoretical computations were carried out to support the experimental results.

  15. Cello-, malto- and xylooligosaccharide fragmentation by collision-induced dissociation using QIT and FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Pasanen, Salla; Jänis, Janne; Vainiotalo, Pirjo

    2007-05-01

    In order to study the effects of the precursor ion type and the carbohydrate structure on the fragmentation of neutral unsubstituted oligosaccharides in collision-induced dissociation (CID), a systematic study of deprotonated, protonated, ammoniated and alkali metal cationized cello-, malto- and xylooligosaccharides was carried out using a quadrupole ion trap (QIT) and Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The fragmentation pathway was highly dependent on the choice of the precursor ion type. Deprotonated precursors gave rise to both glycosidic and cross-ring fragmentation, with clear differences among the three oligosaccharides, therefore being the most prominent for structural analysis. The fragmentation behavior of the xylooligosaccharides differed from that of the cello- and maltooligosaccharides for all the precursor ions studied, most remarkably with the deprotonated and ammoniated precursors. Stereochemical differentiation of cello- and maltooligosaccharides was possible with the use of deprotonated, lithiated and sodiated precursors. In general, as the size of the alkali metal cation increased the amount of structurally informative cross-ring fragmentation increased, but the probability for metal ion loss from the precursor ion also increased. The CID spectra of xylooligosaccharides measured with the QIT and FT-ICR were surprisingly similar.

  16. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.

    PubMed

    Chowdhury, Saiful M; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J; Mayer, M Uljana; Smith, Richard D; Adkins, Joshua N

    2009-07-01

    Chemical cross-linking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of cross-linked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact cross-linkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under conditions where the native complex structure is stable. In this study, we present a novel compact cross-linker that contains two distinct features: (1) an alkyne tag and (2) a small molecule detection tag (NO(2)) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the cross-linked peptides after proteolytic cleavage and coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO(2) moiety provides a secondary means of detecting cross-linked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this cross-linker, which we termed CLIP (click-enabled linker for interacting proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for cross-linked ubiquitin in highly complex E. coli cell lysates. Sequential collision-induced dissociation tandem mass spectrometry (CID-MS/MS) and electron transfer dissociation (ETD)-MS/MS of intercross-linked peptides (two peptides connected with a cross-linker) are also demonstrated for improved automated identification of cross-linked peptides.

  17. Defining the disulfide bonds of insulin-like growth factor-binding protein-5 by tandem mass spectrometry with electron transfer dissociation and collision-induced dissociation.

    PubMed

    Nili, Mahta; Mukherjee, Aditi; Shinde, Ujwal; David, Larry; Rotwein, Peter

    2012-01-06

    The six high-affinity insulin-like growth factor-binding proteins (IGFBPs) comprise a conserved family of secreted molecules that modulate IGF actions by regulating their half-life and access to signaling receptors, and also exert biological effects that are independent of IGF binding. IGFBPs are composed of cysteine-rich amino- (N-) and carboxyl- (C-) terminal domains, along with a cysteine-poor central linker segment. IGFBP-5 is the most conserved IGFBP, and contains 18 cysteines, but only 2 of 9 putative disulfide bonds have been mapped to date. Using a mass spectrometry (MS)-based strategy combining sequential electron transfer dissociation (ETD) and collision-induced dissociation (CID) steps, in which ETD fragmentation preferentially induces cleavage of disulfide bonds, and CID provides exact disulfide linkage assignments between liberated peptides, we now have definitively mapped 5 disulfide bonds in IGFBP-5. In addition, in conjunction with ab initio molecular modeling we are able to assign the other 4 disulfide linkages to within a GCGCCXXC motif that is conserved in five IGFBPs. Because of the nature of ETD fragmentation MS experiments were performed without chemical reduction of IGFBP-5. Our results not only establish a disulfide bond map of IGFBP-5 but also define a general approach that takes advantage of the specificity of ETD and the scalability of tandem MS, and the predictive power of ab initio molecular modeling to characterize unknown disulfide linkages in proteins.

  18. Combined use of ion mobility and collision-induced dissociation to investigate the opening of disulfide bridges by electron-transfer dissociation in peptides bearing two disulfide bonds.

    PubMed

    Massonnet, Philippe; Upert, Gregory; Smargiasso, Nicolas; Gilles, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2015-01-01

    Disulfide bonds are post-translational modifications (PTMs) often found in peptides and proteins. They increase their stability toward enzymatic degradations and provide the structure and (consequently) the activity of such folded proteins. The characterization of disulfide patterns, i.e., the cysteine connectivity, is crucial to achieve a global picture of the active conformation of the protein of interest. Electron-transfer dissociation (ETD) constitutes a valuable tool to cleave the disulfide bonds in the gas phase, avoiding chemical reduction/alkylation in solution. To characterize the cysteine pairing, the present work proposes (i) to reduce by ETD one of the two disulfide bridges of model peptides, resulting in the opening of the cyclic structures, (ii) to separate the generated species by ion mobility, and (iii) to characterize the species using collision-induced dissociation (CID). Results of this strategy applied to several peptides show different behaviors depending on the connectivity. The loss of SH· radical species, observed for all the peptides, confirms the cleavage of the disulfides during the ETD process.

  19. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  20. Collision-induced signal enhancement: a method to increase product ion intensities in MS/MS and MSn experiments.

    PubMed

    Asam, M R; Ray, K L; Glish, G L

    1998-05-01

    Collision-induced signal enhancement (CISE), a new technique to enhance the MSn capabilities of the quadrupole ion trap, is demonstrated. CISE is based on the chemistry, i.e., the dissociation pathways, of the analyte examined. Polysaccharides up to hexamers are used to demonstrate the capabilities of CISE to enhance signal in two distinct functional modes. Mode 1 CISE is designed to enhance the signal of an ion desired for MSn analysis. Mode 2 CISE is designed to enhance structurally significant product ions in an MS/MS spectrum. Two different approaches can be utilized to effect the two functional modes of CISE. Both approaches use conventional resonant excitation techniques to effect dissociation, which is performed nonanalytically, i.e., without isolation of the ions to be dissociated. The two approaches are (1) single-frequency resonance excitation, and (2) broad-band wave form resonant excitation. Experimental results for Mode 1 CISE analysis demonstrate up to a 17.3-fold signal increase for the single-frequency approach and 5.3-fold using broad-band excitation. Mode 2 CISE analysis shows up to a 16.3-fold increase in signal strength with single-frequency excitation and 3.3-fold using broad-band excitation.

  1. Identification of reactive cysteines in a protein using arsenic labeling and collision-induced dissociation tandem mass spectrometry.

    PubMed

    Lu, Meiling; Wang, Hailin; Wang, Zhongwen; Li, Xing-Fang; Le, X Chris

    2008-08-01

    Trivalent arsenicals have high affinity for thiols (such as free cysteines) in proteins. We describe here the use of this property to develop a collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) technique for the identification of reactive cysteines in proteins. A trivalent arsenic species, dimethylarsinous acid (DMA (III)), with a residue mass (103.9607) and mass defect distinct from the normal 20 amino acids, was used to selectively label reactive cysteine residues in proteins. The CID fragment ions of the arsenic-labeled sequences shifted away from the more abundant normal fragments that would otherwise overlap with the ions of interest. Along with the internal and immonium ions, the arsenic-labeled fragment ions served as MS/MS signatures for identification of the binding sites and for assessment of the relative reactivity of individual cysteine residues in a protein. Using this method, we have identified two highly reactive binding sites in rat hemoglobin (Hb): Cys-13alpha and Cys-125beta. Cys-13alpha was bound to DMA (III) in the Hb of rats fed with arsenic, and this binding was responsible for arsenic accumulation in rat blood, while Cys-125beta was found to bind to glutathione in rat blood. This study revealed the relative reactivity of the cysteines in rat Hb in the following decreasing order: Cys-13alpha > Cys-111alpha > Cys-104alpha and Cys-13alpha > Cys-125beta > Cys-93beta. Arsenic-labeling is easy and fast for identification of active binding sites without enzymatic digestion and acid hydrolysis, and useful for characterization and identification of metal binding sites in other proteins.

  2. Collision-induced thermochemistry of reactions of dissociation of glycyl-homopeptides-An experimental and theoretical analysis.

    PubMed

    Ivanova, Bojidarka; Spiteller, Michael

    2017-02-01

    The research draws on experimental and theoretical data about energetics and kinetics of mass spectrometric (MS) reactions of glycyl homopenta- (G5) and glycyl homohexapeptides (G6). It shows the great applicability of the methods of quantum chemistry to predict MS profile of peptides using energetics of collision induced dissociation (CID) fragment species. Mass spectrometry is among irreplaceable methods, providing unambiguous qualitative, quantitative and structural information about analytes, applicable to many scientific areas like environmental chemistry; food chemistry; medicinal chemistry; and more. Our study could be considered of substantial interdisciplinary significance, where MS proteomics is widely used. The experimental design involves electrospray ionization (ESI) and CID MS/MS. Theoretical design is based on ab initio and density functional theory (DFT) methods. Experimental MS and theoretical free Gibbs energies as well as rate constants of fragment reactions are compared. The thermodynamic encompasses gas-phase and polar continuum analysis, including polar protic and aprotic solvents within temperature T = 10-500 K; dielectric constant ε = 0-78, pH, and ionic strengths μ = 0.001-1.0 mol dm(-1) . There are computed and discussed 39 protonated forms of peptides at amide N- and -(NHC)=O centers; corresponding fragment ions studying their thermodynamic stability depending on experimental conditions. A correlation analysis between molecular conformations of parent ions and fragment species; their proton accepting ability and internal energy distribution is carried out. Data about ionization potentials (IPs) and electron affinities (EAs) are discussed, as well.

  3. Electrospray ionization collision-induced dissociation mass spectrometry: a tool to characterize synthetic polyaminocarboxylate ferric chelates used as fertilizers.

    PubMed

    Orera, Irene; Orduna, Jesús; Abadía, Javier; Alvarez-Fernández, Ana

    2010-01-01

    Fertilizers based on synthetic polyaminocarboxylate ferric chelates have been known since the 1950s to be successful in supplying Fe to plants. In commercial Fe(III)-chelate fertilizers, a significant part of the water-soluble Fe-fraction consists of still uncharacterized Fe byproducts, whose agronomical value is unknown. Although collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) is a valuable tool for the identification of such compounds, no fragmentation data have been reported for most Fe(III)-chelate fertilizers. The aim of this study was to characterize the CID-MS(2) fragmentation patterns of the major synthetic Fe(III)-chelates used as Fe-fertilizers, and subsequently use this technique for the characterization of commercial fertilizers. Quadrupole-time-of-flight (QTOF) and spherical ion trap mass analyzers equipped with an electrospray ionization (ESI) source were used. ESI-CID-MS(2) spectra obtained were richer when using the QTOF device. Specific differences were found among Fe(III)-chelate fragmentation patterns, even in the case of positional isomers. The analysis of a commercial Fe(III)-chelate fertilizer by high-performance liquid chromatography (HPLC) coupled to ESI-MS(QTOF) revealed two previously unknown, Fe-containing compounds, that were successfully identified by a comprehensive comparison of the ESI-CID-MS(2)(QTOF) spectra with those of pure chelates. This shows that HPLC/ESI-CID-MS(2)(QTOF), along with the Fe(III)-chelate fragmentation patterns, could be a highly valuable tool to directly characterize the water-soluble Fe fraction in Fe(III)-chelate fertilizers. This could be of great importance in issues related to crop Fe-fertilization, both from an agricultural and an environmental point of view.

  4. Combined Use of Post-Ion Mobility/Collision-Induced Dissociation and Chemometrics for b Fragment Ion Analysis

    NASA Astrophysics Data System (ADS)

    Zekavat, Behrooz; Miladi, Mahsan; Becker, Christopher; Munisamy, Sharon M.; Solouki, Touradj

    2013-09-01

    Although structural isomers may yield indistinguishable ion mobility (IM) arrival times and similar fragment ions in tandem mass spectrometry (MS), it is demonstrated that post-IM/collision-induced dissociation MS (post-IM/CID MS) combined with chemometrics can enable independent study of the IM-overlapped isomers. The new approach allowed us to investigate the propensity of selected b type fragment ions from AlaAlaAlaHisAlaAlaAla-NH2 (AAA(His)AAA) heptapeptide to form different isomers. Principle component analysis (PCA) of the unresolved post-IM/CID profiles indicated the presence of two different isomer types for b4 +, b5 +, and b6 + and a single isomer type for b7 + fragments of AAA(His)AAA. We employed a simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) to calculate the total IM profiles and CID mass spectra of b fragment isomers. The deconvoluted CID mass spectra showed discernible fragmentation patterns for the two isomers of b4 +, b5 +, and b6 + fragments. Under our experimental conditions, calculated percentages of the "cyclic" isomers (at the 95 % confidence level for n = 3) for b4 +, b5 +, and b6 + were 61 (± 5) %, 36 (± 5) %, and 48 (± 2) %, respectively. Results from the SIMPLISMA deconvolution of b5 + species resembled the CID MS patterns of fully resolved IM profiles for the two b5 + isomers. The "cyclic" isomers for each of the two-component b fragment ions were less susceptible to ion fragmentation than their "linear" counterparts.

  5. Structural characterization of glycerophospholipids by combinations of ozone- and collision-induced dissociation mass spectrometry: the next step towards "top-down" lipidomics.

    PubMed

    Pham, Huong T; Maccarone, Alan T; Thomas, Michael C; Campbell, J Larry; Mitchell, Todd W; Blanksby, Stephen J

    2014-01-07

    The complete structural elucidation of complex lipids, including glycerophospholipids, using only mass spectrometry represents a major challenge to contemporary analytical technologies. Here, we demonstrate that product ions arising from the collision-induced dissociation (CID) of the [M + Na](+) adduct ions of phospholipids can be isolated and subjected to subsequent gas-phase ozonolysis - known as ozone-induced dissociation (OzID) - in a linear ion-trap mass spectrometer. The resulting CID/OzID experiment yields abundant product ions that are characteristic of the acyl substitution on the glycerol backbone (i.e., sn-position). This approach is shown to differentiate sn-positional isomers, such as the regioisomeric phosphatidylcholine pair of PC 16:0/18:1 and PC 18:1/16:0. Importantly, CID/OzID provides a sensitive diagnostic for the existence of an isomeric mixture in a given sample. This is of very high value for the analysis of tissue extracts since CID/OzID analyses can reveal changes in the relative abundance of isomeric constituents even within different tissues from the same animal. Finally, we demonstrate the ability to assign carbon-carbon double bond positions to individual acyl chains at specific backbone positions by adding subsequent CID and/or OzID steps to the workflow and that this can be achieved in a single step using a hybrid triple quadrupole-linear ion trap mass spectrometer. This unique approach represents the most complete and specific structural analysis of lipids by mass spectrometry demonstrated to date and is a significant step towards comprehensive top-down lipidomics.

  6. Threshold collision-induced dissociation measurements using a ring ion guide as the collision cell in a triple-quadrupole mass spectrometer.

    PubMed

    Romanov, Vladimir; Verkerk, Udo H; Siu, Chi-Kit; Hopkinson, Alan C; Siu, K W Michael

    2009-08-15

    A triple-quadrupole mass spectrometer has been modified for bond-dissociation energy measurements via threshold collision-induced dissociations (TCIDs) by replacing the conventional collision cell with a ring ion guide. Optimal operating conditions for the ring ion guide were determined or derived, and validated using a set of complexes for which bond dissociation energies are known. A comparison with reference data (within a range of 16-57 kcal/mol) indicates an accuracy approaching that of TCID determined on a guided ion-beam mass spectrometer. Complexes for which bond-dissociation energies were measured include metal ion complexes of simple ligands, amino acids and peptides, as well as of carbonic acid. There is excellent agreement between our experimental data and literature data, as well as theoretical data determined using a high-level computational method.

  7. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

    NASA Astrophysics Data System (ADS)

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  8. Fragmentation behavior of a thiourea-based reagent for protein structure analysis by collision-induced dissociative chemical cross-linking.

    PubMed

    Müller, Mathias Q; Dreiocker, Frank; Ihling, Christian H; Schäfer, Mathias; Sinz, Andrea

    2010-08-01

    The fragmentation behavior of a novel thiourea-based cross-linker molecule specifically designed for collision-induced dissociation (CID) MS/MS experiments is described. The development of this cross-linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross-linked products. The new derivatizing reagent for chemical cross-linking solely contains a thiourea moiety that is flanked by two amine-reactive N-hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N-termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities--a characteristic CNL of 85 u--ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross-linking studies. A detailed examination of the CID behavior of the presented thiourea-based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross-linking of proteins.

  9. Application of MALDI TOF/TOF mass spectrometry and collision-induced dissociation for the identification of disulfide-bonded peptides.

    PubMed

    Janecki, Dariusz J; Nemeth, Jennifer F

    2011-07-01

    This paper describes a method for the fast identification and composition of disulfide-bonded peptides. A unique fragmentation signature of inter-disulfide-bonded peptides is detected using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry and high-energy collision-induced dissociation (CID). This fragmentation pattern identifies peptides with an interconnected disulfide bond and provides information regarding the composition of the peptides involved in the pairing. The distinctive signature produced using CID is a triplet of ions resulting from the cleavage of the disulfide bond to produce dehydroalanine, cysteine or thiocysteine product ions. This method is not applicable to intra-peptide disulfide bonds, as the cleavage mechanism is not the same and a triplet pattern is not observed. This method has been successfully applied to identifying disulfide-bonded peptides in a number of control digestions, as well as study samples where disulfide bond networks were postulated and/or unknown.

  10. Chemical ionization by [NO]+ and subsequent collision-induced dissociation for the selective on-line detection of monoterpenes and linalool.

    PubMed

    Rimetz-Planchon, Juliette; Dhooghe, Frederik; Schoon, Niels; Vanhaecke, Frank; Amelynck, Crist

    2011-03-15

    Existing on-line Chemical Ionization Mass Spectrometry (CIMS) techniques for quantification of atmospheric trace gases, such as Biogenic Volatile Organic Compounds (BVOCs), suffer from difficulty in discriminating between isomeric (and more generally isobaric) compounds. Selective detection of these compounds, however, is important because they can affect atmospheric chemistry in different ways, depending on their chemical structure. In this work, Flowing Afterglow Tandem Mass Spectrometry (FATMS) was used to investigate the feasibility of the selective detection of a series of monoterpenes, an oxygenated monoterpene (linalool) and a sesquiterpene (β-caryophyllene). Ions at m/z 137 from [H(3)O](+) chemical ionization of α-pinene, linalool and β-caryophyllene have been subjected to Collision-Induced Dissociation (CID) with Ar in the collision cell of a tandem mass spectrometer at center-of-mass energies ranging between 0 and 8 eV. Similar fragmentation patterns were obtained, demonstrating that this method is not suited for the selective detection of these compounds. However, CID of the ions at m/z 136 produced via [NO](+) chemical ionization of a series of monoterpenes has revealed promising results. Some tracer-product ions for individual compounds or groups of compounds were found, which can be considered as a step forward towards selective on-line monitoring of BVOCs with CIMS techniques.

  11. Collision-induced dissociation of Lys-Lys intramolecular crosslinked peptides.

    PubMed

    Iglesias, Amadeu H; Santos, Luiz F A; Gozzo, Fabio C

    2009-04-01

    The use of chemical crosslinking is an attractive tool that presents many advantages in the application of mass spectrometry to structural biology. The correct assignment of crosslinked peptides, however, is still a challenge because of the lack of detailed fragmentation studies on resultant species. In this work, the fragmentation patterns of intramolecular crosslinked peptides with disuccinimidyl suberate (DSS) has been devised by using a set of versatile, model peptides that resemble species found in crosslinking experiments with proteins. These peptides contain an acetylated N-terminus followed by a random sequence of residues containing two lysine residues separated by an arginine. After the crosslinking reaction, controlled trypsin digestion yields both intra- and intermolecular crosslinked peptides. In the present study we analyzed the fragmentation of matrix-assisted laser desorption/ionization-generated peptides crosslinked with DSS in which both lysines are found in the same peptide. Fragmentation starts in the linear moiety of the peptide, yielding regular b and y ions. Once it reaches the cyclic portion of the molecule, fragmentation was observed to occur either at the following peptide bond or at the peptide crosslinker amide bond. If the peptide crosslinker bond is cleaved, it fragments as a regular modified peptide, in which the DSS backbone remains attached to the first lysine. This fragmentation pattern resembles the fragmentation of modified peptides and may be identified by common automated search engines using DSS as a modification. If, on the other hand, fragmentation happens at the peptide bond itself, rearrangement of the last crosslinked lysine is observed and a product ion containing the crosslinker backbone and lysine (m/z 222) is formed. The detailed identification of fragment ions can help the development of softwares devoted to the MS/MS data analysis of crosslinked peptides.

  12. Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

    2013-09-01

    Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a

  13. Resonance activation and collision-induced-dissociation of ions using rectangular wave dipolar potentials in a digital ion trap mass spectrometer.

    PubMed

    Xu, Fuxing; Wang, Liang; Dai, Xinhua; Fang, Xiang; Ding, Chuan-Fan

    2014-04-01

    Collision-induced dissociation (CID) of ions by resonance activation in a quadrupole ion trap is usually accomplished by resonance exciting the ions to higher kinetic energy, whereby the high kinetic energy ions collide with a bath gas, such as helium or argon, inside the trap and dissociate to fragments. A new ion activation method using a well-defined rectangular wave dipolar potential formed by dividing down the trapping rectangular waveform is developed and examined herein. The mass-selected parent ions are resonance excited to high kinetic energies by simply changing the frequency of the rectangular wave dipolar potential and dissociation proceeds. A relationship between the ion mass and the activation waveform frequency is also identified and described. This highly efficient (CID) procedure can be realized by simply changing the waveform frequency of the dipolar potential, which could certainly simplify tandem mass spectrometry analysis methods.

  14. Improving collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD) fourier transform MS/MS degradome-peptidome identifications using high accuracy mass information.

    PubMed

    Shen, Yufeng; Tolić, Nikola; Purvine, Samuel O; Smith, Richard D

    2012-02-03

    MS dissociation methods, including collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD), can each contribute distinct peptidome identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant informatics challenges. In this work, we explored utilization of high accuracy fragment ion mass measurements, in this case provided by Fourier transform MS/MS, to improve peptidome peptide data set size and consistency relative to conventional descriptive and probabilistic scoring methods. For example, we identified 20-40% more peptides than SEQUEST, Mascot, and MS_GF scoring methods using high accuracy fragment ion information and the same false discovery rate (FDR) from CID, HCD, and ETD spectra. Identified species covered >90% of the collective identifications obtained using various conventional peptide identification methods, which significantly addresses the common issue of different data analysis methods generating different peptide data sets. Choice of peptide dissociation and high-precision measurement-based identification methods presently available for degradomic-peptidomic analyses needs to be based on the coverage and confidence (or specificity) afforded by the method, as well as practical issues (e.g., throughput). By using accurate fragment information, >1000 peptidome components can be identified from a single human blood plasma analysis with low peptide-level FDRs (e.g., 0.6%), providing an improved basis for investigating potential disease-related peptidome components.

  15. Collision-induced dissociation of fatty acid [M - 2H + Na]- ions: charge-directed fragmentation and assignment of double bond position.

    PubMed

    Thomas, Michael C; Altvater, Jens; Gallagher, Thomas J; Nette, Geoffrey W

    2014-11-01

    The collision-induced dissociation (CID) of cationic fatty acid-metal ion complexes has been extensively studied and, in general, provides rich structural information. In particular, charge-remote fragmentation processes are commonly observed allowing the assignment of double bond position. In a previous manuscript, we presented two methods to doubly deprotonate polyunsaturated fatty acids to form anionic fatty acid-sodium ion complexes, referred to as [M - 2H + Na] (-) ions. In the current manuscript, the CID behavior of these [M - 2H + Na] (-) ions is investigated for the first time. Significantly, we also present a deuterium-labeling experiment, which excludes the possibility that deprotonation occurs predominately at the α-carbon in the formation of fatty acid [M - H + NaF](-) ions. This supports our original proposal where deprotonation occurs at the bis-allylic positions of polyunsaturated fatty acids. CID spectra of polyunsaturated fatty acid [M - 2H + Na](-) ions display abundant product ions arising from acyl chain cleavages. Through the examination of fatty acid isomers, it is demonstrated that double bond position may be unequivocally determined for methylene-interrupted polyunsaturated fatty acids with three or more carbon-carbon double bonds. In addition, CID of [M - 2H + Na](-) ions was applied to 18:3 isomers of Nannochloropsis oculata and three isomers were tentatively identified: ∆(9,12,15)18:3, ∆(6,9,12)18:3, and ∆(5,8,11)18:3. We propose that structurally-informative product ions are formed via charge-driven fragmentation processes at the site of the resonance-stabilized carbanion as opposed to charge-remote fragmentation processes, which could be inferred if deprotonation occurred predominately at the α-carbon.

  16. Formation of the bisulfite anion (HSO(3) (-) , m/z 81) upon collision-induced dissociation of anions derived from organic sulfonic acids.

    PubMed

    Jariwala, Freneil B; Wood, Ryan E; Nishshanka, Upul; Attygalle, Athula B

    2012-04-01

    In the negative-ion collision-induced dissociation mass spectra of most organic sulfonates, the base peak is observed at m/z 80 for the sulfur trioxide radical anion (SO(3) (-·) ). In contrast, the product-ion spectra of a few sulfonates, such as cysteic acid, aminomethanesulfonate, and 2-phenylethanesulfonate, show the base peak at m/z 81 for the bisulfite anion (HSO(3) (-) ). An investigation with an extensive variety of sulfonates revealed that the presence of a hydrogen atom at the β-position relative to the sulfur atom is a prerequisite for the formation of the bisulfite anion. The formation of HSO(3) (-) is highly favored when the atom at the β-position is nitrogen, or the leaving neutral species is a highly conjugated molecule such as styrene or acrylic acid. Deuterium-exchange experiments with aminomethanesulfonate demonstrated that the hydrogen for HSO(3) (-) formation is transferred from the β-position. The presence of a peak at m/z 80 in the spectrum of 2-sulfoacetic acid, in contrast to a peak at m/z 81 in that of 3-sulfopropanoic acid, corroborated the proposed hydrogen transfer mechanism. For diacidic compounds, such as 4-sulfobutanoic acid and cysteic acid, the m/z 81 ion can be formed by an alternative mechanism, in which the negative charge of the carboxylate moiety attacks the α-carbon relative to the sulfur atom. Experiments conducted with deuterium-exchanged and deuterium-labeled analogs of sulfocarboxylic acids demonstrated that the formation of the bisulfite anion resulted either from a hydrogen transfer from the β-carbon, or from a direct attack by the carboxylate moiety on the α-carbon.

  17. Energetics and reaction mechanisms of SiH/sup +/ + D/sub 2/ and SiD/sup +/ + H/sub 2/ and collision-induced dissociation of SiD/sub 3//sup +/

    SciTech Connect

    Boo, B.H.; Armentrout, P.B.

    1987-10-22

    The title reactions are investigated by guided ion beam mass spectrometry. Absolute cross sections are determined as a function of the relative collision energy. In the reaction of SiH/sup +/ with D/sub 2/, the lowest energy process is the near thermoneutral H/D exchange reaction. At energies above about 2 eV, several minor processes are observed: deuterium atom transfer to form SiHD/sup +/, H/D/sub 2/ exchange to yield SiD/sub 2//sup +/, and collision-induced dissociation into Si/sup +/ and H. The reaction of SiD/sup +/ + H/sub 2/ is observed to have analogous product channels with nearly identical energy behaviors. The translational energy dependence of the collision-induced dissociation of SiD/sub 3//sup +/ is shown to correlate well with the reaction of SiH/sup +/ (SiD/sup +/) + D/sub 2/ (H/sub 2/). This supports the intermediacy of SiHD/sub 2//sup +/ (SiH/sub 2/D/sup +/) for the H/D isotope exchange reaction. The thermochemistry of all these reactions is in good agreement with previous studies indicates that there are no activation barriers in excess of the endothermicities.

  18. N-Terminal Derivatization with Structures Having High Proton Affinity for Discrimination between Leu and Ile Residues in Peptides by High-Energy Collision-Induced Dissociation.

    PubMed

    Kitanaka, Atsushi; Miyashita, Masahiro; Kubo, Ayumi; Satoh, Takaya; Toyoda, Michisato; Miyagawa, Hisashi

    2016-01-01

    De novo sequencing is still essential in the identification of peptides and proteins from unexplored organisms whose sequence information is not available. One of the remaining problems in de novo sequencing is discrimination between Leu and Ile residues. The discrimination is possible based on differences in side chain fragmentation between Leu and Ile under high-energy collision-induced dissociation (HE-CID) conditions. However, this is observed only when basic residues, such as Arg and Lys, are present near the N- or C-terminal end. It has been shown that the charge derivatization at the N-terminal end by a quarternary ammonium or phosphonium moiety facilitates the side chain fragmentation by HE-CID. However, the effective backbone fragmentation by low-energy CID (LE-CID) is often hampered in those derivatives with a fixed charge. Previously, we demonstrated that the N-terminal charge derivatization with the structures having high proton affinity induced the preferential formation of b-ions under LE-CID conditions, allowing straightforward interpretation of product ion spectra. In the present study, we further investigated whether the same derivatization approach is also effective for discrimination between Leu and Ile under HE-CID conditions. Consequently, the side chain fragmentation of Leu and Ile residues was most effectively enhanced by the N-terminal derivatization with 4-(guanidinomethyl)benzoic acid among the tested structures. This derivatization approach, which is compatible with both HE- and LE-CID analysis, offers a straightforward and unambiguous de novo peptide sequencing method.

  19. N-Terminal Derivatization with Structures Having High Proton Affinity for Discrimination between Leu and Ile Residues in Peptides by High-Energy Collision-Induced Dissociation

    PubMed Central

    Kitanaka, Atsushi; Miyashita, Masahiro; Kubo, Ayumi; Satoh, Takaya; Toyoda, Michisato; Miyagawa, Hisashi

    2016-01-01

    De novo sequencing is still essential in the identification of peptides and proteins from unexplored organisms whose sequence information is not available. One of the remaining problems in de novo sequencing is discrimination between Leu and Ile residues. The discrimination is possible based on differences in side chain fragmentation between Leu and Ile under high-energy collision-induced dissociation (HE-CID) conditions. However, this is observed only when basic residues, such as Arg and Lys, are present near the N- or C-terminal end. It has been shown that the charge derivatization at the N-terminal end by a quarternary ammonium or phosphonium moiety facilitates the side chain fragmentation by HE-CID. However, the effective backbone fragmentation by low-energy CID (LE-CID) is often hampered in those derivatives with a fixed charge. Previously, we demonstrated that the N-terminal charge derivatization with the structures having high proton affinity induced the preferential formation of b-ions under LE-CID conditions, allowing straightforward interpretation of product ion spectra. In the present study, we further investigated whether the same derivatization approach is also effective for discrimination between Leu and Ile under HE-CID conditions. Consequently, the side chain fragmentation of Leu and Ile residues was most effectively enhanced by the N-terminal derivatization with 4-(guanidinomethyl)benzoic acid among the tested structures. This derivatization approach, which is compatible with both HE- and LE-CID analysis, offers a straightforward and unambiguous de novo peptide sequencing method. PMID:27900234

  20. Comparison of high- and low-energy collision-induced dissociation tandem mass spectrometry in the analysis of glycoalkaloids and their aglycons.

    PubMed

    Claeys, M; Van den Heuvel, H; Chen, S; Derrick, P J; Mellon, F A; Price, K R

    1996-02-01

    Four aglycons (tomatidine, demissidine, solanidine, and solasodine) and three glycoalkaloids (α-tomatine, α-chaconine, and α-solanine) have been analyzed by positive ion liquid secondary ion high-energy and low-energy collision-induced dissociation (CID) tandem mass Spectrometry, performed on a four-sector (EBEB) and a hybrid (EBQQ) instrument, respectively. Both high- and low-energy collision-induced dissociation mass spectra of [M+H](+) ions of these compounds provided structural information that aided the characterization of the different aglycons and of the carbohydrate sequence and linkage sites in the glycoalkaloids. Low-energy CID favors charge-driven fragmentation of the aglycon rings, whilst high-energy CID spectra are more complex and contain additional ions that appear to result from charge-remote fragmentations, multiple cleavages, or complex charge-driven rearrangements. With respect to the structural characterization of the carbohydrate part, low-energy CID fragmentations of sugar residues in the glycoalkaloids generate Y n (+) ions and some low intensity Z n (+) ions; the high-energy spectra also exhibit strong (1,5)X n (+) ions, formed by multiple cleavage of the sugar ring, and significant Z n (+) ions.

  1. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation.

    PubMed

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A; Lambrecht, Marlies A; Koehler, Peter; Delcour, Jan A

    2015-07-20

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing.

  2. Axial spatial distribution focusing: improving MALDI-TOF/RTOF mass spectrometric performance for high-energy collision-induced dissociation of biomolecules

    PubMed Central

    Belgacem, O; Pittenauer, E; Openshaw, M E; Hart, P J; Bowdler, A; Allmaier, G

    2016-01-01

    Rationale For the last two decades, curved field reflectron technology has been used in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers, assisting in the generation of post-source-decay (PSD) or collision-induced dissociation (CID) without decelerating precursor ions, producing true high-energy CID spectra. The result was the generation of product ion mass spectra with product ions typical of high-energy (10 keV and beyond) collision processes. The disadvantage of this approach was the lack of resolution in CID spectra resulting from the excess laser energy deposition used to generate those MS/MS spectra. The work presented in this study overcomes this limitation and includes comprehensive examples of high-energy and high-resolution CID MALDI-MS/MS spectra of biomolecules. Methods The devices used in this study are TOF/RTOF instruments equipped with a high-vacuum MALDI ion source. High-resolution and high-energy CID spectra result from the use of axial spatial distribution focusing (ASDF) in combination with curved field reflectron technology. Results A CID spectrum of the P14R1 peptide exhibits product ion resolution in excess of 10,000 (FWHM) but at the same time yields typical high-energy product ions such as w- and [y–2]-type ion series. High-energy CID spectra of lipids, exemplified by a glycerophospholipid and triglyceride, demonstrate C–C backbone fragmentation elucidating the presence of a hydroxyl group in addition to double-bond positioning. A complex high mannose carbohydrate (Man)8(GlcNAc)2 was also studied at 20 keV collision energy and revealed further high-energy product ions with very high resolution, allowing unambiguous detection and characterization of cross-ring cleavage-related ions. Conclusions This is the first comprehensive study using a MALDI-TOF/RTOF instrument equipped with a curved field reflectron and an ASDF device prior to the reflectron. © 2015 The Authors. Rapid Communications in

  3. Energy-resolved collision-induced dissociation of non-covalent ions: charge- and guest-dependence of decomplexation reaction efficiencies.

    PubMed

    Carroy, Glenn; Lemaur, Vincent; De Winter, Julien; Isaacs, Lyle; De Pauw, Edwin; Cornil, Jérôme; Gerbaux, Pascal

    2016-05-14

    Supramolecular chemistry, and especially host-guest chemistry, has been the subject of great interest in the past few decades leading to the synthesis of host cage molecules such as calixarenes, cyclodextrins and more recently cucurbiturils. Mass spectrometry methods are increasingly used to decipher at the molecular level the non-covalent interactions between the different associated molecules. The present article illustrates that the association between mass spectrometry and computational chemistry techniques proves very complementary to depict the gas-phase dissociation processes of ionic non-covalent complexes when subjected to collisional activation. The selected system associates a nor-seco-cucurbit[10]uril bitopic receptor with different amino compounds (adamantylamine, para-xylylenediamine, and para-phenylenediamine). When subjected to CID experiments, the ternary complexes undergo fragmentation via dissociation of non-covalently bound partners. Interestingly, depending on their charge state, the collisionally excited complexes can selectively expel either a neutral guest molecule or a protonated guest molecule. Moreover, based on energy-resolved CID experiments, it is possible to evaluate the guest molecule dependence on the gas phase dissociation efficiency. We observed that the relative order of gas phase dissociation is charge state dependent, with the adamantylamine-containing complexes being the weakest when triply charged and the strongest when doubly charged. The energetics of the gas-phase dissociation reactions have been estimated by density functional theory (DFT) calculations. We succeeded in theoretically rationalizing the experimental collision-induced dissociation results with a special emphasis on: (i) the charge state of the expelled guest molecule and (ii) the nature of the guest molecule.

  4. Use of collision induced dissociation mass spectrometry as a rapid technique for the identification of pharmacologically active peptides in pharmacopoeial testing.

    PubMed

    Holzgrabe, Ulrike; Nap, Cees-Jan; Almeling, Stefan

    2011-07-15

    The applicability of collision induced dissociation mass spectrometry (CID-MS) for the pharmacopoeial identification of pharmacologically active peptides was examined. Two different classes of related peptides were selected, i.e. four synthetic gonadotropin releasing hormone analogues (gonadorelin, goserelin, buserelin and leuprorelin) being either nona- or decapeptides, and human insulin and 2 insulin analogues (insulin lispro and insulin aspart). For all these substances the pharmacopoeial identification currently requires a combination of several partly rather laborious tests using sophisticated equipment. In contrast, CID-MS as a stand alone test can provide increased reassurance about the identity and is rapid and efficient. Moreover, the substance consumption for testing is significantly lower, which is a non-negligible factor for very expensive substances.

  5. Applications of a matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer. l. Metastable decay and collision-induced dissociation for sequencing peptides.

    PubMed

    Ackloo, Suzanne; Loboda, Alexandre

    2005-01-01

    The use of a high-performance orthogonal time-of-flight (o-TOF) mass spectrometer for sequence analysis is described. The mass spectrometer is equipped with a matrix-assisted laser desorption/ionization (MALDI) source that operates at elevated pressure, 0.01-1 Torr. Ion fragmentation is controlled by varying the pressure of the buffer gas, the laser energy, the voltage difference between the MALDI target and the adjacent sampling cone, and between the cone and the quadrupole ion guide. The peptides were analyzed under optimal ionization conditions to obtain their molecular mass, and under conditions that promote ion dissociation via metastable decomposition or collision-induced dissociation (CID). The fragmentation spectra were used to obtain sequence information. Ion dissociation was promoted via three configurations of the ionization parameters. All methods yielded sequencing-grade b- and y-type ions. Two binary mixtures of peptides were used to demonstrate that: (1) external calibration provides a standard deviation (sigma) of 4 ppm with a mode of 9 ppm; and (2) that peptides with molecular masses that differ by a factor of two may be independently fragmented by appropriately choosing the CID energy and the low-mass cut-off. Analyses of tryptic digests employed liquid chromatography (LC), deposition of the eluant on a target, and finally MALDI-TOF mass spectrometry. The mass fingerprint and the (partial) sequence of the tryptic peptides were matched to their precursor protein via database searches.

  6. Possible conformational change within the desolvated and cationized sBBI/trypsin non-covalent complex during the collision-induced dissociation process.

    PubMed

    Darii, Ekaterina; Saravanamuthu, Gunalini; Afonso, Carlos; Alves, Sandra; Gut, Ivo; Tabet, Jean-Claude

    2011-06-30

    Electrospray ionization mass spectrometry (ESI-MS) has become an analytical technique widely used for the investigation of non-covalent protein-protein and protein-ligand complexes due to the soft desolvation conditions that preserve the stoichiometry of the interacting partners. Dissociation studies of solvated or desolvated complexes (in the source and in the collision cell, respectively) allow access to information on protein conformation and localization of the metal ions involved in protein structure stabilization and biological activity. The complex of bovine trypsin and small soybean Bowman-Birk inhibitor (sBBI) was studied by ESI-MS to determine changes occurring within the complex during its transfer from droplets to the gas phase independently of the ion polarity. Under collision-induced dissociation (CID) conditions, unexpected binding of the Ca(2+) ion (cofactor of native trypsin) to the inhibitor molecule was observed within the desolvated sBBI/trypsin/Ca(2+) complex (with a 1:1:1 stoichiometry). This formal gas-phase migration of the calcium ion from trypsin to the inhibitor may be related to conformational rearrangements in the solvent-free and likely collapsed complex. However, under conditions leading to the increase in complex charge state, the appearance of the cationized trypsin molecule was detected during complex dissociation, thus reflecting different pathways of the evolution of complex conformation.

  7. Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

    2016-11-01

    Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na( n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

  8. Influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions: Threshold collision-induced dissociation and theoretical studies

    NASA Astrophysics Data System (ADS)

    Yang, Zhibo; Rodgers, M. T.

    2005-03-01

    The influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M+(xMeU) with Xe is studied in a guided ion beam mass spectrometer. M+ include the following alkali metal ions: Li+, Na+, and K+. Five methylated uracils are examined, xMeU = 1-methyluracil, 3-methyluracil, 6-methyluracil, 1,3-dimethyluracil, and 5,6-dimethyluracil. In all cases endothermic loss of the intact nucleobase is the dominant reaction pathway, while ligand exchange to produce MXe+ is observed as a minor reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies (BDEs) for M+xMeU after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energies of the reactants, and dissociation lifetimes. Ab initio calculations at the MP2(full)/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the MP2(full)/6-31G* geometries. Excellent agreement between theory and experiment is found for the Na+ and K+ systems, while theory systematically underestimates the strength of binding in the Li+ systems. Theoretical calculations are also performed to examine the influence of methylation on the acidities, proton affinities, and Watson-Crick base pairing energies. The present results are compared to earlier studies of uracil and 5-methyluracil to more fully elucidate the influence of methylation on the properties of uracil, its noncovalent interactions with alkali metal ions, and nucleic acid stability.

  9. Ion mobility mass spectrometry coupled with rapid protein threading predictor structure prediction and collision-induced dissociation for probing chemokine conformation and stability.

    PubMed

    Niñonuevo, Milady R; Leary, Julie A

    2012-04-03

    Unique to ion mobility mass spectrometry (IM-MS) is the ability to provide collision cross section (CCS) data and the capacity to delineate any dissociation and/or unfolding of protein complexes. The strong correlation of the experimentally determined CCS with theory is indicative of the retention of native structure in the gas phase, which in turn, qualifies as a means in evaluating the IM-MS data. The assessment of IM-MS data, however, is currently impeded due to the lack of appropriate structural coordinates to use as input in the in silico calculation of theory. To address this issue, this study involves the use of rapid protein threading predictor (RAPTOR) to generate tertiary structures of closely related monomeric chemokines (MCP-1, MCP-3, MCP-4, and eotaxin) and, subsequently, utilize these models to estimate the theoretical values. Experimental CCS of both the model proteins and chemokines correlate well with theory generated by RAPTOR. All conformations for z = 5+ of chemokines fall within theoretical limits. Of the four chemokines, MCP-4 with z = 6+ appears to adopt an extended conformation, while eotaxin gradually unfolds, and the extended structures of MCP-1 and MCP-3 increase in abundance upon activation. Combining RAPTOR with IM-MS and collision-induced dissociation (CID) enables us to interrogate the conformations of homologous proteins with very similar tertiary structures.

  10. Influence of a 4-aminomethylbenzoic acid residue on competitive fragmentation pathways during collision-induced dissociation of metal-cationized peptides.

    PubMed

    Osburn, Sandra; Ochola, Sila; Talaty, Erach; Van Stipdonk, Michael

    2007-01-01

    Formation of [bn+17+cat]+ is a prominent collision-induced dissociation (CID) pathway for Li+- and Na+-cationized peptides. Dissociation of protonated and Ag+-cationized peptides instead favors formation of the rival bn+/[bn-1+cat]+ species. In this study the influence of a 4-aminomethylbenzoic acid (4AMBz) residue on the relative intensities of [b(3)-1+cat]+ and [b(3)+17+cat]+ fragment ions was investigated using several model tetrapeptides including those with the general formula A(4AMBz)AX and A(4AMBz)GX (where X=G, A, V). For Li+- and Na+-cationized versions of the peptides there was a significant increase in the intensity of [b(3)-1+cat]+ for the peptides that contain the 4AMBz residue, and in some cases the complete elimination of the [b(3)+17+cat]+ pathway. The influence of the 4AMBz residue may be attributed to the fact that [b(3)-1+cat]+ would be a highly conjugated species containing an aromatic ring substituent. Comparison of CID profiles generated from Na+-cationized AAGV and A(4AMBz)GV suggests an apparent decrease in the critical energy for generation of [b(3)-1+Na]+ relative to that of [b(3)+17+Na]+ when the aromatic amino acid occupies a position such that it leads to the formation of the highly conjugated oxazolinone, thus leading to an increase in formation rate for the former compared to the latter.

  11. Enhancement of Ion Activation and Collision-Induced Dissociation by Simultaneous Dipolar Excitation of Ions in x- and y-Directions in a Linear Ion Trap.

    PubMed

    Dang, Qiankun; Xu, Fuxing; Xie, Xiaodong; Xu, Chongsheng; Dai, Xinhua; Fang, Xiang; Ding, Li; Ding, Chuan-Fan

    2015-06-02

    Collision-induced dissociation (CID) in linear ion traps is usually performed by applying a dipolar alternating current (AC) signal to one pair of electrodes, which results in ion excitation mainly in one direction. In this paper, we report simulation and experimental studies of the ion excitation in two coordinate directions by applying identical dipolar AC signals to two pairs of electrodes simultaneously. Theoretical analysis and simulation results demonstrate that the ion kinetic energy is higher than that using the conventional CID method. Experimental results show that more activation energy (as determined by the intensity ratio of the a4/b4 fragments from the CID of protonated leucine enkephalin) can be deposited into parent ions in this method. The dissociation rate constant in this method was about 3.8 times higher than that in the conventional method under the same experimental condition, at the Mathieu parameter qu (where u = x, y) value of 0.25. The ion fragmentation efficiency is also significantly improved. Compared with the conventional method, the smaller qu value can be used in this method to obtain the same internal energy deposited into ions. Consequently, the "low mass cut-off" is redeemed and more fragment ions can be detected. This excitation method can be implemented easily without changing any experimental parameters.

  12. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation

    PubMed Central

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A.; Koehler, Peter; Delcour, Jan A.

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  13. Formation of y + 10 and y + 11 ions in the collision-induced dissociation of peptide ions.

    PubMed

    Kilpatrick, Lisa E; Neta, Pedatsur; Yang, Xiaoyu; Simón-Manso, Yamil; Liang, Yuxue; Stein, Stephen E

    2012-04-01

    Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to y(n-1) + 10 and y(n-1) + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO - H(2)O] and [+ CO - NH(3)], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H(2)O or NH(3). MS(3) spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The y(n-1) + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The y(n-1) + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the y(n-1) + 10 ions decrease with increasing peptide length. These data for y(n-1) + 10 and y(n-1) + 11 ion formation may be used to improve peptide identification from tandem mass spectra.

  14. On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications.

    PubMed

    Wu, Shiaw-Lin; Hühmer, Andreas F R; Hao, Zhiqi; Karger, Barry L

    2007-11-01

    We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as the sequence of large peptide fragments (i.e., 2000-10,000 Da) from complex proteins, such as beta-casein, epidermal growth factor receptor (EGFR), and tissue plasminogen activator (t-PA) at the low femtomol level. The incorporation of an additional CID activation step for a charge-reduced species, isolated from ETD fragment ions, improved ETD fragmentation when precursor ions with high m/z (approximately >1000) were automatically selected for fragmentation. Specifically, the identification of the exact phosphorylation sites was strengthened by the extensive coverage of the peptide sequence with a near-continuous product ion series. The identification of N-linked glycosylation sites in EGFR and an O-linked glycosylation site in t-PA were also improved through the enhanced identification of the peptide backbone sequence of the glycosylated precursors. The new strategy is a good starting survey scan to characterize enzymatic peptide mixtures over a broad range of masses using LC-MS with data-dependent acquisition, as the three activation steps can provide complementary information to each other. In general, large peptides can be extensively characterized by the ETD and CRCID steps, including sites of modification from the generated, near-continuous product ion series, supplemented by the CID-MS2 step. At the same time, small peptides (e.g.,

  15. Threshold collision-induced dissociation of Sr2+(H2O)x complexes (x=1-6): An experimental and theoretical investigation of the complete inner shell hydration energies of Sr2+

    NASA Astrophysics Data System (ADS)

    Carl, D. R.; Chatterjee, B. K.; Armentrout, P. B.

    2010-01-01

    The sequential bond energies of Sr2+(H2O)x complexes, where x =1-6, are determined by threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer equipped with an electrospray ionization source. The electrospray source produces an initial distribution of Sr2+(H2O)x complexes, where x =6-9. Smaller Sr2+(H2O)x complexes, where x =1-5, are accessed using a recently developed in-source fragmentation technique that takes place in the high pressure region of a rf-only hexapole ion guide. This work constitutes the first experimental study for the complete inner shell of any multiply charged ion. The kinetic energy dependent cross sections are determined over a wide energy range to monitor all possible dissociation products and are modeled to obtain 0 and 298 K binding energies for loss of a single water molecule. These binding energies decrease monotonically for the Sr2+(H2O) complex to Sr2+(H2O)6. Our experimental results agree well with previous literature results obtained by equilibrium and kinetic studies for x =5 and 6. Because there has been limited theory for the hydration of Sr2+, we also present an in-depth theoretical study on the energetics of the Sr2+(H2O)x systems by employing several levels of theory with multiple effective core potentials for Sr and different basis sets for the water molecules.

  16. Influence of Equilibration Time in Solution on the Inclusion/Exclusion Topology Ratio of Host-Guest Complexes Probed by Ion Mobility and Collision-Induced Dissociation.

    PubMed

    Carroy, Glenn; Daxhelet, Charlotte; Lemaur, Vincent; De Winter, Julien; De Pauw, Edwin; Cornil, Jérôme; Gerbaux, Pascal

    2016-03-18

    Host-guest complexes are formed by the creation of multiple noncovalent bonds between a large molecule (the host) and smaller molecule(s) or ion(s) (the guest(s)). Ion-mobility separation coupled with mass spectrometry nowadays represents an ideal tool to assess whether the host-guest complexes, when transferred to the gas phase upon electrospray ionization, possess an exclusion or inclusion nature. Nevertheless, the influence of the solution conditions on the nature of the observed gas-phase ions is often not considered. In the specific case of inclusion complexes, kinetic considerations must be taken into account beside thermodynamics; the guest ingression within the host cavity can be characterized by slow kinetics, which makes the complexation reaction kinetically driven on the timescale of the experiment. This is particularly the case for the cucurbituril family of macrocyclic host molecules. Herein, we selected para-phenylenediamine and cucurbit[6]uril as a model system to demonstrate, by means of ion mobility and collision-induced dissociation measurements, that the inclusion/exclusion topology ratio varies as a function of the equilibration time in solution prior to the electrospray process.

  17. Collision induced dissociation-based characterization of nucleotide peptides: fragmentation patterns of microcin C7-C51, an antimicrobial peptide produced by Escherichia coli.

    PubMed

    Petit, Vanessa W; Zirah, Séverine; Rebuffat, Sylvie; Tabet, Jean-Claude

    2008-08-01

    Covalent protein-nucleic acid conjugates form an original class of compounds that occur in nature or can be generated in vitro through cross-linking to investigate domains involved in protein/nucleic acid interactions. Their mass spectrometry fragmentation patterns are poorly characterized. We have used electrospray-ionization mass spectrometry (ESI-MS) combined with collision-induced dissociation (CID) to characterize microcin C7-C51, an antimicrobial nucleotide peptide that targets aspartyl-tRNA synthetase and inhibits translation. The fragments of microcin C7-C51 were analyzed in positive- and negative-ion modes and compared with those of the corresponding unmodified heptapeptide and to the derived aspartyl-adenylate. The positive- and negative-ion mode fragments of microcin C7-C51 provided information on both the nucleotide and peptide moieties. Accurate mass measurement obtained using an LTQ Orbitrap instrument was a key factor for a comprehensive interpretation of the fragments. The experimental results obtained permitted the proposal of stepwise fragmentation pathways involving ion-dipole complexes. The data provide a better understanding of nucleotide peptide fragmentation in the gas phase.

  18. An isomer-specific high-energy collision-induced dissociation MS/MS database for forensic applications: a proof-of-concept on chemical warfare agent markers.

    PubMed

    Subramaniam, Raja; Östin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; Åstot, Crister

    2011-09-01

    Spectra database search has become the most popular technique for the identification of unknown chemicals, minimizing the need for authentic reference chemicals. In the present study, an isomer-specific high-energy collision-induced dissociation (CID) MS/MS spectra database of 12 isomeric O-hexyl methylphosphonic acids (degradation markers of nerve agents) was created. Phosphonate anions were produced by the electrospray ionization of phosphonic acids or negative-ion chemical ionization of their fluorinated derivatives and were analysed in a hybrid magnetic-sector-time-of-flight tandem mass spectrometer. A centre-of-mass energy (E(com)) of 65 eV led to an optimal sequential carbon-carbon bond breakage, which was interpreted in terms of charge remote fragmentation. The proposed mechanism is discussed in comparison with the routinely used low-energy CID MS/MS. Even-mass (odd-electron) charge remote fragmentation ion series were diagnostic of the O-alkyl chain structure and can be used to interpret unknown spectra. Together with the odd-mass ion series, they formed highly reproducible, isomer-specific spectra that gave significantly higher database matches and probability factors (by 1.5 times) than did the EI MS spectra of the trimethylsilyl derivatives of the same isomers. In addition, ionization by negative-ion chemical ionization and electrospray ionization resulted in similar spectra, which further highlights the general potential of the high-energy CID MS/MS technique.

  19. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sidebottom, Ashley M.; Karty, Jonathan A.; Carlson, Erin E.

    2015-11-01

    Siderophores are bacterially secreted, small molecule iron chelators that facilitate the binding of insoluble iron (III) for reuptake and use in various biological processes. These compounds are classified by their iron (III) binding geometry, as dictated by subunit composition and include groups such as the trihydroxamates (hexadentate ligand) and catecholates (bidentate). Small modifications to the core structure such as acetylation, lipid tail addition, or cyclization, make facile characterization of new siderophores difficult by molecular ion detection alone (MS1). We have expanded upon previous fragmentation-directed studies using electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS/MS) and identified diagnostic MS3 features from the trihydroxamate siderophore class for ferrioxamine B and E1 by accurate mass. Diagnostic features for MS3 include C-C, C-N, amide, and oxime cleavage events with proposed losses of water and -CO from the iron (III) coordination sites. These insights will facilitate the discovery of novel trihydroxamate siderophores from complex sample matrices.

  20. A full dimensional time-dependent wave packet study for the H4 four-center, collision induced dissociation, and single exchange reactions: reaction probabilities for J=0.

    PubMed

    Lu, Yunpeng; Lee, Soo-Y; Zhang, Dong H

    2006-01-07

    A time-dependent initial state selected wave packet method has been developed to study the H2(v(1)=10-11,j1=0)+H2'(v2=0,j2=0)-->HH'+HH' four-center (4C) reaction, and two other competing reactions: the H2+H2'-->H+H+H2' collision induced dissociation (CID) and the H2+H2'-->H+HH'+H' single exchange (SE) reaction, in full six dimensions. Initial state-specific total reaction probabilities for these three competing reactions are presented for total angular momentum J=0 and the effects of reagent vibration on reactions are examined. It is found that (a) the CID process is the dominant process over the whole energy range considered in this study, but the 4C and SE processes also have non-negligible probabilities; (b) the SE process has a lower threshold energy than the 4C process, but the SE probability increases slower than the 4C probability as collision energy increases; (c) the vibrational excitation of H2(v1) is much more efficient than translational motion for promoting these processes, in particular to the CID process.

  1. Evaluation of the Influence of Amino Acid Composition on the Propensity for Collision-Induced Dissociation of Model Peptides Using Molecular Dynamics Simulations

    SciTech Connect

    Cannon, William R.; Taasevigen, Danny J.; Baxter, Douglas J.; Laskin, Julia

    2007-09-01

    The dynamical behavior of model peptides was evaluated with respect to their ability to form internal proton donor-acceptor pairs using molecular dynamics simulations. The proton donor-acceptor pairs are postulated to be prerequisites for peptide bond cleavage resulting in formation of b and y ions during low energy collision-induced dissociation in tandem mass spectrometry (MS/MS). The simulations for the polyalanine pentamer Ala5H+ were compared to experimental data from collision energy-resolved surface induced dissociation (SID) studies. The results of the simulation are insightful into the events that likely lead up to the fragmentation of peptides. 9-mer polyalanine-based model peptides were used to examine the dynamical effect of each of the 20 common amino acids on the probability to form donor-acceptor pairs at labile peptide bonds. A continuous range of probabilities was observed as a function of the substituted amino acid. However, the location of the peptide bond involved in the donor-acceptor pair plays a critical role in the dynamical behavior. This influence of position on the probability of forming a donor-acceptor pair would be hard to predict from statistical analyses on experimental spectra of aggregate, diverse peptides. In addition, the inclusion of basic side chains in the model peptides alters the probability of forming donor-acceptor pairs across the entire backbone. In this case there are still more ionizing protons than basic residues, but the side chains of the basic amino acids form stable hydrogen bond networks with the peptide carbonyl oxygens and thus act to prevent free access of “mobile protons” to labile peptide bonds. It is clear from the work that the identification of peptides from low-energy CID using automated computational methods should consider the location of the fragmenting bond as well as the amino acid composition.

  2. Identification of the unpaired cysteine status and complete mapping of the 17 disulfides of recombinant tissue plasminogen activator using LC-MS with electron transfer dissociation/collision induced dissociation.

    PubMed

    Wu, Shiaw-Lin; Jiang, Haitao; Hancock, William S; Karger, Barry L

    2010-06-15

    Recombinant tissue plasminogen (rt-PA) with 35 cysteine residues has been completely assigned by mapping the 17 disulfide linkages and the unpaired cysteine. The result is consistent with the prediction from homology except for the unassigned cysteine, which was identified at Cys83. This cysteine was found to be blocked and paired with either a glutathione or cysteine residue in an approximately 60:40 ratio, respectively. The analysis was conducted using a multifragmentation approach consisting of electron transfer dissociation (ETD) and collision induced dissociation (CID), in combination with a multienzyme digestion strategy (Lys-C, trypsin, and Glu-C). The disulfide-linked peptides, even those containing N- or O-linked glycosylation, could be assigned since the disulfide bonds were still preferably cleaved over the glycosidic cleavages under ETD fragmentation. The use of a multiple and sequential enzymatic digestion strategy was important in producing fragment sizes suitable for analysis. For the analysis of complex intertwined disulfides, the use of CID-MS(3) to target partially disulfide-dissociated peptides from the ETD fragmentation was necessary for linkage assignment. The ability to identify the exact location and status of the unpaired cysteine (free or blocked with a glutathione or cysteine) could shed light on the activation of rt-PA, upon stimulation by either oxidative or ischemic stress.

  3. Surface-Induced Dissociation Shows Potential to be More Informative than Collision-Induced Dissociation for Structural Studies of Large Systems

    PubMed Central

    Wysocki, Vicki H.; Jones, Christopher M.; Galhena, Asiri S.; Blackwell, Anne E.

    2008-01-01

    The ability to preserve non-covalent, macromolecular assemblies intact in the gas-phase has paved the way for mass spectrometry to characterize ions of increasing size and become a powerful tool in the field of structural biology. Tandem mass spectrometry experiments have the potential to expand the capabilities of this technique through the gas-phase dissociation of macromolecular complexes, but collisions with small gas atoms currently provide very limited fragmentation. One alternative for dissociating large ions is to collide them into a surface, a more massive target. Here, we demonstrate the ability and benefit of fragmenting large protein complexes and inorganic salt clusters by surface-induced dissociation (SID). SID provides more extensive fragmentation of these systems and shows promise as an activation method for ions of increasing size. PMID:18598898

  4. Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation.

    PubMed

    Mormann, Michael; Eble, Johannes; Schwöppe, Christian; Mesters, Rolf M; Berdel, Wolfgang E; Peter-Katalinić, Jasna; Pohlentz, Gottfried

    2008-11-01

    Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.

  5. Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation.

    PubMed

    Horton, Andrew Pitchford; Robotham, Scott A; Cannon, Joe R; Holden, Dustin D; Marcotte, Edward M; Brodbelt, Jennifer S

    2017-02-24

    We describe a strategy for de novo peptide sequencing based on matched pairs of tandem mass spectra (MS/MS) obtained by collision induced dissociation (CID) and 351 nm ultraviolet photodissociation (UVPD). Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. To interpret these paired spectra, we modified the UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra, provided a representative set of training data. This machine learning procedure, using random forests, synthesizes information from one or multiple complementary spectra, such as the CID/UVPD pairs, into peptide fragmentation site predictions. In doing so, the burden of fragmentation model definition shifts from programmer to machine and opens up the model parameter space for inclusion of nonobvious features and interactions. This spectral synthesis also serves to transform distinct types of spectra into a common representation for subsequent activation-independent processing steps. Then, independent from precursor activation constraints, UVnovo's de novo sequencing procedure generates and scores sequence candidates for each precursor. We demonstrate the combined experimental and computational approach for de novo sequencing using whole cell E. coli lysate. In benchmarks on the CID/UVPD data, UVnovo assigned correct full-length sequences to 83% of the spectral pairs of doubly charged ions with high-confidence database identifications. Considering only top-ranked de novo predictions, 70% of the pairs were deciphered correctly. This de novo sequencing performance exceeds that of PEAKS and PepNovo on the CID spectra and that of UVnovo on CID or UVPD spectra alone. As presented here, the methods for paired CID/UVPD spectral acquisition and interpretation constitute a powerful workflow for high-throughput and accurate de novo peptide sequencing.

  6. Comparison of laser-induced dissociation and high-energy collision-induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification.

    PubMed

    Macht, Marcus; Asperger, Arndt; Deininger, Sören-Oliver

    2004-01-01

    The fragmentation of peptides under laser-induced dissociation (LID) as well as high-energy collision-induced dissociation (CID) conditions has been investigated. The effect of the different fragmentation mechanisms on the formation of specific fragment ion types and the usability of the resulting spectra, e.g. for high-throughput protein identification, has been evaluated. Also, basic investigations on the influence of the matrix, as well as laser fluence, on the fragment ion formation and the consequences in the spectral appearance are discussed. The preconditions for obtaining 'pure' CID spectra on matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) instruments are evaluated and discussed as well as the differences between LID and CID in the resulting fragment ion types. While containing a wealth of information due to additional fragment ions in comparison with LID, CID spectra are significantly more complex than LID spectra and, due to different fragmentation patterns, the CID spectra are of limited use for protein identification, even under optimized parameter settings, due to significantly lower scores for the individual spectra. Conditions for optimal results regarding protein identification using MALDI-TOF/TOF instruments have been evaluated. For database searches using tandem mass spectrometric data, the use of LID as fragmentation technique in combination with parameter settings supporting the use of internal fragment ions turned out to yield the optimal results.

  7. GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to (13)C-metabolic flux analysis of Escherichia coli central metabolism.

    PubMed

    Okahashi, Nobuyuki; Kawana, Shuichi; Iida, Junko; Shimizu, Hiroshi; Matsuda, Fumio

    2016-09-01

    Stable isotope labeling experiments using mass spectrometry have been employed to investigate carbon flow levels (metabolic flux) in mammalian, plant, and microbial cells. To achieve a more precise (13)C-metabolic flux analysis ((13)C-MFA), novel fragmentations of tert-butyldimethylsilyl (TBDMS)-amino acids were investigated by gas chromatography-tandem mass spectrometry (GC-MS/MS). The product ion scan analyses of 15 TBDMS-amino acids revealed 24 novel fragment ions. The amino acid-derived carbons included in the five fragment ions were identified by the analyses of (13)C-labeled authentic standards. The identification of the fragment ion at m/z 170 indicated that the isotopic abundance of S-methyl carbon in methionine could be determined from the cleavage of C5 in the precursor of [M-159](+) (m/z 218). It was also confirmed that the precision of (13)C-MFA in Escherichia coli central carbon metabolism could be improved by introducing (13)C-labeling data derived from novel fragmentations. Graphical Abstract Novel collision-induced dissociation fragmentations of tert-butyldimethylsilyl amino acids were investigated and identified by GC-MS/MS.

  8. Towards understanding the tandem mass spectra of protonated oligopeptides. 2: The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp).

    PubMed

    Bleiholder, Christian; Suhai, Sándor; Harrison, Alex G; Paizs, Béla

    2011-06-01

    The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.

  9. Simultaneous Transmission Mode Collision-Induced Dissociation and Ion/Ion Reactions for Top-Down Protein Identification/Characterization Using a Quadrupole/Time-of-Flight Tandem Mass Spectrometer

    PubMed Central

    Liu, Jian; Huang, Teng-Yi; McLuckey, Scott A.

    2009-01-01

    Simultaneous transmission mode collision-induced dissociation (CID) and ion/ion proton transfer reactions have been implemented on a quadrupole/time-of-flight (TOF) tandem mass spectrometer. Reagent anions were trapped in a pressurized quadrupole collision cell by applying appropriate DC voltages while multiply protonated protein precursor ions were injected into the collision cell at energies sufficient to give rise to CID. Intact precursor ions as well as fragment ions underwent ion/ion proton transfer reactions during their passage through the collision cell and on to an orthogonal acceleration TOF mass analyzer. The resulting product ion spectrum was then submitted to deconvolution to yield a “zero-charge” spectrum, which was then matched against in silico produced spectra derived from a protein database. Dramatic improvements in the scores associated with correct matches were obtained relative to CID data without benefit of ion/ion reactions for proteins as large as carbonic anhydrase (29 kDa). The parameters that most affect the extent of ion/ion proton transfer during transmission through the instrument include the number of anions stored in the collision cell, the amplitude of the radio-frequency trapping voltage, the voltage of the LINAC potential associated with the collision cell, and the collision gas pressure. This work demonstrates that it is possible to effect whole protein tandem mass spectrometry with simultaneous CID, ion/ion reactions, and mass analysis for high duty cycle top-down protein characterization. PMID:19281259

  10. Structure and end-group analysis of complex hexanediol-neopentylglycol-adipic acid copolyesters by matrix-assisted laser desorption/ionization collision-induced dissociation tandem mass spectrometry.

    PubMed

    Weidner, Steffen M; Falkenhagen, Jana; Knop, Karin; Thünemann, Andreas

    2009-09-01

    Sequences and end groups of complex copolyesters were determined by fragmentation analysis by means of matrix-assisted laser desorption/ionization collision-induced dissociation tandem mass spectrometry (MALDI CID MS/MS). The complexity of the crude copolyester mixture was reduced by a chromatographic separation followed by a MALDI time-of-flight (TOF) investigation of fractions. Due to overlapping compositional and end-group information a clear assignment of end groups was very difficult. However, the fragmentation of suitable precursor ions resulted in typical fragment ion patterns and, therefore, enabled a fast and unambiguous determination of the end groups and composition of this important class of polymers.

  11. Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

    SciTech Connect

    Chowdhury, Saiful M.; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2009-07-01

    Chemical cross-linking combined with mass spectrometric analysis is emerging as a powerful technique for protein-protein interaction and protein structure elucidation studies.1 Cross-linkers covalently link two interacting proteins, often with chemistries specific to certain amino acid side chains. After enzymatic digestion of the proteins, the resulting cross-linked peptides can be subjected to analysis by LC-MS(/MS) to identify cross-linked species.2,3 For studying protein interactions using chemical cross-linking towards global discovery-based applications, the critical needs are the development of cross-linkers that are highly specific, amenable to LC-MS/MS, and resulting spectra are interpretable by bioinformatics tools to automatically assign cross-linked peptides with high confidence.4-10 As recently mentioned by Aebersold and co-workers, due to the low relative abundances of cross-linking products compared to their unmodified counterparts, enrichment of cross-linked species is also highly desirable to improve the likelihood of unambiguous identification of cross-linked peptides.6 Most of the currently available enrichable cross-linkers are bulky and are not amenable to studying protein-protein interactions in vivo. To discover protein-protein interactions with high confidence, there is a need for chemical cross-linkers that can effectively label protein complexes, utilize mass spectrometry based bottom-up proteomics analysis pipelines and also contains enrichment functionality.

  12. Reduction of in-source collision-induced dissociation and thermolysis of sulopenem prodrugs for quantitative liquid chromatography/electrospray ionization mass spectrometric analysis by promoting sodium adduct formation.

    PubMed

    Wujcik, Chad E; Kadar, Eugene P

    2008-10-01

    Six chromatographically resolved sulopenem prodrugs were monitored for their potential to undergo both in-source collision-induced dissociation (CID) and thermolysis. Initial Q1 scans for each prodrug revealed the formation of intense [Prodrug2 + H]+, [Prodrug2 + Na]+, [Prodrug + Na]+, and [Sulopenem + Na]+ ions. Non-adduct-associated sulopenem ([Sulopenem + H]+) along with several additional lower mass ions were also observed. Product ion scans of [Prodrug3 + Na]+ showed the retention of the sodium adduct in the collision cell continuing down to opening of the beta-lactam ring. In-source CID and temperature experiments were conducted under chromatographic conditions while monitoring several of the latter ion transitions (i.e., adducts, dimers and degradants/fragments) for a given prodrug. The resulting ion profiles indicated the regions of greatest stability for temperature and declustering potential (DP) that provided the highest signal intensity for each prodrug and minimized in-source degradation. The heightened stability of adduct ions, relative to their appropriate counterpart (i.e., dimer to dimer adduct and prodrug to prodrug adduct ions), was observed under elevated temperature and DP conditions. The addition of 100 microM sodium to the mobile phase further enhanced the formation of these more stable adduct ions, yielding an optimal [Prodrug + Na]+ ion signal at temperatures from 400 to 600 degrees C. A clinical liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for sulopenem prodrug PF-04064900 in buffered whole blood was successfully validated using sodium-fortified mobile phase and the [PF-04064900 + Na]+ ion for quantitation. A conservative five-fold increase in sensitivity from previously validated preclinical assays using the [PF-04064900 + H]+ precursor ion was achieved.

  13. A novel “correlated ion and neutral time of flight” method: Event-by-event detection of neutral and charged fragments in collision induced dissociation of mass selected ions

    SciTech Connect

    Teyssier, C.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.

    2014-01-15

    A new tandem mass spectrometry (MS/MS) method based on time of flight measurements performed on an event-by-event detection technique is presented. This “correlated ion and neutral time of flight” method allows to explore Collision Induced Dissociation (CID) fragmentation processes by directly identifying not only all ions and neutral fragments produced but also their arrival time correlations within each single fragmentation event from a dissociating molecular ion. This constitutes a new step in the characterization of molecular ions. The method will be illustrated here for a prototypical case involving CID of protonated water clusters H{sup +}(H{sub 2}O){sub n=1–5} upon collisions with argon atoms.

  14. Improved collision-induced dissociation analysis of peptides by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry through 3-sulfobenzoic acid succinimidyl ester labeling.

    PubMed

    Alley, William R; Mechref, Yehia; Klouckova, Iveta; Novotny, Milos V

    2007-01-01

    The sulfonation reagent, a succinimidyl ester of 3-sulfobenzoic acid, has been synthesized for effective peptide sequencing. It is capable of incorporating an additional mobile proton into the peptide backbone, thus, facilitating efficient collision-induced dissociation. This reagent is easily and inexpensively prepared in short time. Tandem mass spectra of the guanidinated and reagent-sulfonated peptides consist mainly of the y-ion series with higher intensities than those observed for solely guanidinated peptides. These enhanced tandem MS attributes significantly improved MASCOT total-ion scores, thus, allowing more confident peptide sequencing. This derivatization was also very effective for the analysis of tryptic digest of human blood serum proteins separated by two-dimensional gel electrophoresis. When used in LC-MALDI/MS/MS format, this type of derivatization does not adversely affect chromatographic efficiencies.

  15. Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

    PubMed

    Somogyi, Arpád

    2008-12-01

    The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

  16. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

    PubMed

    Nose, Holliness; Chen, Yu; Rodgers, M T

    2013-05-23

    The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

  17. Products of Dissociative Recombination in the Ionosphere

    NASA Technical Reports Server (NTRS)

    Cosby, Philip

    1996-01-01

    SRI International undertook a novel experimental measurement of the product states formed by dissociative ro-combination (DR) of C2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and ro-vibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates.

  18. Comparisons and scaling rules between N+N2 and N2+N2 collision induced dissociation cross sections from atomistic studies

    NASA Astrophysics Data System (ADS)

    Esposito, F.; Garcia, E.; Laganà, A.

    2017-04-01

    Quantitative knowledge of elementary processes involved in plasmas are key to successfully perform accurate kinetic simulations. The issue is the huge amount of data to treat, both in the dynamical calculation and in the kinetic simulation. The aim of this paper is to study the dissociation in atom–molecule (AM) and molecule–molecule (MM) collisions involving nitrogen, obtained by molecular dynamics calculations considering vibrational states in the range 10–50 and collision energy up to 10 eV, in order to formulate suitable scaling laws resulting in less expensive computational procedures and easier to handle treatments in kinetic simulations. It is shown that, while a direct substitution of MM dissociation cross sections with AM ones might be acceptable only at very high collision energy, scaling laws application allows to obtain quite good results on almost the whole energy range of interest.

  19. Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry.

    PubMed

    Wang, Dongdong; Hincapie, Marina; Rejtar, Tomas; Karger, Barry L

    2011-03-15

    Site-specific analysis of protein glycosylation is important for biochemical and clinical research efforts. Glycopeptide analysis using liquid chromatography-collision-induced dissociation/electron transfer dissociation mass spectrometry (LC-CID/ETD-MS) allows simultaneous characterization of the glycan structure and attached peptide site. However, due to the low ionization efficiency of glycopeptides during electrospray ionization, 200-500 fmol of sample per injection is needed for a single LC-MS run, which makes it challenging for the analysis of limited amounts of glycoprotein purified from biological matrixes. To improve the sensitivity of LC-MS analysis for glycopeptides, an ultranarrow porous layer open tubular (PLOT) LC column (2.5 m × 10 μm i.d.) was coupled to a linear ion trap (LTQ) collision-induced dissociation/electron transfer dissociation mass spectrometer to provide sensitive analysis of N-linked protein glycosylation heterogeneity. The potential of the developed method is demonstrated by the characterization of site-specific glycosylation using haptoglobin (Hpt) as a model protein. To limit the amount of haptoglobin to low picomole amounts of protein, we affinity purified it from 1 μL of pooled lung cancer patient plasma. A total of 26 glycoforms/glycan compositions on three Hpt tryptic glycopeptides were identified and quantified from 10 LC-MS runs with a consumption of 100 fmol of Hpt digest (13 ng of protein, 10 fmol per injection). Included in this analysis was the determination of the glycan occupancy level. At this sample consumption level, the high sensitivity of the PLOT LC-LTQ-CID/ETD-MS system allowed glycopeptide identification and structure determination, along with relative quantitation of glycans presented on the same peptide backbone, even for low abundant glycopeptides at the ∼100 amol level. The PLOT LC-MS system is shown to have sufficient sensitivity to allow characterization of site-specific protein glycosylation from trace

  20. Selective Production of Electrostatically-Bound Adducts of Alkyl Cations/Polyoxoanions by the Collision-Induced Fragmentations of Their Quaternary Ammonium Counterparts

    NASA Astrophysics Data System (ADS)

    Cao, Jie; Xu, Chong; Fan, YanXuan; Fan, LinYuan; Zhang, XiuHui; Hu, ChangWen

    2013-06-01

    Solutions of the quaternary ammonium salts of a set of classic polyoxometalates (POMs) (Keggin [XM12O40]n-, Dawson [P2W18O62]6-, and Lindqvist [M6O19]2- (X = P, Si; M = W, Mo) were characterized by electrospray mass spectrometry. The gas-phase fragmentations of a series of quaternary ammonium-associated clusters were investigated by their collision-induced dissociations to elucidate their fragmentation mechanisms. It was found that the quaternary ammonium-associated clusters had distinctive dissociation characteristics. Moreover, the mono-quaternary ammonium-associated clusters, {NR4[POMs]}(n-1)-, shared a common fragmentation feature, that is, they decomposed exclusively into their respective alkyl cation-bound clusters irrespective of the different cation sizes and the different natures of the polyoxoanions. The optimized geometries and the binding energies of the mono cation-bound Lindqvist POM-based clusters were obtained by calculations. To the best of our knowledge, this is the first investigation of the gas-phase fragmentations of these noncovalent complexes between organic amines and inorganic POM anions by a combination of theory and mass spectrometry.

  1. The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.

    PubMed

    Cramer, R; Corless, S

    2001-01-01

    Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.

  2. Rapid determination of oxidized methionine residues in recombinant human basic fibroblast growth factor by ultra-performance liquid chromatography and electrospray ionization quadrupole time-of-flight mass spectrometry with in-source collision-induced dissociation.

    PubMed

    Ohkubo, Tsutomu; Inagaki, Shinsuke; Min, Jun Zhe; Kamiya, Daiki; Toyo'oka, Toshimasa

    2009-07-01

    The primary structure of the deteriorated recombinant human basic fibroblast growth factor (rhbFGF) was determined by ultra-performance liquid chromatography and electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) with in-source collision-induced dissociation (CID). The rhbFGFs before and after treatment with hydrogen peroxide (H(2)O(2)) were separated using an ACQUITY UPLC BEH300 C18 column (1.7 microm, 150 mm x 2.1 mm i.d.) with a gradient elution of a mixture of water/acetonitrile containing 0.1% formic acid. The separated proteins were then detected by a SYNAPT High Definition Mass Spectrometry system (SYNAPT-MS). Two methionine (Met) residues in the rhbFGF structure were oxidized to Met-sulfoxide (Met-O) in 0.03% H(2)O(2) at pH 2.0. As the result, three peaks, except for the peak of rhbFGF, appeared on the chromatogram. The three proteins corresponding to each peak were estimated as the denatured rhbFGFs including the Met-O residue(s) with TOF-MS. Furthermore, the position of the Met-O residue(s) was efficiently identified by UPLC/ESI-QTOF-MS using the in-source CID technique. The proposed method seems to be very useful for the structural elucidation of proteins, because the oxidized Met residues in rhbFGF were easily and rapidly identified.

  3. Online immunoaffinity liquid chromatography/tandem mass spectrometry determination of a type II collagen peptide biomarker in rat urine: Investigation of the impact of collision-induced dissociation fluctuation on peptide quantitation.

    PubMed

    Berna, Michael; Schmalz, Chris; Duffin, Kevin; Mitchell, Peter; Chambers, Mark; Ackermann, Brad

    2006-09-15

    Proteolytic fragments of type II collagen, a major component of joint tissue, have recently been identified as biomarkers for osteoarthritis, a progressive disease associated with cartilage degeneration. A liquid chromatography/tandem mass spectrometry (MS/MS) assay that utilizes online immunoaffinity chromatography and column switching was developed in our laboratory for the neoepitope of type II collagen (NET2C). During method development, peptide collision-induced dissociation (CID) was found to be a significant source of assay variation, which exceeded 10% CV, despite the fact that a stable-isotope-labeled (SIL) internal standard was used to minimize imprecision. This phenomenon was studied in detail using peptides and associated SIL internal standards of varying lengths and amino acid compositions. Variability in peptide CID necessitated the monitoring of multiple MS/MS transitions to obtain acceptable assay precision. The assay was subsequently validated to measure NET2C concentrations in rat urine over the range of 0.1 to 10 ng/mL. The interday accuracy and precision ranged from 3.9 to 13.1 (%CV) and 10.7 to 5.3 (%RE), respectively, across the range of validated concentrations. A specific application of the assay is presented in which the role of estrogen deficiency in the development and progression of osteoarthritis was investigated. In this study, the effect of estrogen on lowering NET2C concentrations in urine in ovariectomized rats was demonstrated.

  4. Development and Optimization of an UPLC-QTOF-MS/MS Method Based on an In-Source Collision Induced Dissociation Approach for Comprehensive Discrimination of Chlorogenic Acids Isomers from Momordica Plant Species

    PubMed Central

    Madala, N. E.; Tugizimana, F.; Steenkamp, P. A.

    2014-01-01

    Chlorogenic acids (CGA) have been profiled in the leaves of Momordica balsamina, Momordica charantia, and Momordica foetida. All three species were found to contain the trans and cis isomers of 4-acyl para-coumaroylquinic acid (pCoQA), caffeoylquinic acid (CQA), and feruloylquinic acid (FQA). To the best of our knowledge, this is the first report of pCoQA and FQA and their cis isomers in these Momordica species. These profiles were obtained by a newly developed UPLC-qTOF-MS method based on the in-source collision induced dissociation (ISCID) method optimized to mimic the MS2 and MS3 fragmentation of an ion trap-based MS. The presence of the cis isomers is believed to be due to high UV exposure of these plants. Furthermore, the absence of the 3-acyl and 5-acyl CGA molecules points to a metabolic mark that is unusual and represents a very interesting biochemical phenotype of these species. Our optimized ISCID method was also shown to be able to distinguish between the geometrical isomers of all three forms of CGA, a phenomenon previously deemed impossible with other common mass spectrometry systems used for CGA analyses. PMID:25295221

  5. A simultaneous determination method for 5-fluorouracil and its metabolites in human plasma with linear range adjusted by in-source collision-induced dissociation using hydrophilic interaction liquid chromatography-electrospray ionization-tandem mass spectrometry.

    PubMed

    Ishii, Hideaki; Shimada, Miki; Yamaguchi, Hiroaki; Mano, Nariyasu

    2016-11-01

    We applied a new technique for quantitative linear range shift using in-source collision-induced dissociation (CID) to complex biological fluids to demonstrate its utility. The technique was used in a simultaneous quantitative determination method of 5-fluorouracil (5-FU), an anticancer drug for various solid tumors, and its metabolites in human plasma by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). To control adverse effects after administration of 5-FU, it is important to monitor the plasma concentration of 5-FU and its metabolites; however, no simultaneous determination method has yet been reported because of vastly different physical and chemical properties of compounds. We developed a new analytical method for simultaneously determining 5-FU and its metabolites in human plasma by LC/ESI-MS/MS coupled with the technique for quantitative linear range shift using in-source CID. Hydrophilic interaction liquid chromatography using a stationary phase with zwitterionic functional groups, phosphorylcholine, was suitable for separation of 5-FU from its nucleoside and interfering endogenous materials. The addition of glycerin into acetonitrile-rich eluent after LC separation improved the ESI-MS response of high polar analytes. Based on the validation results, linear range shifts by in-source CID is the reliable technique even with complex biological samples such as plasma. Copyright © 2016 John Wiley & Sons Ltd.

  6. Fully converged integral cross sections of collision induced dissociation, four-center, and single exchange reactions, and accuracy of the centrifugal sudden approximation in H2 + D2 reaction.

    PubMed

    Song, Hongwei; Lu, Yunpeng; Lee, Soo-Y

    2012-03-21

    The initial state selected time-dependent wave packet method was employed to calculate the integral cross sections for the H(2) + D(2) reaction with and without the centrifugal sudden (CS) approximation by including all important K (the projection of the total angular momentum on the body-fixed axis) blocks. With a full-dimensional model, the first fully converged coupled-channel (CC) cross sections for different competitive processes from the ground rotational state were obtained: collision induced dissociation (CID), four-center (4C) reaction and single exchange (SE) reaction. The effect of the total angular momentum J on the reaction dynamics of H(2) + D(2) and the accuracy of the CS approximation have also been studied. It was found that the CID and SE processes occur in a wide range of J values while the 4C process can only take place in a narrow window of J values. For this reason, the CC cross section for the 4C channel is merely comparable to the SE channel. A comparison of the integral cross sections from CC and CS calculations showed that the CS approximation works well for the CID process but not for the 4C and SE processes, and the discrepancy between the CC and CS cross sections grows larger as the translational energy and/or the vibrational energy increase(s).

  7. Angle and energy resolved studies of the collision-induced dissociation of polyatomic molecular ions: Baseline studies of CH[sub 4][sup +] and C[sub 3]H[sub 8][sup +

    SciTech Connect

    Anderson, S.G.

    1992-01-01

    A deeper fundamental understanding of the collision process and subsequent dissociation for polyatomic ions is essential to optimize future studies of collision induced dissociation (CID). An instrument was developed with an unique system of electrostatic lenses that allows CID to be observed in the energy range from a few tenths of an eV to several thousand eV. The instrument permits daughter ion distributions to be mapped in angle and energy. The CID spectra of methane and propane were investigated at keV energies using a commercial tandem mass spectrometer. The relative abundances of the daughter ions, the energy deposition, and kinetic energy release were determined as a function of collision gas was also investigated and interpreted in terms of center of mass (CM) collision energy and the Massey adiabatic criterion most probable energy deposition. The daughter ion abundance, kinetic energy transfer, and kinetic energy release were observed as a function of collision gas, CM collision energy and attenuation of the primary ion beam. A simple model is proposed to describe the effect of multiple collisions on the CID process. Propane molecular ion CID was investigated with the new instrument at laboratory energies ranging from 18 eV to 1 keV and CM collision energies ranging from 1.5 eV to 450 eV. The daughter ion distributions obtained from these experiments show that there is no change in mechanism between CID observed in quadrupole instruments at eV energies and CID observed in sector instruments at keV lab energies. The energy and angular distribution of CID daughter ions is close to the CM with large CM scattering angles at low energy and shifts to near the elastic scattering circle and small CM scattering angles at high lab energies.

  8. High-energy and low-energy collision-induced dissociation of protonated flavonoids generated by MALDI and by electrospray ionization

    NASA Astrophysics Data System (ADS)

    March, Raymond E.; Li, Hongxia; Belgacem, Omar; Papanastasiou, Dimitris

    2007-04-01

    Product ion mass spectra of a series of nine protonated flavonoids have been observed by electrospray ionization combined with quadrupole/time-of-flight (ESI QTOF), and matrix-assisted laser desorption ionization combined either with quadrupole ion trap (MALDI QIT) tandem mass spectrometry or time-of-flight tandem mass spectrometry (MALDI TOF ReTOF). The compounds examined are 3,6-, 3,2'-, and 3,3'-dihydoxyflavone, apigenin (5,7,4'-trihydroxyflavone), luteolin (5,7,3',4'-tetrahydroxyflavone), apigenin-7-O-glucoside, hesperidin (5,7,3'-trihydroxy-4'-methoxyflavanone), daidzen (7,4'-dihydroxyisoflavone), and rutin (quercitin-3-O-rutinoside) where quercitin is 3,5,7,3',4'-pentahydroxyflavone; sodiated rutin was examined also. The center-of-mass energies in ESI QTOF and MALDI QIT are similar (1-4 eV) and their product ion mass spectra are virtually identical. In the MALDI TOF ReTOF instrument, center-of-mass energies range from 126-309 eV for sodiated rutin to protonated dihydroxyflavones, respectively. Due to the high center-of-mass energies available with the MALDI TOF ReTOF instrument, some useful structural information may be obtained; however, with increasing precursor mass/charge ratio, product ion mass spectra become simplified so as to be of limited structural value. Electronic excitation of the protonated (and sodiated) species examined here offers an explanation for the very simple product ion mass spectra observed particularly for glycosylated flavonoids.

  9. Photo and Collision Induced Isomerization of a Cyclic Retinal Derivative: An Ion Mobility Study

    NASA Astrophysics Data System (ADS)

    Coughlan, Neville J. A.; Scholz, Michael S.; Hansen, Christopher S.; Trevitt, Adam J.; Adamson, Brian D.; Bieske, Evan J.

    2016-09-01

    A cationic degradation product, formed in solution from retinal Schiff base (RSB), is examined in the gas phase using ion mobility spectrometry, photoisomerization action spectroscopy, and collision induced dissociation (CID). The degradation product is found to be N- n-butyl-2-(β-ionylidene)-4-methylpyridinium (BIP) produced through 6π electrocyclization of RSB followed by protonation and loss of dihydrogen. Ion mobility measurements show that BIP exists as trans and cis isomers that can be interconverted through buffer gas collisions and by exposure to light, with a maximum response at λ = 420 nm.

  10. Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID-MS/MS) for the identification of proteins.

    PubMed

    Creese, Andrew J; Cooper, Helen J

    2007-05-01

    Electron capture dissociation (ECD) offers many advantages over the more traditional fragmentation techniques for the analysis of peptides and proteins, although the question remains: How suitable is ECD for incorporation within proteomic strategies for the identification of proteins? Here, we compare LC-ECD-MS/MS and LC-CID-MS/MS as techniques for the identification of proteins. Experiments were performed on a hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer. Replicate analyses of a six-protein (bovine serum albumin, apo-transferrin, lysozyme, cytochrome c, alcohol dehydrogenase, and beta-galactosidase) tryptic digest were performed and the results analyzed on the basis of overall protein sequence coverage and sequence tag lengths within individual peptides. The results show that although protein coverage was lower for LC-ECD-MS/MS than for LC-CID-MS/MS, LC-ECD-MS/MS resulted in longer peptide sequence tags, providing greater confidence in protein assignment.

  11. Products of Dissociative Recombination in the Ionosphere

    NASA Technical Reports Server (NTRS)

    Cosby, Philip

    1996-01-01

    SRI International undertook a novel experimental measurement of the product states formed by dissociative recombination (DR) of O2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and rovibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates. For a molecular ion such as O2(+), the dissociation recombination reaction is (1) O2(+) + e yields O + O + W. The atomic products of this reaction, in this case two oxygen atoms, can be produced in a variety of excited states and with a variety of kinetic energies, as represented by W in Eq. (1). These atoms are not only active in the neutral chemistry of the ionosphere, but are also especially important because their optical emissions are often used to infer in situ concentrations of the parent molecular ion and ambient electron densities. Many laboratory measurements have been made of DR reaction rates under a wide range of electron temperatures, but very little is known about the actual distributions among the final states of the atomic products. This lack of knowledge seriously limits the validity and effectiveness of efforts to model both natural and man-made ionospheric disturbances. Bates recently identified major deficiencies in the currently accepted branching ratios for O2(+) as they relate to blue and green line emission measurements in the nocturnal F-region. During our two-year effort, we partially satisfied our ambitious goals. We constructed and operated a variable pressure, electron-impact ion source and a high pressure, hollow-cathode discharge ion

  12. Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins.

    PubMed

    Singh, Charandeep; Zampronio, Cleidiane G; Creese, Andrew J; Cooper, Helen J

    2012-09-07

    Large scale mass spectrometry analysis of N-linked glycopeptides is complicated by the inherent complexity of the glycan structures. Here, we evaluate a mass spectrometry approach for the targeted analysis of N-linked glycopeptides in complex mixtures that does not require prior knowledge of the glycan structures or pre-enrichment of the glycopeptides. Despite the complexity of N-glycans, the core of the glycan remains constant, comprising two N-acetylglucosamine and three mannose units. Collision-induced dissociation (CID) mass spectrometry of N-glycopeptides results in the formation of the N-acetylglucosamine (GlcNAc) oxonium ion and a [mannose+GlcNAc] fragment (in addition to other fragments resulting from cleavage within the glycan). In ion-trap CID, those ions are not detected due to the low m/z cutoff; however, they are detected following the beam-type CID known as higher energy collision dissociation (HCD) on the orbitrap mass spectrometer. The presence of these product ions following HCD can be used as triggers for subsequent electron transfer dissociation (ETD) mass spectrometry analysis of the precursor ion. The ETD mass spectrum provides peptide sequence information, which is unobtainable from HCD. A Lys-C digest of ribonuclease B and trypsin digest of immunoglobulin G were separated by ZIC-HILIC liquid chromatography and analyzed by HCD product ion-triggered ETD. The data were analyzed both manually and by search against protein databases by commonly used algorithms. The results show that the product ion-triggered approach shows promise for the field of glycoproteomics and highlight the requirement for more sophisticated data mining tools.

  13. Absolute Emission Spectroscopy of Electronically Excited Products of Dissociative Recombination

    NASA Astrophysics Data System (ADS)

    Skrzypkowski, M. P.; Gougousi, T.; Golde, M. F.; Johnsen, R.

    1997-10-01

    We have employed spatially-resolved optical emission spectroscopy in a flowing afterglow plasma to investigate radiations in the 200-400 nm range resulting from electron-ion dissociative recombination. Calibrated emission data combined with Langmuir probe electron-density measurements are analyzed to obtain branching ratios for electronically excited recombination products. In particular, we will report absolute yields of CO(a^3Π) resulting from recombining CO_2^+ ions, NO(B^2Π) from N_2O^+, OH(A^2Σ^+) from HCO_2^+, as well as NH(A^3Π_i), and OH(A^2Σ^+) from the recombination of N_2OH^+ ions.

  14. Origin of collision-induced molecular orientation.

    PubMed

    Brouard, M; Hornung, B; Aoiz, F J

    2013-11-01

    Collision-induced rotational angular momentum orientation is a fundamental property of molecular scattering, which is sensitive to the balance between attractive and repulsive forces at play during collision. Here, we quantify a new mechanism leading to orientation, which is purely quantum mechanical in origin. Although the new mechanism is quite general, and will operate more widely in atomic and molecular scattering, it is observed here for impulsive hard shell collisions, for which the orientation vanishes classically. The quantum mechanism can thus be studied in isolation from other processes. The orientation is proposed to originate from the nonlocal nature of the quantum mechanical collision encounter.

  15. Energy-Dependent Electron Activated Dissociation of Metal-Adducted Permethylated Oligosaccharides

    PubMed Central

    Yu, Xiang; Huang, Yiqun; Lin, Cheng; Costello, Catherine E.

    2013-01-01

    The effects of varying the electron energy and cationizing agents on electron activated dissociation (ExD) of metal-adducted oligosaccharides were explored, using permethylated maltoheptaose as the model system. Across the examined range of electron energy, the metal-adducted oligosaccharide exhibited several fragmentation processes, including electron capture dissociation (ECD) at low energies, hot-ECD at intermediate energies, and electronic excitation dissociation (EED) at high energies. The dissociation threshold depended on the metal charge carrier(s), whereas the types and sequence spans of product ions were influenced by the metal-oligosaccharide binding pattern. Theoretical modeling contributed insight into the metal-dependent behavior of carbohydrates during low-energy ECD. When ExD was applied to a permethylated high mannose N-linked glycan, EED provided more structural information than either collision-induced dissociation (CID) or low-energy ECD, thus demonstrating its potential for oligosaccharide linkage analysis. PMID:22881449

  16. Dissociative Experiences, Creative Imagination, and Artistic Production in Students of Fine Arts

    ERIC Educational Resources Information Center

    Perez-Fabello, Maria Jose; Campos, Alfredo

    2011-01-01

    The current research was designed to assess the influence of dissociative experiences and creative imagination on the artistic production of Fine Arts students of the University of Vigo (Spain). The sample consisted of 81 students who were administered the Creative Imagination Scale and The Dissociative Experiences Scale. To measure artistic…

  17. Dissociative Ionization and Product Distributions of Benzene and Pyridine by Electron Impact

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Huo, Winifred M.; Fletcher, Graham D.

    2003-01-01

    We report a theoretical study of the dissociative ionization (DI) and product distributions of benzene (C6H6) and pyridine (C5H5N) from their low-lying ionization channels. Our approach makes use of the fact that electronic motion is much faster than nuclear motion allowing DI to be treated as a two-step process. The first step is the electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step, the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64,042719-I (2001)]. For the unimolecular dissociation, we use multiconfigurational self-consistent field (MCSCF) methods to determine the steepest descent pathways to the possible product channels. More accurate methods are then used to obtain better energetics of the paths which are used to determine unimolecular dissociation probabilities and product distributions. Our analysis of the dissociation products and the thresholds of their productions for benzene are compared with the recent dissociative photoionization meausurements of benzene by Feng et al. [R. Feng, G. Cooper, C.E. Brion, J. Electron Spectrosc. Relat. Phenom. 123,211 (2002)] and the dissociative photoionization measurements of pyridine by Tixier et al. [S. Tixier, G. Cooper, R. Feng, C.E. Brion, J. Electron Spectrosc. Relat. Phenom. 123,185 (2002)] using dipole (e,e+ion) coincidence spectroscopy.

  18. Determination of the dissociation kinetics of a transient intermediate.

    PubMed

    Asam, M R; Glish, G L

    1999-02-01

    Tandem mass spectrometry provides information on the dissociation pathways of gas-phase ions by providing a link between product ions and parent ions. However, there exists a distinct possibility that a parent ion does not dissociate directly to the observed product ion, but that the reaction proceeds through unobserved reaction intermediates. This work describes the discovery and kinetic analysis of an unobserved reaction intermediate with a quadrupole ion trap. [a4 - NH3] ions formed from [YG beta FL + H] ions dissociate to [(F*YG - NH3) - CO] ions. It is expected, however, from previous results, that [F*YG - NH3] ions should form prior to [(F*YG - NH3) - CO] ions. Double-resonance experiments are used to demonstrate the existence of intermediate [F*YG - NH3] ions. Various kinetic analyses are then performed using traditional collision-induced dissociation kinetics and double-resonance experiments. The phenomenological rates of formation and decay of peptide rearrangement ion dissociation products are determined by curve fitting decay and formation data generated with the kinetics experiments. The data generated predict an observable level of the intermediate in a time frame accessible but previously not monitored. By examining early product-ion formation, the intermediate ions, [F*YG - NH3]+, are observed.

  19. Thermal regulation of methane hydrate dissociation: Implications for gas production models

    USGS Publications Warehouse

    Circone, S.; Kirby, S.H.; Stern, L.A.

    2005-01-01

    Thermal self-regulation of methane hydrate dissociation at pressure, temperature conditions along phase boundaries, illustrated by experiment in this report, is a significant effect with potential relevance to gas production from gas hydrate. In surroundings maintained at temperatures above the ice melting point, the temperature in the vicinity of dissociating methane hydrate will decrease because heat flow is insufficient to balance the heat absorbed by the endothermic reaction: CH4??nH2O (s) = CH4 (g) + nH2O (l). Temperature decreases until either all of the hydrate dissociates or a phase boundary is reached. At pressures above the quadruple point, the temperature-limiting phase boundary is that of the dissociation reaction itself. At lower pressures, the minimum temperature is limited by the H2O solid/liquid boundary. This change in the temperature-limiting phase boundary constrains the pressure, temperature conditions of the quadruple point for the CH4-H2O system to 2.55 ?? 0.02 MPa and 272.85 ?? 0.03 K. At pressures below the quadruple point, hydrate dissociation proceeds as the liquid H2O produced by dissociation freezes. In the laboratory experiments, dissociation is not impeded by the formation of ice byproduct per se; instead rates are proportional to the heat flow from the surroundings. This is in contrast to the extremely slow dissociation rates observed when surrounding temperatures are below the H2O solid/liquid boundary, where no liquid water is present. This "anomalous" or "self" preservation behavior, most pronounced near 268 K, cannot be accessed when surrounding temperatures are above the H2O solid/liquid boundary. ?? 2005 American Chemical Society.

  20. Dissociation techniques in mass spectrometry-based proteomics.

    PubMed

    Jones, Andrew W; Cooper, Helen J

    2011-09-07

    The field of proteomics, the large-scale analysis of proteins, has undergone a huge expansion over the past decade. Mass spectrometry-based proteomics relies on the dissociation of peptide and/or protein ions to provide information on primary sequence and sites of post-translational modifications. Fragmentation techniques include collision-induced dissociation, electron capture dissociation and electron transfer dissociation. Here, we describe each of these techniques and their use in proteomics. The principles, advantages, limitations, and applications are discussed.

  1. Degradation process of grease due to SF/sub 6/ gas dissociation products

    SciTech Connect

    Suzuki, T.; Koyama, A.; Tomimuro, S.; Yoshiba, H.

    1982-08-01

    It is known that some insulating materials are degraded due to dissociation products of SF/sub 6/ gas. Many studies related to the degradation of insulating materials have been accomplished. But no studies related to sealing materials, for instance (lubricating) grease and rubber have been made. This paper presents the degradation process of grease as follows. Properties of Lithium grease easily change in SF/sub 6/ gas including dissociation products owing to the degradation of Lithium soap used as thickner of grease. However, in the case of Bentonite grease and Urea grease, any changes of properties are not observed.

  2. The contribution of dissociative processes to the production of atomic lines in hydrogen plasmas

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1985-01-01

    The contribution of molecular dissociative processes to the production of atomic lines is considered for a steady-state hydrogen plasma. If the contribution of dissociative processes is dominant, a substantial simplification in plasma diagnostics can be achieved. Numerical calculations have been performed for the production of Balmer alpha, beta, and gamma lines in hydrogen plasmas with medium and large degrees of ionization (x greater than about 0.0001) and for electron temperatures of 5000-45,000 K and electron densities of 10 to the 10th to 10 to the 16th/cu cm.

  3. Dissociative-recombination product states and the dissociation energy D0 of Ne2+

    SciTech Connect

    Hardy, K. A.; Peterson, J. R.; Ramos, G.; Sheldon, J. W.

    1998-02-28

    Final product states of Ne2+ dissociative recombination were studied using time-of-flight spectroscopy to determine the kinetic energies released. The dissociative recombination occurred in a sustained discharge in the presence of a variable magnetic field and discharge voltage, at pressures of 5-15 mTorr. Under different conditions various excited states were observed ranging from the lowest 3s metastable states to higher Rydbcrg states within 0.000 54 eV of the dissociation limit. From their narrow widths, it is deduced that these higher states arose from Ne2+ ions with subthermal energies. From two of these narrow distributions, we obtain an improved value for the dissociation limit D0(Ne2+)= 1.26±0.02 eV.

  4. Standard enthalpies of formation for glycyl-tyrosine and products of its dissociation in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Kochergina, L. A.; Badelin, V. G.; Krutova, O. N.; Volkov, A. V.; Damrina, K. V.

    2015-07-01

    The enthalpies of solution of crystalline glycyl-tyrosine in water and potassium hydroxide aqueous solutions are determined at 298.15 K by means of direct calorimetry. Standard enthalpies of formation for dipeptide and its products of dissociation in an aqueous solution are calculated.

  5. Surface Induced Dissociation Yields Quaternary Substructure of Refractory Noncovalent Phosphorylase B and Glutamate Dehydrogenase Complexes

    NASA Astrophysics Data System (ADS)

    Ma, Xin; Zhou, Mowei; Wysocki, Vicki H.

    2014-03-01

    Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.

  6. Interpretation of collision-induced fragmentation tandem mass spectra of posttranslationally modified peptides.

    PubMed

    Bunkenborg, Jakob; Matthiesen, Rune

    2007-01-01

    Tandem collision-induced dissociation (CID) mass spectrometry (MS) provides a sensitive means of analyzing the amino acid sequence of peptides. Modern MS instrumentation is capable of rapidly generating many thousands of tandem mass spectra, and protein database search engines have been developed to cope with this avalanche of data. In most studies, there is a schism between discarding perfectly valid data and including nonsensical peptide identifications--this is currently a major bottleneck in data analysis and it calls for manual evaluation of the data. Especially for posttranslationally modified peptides, there is a need for manual validation of the data because search algorithms seldom have been optimized for the identification of modified peptides and because there are many pitfalls for the unwary. This chapter describes some of the issues that should be considered when interpreting and validating low-energy CID tandem mass spectra and gives some useful tables to aid this process.

  7. Production of oxygen by electronically induced dissociations in ice.

    PubMed

    Johnson, R E; Cooper, P D; Quickenden, T I; Grieves, G A; Orlando, T M

    2005-11-08

    A solid-state chemical model is given for the production of O2 by electronic excitation of ice, a process that occurs on icy bodies in the outer solar system. Based on a review of the relevant available laboratory data, we propose that a trapped oxygen atom-water complex is the principal precursor for the formation of molecular oxygen in low-temperature ice at low fluences. Oxygen formation then occurs through direct excitation of this complex or by its reaction with a freshly produced, nonthermal O from an another excitation event. We describe a model for the latter process that includes competition with precursor destruction and the effect of sample structure. This allows us to put the ultraviolet photon, low-energy electron, and fast-ion experiments on a common footing for the first time. The formation of the trapped oxygen atom precursor is favored by the preferential loss of molecular hydrogen and is quenched by reactions with mobile H. The presence of impurity scavengers can limit the trapping of O, leading to the formation of oxygen-rich molecules in ice. Rate equations that include these reactions are given and integrated to obtain an analytic approximation for describing the experimental results on the production and loss of molecular oxygen from ice samples. In the proposed model, the loss rate varies, roughly, inversely with solid-state defect density at low temperatures, leading to a yield that increases with increasing temperature as observed. Cross sections obtained from fits of the model to laboratory data are evaluated in light of the proposed solid-state chemistry.

  8. Similarity Solution for Gas Production From Dissociating Hydrates in Geologic Media

    NASA Astrophysics Data System (ADS)

    Moridis, G. J.; Reagan, M. T.

    2007-12-01

    By using the Boltzman transformation, the nonlinear partial differential equations governing multicomponent mass flow, energy transport and phase changes in a geologic system involving methane hydrate dissociation can be reduced to simpler ordinary differential equations, without resorting to simplifications or approximations that require removal of any of the nonlinearities. This capability indicates that the problem admits a similarity solution, which results in invariance of any of the parameters (e.g., pressure, temperature, phase saturations) with respect to the similarity variable r/t1/2. The similarity solution is confirmed in test problems involving gas production from hydrate deposits undergoing dissociation by depressurization and thermal stimulation. The existence of the similarity solution provides a robust estimator of the gas production potential of natural hydrate accumulations, in addition to a reliable tool for the evaluation of the validity of numerical simulators of gas hydrate behavior in porous media.

  9. Cross sections for H(-) and Cl(-) production from HCl by dissociative electron attachment

    NASA Technical Reports Server (NTRS)

    Orient, O. J.; Srivastava, S. K.

    1985-01-01

    A crossed target beam-electron beam collision geometry and a quadrupole mass spectrometer have been used to conduct dissociative electron attachment cross section measurements for the case of H(-) and Cl(-) production from HCl. The relative flow technique is used to determine the absolute values of cross sections. A tabulation is given of the attachment energies corresponding to various cross section maxima. Error sources contributing to total errors are also estimated.

  10. Hydrogen production by water dissociation using ceramic membranes - annual report for FY 2008.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.; Energy Systems

    2009-03-25

    The objective of this project is to develop dense ceramic membranes that, without using an external power supply or circuitry, can produce hydrogen via coal/coal gas-assisted water dissociation. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  11. Hydrogen production by water dissociation using ceramic membranes. Annual report for FY 2009.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.; Energy Systems

    2010-04-20

    The objective of this project is to develop dense ceramic membranes that can produce hydrogen via coal/coal gas-assisted water dissociation without using an external power supply or circuitry. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  12. Hydrogen production by water dissociation using ceramic membranes - annual report for FY 2010.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.

    2011-03-14

    The objective of this project is to develop dense ceramic membranes that can produce hydrogen via coal/coal gas-assisted water dissociation without using an external power supply or circuitry. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen using OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  13. Collision--induced absorption in dense atmospheres of cool stars

    SciTech Connect

    Borysow, Aleksandra; Joergensen, Uffe Graae

    1999-04-01

    In the atmosphere of the Sun the major interaction between the matter and the radiation is through light absorption by ions (predominantly the negative ion of hydrogen atoms), neutral atoms and a small amount of polar molecules. The majority of stars in the universe are, however, cooler and denser than our Sun, and for a large fraction of these, the above absorption processes are very weak. Here, collision-induced absorption (CIA) becomes the dominant opacity source. The radiation is absorbed during very short mutual passages ('collisions') of two non-polar molecules (and/or atoms), while their electric charge distributions are temporarily distorted which gives rise to a transient dipole moment. We present here a review of the present-day knowledge about the impact of collision-induced absorption processes on the structure and the spectrum of such stars.

  14. Partial dissociative emission cross sections and product state distributions of the resulting photofragments

    NASA Astrophysics Data System (ADS)

    Picconi, David; Grebenshchikov, Sergy Yu.

    2016-12-01

    This paper relates the partial cross section of a continuous optical emission into a given scattering channel of the lower electronic state to the photofragment population. This allows one to infer partial emission cross sections 'non-optically' from product state distributions; in computations, explicit construction of exact scattering states is therefore avoided. Applications to the emission spectra of NaI, CO2, and pyrrole are given. It is also demonstrated that a similar relationship holds between partial cross sections of dissociative photoionization and distributions of ionic fragments over final product channels.

  15. Wavepacket theory of collisional dissociation in molecules

    SciTech Connect

    Kulander, K.

    1980-01-01

    An explicit integration scheme is used to solve the time dependent Schroedinger equation for wavepackets which model collisions in the collinear H + H/sub 2/ system. A realistic LEPS-type potential energy surface is used. Collision energies considered are above the dissociation threshold and probabilities for collision induced dissociation are reported. Also quantum mechanical state-to-state transition probabilities are generated. These results are compared to extensive classical trajectory calculations performed on this same system. The time evolution of the wavepacket densities is studied to understand the dynamics of the collinear collisional dissociation process.

  16. Repeatability and reproducibility of product ion abundances in electron capture dissociation mass spectrometry of peptides.

    PubMed

    Ben Hamidane, Hisham; Vorobyev, Aleksey; Tsybin, Yury O

    2011-01-01

    Site-specific reproducibility and repeatability of electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) are of fundamental importance for product ion abundance (PIA)-based peptide and protein structure analysis. However, despite the growing interest in ECD PIA-based applications, these parameters have not yet been investigated in a consistent manner. Here, we first provide a detailed description of the experimental parameters for ECD-based tandem mass spectrometry performed on a hybrid linear ion trap (LTQ) FT-ICR MS. In the following, we describe the evaluation and comparison of ECD and infrared multiphoton dissociation (IRMPD) PIA methodologies upon variation of a number of experimental parameters, for example, cathode potential (electron energy), laser power, electron and photon irradiation periods and pre- irradiation delays, as well as precursor ion number. Ranges of experimental parameters that yielded an average PIA variation below 5% and 15% were determined for ECD and IRMPD, respectively. We report cleavage site-dependent ECD PIA variation below 20% and correlation coefficients between fragmentation patterns superior to 0.95 for experiments performed on three FT-ICR MS instruments. Overall, the encouraging results obtained for ECD PIA reproducibility and repeatability support the use of ECD PIA as a complementary source of information to m/z data in radical-induced dissociation applied for peptide and protein structure analysis.

  17. Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products

    NASA Astrophysics Data System (ADS)

    Kidwell, Nathanael M.; Li, Hongwei; Wang, Xiaohong; Bowman, Joel M.; Lester, Marsha I.

    2016-05-01

    The hydroxyl radical is an important atmospheric oxidant, and a significant source of its production occurs through alkene ozonolysis. This takes place via a cycloaddition reaction and subsequent fragmentation to form an energized carbonyl oxide (for example, CH3CHOO), known as a Criegee intermediate, which can then either react with another atmospheric species or decay and, in doing so, produce the hydroxyl radical. Here, we examine the dissociation dynamics of a prototypical Criegee intermediate by characterizing the translational and internal energy distributions of the OH radical products, which reflect critical configurations along the reaction pathway. Experimentally, the kinetic energy release to OH products is ascertained through velocity map imaging. Theoretically, quasi-classical trajectories are performed on a new full-dimensional, ab initio potential energy surface. Both experiment and theory show that most of the available energy flows into internal excitation of the vinoxy products. The isotropic angular distribution of OH fragments indicates that dissociation occurs in ≥2 ps, in agreement with theory.

  18. Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products.

    PubMed

    Kidwell, Nathanael M; Li, Hongwei; Wang, Xiaohong; Bowman, Joel M; Lester, Marsha I

    2016-05-01

    The hydroxyl radical is an important atmospheric oxidant, and a significant source of its production occurs through alkene ozonolysis. This takes place via a cycloaddition reaction and subsequent fragmentation to form an energized carbonyl oxide (for example, CH3CHOO), known as a Criegee intermediate, which can then either react with another atmospheric species or decay and, in doing so, produce the hydroxyl radical. Here, we examine the dissociation dynamics of a prototypical Criegee intermediate by characterizing the translational and internal energy distributions of the OH radical products, which reflect critical configurations along the reaction pathway. Experimentally, the kinetic energy release to OH products is ascertained through velocity map imaging. Theoretically, quasi-classical trajectories are performed on a new full-dimensional, ab initio potential energy surface. Both experiment and theory show that most of the available energy flows into internal excitation of the vinoxy products. The isotropic angular distribution of OH fragments indicates that dissociation occurs in ≥2 ps, in agreement with theory.

  19. Competitive Hydrogen Atom Migrations Accompanying Cascade Dissociations of Peptide Cation-Radicals of the z(+•) Type.

    PubMed

    Ledvina, Aaron R; Coon, Joshua J; Tureček, František

    2015-02-01

    We report a combined experimental and computational study of energy-resolved collision-induced dissociation (ER-CID) and time-resolved infrared multiphoton dissociation (TR-IRMPD) of z4 ions prepared by electron transfer dissociation of peptide (Ala-Ala-Asn-Ala-Arg + 2H)(2+) ions. The z4 cation-radicals, (•)ANAR(+), undergo competitive dissociations by backbone cleavage and loss of a CONH2 radical from the Asn side chain. The backbone cleavage proceeds by radical-assisted dissociation of the Asn Cα-CO bond, forming an x2 ion intermediate which rapidly dissociates by HNCO elimination to yield a stable z2 fragment ion, (•)AR(+). The ER-CID and TR-IRMPD data were consistent with the consecutive nature of the backbone dissociation but showed different branching ratios for the two major fragmentations. The ER-CID data showed branching ratios 0.6-1.0 for the side-chain and backbone cleavages whereas the TR-IRMPD data showed an earlier onset for the latter dissociation. Computational analysis of the potential energy surface with density functional theory and ab initio calculations was carried out to provide structures and energies for the reactant ions as well as several intermediates, products, and transition states. Dissociation pathways for cis and trans amide conformers were distinguished and their energies were evaluated. The threshold dissociation energies for the backbone and side-chain dissociations were similar in accordance with the experimental ER-CID branching ratio. The TR-IRMPD data were interpreted by different absorbances of intermediates produced by hydrogen atom migrations along the dissociation pathways.

  20. Competitive Hydrogen Atom Migrations Accompanying Cascade Dissociations of Peptide Cation-Radicals of the z+• Type

    PubMed Central

    Ledvina, Aaron R.; Coon, Joshua J.

    2014-01-01

    We report a combined experimental and computational study of energy-resolved collision-induced dissociation (ER-CID) and time-resolved infrared multiphoton dissociation (TR-IRMPD) of z4 ions prepared by electron transfer dissociation of peptide (Ala-Ala-Asn-Ala-Arg + 2H)2+ ions. The z4 cation-radicals, •ANAR+, undergo competitive dissociations by backbone cleavage and loss of a CONH2 radical from the Asn side chain. The backbone cleavage proceeds by radical-assisted dissociation of the Asn Cα—CO bond, forming an x2 ion intermediate which rapidly dissociates by HNCO elimination to yield a stable z2 fragment ion, •AR+. The ER-CID and TR-IRMPD data were consistent with the consecutive nature of the backbone dissociation but showed different branching ratios for the two major fragmentations. The ER-CID data showed branching ratios 0.6-1.0 for the side-chain and backbone cleavages whereas the TR-IRMPD data showed an earlier onset for the latter dissociation. Computational analysis of the potential energy surface with density functional theory and ab initio calculations was carried out to provide structures and energies for the reactant ions as well as several intermediates, products, and transition states. Dissociation pathways for cis and trans amide conformers were distinguished and their energies were evaluated. The threshold dissociation energies for the backbone and side-chain dissociations were similar in accordance with the experimental ER-CID branching ratio. The TR-IRMPD data were interpreted by different absorbances of intermediates produced by hydrogen atom migrations along the dissociation pathways. PMID:25844055

  1. Assignment of the stereochemistry and anomeric configuration of structurally informative product ions derived from disaccharides: infrared photodissociation of glycosyl-glycolaldehydes in the negative ion mode.

    PubMed

    Bendiak, Brad; Fang, Tammy T

    2010-11-02

    Using mass spectrometry in the negative ion mode, m/z 221 ions are frequently observed as product ion substructures derived from reducing disaccharides having 2, 4, or 6 linkages. The ions have been shown to be glycosyl-glycolaldehydes. All 16 stereochemical variants of their pyranosides were prepared and evaluated by infrared photodissociation, in addition to HexNAc-glycolaldehyde variants (m/z 262) of 2-acetamido-2-deoxy-d-glucose and 2-acetamido-2-deoxy-d-galactose. The stereochemistry and anomeric configuration of these ions were differentiated in the gas phase using a Fourier transform ion cyclotron resonance spectrometer with infrared multiphoton dissociation at 10.6 μm. Results were compared to those obtained by collision-induced dissociation. In some cases, differentiation was far preferable using infrared photodissociation; in others, collision-induced dissociation was preferred. Using an instrument that interfaced a linear trap with a Fourier transform ion cyclotron resonance spectrometer, either dissociation technique could be used to optimally discriminate between isomers. With infrared photodissociation, spectral differences were highly statistically significant, even between pairs of isomers having spectra that appeared to be visually somewhat similar (p<1×10⁻⁹, student's t-test for key discriminatory ions). Comparisons among different instruments suggest that physical standards of the stereochemical variants of these ions will be required for their detailed structural assignments in unknowns, as some variation was observed among instruments, both using infrared photodissociation and collision-induced dissociation.

  2. Efficient Production of O- by Dissociative Attachment of Slow Electrons to Highly Excited Metastable Oxygen Molecules

    NASA Astrophysics Data System (ADS)

    Hayashi, Daiyu; Kadota, Kiyoshi

    1999-01-01

    In this paper, the mechanism for efficient production of O- in the afterglow of a low-pressure and high-density oxygen plasma has been described. We proposed a new production process, the dissociative attachment of slow electrons to highly excited metastable oxygen molecules O2 (A3 Σu+, A'3Δu, c1Σu-). The electron attachment frequency has been obtained from the experimental results, and was significantly high for the electron temperature of less than 2 eV. The cross section, σDA, for this process was evaluated by a quantum mechanical approach. σDA at 0.1 eV was larger by two-orders of magnitude than the peak value at 6.7 eV for the ground state O2 (X3Σg+). The enhancement of the electron attachment frequency at low temperature can be explained by dissociative attachment of slow electrons to O2 (A3Σu+, A'3Δu, c1Σu-).

  3. Hydrogen production by water dissociation using ceramic membranes. Annual report for FY 2007.

    SciTech Connect

    Balachandran, U.; Chen, L.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Park, C. Y.; Picciolo, J. J.; Song, S. J.; Energy Systems

    2008-03-04

    The objective of this project is to develop dense ceramic membranes that, without using an external power supply or circuitry, can produce hydrogen via coal/coal gas-assisted water dissociation. This project grew out of an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions [1]. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen to be produced by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting [1, 2]. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  4. Methane dissociation process in inductively coupled Ar/H2/CH4 plasma for graphene nano-flakes production

    NASA Astrophysics Data System (ADS)

    Mohanta, Antaryami; Lanfant, Briac; Asfaha, Mehari; Leparoux, Marc

    2017-02-01

    The role of hydrogen and methane dissociation process in induction plasma synthesis of graphene nano-flakes (GNF) is studied by the optical emission spectroscopy of Ar/H2/CH4 plasma. The condensation of C2 species formed due to methane decomposition produces GNF, which depends on pressure. Electron impact and dehydrogenation processes dissociate methane, which promotes and hinders the GNF production, respectively. The effect of hydrogen is insignificant on quality, size and morphology of the GNF. The CH4 flow rate has no influence on particle temperature but has effect on cooling rate at the point of nucleation and, therefore, on production rate and thickness of GNF.

  5. Apparatus for hydrogen and carbon production via carbon aerosol-catalyzed dissociation of hydrocarbons

    NASA Technical Reports Server (NTRS)

    Muradov, Nazim Z. (Inventor); Smith, Franklyn (Inventor); Tabatabaie-Raissi, Ali (Inventor)

    2012-01-01

    A novel process and apparatus is disclosed for sustainable, continuous production of hydrogen and carbon by catalytic dissociation or decomposition of hydrocarbons at elevated temperatures using in-situ generated carbon particles. Carbon particles are produced by decomposition of carbonaceous materials in response to an energy input. The energy input can be provided by at least one of a non-oxidative and oxidative means. The non-oxidative means of the energy input includes a high temperature source, or different types of plasma, such as, thermal, non-thermal, microwave, corona discharge, glow discharge, dielectric barrier discharge, or radiation sources, such as, electron beam, gamma, ultraviolet (UV). The oxidative means of the energy input includes oxygen, air, ozone, nitrous oxide (NO.sub.2) and other oxidizing agents. The method, apparatus and process of the present invention is applicable to any gaseous or liquid hydrocarbon fuel and it produces no or significantly less CO.sub.2 emissions compared to conventional processes.

  6. Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer.

    PubMed

    Gardner, Myles W; Smith, Suncerae I; Ledvina, Aaron R; Madsen, James A; Coon, Joshua J; Schwartz, Jae C; Stafford, George C; Brodbelt, Jennifer S

    2009-10-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells-the first a high pressure cell operated at nominally 5 x 10(-3) Torr and the second a low pressure cell operated at nominally 3 x 10(-4) Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y(1) fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of approximately 100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra.

  7. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

    PubMed Central

    Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

    2009-01-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

  8. Collision-induced stimulated photon echo in magnetic field

    NASA Astrophysics Data System (ADS)

    Reshetov, V. A.

    2015-12-01

    The action of the longitudinal magnetic field on the collision-induced stimulated photon echo formed on the transition with the angular momentum change {{J}a}=0\\to {{J}b}=1 is studied theoretically. It is shown that this action depends essentially on the sign of the difference in the orientation Γb(1) and alignment Γb(2) relaxation rates of the excited level b. If Γb(2)>Γb(1) , then the echo intensity in a weak magnetic field increases with the increase in the magnetic field strength, while in the alternative case Γb(2)<Γb(1) it decreases up to zero value. The formulae enabling the determination of the magnitude of the difference Γb(1)-Γb(2) from the experimental study of the oscillations of the echo intensity with the increase in the magnetic field strength are obtained.

  9. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    SciTech Connect

    McGuire, S. Miles, R.

    2014-12-28

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}Π{sub g} ← X{sup 1}Σ{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ″1}Σ{sub g}{sup +} electronic state.

  10. Ultrafast laser-collision-induced fluorescence in atmospheric pressure plasma

    NASA Astrophysics Data System (ADS)

    Barnat, E. V.; Fierro, A.

    2017-04-01

    The implementation and demonstration of laser-collision-induced fluorescence (LCIF) generated in atmospheric pressure helium environments is presented in this communication. As collision times are observed to be fast (~10 ns), ultrashort pulse laser excitation (<100 fs) of the 23S to 33P (388.9 nm) is utilized to initiate the LCIF process. Both neutral-induced and electron-induced components of the LCIF are observed in the helium afterglow plasma as the reduced electric field (E/N) is tuned from  <0.1 Td to over 5 Td. Under the discharge conditions presented in this study (640 Torr He), the lower limit of electron density detection is ~1012 e cm‑3. The spatial profiles of the 23S helium metastable and electrons are presented as functions of E/N to demonstrate the spatial resolving capabilities of the LCIF method.

  11. Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation.

    PubMed

    Srikanth, R; Wilson, Jonathan; Bridgewater, Juma D; Numbers, Jason R; Lim, Jihyeon; Olbris, Mark R; Kettani, Ali; Vachet, Richard W

    2007-08-01

    Oxidative modifications to the side chains of sulfur-containing amino acids often limit the number of product ions formed during collision-induced dissociation (CID) and thus make it difficult to obtain sequence information for oxidized peptides. In this work, we demonstrate that electron-transfer dissociation (ETD) can be used to improve the sequence information obtained from peptides with oxidized cysteine and methionine residues. In contrast to CID, ETD is found to be much less sensitive to the side-chain chemistry, enabling extensive sequence information to be obtained in cases where CID fails to provide this information. These results indicate that ETD is a valuable technique for studying oxidatively modified peptides and proteins. In addition, we report a unique and very abundant product ion that is formed in the CID spectra of peptides having N-terminal cysteine sulfinic acid residues. The mechanism for this unique dissociation pathway involves a six-membered cyclic intermediate and leads to the facile loss of NH(3) and SO(2), which corresponds to a mass loss of 81 Da. While the facile nature of this dissociation pathway limits the sequence information present in CID spectra of peptides with N-terminal cysteine sulfinic acid residues, extensive sequence information for these peptides can be obtained with ETD.

  12. Major Effects in the Thermodynamics of Detonation Products: Phase Segregation versus Ionic Dissociation

    SciTech Connect

    Bastea, S; Fried, L E

    2010-03-09

    Water (H{sub 2}O) and nitrogen (N{sub 2}) are major detonation products of high explosives and it has long been conjectured that they may phase segregate at high enough temperatures and pressures to influence detonation properties of common explosives. We analyze the phase diagram of H{sub 2}O-N{sub 2} mixtures using a thermodynamic theory for polar-nonpolar mixtures and find that phase segregation is unlikely to occur above approximately 1600K. Therefore, H{sub 2}O-N{sub 2} immiscibility is not likely to be relevant for detonation predictions. We propose instead that the high pressure ionic dissociation of water plays an important role in detonation, and model it using a new ionic thermodynamics. We employ this model in chemical equilibrium calculations of standard high explosives, e.g. PETN, HMX and RDX, and find that it performs very well under a wide range of conditions. Thus, although it may require further development, it is likely that explicitly ionic thermodynamics will become a standard tool for explosives modeling.

  13. Spectroscopic studies of neutral products of electron-ion dissociative recombination

    NASA Astrophysics Data System (ADS)

    Rosati, Richard E.

    The Flowing Afterglow Langmuir Probe (FALP) technique, in conjunction with spatially resolved absolute spectroscopy, has been applied to the dissociative recombination of CO2+, N2H+, HCO+, and HCO+ ions with thermal-energy electrons. The principal aim was to determine the radiative cascading contribution from high-lying triplet states, mainly CO(a' 3Sigma+) and CO(d 3Delta i), to the total yield of the long-lived CO(a 3pir) state. In the case of CO2+, the sum of the yields of the triplet states, which radiate exclusively into CO(a 3pir), relative to that of CO(a 3pir) was found to be 0.63 +/- 0.08. That is, approximately 0.63 of the total CO(a ) yield is due to radiative cascade contributions from the triplet states. When combined with our previously reported value of 0.29 +/- 0.101 for the total absolute yield of CO(a), the sum of absolute yields of the triplet states was found to be 0.18 +/- 0.06. A similar, but more complex analysis has been performed on HCO +/HOC+ recombination. The results indicate that CO( a) is populated mainly by direct formation from the recombination of the lower-energy isomer, HCO+. The total absolute yield of CO(a') and CO(d) from HOC+ recombination was found to be 0.64 +/- 0.20. This value represents a lower limit as not all emissions from CO( a') could be included in the determination. The indication is that there is little direct formation of CO(a) from HOC+ recombination. Upper and lower limits for the yield of N2(B 3pig) from N2H+ recombination were obtained, which place the absolute yield between 0.20 and 0.33. The following vibrational distributions for products of dissociative recombination were determined: CO(d 3Deltai, nu ' = 0--5) and CO(a' 3Sigma+, nu' = 4--7) from CO2+ recombination, CO(d 3Deltai, nu' = 0--5) and CO(a' 3Sigma +, nu' = 5--7) from HOC+ recombination, and N2(B 3pi g, nu' = 1--6) from N2 H+ recombination. An analysis of the O-atom yield from the dissociative recombination of H3O+ ions employing a (2 + 1

  14. Collision-induced squeezing in a harmonic oscillator

    NASA Technical Reports Server (NTRS)

    Lee, Hai-Woong

    1993-01-01

    The concept of squeezing has so far been applied mainly to light, as is evidenced by the number of research works on the subject of squeezed light. Since, in quantum mechanics, both light and the simple harmonic oscillator are described within the same mathematical framework, there is of course no difficulty in applying the concept to the simple harmonic oscillator as well. In fact, the theoretical development of squeezed states and squeezed light owes much to the physical insights that one obtains as the analogy between light and the harmonic oscillator is exploited. The example presented shows clearly that two states with different phases in general have different degrees of squeezing, even if they have the same state distribution. This means that, even if one considers collision processes that produce the same state distribution, the degree of squeezing obtained during and after the collisions can be quite different, depending on how the phases phi(sub n) of the probability amplitudes develop in time as the collisions proceed. It is therefore evident that, for a detailed study of collision-induced squeezing, further study on the time development of the phases in collisions and its relation to collision parameters such as potential energy surfaces and collision energy is needed.

  15. A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination

    NASA Astrophysics Data System (ADS)

    Yu, Hua-Gen

    2008-05-01

    A spherical electron cloud hopping (SECH) model is proposed to study the product branching ratios of dissociative recombination (DR) of polyatomic systems. In this model, the fast electron-captured process is treated as an instantaneous hopping of a cloud of uniform spherical fractional point charges onto a target M+q ion (or molecule). The sum of point charges (-1) simulates the incident electron. The sphere radius is determined by a critical distance (ReMc) between the incoming electron (e -) and the target, at which the potential energy of the e--M+q system is equal to that of the electron-captured molecule M+q-1 in a symmetry-allowed electronic state with the same structure as M+q. During the hopping procedure, the excess energies of electron association reaction are dispersed in the kinetic energies of M+q-1 atoms to conserve total energy. The kinetic energies are adjusted by linearly adding atomic momenta in the direction of driving forces induced by the scattering electron. The nuclear dynamics of the resultant M+q-1 molecule are studied by using a direct ab initio dynamics method on the adiabatic potential energy surface of M+q-1, or together with extra adiabatic surface(s) of M+q-1. For the latter case, the "fewest switches" surface hopping algorithm of Tully was adapted to deal with the nonadiabaticity in trajectory propagations. The SECH model has been applied to study the DR of both CH + and H3O+(H2O)2. The theoretical results are consistent with the experiment. It was found that water molecules play an important role in determining the product branching ratios of the molecular cluster ion.

  16. A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination.

    PubMed

    Yu, Hua-Gen

    2008-05-21

    A spherical electron cloud hopping (SECH) model is proposed to study the product branching ratios of dissociative recombination (DR) of polyatomic systems. In this model, the fast electron-captured process is treated as an instantaneous hopping of a cloud of uniform spherical fractional point charges onto a target M+q ion (or molecule). The sum of point charges (-1) simulates the incident electron. The sphere radius is determined by a critical distance (Rc eM) between the incoming electron (e-) and the target, at which the potential energy of the e(-)-M+q system is equal to that of the electron-captured molecule M+q(-1) in a symmetry-allowed electronic state with the same structure as M(+q). During the hopping procedure, the excess energies of electron association reaction are dispersed in the kinetic energies of M+q(-1) atoms to conserve total energy. The kinetic energies are adjusted by linearly adding atomic momenta in the direction of driving forces induced by the scattering electron. The nuclear dynamics of the resultant M+q(-1) molecule are studied by using a direct ab initio dynamics method on the adiabatic potential energy surface of M+q(-1), or together with extra adiabatic surface(s) of M+q(-1). For the latter case, the "fewest switches" surface hopping algorithm of Tully was adapted to deal with the nonadiabaticity in trajectory propagations. The SECH model has been applied to study the DR of both CH+ and H3O+(H2O)2. The theoretical results are consistent with the experiment. It was found that water molecules play an important role in determining the product branching ratios of the molecular cluster ion.

  17. Electron capture dissociation mass spectrometry of tyrosine nitrated peptides.

    PubMed

    Jones, Andrew W; Mikhailov, Victor A; Iniesta, Jesus; Cooper, Helen J

    2010-02-01

    In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.

  18. Electron transfer dissociation of modified peptides and proteins.

    PubMed

    Zhou, Yuping; Dong, Jia; Vachet, Richard W

    2011-10-01

    Mass spectrometry is the method of choice for sequencing peptides and proteins and is the preferred choice for characterizing post-translational modifications (PTMs). The most commonly used dissociation method to characterize peptides (i.e. collision-induced dissociation (CID)), however, has some limitations when it comes to analyzing many PTMs. Because CID chemistry is influenced by amino acid side-chains, some modifications can alter or inhibit dissociation along the peptide backbone, thereby limiting sequence information and hindering identification of the modification site. Electron transfer dissociation (ETD) has emerged as an alternate dissociation technique that, in most cases, overcomes these limitations of CID because it is less affected by side chain chemistry. Here, we review recent applications of ETD for characterizing peptide and protein PTMs with a particular emphasis on the advantages of ETD over CID, the ways in which ETD and CID have been used in a complementary manner, and how peptide modifications can still influence ETD dissociation pathways.

  19. Production of and Dissociative Electron Attachment to the Simplest Criegee Intermediate in an Afterglow.

    PubMed

    Wiens, Justin P; Shuman, Nicholas S; Viggiano, Albert A

    2015-02-05

    The simplest Criegee intermediate, CH2OO, has been produced in a flowing afterglow using a novel technique. CH2I is produced by dissociative electron attachment to CH2I2, leading to the established reaction CH2I + O2 → CH2OO + I. The presence of CH2OO is established by observation of dissociative electron attachment to yield O(-) using the variable electron and neutral density attachment mass spectrometry (VENDAMS) technique. The measurements establish the electron attachment rate coefficient of thermal electrons at 300 K to CH2OO as 1.2 ± 0.3 × 10(-8) cm(3) s(-1). Thermal electron attachment is solely dissociative and is not a promising route to producing stable CH2OO(-). The results open the possibility of measuring ion-molecule chemistry involving Criegee intermediates, as well as the reactivity of other unstable radicals produced in an analogous manner.

  20. Collision-induced vibrational absorption in molecular hydrogens

    SciTech Connect

    Reddy, S.P.

    1993-05-01

    Collision induced absorption (CIA) spectra of the first overtone bands of H{sub 2}, D{sub 2}, and HD have been recorded for gas densities up to 500 amagat at 77-300 K. Analyses of these spectra reveal that (1) contrary to the observations in the fundamental bands, the contribution of the isotropic overlap interaction to the first overtone bands is negligible, (2) the squares of the matrix elements B{sub 32}(R)/ea{sub o} [= {lambda}{sub 32} exp(-(R-{sigma})/{rho}{sub 32}) + 3 (R/a{sub o}){sup -4}] where the subscripts 3 and 2 represent L and {lambda}, respectively, account for the absorption intensity of the bands and (3) the mixed term, 2,3 {lambda}{sub 32} exp (-(R-{sigma})/{rho}{sub 32}) <{vert_bar}Q{vert_bar}> <{alpha}> (R/a){sup -4}, gives a negative contribution. In the CIA spectra of H{sub 2} in its second overtone region recorded at 77, 201 and 298 K for gas densities up to 1000 amagat, a dip in the Q branch with characteristic Q{sub p} and Q{sub R} components has been observed. The analysis of the absorption profiles reveals, in addition to the previously known effects, the occurrence of the triple-collision transitions of H{sub 2} of the type Q{sub 1}(J) + Q{sub 1}(J) + Q{sub 1}(J) for the first time. From the profile analysis the absorption coefficient of these transitions is obtained.

  1. Coordination Sphere Tuning of the Electron Transfer Dissociation Behavior of Cu(II)-Peptide Complexes

    NASA Astrophysics Data System (ADS)

    Dong, Jia; Vachet, Richard W.

    2012-02-01

    In contrast to previous electron capture dissociation (ECD) studies, we find that electron transfer dissociation (ETD) of Cu(II)-peptide complexes can generate c- and z-type product ions when the peptide has a sufficient number of strongly coordinating residues. Double-resonance experiments, ion-molecule reactions, and collision-induced dissociation (CID) prove that the c and z product ions are formed via typical radical pathways without the associated reduction of Cu(II), despite the high second ionization energy of Cu. A positive correlation between the number of Cu(II) binding groups in the peptide sequence and the extent of c and z ion formation was also observed. This trend is rationalized by considering that the recombination energy of Cu(II) can be lowered by strong binding ligands to an extent that enables electron transfer to non-Cu sites (e.g., protonation sites) to compete with Cu(II) reduction, thereby generating c/z ions in a manner similar to that observed for protonated (i.e., nonmetalated) peptides.

  2. Dissociative Disorders

    MedlinePlus

    ... of continuity between thoughts, memories, surroundings, actions and identity. People with dissociative disorders escape reality in ways ... at bay. Symptoms — ranging from amnesia to alternate identities — depend in part on the type of dissociative ...

  3. Surface-induced dissociation of ion mobility-separated noncovalent complexes in a quadrupole/time-of-flight mass spectrometer.

    PubMed

    Zhou, Mowei; Huang, Chengsi; Wysocki, Vicki H

    2012-07-17

    A custom in-line surface-induced dissociation (SID) device has been incorporated into a commercial ion mobility quadrupole/time-of-flight mass spectrometer in order to provide an alternative and potentially more informative activation method than the commonly used collision-induced dissociation (CID). Complicated sample mixtures can be fractionated by ion mobility (IM) and then dissociated by CID or SID for further structural analysis. Interpretation of SID spectra for cesium iodide clusters was greatly simplified with IM prior to dissociation because products originating from different precursors and overlapping in m/z but separated in drift time can be examined individually. Multiple conformations of two protein complexes, source-activated transthyretin tetramer and nativelike serum amyloid P decamer, were separated in ion mobility and subjected to CID and SID. CID spectra of the mobility separated conformations are similar. However, drastic differences can be observed for SID spectra of different conformations, implying different structures in the gas phase. This work highlights the potential of utilizing IM-SID to study quaternary structures of protein complexes and provides information that is complementary to our recently reported SID-IM approach.

  4. Collision-induced absorption in the far infrared spectrum of Titan

    NASA Technical Reports Server (NTRS)

    Hunt, J. L.; Poll, J. D.; Goorvitch, D.; Tipping, R. H.

    1983-01-01

    The effects of collision-induced absorption on the far infrared spectrum of Titan have been investigated. After a review of the procedure for the theoretical calculation of the N2 translation-rotational spectrum, new results for the temperature range o 70 to 120 K are reported. These are used as input data for a simple atmospheric model in order to compute the far infrared radiance, brightness temperature, and specral limb function. This source of opacity alone is not capable of explaining the Voyager results. When the collision-induced methane is included, the results are in closer agreement in the range between 200 and 300/cm, suggesting that a more complete treatment of collision-induced absorption including particularly CH4-N2, N2-H2, and H2-H2 results, may provide sufficient opacity to reduce or obviate the need for opacities due to clouds or aerosols in order to explain the observed spectra.

  5. Dissociative disorders.

    PubMed

    Kihlstrom, John F

    2005-01-01

    The dissociative disorders, including "psychogenic" or "functional" amnesia, fugue, dissociative identity disorder (DID, also known as multiple personality disorder), and depersonalization disorder, were once classified, along with conversion disorder, as forms of hysteria. The 1970s witnessed an "epidemic" of dissociative disorder, particularly DID, which may have reflected enthusiasm for the diagnosis more than its actual prevalence. Traditionally, the dissociative disorders have been attributed to trauma and other psychological stress, but the existing evidence favoring this hypothesis is plagued by poor methodology. Prospective studies of traumatized individuals reveal no convincing cases of amnesia not attributable to brain insult, injury, or disease. Treatment generally involves recovering and working through ostensibly repressed or dissociated memories of trauma; at present, there are few quantitative or controlled outcome studies. Experimental studies are few in number and have focused largely on state-dependent and implicit memory. Depersonalization disorder may be in line for the next "epidemic" of dissociation.

  6. Anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) and product branching ratio calculations for the partially deuterated protonated water dimers: Dissociation and isomerization

    NASA Astrophysics Data System (ADS)

    Song, Di; Su, Hongmei; Kong, Fan-ao; Lin, Sheng-Hsien

    2013-03-01

    Partially deuterated protonated water dimers, H2O.H+.D2O, H2O.D+.HDO, and HDO.H+.HDO, as important intermediates of isotopic labeled reaction of H3O+ + D2O, undergo direct dissociation and indirect dissociation, i.e., isomerization before the dissociation. With Rice-Ramsperger-Kassel-Marcus theory and ab initio calculations, we have computed their dissociation and isomerization rate constants separately under the harmonic and anharmonic oscillator models. On the basis of the dissociation and isomerization rate constants, branching ratios of two primary products, [HD2O+]/[H2DO+], are predicted under various kinetics models with the harmonic or anharmonic approximation included. The feasible kinetics model accounting for experimental results is shown to include anharmonic effect in describing dissociation, while adopting harmonic approximation for isomerization. Thus, the anharmonic effect is found to play important roles affecting the dissociation reaction, while isomerization rates are shown to be insensitive to whether the anharmonic or harmonic oscillator model is being applied.

  7. Formation and Dissociation of Phosphorylated Peptide Radical Cations

    NASA Astrophysics Data System (ADS)

    Kong, Ricky P. W.; Quan, Quan; Hao, Qiang; Lai, Cheuk-Kuen; Siu, Chi-Kit; Chu, Ivan K.

    2012-12-01

    In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal-ligand phosphorylated peptide complexes [CuII(terpy) p M]·2+ and [CoIII(salen) p M]·+ [ p M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N, N '-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ( p M·+) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M - H3PO4]·+ species through phosphate ester bond cleavage. The CID spectra of the p M·+ species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H3PO4 loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H3PO4 from a prototypical model— N-acetylphosphorylserine methylamide—revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms.

  8. Dissociative amnesia.

    PubMed

    Staniloiu, Angelica; Markowitsch, Hans J

    2014-08-01

    Dissociative amnesia is one of the most enigmatic and controversial psychiatric disorders. In the past two decades, interest in the understanding of its pathophysiology has surged. In this report, we review new data about the epidemiology, neurobiology, and neuroimaging of dissociative amnesia and show how advances in memory research and neurobiology of dissociation inform proposed pathogenetic models of the disorder. Dissociative amnesia is characterised by functional impairment. Additionally, preliminary data suggest that affected people have an increased and possibly underestimated suicide risk. The prevalence of dissociative amnesia differs substantially across countries and populations. Symptoms and disease course also vary, indicating a possibly heterogeneous disorder. The accompanying clinical features differ across cultural groups. Most dissociative amnesias are retrograde, with memory impairments mainly involving the episodic-autobiographical memory domain. Anterograde dissociative amnesia occurring without significant retrograde memory impairments is rare. Functional neuroimaging studies of dissociative amnesia with prevailing retrograde memory impairments show changes in the network that subserves autobiographical memory. At present, no evidence-based treatments are available for dissociative amnesia and no broad framework exists for its rehabilitation. Further research is needed into its neurobiology, course, treatment options, and strategies to improve differential diagnoses.

  9. Efficient structural characterization of poly(methacrylic acid) by activated-electron photodetachment dissociation.

    PubMed

    Girod, Marion; Brunet, Claire; Antoine, Rodolphe; Lemoine, Jérôme; Dugourd, Philippe; Charles, Laurence

    2012-01-01

    Characterization of end-groups in poly(methacrylic acid) (PMAA) was achieved using tandem mass spectrometry after activated-electron photodetachment dissociation (activated-EPD). In this technique, multiply deprotonated PMAA oligomers produced in the negative-ion mode of electrospray ionization were oxidized into radical anions upon electron photodetachment using a 220 nm laser wavelength, and further activated by collision. In contrast to conventional collision induced dissociation of negatively charged PMAA, which mainly consists of multiple dehydration steps, fragmentation of odd-electron species is shown to proceed via a radical-induced decarboxylation, followed by reactions involving backbone bond cleavages, giving rise to product ions containing one or the other oligomer termination. A single radical-induced mechanism accounts for the four main fragment series observed in MS/MS. The relative position of the radical and of the anionic center in distonic precursor ions determines the nature of the reaction products. Experiments performed using PMAA sodium salts allowed us to account for relative abundances of product ions in series obtained from PMAA, revealing that ion stability is ensured by hydrogen bonds within pairs of MAA units.

  10. Strong-field control over the product branching ratios in molecular dissociation

    NASA Astrophysics Data System (ADS)

    Rigsbee, Brandon; Zohrabi, Mohammad; Ablikim, Utuq; Guevara, Nicolais; Carnes, Kevin; Ben-Itzhak, Itzik; Esry, Brett

    2012-06-01

    We present a theoretical and experimental study of strong-field control over the fragmentation channel in molecular dissociation by intense, single-color laser fields with emphasis on the effect of chirped pulses. In particular, the branching ratio between H+D^+ and H^++D from an HD^+ target is examined as a function of kinetic energy release for 790 nm pulses with intensities on the order of 10^14 W/cm^2 and pulse lengths ranging from 25 to 65 fs. Theoretical calculations based on numerical solutions of the time-dependent Schr"odinger equation in the Born-Oppenheimer approximation are compared to measurements using a coincidence 3-D momentum imaging technique. Both demonstrate that control is indeed possible and depends, as expected, on details of the laser pulse such as its chirp.

  11. Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides.

    PubMed

    Cook, Shannon L; Zimmermann, Carolyn M; Singer, David; Fedorova, Maria; Hoffmann, Ralf; Jackson, Glen P

    2012-06-01

    The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.

  12. Collision-induced desorption in 193-nm photoinduced reactions in (O{sub 2}+CO) adlayers on Pt(112)

    SciTech Connect

    Han Song; Ma Yunsheng; Matsushima, Tatsuo

    2005-09-01

    The spatial distribution of desorbing O{sub 2} and CO{sub 2} was examined in 193-nm photoinduced reactions in O{sub 2}+CO adlayers on stepped Pt (112)=[(s)3(111)x(001)]. The O{sub 2} desorption collimated in inclined ways in the plane along the surface trough, confirming the hot-atom collision mechanism. In the presence of CO(a), the product CO{sub 2} desorption also collimated in an inclined way, whereas the inclined O{sub 2} desorption was suppressed. The inclined O{sub 2} and CO{sub 2} desorption is explained by a common collision-induced desorption model. At high O{sub 2} coverage, the CO{sub 2} desorption collimated closely along the (111) terrace normal.

  13. Dissociative recombination in aeronomy

    NASA Technical Reports Server (NTRS)

    Fox, J. L.

    1989-01-01

    The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

  14. Three products are better than two: entropic advantages in the competing dissociation reactions of ionized azo-t-butane.

    PubMed

    Rabaev, Madlena; Boulanger, Anne-Marie; Holland, David M P; Shaw, David A; Mayer, Paul M

    2009-02-26

    Ionized azo-t-butane (m/z 142) undergoes three dissociation reactions: competitive cleavage of the N-C bond to form (1) the t-butyl cation ((CH(3))(3)C(+), m/z 57) plus a neutral that is nominally (CH(3))(3)CN(2)(*) (85 Da); (2) m/z 85 cation, (CH(3))(3)CN(2)(+), plus the neutral t-butyl radical; and (3) a minor rearrangement reaction leading to ionized butene. The competition between channels (1) and (2) is governed by both energetic and entropic considerations as the 85 Da neutral lies in a 1 kJ mol(-1) potential energy well and when formed dissociates into the t-butyl radical and N(2). This gives channel 1 an entropic advantage over channel 2, as long as the transition states for these processes reside close to products, a conclusion supported by threshold photoelectron photoion coincidence spectroscopy, tandem mass spectrometry, and ab initio calculations.

  15. Anisotropic collision-induced Raman scattering by the Kr:Xe gas mixture.

    PubMed

    Dixneuf, S; Chrysos, M; Rachet, F

    2009-08-21

    We report anisotropic collision-induced Raman scattering intensities by the Kr-Xe atomic pair recorded in a gas mixture of Kr and Xe at room temperature. We compare them to quantum-mechanical calculations on the basis of modern incremental polarizability models of either ab initio post-Hartree-Fock or density functional theory methods.

  16. Electron-induced dissociation of singly charged organic cations as a tool for structural characterization of pharmaceutical type molecules.

    PubMed

    Mosely, Jackie A; Smith, Michael J P; Prakash, Aruna S; Sims, Martin; Bristow, Anthony W T

    2011-06-01

    Collision-induced dissociation (CID) and electron-induced dissociation (EID) have been investigated for a selection of small, singly charged organic molecules of pharmaceutical interest. Comparison of these techniques has shown that EID carried out on an FTICR MS and CID performed on a linear ion trap MS produce complementary data. In a study of 33 molecule-cations, EID generated over 300 product ions compared to 190 product ions by CID with an average of only 3 product ions per precursor ion common to both tandem MS techniques. Even multiple stages of CID failed to generate many of the product ions observed following EID. The charge carrying species is also shown to have a very significant effect on the degree of fragmentation and types of product ion resulting from EID. Protonated species behave much like the ammonium adduct with suggestion of a hydrogen atom from the charge carrying species strongly affecting the fragmentation mechanism. Sodium and potassium are retained by nearly every product ion formed from [M + Na](+) or [M + K](+) and provide information to complement the EID of [M + H](+) or [M + NH(4)](+). In summary, EID is proven to be a fitting partner to CID in the structural elucidation of small singly charged ions and by studying EID of a molecule-ion holding different charge carrying species, an even greater depth of detail can be obtained for functional groups commonly used in synthetic chemistry.

  17. Using Electron Induced Dissociation (EID) on an LC Time-Scale to Characterize a Mixture of Analogous Small Organic Molecules

    NASA Astrophysics Data System (ADS)

    Prakash, Aruna S.; Smith, Michael J. P.; Kaabia, Zied; Hurst, Glenn; Yan, Ci; Sims, Martin; Bristow, Anthony W. T.; Stokes, Peter; Parker, David; Mosely, Jackie A.

    2012-05-01

    LC ESI FTICR MS of a sample of cediranib identified this pharmaceutical target molecule plus an additional 10 compounds of interest, all of which were less than 10% total ion current (TIC) peak intensity relative to cediranib. LC FTICR tandem mass spectrometry using electron induced dissociation (EID) has been achieved and has proven to be the best way to generate useful product ion information for all of these singly protonated molecules. Cediranib [M + H]+ fragmented by EID to give 29 product ions whereas QTOF-CID generated only one very intense product ion, and linear ion trap-CID, which generated 10 product ions, but all with poor S/N. Twenty-six of the EID product ions were unique to this fragmentation technique alone. By considering the complementary LC-EID and LC-CID data together, all 10 unknown compounds were structurally characterized and proven to be analogous to cediranib. Of particular importance, EID produced unique product ion information for one of the low level cediranib analogues that enabled full characterization of the molecule such that the presence of an extra propylpyrrolidine group was discovered and proven to be located on the pyrrolidine ring of cediranib, solving an analytical problem that could not be solved by collision induced dissociation (CID). Thus, it has been demonstrated that EID is in harmony with the chromatography duty-cycle and the dynamic concentration range of synthetic compounds containing trace impurities, providing crucial analytical information that cannot be obtained by more traditional methodologies.

  18. Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Frolov, Andrej; Tang, Ning; Hoffman, Ralf; van der Goor, Tom; Metz, Thomas O.; Smith, Richard D.

    2007-03-15

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in diabetes mellitus research, particularly in the context of development of diabetic complications. The fragmentation behavior of glycated peptides produced from reaction of D-glucose with lysine residues was investigated by electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was found that high abundance ions corresponding to various degrees of neutral water losses, as well as furylium ion production, dominate the CID spectra, and that the sequence informative b and y ions were rarely observed when Amadori-modified peptides were fragmented. Contrary to what was observed under CID conditions, ions corresponding to neutral losses of water or furylium ion production were not observed in the ETD spectra. Instead, abundant and almost complete series of c and z type ions were observed regardless of whether the modification site was located in the middle of the sequence or close to the N-terminus, greatly facilitating the peptide sequencing. This study strongly suggests that ETD is a better technique for proteomics studies of non-enzymatically glycated peptides and proteins.

  19. Dynamics of production of iodine atoms by dissociation of iodides in a pulsed self-sustained discharge

    SciTech Connect

    Vagin, Nikolai P; Kochetov, Igor' V; Napartovich, A P; Yuryshev, Nikolai N

    2013-07-31

    Absorption at the laser transition has been used for the first time to assess the evolution of concentration of iodine atoms in a pulsed self-sustained discharge in mixtures of iodides with a buffer gas such as molecular nitrogen and helium. Dynamics of the iodine atom production is studied by the method of absorption spectroscopy. The dissociation of C{sub n}F{sub 2n+1}I and CnH{sub 2n+1}I (n = 1, 2) iodides is investigated. The energy required to produce atomic iodine is evaluated. The experimental data obtained for CF{sub 3}I are compared with the results of numerical simulations, their reasonable agreement being demonstrated. (active media)

  20. The Harvard Beat Assessment Test (H-BAT): a battery for assessing beat perception and production and their dissociation.

    PubMed

    Fujii, Shinya; Schlaug, Gottfried

    2013-01-01

    Humans have the abilities to perceive, produce, and synchronize with a musical beat, yet there are widespread individual differences. To investigate these abilities and to determine if a dissociation between beat perception and production exists, we developed the Harvard Beat Assessment Test (H-BAT), a new battery that assesses beat perception and production abilities. H-BAT consists of four subtests: (1) music tapping test (MTT), (2) beat saliency test (BST), (3) beat interval test (BIT), and (4) beat finding and interval test (BFIT). MTT measures the degree of tapping synchronization with the beat of music, whereas BST, BIT, and BFIT measure perception and production thresholds via psychophysical adaptive stair-case methods. We administered the H-BAT on thirty individuals and investigated the performance distribution across these individuals in each subtest. There was a wide distribution in individual abilities to tap in synchrony with the beat of music during the MTT. The degree of synchronization consistency was negatively correlated with thresholds in the BST, BIT, and BFIT: a lower degree of synchronization was associated with higher perception and production thresholds. H-BAT can be a useful tool in determining an individual's ability to perceive and produce a beat within a single session.

  1. Effects of Carbonyl Bond and Metal Cluster Dissociation and Evaporation Rates on Predictions of Nanotube Production in HiPco

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2002-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNT) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the co-formation of CO2. It is shown that the production of CO2 is significantly greater for FeCO due to its lower bond energy as compared with that ofNiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  2. The Harvard Beat Assessment Test (H-BAT): a battery for assessing beat perception and production and their dissociation

    PubMed Central

    Fujii, Shinya; Schlaug, Gottfried

    2013-01-01

    Humans have the abilities to perceive, produce, and synchronize with a musical beat, yet there are widespread individual differences. To investigate these abilities and to determine if a dissociation between beat perception and production exists, we developed the Harvard Beat Assessment Test (H-BAT), a new battery that assesses beat perception and production abilities. H-BAT consists of four subtests: (1) music tapping test (MTT), (2) beat saliency test (BST), (3) beat interval test (BIT), and (4) beat finding and interval test (BFIT). MTT measures the degree of tapping synchronization with the beat of music, whereas BST, BIT, and BFIT measure perception and production thresholds via psychophysical adaptive stair-case methods. We administered the H-BAT on thirty individuals and investigated the performance distribution across these individuals in each subtest. There was a wide distribution in individual abilities to tap in synchrony with the beat of music during the MTT. The degree of synchronization consistency was negatively correlated with thresholds in the BST, BIT, and BFIT: a lower degree of synchronization was associated with higher perception and production thresholds. H-BAT can be a useful tool in determining an individual's ability to perceive and produce a beat within a single session. PMID:24324421

  3. Dissociation energy for O2 release from gas-phase iron oxide clusters measured by temperature-programmed desorption experiments

    NASA Astrophysics Data System (ADS)

    Koyama, Kohei; Kudoh, Satoshi; Miyajima, Ken; Mafuné, Fumitaka

    2015-04-01

    Thermal dissociation of gas phase iron oxide cluster ions, FenOm+ (n = 2-6), was observed by mass spectrometry. The dissociation processes were investigated by temperature-programmed desorption (TPD) measurements for different sized clusters. Oxygen molecules were found to be released from the cluster ions. The threshold energy required for dissociation, determined by analyzing TPD, was compared with the energies obtained by experiments of collision-induced dissociation and by calculations of density functional theory. The agreement of the energies indicates that the oxygen atoms bonded to the terminal site of clusters are more readily released into the gas phase than those in the bridge site.

  4. Comparative study of the dissociation energies of Ni2 and Ni2(+)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

    1992-01-01

    Computations at the internally contracted averaged coupled-pair-functional level of theory yield a dissociation energy (Do) for Ni2(+) that is 0.17 eV larger than that of Ni2. This finding is consistent with the collision-induced dissociation experiments of Lian, Su, and Armentrout, but rules out the results from the resonant two-photon dissociation experiments of Lessen and Brucat, which predict that the Do value of Ni2(+) is about 1 eV larger than that of Ni2.

  5. Dissociation of dicarboxylate and disulfonate dianions.

    PubMed

    Ard, Shaun; Mirsaleh-Kohan, Nasrin; Steill, Jeffrey D; Oomens, Jos; Nielsen, Steen Brøndsted; Compton, R N

    2010-03-07

    Collision-induced dissociation (CID), along with infrared multiple photon dissociation/detachment (IRMPD) techniques, is utilized to study a series of doubly substituted aromatic dianions containing sulfonate and carboxylate functionalities (1,2- and 1,3-benzenedisulfonate, 1,5-naphthalenedisulfonate, 2,6-naphthalenedisulfonate, 4-sulfobenzoate, 2,6-naphthalenedicarboxylate, and terephthalate dianions). The molecules were chosen because of the electronegativity of the CO(2) and SO(3) moieties along with their varied spatial separation in order to investigate the effect of the repulsive Coulomb barrier (RCB) on the dianions' respective dissociation pathways. Density functional theory calculations of the structures, electron detachment and dissociation energies, as well as vibrational frequencies are performed. Calculated infrared active vibrational frequencies are largely in agreement with the IRMPD spectra which provide support for interpretations based upon computed energies. Calculated and experimental results show that fragmentation dominates over electron detachment as the lowest energy dissociation pathway for these systems and the nature of this dissociation is dictated by properties of the substituent group. CID and IRMPD of dianions with two sulfonate groups (SO(3)(-)) resulted in a single dissociation channel leading to observation of SO(3)(-) and its anion conjugate pair, whereas the carboxylate (CO(2)(-)) containing dianions dissociated via loss of one or both CO(2) molecules and an electron. The SO(3)(-) collisional dissociation exhibited a clear energetic threshold toward ionic fragmentation with an isomeric dependence that is in reasonable agreement with a simple electrostatic model of the RCB, as well as with published reports on electron photodetachment. The loss of one or both CO(2) units and an electron from CID of the carboxylate dianions appeared with no threshold (dissociation occurs with no collision gas), implying these dianions to be

  6. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer.

    PubMed

    Voinov, Valery G; Hoffman, Peter D; Bennett, Samuel E; Beckman, Joseph S; Barofsky, Douglas F

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer. Graphical Abstract ᅟ.

  7. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Voinov, Valery G.; Hoffman, Peter D.; Bennett, Samuel E.; Beckman, Joseph S.; Barofsky, Douglas F.

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer.

  8. Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides.

    PubMed

    Kowalewska, Karolina; Stefanowicz, Piotr; Ruman, Tomasz; Fraczyk, Tomasz; Rode, Wojciech; Szewczuk, Zbigniew

    2010-12-01

    Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by 1H NMR and 31P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD-MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested.

  9. Collision-induced hyper-Rayleigh spectrum of H(2)-Ar gas mixture.

    PubMed

    Bancewicz, Tadeusz; Głaz, Waldemar; Godet, Jean-Luc; Maroulis, George

    2008-09-28

    The collision-induced hyper-Rayleigh (CIHR) spectra of the gaseous H(2)-Ar mixture are discussed in the binary regime on the basis of our ab initio computed H(2)-Ar collision-induced (CI) first dipole hyperpolarizability tensor Deltabeta(R). A method for the computation of the spherical, rotationally adapted components Deltabeta(lambdaL) ((s,K))(R) of Deltabeta(R) needed for spectroscopic line shape analysis is proposed. Both the vector and the septor parts of the H(2)-Ar CIHR spectrum are evaluated at room (T=295 K) temperature. The spectra are calculated assuming the full quantum computations based on the Schrodinger equation of the relative translational motion of H(2)-Ar as well as semiclassical methods (classical trajectory approach and Birnbaum-Cohen model translational profiles). The H(2)-Ar pair CIHR septor spectrum has been found stronger than the vector one.

  10. Theory of collision-induced translation-rotation spectra: H2-He

    NASA Technical Reports Server (NTRS)

    Birnbaum, G.; Chu, S.-I.; Dalgarno, A.; Frommhold, L.; Wright, E. L.

    1984-01-01

    An adiabatic quantal theory of spectral line shapes in collision-induced absorption and emission is presented which incorporates the induced translation-rotation and translation-vibration spectra. The generalization to account for the anisotropy of the scattering potential is given. Calculations are carried out of the collision-induced absorption spectra of He in collisions with H2 with ab initio electric dipole functions and realistic potentials. The anisotropy of the interaction potential is small and is not included in the calculations. The predicted spectra are in satisfactory agreement with experimental data though some deviations occur which may be significant. The rotational line shapes have exponential wings and are not Lorentzian. The connection between the quantal and classical theories is written out explicitly for the isotropic overlap induction.

  11. Renormalization screening and collision-induced quantum interference in dense plasmas

    SciTech Connect

    Jung, Young-Dae; Rasheed, A.; Jamil, M.

    2014-07-15

    The influence of renormalization screening and collision-induced quantum interference in electron-electron collisions is investigated in partially ionized dense hydrogen plasmas. The effective interaction potential with the total spin-states of the collision system is considered to obtain the differential electron-electron scattering cross section. The results show that the renormalization plasma screening effect suppresses the electron-electron scattering cross section, including the quantum interference effect, especially, except for the forward and backward scattering directions. It is also shown that the renormalization plasma screening effect on the scattering cross section decreases with increasing collision energy. However, the renormalization screening effect is found to be important for the forward directions in the scattering cross section neglecting the quantum interference effect. The variations of the renormalization screening and collision-induced quantum interference effects are also discussed.

  12. Infrared Ion Spectroscopy at Felix: Applications in Peptide Dissociation and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Oomens, Jos

    2016-06-01

    Infrared free electron lasers such as those in Paris, Berlin and Nijmegen have been at the forefront of the development of infrared ion spectroscopy. In this contribution, I will give an overview of new developments in IR spectroscopy of stored ions at the FELIX Laboratory. In particular, I will focus on recent developments made possible by the coupling of a new commercial ion trap mass spectrometer to the FELIX beamline. The possibility to record IR spectra of mass-selected molecular ions and their reaction products has in recent years shed new light on our understanding of collision induced dissociation (CID) reactions of protonated peptides in mass spectrometry (MS). We now show that it is possible to record IR spectra for the products of electron transfer dissociation (ETD) reactions [M + nH]n+ + A- → [M + nH](n-1)+ + A → {dissociation of analyte} These reactions are now widely used in novel MS-based protein sequencing strategies, but involve complex radical chemistry. The spectroscopic results allow stringent verification of computationally predicted product structures and hence reaction mechanisms and H-atom migration. The sensitivity and high dynamic range of a commercial mass spectrometer also allows us to apply infrared ion spectroscopy to analytes in complex "real-life" mixtures. The ability to record IR spectra with the sensitivity of mass-spectrometric detection is unrivalled in analytical sciences and is particularly useful in the identification of small (biological) molecules, such as in metabolomics. We report preliminary results of a pilot study on the spectroscopic identification of small metabolites in urine and plasma samples.

  13. Collision-induced stimulated photon echo on the broad spectral line

    NASA Astrophysics Data System (ADS)

    Reshetov, V. A.

    2017-01-01

    The collision-induced stimulated photon echo formed on the broad spectral line on the transition with the angular momentum change {{J}a}=0\\to {{J}b}=1 is studied theoretically. The dependencies of the echo intensity on the areas of exciting pulses and on the strength of the external magnetic field under the conditions of experiments in ytterbium (174Yb) vapor are obtained. The ways to measure orientation and alignment relaxation rates of the excited atomic level are discussed.

  14. Dissociation and Re-Aggregation of Multicell-Ensheathed Fragments Responsible for Rapid Production of Massive Clumps of Leptothrix Sheaths.

    PubMed

    Kunoh, Tatsuki; Nagaoka, Noriyuki; McFarlane, Ian R; Tamura, Katsunori; El-Naggar, Mohamed Y; Kunoh, Hitoshi; Takada, Jun

    2016-08-01

    Species of the Fe/Mn-oxidizing bacteria Leptothrix produce tremendous amounts of microtubular, Fe/Mn-encrusted sheaths within a few days in outwells of groundwater that can rapidly clog water systems. To understand this mode of rapid sheath production and define the timescales involved, behaviors of sheath-forming Leptothrix sp. strain OUMS1 were examined using time-lapse video at the initial stage of sheath formation. OUMS1 formed clumps of tangled sheaths. Electron microscopy confirmed the presence of a thin layer of bacterial exopolymer fibrils around catenulate cells (corresponding to the immature sheath). In time-lapse videos, numerous sheath filaments that extended from the periphery of sheath clumps repeatedly fragmented at the apex of the same fragment, the fragments then aggregated and again elongated, eventually forming a large sheath clump comprising tangled sheaths within two days. In this study, we found that fast microscopic fragmentation, dissociation, re-aggregation and re-elongation events are the basis of the rapid, massive production of Leptothrix sheaths typically observed at macroscopic scales.

  15. Dissociation and Re-Aggregation of Multicell-Ensheathed Fragments Responsible for Rapid Production of Massive Clumps of Leptothrix Sheaths

    PubMed Central

    Kunoh, Tatsuki; Nagaoka, Noriyuki; McFarlane, Ian R.; Tamura, Katsunori; El-Naggar, Mohamed Y.; Kunoh, Hitoshi; Takada, Jun

    2016-01-01

    Species of the Fe/Mn-oxidizing bacteria Leptothrix produce tremendous amounts of microtubular, Fe/Mn-encrusted sheaths within a few days in outwells of groundwater that can rapidly clog water systems. To understand this mode of rapid sheath production and define the timescales involved, behaviors of sheath-forming Leptothrix sp. strain OUMS1 were examined using time-lapse video at the initial stage of sheath formation. OUMS1 formed clumps of tangled sheaths. Electron microscopy confirmed the presence of a thin layer of bacterial exopolymer fibrils around catenulate cells (corresponding to the immature sheath). In time-lapse videos, numerous sheath filaments that extended from the periphery of sheath clumps repeatedly fragmented at the apex of the same fragment, the fragments then aggregated and again elongated, eventually forming a large sheath clump comprising tangled sheaths within two days. In this study, we found that fast microscopic fragmentation, dissociation, re-aggregation and re-elongation events are the basis of the rapid, massive production of Leptothrix sheaths typically observed at macroscopic scales. PMID:27490579

  16. COLLISION-INDUCED MAGNETIC RECONNECTION AND A UNIFIED INTERPRETATION OF POLARIZATION PROPERTIES OF GRBs AND BLAZARS

    DOE PAGES

    Deng; Zhang; Zhang; ...

    2016-04-11

    The jet composition and energy dissipation mechanism of gamma-ray bursts (GRBs) and blazars are fundamental questions that remain not fully understood. One plausible model is to interpret the γ-ray emission of GRBs and optical emission of blazars as synchrotron radiation of electrons accelerated from the collision-induced magnetic dissipation regions in Poynting-flux-dominated jets. The polarization observation is an important and independent information to test this model. Based on our recent 3D relativistic MHD simulations of collision-induced magnetic dissipation of magnetically dominated blobs, here we perform calculations of the polarization properties of the emission in the dissipation region and apply the resultsmore » to model the polarization observational data of GRB prompt emission and blazar optical emission. In this article, we show that the same numerical model with different input parameters can reproduce well the observational data of both GRBs and blazars, especially the 90° polarization angle (PA) change in GRB 100826A and the 180° PA swing in blazar 3C279. This supports a unified model for GRB and blazar jets, suggesting that collision-induced magnetic reconnection is a common physical mechanism to power the relativistic jet emission from events with very different black hole masses.« less

  17. COLLISION-INDUCED MAGNETIC RECONNECTION AND A UNIFIED INTERPRETATION OF POLARIZATION PROPERTIES OF GRBs AND BLAZARS

    SciTech Connect

    Deng, Wei; Zhang, Bing; Zhang, Haocheng; Li, Hui E-mail: zhang@physics.unlv.edu E-mail: hz193909@ohio.edu

    2016-04-10

    The jet composition and energy dissipation mechanism of gamma-ray bursts (GRBs) and blazars are fundamental questions that remain not fully understood. One plausible model is to interpret the γ-ray emission of GRBs and optical emission of blazars as synchrotron radiation of electrons accelerated from the collision-induced magnetic dissipation regions in Poynting-flux-dominated jets. The polarization observation is an important and independent information to test this model. Based on our recent 3D relativistic MHD simulations of collision-induced magnetic dissipation of magnetically dominated blobs, here we perform calculations of the polarization properties of the emission in the dissipation region and apply the results to model the polarization observational data of GRB prompt emission and blazar optical emission. We show that the same numerical model with different input parameters can reproduce well the observational data of both GRBs and blazars, especially the 90° polarization angle (PA) change in GRB 100826A and the 180° PA swing in blazar 3C279. This supports a unified model for GRB and blazar jets, suggesting that collision-induced magnetic reconnection is a common physical mechanism to power the relativistic jet emission from events with very different black hole masses.

  18. COLLISION-INDUCED MAGNETIC RECONNECTION AND A UNIFIED INTERPRETATION OF POLARIZATION PROPERTIES OF GRBs AND BLAZARS

    SciTech Connect

    Deng , Wei; Zhang , Haocheng; Zhang , Bing; Li , Hui

    2016-04-11

    The jet composition and energy dissipation mechanism of gamma-ray bursts (GRBs) and blazars are fundamental questions that remain not fully understood. One plausible model is to interpret the γ-ray emission of GRBs and optical emission of blazars as synchrotron radiation of electrons accelerated from the collision-induced magnetic dissipation regions in Poynting-flux-dominated jets. The polarization observation is an important and independent information to test this model. Based on our recent 3D relativistic MHD simulations of collision-induced magnetic dissipation of magnetically dominated blobs, here we perform calculations of the polarization properties of the emission in the dissipation region and apply the results to model the polarization observational data of GRB prompt emission and blazar optical emission. In this article, we show that the same numerical model with different input parameters can reproduce well the observational data of both GRBs and blazars, especially the 90° polarization angle (PA) change in GRB 100826A and the 180° PA swing in blazar 3C279. This supports a unified model for GRB and blazar jets, suggesting that collision-induced magnetic reconnection is a common physical mechanism to power the relativistic jet emission from events with very different black hole masses.

  19. Collision-induced light scattering spectra of krypton layer confined between graphite slabs - MD simulation

    NASA Astrophysics Data System (ADS)

    Dawid, A.; Wojcieszyk, D.; Gburski, Z.

    2016-12-01

    We have used the molecular dynamics (MD) simulation method to obtain the collision-induced light scattering spectra of the thin krypton layer confined between two parallel graphite slabs. The simulations have been made under constant density, pressure and temperature condition. We have investigated four thin krypton layers of the thickness ranging from 13 to 24 Å. The 2-, 3- and 4-body correlation functions of collision-induced polarizability anisotropy were calculated. The spectra of colliding krypton atoms were simulated as cosine Fourier transform of the total polarizability anisotropy correlation function. The calculated correlation functions and their spectra show substantial dependence on the distance between graphite slabs. The collision-induced light scattering spectrum of krypton bulk sample was also simulated and compared with the krypton layer between graphite walls. The striking differences between these two systems are observed. We have further extended our analysis of krypton movement between graphite slabs by calculating the mean square displacement functions and diffusion coefficients. The decrease of the diffusion of krypton atoms with the increasing distance between graphite walls has been found. The structure of krypton layer has been also investigated by calculating the density profile and pressure tension across the rift. The distance between graphite slabs, for which the highest mobility of krypton's atoms occurred, has been found.

  20. Collision-induced stimulated photon echo at the transition 0-1 in ytterbium: application to depolarizing collisions

    NASA Astrophysics Data System (ADS)

    Rubtsova, N. N.; Gol'dort, V. G.; Khvorostov, E. B.; Kochubei, S. A.; Reshetov, V. A.

    2017-02-01

    A new idea based on the collision-induced stimulated photon echo in the presence of weak longitudinal magnetic field is applied to the depolarizing collisions research in a gaseous mixture of ytterbium vapour with xenon. Comparison of experimental data with theoretical prediction for the collision-induced stimulated photon echo in the weak magnetic field shows that the alignment decay rate of state 3P1 in 174Yb is higher than the orientation decay rate.

  1. Dissociation of CH4 by electron impact: Production of metastable hydrogen and carbon fragments

    NASA Technical Reports Server (NTRS)

    Finn, T. G.; Carnahan, B. L.; Zipf, E. C.

    1974-01-01

    Metastable fragments produced by electron impact excitation of CH4 have been investigated for incident electron energies from threshold to 300 eV. Only metastable hydrogen and carbon atoms were observed. Onset energies for the production of metastable hydrogen atoms were observed at electron impact energies of 22.0 + or - .5 eV, 25.5 + or - .6 eV, 36.7 + or - .6 eV and 66 + or - 3 eV, and at 26.6 + or - .6 eV for the production of metastable carbon atoms. Most of the fragments appear to have been formed in high-lying Rydberg states. The total metastable hydrogen cross section reaches a maximum value of approximately 1 X 10 to the minus 18th power sq cm at 100 eV. At the same energy, the metastable carbon cross section is 2 x 10 to the minus 19th power sq cm.

  2. Super-dissociative recombination of H2+?

    NASA Astrophysics Data System (ADS)

    Mitchell, J. B. A.; Yousif, F. B.; van der Donk, P. J. T.; Morgan, T. J.; Chibisov, M. I.

    1995-11-01

    The dissociative recombination of vibrationally excited H2+ ions to form products in high Rydberg states has been measured. Surprisingly large cross-sections are found for this channel. This seems to be an example of super-dissociative recombination.

  3. First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

    NASA Astrophysics Data System (ADS)

    Varghese, Jithin J.; Mushrif, Samir H.

    2015-05-01

    Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cun where n = 2-12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C-H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH3 and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CHx (x = 1-3) species and recombination of H with CHx have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.

  4. Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases.

    PubMed

    Zhang, Zhongqi; Bordas-Nagy, Joseph

    2006-06-01

    A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive alpha-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases.

  5. Calcium and melatonin production in dissociated trout pineal photoreceptor cells in culture.

    PubMed

    Bégay, V; Bois, P; Collin, J P; Lenfant, J; Falcón, J

    1994-07-01

    Trout pineal cells maintained in primary culture produce melatonin in high amounts during night time and low amounts during daytime. The dark-induced increase in melatonin production was enhanced, in a dose-dependent manner, by elevating extracellular calcium concentration. Low external calcium concentration reduced nocturnal and diurnal melatonin production. Bay K 8644 increased, in a dose-dependent manner, the dark-induced rise in melatonin output, and this effect was antagonized by nifedipine and verapamil. This suggests a role for the dihydropyridine calcium channels in the regulation of the melatonin output. To confirm this, patch-clamp recordings (whole-cell perforated) were run in a 20 mmol/l barium medium at different holding potentials from -80 mV. A voltage-dependent inward current was activated from -30 mV to +40 mV with a maximal amplitude being observed at 0 mV. This current was drastically increased in the presence of Bay K 8644. Nifedipine inhibited the current both in the absence or in the presence of Bay K 8644. Our results are consistent with the idea that extracellular calcium participates in the control of melatonin secretion by photoreceptor cells. It is suggested that activation of the voltage-dependent L-type channel may modulate this secretion.

  6. Dissociation of doubly charged clusters of lithium acetate: Asymmetric fission and breakdown of the liquid drop model: Dissociation of doubly charged clusters of lithium acetate

    SciTech Connect

    Shukla, Anil

    2016-06-08

    Unimolecular and collision-induced dissociation of doubly charged lithium acetate clusters, (CH3COOLi)nLi22+, demonstrated that Coulomb fission via charge separation is the dominant dissociation process with no contribution from the neutral evaporation processes for all such ions from the critical limit to larger cluster ions, although latter process have normally been observed in all earlier studies. These results are clearly in disagreement with the Rayleigh’s liquid drop model that has been used successfully to predict the critical size and explain the fragmentation behavior of multiply charged clusters.

  7. Introduction to dissociative recombination

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.; Mitchell, J. Brian A.

    1989-01-01

    Dissociative recombination (DR) of molecular ions with electrons has important consequences in many areas of physical science. Ab-initio calculations coupled with resonant scattering theory and multichannel quantum defect studies have produced detailed results illuminating the role of ion vibrational excitation, the quantum yields of the DR products, and the role of Rydberg states. The theoretical and experimental results are discussed.

  8. Dissociation of CH4 and CD4 by electron impact - Production of metastable and high-Rydberg hydrogen and carbon fragments

    NASA Technical Reports Server (NTRS)

    Finn, T. G.; Carnahan, B. L.; Wells, W. C.; Zipf, E. C.

    1975-01-01

    Production of hydrogen and carbon atoms in metastable and high-lying Rydberg states by electron-impact dissociation of methane and deuterated methane is investigated for incident electron energies ranging from threshold values to 300 eV. Threshold energies for five different processes resulting in metastable hydrogen and carbon atoms are determined in the energy range from 20 to 70 eV, and it is shown that metastable hydrogen atoms are produced in four of these collisional processes while metastable carbon atoms are produced in the other. The nature of each collisional process is described, differential cross sections are derived for the dissociative excitation of both types of atoms to metastable and high-Rydberg states at 100 eV, and the onset energy for UV photon production is measured. Much of the data is interpreted in terms of the ion core model suggested by Kupriyanov (1968) and developed by Freund (1971).

  9. Sequential bond energies and barrier heights for the water loss and charge separation dissociation pathways of Cd2+(H2O)n, n = 3-11

    NASA Astrophysics Data System (ADS)

    Cooper, Theresa E.; Armentrout, P. B.

    2011-03-01

    The bond dissociation energies for losing one water from Cd2+(H2O)n complexes, n = 3-11, are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer coupled with a thermal electrospray ionization source. Kinetic energy dependent cross sections are obtained for n = 4-11 complexes and analyzed to yield 0 K threshold measurements for loss of one, two, and three water ligands after accounting for multiple collisions, kinetic shifts, and energy distributions. The threshold measurements are converted from 0 to 298 K values to give the hydration enthalpies and free energies for sequentially losing one water from each complex. Theoretical geometry optimizations and single point energy calculations are performed on reactant and product complexes using several levels of theory and basis sets to obtain thermochemistry for comparison to experiment. The charge separation process, Cd2+(H2O)n → CdOH+(H2O)m + H+(H2O)n-m-1, is also observed for n = 4 and 5 and the competition between this process and water loss is analyzed. Rate-limiting transition states for the charge separation process at n = 3-6 are calculated and compared to experimental threshold measurements resulting in the conclusion that the critical size for this dissociation pathway of hydrated cadmium is ncrit = 4.

  10. Collision-induced release, ion mobility separation, and amino acid sequence analysis of subunits from mass-selected noncovalent protein complexes.

    PubMed

    Rathore, Deepali; Dodds, Eric D

    2014-09-01

    In recent years, mass spectrometry has become a valuable tool for detecting and characterizing protein-protein interactions and for measuring the masses and subunit stoichiometries of noncovalent protein complexes. The gas-phase dissociation of noncovalent protein assemblies via tandem mass spectrometry can be useful in confirming subunit masses and stoichiometries; however, dissociation experiments that are able to yield subunit sequence information must usually be conducted separately. Here, we furnish proof of concept for a method that allows subunit sequence information to be directly obtained from a protein aggregate in a single gas-phase analysis. The experiments were carried out using a quadrupole time-of-flight mass spectrometer equipped with a traveling-wave ion mobility separator. This instrument configuration allows for a noncovalent protein assembly to be quadrupole selected, then subjected to two successive rounds of collision-induced dissociation with an intervening stage of ion mobility separation. This approach was applied to four model proteins as their corresponding homodimers: glucagon, ubiquitin, cytochrome c, and β-lactoglobulin. In each case, b- and y-type fragment ions were obtained upon further collisional activation of the collisionally-released subunits, resulting in up to 50% sequence coverage. Owing to the incorporation of an ion mobility separation, these results also suggest the intriguing possibility of measuring complex mass, complex collisional cross section, subunit masses, subunit collisional cross sections, and sequence information for the subunits in a single gas-phase experiment. Overall, these findings represent a significant contribution towards the realization of protein interactomic analyses, which begin with native complexes and directly yield subunit identities.

  11. Collision-Induced Release, Ion Mobility Separation, and Amino Acid Sequence Analysis of Subunits from Mass-Selected Noncovalent Protein Complexes

    NASA Astrophysics Data System (ADS)

    Rathore, Deepali; Dodds, Eric D.

    2014-09-01

    In recent years, mass spectrometry has become a valuable tool for detecting and characterizing protein-protein interactions and for measuring the masses and subunit stoichiometries of noncovalent protein complexes. The gas-phase dissociation of noncovalent protein assemblies via tandem mass spectrometry can be useful in confirming subunit masses and stoichiometries; however, dissociation experiments that are able to yield subunit sequence information must usually be conducted separately. Here, we furnish proof of concept for a method that allows subunit sequence information to be directly obtained from a protein aggregate in a single gas-phase analysis. The experiments were carried out using a quadrupole time-of-flight mass spectrometer equipped with a traveling-wave ion mobility separator. This instrument configuration allows for a noncovalent protein assembly to be quadrupole selected, then subjected to two successive rounds of collision-induced dissociation with an intervening stage of ion mobility separation. This approach was applied to four model proteins as their corresponding homodimers: glucagon, ubiquitin, cytochrome c, and β-lactoglobulin. In each case, b- and y-type fragment ions were obtained upon further collisional activation of the collisionally-released subunits, resulting in up to 50% sequence coverage. Owing to the incorporation of an ion mobility separation, these results also suggest the intriguing possibility of measuring complex mass, complex collisional cross section, subunit masses, subunit collisional cross sections, and sequence information for the subunits in a single gas-phase experiment. Overall, these findings represent a significant contribution towards the realization of protein interactomic analyses, which begin with native complexes and directly yield subunit identities.

  12. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes.

    PubMed

    Loo, Rachel R Ogorzalek; Loo, Joseph A

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ.

  13. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

    NASA Astrophysics Data System (ADS)

    Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

  14. Characterization of the iron-binding properties of pyoverdine using electron-capture dissociation-tandem mass spectrometry.

    PubMed

    Qi, Yulin; Hayen, Heiko; Volmer, Dietrich A

    2016-02-01

    Pyoverdines (PVD) are a group of siderophores produced by fluorescent Pseudomonads. Identification of PVD variants mostly relies on liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID). Here, both CID and the novel dissociation technique electron-capture dissociation (ECD) were applied to characterize PVD succinamide and its Fe(III)-chelated complex. The results clearly showed that ECD produced diagnostic side chain fragmentation of the PVD peptide chain and preserved the labile Fe(III) binding to the chromophore in contrast to CID. The ECD technique is therefore expected to support the understanding of strain-specific Fe(III) transport processes of PVDs.

  15. Quantum study of Eley-Rideal reaction and collision induced desorption of hydrogen atoms on a graphite surface. II. H-physisorbed case.

    PubMed

    Martinazzo, Rocco; Tantardini, Gian Franco

    2006-03-28

    Following previous investigation of collision induced (CI) processes involving hydrogen atoms chemisorbed on graphite [R. Martinazzo and G. F. Tantardini, J. Chem. Phys. 124, 124702 (2006)], the case in which the target hydrogen atom is initially physisorbed on the surface is considered here. Several adsorbate-substrate initial states of the target H atom in the physisorption well are considered, and CI processes are studied for projectile energies up to 1 eV. Results show that (i) Eley-Rideal cross sections at low collision energies may be larger than those found in the H-chemisorbed case but they rapidly decrease as the collision energy increases; (ii) product hydrogen molecules are vibrationally very excited; (iii) collision induced desorption cross sections rapidly increase, reaching saturation values greater than 10 A2; (iv) trapping of the incident atoms is found to be as efficient as the Eley-Rideal reaction at low energies and remains sizable (3-4 A2) at high energies. The latter adsorbate-induced trapping results mainly in formation of metastable hot hydrogen atoms, i.e., atoms with an excess energy channeled in the motion parallel to the surface. These atoms might contribute in explaining hydrogen formation on graphite.

  16. Computation of Collision-Induced Absorption by Simple Molecular Complexes, for Astrophysical Applications

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2012-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of various types of planets and cool stars, such as late stars, low-mass stars, brown dwarfs, cool white dwarf stars, the ambers of the smaller, burnt out main sequence stars, exoplanets, etc., and therefore of special astronomical interest The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. First results for H_2-He complexes have already been applied to astrophysical models have shown great improvements in these models. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin, Int. J. of Spect., vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin, J. Phys. Chem. A, 115, 6805-6812, 2011} L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Infrared absorption by collisional H_2-He complexes

  17. The temperature dependence of collision-induced absorption by oxygen near 6 microns

    NASA Technical Reports Server (NTRS)

    Orlando, John J.; Tyndall, Geoffrey S.; Nickerson, Karen E.; Calvert, Jack G.

    1991-01-01

    Coefficients for oxygen absorption in the infrared induced by collisions with O2 and N2 are reported over the range 1400-1800/cm and 225-356 K. These coefficients are used to calculate the absorption for O2 in air as a function of temperature and wavenumber, and comparisons are made with previous determinations. In addition, structured absorption features superimposed on the broad collision-induced absorption band, which were observed at all temperatures studied, are interpreted in terms of the presence of (O2)2 and O2-N2 van der Waals molecules.

  18. Fusion reactions in collisions induced by Li isotopes on Sn targets

    SciTech Connect

    Fisichella, M.; Shotter, A. C.; Di Pietro, A.; Figuera, P.; Lattuada, M.; Marchetta, C.; Musumarra, A.; Pellegriti, M. G.; Ruiz, C.; Scuderi, V.; Strano, E.; Torresi, D.; Zadro, M.

    2012-10-20

    Fusion cross sections for the {sup 6}Li+{sup 120}Sn and {sup 7}Li+{sup 119}Sn systems have been measured. We aim to search for possible effects due to the different neutron transfer Q-values, by comparing the fusion cross sections for the two systems below the barrier. This experiment is the first step of a wider systematic aiming to study the above problems in collisions induced by stable and unstable Li isotopes on tin all forming the same compound nucleus.

  19. Shock induced dissociation of polyethylene

    SciTech Connect

    Morris, C.E.; Loughran, E.D.; Mortensen, G.F.; Gray, G.T. III; Shaw, M.S.

    1989-01-01

    To identify the physical processes occurring on the Hugoniot, shock-recovery experiments were performed. Cylindrical recovery systems were used that enabled a wide range of single-shock Hugoniot states to be examined. Mass spectroscopy was used to examine the gaseous dissociation products. X-ray and TEM measurements were made to characterize the post-shock carbon structures. A dissociation product equation of state is presented to interpret the observed results. Polyethylene (PE) samples that were multiply shocked to their final states dissociated at much higher pressures than single-shocked samples. 5 refs., 2 figs., 1 tab.

  20. Dissociation Rates of Diatomic Molecules

    DTIC Science & Technology

    1992-12-01

    relatively simple design that we have used extensively in earlier research; its characteristics were recently described in detail. 10 This source is by...the dominant dissociation background when observing electron- impact dissociation products. This background constitutes the single greatest impediment...a3aF) + o(3P) at 11.385 eV. Photoexcitation studies indeed find that O(1S) and CO(a) are the dominant photodissociation products. 32,33 If the energy

  1. Scapholunate Dissociation.

    PubMed

    Ramponi, Denise; McSwigan, Tara

    2016-01-01

    Wrist injuries are a common complaint in the emergency setting. Any disruption of the anatomy of the carpal bones can impair hand function, leading to pain, weakness, and complications. One of the most common forms of carpal bone instability is scapholunate dissociation. This injury can lead to significant morbidity including avascular necrosis, impaired healing, limited function, and arthritis. These diagnostic findings may be subtle, thus identifying high-risk mechanisms of injury, and clinical manifestations will assist the emergency practitioner with early diagnosis and treatment of this high-risk injury.

  2. Theoretical development of a simplified wheelset model to evaluate collision-induced derailments of rolling stock

    NASA Astrophysics Data System (ADS)

    Koo, Jeong Seo; Choi, Se Young

    2012-06-01

    A theoretical method is proposed to predict and evaluate collision-induced derailments of rolling stock by using a simplified wheelset model and is verified with dynamic simulations. Because the impact forces occurring during collision are transmitted from the car body to the bogies and axles through suspensions, rolling stock leads to derailment as a result of the combination of horizontal and vertical impact forces applied to the axle and a simplified wheelset model enforced at the axle can be used to theoretically formulate derailment behaviors. The derailment type depends on the combination of the horizontal and vertical forces, the flange angle and the friction coefficient. According to collision conditions, wheel-climb, wheel-lift or roll-over derailment can occur between the wheel and the rail. In this theoretical derailment model of a simplified wheelset, the derailment types are classified as Slip-up, Slip/roll-over, Climb-up, Climb/roll-over and pure Roll-over according to the derailment mechanisms between the wheel and the rail and the theoretical conditions needed to generate each derailment mechanism are proposed. The theoretical wheelset model is verified by dynamic simulation and its applicability is demonstrated by comparing the simulation results of the theoretical wheelset model with those of an actual wheelset model. The theoretical derailment wheelset model is in good agreement with the virtual testing model simulation for a collision-induced derailment of rolling stock.

  3. Collision-Induced Infrared Absorption by Hydrogen-Helium gas mixtures at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2010-10-01

    The interaction-induced absorption by collisional pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets and cool stars ^[1]. The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H2--H2, H2--He, and H2--H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin ^[2]. Laboratory measurements of interaction-induced absorption spectra by H2 pairs exist only at room temperature and below. We show that our results reproduce these measurements closely ^[2], so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures ^[2]. [1] L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 [2] Xiaoping Li, Katharine L. C. Hunt, Fei Wang, Martin Abel, and Lothar Frommhold, ``Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin'', International Journal of Spectroscopy, vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201

  4. Production of C2H4Cl+ by dissociative photoionization of weak molecular complexes in C2H4 + HCl mixtures

    NASA Astrophysics Data System (ADS)

    Walters, E. A.; Grover, J. R.; Arneberg, D. L.; Santandrea, C. J.; White, M. G.

    1990-12-01

    The photoionization efficiency (PIE) spectrum from 600 to 1200 Å for the production of the ion C2H4Cl+ by dissociative photoionization of the products of room-temperature jet expansions of a 1:4 mixture of C2H4 and HCl was measured at several nozzle pressures. The results were resolved into the PIE yield curve for the heterodimer process C2H4·HCl+ hv→C2H4Cl++H+ e. This reaction is necessarily characterized by a large change in geometry between neutral complex and ionic product. The observed spectrum exhibits an unusual and conspicuous peak at 15.2 eV that is characterized by a sharp cutoff to the high energy side. This feature points to the onset of strongly nonstatistical channels for the production of C2H4Cl+ at this energy such that product formation proceeds through very few states. The observed onset of C2H4Cl+ at 11.92±0.24 eV is 17±6 kcal mol-1 above the true threshold. An important conclusion is that at all energies above the onset the yield of dissociative ionization of the heterodimer to the cation C2H4Cl+ is determined by dynamical factors.

  5. Reliable Determination of Site-Specific In Vivo Protein N-Glycosylation Based on Collision-Induced MS/MS and Chromatographic Retention Time

    NASA Astrophysics Data System (ADS)

    Wang, Benlian; Tsybovsky, Yaroslav; Palczewski, Krzysztof; Chance, Mark R.

    2014-05-01

    Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures.

  6. Reliable determination of site-specific in vivo protein N-glycosylation based on collision-induced MS/MS and chromatographic retention time.

    PubMed

    Wang, Benlian; Tsybovsky, Yaroslav; Palczewski, Krzysztof; Chance, Mark R

    2014-05-01

    Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures.

  7. Theoretical study of the unimolecular dissociation of HCO

    NASA Astrophysics Data System (ADS)

    Whittier, Gregory Scott

    This thesis offers a detailed theoretical study of the unimolecular dissociation of formyl radical, HCO, which is an important intermediate in combustion chemistry. A quantum mechanical treatment of the dissociation of isolated HCO is presented along with a mixed quantum/classical study of the excitation and deexcitation of HCO in collisions of HCO with the bath gas Ar. The results are then used to model the kinetics of the collision-induced dissociation of HCO by Ar. Resonance states of HCO are calculated for total angular momentum J = 0, 1, and 3 using the artificial boundary inhomogeneity (ABI) method of Jang and Light [J. Chem. Phys. 102, 3262 (1995)]. Resonance energies and widths are determined by analyzing the Smith lifetime matrix. A resonance search algorithm and a method for resolving overlapping resonances are described. The accurate prediction of J = 3 resonances from J = 0 and 1 data is tested with good results for excited stretch resonance and less accurate results for bending resonances, demonstrating the degree of separability of vibration from overall rotation for these quasi-bound states. A quantum/classical time-dependent self-consistent field (Q/C TDSCF) approach is used to simulate the dynamics of collisions of Ar with HCO. State-to-state cross sections and thermal rate constants for vibrational transitions are presented. Using this model together with assumptions about the rotational energy transfer and a master equation treatment of the kinetics, the low-pressure thermal rate of collision-induced dissociation was calculated over the 300-4000 K temperature range. Comparison with experiment shows good agreement at high temperatures and poor agreement at low temperatures. The high temperature results were sufficient to obtain an Arrhenius expression for the rate that agrees with all experimental results of which we are aware.

  8. Structure Effects in Collisions Induced by Halo and Weakly Bound Nuclei around the Coulomb Barrier

    NASA Astrophysics Data System (ADS)

    Scuderi, V.; di Pietro, A.; Acosta, L.; Amorini, F.; Borge, M. J. G.; Figuera, P.; Fisichella, M.; Fraile, L. M.; Gomez-Camacho, J.; Jeppesen, H.; Lattuada, M.; Martel, I.; Milin, M.; Musumarra, A.; Papa, M.; Pellegriti, M. G.; Raabe, R.; Randisi, G.; Rizzo, F.; Santonocito, D.; Sanchez, E. M. R.; Scalia, G.; Tengblad, O.; Torresi, D.; Vidal, A. M.; Zadro, M.

    In this contribution, results concerning different reaction channels for the collisions induced by the three Be isotopes, 9,10,11Be, on a 64Zn target at energies around the Coulomb barrier will be presented. The experiments with the radioactive 10,11Be beams were performed at REX-ISOLDE (CERN) whereas the experiment with the stable weakly bound 9Be beam was performed at LNS Catania. Elastic scattering angular distributions have been measured for the three systems 9,10,11Be + 64Zn at the same center of mass energy. The angular distributions were analyzed with optical potentials and reaction cross sections were obtained from optical model calculations, performed with the code PTOLEMY. For the 11Be + 64Zn reaction, the break-up angular distribution was also measured.

  9. Depolarized light scattering studies of the collision induced polarizability anisotropy of atoms and spherical top molecules

    NASA Astrophysics Data System (ADS)

    Dunmur, D. A.; Manterfield, M. R.; Robinson, D. J.

    New measurements are reported of the density dependent depolarization ratio for argon, krypton, xenon, methane and sulphur hexafluoride, and the results are analysed to provide values for the second and third depolarization virial coefficients. The relationships between the second depolarization virial coefficient, the zeroth moment of the two-body Rayleigh spectrum and the second Kerr virial coefficient are considered, and it is shown that they now provide consistent results for the collision-induced pair polarizability anisotropy. Former inconsistencies are attributed to insufficient allowance for the effects of three-body interactions. Calculations of the second and third depolarization virial coefficients based on the DID model and using the Maitland-Smith potential are in excellent agreement with the experimental results for argon, krypton and xenon.

  10. Computer Simulation of the far Infrared Collision Induced Absorption Spectra of Gaseous CO2

    NASA Technical Reports Server (NTRS)

    Gruszka, Marcin; Borysow, Aleksandra

    1998-01-01

    Far infrared collision induced absorption spectra of gaseous CO2 were computed using molecular dynamics simulations. The quadrupole and hexadecapole multipolar induction, through the trace, and the anisotropy of the molecular polarizability were found to be insufficient to represent properly the dipole induction mechanism. For a detailed analysis of the induction process the spectra obtained were decomposed into components resulting from different terms of the induced dipole. Based on this decomposition, all additional overlap contribution for each term was proposed. When spectra were recomputed including such overlap, good agreement between experiment and simulation was achieved over the temperature range at which measurements exist (233-400 K). The use of an anisotropic intermolecular potential was found to be of critical importance for obtaining the right shape of the far wings of the spectra.

  11. 2D laser-collision induced fluorescence in low-pressure argon discharges

    SciTech Connect

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Td to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.

  12. 2D laser-collision induced fluorescence in low-pressure argon discharges

    DOE PAGES

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Tdmore » to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.« less

  13. Collision-induced photon echo at the transition 0{r_reversible}1 in ytterbium vapor: Direct proof of depolarizing collision anisotropy

    SciTech Connect

    Rubtsova, N. N.; Gol'dort, V. G.; Ishchenko, V. N.; Khvorostov, E. B.; Kochubei, S. A.; Reshetov, V. A.; Yevseyev, I. V.

    2011-09-15

    A collision-induced photon echo arising at the transition 0{r_reversible}1 of ytterbium in the presence of heavy atomic buffer is investigated. Collision-induced echo signal appears in the case of mutually orthogonal linear polarizations of exciting pulses and it is absent without buffer. Collision-induced echo power grows with buffer pressure up to the maximum value and decays exponentially at further buffer pressure growth. Collision-induced echo power is essentially less than that of the ordinary echo generated by pulses with parallel polarizations in the same mixture, and its polarization is linear with the polarization vector directed along that of the first exciting pulse. All the properties of collision-induced photon echo are explained on the basis of collision relaxation dependence on the direction of active atom velocity.

  14. Catalytic recombination of dissociation products with Pt/SnO2 for rare and common isotope long-life, closed-cycle CO2 lasers

    NASA Technical Reports Server (NTRS)

    Brown, Kenneth G.; Sidney, B. D.; Schryer, D. R.; Upchurch, B. T.; Miller, I. M.

    1986-01-01

    This paper reports results on recombination of pulsed CO2 laser dissociation products with Pt/SnO2 catalysts, and supporting studies in a surrogate laboratory catalyst reactor. The closed-cycle, pulsed CO2 laser has been continuously operated for one million pulses with an overall power degradation of less than 5 percent by flowing the laser gas mixture through a 2-percent Pt/SnO2 catalyst bed. In the surrogate laboratory reactor, experiments have been conducted to determine isotopic exchange with the catalyst when using rare-isotope gases. The effects of catalyst pretreatment, sample weight, composition, and temperature on catalyst efficiency have also been determined.

  15. Vibrational nonequilibrium effects on diatomic dissociation rates

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1993-01-01

    The collision-induced dissociation rate of diatomic molecules from a ladder of rotational and anharmonic vibrational states is developed, and the correction for vibrational nonequilibrium is considered. The result is similar to an analytic correction derived by Hammerling et al. (1959) for harmonic oscillators. An empirical correction algorithm suggested by Park (1987, 1990) gives similar results when vibrational temperature is comparable to kinetic temperature but underestimates the dissociation rate when vibrational temperature is small compared with the kinetic temperature. This algorithm uses an effective temperature in the experimentally determined Arrhenius expression for the rate coefficient, which is a weighted average of the vibrational and kinetic temperature, whereas theory indicates that kinetic temperature should appear only in the exponential term of the Arrhenius expression. Nevertheless, an effective temperature can always be found that will numerically duplicate the proper rate coefficient at any given condition, but a constant weighting factor cannot be expected to provide this. However, the algorithm can he adjusted to give reasonable results over a range of conditions if the geometric weighting factor is taken to be a simple linear function of the ratio of vibrational to kinetic temperature in the gas.

  16. Cross sections for production of H(2p, 2s, 1s) by electron collisional dissociation of H2

    NASA Technical Reports Server (NTRS)

    Ajello, J. M.; James, G. K.; Shemansky, D. E.

    1991-01-01

    The excitation function of H Ly-alpha from the astrophysically important dissociation of electron-excited H2 over the range 10-700 eV has been measured. The analysis predicts the cross section to energies higher than the present experimental limit, and it is found that the predicted shape is in close agreement with measured results. At 6 eV the cross section is dominated by the electric dipole first Born component, while at 100 eV the electric dipole component constitutes 73 percent of the total H(2p) cross section. The cross sections of the H(2s) and H(1s) components are calculated.

  17. Ozone-induced dissociation: elucidation of double bond position within mass-selected lipid ions.

    PubMed

    Thomas, Michael C; Mitchell, Todd W; Harman, David G; Deeley, Jane M; Nealon, Jessica R; Blanksby, Stephen J

    2008-01-01

    Ions formed from lipids during electrospray ionization of crude lipid extracts have been mass-selected within a quadrupole linear ion trap mass spectrometer and allowed to react with ozone vapor. Gas-phase ion-molecule reactions between unsaturated lipid ions and ozone are found to yield two primary product ions for each carbon-carbon double bond within the molecule. The mass-to-charge ratios of these chemically induced fragments are diagnostic of the position of unsaturation within the precursor ion. This novel analytical technique, dubbed ozone-induced dissociation (OzID), can be applied both in series and in parallel with conventional collision-induced dissociation (CID) to provide near-complete structural assignment of unknown lipids within complex mixtures without prior fractionation or derivatization. In this study, OzID is applied to a suite of complex lipid extracts from sources including human lens, bovine kidney, and commercial olive oil, thus demonstrating the technique to be applicable to a broad range of lipid classes including both neutral and acidic glycerophospholipids, sphingomyelins, and triacylglycerols. Gas-phase ozonolysis reactions are also observed with different types of precursor ions including [M+H]+, [M+Li]+, [M+Na]+, and [M-H]-: in each case yielding fragmentation data that allow double bond position to be unambiguously assigned. Within the human lens lipid extract, three sphingomyelin regioisomers, namely SM(d18:0/15Z-24:1), SM(d18:0/17Z-24:1), and SM(d18:0/19Z-24:1), and a novel phosphatidylethanolamine alkyl ether, GPEtn(11Z-18:1e/9Z-18:1), are identified using a combination of CID and OzID. These discoveries demonstrate that lipid identification based on CID alone belies the natural structural diversity in lipid biochemistry and illustrate the potential of OzID as a complementary approach within automated, high-throughput lipid analysis protocols.

  18. Hybrid quadrupole mass filter/quadrupole ion trap/time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions

    SciTech Connect

    Gulyuz, Kerim; Stedwell, Corey N.; Wang Da; Polfer, Nick C.

    2011-05-15

    We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator/amplifier (OPO/A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure ({approx}10{sup -5} Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH{sup +}, as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.

  19. Dissociative phenomenology of dissociative identity disorder.

    PubMed

    Dell, Paul F

    2002-01-01

    The goal of this study was to investigate the dissociative phenomenology of dissociative identity disorder (DID). The Multidimensional Inventory of Dissociation (MID) was administered to 34 patients with DID, 23 patients with dissociative disorder not otherwise specified (DDNOS), 52 patients with mixed psychiatric disorders, and 58 normal individuals. DID patients obtained significantly higher scores than the other three groups on 27 dissociation-related variables. DDNOS patients had significantly higher scores than normals and mixed psychiatric patients on 17 and 15 dissociation-related variables, respectively. The findings of the present study are virtually identical to a large body of replicated findings about the dissociative phenomenology of DID. This broad range of dissociation-related phenomena, which routinely occurs in individuals with DID, is largely absent from the DSM-IV-TR account of DID. Factor analysis of the 11 dimensions of dissociation that are measured by the MID extracted only one factor that accounted for 85% of the variance. It was concluded that dissociation is a unifactorial taxon or natural type that has different aspects or epiphenomena (i.e., amnesia, depersonalization, voices, trance, etc.).

  20. Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides

    PubMed Central

    Liu, Jian; McLuckey, Scott A.

    2012-01-01

    The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation. PMID:23264749

  1. The Binary Collision-Induced Second Overtone Band of Gaseous Hydrogen: Modelling and Laboratory Measurements

    NASA Technical Reports Server (NTRS)

    Brodbeck, C.; Bouanich, J.-P.; Nguyen, Van Thanh; Borysow, Aleksandra

    1999-01-01

    Collision-induced absorption (CIA) is the major source of the infrared opacity of dense planetary atmospheres which are composed of nonpolar molecules. Knowledge of CIA absorption spectra of H2-H2 pairs is important for modelling the atmospheres of planets and cold stars that are mainly composed of hydrogen. The spectra of hydrogen in the region of the second overtone at 0.8 microns have been recorded at temperatures of 298 and 77.5 K for gas densities ranging from 100 to 800 amagats. By extrapolation to zero density of the absorption coefficient measured every 10 cm(exp -1) in the spectral range from 11100 to 13800 cm(exp -1), we have determined the binary absorption coefficient. These extrapolated measurements are compared with calculations based on a model that was obtained by using simple computer codes and lineshape profiles. In view of the very weak absorption of the second overtone band, we find the agreement between results of the model and experiment to be reasonable.

  2. High-energy limit of collision-induced false vacuum decay

    NASA Astrophysics Data System (ADS)

    Demidov, Sergei; Levkov, Dmitry

    2015-06-01

    We develop a consistent semiclassical description of field-theoretic collision-induced tunneling at arbitrary high collision energies. As a playground we consider a (1 + 1)-dimensional false vacuum decay initiated by a collision of N particles at energy E, paying special attention to the realistic case of N = 2 particles. We demonstrate that the cross section of this process is exponentially suppressed at all energies. Moreover, the respective suppressesion exponent F N ( E) exhibits a specific behavior which is significant for our semiclassical method and assumed to be general: it decreases with energy, reaches absolute minimum F = F min( N ) at a certain threshold energy E = E rt( N ), and stays constant at higher energies. We show that the minimal suppression F min( N ) and threshold energy can be evaluated using a special class of semiclassical solutions which describe exponentially suppressed transitions but nevertheless evolve in real time. Importantly, we argue that the cross section at energies above E rt( N ) is computed perturbatively in the background of the latter solutions, and the terms of this perturbative expansion stay bounded in the infinite-energy limit. Transitions in the high-energy regime proceed via emission of many soft quanta with total energy E rt; the energy excess E - E rt remains in the colliding particles till the end of the process.

  3. Collision-induced absorption in mixtures of symmetrical linear and tetrahedral molecules - Methane-nitrogen

    NASA Technical Reports Server (NTRS)

    Birnbaum, G.; Borysow, A.; Buechele, A.

    1993-01-01

    The far infrared absorption of a CH4-N2 mixture was measured at 297, 195, and 162 K from 30 to 650/cm. The spectral invariants gamma1 and alpha1, proportional, respectively, to the zeroth and first spectral moments, due to bimolecular collisions between CH4 and N2 were obtained from these data and compared with theoretical values. The theory for collision-induced dipoles between a tetrahedral and a diatomic or symmetrical linear molecule includes contributions not previously considered. Whereas the theoretical values of gamma1 are only somewhat greater than experiment at all temperatures, the theoretical values of alpha1 are significantly lower than the experimental values. From the theoretical spectral moments for the various induced dipole components, the parameters of the BC shape were computed, and theoretical spectra were constructed. Good agreement was obtained at the lower frequencies, but with increasing frequencies the theoretical spectra were increasingly less intense than the experimental spectra. Although the accuracy of the theoretical results may suffer from the lack of a reliable potential function, it does not appear that this high frequency discrepancy can be removed by any conceivable modification in the potential.

  4. Collision-induced Absorption in the Infrared: A Data Base for Modelling Planetary and Stellar Atmospheres

    NASA Astrophysics Data System (ADS)

    Borysow, Aleksandra

    1998-12-01

    Accurate knowledge of certain collision-induced absorption continua of molecular pairs such as H2-H2, H2-He, H2-CH4, CO2-CO2, etc., is a prerequisite for most spectral analyses and modelling attempts of atmospheres of planets and cold stars. We collect and regularly update simple, state of the art computer programs for the calculation of the absorption coefficient of such molecular pairs over a broad range of temperatures and frequencies, for the various rotovibrational bands. The computational results are in agreement with the existing laboratory measurements of such absorption continua, recorded with a spectral resolution of a few wavenumbers, but reliable computational results may be expected even in the far wings, and at temperatures for which laboratory measurements do not exist. Detailed information is given concerning the systems thus studied, the temperature and frequency ranges considered, the rotovibrational bands thus modelled, and how one may obtain copies of the FORTRAN77 computer programs by e-mail.

  5. Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Hunt, Katharine L. C.; Li, Xiaoping; Frommhold, Lothar

    2010-03-01

    The interaction-induced absorption by collisional pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets and cool stars [1]. The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H2---H2, H2---He, and H2---H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H2 pairs exist only at temperatures below 300 K. We show that our results reproduce these measurements closely so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. This work has been supported in part by the National Science Foundation through Grants AST-0709106 and AST-0708496.[4pt] [1] L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006

  6. Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Hunt, Katharine L. C.; Li, Xiaoping; Frommhold, Lothar

    2010-03-01

    The interaction-induced absorption by collisional pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets and cool stars.ootnotetextL. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H2---H2, H2---He, and H2---H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H2 pairs exist only at temperatures below 300 K. We show that our results reproduce these measurements closely so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. This work has been supported in part by the National Science Foundation through Grants AST-0709106 and AST-0708496.

  7. Collision-induced light scattering in a thin xenon layer between graphite slabs - MD study.

    PubMed

    Dawid, A; Górny, K; Wojcieszyk, D; Dendzik, Z; Gburski, Z

    2014-08-14

    The collision-induced light scattering many-body correlation functions and their spectra in thin xenon layer located between two parallel graphite slabs have been investigated by molecular dynamics computer simulations. The results have been obtained at three different distances (densities) between graphite slabs. Our simulations show the increased intensity of the interaction-induced light scattering spectra at low frequencies for xenon atoms in confined space, in comparison to the bulk xenon sample. Moreover, we show substantial dependence of the interaction-induced light scattering correlation functions of xenon on the distances between graphite slabs. The dynamics of xenon atoms in a confined space was also investigated by calculating the mean square displacement functions and related diffusion coefficients. The structural property of confined xenon layer was studied by calculating the density profile, perpendicular to the graphite slabs. Building of a fluid phase of xenon in the innermost part of the slot was observed. The nonlinear dependence of xenon diffusion coefficient on the separation distance between graphite slabs has been found.

  8. Collision-induced migration of adsorbates on solid surfaces: an experimental approach.

    PubMed

    Danziger, I M; Asscher, M

    2006-07-13

    Collision-induced migration (CIM) is a process in which energetic gas-phase atoms or molecules at the tail of the Boltzmann distribution enhance surface migration of adsorbates upon collision. It is believed to exist and play an important role in any realistic high pressure-high-temperature heterogeneous catalytic system. Combining supersonic beam-surface collision setup with in-situ optical second harmonic generation diffraction technique from a coverage grating, we have shown, for the first time, that indeed energetic collisions (Kr seeded in He) promote surface mobility of CO-K surface complex on Ru(001) with a threshold total kinetic energy of 3 eV. An average migration distance/collision of more than 30 adsorption sites was estimated from the experimental data at Kr total energy of 3.8 eV. This long-range migration distance per collision is understood in terms of a cascade migration mechanism, where adsorbed CO molecules collide and push their neighbors from high to low coverage areas, in a direction dictated by the collision momentum vector. A similar mechanism has recently been suggested to explain adsorbate mobility at high coverage induced by an STM tip.

  9. Collision-induced Absorption in the Infrared: A Data Base for Modelling Planetary and Stellar Atmospheres

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra

    1998-01-01

    Accurate knowledge of certain collision-induced absorption continua of molecular pairs such as H2-H2, H2-He, H2-CH4, CO2-CO2, etc., is a prerequisite for most spectral analyses and modelling attempts of atmospheres of planets and cold stars. We collect and regularly update simple, state of the art computer programs for the calculation of the absorption coefficient of such molecular pairs over a broad range of temperatures and frequencies, for the various rotovibrational bands. The computational results are in agreement with the existing laboratory measurements of such absorption continua, recorded with a spectral resolution of a few wavenumbers, but reliable computational results may be expected even in the far wings, and at temperatures for which laboratory measurements do not exist. Detailed information is given concerning the systems thus studied, the temperature and frequency ranges considered, the rotovibrational bands thus modelled, and how one may obtain copies of the FORTRAN77 computer programs by e-mail.

  10. Collision-induced signal enhancement (CISE): the use of boundary activation to effect non-resonant CISE.

    PubMed

    Asam, Michael R; Glish, Gary L

    2002-06-01

    An alternative to resonant excitation collision-induced signal enhancement (CISE) is presented. This alternative utilizes boundary activation instead of resonant excitation to effect CISE and is called boundary activated collision induced signal enhancement (BA-CISE). There are three ways to effect BA-CISE to enhance the signal for an MS(n+1) experiment. Each technique utilizes the beta(z) = 0 boundary, which ions encounter from high to low mass/charge ratio. BA-CISE is shown to produce an almost 900% increase in the C2 ion of [maltohexaose + Li]+. The use of a heavy collision gas in addition to the helium bath gas generally produced a signal enhancement inferior to the same experiment without the heavy gas.

  11. Interacting He and Ar atoms: Revised theoretical interaction potential, dipole moment, and collision-induced absorption spectra

    SciTech Connect

    Meyer, Wilfried; Frommhold, Lothar

    2015-09-21

    Coupled cluster quantum chemical calculations of the potential energy surface and the induced dipole surface are reported for the He–Ar van der Waals collisional complex. Spectroscopic parameters are derived from global analytical fits while an accurate value for the long-range dipole coefficient D{sub 7} is obtained by perturbation methods. Collision-induced absorption spectra are computed quantum mechanically and compared with existing measurements.

  12. Interacting He and Ar atoms: Revised theoretical interaction potential, dipole moment, and collision-induced absorption spectra.

    PubMed

    Meyer, Wilfried; Frommhold, Lothar

    2015-09-21

    Coupled cluster quantum chemical calculations of the potential energy surface and the induced dipole surface are reported for the He-Ar van der Waals collisional complex. Spectroscopic parameters are derived from global analytical fits while an accurate value for the long-range dipole coefficient D7 is obtained by perturbation methods. Collision-induced absorption spectra are computed quantum mechanically and compared with existing measurements.

  13. First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

    SciTech Connect

    Varghese, Jithin J.; Mushrif, Samir H.

    2015-05-14

    Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.

  14. Quantum mechanical calculation of the collision-induced absorption spectra of N{sub 2}–N{sub 2} with anisotropic interactions

    SciTech Connect

    Karman, Tijs; Groenenboom, Gerrit C.; Avoird, Ad van der; Miliordos, Evangelos; Hunt, Katharine L. C.

    2015-02-28

    We present quantum mechanical calculations of the collision-induced absorption spectra of nitrogen molecules, using ab initio dipole moment and potential energy surfaces. Collision-induced spectra are first calculated using the isotropic interaction approximation. Then, we improve upon these results by considering the full anisotropic interaction potential. We also develop the computationally less expensive coupled-states approximation for calculating collision-induced spectra and validate this approximation by comparing the results to numerically exact close-coupling calculations for low energies. Angular localization of the scattering wave functions due to anisotropic interactions affects the line strength at low energies by two orders of magnitude. The effect of anisotropy decreases at higher energy, which validates the isotropic interaction approximation as a high-temperature approximation for calculating collision-induced spectra. Agreement with experimental data is reasonable in the isotropic interaction approximation, and improves when the full anisotropic potential is considered. Calculated absorption coefficients are tabulated for application in atmospheric modeling.

  15. Protonation sites and dissociation mechanisms of t-butylcarbamates in tandem mass spectrometric assays for newborn screening.

    PubMed

    Spáčil, Zdeněk; Hui, Renjie; Gelb, Michael H; Tureček, František

    2011-10-01

    Structures of tert-butylcarbamate ions in the gas-phase and methanol solution were studied for simple secondary and tertiary carbamates as well as for carbamate-containing products and internal standards for lysosomal enzyme assays used in newborn screening of a α-galactosidase A deficiency (Fabry disease), mucopolysaccharidosis I (Hurler disease), and mucopolysaccharidosis II (Hunter disease). The protonation of simple t-butylcarbamates can occur at the carbonyl group, which is the preferred site in the gas phase. Protonation in methanol solution is more favorable if occurring at the carbamate nitrogen atom. The protonation of more complex t-butylcarbamates occurs at amide and carbamate carbonyl groups, and the ions are stabilized by intramolecular hydrogen bonding, which is affected by solvation. Tertiary carbamates containing aminophenol amide groups were calculated to have substantially greater gas-phase basicities than secondary carbamates containing coumarin amide groups. The main diagnostically important ion dissociation by elimination of 2-methylpropene (isobutylene, i-C(4)H(8)) and carbon dioxide is shown by experiment and theory to proceed in two steps. Energy-resolved collision-induced dissociation of the Hurler's disease enzymatic product ion, which is a coumarin-diamine linker-t-butylcarbamate conjugate (3a(+)), indicated separate energy thresholds for the loss of i-C(4)H(8) and CO(2). Computational investigation of the potential energy surface along two presumed reaction pathways indicated kinetic preference for the migration of a t-butyl hydrogen atom to the carbamate carbonyl resulting in the isobutylene loss. The consequent loss of CO(2) required further proton migrations that had to overcome energy barriers.

  16. Effects of carbonyl bond, metal cluster dissociation, and evaporation rates on predictions of nanotube production in high-pressure carbon monoxide

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2003-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNTs) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the conformation of CO2. It is shown that the production of CO2 is significantly greater for FeCO because of its lower bond energy as compared with that of NiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  17. Wave packet dynamics of H2(v1=8-14)+H2(v2=0-2): the role of the potential energy surface on different reactive and dissociative processes.

    PubMed

    Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José

    2005-02-08

    A time-dependent wave packet method has been used to study different competing products of H(2)+H(2) collisions: four center reaction, collision induced dissociation, reactive dissociation, and three-body complex formation. A three-degree-of-freedom reduced dimensionality model has been used for five different geometries of the colliding complex (parallel H, crossed X, collinear L, and two T-shaped geometries T(I) and T(II)), with reactants in selected vibrational states with one diatom vibrationally "hot" and the other one vibrationally "cold." Product probabilities have been calculated using two potential energy surfaces [J. Chem. Phys. 101, 4004 (1994); J. Chem. Phys. 116, 666 (2002)] in order to compare their performance in the dynamics. The regions of the potential energy surfaces responsible of the threshold behavior of the probabilities have been identified. Overall, we have found that the most recent potential energy surface is less anisotropic, provides a smaller propensity for insertion-type processes, and gives lower energy thresholds.

  18. Central production of ρ0 in p p collisions with single proton diffractive dissociation at the LHC

    NASA Astrophysics Data System (ADS)

    Lebiedowicz, Piotr; Nachtmann, Otto; Szczurek, Antoni

    2017-02-01

    We consider the p p →p p ρ0π0 and p p →p n ρ0π+ processes at LHC energies. Our description is based on the nonperturbative framework of tensor pomeron and tensor reggeon exchanges. We discuss the Drell-Hiida-Deck type mechanism with centrally produced ρ0 meson associated with a very forward/backward π N system. The considered processes constitute an inelastic (nonexclusive) background to the p p →p p ρ0 reaction in the case when only the centrally produced ρ0 meson decaying into π+π- is measured, the final state protons are not observed, and only rapidity-gap conditions are checked experimentally. We compare our results for the γ π+→ρ0π+ reaction with the experimental data obtained by the H1 collaboration at HERA. We present several differential distributions for the p p →p n ρ0π+ reaction and estimate the size of the proton dissociative background to the exclusive p p →p p ρ0 process. The ratio of integrated cross sections for the inelastic p p →p N ρ0π processes, where p N ρ0π stands for p n ρ0π+ plus p p ρ0π0, to the reference reaction p p →p p ρ0 is of order of (7-10)%. We present also the ratios of the ρ0 rapidity and transverse momentum distributions for the inelastic p p →p N ρ0π versus the elastic p p →p p ρ0 reaction. Our results may be used to investigate the γ π →ρ0π process at LHC energies.

  19. Dissociative Electron Attachment to chloroacetylene

    NASA Astrophysics Data System (ADS)

    Ngassam, V.; Orel, A. E.

    2007-06-01

    The production of two fragments with σ symmetry from electron-impact dissociation of C2H2, which has only a low lying &*circ; resonance at equilibrium geometry, has been explained by the existence of interactions with &*circ; resonances at bent geometries. We are investigating the presence of such multidimensional effects in the dissociative attachment of chloroacetylene (C2HCl). We have performed electron scattering calculations using the Complex Kohn variational method to determine the resonance energies and widths of the chloroacetylene resonances as a function of both the Cl--C2H bond distance as well as the variation with C-C stretch and bend. We will discuss our results and our prediction of the dissociation dynamics in comparison to the findings for for C2H2. This work was supported by the U.S. DOE Office of Basic Energy Sciences, Division of Chemical Sciences and the National Science Foundation, PHY-05-55401.

  20. Dissociative Electron Attachment

    NASA Astrophysics Data System (ADS)

    Arreola, Esmeralda; Esmeralda Arreola Collaboration; Leigh Hargreaves Collaboration

    Since the pioneering work of Boudiaffa et al., it has been understood that electrons, even with energies near or below the ionization threshold, are capable of initiating strand-breaks in human DNA. This discovery raised important questions for cancer treatments, since sub-ionizing electrons are known to be the most copiously produced secondary product of radiation therapy. But even to date these factors are largely excluded from dosimetry calculations. This lack of inclusion is, at least in part, certainly due to the dearth of fundamental data describing low-energy electron interactions with nucleotide molecules that form the basis of DNA. Understanding of how such slow electrons are able to damage DNA remains incomplete, but the strongly peaked nature of Boudiaffa et al.'s data gives strong hints at resonantly driven collision processes. DNA damage is therefore most likely driven by ``dissociative electron attachment'' (DEA). DEA is a rather complicated process to model due to the coupling of electronic and nuclear degrees of freedom in the molecule. At the California State University Fullerton, we are currently commissioning a new spectrometer to study dissociation channels, reaction rates and orientation effects in DEA collisions between slow electrons and nucleotide molecules. At the meeting we will present design parameters and commissioning data for this new apparatus.

  1. Neural Dissociation in the Production of Lexical versus Classifier Signs in ASL: Distinct Patterns of Hemispheric Asymmetry

    ERIC Educational Resources Information Center

    Hickok, Gregory; Pickell, Herbert; Klima, Edward; Bellugi, Ursula

    2009-01-01

    We examine the hemispheric organization for the production of two classes of ASL signs, lexical signs and classifier signs. Previous work has found strong left hemisphere dominance for the production of lexical signs, but several authors have speculated that classifier signs may involve the right hemisphere to a greater degree because they can…

  2. Standard enthalpies of formation for L-tyrosine, DL-norleucine, DL-tryptophan, DL-α-alanyl-DL-norleucine, and products of their dissociation in an aqueous solution

    NASA Astrophysics Data System (ADS)

    Kochergina, L. A.; Krutova, O. N.; Damrina, K. V.

    2015-05-01

    Enthalpies of dissolution are determined for a series of crystal amino acids (L-tyrosine, DL-norleucine, and DL-tryptophan) and a DL-α-alanyl-DL-norleucine dipeptide in aqueous solutions of KOH at 298.15 K by means of direct calorimetry. Standard enthalpies of formation are determined for bioligands and products of their dissociation.

  3. The role of proton mobility in determining the energy-resolved vibrational activation/dissociation channels of N-glycopeptide ions.

    PubMed

    Kolli, Venkata; Roth, Heidi A; De La Cruz, Gabriela; Fernando, Ganga S; Dodds, Eric D

    2015-10-08

    Site-specific glycoproteomic analysis largely hinges on the use of tandem mass spectrometry (MS/MS) to identify glycopeptides. Experiments of this type are usually aimed at drawing connections between individual oligosaccharide structures and their specific sites of attachment to the polypeptide chain. These determinations inherently require ion dissociation methods capable of interrogating both the monosaccharide and amino acid connectivity of the glycopeptide. Collision-induced dissociation (CID) shows potential to satisfy this requirement, as the vibrational activation/dissociation of protonated N-glycopeptides has been observed to access cleavage of either glycosidic bonds of the glycan or amide bonds of the peptide in an energy-resolved manner. Nevertheless, the relative energy requirement for these fragmentation pathways varies considerably among analytes. This research addresses the influence of proton mobility on the vibrational energy necessary to achieve either glycan or peptide cleavage in a collection of protonated N-glycopeptide ions. While greater proton mobility of the precursor ion was found to correlate with lower energy requirements for precursor ion depletion and appearance of glycosidic fragments, the vibrational energy deposition necessary for appearance of peptide backbone fragments showed no relation to the precursor ion proton mobility. These results are consistent with observations suggesting that peptide fragments arise from an intermediate fragment which is generally of lower proton mobility than the precursor ion. Such findings have potential to facilitate the rational selection of CID conditions which are best suited to provide either glycan or peptide cleavage products in MS/MS based N-glycoproteomic analysis.

  4. Trajectory study of energy transfer and unimolecular dissociation of highly excited allyl with argon.

    PubMed

    Conte, Riccardo; Houston, Paul L; Bowman, Joel M

    2014-09-11

    The influence of rotational excitation on energy transfer in single collisions of allyl with argon and on allyl dissociation is investigated. About 90,000 classical scattering simulations are performed in order to determine collision-induced changes in internal energy and in allyl rotational angular momentum. Dissociation is studied by means of about 50,000 additional trajectories evolved for the isolated allyl under three different conditions: allyl with no angular momentum (J = 0); allyl with the same microcanonically sampled initial conditions used for the collisions (J*); allyl evolving from the corresponding exit conditions after the collision. The potential energy surface is the sum of an intramolecular potential and an interaction one, and it has already been used in a previous work on allyl-argon scattering (Conte, R.; Houston, P. L.; Bowman, J. M. J. Phys. Chem. A 2013, 117, 14028-14041). Energy transfer data show that increased initial rotation favors, on average, increased relaxation of the excited molecule. The availability of a high-level intramolecular potential energy surface permits us to study the dependence of energy transfer on the type of starting allyl isomer. A turning point analysis is presented, and highly efficient collisions are detected. Collision-induced variations in the allyl rotational angular momentum may be quite large and are found to be distributed according to three regimes. The roles of rotational angular momentum, collision, and type of isomer on allyl unimolecular dissociation are considered by looking at dissociations times, kinetic energies of the fragments, and branching ratios. Generally, rotational angular momentum has a strong influence on the dissociation dynamics, while the single collision and the type of starting isomer are less influential.

  5. Guilt by dissociation: guilt primes augment the relationship between dissociative tendencies and state dissociation.

    PubMed

    Rugens, Alex; Terhune, Devin Blair

    2013-03-30

    We examined the influence of guilt on the relationship between dissociative tendencies and state dissociation during mirror-gazing in a non-clinical sample. Dissociative tendencies correlated with state dissociation following guilt primes, but not after negative or neutral primes. This suggests that guilt augments the relationship between dissociative tendencies and state dissociation.

  6. Thermal device and method for production of carbon monoxide and hydrogen by thermal dissociation of hydrocarbon gases

    DOEpatents

    Detering, Brent A.; Kong, Peter C.

    2001-01-01

    Carbon monoxide is produced in a fast quench reactor. The production of carbon monoxide includes injecting carbon dioxide and some air into a reactor chamber having a high temperature at its inlet and a rapidly expanding a reactant stream, such as a restrictive convergent-divergent nozzle at its outlet end. Carbon dioxide and other reactants such as methane and other low molecular weight hydrocarbons are injected into the reactor chamber. Other gas may be added at different stages in the process to form a desired end product and prevent back reactions. The resulting heated gaseous stream is then rapidly cooled by expansion of the gaseous stream.

  7. Photodissociation of gaseous CH{sub 3}COSH at 248 nm by time-resolved Fourier-transform infrared emission spectroscopy: Observation of three dissociation channels

    SciTech Connect

    Hu, En-Lan; Tsai, Po-Yu; Fan, He; Lin, King-Chuen

    2013-01-07

    Upon one-photon excitation at 248 nm, gaseous CH{sub 3}C(O)SH is dissociated following three pathways with the products of (1) OCS + CH{sub 4}, (2) CH{sub 3}SH + CO, and (3) CH{sub 2}CO + H{sub 2}S that are detected using time-resolved Fourier-transform infrared emission spectroscopy. The excited state {sup 1}(n{sub O}, {pi}{sup *}{sub CO}) has a radiative lifetime of 249 {+-} 11 ns long enough to allow for Ar collisions that induce internal conversion and enhance the fragment yields. The rate constant of collision-induced internal conversion is estimated to be 1.1 Multiplication-Sign 10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}. Among the primary dissociation products, a fraction of the CH{sub 2}CO moiety may undergo further decomposition to CH{sub 2}+ CO, of which CH{sub 2} is confirmed by reaction with O{sub 2} producing CO{sub 2}, CO, OH, and H{sub 2}CO. Such a secondary decomposition was not observed previously in the Ar matrix-isolated experiments. The high-resolution spectra of CO are analyzed to determine the ro-vibrational energy deposition of 8.7 {+-} 0.7 kcal/mol, while the remaining primary products with smaller rotational constants are recognized but cannot be spectrally resolved. The CO fragment detected is mainly ascribed to the primary production. A prior distribution method is applied to predict the vibrational distribution of CO that is consistent with the experimental findings.

  8. The role of angular momentum in collision-induced vibration-rotation relaxation in polyatomics.

    PubMed

    McCaffery, Anthony J; Osborne, Mark A; Marsh, Richard J; Lawrance, Warren D; Waclawik, Eric R

    2004-07-01

    Vibrational relaxation of the 6(1) level of S(1)((1)B(2u)) benzene is analyzed using the angular momentum model of inelastic processes. Momentum-(rotational) angular momentum diagrams illustrate energetic and angular momentum constraints on the disposal of released energy and the effect of collision partner on resultant benzene rotational excitation. A kinematic "equivalent rotor" model is introduced that allows quantitative prediction of rotational distributions from inelastic collisions in polyatomic molecules. The method was tested by predicting K-state distributions in glyoxal-Ne as well as J-state distributions in rotationally inelastic acetylene-He collisions before being used to predict J and K distributions from vibrational relaxation of 6(1) benzene by H(2), D(2), and CH(4). Diagrammatic methods and calculations illustrate changes resulting from simultaneous collision partner excitation, a particularly effective mechanism in p-H(2) where some 70% of the available 6(1)-->0(0) energy may be disposed into 0-->2 rotation. These results support the explanation for branching ratios in 6(1)-->0(0) relaxation given by Waclawik and Lawrance and the absence of this pathway for monatomic partners. Collision-induced vibrational relaxation in molecules represents competition between the magnitude of the energy gap of a potential transition and the ability of the colliding species to generate the angular momentum (rotational and orbital) needed for the transition to proceed. Transition probability falls rapidly as DeltaJ increases and for a given molecule-collision partner pair will provide a limit to the gap that may be bridged. Energy constraints increase as collision partner mass increases, an effect that is amplified when J(i)>0. Large energy gaps are most effectively bridged using light collision partners. For efficient vibrational relaxation in polyatomics an additional requirement is that the molecular motion of the mode must be capable of generating molecular

  9. Collision-Induced Infrared Absorption by Collisional Complexes in Dense Hydrogen-Helium Gas Mixtures at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2011-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of the outer planets and cool stars. The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 Xiaoping Li, Katharine L. C. Hunt, Fei Wang, Martin Abel, and Lothar Frommhold, "Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin", International Journal of Spectroscopy, vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, "Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin," J. Phys. Chem. A, published online, DOI: 10.1021/jp109441f L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010

  10. Dissociation heat transfer characteristics of methane hydrates

    SciTech Connect

    Kamath, V.A.; Holder, G.D.

    1987-02-01

    Knowledge of the interfacial heat transfer phenomenon during the dissociation of gas hydrates is essential in modeling the hydrate dissociation process. Such knowledge has applications in natural gas processing, storage, or transportation; in the drilling and recovery of oil and gas in the presence of gas hydrates; in the desalination of sea water; and in the production of natural gas from hydrate reservoirs. The process of hydrate dissociation is a unique phenomenon in which gas and water are simultaneously produced at the dissociated hydrate surface and play an important role in the mechanism of heat transfer to hydrates. An earlier study of propane hydrate dissociation showed that hydrate dissociation is a heat-transfer-limited process and somewhat similar to the nucleate boiling of liquids. In the present study, heat transfer limitations for methane hydrate dissociation were studied for two reasons. First, a comparison of the results of this study with propane hydrate was desired. Second, the effect of hydrate structure and gas molecule type on the rate of heat transfer during hydrate dissociation was sought.

  11. Characterization of drug-product-related impurities and variants of a therapeutic monoclonal antibody by higher energy C-trap dissociation mass spectrometry.

    PubMed

    Wang, Deyun; Wynne, Colin; Gu, Flora; Becker, Chris; Zhao, Jia; Mueller, Hans-Martin; Li, Huijuan; Shameem, Mohammed; Liu, Yan-Hui

    2015-01-20

    Mass spectrometry (MS) characterization of recombinant monoclonal antibody (mAb) drugs and their degraded and/or post-translationally modified counterparts, drug-product-related impurities and variants, is critical for successful development of biotherapeutics. Specifically in this study, drug-product-related impurities of an anti-Clostridium difficile IgG1 mAb drug substance were profiled by cation-exchange liquid chromatography (CEX) followed by the CEX peaks being fraction-collected for MS characterization. A reversed-phase liquid chromatography/mass spectrometry (LC/MS) methodology was developed on a Thermo Q-Exactive orbitrap mass spectrometer for (1) accurate mass measurements of the mAb, its CEX fractionated impurities, and their respective heavy chains and light chains and (2) middle-down LC/MS/MS of the light chains and the heavy chains using higher energy C-trap dissociation (HCD). The accurate mass measurements and the HCD middle-down MS/MS experiments identify that major impurities and variants of the anti-C. difficile mAb are degradation species of the heavy chains at residue Asn101 as well as at the hinge region amino acids, including Cys222, Lys224, His226, and Thr227, with levels ranging from 0.3% to 6.2% of the total drug substance. Additional impurities were identified as light chain C-terminal truncation at Gly93 and oxidized heavy chains at Met40, Met93, and Met430. Our impurity characterization results demonstrate that the middle-down MS method allows direct and accurate identification of drug-product-related impurities of therapeutic mAbs. It is particularly useful for those low-level impurities and variants that are not suitable for further fractionation and characterization by bottom-up MS.

  12. Computational prediction of one-electron reduction potentials and acid dissociation constants for guanine oxidation intermediates and products.

    PubMed

    Psciuk, Brian T; Schlegel, H Bernhard

    2013-08-15

    Reduction potentials and pK(a) values were calculated for intermediates and products along three major pathways for guanine oxidation using the B3LYP and CBS-QB3 levels of theory with the SMD implicit solvation model. N-methylated nucleobases were used as models for nucleoside species. Ensemble averaged reduction potentials at pH 7 (E7) were obtained by combining calculated standard reduction potentials with calculated pKa values in addition to accounting for tautomerization energies. Calculated pK(a) values are reasonable based on experimental estimates and chemical intuition. Pathway A leads to guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp). The first step is the oxidation of 8-oxoguanine which proceeds by the loss of an electron followed by the loss of two protons and loss of another electron, yielding 8-oxopurine. The calculated E7 values for the remaining intermediates and products are at least 0.3 V higher than that of guanine, indicating that further oxidation of these species is unlikely. Pathway B leads to two formamidopyrimidine isomers (FAPyG and 2,5FAPyG). Species along this pathway have calculated reduction potentials that are much lower than the oxidation potential for guanine and would likely be very short-lived in an oxidatively stressed environment. Pathway C leads to reduced spiroiminodihydantoin and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). Similar to pathway A, the calculated reduction potentials for species along this pathway are at least 0.4 V higher than that of guanine.

  13. Optimization of electron transfer dissociation via informed selection of reagents and operating parameters.

    PubMed

    Compton, Philip D; Strukl, Joseph V; Bai, Dina L; Shabanowitz, Jeffrey; Hunt, Donald F

    2012-02-07

    Electron transfer dissociation (ETD) has improved the mass spectrometric analysis of proteins and peptides with labile post-translational modifications and larger intact masses. Here, the parameters governing the reaction rate of ETD are examined experimentally. Currently, due to reagent injection and isolation events as well as longer reaction times, ETD spectra require significantly more time to acquire than collision-induced dissociation (CID) spectra (>100 ms), resulting in a trade-off in the dynamic range of tandem MS analyses when ETD-based methods are compared to CID-based methods. Through fine adjustment of reaction parameters and the selection of reagents with optimal characteristics, we demonstrate a drastic reduction in the time taken per ETD event. In fact, ETD can be performed with optimal efficiency in nearly the same time as CID at low precursor charge state (z = +3) and becomes faster at higher charge state (z > +3).

  14. Assessing the weights of visual neglect: a new approach to dissociate defective symptoms from productive phenomena in length estimation.

    PubMed

    Charras, Pom; Lupiáñez, Juan; Bartolomeo, Paolo

    2010-09-01

    Right hemisphere damage often provokes signs of visual neglect, characterized by a prominent left-right imbalance in information processing. Neglect patients are biased towards right-sided objects and ignore left-sided events. Left-right imbalance may not only result from left neglect but also from right attraction, which have been considered as, respectively, defective and productive phenomena in neglect patients. However, the relative contributions of these two mechanisms to the final left-right imbalance remain uncertain. Using a novel experimental paradigm, we were able to separately test the contribution of left neglect and right attraction to neglect behavior. We used horizontal and vertical lines implemented in L shapes in a line extension task. The use of L shapes oriented either to the left or to the right made it possible to measure the left bias by comparing the length of a left-sided horizontal line to that of a centered vertical line, and to measure the right bias by comparing a centered vertical to a rightwards horizontal line. Our results showed that, in this experimental set, the left-right discrepancy is supported more by left neglect than by right attraction, with important implications about the role of left-right competition on the deployment of left neglect and right attraction.

  15. Relativistic MHD Simulations of Collision-induced Magnetic Dissipation in Poynting-flux-dominated Jets/outflows

    NASA Astrophysics Data System (ADS)

    Deng, Wei; Li, Hui; Zhang, Bing; Li, Shengtai

    2015-06-01

    We perform 3D relativistic ideal magnetohydrodynamics (MHD) simulations to study the collisions between high-σ (Poynting-flux-dominated (PFD)) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable PFD jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvénic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in the relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. Our results give support to the proposed astrophysical models that invoke significant magnetic energy dissipation in PFD jets, such as the internal collision-induced magnetic reconnection and turbulence model for gamma-ray bursts, and reconnection triggered mini jets model for active galactic nuclei. The simulation movies are shown in http://www.physics.unlv.edu/∼deng/simulation1.html.

  16. Relativistic MHD simulations of collision-induced magnetic dissipation in poynting-flux-dominated jets/outflows

    DOE PAGES

    Deng, Wei; Li, Hui; Zhang, Bing; ...

    2015-05-29

    We perform 3D relativistic ideal MHD simulations to study the collisions between high-σ (Poynting- ux-dominated) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable Poynting- ux-dominated jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvenic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in themore » relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini-jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. In conclusion, our results give support to the proposed astrophysical models that invoke signi cant magnetic energy dissipation in Poynting- ux-dominated jets, such as the internal collision-induced magnetic reconnection and turbulence (ICMART) model for GRBs, and reconnection triggered mini-jets model for AGNs.« less

  17. RELATIVISTIC MHD SIMULATIONS OF COLLISION-INDUCED MAGNETIC DISSIPATION IN POYNTING-FLUX-DOMINATED JETS/OUTFLOWS

    SciTech Connect

    Deng, Wei; Zhang, Bing; Li, Hui; Li, Shengtai E-mail: zhang@physics.unlv.edu E-mail: sli@lanl.gov

    2015-06-01

    We perform 3D relativistic ideal magnetohydrodynamics (MHD) simulations to study the collisions between high-σ (Poynting-flux-dominated (PFD)) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable PFD jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvénic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in the relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. Our results give support to the proposed astrophysical models that invoke significant magnetic energy dissipation in PFD jets, such as the internal collision-induced magnetic reconnection and turbulence model for gamma-ray bursts, and reconnection triggered mini jets model for active galactic nuclei. The simulation movies are shown in http://www.physics.unlv.edu/∼deng/simulation1.html.

  18. Far-infrared collision-induced absorption in rare gas mixtures: Quantum and semi-classical calculations

    SciTech Connect

    Buryak, Ilya; Frommhold, Lothar; Vigasin, Andrey A.

    2014-04-21

    We compare calculations of the translational collision-induced spectra and their integrated intensities of both He–Ar and Ne–Ar collisional complexes, using the quantum mechanical and a semiclassical formalism. Advanced potential energy and induced dipole functions are used for the calculations. The quantum method used is as described previously [L. Frommhold, Collision-induced Absorption in Gases (Cambridge University Press, 1993 and 2006)]. The semiclassical method is based on repeated classical atom-atom scattering calculations to simulate an ensemble average; subsequent Fourier transform then renders the binary absorption coefficient as a function of frequency. The problem of classical calculations is the violation of the principle of detailed balance, which may be introduced only artificially in classical calculations. Nevertheless, it is shown that the use of classical trajectories permits a fairly accurate reproduction of the experimental spectra, comparable to the quantum mechanical results at not too low temperatures and for collisional pairs of not too small reduced mass. Inexpensive classical calculations may thus be promising to compute spectra also of molecular pairs, or even of polyatomic collisional pairs with anisotropic intermolecular interactions, for which the quantum approach is still inefficient or impractical.

  19. Relativistic MHD simulations of collision-induced magnetic dissipation in poynting-flux-dominated jets/outflows

    SciTech Connect

    Deng, Wei; Li, Hui; Zhang, Bing; Li, Shengtai

    2015-05-29

    We perform 3D relativistic ideal MHD simulations to study the collisions between high-σ (Poynting- ux-dominated) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable Poynting- ux-dominated jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvenic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in the relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini-jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. In conclusion, our results give support to the proposed astrophysical models that invoke signi cant magnetic energy dissipation in Poynting- ux-dominated jets, such as the internal collision-induced magnetic reconnection and turbulence (ICMART) model for GRBs, and reconnection triggered mini-jets model for AGNs.

  20. Thermal Dissociation of Halogen Azides

    DTIC Science & Technology

    1994-09-01

    inefficient due to the low gain provided by this emitter and the short duration of the shock tube experiment . Much higher gain coefficients were...with the SF6 sensitizers (in the C02 laser triggered experiment ) and thermal dissociation of the tetraazldodiborane donor ;nto non-productive...Excitation of FN3/S2CI 2/SF6 gas mixtures by the pulsed C02 laser yielded NS(B-X) chemiluminescence 5 . Cold trap experiments showed that small levels

  1. Dissociative Ionization of Pyridine by Electron Impact

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher; Huo, Winifred; Kwak, Dochan (Technical Monitor)

    2002-01-01

    In order to understand the damage of biomolecules by electrons, a process important in radiation damage, we undertake a study of the dissociative ionization (DI) of pyridine (C5H5N) from the low-lying ionization channels. The methodology used is the same as in the benzene study. While no experimental DI data are available, we compare the dissociation products from our calculations with the dissociative photoionization measurements of Tixier et al. using dipole (e, e(+) ion) coincidence spectroscopy. Comparisons with the DI of benzene is also made so as to understand the difference in DI between a heterocyclic and an aromatic molecule.

  2. Collision-induced absorption with exchange effects and anisotropic interactions: Theory and application to H{sub 2} − H{sub 2}

    SciTech Connect

    Karman, Tijs; Avoird, Ad van der; Groenenboom, Gerrit C.

    2015-02-28

    We discuss three quantum mechanical formalisms for calculating collision-induced absorption spectra. First, we revisit the established theory of collision-induced absorption, assuming distinguishable molecules which interact isotropically. Then, the theory is rederived incorporating exchange effects between indistinguishable molecules. It is shown that the spectrum can no longer be written as an incoherent sum of the contributions of the different spherical components of the dipole moment. Finally, we derive an efficient method to include the effects of anisotropic interactions in the computation of the absorption spectrum. This method calculates the dipole coupling on-the-fly, which allows for the uncoupled treatment of the initial and final states without the explicit reconstruction of the many-component wave functions. The three formalisms are applied to the collision-induced rotation-translation spectra of hydrogen molecules in the far-infrared. Good agreement with experimental data is obtained. Significant effects of anisotropic interactions are observed in the far wing.

  3. Narrative, dialogue, and dissociation.

    PubMed

    Gedo, Paul M

    2014-02-01

    This paper explores dissociative phenomena as disruptions of dialogue between persons, and disruptions of internal narratives. A dissociating patient temporarily loses ability to convey his or her inner experience to the therapist. The disconnection between dialogue and internal experience can mislead both participants, or distract them from underlying connotations. Dissociation also disrupts the patient's sense of internal coherence and internal conversation. Dissociation represents a regression to an early, preverbal mode of (internal and external) communication. The challenge for the dyad is to restore dialogue and then to discern the multiply determined meanings of the dissociative communication. This therapeutic work allows the patient to achieve a more coherent sense of self and of his or her life course.

  4. Dissociative Ionization of Benzene by Electron Impact

    NASA Technical Reports Server (NTRS)

    Huo, Winifred; Dateo, Christopher; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We report a theoretical study of the dissociative ionization (DI) of benzene from the low-lying ionization channels. Our approach makes use of the fact that electron motion is much faster than nuclear motion and DI is treated as a two-step process. The first step is electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model. For the unimolecular dissociation step, we study the steepest descent reaction path to the minimum of the ion potential energy surface. The path is used to analyze the probability of unimolecular dissociation and to determine the product distributions. Our analysis of the dissociation products and the thresholds of the productions are compared with the result dissociative photoionization measurements of Feng et al. The partial oscillator strengths from Feng et al. are then used in the iBED cross section calculations.

  5. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.

    PubMed

    Tabb, David L; Huang, Yingying; Wysocki, Vicki H; Yates, John R

    2004-03-01

    The primary utility of trypsin digestion in proteomics is that it cleaves proteins at predictable locations, but it is also notable for yielding peptides that terminate in basic arginine and lysine residues. Tryptic peptides fragment in ion trap tandem mass spectrometry to produce prominent C-terminal y series ions. Alternative proteolytic digests may produce peptides that do not follow these rules. In this study, we examine 2568 peptides generated through proteinase K digestion, a technique that produces a greater diversity of basic residue content in peptides. We show that the position of basic residues within peptides influences the peak intensities of b and y series ions; a basic residue near the N-terminus of a peptide can lead to prominent b series peaks rather than the intense y series peaks associated with tryptic peptides. The effects of presence and position for arginine, lysine, and histidine are explored separately and in combination. Arg shows the most dominant effects followed by His and then by Lys. Fragment ions containing basic residues produce more intense peaks than those without basic residues. Doubly charged precursor ions have generally been modeled as producing only singly charged fragment ions, but fragment ions that contain two basic residues may accept both protons during fragmentation. By characterizing the influence of basic residues on gas-phase fragmentation of peptides, this research makes possible more accurate fragmentation models for peptide identification algorithms.

  6. ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer.

    PubMed

    Zhang, Ning; Li, Xiao-jun; Ye, Mingliang; Pan, Sheng; Schwikowski, Benno; Aebersold, Ruedi

    2005-11-01

    In MS/MS experiments with automated precursor ion, selection only a fraction of sequencing attempts lead to the successful identification of a peptide. A number of reasons may contribute to this situation. They include poor fragmentation of the selected precursor ion, the presence of modified residues in the peptide, mismatches with sequence databases, and frequently, the concurrent fragmentation of multiple precursors in the same CID attempt. Current database search engines are incapable of correctly assigning the sequences of multiple precursors to such spectra. We have developed a search engine, ProbIDtree, which can identify multiple peptides from a CID spectrum generated by the concurrent fragmentation of multiple precursor ions. This is achieved by iterative database searching in which the submitted spectra are generated by subtracting the fragment ions assigned to a tentatively matched peptide from the acquired spectrum and in which each match is assigned a tentative probability score. Tentatively matched peptides are organized in a tree structure from which their adjusted probability scores are calculated and used to determine the correct identifications. The results using MALDI-TOF-TOF MS/MS data demonstrate that multiple peptides can be effectively identified simultaneously with high confidence using ProbIDtree.

  7. Identification of Foodborne Bacteria by High Energy Collision-Induced Dissociation of Their Protein Biomarkers by MALDI Tandem-Time-of-Flight Mass Spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of methods for rapid identification of foodborne bacteria is an important area of analytical science and food safety. MALDI-TOF-MS has been utilized to rapidly identify pathogens including foodborne bacteria. Identification typically involves detection of high copy cytosolic proteins i...

  8. Structural analysis of a heteropolysaccharide from Saccharina japonica by electrospray mass spectrometry in tandem with collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS).

    PubMed

    Jin, Weihua; Wang, Jing; Ren, Sumei; Song, Ni; Zhang, Quanbin

    2012-10-01

    A fucoidan extracted from Saccharina japonica was fractionated by anion exchange chromatography. The most complex fraction F0.5 was degraded by dilute sulphuric acid and then separated by use of an activated carbon column. Fraction Y1 was fractionated by anion exchange and gel filtration chromatography while Fraction Y2 was fractionated by gel filtration chromatography. The fractions were determined by ESI-MS and analyzed by ESI-CID-MS/MS. It was concluded that F0.5 had a backbone of alternating 4-linked GlcA and 2-linked Man with the first Man residue from the nonreducing end accidentally sulfated at C6. In addition, F0.5 had a 3-linked glucuronan, in accordance with a previous report by NMR. Some other structural characteristics included GlcA 1→3 Man 1→4 GlcA, Man 1→3 GlcA 1→4 GlcA, Fuc 1→4 GlcA and Fuc 1→3 Fuc. Finally, it was shown that fucose was sulfated at C2 or C4 while galactose was sulfated at C2, C4 or C6.

  9. An Unusual Family of Glycosylated Peptides Isolated from Dendroaspis angusticeps Venom and Characterized by Combination of Collision Induced and Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Quinton, Loïc; Gilles, Nicolas; Smargiasso, Nicolas; Kiehne, Andrea; de Pauw, Edwin

    2011-11-01

    This study describes the structural characterization of a totally new family of peptides from the venom of the snake green mamba ( Dendroaspis angusticeps). Interestingly, these peptides differ in several points from other already known mamba toxins. First of all, they exhibit very small molecular masses, ranging from 1.3 to 2.4 kDa. The molecular mass of classical mamba toxins is in the range of 7 to 25 kDa. Second, the new peptides do not contain disulfide bonds, a post-translational modification commonly encountered in animal toxins. The third difference is the very high proportion of proline residues in the sequence accounting for about one-third of the sequence. Finally, these new peptides reveal a carbohydrate moiety, indicating a glycosylation in the sequence. The last two features have made the structural characterization of the new peptides by mass spectrometry a real analytical challenge. Peptides were characterized by a combined use of MALDI- TOF/TOF and nanoESI-IT-ETD experiments to determine not only the peptide sequence but also the composition and the position of the carbohydrate moiety. Anyway, such small glycosylated and proline-rich toxins are totally different from any other known snake peptide and form, as a consequence, a new family of peptides.

  10. Dissociative Identity Disorder

    PubMed Central

    2009-01-01

    A brief description of the controversies surrounding the diagnosis of dissociative identity disorder is presented, followed by a discussion of the proposed similarities and differences between dissociative identity disorder and borderline personality disorder. The phenomenon of autohypnosis in the context of early childhood sexual trauma and disordered attachment is discussed, as is the meaning of alters or alternate personalities. The author describes recent neurosciences research that may relate the symptoms of dissociative identity disorder to demonstrable disordered attention and memory processes. A clinical description of a typical patient presentation is included, plus some recommendations for approaches to treatment. PMID:19724751

  11. Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides.

    PubMed

    Ledvina, Aaron R; Chung, Thomas W; Hui, Renjie; Coon, Joshua J; Tureček, Frantisek

    2012-08-01

    Dissociations of z(4) ions from pentapeptides AAXAR where X=H, Y, F, W, and V produce dominant z(2) ions that account for >50 % of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z(4) ions proceed by amide trans→cis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable C(β) radical intermediates. These undergo rate-determining cleavage of the C(α)-CO bond at the X residue followed by loss of the neutral AX fragment, forming x(2) intermediates. The latter were detected by energy-resolved resonant excitation collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments. The x(2) intermediates undergo facile loss of HNCO to form z(2) fragment ions, as also confirmed by energy-resolved CID and IRMPD MS(4) experiments. The loss of HNCO from the x(2) ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate.

  12. Dissociation of biomolecules using a ultraviolet matrix-assisted laser desorption/ionisation time-of-flight/curved field reflectron tandem mass spectrometer equipped with a differential-pumped collision cell.

    PubMed

    Belgacem, Omar; Bowdler, Andrew; Brookhouse, Ian; Brancia, Francesco L; Raptakis, Emmanuel

    2006-01-01

    A commercial matrix-assisted laser desorption/ionisation time-of-flight (MALDI-ToF) instrument equipped with a curved field reflectron (CFR) was modified in order to perform collision-induced dissociation (CID) on a variety of biomolecules. The incorporation of a high-resolution ion gate together with a collision cell within the field-free region allowed tandem mass analysis (MS/MS), without the necessity to decelerate the precursor ions prior to activation. The simultaneous detection of all product ions remained possible by using the CFR. To test the MS/MS performances, ACTH (fragment 1-17), a complex high mannose carbohydrate (Man)(8)(GlcNac)(2) and a lysophosphatidylcholine lipid (18:1) were analysed on the modified instrument. Direct comparison with the low-energy product ion spectra, acquired on a MALDI quadrupole ion trap (QIT) two-stage reflectron time-of flight (ReToF) mass spectrometer, showed significant differences in the types of product ions observed. The additional ions detected were a clear indication of the high-energy fragmentation processes occurring in the collision cell.

  13. ION PAIR DISSOCIATION: Spectroscopy and Dynamics

    NASA Astrophysics Data System (ADS)

    Suits, Arthur G.; Hepburn, John W.

    2006-05-01

    Ion pair dissociation processes may be studied using coherent vacuum ultraviolet laser sources in a manner entirely analogous to photoelectron spectroscopy, albeit with the anion playing the role of a heavy electron. If the excitation energy is above the dissociation energy and the kinetic energy of the fragment is measured using ion imaging, this approach is termed ion pair imaging spectroscopy (IPIS) and is related to conventional photoelectron spectroscopy. If the excitation energy is just below the dissociation energy and pulsed-field dissociation is employed, this approach is analogous to mass analyzed threshold ionization (MATI) spectroscopy and is termed threshold ion pair production spectroscopy (TIPPS). These approaches provide a novel means of investigating ion thermochemistry and spectroscopy and superexcited state decay dynamics at high resolution.

  14. Infrared collision-induced absorption by O2 near 6.4 microm for atmospheric applications: measurements and empirical modeling.

    PubMed

    Thibault, F; Menoux, V; Le Doucen, R; Rosenmann, L; Hartmann, J M; Boulet, C

    1997-01-20

    Accurate measurements of collision-induced absorption by O(2) and O(2)-N(2) mixtures in the fundamental band near 6.4 microm have been made. A Fourier-transform spectrometer was used with a resolution of 0.5 cm(-1). Absorption has been investigated in the 0-20-atm and 193-293 K pressure and temperature ranges, respectively. The current measurements confirm that the broad O(2) continuum carries small features whose attribution is not yet clear. Available experimental data in the 190-360 K temperature range have been used to build a simple, low cost computer, empirical model that is well adapted for computation of atmospheric O(2) absorption. Tests show that it is accurate, contrary to predictions of widely used atmospheric transmission codes.

  15. Modeling of collision induced absorption spectra of CO2-CO2 pairs for planetary atmosphere of Venus

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra

    1995-01-01

    The objective of the proposal was to model the rototranslational and rotovibrational collision induced absorption spectral bands of importance for the radiative transfer analysis of the atmosphere of Venus. Our main task has involved CO2 pairs. The approach is not straightforward: whereas computational techniques to compute CIA spectra of small linear molecules exist, and were successfully applied to molecules like H2 or N2, they fail when applied to large molecules like CO2. For small molecules one can safely assume that the interaction potential is isotropic. The same approximation does not work for CO2, and when employed, it gives an incorrect band shape and only 50 percent of the CIA intensity.

  16. Collision-induced absorption by N2 near 2.16 µm: Calculations, model, and consequences for atmospheric remote sensing

    NASA Astrophysics Data System (ADS)

    Hartmann, J.-M.; Boulet, C.; Toon, G. C.

    2017-02-01

    Classical molecular dynamics simulations (CMDS) are used for calculations of the collision-induced absorption (CIA) by pure N2 in the (2.1-2.2 µm) region of the first overtone band. They lead to reasonable (±15%) agreement with the only two laboratory measurements available, at 97 K and room temperature. Based on these experiment/theory comparisons, empirical corrections are made to the CMDS-calculated CIA of pure N2 in the 200-300 K temperature range. In addition, the contribution of N2-O2 collisions is, in the absence of any laboratory measurement, calculated and a simple semiempirical model (the first of its kind) is built in order to predict the CIA of N2 under Earth atmosphere conditions. This is successfully validated by comparisons with ground-based atmospheric transmission spectra in the 2.1-2.2 µm region.

  17. Mechanistic examination of Cβ-Cγ bond cleavages of tryptophan residues during dissociations of molecular peptide radical cations.

    PubMed

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [G(n)W](•+) (n = 2-4) and [GXW](•+) (X = C, S, L, F, Y, Q) species. The C(β)-C(γ) bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO(2)](•+)) can generate [M - CO(2) - 116](+), [M - CO(2) - 117](•+), and [1H-indole](•+) (m/z 117) species as possible product ions. Competition between the formation of [M - CO(2) - 116](+) and [1H-indole](•+) systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2, the decarboxylated species that is active against C(β)-C(γ) bond cleavage, can efficiently isomerize to form a more stable π-radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The C(β)-C(γ) bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WG(n)R](•+) (n = 1-3) radical cations consistently resulted in predominant formation of [M - 116](+) product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote C(β)-C(γ) bond cleavage to prevail over the charge-directed one. DFT calculations predicted that the barrier for the former is 6.2 kcal mol(-1) lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  18. Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

    SciTech Connect

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  19. Dissociative Recombination Chemistry and Plasma Dynamics

    DTIC Science & Technology

    2008-06-16

    the fractional square of product momentum with product momentum vectors . Qx and Qy denote the degenerate bend two-body dissociation limits...with product momentum vectors . Qx and Qy denote the degenerate bend normal modes for C2v symmetry H2D and HD2 isomers of H3. symmetry for the Qx...heavy (D atom) products in general receive a greater partitioning of energy than the light product. This may have important implications for

  20. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF).

  1. Dissociative disorders in medical settings.

    PubMed

    MacPhee, Edward

    2013-10-01

    Despite the challenges of conducting research on dissociation and the dissociative disorders, our understanding has grown greatly over the past three decades, including our knowledge of the often overlooked sensorimotor manifestations of dissociation, more commonly referred to as somatoform dissociation. This article will first review the definitions and presentations of dissociation in general along with recent research on the concept of somatoform dissociation. Then, each of the dissociative disorders and conversion disorder will be discussed in further detail as well as how they might present in a medical setting. Current recommendations for diagnosis and treatment will also be provided.

  2. The role of water in gas hydrate dissociation

    USGS Publications Warehouse

    Circone, S.; Stern, L.A.; Kirby, S.H.

    2004-01-01

    When raised to temperatures above the ice melting point, gas hydrates release their gas in well-defined, reproducible events that occur within self-maintained temperature ranges slightly below the ice point. This behavior is observed for structure I (carbon dioxide, methane) and structure II gas hydrates (methane-ethane, and propane), including those formed with either H2O- or D2O-host frameworks, and dissociated at either ambient or elevated pressure conditions. We hypothesize that at temperatures above the H2O (or D2O) melting point: (1) hydrate dissociation produces water + gas instead of ice + gas, (2) the endothermic dissociation reaction lowers the temperature of the sample, causing the water product to freeze, (3) this phase transition buffers the sample temperatures within a narrow temperature range just below the ice point until dissociation goes to completion, and (4) the temperature depression below the pure ice melting point correlates with the average rate of dissociation and arises from solution of the hydrate-forming gas, released by dissociation, in the water phase at elevated concentrations. In addition, for hydrate that is partially dissociated to ice + gas at lower temperatures and then heated to temperatures above the ice point, all remaining hydrate dissociates to gas + liquid water as existing barriers to dissociation disappear. The enhanced dissociation rates at warmer temperatures are probably associated with faster gas transport pathways arising from the formation of water product.

  3. Dissociation of diatomic gases

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1991-01-01

    The Landau-Zener theory of reactive cross sections has been applied to diatomic molecules dissociating from a ladder of rotational and vibrational states. Although the preexponential factor of the Arrhenius rate expression is shown to be a complex function of the dimensionless activation energy, the average over all states in the ladder is well represented by a single factor that varies about as T exp (-n), where the coefficient n is the order of unity. This relation agrees very well with experimental data for dissociation of O2 and N2, for example. The results validate previous empirical assignment of a single preexponential factor in the Arrhenius expression and justify the extrapolation of the expression well beyond the range of data. The theory is then used to calculate the effect of vibrational nonequilibrium on dissociation rate. For Morse oscillators the results are about the same as for harmonic oscillators, and the dissociation from a ladder of equilibrium rotational and nonequilibrium vibrational states is close to an analytic approximation provided by Hammerling, Kivel, and Teare for harmonic oscillators all dissociating from the ground rotational state.

  4. Isotope separation by photoselective dissociative electron capture

    DOEpatents

    Stevens, Charles G. [Pleasanton, CA

    1978-08-29

    A method of separating isotopes based on photoselective electron capture dissociation of molecules having an electron capture cross section dependence on the vibrational state of the molecule. A molecular isotope source material is irradiated to selectively excite those molecules containing a desired isotope to a predetermined vibrational state having associated therewith an electron capture energy region substantially non-overlapping with the electron capture energy ranges associated with the lowest vibration states of the molecules. The isotope source is also subjected to electrons having an energy corresponding to the non-overlapping electron capture region whereby the selectively excited molecules preferentially capture electrons and dissociate into negative ions and neutrals. The desired isotope may be in the negative ion product or in the neutral product depending upon the mechanism of dissociation of the particular isotope source used. The dissociation product enriched in the desired isotope is then separated from the reaction system by conventional means. Specifically, .sup.235 UF.sub.6 is separated from a UF.sub.6 mixture by selective excitation followed by dissociative electron capture into .sup.235 UF.sub.5 - and F.

  5. Isotope separation by photoselective dissociative electron capture

    DOEpatents

    Stevens, C.G.

    1978-08-29

    Disclosed is a method of separating isotopes based on photoselective electron capture dissociation of molecules having an electron capture cross section dependence on the vibrational state of the molecule. A molecular isotope source material is irradiated to selectively excite those molecules containing a desired isotope to a predetermined vibrational state having associated therewith an electron capture energy region substantially non-overlapping with the electron capture energy ranges associated with the lowest vibration states of the molecules. The isotope source is also subjected to electrons having an energy corresponding to the non-overlapping electron capture region whereby the selectively excited molecules preferentially capture electrons and dissociate into negative ions and neutrals. The desired isotope may be in the negative ion product or in the neutral product depending upon the mechanism of dissociation of the particular isotope source used. The dissociation product enriched in the desired isotope is then separated from the reaction system by conventional means. Specifically, [sup 235]UF[sub 6] is separated from a UF[sub 6] mixture by selective excitation followed by dissociative electron capture into [sup 235]UF[sub 5]- and F. 2 figs.

  6. Formation, isomerization, and dissociation of alpha-carbon-centered and pi-centered glycylglycyltryptophan radical cations

    SciTech Connect

    Ng, Dominic C.; Song, Tao; Siu, Shiu On; Siu, Chi-Kit; Laskin, Julia; Chu, Ivan K.

    2010-02-11

    Gas phase fragmentations of two isomeric radical cationic tripeptides of glycylglycyltryptophan-G•GW+ and [GGW]•+—with well-defined initial radical sites at the α-carbon atom and the 3-methylindole ring, respectively, have been studied using collision-induced dissociation (CID), density functional theory (DFT), and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Substantially different low-energy CID spectra were obtained for these two isomeric GGW structures, suggesting that they did not interconvert on the time scale of these experiments. DFT and RRKM calculations were used to investigate the influence of the kinetics, stabilities, and locations of the radicals on the competition between the isomerization and dissociation channels. The calculated isomerization barrier between the GGW radical cations (>35.4 kcal/mol) was slightly higher than the barrier for competitive dissociation of these species (<30.5 kcal/mol); the corresponding microcanonical rate constants for isomerization obtained from RRKM calculations were all considerably lower than the dissociation rates at all internal energies. Thus, interconversion between the GGW isomers examined in this study cannot compete with their fragmentations.

  7. Alternate dissociation pathways identified in charge-reduced protein complex ions.

    PubMed

    Pagel, Kevin; Hyung, Suk-Joon; Ruotolo, Brandon T; Robinson, Carol V

    2010-06-15

    Tandem mass spectrometry (MS) of large protein complexes has proven to be capable of assessing the stoichiometry, connectivity, and structural details of multiprotein assemblies. While the utility of tandem MS is without question, a deeper understanding of the mechanism of protein complex dissociation will undoubtedly drive the technology into new areas of enhanced utility and information content. We present here the systematic analysis of the charge state dependent decay of the noncovalently associated complex of human transthyretin, generated by collision-induced dissociation (CID). A crown ether based charge reduction approach was applied to generate intact transthyretin tetramers with charge states ranging from 15+ to 7+. These nine charge states were subsequently analyzed by means of tandem MS and ion mobility spectrometry. Three different charge-dependent mechanistic regimes were identified: (1) common asymmetric dissociation involving ejection of unfolded monomers, (2) expulsion of folded monomers from the intact tetramer, and (3) release of C-terminal peptide fragments from the intact complex. Taken together, the results presented highlight the potential of charge state modulation as a method for directing the course of gas-phase dissociation and unfolding of protein complexes.

  8. Characterization of Tyrosine Nitration and Cysteine Nitrosylation Modifications by Metastable Atom-Activation Dissociation Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Cook, Shannon L.; Jackson, Glen P.

    2011-02-01

    The fragmentation behavior of nitrated and S-nitrosylated peptides were studied using collision induced dissociation (CID) and metastable atom-activated dissociation mass spectrometry (MAD-MS). Various charge states, such as 1+, 2+, 3+, 2-, of modified and unmodified peptides were exposed to a beam of high kinetic energy helium (He) metastable atoms resulting in extensive backbone fragmentation with significant retention of the post-translation modifications (PTMs). Whereas the high electron affinity of the nitrotyrosine moiety quenches radical chemistry and fragmentation in electron capture dissociation (ECD) and electron transfer dissociation (ETD), MAD does produce numerous backbone cleavages in the vicinity of the modification. Fragment ions of nitrosylated cysteine modifications typically exhibit more abundant neutral losses than nitrated tyrosine modifications because of the extremely labile nature of the nitrosylated cysteine residues. However, compared with CID, MAD produced between 66% and 86% more fragment ions, which preserved the labile -NO modification. MAD was also able to differentiate I/L residues in the modified peptides. MAD is able to induce radical ion chemistry even in the presence of strong radical traps and therefore offers unique advantages to ECD, ETD, and CID for determination of PTMs such as nitrated and S-nitrosylated peptides.

  9. Rapidly Alternating Transmission Mode Electron Transfer Dissociation and Collisional Activation for the Characterization of Polypeptide Ions

    PubMed Central

    Han, Hongling; Xia, Yu; Yang, Min; McLuckey, Scott A.

    2009-01-01

    Cation transmission/electron transfer reagent anion storage mode electron transfer ion/ion reactions and beam-type collisional activation of the polypeptide ions are performed in rapid succession in the high pressure collision cell (Q2) of a quadrupole/time-of-flight tandem mass spectrometer (QqTOF), where the electron transfer reagent anions are accumulated. Duty cycles for both electron transfer dissociation (ETD) and collision-induced dissociation (CID) experiments are improved relative to ion trapping approaches since there are no discrete ion storage and reaction steps for ETD experiments and no discrete ion storage step and frequency tuning for CID experiments. For this technique, moderately high resolution and mass accuracy are also obtained due to mass analysis via the TOF analyzer. This relatively simple approach has been demonstrated with a triply charged tryptic peptide, a triply charged tryptic phosphopeptide, and a triply charged tryptic N-linked glycopeptide. For the tryptic peptide, the sequence is identified with more certainty than would be available from a single method alone due to the complementary information provided by these two dissociation methods. Because of the complementary information derived from both ETD and CID dissociation methods, peptide sequence and post-translational modification (PTM) sites for the phosphopeptide are identified. This combined ETD and CID approach is particularly useful for characterizing glycopeptides because ETD generates information about both peptide sequence and locations of the glycosylation sites while CID provides information about the glycan structure. PMID:18396915

  10. Psychophysiology of dissociated consciousness.

    PubMed

    Bob, Petr

    2014-01-01

    Recent study of consciousness provides an evidence that there is a limit of consciousness, which presents a barrier between conscious and unconscious processes. This barrier likely is specifically manifested as a disturbance of neural mechanisms of consciousness that through distributed brain processing, attentional mechanisms and memory processes enable to constitute integrative conscious experience. According to recent findings a level of conscious integration may change during certain conditions related to experimental cognitive manipulations, hypnosis, or stressful experiences that can lead to dissociation of consciousness. In psychopathological research the term dissociation was proposed by Pierre Janet for explanation of processes related to splitting of consciousness due to traumatic events or during hypnosis. According to several recent findings dissociation of consciousness likely is related to deficits in global distribution of information and may lead to heightened levels of "neural complexity" that reflects brain integration or differentiation based on numbers of independent neural processes in the brain that may be specifically related to various mental disorders.

  11. Communication: Quasiclassical trajectory calculations of correlated product-state distributions for the dissociation of (H2O)2 and (D2O)2

    NASA Astrophysics Data System (ADS)

    Czakó, Gábor; Wang, Yimin; Bowman, Joel M.

    2011-10-01

    Stimulated by recent experiments [B. E. Rocher-Casterline, L. C. Ch'ng, A. K. Mollner, and H. Reisler, J. Chem. Phys. 134, 211101 (2011)], we report quasiclassical trajectory calculations of the dissociation dynamics of the water dimer, (H2O)2 (and also (D2O)2) using a full-dimensional ab initio potential energy surface. The dissociation is initiated by exciting the H-bonded OH(OD)-stretch, as done experimentally for (H2O)2. Normal mode analysis of the fragment pairs is done and the correlated vibrational populations are obtained by (a) standard histogram binning (HB), (b) harmonic normal-mode energy-based Gaussian binning (GB), and (c) a modified version of (b) using accurate vibrational energies obtained in the Cartesian space. We show that HB allows opening quantum mechanically closed states, whereas GB, especially via (c), gives physically correct results. Dissociation of both (H2O)2 and (D2O)2 mainly produces either fragment in the bending excited (010) state. The H2O(J) and D2O(J) rotational distributions are similar, peaking at J = 3-5. The computations do not show significant difference between the ro-vibrational distributions of the donor and acceptor fragments. Diffusion Monte Carlo computations are performed for (D2O)2 providing an accurate zero-point energy of 7247 cm-1, and thus, a benchmark D0 of 1244 ± 5 cm-1.

  12. Reading aloud in jargonaphasia: an unusual dissociation in speech output.

    PubMed Central

    Semenza, C; Cipolotti, L; Denes, G

    1992-01-01

    A patient is described who showed several dissociations between oral and written language processing after bilateral retrorolandic vascular lesion. Dissociation was firstly between abolished auditory comprehension and preserved written comprehension and then involved confrontation naming, clearly superior in the written modality. The third striking dissociation involved oral output; spontaneous speech, although fluent and well articulated, consisted of neologistic jargon, while reading aloud was clearly superior though not perfect. Data are discussed with reference to a cognitive model of word processing. The pattern of dissociation in word production may be due to a failure in retrieving the phonological word form from the semantic system. Images PMID:1564482

  13. Reading aloud in jargonaphasia: an unusual dissociation in speech output.

    PubMed

    Semenza, C; Cipolotti, L; Denes, G

    1992-03-01

    A patient is described who showed several dissociations between oral and written language processing after bilateral retrorolandic vascular lesion. Dissociation was firstly between abolished auditory comprehension and preserved written comprehension and then involved confrontation naming, clearly superior in the written modality. The third striking dissociation involved oral output; spontaneous speech, although fluent and well articulated, consisted of neologistic jargon, while reading aloud was clearly superior though not perfect. Data are discussed with reference to a cognitive model of word processing. The pattern of dissociation in word production may be due to a failure in retrieving the phonological word form from the semantic system.

  14. The dissociative recombination of ?

    NASA Astrophysics Data System (ADS)

    Laubé, S.; Lehfaoui, L.; Rowe, B. R.; Mitchell, J. B. A.

    1998-09-01

    The dissociative recombination rate coefficient for 0953-4075/31/18/016/img2 has been measured at 300 K using a flowing afterglow Langmuir probe-mass spectrometer apparatus. A value of 0953-4075/31/18/016/img3 has been found.

  15. Dissociative Identity Disorder

    ERIC Educational Resources Information Center

    Schmidt, Tom

    2007-01-01

    Few psychological disorders in the Diagnostic Statistical Manual have generated as much controversy as Dissociative Identity Disorder (DID). For the past 35 years diagnoses of DID, previously referred to as Multiple Personality Disorder (MPD), have increased exponentially, causing various psychological researchers and clinicians to question the…

  16. Functional (dissociative) retrograde amnesia.

    PubMed

    Markowitsch, H J; Staniloiu, A

    2017-01-01

    Retrograde amnesia is described as condition which can occur after direct brain damage, but which occurs more frequently as a result of a psychiatric illness. In order to understand the amnesic condition, content-based divisions of memory are defined. The measurement of retrograde memory is discussed and the dichotomy between "organic" and "psychogenic" retrograde amnesia is questioned. Briefly, brain damage-related etiologies of retrograde amnesia are mentioned. The major portion of the review is devoted to dissociative amnesia (also named psychogenic or functional amnesia) and to the discussion of an overlap between psychogenic and "brain organic" forms of amnesia. The "inability of access hypothesis" is proposed to account for most of both the organic and psychogenic (dissociative) patients with primarily retrograde amnesia. Questions such as why recovery from retrograde amnesia can occur in retrograde (dissociative) amnesia, and why long-term new learning of episodic-autobiographic episodes is possible, are addressed. It is concluded that research on retrograde amnesia research is still in its infancy, as the neural correlates of memory storage are still unknown. It is argued that the recollection of episodic-autobiographic episodes most likely involves frontotemporal regions of the right hemisphere, a region which appears to be hypometabolic in patients with dissociative amnesia.

  17. Dissociative Reactions to Incest.

    ERIC Educational Resources Information Center

    Hall, J. Mark

    In contrast to Freud's later and revised view of the etiology of hysterical, or dissociative, symptoms, it is now known that real, and not fantasized, sexual experiences in childhood are experienced in disociative symptomatology. It is useful to understand that incest involves both traumatic events, that is, incidents of sexual violation per se,…

  18. Pathological Dissociation as Measured by the Child Dissociative Checklist

    ERIC Educational Resources Information Center

    Wherry, Jeffrey N.; Neil, Debra A.; Taylor, Tamara N.

    2009-01-01

    The component structure of the Child Dissociative Checklist was examined among abused children. A factor described as pathological dissociation emerged that was predicted by participants being male. There also were differences in pathological dissociation between groups of sexually abused and physically abused children. Replication of this factor…

  19. Dissociation and psychosis in dissociative identity disorder and schizophrenia.

    PubMed

    Laddis, Andreas; Dell, Paul F

    2012-01-01

    Dissociative symptoms, first-rank symptoms of schizophrenia, and delusions were assessed in 40 schizophrenia patients and 40 dissociative identity disorder (DID) patients with the Multidimensional Inventory of Dissociation (MID). Schizophrenia patients were diagnosed with the Structured Clinical Interview for the DSM-IV Axis I Disorders; DID patients were diagnosed with the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised. DID patients obtained significantly (a) higher dissociation scores; (b) higher passive-influence scores (first-rank symptoms); and (c) higher scores on scales that measure child voices, angry voices, persecutory voices, voices arguing, and voices commenting. Schizophrenia patients obtained significantly higher delusion scores than did DID patients. What is odd is that the dissociation scores of schizophrenia patients were unrelated to their reports of childhood maltreatment. Multiple regression analyses indicated that 81% of the variance in DID patients' dissociation scores was predicted by the MID's Ego-Alien Experiences Scale, whereas 92% of the variance in schizophrenia patients' dissociation scores was predicted by the MID's Voices Scale. We propose that schizophrenia patients' responses to the MID do not index the same pathology as do the responses of DID patients. We argue that neither phenomenological definitions of dissociation nor the current generation of dissociation instruments (which are uniformly phenomenological in nature) can distinguish between the dissociative phenomena of DID and what we suspect are just the dissociation-like phenomena of schizophrenia.

  20. Electron Transfer Dissociation of All Ions at All Times, MSETD, in a Quadrupole Time-of-Flight (Q-ToF) Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Cramer, Christian N.; Brown, Jeffery M.; Tomczyk, Nick; Nielsen, Peter Kresten; Haselmann, Kim F.

    2017-02-01

    Data-independent mass spectral acquisition is particularly powerful when combined with ultra-performance liquid chromatography (LC) that provides excellent separation of most components present in a given sample. Data-independent analysis (DIA) consists of alternating full MS scans and scans with fragmentation of all ions within a selected m/z range, providing precursor masses and structure information, respectively. Fragmentation spectra are acquired either by sequential isolation and fragmentation of sliding m/z ranges or fragmenting all ions entering the MS instrument with no ion isolation, termed broadband DIA. Previously, broadband DIA has only been possible using collision induced dissociation (CID). Here, we report the use of electron transfer dissociation (ETD) as the fragmentation technique in broadband DIA instead of traditional collision induced dissociation (CID) during MSE. In this approach, which we refer to as MSETD, we implement the inherent benefits provided by ETD, such as discrimination of leucine and isoleucine, in a DIA setup. The combination of DIA analysis and ETD fragmentation with supplemental CID energy provides a powerful platform to obtain information on all precursors and their sequence from a single experiment.

  1. Mechanism and dynamics of the reaction of XeF2 with fluorinated Si(100): possible role of gas phase dissociation of a surface reaction product in plasmaless etching.

    PubMed

    Hefty, R C; Holt, J R; Tate, M R; Ceyer, S T

    2009-04-28

    Xenon difluoride is observed to react with Si-Si sigma-dimer and sigma-lattice bonds of Si(100)2 x 1 at 150 K by single and two atom abstraction at F coverages above 1 ML. As in the limit of zero F coverage, a measurable fraction of the scattered, gas phase product of single atom abstraction, XeF, is sufficiently internally excited to dissociate into F and Xe atoms before detection. Using the XeF internal energy and orientation distributions determined in the limit of zero coverage, the laws of conservation of momentum, energy, and mass are applied to the measured F velocity and angular distributions at higher coverage to simulate the Xe atom velocity and angular distributions and their intensities at higher coverage. The simulation predicts the observed Xe atom velocity and angular distributions at high coverage reasonably well, largely because the exothermicity channeled to XeF remains approximately constant as the coverage increases. This constancy is an opportune consequence of the trade-off between the attractiveness of the potential energy surface as the coverage is increased and the dynamics of the XeF product along the potential surface. The energy, momentum, and mass conservation analysis is also used to distinguish between Xe atoms that arise from XeF gas phase dissociation and Xe atoms that are produced by two atom abstraction. This distinction enables the calculation of percentages of the single and two atom abstraction pathways, as well as the percentages of the two pathways available to the Xe atom produced by two atom abstraction, inelastic scattering, and desorption. Finally, the simulation reveals that between 9% and 12% of F atoms produced by gas phase dissociation of XeF are scattered back toward the surface. These F atoms likely react readily with Si to form the higher fluorides that ultimately lead to etching. Gas phase dissociation of the scattered product of a surface reaction is a novel mechanism to explain the unique reactivity of XeF(2) to

  2. Rototranslational collision-induced absorption by H2-H2 pairs at temperatures from 600 to 7000 K

    NASA Technical Reports Server (NTRS)

    Zheng, Chunguang; Borysow, Aleksandra

    1995-01-01

    The computation of the far-infrared, rototranslational (RT) collision-induced absorption (CIA) spectra of H2-H2 pairs is presented at temperatures from 600 to 7000 K for the first time. Theoretical results are based on the quantum mechanical and semiclassical, three lowest translational spectral moments obtained for H2 pairs. The effective, isotropic H2-H2 interaction potential, suitable for the high-temperature computations, and the ab initio induced dipoles, have been used as input. Special effort has been made to account for the rotational and vibrational states dependence of the dipoles, since it was found to be relevant at the high temperatures employed. The computations of the entire RT band account for all populated vibrational states of hydrogen molecule and include vibrational transitions v tends towards v-prime = v, with v = 0, 1, 2 and 3. The described method makes use of the adequately selected model line shapes with the temperature-dependent parameters. The presented model is useful for the 'model atmospheres' of zero- and low-metallicity, cool and dense stellar atmospheres, where CIA is known to be imporatnt.

  3. Spectral Moments of Collision-Induced Absorption of CO2 Pairs: The Role of the Intermolecular Potential

    NASA Technical Reports Server (NTRS)

    Gruszka, Marcin; Borysow, Aleksandra

    1994-01-01

    In this paper we examine the role of the anisotropy of the intermolecular potential in the rototranslational collision-induced absorption of the CO2 pairs. Using newly developed formulas that include the effects of anisotropy of the potential to all orders, we calculate the two lowest spectral moments gamma(prime), and alpha(prime), for four different classes of C02 pair potentials and compare the results with the experimental values. We assumed only multipolar induction in the process of forming the induced dipole, with the second-order contributions included. Using a site-site LJ and a site-site semi-ab initio intermolecular potentials we were able to reproduce the experimental values of gamma(prime), and alpha(prime) moments over entire temperature range from 230 to 330 K. Also, the role of an electrostatic interaction between two C02 molecules and its impact on the spectral moments is thoroughly investigated. An isotropic core with a point quadrupole centered at each molecule is shown to be an inadequate representation of the C02-CO2 potential. Additionally, we show the results obtained with the first- and second-order perturbation theory to be more than twice too small.

  4. Relativistic MHD simulations of collision-induced magnetic dissipation in Poynting-flux-dominated jets/outflows

    SciTech Connect

    Deng, Wei

    2015-07-21

    The question of the energy composition of the jets/outflows in high-energy astrophysical systems, e.g. GRBs, AGNs, is taken up first: Matter-flux-dominated (MFD), σ < 1, and/or Poynting-flux-dominated (PFD), σ >1? The standard fireball IS model and dissipative photosphere model are MFD, while the ICMART (Internal-Collision-induced MAgnetic Reconnection and Turbulence) model is PFD. Motivated by ICMART model and other relevant problems, such as “jets in a jet” model of AGNs, the author investigates the models from the EMF energy dissipation efficiency, relativistic outflow generation, and σ evolution points of view, and simulates collisions between high-σ blobs to mimic the situation of the interactions inside the PFD jets/outflows by using a 3D SRMHD code which solves the conservative form of the ideal MHD equations. σb,f is calculated from the simulation results (threshold = 1). The efficiency obtained from this hybrid method is similar to the efficiency got from the energy evolution of the simulations (35.2%). Efficiency is nearly σ independent, which is also confirmed by the hybrid method. σb,i - σb,f provides an interesting linear relationship. Results of several parameter studies of EMF energy dissipation efficiency are shown.

  5. Collision-induced Raman scattering and the peculiar case of neon: Anisotropic spectrum, anisotropy, and the inverse scattering problem

    SciTech Connect

    Dixneuf, Sophie; Rachet, Florent; Chrysos, Michael

    2015-02-28

    Owing in part to the p orbitals of its filled L shell, neon has repeatedly come on stage for its peculiar properties. In the context of collision-induced Raman spectroscopy, in particular, we have shown, in a brief report published a few years ago [M. Chrysos et al., Phys. Rev. A 80, 054701 (2009)], that the room-temperature anisotropic Raman lineshape of Ne–Ne exhibits, in the far wing of the spectrum, a peculiar structure with an aspect other than a smooth wing (on a logarithmic plot) which contrasts with any of the existing studies, and whose explanation lies in the distinct way in which overlap and exchange interactions interfere with the classical electrostatic ones in making the polarizability anisotropy, α{sub ∥} − α{sub ⊥}. Here, we delve deeper into that study by reporting data for that spectrum up to 450 cm{sup −1} and for even- and odd-order spectral moments up to M{sub 6}, as well as quantum lineshapes, generated from SCF, CCSD, and CCSD(T) models for α{sub ∥} − α{sub ⊥}, which are critically compared with the experiment. On account of the knowledge of the spectrum over the augmented frequency domain, we show how the inverse scattering problem can be tackled both effectively and economically, and we report an analytic function for the anisotropy whose quantum lineshape faithfully reproduces our observations.

  6. Dissociative recombination: Results from storage rings

    SciTech Connect

    Larsson, Mats

    2005-05-27

    The focus of this article is on the measurement of product branching ratios in the dissociative recombination of polyatomic molecular ions with electrons by means of ion storage rings. Recombination of ions of interest in astrophysics, plasma-assisted combustion, thermonuclear fusion, protein fragmentation, and atmospheric physics are reviewed and discussed.

  7. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS

    NASA Astrophysics Data System (ADS)

    Hage, Christoph; Ihling, Christian H.; Götze, Michael; Schäfer, Mathias; Sinz, Andrea

    2017-01-01

    We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids.

  8. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS.

    PubMed

    Hage, Christoph; Ihling, Christian H; Götze, Michael; Schäfer, Mathias; Sinz, Andrea

    2017-01-01

    We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS(3) experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.

  9. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides.

    PubMed

    Aboufazeli, Forouzan; Kolli, Venkata; Dodds, Eric D

    2015-04-01

    Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

  10. A Comparison of Energy-Resolved Vibrational Activation/Dissociation Characteristics of Protonated and Sodiated High Mannose N-Glycopeptides

    NASA Astrophysics Data System (ADS)

    Aboufazeli, Forouzan; Kolli, Venkata; Dodds, Eric D.

    2015-04-01

    Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

  11. Three dimensions of dissociative amnesia.

    PubMed

    Dell, Paul F

    2013-01-01

    Principal axis factor analysis with promax rotation extracted 3 factors from the 42 memory and amnesia items of the Multidimensional Inventory of Dissociation (MID) database (N = 2,569): Discovering Dissociated Actions, Lapses of Recent Memory and Skills, and Gaps in Remote Memory. The 3 factors' shared variance ranged from 36% to 64%. Construed as scales, the 3 factor scales had Cronbach's alpha coefficients of .96, .94, and .93, respectively. The scales correlated strongly with mean Dissociative Experiences Scale scores, mean MID scores, and total scores on the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised (SCID-D-R). What is interesting is that the 3 amnesia factors exhibited a range of correlations with SCID-D-R Amnesia scores (.52, .63, and .70, respectively), suggesting that the SCID-D-R Amnesia score emphasizes gaps in remote memory over amnesias related to dissociative identity disorder. The 3 amnesia factor scales exhibited a clinically meaningful pattern of significant differences among dissociative identity disorder, dissociative disorder not otherwise specified-1, dissociative amnesia, depersonalization disorder, and nonclinical participants. The 3 amnesia factors may have greater clinical utility for frontline clinicians than (a) amnesia as discussed in the context of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, nosology of the dissociative disorders or (b) P. Janet's (1893/1977 ) 4-fold classification of dissociative amnesia. The author recommends systematic study of the phenomenological differences within specific dissociative symptoms and their differential relationship to specific dissociative disorders.

  12. Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes

    SciTech Connect

    Rios, Daniel; Schoendorff, George E.; Van Stipdonk, Michael J.; Gordon, Mark S.; Windus, Theresa L.; Gibson, John K.; De Jong, Wibe A.

    2012-12-03

    Combined collision-induced dissociation mass-spectrometry experiments and DFT calculations were employed to elucidate the molecular structure of "hypercoordinated" species and the energetics of water-elimination reactions of uranyl acetone complexes observed in earlier work (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). It is shown that the "hypercoordinated" species contain diacetone alcohol ligands bonded in either bidentate or monodentate fashion, which are indistinguishable from (acetone)2 in mass spectrometry. Calculations confirm that four diacetone ligands can form stable complexes, but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Diacetone alcohol ligands are shown to form mesityl oxide ligands and alkoxide species through the elimination of water, providing an explanation for the observed water-elimination reactions.

  13. Zero-Point Energy Constraint for Unimolecular Dissociation Reactions. Giving Trajectories Multiple Chances To Dissociate Correctly.

    PubMed

    Paul, Amit K; Hase, William L

    2016-01-28

    A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

  14. Modeling the electron-impact dissociation of methane

    NASA Astrophysics Data System (ADS)

    Ziółkowski, Marcin; Vikár, Anna; Mayes, Maricris Lodriguito; Bencsura, Ákos; Lendvay, György; Schatz, George C.

    2012-12-01

    The product yield of the electron-impact dissociation of methane has been studied with a combination of three theoretical methods: R-matrix theory to determine the electronically inelastic collisional excitation cross sections, high-level electronic structure methods to determine excited states energies and derivative couplings, and trajectory surface hopping (TSH) calculations to determine branching in the dissociation of the methane excited states to give CH3, CH2, and CH. The calculations involve the lowest 24 excited-state potential surfaces of methane, up to the ionization energy. According to the R-matrix calculations, electron impact preferentially produces triplet excited states, especially for electron kinetic energies close to the dissociation threshold. The potential surfaces of excited states are characterized by numerous avoided and real crossings such that the TSH calculations show rapid cascading down to the lowest excited singlet or triplet states, and then slower the dissociation of these lowest states. Product branching for electron-impact dissociation was therefore estimated by combining the electron-impact excitation cross sections with TSH product branching ratios that were obtained from the lowest singlet and triplet states, with the singlet dissociation giving a comparable formation of CH2 and CH3 while triplet dissociation gives CH3 exclusively. The overall branching in electron-impact dissociation is dominated by CH3 over CH2. A small branching yield for CH is also predicted.

  15. Controllable dissociations of PH3 molecules on Si(001)

    NASA Astrophysics Data System (ADS)

    Liu, Qin; Lei, Yanhua; Shao, Xiji; Ming, Fangfei; Xu, Hu; Wang, Kedong; Xiao, Xudong

    2016-04-01

    We demonstrate for the first time to our knowledge that controllable dissociation of PH3 adsorption products PH x (x = 2, 1) can be realized by STM (scanning tunneling microscope) manipulation techniques at room temperature. Five dissociative products and their geometric structures are identified via combining STM experiments and first-principle calculations and simulations. In total we realize nine kinds of controllable dissociations by applying a voltage pulse among the PH3-related structures on Si(001). The dissociation rates of the five most common reactions are measured by the I-t spectrum method as a function of voltage. The suddenly increased dissociation rate at 3.3 V indicates a transition from multivibrational excitation to single-step excitation induced by inelastic tunneling electrons. Our studies prove that selectively breaking the chemical bonds of a single molecule on semiconductor surface by STM manipulation technique is feasible.

  16. Mechanism of Formation of the Major Estradiol Product Ions Following Collisional Activation of the Molecular Anion in a Tandem Quadrupole Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Wooding, Kerry M.; Barkley, Robert M.; Hankin, Joseph A.; Johnson, Christopher A.; Bradford, Andrew P.; Santoro, Nanette; Murphy, Robert C.

    2013-10-01

    The importance of the mass spectral product ion structure is highlighted in quantitative assays, which typically use multiple reaction monitoring (MRM), and in the discovery of novel metabolites. Estradiol is an important sex steroid whose quantitation and metabolite identification using tandem mass spectrometry has been widely employed in numerous clinical studies. Negative electrospray ionization tandem mass spectrometry of estradiol (E2) results in several product ions, including the abundant m/z 183 and 169. Although m/z 183 is one of the most abundant product ions used in many quantitative assays, the structure of m/z 183 has not been rigorously examined. We suggest a structure for m/z 183 and a mechanism of formation consistent with collision induced dissociation (CID) of E2 and several stable isotopes ([D4]-E2, [13C6]-E2, and [D1]-E2). An additional product ion from E2, namely m/z 169, has also been examined. MS3 experiments indicated that both m/z 183 and m/z 169 originate from only E2 [M - H]- m/z 271. These ions, m/z 183 and m/z 169, were also present in the collision induced decomposition mass spectra of other prominent estrogens, estrone (E1) and estriol (E3), indicating that these two product ions could be used to elucidate the estrogenic origin of novel metabolites. We propose two fragmentation schemes to explain the CID data and suggest a structure of m/z 183 and m/z 169 consistent with several isotopic variants and high resolution mass spectrometric measurements.

  17. Dissociation: cognitive capacity or dysfunction?

    PubMed

    de Ruiter, Michiel B; Elzinga, Bernet M; Phaf, R Hans

    2006-01-01

    Dissociative experiences are mostly studied as a risk factor for dissociative pathology. Nonpathological dissociation is quite common in the general population, however, and may reflect a constitutionally determined cognitive style rather than a pathological trait acquired through the experience of adverse life events. In a theoretical model, we propose that nonpathological dissociation is characterized by high levels of elaboration learning and reconstructive retrieval, for which enhanced levels of attentional and working memory abilities are a prerequisite. These characteristics, in general, seem to be representative for a higher ability to (re-)construct conscious experiences. We review some of our behavioral as well as neural (i.e., fMRI, ERPs) studies, suggesting that high dissociative individuals are characterized by heightened levels of attention, working memory and episodic memory. In nonpathological conditions a person may benefit from these dissociative abilities, although after adverse (e.g., traumatic) events the disposition may develop into dissociative pathology.

  18. Use of Doubly Charged Precursors to Validate Dissociation Mechanisms of Singly Charged Poly(Dimethylsiloxane) Oligomers

    NASA Astrophysics Data System (ADS)

    Fouquet, Thierry; Toniazzo, Valérie; Ruch, David; Charles, Laurence

    2013-07-01

    Collision-induced dissociation of doubly charged poly(dimethylsiloxane) (PDMS) molecules was investigated to provide experimental evidence for fragmentation reactions proposed to occur upon activation of singly charged oligomers. This study focuses on two PDMS species holding trimethylsilyl or methoxy end-groups and cationized with ammonium. In both cases, introduction of the additional charge did not induce significant differences in dissociation behavior, and the use of doubly charged precursors enabled the occurrence of charge-separation reactions, allowing molecules always eliminated as neutrals upon activation of singly charged oligomers to be detected as cationized species. In the case of trimethylsilyl-terminated oligomers, random location of the adducted charge combined with rapid consecutive reactions proposed to occur from singly charged precursors could be validated based on MS/MS data of doubly charged oligomers. In the case of methoxy-terminated PDMS, favored interaction of the adducted ammonium with both end-groups, proposed to rationalize the dissociation behavior of singly charged molecules, was also supported by MS/MS data obtained for molecules adducted with two ammonium cations.

  19. Thermal dissociation behavior and dissociation enthalpies of methane-carbon dioxide mixed hydrates

    SciTech Connect

    Kwon, T.H.; Kneafsey, T.J.; Rees, E.V.L.

    2011-02-15

    Replacement of methane with carbon dioxide in hydrate has been proposed as a strategy for geologic sequestration of carbon dioxide (CO{sub 2}) and/or production of methane (CH{sub 4}) from natural hydrate deposits. This replacement strategy requires a better understanding of the thermodynamic characteristics of binary mixtures of CH{sub 4} and CO{sub 2} hydrate (CH{sub 4}-CO{sub 2} mixed hydrates), as well as thermophysical property changes during gas exchange. This study explores the thermal dissociation behavior and dissociation enthalpies of CH{sub 4}-CO{sub 2} mixed hydrates. We prepared CH{sub 4}-CO{sub 2} mixed hydrate samples from two different, well-defined gas mixtures. During thermal dissociation of a CH{sub 4}-CO{sub 2} mixed hydrate sample, gas samples from the head space were periodically collected and analyzed using gas chromatography. The changes in CH{sub 4}-CO{sub 2} compositions in both the vapor phase and hydrate phase during dissociation were estimated based on the gas chromatography measurements. It was found that the CO{sub 2} concentration in the vapor phase became richer during dissociation because the initial hydrate composition contained relatively more CO{sub 2} than the vapor phase. The composition change in the vapor phase during hydrate dissociation affected the dissociation pressure and temperature; the richer CO{sub 2} in the vapor phase led to a lower dissociation pressure. Furthermore, the increase in CO{sub 2} concentration in the vapor phase enriched the hydrate in CO{sub 2}. The dissociation enthalpy of the CH{sub 4}-CO{sub 2} mixed hydrate was computed by fitting the Clausius-Clapeyron equation to the pressure-temperature (PT) trace of a dissociation test. It was observed that the dissociation enthalpy of the CH{sub 4}-CO{sub 2} mixed hydrate lays between the limiting values of pure CH{sub 4} hydrate and CO{sub 2} hydrate, increasing with the CO{sub 2} fraction in the hydrate phase.

  20. Temperature dependences of mechanisms responsible for the water-vapor continuum absorption. II. Dimers and collision-induced absorption.

    PubMed

    Leforestier, C; Tipping, R H; Ma, Q

    2010-04-28

    We investigated the magnitude and temperature dependence (T dependence) of the dimer absorption in the region of 0-600 cm(-1) and the collision-induced absorption (CIA) in the region of 0-1150 cm(-1). Together with our previous study of the self water-vapor continuum contributions resulting from far-wing line shapes of the allowed H(2)O lines in the infrared window between 800 and 1150 cm(-1), we find that the three mechanisms have completely different T dependence behaviors. The dimer absorption has the strongest negative T dependence and the continuum absorption from far wings of the allowed lines has a moderately strong negative one. Meanwhile, the CIA exhibits a mild T dependence. In addition, their T dependence patterns are quite different. The T dependence of the far-wing theory varies significantly as the frequency of interest omega varies. For CIA, in general, its T dependence is mildly negative, but becomes slightly positive in the window region between the H(2)O bands. In contrast, the T dependence of the dimer absorption varies slightly as omega varies. In the microwave and submillimeter region, its T dependence becomes uniform. Concerning the relative importance for each of these three mechanisms, we find that in the infrared widow, the far-wing contributions are the dominant source of the self-continuum. Within the band, its contributions are definitely responsible for the measured continuum data. But, it is impossible to draw quantitatively conclusions on its relative importance unless one is able to improve the accuracy of the local line calculations significantly. On the other hand, within the pure rotational band, the dimer absorptions are a minor contributor to the self-continuum measurements, and its role becomes more important in the microwave and submillimeter regions. Finally, based on our study we conclude that contributions to the self-continuum from CIA in the frequency region of 0-1150 cm(-1) are negligible.

  1. The Dissociative Recombination of OH(+)

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1995-01-01

    Theoretical quantum chemical calculations of the cross sections and rates for the dissociative recombination of the upsilon = 0 level of the ground state of OH(+) show that recombination occurs primarily along the 2 (2)Pi diabatic route. The products are 0((1)D) and a hot H atom with 6.1 eV kinetic energy. The coupling to the resonances is very small and the indirect recombination mechanism plays only a minor role. The recommended value for the rate coefficient is (6.3 +/- 0.7) x 10(exp -9)x (T(e)/1300)(exp -0.48) cu.cm/s for 10 less than T(e) less than 1000 K.

  2. Dissociative absorption: An empirically unique, clinically relevant, dissociative factor.

    PubMed

    Soffer-Dudek, Nirit; Lassri, Dana; Soffer-Dudek, Nir; Shahar, Golan

    2015-11-01

    Research of dissociative absorption has raised two questions: (a) Is absorption a unique dissociative factor within a three-factor structure, or a part of one general dissociative factor? Even when three factors are found, the specificity of the absorption factor is questionable. (b) Is absorption implicated in psychopathology? Although commonly viewed as "non-clinical" dissociation, absorption was recently hypothesized to be specifically associated with obsessive-compulsive symptoms. To address these questions, we conducted exploratory and confirmatory factor analyses on 679 undergraduates. Analyses supported the three-factor model, and a "purified" absorption scale was extracted from the original inclusive absorption factor. The purified scale predicted several psychopathology scales. As hypothesized, absorption was a stronger predictor of obsessive-compulsive symptoms than of general psychopathology. In addition, absorption was the only dissociative scale that longitudinally predicted obsessive-compulsive symptoms. We conclude that absorption is a unique and clinically relevant dissociative tendency that is particularly meaningful to obsessive-compulsive symptoms.

  3. Protein Identification Via Surface-Induced Dissociation in an FT-ICR Mass Spectrometer and a Patchwork Sequencing Approach

    SciTech Connect

    Fernandez, Facundo; Wysocki, Vicki H.; Futrell, Jean H.; Laskin, Julia

    2006-05-01

    Surface-induced dissociation (SID) and collision-induced dissociation (CID) are ion activation techniques based on energetic collisions with a surface or gas molecules, respectively. One noticeable difference between CID and SID is that SID does not require a collision gas for ion activation and is therefore directly compatible with the high vacuum requirement of Fourier Transform Ion Cyclotron Resonance mass spectrometers (FT-ICR MS). Eliminating the introduction of collision gas into the ICR cell for collisional activation dramatically shortens the acquisition time for MS/MS experiments, suggesting that SID could be utilized for high-throughput MS/MS studies in FT-ICR MS. We demonstrate for the first time the utility of SID combined with FT-ICR MS for protein identification. Tryptic digests of standard proteins were analyzed using a hybrid 6-Tesla FT-ICR MS with SID and CID capabilities. SID spectra of mass-selected singly and doubly charged peptides were obtained using a diamond-coated target mounted at the rear trapping plate of the ICR cell. The broad internal energy distribution deposited into the precursor ion following collision with the diamond surface allowed a variety of fragmentation channels to be accessed by SID. Composition and sequence qualifiers produced by SID of tryptic peptides were used to improve the statistical significance of database searches. Protein identification MASCOT scores obtained using SID were comparable or better than scores obtained using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) –the conventional ion activation technique in FT-ICR MS.

  4. Dissociation of motor maturation.

    PubMed

    DiMario, Francis J

    2003-06-01

    We prospectively acquired clinical data regarding the presentation, evaluation, and developmental progress of all patients identified with dissociated motor maturation to define their clinical outcomes. Children (N = 8) referred for evaluation of suspected cerebral palsy because of delayed sitting or walking and identified to have dissociated motor maturation were followed with serial clinical examination. All displayed the characteristic "sitting on air" posture while held in vertical suspension and had otherwise normal developmental assessments. This posture is composed of the hips held in flexion and abduction with the knees extended and feet plantar or dorsiflexed. Three children were initially evaluated at 10 months of age owing to absence of sitting and five other children were evaluated at a mean of 14 months (range 12-19 months) owing to inability to stand. Follow-up evaluations were conducted over a mean of 10.5 months (range 5-34 months). Five children were born prematurely at 34 to 36 weeks gestation. Denver Developmental Screening Test and general and neurologic examinations were normal except to note hypotonia in six children and the "sitting on air" posture in all of the children. Four children have older siblings or parents who "walked late" (after 15 months). On average, the children attained sitting by 8 months (range 7-10 months). One child did not crawl prior to independent walking, two children scooted rather than crawled, and five children crawled at an average of 13.5 months (range 10-16 months). All children cruised by a mean of 18 months (range 16-21.5 months) and attained independent walking by 20.1 months (range 18-25 months). Neuroimaging and serum creatine kinase enzyme testing were normal in two children who were tested. These eight children conform to the syndrome of dissociated motor maturation. The "sitting on air" posture serves as a diagnostic sign and anticipated excellent prognosis, but follow-up is required to ensure a normal

  5. Electron-driven excitation and dissociation of molecules

    NASA Astrophysics Data System (ADS)

    Orel, Ann

    2009-10-01

    Due to the large difference in mass between the electron and the nuclei, when an electron collides with a molecule or molecular ion, there is inefficient transfer of energy from the electron into the motion of the nuclei, leading to little vibrational excitation or dissociation. However, in certain special cases, the electron can temporarily attach to the molecule and change the forces felt between its atoms for a period of time comparable to a vibrational period. This can lead to resonant vibrational excitation and dissociative attachment, for neutral targets, or dissociative recombination in the case of ions. Studies of dissociative recombination and attachment in several polyatomic systems have shown that simple one-dimensional models can fail to capture the correct dissociation dynamics. In our treatment of these processes we first carry out ab initio electron scattering calculations at fixed internuclear geometries to determine the resonant energy surfaces and the corresponding surface of autoionization widths using the Complex Kohn variational method. These resonance positions and widths are then used as input to a dynamics study to determine the cross-section and product distributions for the dissociation or excitation process. We will present results on a number of systems, including HCCH, HCN/HNC and HCCCN as examples of dissociative attachment and N2H^+ and H2O^+ for dissociative recombination.

  6. [Dissociative disorders and affective disorders].

    PubMed

    Montant, J; Adida, M; Belzeaux, R; Cermolacce, M; Pringuey, D; Da Fonseca, D; Azorin, J-M

    2014-12-01

    The phenomenology of dissociative disorders may be complex and sometimes confusing. We describe here two cases who were initially misdiagnosed. The first case concerned a 61 year-old woman, who was initially diagnosed as an isolated dissociative fugue and was actually suffering from severe major depressive episode. The second case concerned a 55 year-old man, who was suffering from type I bipolar disorder and polyvascular disease, and was initially diagnosed as dissociative fugue in a mooddestabilization context, while it was finally a stroke. Yet dissociative disorders as affective disorder comorbidity are relatively unknown. We made a review on this topic. Dissociative disorders are often studied through psycho-trauma issues. Litterature is rare on affective illness comorbid with dissociative disorders, but highlight the link between bipolar and dissociative disorders. The later comorbidity often refers to an early onset subtype with also comorbid panic and depersonalization-derealization disorder. Besides, unipolar patients suffering from dissociative symptoms have more often cyclothymic affective temperament. Despite the limits of such studies dissociative symptoms-BD association seems to correspond to a clinical reality and further works on this topic may be warranted.

  7. A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry.

    PubMed

    Hart-Smith, Gene

    2014-01-15

    Mass spectrometry (MS)-based studies of synthetic polymers often characterise detected polymer components using mass data alone. However when mass-based characterisations are ambiguous, tandem MS (MS/MS) offers a means by which additional analytical information may be collected. This review provides a synopsis of two particularly promising methods of dissociating polymer ions during MS/MS: electron-capture and electron-transfer dissociation (ECD and ETD, respectively). The article opens with a summary of the basic characteristics and operating principles of ECD and ETD, and relates these techniques to other methods of dissociating gas-phase ions, such as collision-induced dissociation (CID). Insights into ECD- and ETD-based MS/MS, gained from studies into proteins and peptides, are then discussed in relation to polymer chemistry. Finally, ECD- and ETD-based studies into various classes of polymer are summarised; for each polymer class, ECD- and ETD-derived data are compared to CID-derived data. These discussions identify ECD and ETD as powerful means by which unique and diagnostically useful polymer ion fragmentation data may be generated, and techniques worthy of increased utilisation by the polymer chemistry community.

  8. Hyperglycemia associated dissociative fugue (organic dissociative disorder) in an elderly.

    PubMed

    Ram, Dushad; Ashoka, H G; Gowdappa, Basavnna

    2015-01-01

    Inadequate glycemic control in patients with diabetes is known to be associated with psychiatric disorders such as depression, anxiety disorder, and cognitive impairment. However, dissociative syndrome has not been reported so far. Here we are reporting a case of repeated dissociative fugue associated with hyperglycemia, in an elderly with type II diabetes. Possible neurobiological mechanism has been discussed.

  9. Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions.

    PubMed

    Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

    2015-08-01

    A series of different types of wax esters (represented by RCOOR') were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS(3) (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2](+), [RCO](+) and [RCO-H2O](+) that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: (1) [RCOOH2](+) for saturated wax esters, (2) [RCOOH2](+), [RCO](+) and [RCO-H2O](+) for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and (3) [RCOOH2](+) and [RCO](+) for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R'](+) and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2](+) ions for all types of wax esters and [R'-2H](+) ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions.

  10. Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions

    PubMed Central

    Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

    2015-01-01

    A series of different types of wax esters (represented by RCOOR′) were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS3 (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2]+, [RCO]+ and [RCO – H2O]+ that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: 1) [RCOOH2]+ for saturated wax esters, 2) [RCOOH2]+, [RCO]+ and [RCO – H2O]+ for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and 3) [RCOOH2]+ and [RCO]+ for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R′]+ and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2]+ ions for all types of wax esters and [R′ – 2H]+ ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions. PMID:26178197

  11. Analysis of the collision-induced absorption spectra in the second overtone region of H2-H2 at 298 K

    NASA Astrophysics Data System (ADS)

    Abu-Kharma, M.

    2015-02-01

    The collision-induced absorption (CIA) spectra of the second overtone band of normal hydrogen in a pure gas were recorded for a number of gas densities up to 750 amagat (1 amagat = 44.614981 mol/m3) with a two meter stainless steel absorption cell at 298 K. The profile analyses of these spectra were carried out using the Birnbaum-Cohen line shape function for the quadrupolar vibrational transitions and the Levine-Birnbaum line shape function for the overlap transitions.

  12. Modeling of collision-induced infrared absorption spectra of H2-H2 pairs in the fundamental band at temperatures from 20 to 300 K. [Planetary atmospheres

    SciTech Connect

    Borysow, A. )

    1991-08-01

    The 20-300 K free-free rotovibrational collision-induced absorption (RV CIA) spectra of H2-H2 pairs are presently obtained by a numerical method which, in addition to closely matching known CIA spectra of H2-H2, can reproduce the results of the quantum-mechanical computations to within a few percent. Since the spectral lineshape parameters are derivable by these means from the lowest three quantum-mechanical spectral moments, these outer-planet atmosphere-pertinent model spectra may be computed on even small computers. 35 refs.

  13. Coupled cluster investigation on the thermochemistry of dimethyl sulphide, dimethyl disulphide and their dissociation products: the problem of the enthalpy of formation of atomic sulphur

    NASA Astrophysics Data System (ADS)

    Denis, Pablo A.

    2014-04-01

    By means of coupled cluster theory and correlation consistent basis sets we investigated the thermochemistry of dimethyl sulphide (DMS), dimethyl disulphide (DMDS) and four closely related sulphur-containing molecules: CH3SS, CH3S, CH3SH and CH3CH2SH. For the four closed-shell molecules studied, their enthalpies of formation (EOFs) were derived using bomb calorimetry. We found that the deviation of the EOF with respect to experiment was 0.96, 0.65, 1.24 and 1.29 kcal/mol, for CH3SH, CH3CH2SH, DMS and DMDS, respectively, when ΔHf,0 = 65.6 kcal/mol was utilised (JANAF value). However, if the recently proposed ΔHf,0 = 66.2 kcal/mol was used to estimate EOF, the errors dropped to 0.36, 0.05, 0.64 and 0.09 kcal/mol, respectively. In contrast, for the CH3SS radical, a better agreement with experiment was obtained if the 65.6 kcal/mol value was used. To compare with experiment avoiding the problem of the ΔHf,0 (S), we determined the CH3-S and CH3-SS bond dissociation energies (BDEs) in CH3S and CH3SS. At the coupled cluster with singles doubles and perturbative triples correction level of theory, these values are 48.0 and 71.4 kcal/mol, respectively. The latter BDEs are 1.5 and 1.2 kcal/mol larger than the experimental values. The agreement can be considered to be acceptable if we take into consideration that these two radicals present important challenges when determining their EOFs. It is our hope that this work stimulates new studies which help elucidate the problem of the EOF of atomic sulphur.

  14. Ab initio calculations of dissociative attachment and dissociative recombination of electrons and polyatomic species

    NASA Astrophysics Data System (ADS)

    Haxton, Daniel

    2009-05-01

    Interactions of free electrons with neutral and positively charged molecular species play a role in various physical systems. In interstellar space, reactions such as dissociative recombination determine the balance of various charged and neutral species. In a laboratory equipped with an apparatus like a COLTRIMS device, the dissociative attachment process can be used as a microscope to study polyatomic molecular dynamics. We discuss the theoretical and numerical methods used to calculate dissociative attachment and dissociative recombination of electrons with larger molecules from first principles. Studies using these methods are complimentary to other methods that yield more approximate reaction rates at greatly lesser numerical cost; they may yield precise information about the dissociation dynamics, product distribution, and differential cross section that approximate methods cannot. We discuss calculations performed to date on the target species H2O, NO2, and LiH2^+. We discuss the scaling of our numerical methods with the number of atoms, and the prospects of applying them to tetra-atomics.

  15. Dissociative States and Neural Complexity

    ERIC Educational Resources Information Center

    Bob, Petr; Svetlak, Miroslav

    2011-01-01

    Recent findings indicate that neural mechanisms of consciousness are related to integration of distributed neural assemblies. This neural integration is particularly vulnerable to past stressful experiences that can lead to disintegration and dissociation of consciousness. These findings suggest that dissociation could be described as a level of…

  16. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

    NASA Astrophysics Data System (ADS)

    Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v

  17. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions.

    PubMed

    Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V

    2015-08-07

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability

  18. High resolution parallel reaction monitoring with electron transfer dissociation for middle-down proteomics.

    PubMed

    Sweredoski, Michael J; Moradian, Annie; Raedle, Matthias; Franco, Catarina; Hess, Sonja

    2015-08-18

    In recent years, middle-down proteomics has emerged as a popular technique for the characterization and quantification of proteins not readily amenable to typical bottom-up approaches. So far, all high resolution middle-down approaches are done in data-dependent acquisition mode, using both collision-induced dissociation or electron capture/transfer dissociation techniques. Here, we explore middle-down proteomics with electron transfer dissociation using a targeted acquisition mode, parallel reaction monitoring (PRM), on an Orbitrap Fusion. As an example of a highly modified protein, we used histone H3 fractions from untreated and DMSO-treated Murine ErythroLeukemia (MEL) cells. We first determined optimized instrument parameters to obtain high sequence coverage using a synthetic standard peptide. We then setup a combined method of both MS1 scans and PRM scans of the 20 most abundant combinations of methylation and acetylation of the +10 charge state of the N-terminal tail of H3. Weak cation exchange hydrophilic interaction chromatography was used to separate the N-terminal H3 tail, primarily, by its acetylation and, to a secondary degree, by its methylation status, which aided in the interpretation of the results. After deconvolution of the highly charged ions, peaks were annotated to a minimum set of 254 H3 proteoforms in the untreated and treated samples. Upon DMSO treatment, global quantitation changes from the MS1 level show a relative decrease of 2, 3, 4, and 5 acetylations and an increase of 0 and 1 acetylations. A fragment ion map was developed to visualize specific differences between treated and untreated samples. Taken together, the data presented here show that middle-down proteomics with electron transfer dissociation using PRM is a novel, attractive method for the effective analysis and quantification of large and highly modified peptides.

  19. Dissociative electron attachment to water

    NASA Astrophysics Data System (ADS)

    Haxton, Daniel James

    Dissociative electron attachment to water, H2O+e-→ H+OH-3.27eV H2+O-3.56eV H-+OHX P2 4.35eVH+H+O-8.04e VH-+OH* S2 8.38eVH-+H+O 8.75eV 0.1 is a physical process that has been studied since 1930[1]. It may be viewed as an inherently is non-Born-Oppenheimer process, for the initial state belongs to the electronic continuum, and the final state is electronically bound. As such, it presents a particular challenge for theory. We present a first-principles theoretical treatment of this process, in which we calculate the cross sections for production of the three major atom - diatom products observed by experiment, H2 + O-, H- + OH (X 2pi), and H- + OH (2Sigma). These states comprise the bulk of the experimentally determined cross section. In the present work we employ a Born-Oppenheimer expansion of the wavefunction for nuclear and electronic motion, and treat both quantum mechanically. The adiabatic treatment of the electronic motion incorporates multiconfiguration, correlated wavefunctions and includes an explicit treatment of the electronic continuum. For the nuclear dynamics we incorporate the full dimensionality of nuclear motion, including the three internal degrees of freedom and the effect of rotation. This is the first ab initio treatment of dissociative electron attachment which incorporates more than one degree of freedom in the nuclear dynamics. The first step in our Born-Oppenheimer treatment is to calculate adiabatic potential energy surfaces for the three metastable electronic states which are involved, the 2B1, 2A1, and 2B 2 electronic Feshbach resonances. Global potential energy surfaces are defined which incorporate the results of fixed-nuclei, ab initio calculations: quantum-mechanical electron scattering calculations using the complex Kohn method are performed and augmented by the results of large-scale configuration-interaction calculations performed in a restricted Hilbert space. The global surfaces are defined by a very accurate fit combining a 35

  20. Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers.

    PubMed

    Hopley, Chris; Bristow, Tony; Lubben, Anneke; Simpson, Alec; Bull, Elaine; Klagkou, Katerina; Herniman, Julie; Langley, John

    2008-06-01

    Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments - a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns. The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS. The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC

  1. Quantum/classical time-dependent self-consistent field treatment of Ar+HCO inelastic and dissociative scattering

    NASA Astrophysics Data System (ADS)

    Whittier, Gregory S.; Light, John C.

    1999-03-01

    A quantum/classical time-dependent self-consistent field (Q/C TDSCF) approach is used to simulate the dynamics of collisions of Ar with HCO. We present state-to-state cross sections and thermal rate constants for vibrational transitions. Using this model together with assumptions about the rotational energy transfer and a master equation treatment of the kinetics, the low-pressure thermal rate of collision-induced dissociation (CID) was calculated over the 300-4000 K temperature range. A comparison with experiment shows good agreement at high temperatures and poor agreement at low temperatures. The high temperature results were sufficient to obtain an Arrhenius expression for the rate that agrees with all experimental results of which we are aware.

  2. Precursor charge state prediction for electron transfer dissociation tandem mass spectra.

    PubMed

    Sharma, Vagisha; Eng, Jimmy K; Feldman, Sergey; von Haller, Priska D; MacCoss, Michael J; Noble, William S

    2010-10-01

    Electron-transfer dissociation (ETD) induces fragmentation along the peptide backbone by transferring an electron from a radical anion to a protonated peptide. In contrast with collision-induced dissociation, side chains and modifications such as phosphorylation are left intact through the ETD process. Because the precursor charge state is an important input to MS/MS sequence database search tools, the ability to accurately determine the precursor charge is helpful for the identification process. Furthermore, because ETD can be applied to large, highly charged peptides, the need for accurate precursor charge state determination is magnified. Otherwise, each spectrum must be searched repeatedly using a large range of possible precursor charge states. To address this problem, we have developed an ETD charge state prediction tool based on support vector machine classifiers that is demonstrated to exhibit superior classification accuracy while minimizing the overall number of predicted charge states. The tool is freely available, open source, cross platform compatible, and demonstrated to perform well when compared with an existing charge state prediction tool. The program is available from http://code.google.com/p/etdz/.

  3. Infrared Multiple-Photon Dissociation spectroscopy of group II metal complexes with salicylate

    SciTech Connect

    Ryan P. Dain; Gary Gresham; Gary S. Groenewold; Jeffrey D. Steill; Jos Oomens; Michael J. van Stipdonk

    2011-07-01

    Ion-trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations were used to characterize singly-charged, 1:1 complexes of Ca2+, Sr2+ and Ba2+ with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO2 and (b) formation of [MOH]+ where M=Ca2+, Sr2+ or Ba2+. DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cation is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 – 1650 cm-1, and the best correlation between theoretical and experimental spectra for the structure that features coordination of the metal ion by phenoxide and the carbonyl group of the carboxylic acid group, consistent with calculated energies for the respective species.

  4. Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

    NASA Astrophysics Data System (ADS)

    Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.

    2013-10-01

    The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein

  5. Are major dissociative disorders characterized by a qualitatively different kind of dissociation?

    PubMed

    Rodewald, Frauke; Dell, Paul F; Wilhelm-Gossling, Claudia; Gast, Ursula

    2011-01-01

    A total of 66 patients with a major dissociative disorder, 54 patients with nondissociative disorders, and 30 nonclinical controls were administered the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised, the Dissociative Experiences Scale, the Multidimensional Inventory of Dissociation, and the Symptom Checklist 90-Revised. Dissociative patients reported significantly more dissociative and nondissociative symptoms than did nondissociative patients and nonclinical controls. When general psychopathology was controlled, the dissociation scores of dissociative patients were still significantly higher than those of both other groups, whereas the dissociation scores of nondissociative patients and nonclinical controls no longer differed. These findings appear to be congruent with a typological model of dissociation that distinguishes between 2 qualitatively different kinds of dissociation. Specifically, the results of this study suggest that the dissociation that occurs in major dissociative disorders (i.e., dissociative identity disorder [DID] and dissociative disorder not otherwise specified, Type 1 [DDNOS-1]) is qualitatively different from the dissociation that occurs in persons who do not have a dissociative disorder. In contrast to previous research, the dissociation of persons who do not have a dissociative disorder is not limited to absorption; it covers a much wider range of phenomena. The authors hypothesize that different mechanisms produce the dissociation of persons with DID and DDNOS-1 as opposed to the dissociation of persons who do not have a dissociative disorder.

  6. Dissociative recombination and the decay of a molecular ultracold plasma

    NASA Astrophysics Data System (ADS)

    Rennick, C. J.; Saquet, N.; Morrison, J. P.; Ortega-Arroyo, J.; Godin, P.; Fu, L.; Schulz-Weiling, M.; Grant, E. R.

    2011-07-01

    Double-resonant photoexcitation of nitric oxide in a molecular beam creates a dense ensemble of 51f(2) Rydberg states, which evolves to form a plasma of free electrons trapped in the potential well of an NO+ spacecharge. The plasma travels at the velocity of the molecular beam, and, on passing through a grounded grid, yields an electron time-of-flight signal that gauges the plasma size and quantity of trapped electrons. This plasma expands at a rate that fits with an electron temperature as low as 5 K. Dissociative recombination of NO+ ions with electrons provides the primary dissipation mechanism for the plasma. We have identified three dissociation pathways, and quantified their relative contributions to the measured rate: Two-body dissociative recombination competes with direct three-body recombination to neutral dissociation products, and with a process in which three-body recombination and electron-impact ionization form an equilibrium population of high-Rydberg states that decays by predissociation. Using available collision-theory rate constants for three-body recombination and ionization, together with quantum mechanical estimates of predissociation rates, we predict that the relaxation of the plasma to a high-Rydberg equilibrium outpaces direct three-body dissociative recombination, and, among second-order processes, the rate of two-body electron-cation dissociative recombination substantially exceeds the rate at which the high-Rydberg equilibrium dissociatively relaxes. The rate constant for dissociative recombination extracted from these data conforms with predictions drawn from theory for isolated electron-ion collisions. Methods based on the dissipation of molecular ultracold plasmas may provide a means for estimating rates of dissociative recombination for a variety of complex molecules.

  7. Recurrent Episodes of Dissociative Fugue

    PubMed Central

    Angothu, Hareesh; Pabbathi, Lokeswar Reddy

    2016-01-01

    Dissociative fugue is rare entity to encounter with possible differentials of epilepsy and malingering. It is one of the dissociative disorders rarely seen in clinical practice more often because of the short lasting nature of this condition. This might also be because of organized travel of the individuals during the episodes and return to their families after the recovery from episodes. This is a case description of a patient who has experienced total three episodes of dissociative fugue. The patient has presented during the third episode and two prior episodes were diagnosed as fugue episodes retrospectively based on the history. Planned travel in this case by the patient to a distant location was prevented because of early diagnosis and constant vigilance till the recovery. As in this case, it may be more likely that persons with Dissociative fugue may develop similar episodes if they encounter exceptional perceived stress. However, such conclusions may require follow-up studies. PMID:27114633

  8. Electron-driven excitation and dissociation of molecules

    NASA Astrophysics Data System (ADS)

    Chourou, S.; Larson, Å.; Orel, A. E.

    2010-01-01

    In the collision of electrons with molecules and molecular ions, excitation and dissociation are dominated by resonant processes, where the electron becomes temporarily trapped, changing the forces felt by the nuclei. In this paper, we will outline our method for treating these collision processes, where one or more resonant states exist. We separate the problem into two steps. First we carry out ab initio electron scattering calculations at fixed internuclear geometries to determine the resonant energy surfaces and the corresponding surface of autoionization widths, using the Complex Kohn variational method. These resonance positions and widths are then used as input to a dynamics study to determine the cross section and product distributions for the dissociation or excitation process. We will present results on a number of systems, including HCCH, HCN/HNC and HCCCN as examples of dissociative attachment, and H2O+ for dissociative recombination.

  9. Dissociation of LPS-induced monocytic ex vivo production of granulocyte colony-stimulating factor (G-CSF) and TNF-alpha in patients with septic shock.

    PubMed

    Weiss, M; Fischer, G; Barth, E; Boneberg, E; Schneider, E M; Georgieff, M; Hartung, T

    2001-01-07

    Over a 6 month period, in 192 patients admitted to the intensive care unit (ICU), a longitudinal analysis of whole blood lipopolysaccharide (LPS)-induced ex vivo cytokine production was performed on a daily basis until discharge from the ICU or death. Twenty-one patients with proven infections were in septic shock for the first time and for at least 3 days' duration. Ex vivo LPS-inducible release of granulocyte colony-stimulating factor (G-CSF) was upregulated and that of TNF-alpha was downregulated in patients with septic shock, regardless whether they survived or died. In conclusion, LPS-induced ex vivo TNF-alpha and G-CSF cytokine release by monocytes is regulated differentially in patients with septic shock. Since upregulation of LPS-induced production of G-CSF occurred earlier in survivors than in non-survivors, rapidly elevated and sustained G-CSF responsiveness may contribute to survival in septic shock.

  10. Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments.

    PubMed

    Kandasamy, Kumaran; Pandey, Akhilesh; Molina, Henrik

    2009-09-01

    Electron transfer dissociation (ETD) is increasingly becoming popular for high-throughput experiments especially in the identification of the labile post-translational modifications. Most search algorithms that are currently in use for querying MS/MS data against protein databases have been optimized on the basis of matching fragment ions derived from collision induced dissociation of peptides, which are dominated by b and y ions. However, electron transfer dissociation of peptides generates completely different types of fragments: c and z ions. The goal of our study was to test the ability of different search algorithms to handle data from this fragmentation method. We compared four MS/MS search algorithms (OMSSA, Mascot, Spectrum Mill, and X!Tandem) using approximately 170,000 spectra generated from a standard protein mix, as well as from complex proteomic samples which included a large number of phosphopeptides. Our analysis revealed (1) greater differences between algorithms than has been previously reported for CID data, (2) a significant charge state bias resulting in >60-fold difference in the numbers of matched doubly charged peptides, and (3) identification of 70% more peptides by the best performing algorithm than the algorithm identifying the least number of peptides. Our results indicate that the search engines for analyzing ETD derived MS/MS spectra are still in their early days and that multiple search engines could be used to reduce individual biases of algorithms.

  11. Dissociative disorders in DSM-5.

    PubMed

    Spiegel, David; Lewis-Fernández, Roberto; Lanius, Ruth; Vermetten, Eric; Simeon, Daphne; Friedman, Matthew

    2013-01-01

    The rationale, research literature, and proposed changes to the dissociative disorders and conversion disorder in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) are presented. Dissociative identity disorder will include reference to possession as well as identity fragmentation, to make the disorder more applicable to culturally diverse situations. Dissociative amnesia will include dissociative fugue as a subtype, since fugue is a rare disorder that always involves amnesia but does not always include confused wandering or loss of personality identity. Depersonalization disorder will include derealization as well, since the two often co-occur. A dissociative subtype of posttraumatic stress disorder (PTSD), defined by the presence of depersonalization or derealization in addition to other PTSD symptoms, is being recommended, based upon new epidemiological and neuroimaging evidence linking it to an early life history of adversity and a combination of frontal activation and limbic inhibition. Conversion disorder (functional neurological symptom disorder) will likely remain with the somatic symptom disorders, despite considerable dissociative comorbidity.

  12. Electron induced dissociation of singly deprotonated peptides.

    PubMed

    Kalli, Anastasia; Grigorean, Gabriela; Håkansson, Kristina

    2011-12-01

    Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion-electron and ion-ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.

  13. Global functioning and disability in dissociative disorders.

    PubMed

    Mueller-Pfeiffer, Christoph; Rufibach, Kaspar; Perron, Noelle; Wyss, Daniela; Kuenzler, Cornelia; Prezewowsky, Cornelia; Pitman, Roger K; Rufer, Michael

    2012-12-30

    Dissociative disorders are frequent comorbid conditions of other mental disorders. Yet, there is controversy about their clinical relevance, and little systematic research has been done on how they influence global functioning. Outpatients and day care patients (N=160) of several psychiatric units in Switzerland were assessed with the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV Axis I Disorders, Structured Clinical Interview for DSM-IV Dissociative Disorders, Global Assessment of Functioning Scale, and World Health Organization Disability Assessment Schedule-II. The association between subjects with a dissociative disorder (N=30) and functional impairment after accounting for non-dissociative axis I disorders was evaluated by linear regression models. We found a proportion of 18.8% dissociative disorders (dissociative amnesia=0%, dissociative fugue=0.6%, depersonalization disorder=4.4%, dissociative identity disorder=7.5%, dissociative disorder-not-otherwise-specified=6.3%) across treatment settings. Adjusted for other axis I disorders, subjects with a comorbid dissociative identity disorder or dissociative disorder-not-otherwise-specified had a median global assessment of functioning score that was 0.86 and 0.88 times, respectively, the score of subjects without a comorbid dissociative disorder. These findings support the hypothesis that complex dissociative disorders, i.e., dissociative identity disorder and dissociative disorder-not-otherwise-specified, contribute to functional impairment above and beyond the impact of co-existing non-dissociative axis I disorders, and that they qualify as "serious mental illness".

  14. Does dissociation further our understanding of PTSD?

    PubMed

    Bryant, Richard A

    2007-01-01

    Peritraumatic dissociation, and other dissociative reactions, refer to alterations in awareness in the context of a traumatic experience. This review provides an overview of the current conceptualization of dissociation, critiques methodological approaches to studying dissociation, and reviews the evidence for the purported relationship between dissociative reactions and posttraumatic stress disorder. The evidence challenges the notion that a linear relationship exists between dissociation and psychiatric morbidity. Future research should abandon the global construct of dissociation, and study the specific responses that involve altered awareness under experimental conditions.

  15. Involuntariness in hypnotic responding and dissociative symptoms.

    PubMed

    Dell, Paul F

    2010-01-01

    Clark Hull's (1933) research on dissociation was based on a 'straw man' formulation of dissociation; he claimed that dissociation requires noninterference. Hull completely ignored the then-current paradigm of dissociation--dissociation as automatism--and claimed that he had refuted the validity of the phenomenon of dissociation. Hull's view of dissociation held sway in the hypnosis field for 60 years. This essay seeks to retrieve the Janetian paradigm of dissociation as automatism. Automatisms are unexpected, uninitiated, involuntary behaviors that just 'happen.' The author argues that human sensitivity to the experience of involuntariness (a) is quite important, (b) was selected by evolution, and (c) is central to both hypnotic responses and dissociative symptoms. This editorial urges the hypnosis field and the dissociation field to jointly undertake a renewed investigation of the experience of involuntariness and to follow recent neuroimaging studies which indicate that the parietal cortex underlies the experience of involuntariness.

  16. Investigating gas phase dissociation pathways of crosslinked peptides : application to protein complex determination.

    SciTech Connect

    Young, Malin M.; Gaucher, Sara P.; Hadi, Masood Z.

    2005-02-01

    Chemical crosslinking is an important tool for probing protein structure and protein-protein interactions. The approach usually involves crosslinking of specific amino acids within a folded protein or protein complex, enzymatic digestion of the crosslinked protein(s), and identification of the resulting crosslinked peptides by liquid chromatography/mass spectrometry (LC/MS). In this manner, distance constraints are obtained for residues that must be in close proximity to one another in the native structure or complex. As the complexity of the system under study increases, for example, a large multi-protein complex, simply measuring the mass of a crosslinked species will not always be sufficient to determine the identity of the crosslinked peptides. In such a case, tandem mass spectrometry (MS/MS) could provide the required information if the data can be properly interpreted. In MS/MS, a species of interest is isolated in the gas phase and allowed to undergo collision induced dissociation (CID). Because the gas-phase dissociation pathways of peptides have been well studied, methods are established for determining peptide sequence by MS/MS. However, although crosslinked peptides dissociate through some of the same pathways as isolated peptides, the additional dissociation pathways available to the former have not been studied in detail. Software such as MS2Assign has been written to assist in the interpretation of MS/MS from crosslinked peptide species, but it would be greatly enhanced by a more thorough understanding of how these species dissociate. We are thus systematically investigating the dissociation pathways open to crosslinked peptide species. A series of polyalanine and polyglycine model peptides have been synthesized containing one or two lysine residues to generate defined inter- and intra-molecular crosslinked species, respectively. Each peptide contains 11 total residues, and one arginine residue is present at the carboxy terminus to mimic species

  17. Dissociative disorders among alcohol-dependent inpatients.

    PubMed

    Evren, Cuneyt; Sar, Vedat; Karadag, Figen; Tamar Gurol, Defne; Karagoz, Mustafa

    2007-08-30

    The aim of this study was to determine the prevalence of dissociative disorders among inpatients with alcohol dependency. The Dissociative Experiences Scale was used to screen 111 alcohol-dependent patients consecutively admitted to the inpatient unit of a dependency treatment center. Subgroups of 29 patients who scored 30.0 or above and 25 patients who scored below 10.0 were then evaluated with the Dissociative Disorders Interview Schedule and the Structured Interview for DSM-IV Dissociative Disorders. The interviewers were blind to the Dissociative Experiences Scale scores. Of the 54 patients evaluated, 10 (9.0% of the original 111) patients had a dissociative disorder. A considerable number of the remaining patients reported a high level of dissociative experiences. Among the dissociative disorder group, nine patients had dissociative disorder not otherwise specified and one patient had depersonalization disorder. Female gender, younger age, history of suicide attempt, childhood emotional and sexual abuse, and neglect were more frequent in the dissociative disorder group than among non-dissociative patients. The dissociative disorder group also had somatization disorder, borderline personality disorder, and lifetime major depression more frequently. For 9 of the 10 dissociative patients, dissociative symptoms started before the onset of alcohol use. Although the probability of having a comorbid dissociative disorder was not higher among alcohol-dependent inpatients than among the general psychiatric inpatients, the dissociative subgroup had distinct features. Many patients without a dissociative disorder diagnosis (predominantly men) provided hints of subtle dissociative psychopathology. Implications of comorbid dissociative disorders and dissociative experiences on prevention and treatment of alcohol dependency and the importance of gender-specific characteristics in this relationship require further study.

  18. Collision-Induced Absorption by H2 Pairs in the Second Overtone Band at 298 and 77.5 K: Comparison between Experimental and Theoretical Results

    NASA Technical Reports Server (NTRS)

    Brodbeck, C.; Bouanich, J.-P.; van-Thanh, Nguyen; Fu, Y.; Borysow, A.

    1999-01-01

    The collision-induced spectra of hydrogen in the region of the second overtone at 0.8 microns have been recorded at temperatures of 298 and 77.5 K and for gas densities ranging from 100 to 800 amagats. The spectral profile defined by the absorption coefficient per squared density varies significantly with the density, so that the binary absorption coefficient has been determined by extrapolations to zero density of the measured profiles. Our extrapolated measurements and our recent ab initio quantum calculation are in relatively good agreement with one another. Taking into account the very weak absorption of the second overtone band, the agreement is, however, not as good as it has become (our) standard for strong bands.

  19. Collision-induced infrared spectra of H2-He pairs at temperatures from 18 to 7000 K. II. Overtone and hot bands

    SciTech Connect

    Borysow, A.; Frommhold, L.; Texas Univ., Austin )

    1989-06-01

    The three lowest spectral moments of the collision induced absorption (CIA) spectra of H2-He pairs have been computed from first principles for temperatures T from 18 to 7000 K for a number of hydrogen overtone and hot bands involving vibrational quantum numbers nu = 0, 1, 2, 3 yields nu-prime = 0, 1, 2, 3. The data are given in a form suitable for the computation of CIA spectra of H2-He as function of frequency and temperature, using simple computer codes and model line shapes. The work is of interest for the spectroscopy of the atmospheres of the outer planets and of stars that contain neutral molecular hydrogen and helium (late stars, white dwarfs, and Population II stars) in the infrared and visible region of the spectrum. 13 refs.

  20. Collision-induced Raman scattering by rare-gas atoms: The isotropic spectrum of Ne–Ne and its mean polarizability

    SciTech Connect

    Rachet, Florent; Chrysos, Michael; Dixneuf, Sophie

    2015-05-07

    We report the room-temperature isotropic collision-induced light scattering spectrum of Ne–Ne over a wide interval of Raman shifts, and we compare it with the only available experimental spectrum for that system as well as with spectra calculated quantum-mechanically with the employ of advanced ab initio-computed data for the incremental mean polarizability. The spectral range previously limited to 170 cm{sup −1} is now extended to 485 cm{sup −1} allowing us to successfully solve the inverse-scattering problem toward an analytic model for the mean polarizability that perfectly matches our measurements. We also report the depolarization ratio of the scattering process, lingering over the usefulness of this property for more stringent checks between the various polarizability models.

  1. Dissociative symptomatology in cancer patients

    PubMed Central

    Civilotti, Cristina; Castelli, Lorys; Binaschi, Luca; Cussino, Martina; Tesio, Valentina; Di Fini, Giulia; Veglia, Fabio; Torta, Riccardo

    2015-01-01

    Introduction: The utilization of the post-traumatic stress disorder (PTSD) diagnostic spectrum is currently being debated to categorize psychological adjustment in cancer patients. The aims of this study were to: (1) evaluate the presence of cancer-related traumatic dissociative symptomatology in a sample of cancer patients; (2) examine the correlation of cancer-related dissociation and sociodemographic and medical variables, anxiety, depression, and post-traumatic stress symptomatology; (3) investigate the predictors of cancer-related dissociation. Methods: Ninety-two mixed cancer patients (mean age: 58.94, ds = 10.13) recruited from two hospitals in northern Italy were administered a questionnaire on sociodemographic and medical characteristics, the Karnofsky Scale to measure the level of patient activity and medical care requirements, the Hospital Anxiety and Depression Scale (HADS) to evaluate the presence of anxiety and depression, the Impact of Event Scale Revised (IES-R) to assess the severity of intrusion, avoidance, and hypervigilance, and the Peritraumatic Dissociative Experiences Questionnaire (PDEQ) to quantify the traumatic dissociative symptomatology. Results: 31.5% of participants report a PDEQ score above the cutoff. The results indicated that dissociative symptomatology was positively correlated with HADS scores (HADS-Anxiety: r = 0.476, p < 0.001; HADS-Depression: r = 0.364, p < 0.001) and with IES-R scores (IES-R-Intrusion: r = 0.698, p < 0.001; IES-R-Avoidance: r = 0.619, p < 0.001; IES-R- Hypervigilance: r = 0.681, p < 0.001). A stepwise regression analysis was performed in order to find the predictors of cancer-related traumatic dissociative symptomatology. The results converged on a three predictor model revealing that IES-R-Intrusion, IES-R-Avoidance, and IES-R-Hyperarousal accounted for 53.9% of the explained variance. Conclusion: These findings allow us to hypothesize a specific psychological reaction which may be ascribed to the traumatic

  2. Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.

    PubMed Central

    Gao, J; Wu, Q; Carbeck, J; Lei, Q P; Smith, R D; Whitesides, G M

    1999-01-01

    This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) was used to determine the energetics of dissociation of these CAII-sulfonamide complexes in the gas phase. When two molecules of a benzenesulfonamide (1) were bound simultaneously to one molecule of CAII, one of them was found to exhibit significantly weaker binding (DeltaE50 = 0.4 V, where E50 is defined as the amplitude of sustained off-resonance irradiation when 50% of the protein-ligand complexes are dissociated). In solution, the benzenesulfonamide group coordinates as an anion to a Zn(II) ion bound at the active site of the enzyme. The gas phase stability of the complex with the weakly bound inhibitor was the same as that of the inhibitor complexed with apoCAII (i.e., CAII with the Zn(II) ion removed from the binding site). These results indicate that specific interactions between the sulfonamide group on the inhibitor and the Zn(II) ion on CAII were preserved in the gas phase. Experiments also showed a higher gas phase stability for the complex of para-NO2-benzenesulfonamide-CAII than that for ortho-NO2-benzenesulfonamide-CAII complex. This result further suggests that steric interactions of the inhibitors with the binding pocket of CAII parallel those in solution. Overall, these results are consistent with the hypothesis that CAII retains, at least partially, the structure of its binding pocket in the gas phase on the time scale (seconds to minutes) of the ESI-FTICR measurements. PMID:10354450

  3. Ancient pottery from archaeological sites in Southern Italy: first evidence of red grape products markers.

    PubMed

    Bianco, Giuliana; Granafei, Sara; Colivicchi, Fabio; Catald, Tommaso; Buchicchio, Alessandro

    2015-01-01

    The chemical analysis of tartaric acid (TA) and syringic acid (SA), as grape product markers in ancient ceramic vessels from the sites of Manduria and Torre di Satriano (southern Italy), was successfully performed. Firstly, the fragmentation behaviour of TA and SA as deprotonated molecules, [M-H](-), obtained by collision-induced dissociation, was investigated. Then, reversed-phase liquid chromatography (RPLC) with electrospray ionization (ESI) in negative ion mode, using a quadrupole linear ion trap in multiple reaction monitoring (MRM), was employed. A binary mobile phase composed of water-acetonitrile with 0.1% (v/v) acetic acid enabled the optimum ESI efficiency of SA, greatly improving its identification when it occurs in trace amounts. Chemical analysis of ancient pottery fragments is a valid method for establishing the existence of preserved organic residues, which is valuable new evidence for the culture and customs of ancient populations, in this case those of southern Italy. The proposed RPLC-ESI-MRM method allowed a systematic investigation of ceramic fragments of both archaeological sites, thus providing positive evidence for the presence of TA and SA as grape product markers in storage vessels dating back to the ninth to third centuries BC.

  4. Are the Radical Centers in Peptide Radical Cations Mobile? The Generation, Tautomerism, and Dissociation of Isomeric α-Carbon-Centered Triglycine Radical Cations in the Gas Phase

    SciTech Connect

    Chu, Ivan K.; Zhao, Junfang; Xu, Minjie; Siu, Shiu On; Hopkinson, Alan C.; Siu , K W Michael

    2008-05-31

    The mobility of the radical center in three isomeric triglycine radical cationss[G•GG]+, [GG•G]+, and [GGG•]+shas been investigated theoretically via density functional theory (DFT) and experimentally via tandem mass spectrometry. These radical cations were generated by collision-induced dissociations (CIDs) of Cu(II)-containing ternary complexes that contain the tripeptides YGG, GYG, and GGY, respectively (G and Y are the glycine and tyrosine residues, respectively). Dissociative electron transfer within the complexes led to observation of [Y•GG]+, [GY•G]+, and [GGY•]+; CID resulted in cleavage of the tyrosine side chain as p-quinomethide, yielding [G•GG]+, [GG•G]+, and [GGG•]+, respectively. Interconversions between these isomeric triglycine radical cations have relatively high barriers (g44.7 kcal/mol), in support of the thesis that isomerically pure [G•GG]+, [GG•G]+, and [GGG•]+ can be experimentally produced. This is to be contrasted with barriers < 17 kcal/mol that were encountered in the tautomerism of protonated triglycine [Rodriquez C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The CID spectra of [G•GG]+, [GG•G]+, and [GGG•]+ were substantially different, providing experimental proof that initially these ions have distinct structures. DFT calculations showed that direct dissociations are competitive with interconversions followed by dissociation.

  5. Diffraction dissociation at the LHC

    SciTech Connect

    Jenkovszky, Laszlo; Orava, Risto; Salii, Andrii

    2013-04-15

    We report on recent calculations of low missing mass single (SD) and double (DD) diffractive dissociation at LHC energies. The calculations are based on a dual-Regge model, dominated by a single Pomeron exchange. The diffractively excited states lie on the nucleon trajectory N*, appended by the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing mass dependence of the differential and integrated single-and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

  6. [Dissociative identity disorder or schizophrenia?].

    PubMed

    Tschöke, S; Steinert, T

    2010-01-01

    We present a case of dissociative identity disorder in which Schneiderian first rank symptoms were present besides of various states of consciousness. Thus the diagnosis of schizophrenia had to be considered. Formally, the symptoms met ICD-10 criteria for schizophrenia. However, taking into account the lack of formal thought disorder and of negative symptoms as well as a typical history of severe and prolonged traumatisation, we did not diagnose a co-morbid schizophrenic disorder. There is good evidence for the existence of psychotic symptoms among patients with dissociative disorders. However, in clinical practice this differential diagnosis is rarely considered.

  7. Electron-impact dissociation and ionization of NO+ ions

    NASA Astrophysics Data System (ADS)

    Belic, D. S.; Urbain, X.; Cherkani-Hassani, H.; Defrance, P.

    2016-07-01

    Absolute cross sections for electron-impact ionization and dissociation of NO+ ions are reported. Simple ionization to NO2+ ion and production of singly charged N+ and O+ and doubly charged N2+ and O2+ fragments have been investigated. The animated electron-ion crossed-beam method is applied in the energy range from the respective thresholds up to 2.5 keV. The maximum of the simple ionization cross section is found to be (3.49 ± 0.07) × 10-17 cm2 at 135 eV. The total cross sections for N+ and O+ fragments at the maximum are found to be (13.9 ± 1.0) × 10-17 cm2 and (14.0 ± 1.4) × 10-17 cm2, respectively, both at an energy of 85 eV. By performing careful magnetic field scans of the detected signal, contributions of dissociative excitation and dissociative ionization to N+ and O+ production are determined separately. The cross sections for asymmetric dissociative ionization to N2+ and O2+ are found to be over one order of magnitude smaller. Distributions of the kinetic energy release to the fragments are determined for all dissociation processes.

  8. A Strategy Combining Higher Energy C-Trap Dissociation with Neutral Loss- and Product Ion-Based MS(n) Acquisition for Global Profiling and Structure Annotation of Fatty Acids Conjugates.

    PubMed

    Bi, Qi-Rui; Hou, Jin-Jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-Hong; Dai, Zhuo; Yan, Bing-Peng; Wang, Jian-Wei; Shi, Xiao-Jian; Wu, Wan-Ying; Guo, De-An

    2017-03-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MS(n) (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MS(n) acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB. Graphical Abstract ᅟ.

  9. A Strategy Combining Higher Energy C-Trap Dissociation with Neutral Loss- and Product Ion-Based MSn Acquisition for Global Profiling and Structure Annotation of Fatty Acids Conjugates

    NASA Astrophysics Data System (ADS)

    Bi, Qi-rui; Hou, Jin-jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-hong; Dai, Zhuo; Yan, Bing-peng; Wang, Jian-wei; Shi, Xiao-jian; Wu, Wan-ying; Guo, De-an

    2017-03-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MSn (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MSn acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB.

  10. A Strategy Combining Higher Energy C-Trap Dissociation with Neutral Loss- and Product Ion-Based MSn Acquisition for Global Profiling and Structure Annotation of Fatty Acids Conjugates

    NASA Astrophysics Data System (ADS)

    Bi, Qi-rui; Hou, Jin-jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-hong; Dai, Zhuo; Yan, Bing-peng; Wang, Jian-wei; Shi, Xiao-jian; Wu, Wan-ying; Guo, De-an

    2016-12-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MSn (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MSn acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C9) and sebacic acid (C10)] and three unsaturated dicarboxylic acids (u-C8, u-C9, and u-C10). All these results greatly enriched the structures of DACBs in VB.

  11. [Gender differences in dissociative disorders].

    PubMed

    Spitzer, C; Freyberger, H J

    2008-01-01

    The relationship between mental illness, on the one hand, and sex and gender, on the other hand, has received interest since the beginning of medicine in antique times. A prototypical example of a seemingly woman-specific disease is hysteria. The term itself, which is derived from the Greek word for womb, denotes a psychosexual dimension comprising the current attitude towards sexuality and the dominating gender relationship. In addition, the colourful history of hysteria indicates that illness is not exclusively determined by biological factors, but also significantly by socio-cultural influences, for example in the treatment of hysterical women. Even nowadays, there is a wide-spread belief that dissociative symptoms and disorders, which have succeeded hysteria in current classification systems, are predominantly seen in women. However, empirical studies in the general population and in different clinical samples using sound instruments have indicated that dissociative symptoms do not differ between the genders. The seemingly dominance of dissociative disorders in women may also depend on the socio-cultural context, because men with dissociative disorders usually do not enter the general health system, but rather the legal system, i.e. they can be found in jail or forensic institutions.

  12. Modelling of Collision Induced Absorption Spectra Of H2-H2 Pairs for the Planetary Atmospheres Structure: The Second Overtone Band

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra; Borysow, Jacek I.

    1998-01-01

    The main objective of the proposal was to model the collision induced, second overtone band of gaseous hydrogen at low temperatures. The aim of this work is to assist planetary scientists in their investigation of planetary atmospheres, mainly those of Uranus and Neptune. The recently completed extended database of collision induced dipole moments of hydrogen pairs allowed us, for the first time, to obtain dipole moment matrix elements responsible for the roto-vibrational collision induced absorption spectra of H2-H2 in the second overtone band. Despite our numerous attempts to publish those data, the enormous volume of the database did not allow us to do this. Instead, we deposited the data on a www site. The final part of this work has been partially supported by NASA, Division for Planetary Atmospheres. In order to use our new data for modelling purpose, we first needed to test how well we can reproduce the existing experimental data from theory, when using our new input data. Two papers resulted from this work. The obtained agreement between theoretical results and the measurements appeared to be within 10-30%. The obviously poorer agreement than observed for the first H2 overtone, the fundamental, and the rototranslational bands can be attributed to the fact that dipole moments responsible for the second overtone are much weaker, therefore susceptible to larger numerical uncertainties. At the same time, the intensity of the second overtone band is much weaker and therefore it is much harder to be measured accurately in the laboratory. We need to point out that until now, no dependable model of the 2nd overtone band was available for modelling of the planetary atmospheres. The only one, often referred to in previous works on Uranian and Neptune's atmospheres, uses only one lineshape, with one (or two) parameter(s) deduced at the effective temperature of Uranus (by fitting the planetary observation). After that, the parameter(s) was(were) made temperature

  13. On the statistical nature of collision and surface-induced dissociation: a theoretical investigation of aluminum clusters.

    PubMed

    Larrégaray, Pascal; Peslherbe, Gilles H

    2006-02-02

    The unimolecular dissociation dynamics of aluminum clusters following collision with either a rare gas atom or a surface is investigated by classical trajectory simulations with model potentials. Two conformers of Al(6) with very distinct shapes, i.e., the spherical O(h) and planar C(2)(h) clusters, are considered in this work. The initial vibrational energy and angular momentum distributions resulting from collision, as well as the energy and angular momentum resolved lifetime distributions, of excited clusters were determined for both collision-induced dissociation (CID) and surface-induced dissociation (SID) processes. The partitioning of excitation energy acquired upon collision was found to depend on the excitation mechanism (CID or SID), as well as on the cluster molecular shape, especially in the case of CID. For both types of processes, the energy and angular momentum resolved excited cluster lifetime distributions were found to decay exponentially, in agreement with statistical theories of chemical reactions, suggesting intrinsic Rice-Ramsperger-Kassel-Marcus (RRKM) behavior. Moreover, the simulated microcanonical rate constants determined from the cluster lifetime distributions are in good agreement with the predictions of the orbiting transition state model of phase space theory (OTS/PST), which further supports the statistical character of cluster CID and SID. Thus, in the CID and SID of highly fluxional systems such as aluminum clusters, the rate of intramolecular vibrational energy redistribution (IVR) is much faster than the dissociation rate, which validates one of the key assumptions, i.e., post-collision statistical behavior, underlying the models that are routinely used to determine cluster binding energies from experimental CID/SID cross sections.

  14. Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC4Ym) Monitored with Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Cao, Yanwei; Qin, Yujiao; Bruist, Michael; Gao, Shang; Wang, Bing; Wang, Huixin; Guo, Xinhua

    2015-06-01

    Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(XnC4Ym) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (Tm) obtained in solution show that a non-C base residue located at 5' end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3' end. Detection of penta- and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH = 4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.

  15. Mass Spectrometry as a Powerful Analytical Technique for the Structural Characterization of Synthesized and Natural Products

    NASA Astrophysics Data System (ADS)

    Es-Safi, Nour-Eddine; Essassi, El Mokhtar; Massoui, Mohamed; Banoub, Joseph

    Mass spectrometry is an important tool for the identification and structural elucidation of natural and synthesized compounds. Its high sensitivity and the possibility of coupling liquid chromatography with mass spectrometry detection make it a technique of choice for the investigation of complex mixtures like raw natural extracts. The mass spectrometer is a universal detector that can achieve very high sensitivity and provide information on the molecular mass. More detailed information can be subsequently obtained by resorting to collision-induced dissociation tandem mass spectrometry (CID-MS/MS). In this review, the application of mass spectrometric techniques for the identification of natural and synthetic compounds is presented. The gas-phase fragmentation patterns of a series of four natural flavonoid glycosides, three synthesized benzodiazepines and two synthesized quinoxalinone derivatives were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry techniques. Exact accurate masses were measured using a modorate resolution quadrupole orthogonal time-of-flight QqTOF-MS/MS hybrid mass spectrometer instrument. Confirmation of the molecular masses and the chemical structures of the studied compounds were achieved by exploring the gas-phase breakdown routes of the ionized molecules. This was rationalized by conducting low-energy collision CID-MS/MS analyses (product ion- and precursor ion scans) using a conventional quadrupole hexapole-quadrupole (QhQ) tandem mass spectrometer.

  16. Correction of precursor and product ion relative abundances in order to standardize CID spectra and improve Ecom50 accuracy for non-targeted metabolomics

    PubMed Central

    Dubey, Ritvik; Hill, Dennis W.; Lai, Steven; Ming-Hui, Chen; Grant, David F.

    2014-01-01

    Quantitative biases in the abundance of precursor and product ions due to mass discrimination in RF-only ion guides results in inaccurate collision induced dissociation (CID) spectra. We evaluated the effects of collision cell RF voltage and collision energy on CID spectra using ten singly protonated compounds (46–854 Da) in an orthogonal acceleration time-of-flight mass spectrometer. The relative ion transfer efficiency, i.e. the relative amount of ions transferred through the ion guide at any particular RF voltage was shown to be dependent on the ion’s m/z. We developed an algorithm to correct for the mass discriminating effects of RF voltage on CID spectra. The algorithm was tested for both precursor and product ions at multiple RF voltages and collision energies in order to ensure reliability. Our results suggest that compounds that generate major product ions with m/z values <150 have peak intensities that deviate substantially from their actual abundance. This has implications for small molecule metabolomics research, particularly for studies that rely on CID spectra matching methods for structure identification. PMID:25960696

  17. Self-Entanglement and the Dissociation of Homonuclear Diatomic Molecules

    SciTech Connect

    Gonis, Antonios; Zhang, Xiaoguang; Nicholson, Don M; Stocks, George Malcolm

    2014-01-01

    The concept of self-entanglement is introduced to describe a mixed state or ensemble density as a pure state in an augmented Hilbert space formed by the products of the individual states forming a mixed state (or ensemble). We use this representation of mixed states to show that upon dissociation a neutral homonuclear diatomic molecule will separate into two neutral atoms.

  18. Dissociative attachment of electrons to N2O

    NASA Technical Reports Server (NTRS)

    Krishnakumar, E.; Srivastava, S. K.

    1990-01-01

    Cross sections for the production of O(-) from N2O by the process of dissociative electron attachment have been measured for electron-impact energies ranging from 0 to 50 eV. Three new O(-) peaks are observed. The present data above 5-eV electron-impact energy differ considerably from the previous measurements.

  19. Progress in the measurement of temperature-dependent N2-N2 collision-induced absorption and H2-broadening of cold and hot CH4

    NASA Astrophysics Data System (ADS)

    Sung, Keeyoon; Wishnow, Ed; Venkataraman, Malathy; Brown, Linda R.; Ozier, Irving; Benner, D. Chris; Crawford, Tomithy J.; Mantz, Arlan; Smith, Mary-Ann H.

    2016-10-01

    We report preliminary measurements from two separate laboratory studies: (A) collision-induced absorption (CIA) of nitrogen in the far-infrared at temperatures between 78 and 130 K; and (B) temperature dependence of H2-broadening of CH4 in the near infrared at temperatures between 100 and 370 K.(A) Nitrogen collision-induced absorption provides the primary opacity of Titan at long wavelengths, thereby playing a critical role in determining the heat balance as well as the atmospheric composition and dynamics. Our new measurements of the nitrogen absorption spectrum at temperatures from 78 to 130 K are consistently ~20% higher than predictions made using theoretical models of Borysow and Frommhold (1986) [ApJ, 311, 1043] and of Karman et al. (2015)[J Chem Phys, 142, 084306]. However, the new data are consistent with the previous measurements at 78 K by the UBC group (Wishnow et al. 1996)[J Chem Phys, 104, 3511]. We present preliminary results for the N2-N2 CIA coefficients and their temperature dependence between 78 and 130 K, and comparisons with the above theoretical calculations.(B) In support of the Jovian and exoplanet atmospheric remote sensing in the near infrared, we have measured the temperature dependence of H2-broadened half width and pressure shift coefficients of CH4, both of which are known to be rotational quantum number dependent. We studied both cold and hot CH4 in the K band (~2.2 μm) with the focus on a) weaker lines in the v2+v3 band at low temperatures for cold giant planets and b) stronger lines in the v3+v4 band at elevated temperatures for extra-solar planets (e.g., hot-Jupiters). Three custom-built gas absorption cells (two cold and one hot) were used to obtain the spectra of CH4 and H2 mixtures at temperatures between 100 and 370 K. We will discuss our on-going spectrum analysis for a few select J manifolds and provide comparisons with published values, which are available only at room temperature.

  20. Dissociative Mothers' Subjective Experience of Parenting.

    ERIC Educational Resources Information Center

    Benjamin, Lynn R.; And Others

    1996-01-01

    A study of 54 mothers with a dissociative disorder, 20 mothers with other mental problems, and 20 normal mothers investigated what effect, if any, dissociation had on parenting. When tested on the Subjective Experiences of Parenting Scale, mothers with dissociation presented significantly more negative parenting behavior and attitudes. (CR)

  1. Surface-induced dissociation of peptides and protein complexes in a quadrupole/time-of-flight mass spectrometer.

    PubMed

    Galhena, Asiri S; Dagan, Shai; Jones, Christopher M; Beardsley, Richard L; Wysocki, Vicki H

    2008-03-01

    A novel in-line surface-induced dissociation (SID) device was designed and implemented in a commercial QTOF instrument (Waters/Micromass QTOF II). This new setup allows efficient SID for a broad range of molecules. It also allows direct comparison with conventional collision-induced dissociation (CID) on the same instrument, taking advantage of the characteristics of QTOF instrumentation, including extended mass range, improved sensitivity, and better resolution compared with quadrupole analyzers and ion traps. Various peptides and a noncovalent protein complex have been electrosprayed and analyzed with the new SID setup. Here we present SID of leucine enkephalin, fibrinopeptide A, melittin, insulin chain-B, and a noncovalent protein complex from wheat, heat shock protein 16.9. The SID spectra were also compared to CID spectra. With the SID setup installed, ion transmission proved to be efficient. SID fragmentation patterns of peptides are, in general, similar to CID, with differences in the relative intensities of some peaks such as immonium ions, backbone cleavage b- versus y-type ions, and y- versus y-NH3 ions, suggesting enhanced accessibility to high-energy/secondary fragmentation channels with SID. Furthermore, these results demonstrate that the in-line SID setup is a valid substitute for CID, with potential advantages for activation of singly/multiply charged peptides and larger species such as noncovalent protein complexes.

  2. Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

    SciTech Connect

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John; Smith, Richard D.; Metz, Thomas O.

    2007-06-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resulted in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.

  3. Dissociative Ionization of Aromatic and Heterocyclic Molecules

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    2003-01-01

    Space radiation poses a major health hazard to humans in space flight. The high-energy charged particles in space radiation ranging from protons to high atomic number, high-energy (HZE) particles, and the secondary species they produce, attack DNA, cells, and tissues. Of the potential hazards, long-term health effects such as carcinogenesis are likely linked to the DNA lesions caused by secondary electrons in the 1 - 30 eV range. Dissociative ionization (DI) is one of the electron collision processes that can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. To understand this process, we have developed a theoretical model for DI. Our model makes use of the fact that electron motion is much faster than nuclear motion and assumes DI proceeds through a two-step process. The first step is electron-impact ionization resulting in a particular state of the molecular ion in the geometry of the neutral molecule. In the second step the ion undergoes unimolecular dissociation. Thus the DI cross section sigma(sup DI)(sub a) for channel a is given by sigma(sup DI)(sub a) = sigma(sup I)(sub a) P(sub D) with sigma(sup I)(sub a) the ionization cross section of channel a and P(sub D) the dissociation probability. This model has been applied to study the DI of H2O, NH3, and CH4, with results in good agreement with experiment. The ionization cross section sigma(sup I)(sub a) was calculated using the improved binary encounter-dipole model and the unimolecular dissociation probability P(sub D) obtained by following the minimum energy path determined by the gradients and Hessians of the electronic energy with respect to the nuclear coordinates of the ion. This model is used to study the DI from the low-lying channels of benzene and pyridine to understand the different product formation in aromatic and heterocyclic molecules. DI study of the DNA base thymine is underway. Solvent effects will also be discussed.

  4. Effective novel dissociation methods for intact protein: heat-assisted nozzle-skimmer collisionally induced dissociation and infrared multiphoton dissociation using a Fourier transform ion cyclotron resonance mass spectrometer equipped with a micrometal electrospray ionization emitter.

    PubMed

    Yamada, Naoyuki; Suzuki, Ei-Ichiro; Hirayama, Kazuo

    2006-01-01

    Heating of a nano-electrospray ionization (nanoESI) source can improve the dissociation efficiency of collisionally induced dissociation (CID) methods, such as nozzle-skimmer CID (NS-CID) and infrared multiphoton dissociation (IRMPD), for large biomolecule fragmentation. A metal nanoESI emitter was used due to its resistance to heating above 250 degrees C. This novel method for the dissociation of large biomolecular ions is termed "heat-assisted NS-CID" (HANS-CID) or "heat-assisted IRMPD" (HA-IRMPD). Multiple charged nonreduced protein ions (8.6 Da ubiquitin, 14 kDa lysozyme, and 67 kDa bovine serum albumin) were directly dissociated by HANS-CID and HA-IRMPD to effectively yield fragment ions that could be assigned. The fragment ions of ubiquitin by HANS-CID can be analyzed by tandem mass spectrometry (MS/MS) using sustained off-resonance irradiation CID (SORI-CID) and IRMPD. In addition, a native large protein, immunoglobulin G (IgG, 150 kDa), was efficiently dissociated by HA-IRMPD. The product ions that were obtained reflected the domain structure of IgG. However, these product ions of IgG and lysozyme were not dissociated by MS/MS using the same heating energetic methods such as IRMPD and SORI-CID.

  5. Peritraumatic versus persistent dissociation in acute stress disorder.

    PubMed

    Panasetis, Paula; Bryant, Richard A

    2003-12-01

    The DSM-IV definition of acute stress disorder (ASD) regards dissociation that occurs during a trauma (peritraumatic dissociation) comparably to persistent dissociation. This study investigated the relative contributions of peritraumatic dissociation and persistent dissociation to acute posttraumatic stress reactions. Civilian trauma (N = 53) survivors with either acute stress disorder (ASD), subclinical ASD, or no ASD were administered modified versions of the Peritraumatic Dissociative Experiences Questionnaire that indexed both dissociation during the trauma and dissociation at the time of assessment. Persistent dissociation was more strongly associated with ASD severity and intrusive symptoms than peritraumatic dissociation. These results are consistent with the proposition that persistent, rather than peritraumatic, dissociation is associated with posttraumatic psychopathology.

  6. Dissociative recombination of molecular ions with electrons

    NASA Technical Reports Server (NTRS)

    Johnsen, Rainer

    1990-01-01

    An overview is presented for the present state of the art of laboratory measurements of the dissociative recombination of molecular ions with electrons. Most work has focussed on obtaining rates and their temperature dependence, as these are of primary interest for model calculations of ionospheres. A comparison of data obtained using the microwave afterglow method, the flowing afterglow technique, and the merged beam technique shows that generally the agreement is quite good, but there are some serious discrepancies, especially in the case of H(3+) recombination, that need to be resolved. Results of some earlier experimental work need to be reexamined in the light of more recent developments. Such cases are pointed out and a compilation of rate coefficients that have withstood scrutiny is presented. Recent advances in experimental methods, such as the use of laser-in-duced fluorescence, make it possible to identify some neutral products of dissociative recombination. What has been done so far and what results one might expect from future work are briefly reviewed.

  7. Studying dissociative electron attachment through formation of heavy-Rydberg ion-pair states

    NASA Astrophysics Data System (ADS)

    Kelley, Michael; Buathong, Sitti; Dunning, F. Barry

    2016-05-01

    Following dissociative electron transfer in collisions between Rydberg atoms and electron-attaching targets, it is possible for the resulting pair of ions to remain electrostatically bound, forming heavy-Rydberg ion-pair states. Precise measurement of the velocity distributions of such ion-pair states provides information concerning the dissociation dynamics of the excited intermediates initially created by electron transfer. Here, electric-field-induced dissociation is used to detect the product ion pairs and observe their velocity distributions. These distributions are analyzed with the aid of a Monte Carlo collision code that models the electron transfer. Measurements with a number of different target species show that through this analysis, dissociation energetics, the branching ratios into different dissociation products, and the lifetimes of the excited intermediates can be examined. Research supported by the Robert A. Welch Foundation.

  8. Radiative capture versus Coulomb dissociation.

    SciTech Connect

    Esbensen, H.; Physics

    2006-01-01

    Measurements of the Coulomb dissociation of {sup 8}B have been used to infer the rate of the inverse radiative proton capture on {sup 7}Be. The analysis is usually based on the assumptions that the two processes are related by detailed balance and described by E1 transitions. However, there are corrections to this relation. The Coulomb form factors for the two processes, for example, are not identical. There are also E2 transitions and higher-order effects in the Coulomb dissociation, and the nuclear induced breakup cannot always be ignored. While adding first-order E2 transitions enhances the decay energy spectrum, the other mechanisms cause a suppression at low relative energies. The net result may accidentally be close to the conventional first-order E1 calculation, but there are differences which cannot be ignored if accuracies of 10% or better are needed.

  9. Dissociation of H{sub 2} on carbon doped aluminum cluster Al{sub 6}C

    SciTech Connect

    Yang, Huihui; Zhang, Yan; Chen, Hongshan

    2014-08-14

    The dissociation of H{sub 2} molecule is the first step for chemical storage of hydrogen, and the energy barrier of the dissociation is the key factor to decide the kinetics of the regeneration of the storage material. As a light element, aluminum is an important candidate component for storage materials with high gravimetric density. This paper investigates the adsorption and dissociation of H{sub 2} on carbon doping aluminum cluster Al{sub 6}C. The study shows that doping carbon into aluminum cluster can significantly change the electronic structure and increase the stability. Al{sub 6}C has a few stable isomers with close energies and their structures are quite flexible. The molecular adsorption of H{sub 2} on Al{sub 6}C is very weak, but the H{sub 2} molecule can be dissociated easily on this cluster. The stable product of the dissociated adsorption is searched and the different paths for the dissociation are investigated. During the dissociation of H{sub 2}, the structure of the cluster adjusts accordingly, and strong orbital interaction between the hydrogen and the cluster occurs. The calculated energy barrier for the dissociation is only 0.30 eV, which means the dissociation can take place at moderate temperatures.

  10. Modeling of collision-induced infrared absorption spectra of H2 pairs in the first overtone band at temperatures from 20 to 500 K

    NASA Technical Reports Server (NTRS)

    Zheng, Chunguang; Borysow, Aleksandra

    1995-01-01

    A simple formalism is presented that permits quick computations of the low-resolution, rotovibrational collision-induced absorption (RV CIA) spectra of H2 pairs in the first overtone band of hydrogen, at temperatures from 20 to 500 K. These spectra account for the free-free transitions. The sharp dimer features, originating from the bound-free, free-bound, and bound-bound transitions are ignored, though their integrated intensities are properly accounted for. The method employs spectral model line- shapes with parameters computed from the three lowest spectral moments. The moments are obtained from first principles expressed as analytical functions of temperature. Except for the sharp dimer features, which are absent in this model, the computed spectra reproduce closely the results of exact quantum mechanical lineshape computations. Comparisons of the computed spectra with existing experimental data also show good agreement. The work interest for the modeling of the atmospheres of the outer planets in the near-infrared region of the spectrum. The user-friendly Fortran program developed here is available on request from the authors.

  11. Ab initio 3D potential energy and dipole moment surfaces for the CH4-Ar complex: Collision-induced intensity and dimer content.

    PubMed

    Kalugina, Yulia N; Lokshtanov, Sergei E; Cherepanov, Victor N; Vigasin, Andrey A

    2016-02-07

    We present new three-dimensional potential energy surface (PES) and dipole moment surfaces (DMSs) for the CH4-Ar van der Waals system. Ab initio calculations of the PES and DMS were carried out using the closed-shell single- and double-excitation coupled cluster approach with non-iterative perturbative treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = D,T,Q) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. The dipole moment surface was obtained using aug-cc-pVTZ basis set augmented with mid-bond functions for better description of exchange interactions. The second mixed virial coefficient was calculated and compared to available experimental data. The equilibrium constant for true dimer formation was calculated using classical partition function based on the knowledge of ab initio PES. Temperature variations of the zeroth spectral moment of the rototranslational collision-induced band as well as its true dimer constituent were traced with the use of the Boltzmann-weighted squared induced dipole properly integrated over respective phase space domains. Height profiles for N2-N2, N2-H2, CH4-N2, (CH4)2, and CH4-Ar true bound dimers in Titan's atmosphere were calculated with the use of reliable ab initio  PESs.

  12. The HD spectrum near 2.3 μm by CRDS-VECSEL: Electric quadrupole transition and collision-induced absorption

    NASA Astrophysics Data System (ADS)

    Vasilchenko, S.; Mondelain, D.; Kassi, S.; Čermák, P.; Chomet, B.; Garnache, A.; Denet, S.; Lecocq, V.; Campargue, A.

    2016-08-01

    The HD absorption spectrum is investigated near 2.3 μm with the help of a newly developed Cavity Ring Down Spectrometer (CRDS) using a VECSEL (Vertical External Cavity Surface Emitting Laser) as light source. The HD CRDS spectra were recorded for a series of ten pressure values in the range 50-650 Torr. The sensitivity of the recordings - noise equivalent absorption of the spectra on the order of αmin ≈ 5 × 10-10 cm-1 - has allowed for the first detection of the S(3) quadrupole electric transition of the HD fundamental band, at 4359.940 cm-1. The line center determined with an uncertainty of 0.002 cm-1 agrees with the most recent theoretical calculations. The retrieved value of the line intensity (2.5 × 10-27 cm/molecule at 296 K) agrees within 12% with the ab initio values included in the HITRAN spectroscopic database. We take the opportunity of this contribution to provide an exhaustive review of seventy-three HD absorption lines previously detected up to 20,000 cm-1. From the pressure dependence of the baseline of the CRDS spectra, the binary absorption coefficient of the HD collision induced absorption band is determined to be 1.17(4) × 10-6 cm-1amagat-2 at 4360 cm-1.

  13. Collision-Induced Absorption by Supermolecular Complexes from a New Potential Energy and Induced Dipole Surface, Suited for Calculations up to Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Wang, Fei; Gustafsson, Magnus; Li, Xiaoping; Hunt, Katharine L. C.

    2010-10-01

    Absorption by pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets, and thus of special astronomical interest. The emission spectra of cool white dwarf stars differ significantly from the expected blackbody spectra, amongst other reasons due to absorption by H2-H2, H2-He, and H2-H collisional complexes in the stellar atmospheres. To model the radiative processes in these atmospheres, which have temperatures of several thousand kelvin, one needs accurate knowledge of the induced dipole (ID) and potential energy surfaces (PES) of such collisional complexes. These come from quantum-chemical calculations with the H2 bonds stretched or compressed far from equilibrium. Laboratory measurements of collision-induced (CI) absorption exist only at much lower temperature. For H2 pairs at room temperature, the calculated spectra of the rototranslational band, the fundamental band, and the first overtone match the experimental data very well. In addition, with the newly obtained IDS it became possible to reproduce the measurements in the far blue wing of the rototranslational spectrum of H2 at 77.5 K, as well as at 300 K. Similarly good agreement between theory and measurement is seen in the fundamental band of molecular deuterium at room temperature. Furthermore, we also show the calculated absorption spectra of H2-He at 600 K and of H2-H2 at 2,000 K, for which there are no experimental data for comparison.

  14. Ab initio 3D potential energy and dipole moment surfaces for the CH4-Ar complex: Collision-induced intensity and dimer content

    NASA Astrophysics Data System (ADS)

    Kalugina, Yulia N.; Lokshtanov, Sergei E.; Cherepanov, Victor N.; Vigasin, Andrey A.

    2016-02-01

    We present new three-dimensional potential energy surface (PES) and dipole moment surfaces (DMSs) for the CH4-Ar van der Waals system. Ab initio calculations of the PES and DMS were carried out using the closed-shell single- and double-excitation coupled cluster approach with non-iterative perturbative treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = D,T,Q) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. The dipole moment surface was obtained using aug-cc-pVTZ basis set augmented with mid-bond functions for better description of exchange interactions. The second mixed virial coefficient was calculated and compared to available experimental data. The equilibrium constant for true dimer formation was calculated using classical partition function based on the knowledge of ab initio PES. Temperature variations of the zeroth spectral moment of the rototranslational collision-induced band as well as its true dimer constituent were traced with the use of the Boltzmann-weighted squared induced dipole properly integrated over respective phase space domains. Height profiles for N2-N2, N2-H2, CH4-N2, (CH4)2, and CH4-Ar true bound dimers in Titan's atmosphere were calculated with the use of reliable ab initio PESs.

  15. NEW H{sub 2} COLLISION-INDUCED ABSORPTION AND NH{sub 3} OPACITY AND THE SPECTRA OF THE COOLEST BROWN DWARFS

    SciTech Connect

    Saumon, Didier; Marley, Mark S.; Abel, Martin; Frommhold, Lothar; Freedman, Richard S. E-mail: Mark.S.Marley@nasa.gov E-mail: frommhold@physics.utexas.edu

    2012-05-01

    We present new cloudy and cloudless model atmospheres for brown dwarfs using recent ab initio calculations of the line list of ammonia (NH{sub 3}) and of the collision-induced absorption of molecular hydrogen (H{sub 2}). We compare the new synthetic spectra with models based on an earlier description of the H{sub 2} and NH{sub 3} opacities. We find a significant improvement in fitting the nearly complete spectral energy distribution of the T7p dwarf Gliese 570D and in near-infrared color-magnitude diagrams of field brown dwarfs. We apply these new models to the identification of NH{sub 3} absorption in the H-band peak of very late T dwarfs and the new Y dwarfs and discuss the observed trend in the NH{sub 3}-H spectral index. The new NH{sub 3} line list also allows a detailed study of the medium-resolution spectrum of the T9/T10 dwarf UGPS J072227.51-054031.2 where we identify several specific features caused by NH{sub 3}.

  16. [Differential diagnosis between dissociative disorders and schizophrenia].

    PubMed

    Shibayama, Masatoshi

    2011-01-01

    The differential diagnosis of dissociative disorders includes many psychiatric disorders, such as schizophrenia, bipolar disorders (especially bipolar II disorder), depressive disorder (especially atypical depression), epilepsy, Asperger syndrome, and borderline personality disorder. The theme of this paper is the differential diagnosis between dissociative disorders and schizophrenia. Schneiderian first-rank symptoms in schizophrenia are common in dissociative disorders, especially in dissociative identity disorder (DID). Many DID patients have been misdiagnosed as schizophrenics and treated with neuroleptics. We compared and examined Schneiderian symptoms of schizophrenia and those of dissociative disorders from a structural viewpoint. In dissociative disorders, delusional perception and somatic passivity are not seen. "Lateness" and "Precedence of the Other" originated from the concept of "Pattern Reversal" (H. Yasunaga)" is characteristic of schizophrenia. It is important to check these basic structure of schizophrenia in subjective experiences in differential diagnosis between dissociative disorders and schizophrenia.

  17. The role of metal cation in electron-induced dissociation of tryptophan

    NASA Astrophysics Data System (ADS)

    Feketeová, L.; Wong, M. W.; O'Hair, R. A. J.

    2010-10-01

    The fragmentation of tryptophan (Trp) - metal complexes [Trp+M]+, where M = Cs, K, Na, Li and Ag, induced by 22 eV energy electrons was compared to [Trp+H]+. Additional insights were obtained through the study of collision-induced dissociation (CID) of [Trp+M]+ and through deuterium labelling. The electron-induced dissociation (EID) of [Trp+M]+ resulted in the formation of radical cations via the following pathways: (i) loss of M to form Trp+•, (ii) loss of an H atom to form [(Trp-H)+M]+•, and (iii) bond homolysis to form C2H4NO2M+•. Deuterium labelling suggests that H atom loss can occur from heteroatom and/or C-H positions. Other types of fragment ions observed include: C9H7NM+, C9H8N+, M+, C2H3NO2M+, CO2M+, C10H11N2M+, C10H9NOM+. Formation of C2H4NO2M+• and C9H7NM+ cations suggests that the metal interacts with both the backbone and aromatic side chain, thus implicating π-interactions for all M. CID of [Trp+M]+ resulted in: loss of metal cation (for M = Cs and K); successive loss of NH3 and CO as the dominant channel for M = Na, Li and Ag; formation of C2H3NO2M+. Preliminary DFT calculations were carried out on [Trp+Na]+ and [(Trp-H)+Na]+• which reveal that: the most stable conformation involves chelation by the backbone together with a π -interaction with the indole side chain; loss of H atom from α -CH of the side chain is thermodynamically favoured over losses from other positions, with the resultant radical cation maintaining a (N, O, ring) chelated structure which is stabilized by conjugation.

  18. Large-scale identification of endogenous secretory peptides using electron transfer dissociation mass spectrometry.

    PubMed

    Sasaki, Kazuki; Osaki, Tsukasa; Minamino, Naoto

    2013-03-01

    Mass spectrometry-based unbiased analysis of the full complement of secretory peptides is expected to facilitate the identification of unknown biologically active peptides. However, tandem MS sequencing of endogenous peptides in their native form has proven difficult because they show size heterogeneity and contain multiple internal basic residues, the characteristics not found in peptide fragments produced by in vitro digestion. Endogenous peptides remain largely unexplored by electron transfer dissociation (ETD), despite its widespread use in bottom-up proteomics. We used ETD, in comparison to collision induced dissociation (CID), to identify endogenous peptides derived from secretory granules of a human endocrine cell line. For mass accuracy, both MS and tandem MS were analyzed on an Orbitrap. CID and ETD, performed in different LC-MS runs, resulted in the identification of 795 and 569 unique peptides (ranging from 1000 to 15000 Da), respectively, with an overlap of 397. Peptides larger than 3000 Da accounted for 54% in CID and 46% in ETD identifications. Although numerically outperformed by CID, ETD provided more extensive fragmentation, leading to the identification of peptides that are not reached by CID. This advantage was demonstrated in identifying a new antimicrobial peptide from neurosecretory protein VGF (non-acronymic), VGF[554-577]-NH2, or in differentiating nearly isobaric peptides (mass difference less than 2 ppm) that arise from alternatively spliced exons of the gastrin-releasing peptide gene. CID and ETD complemented each other to add to our knowledge of the proteolytic processing sites of proteins implicated in the regulated secretory pathway. An advantage of the use of both fragmentation methods was also noted in localization of phosphorylation sites. These findings point to the utility of ETD mass spectrometry in the global study of endogenous peptides, or peptidomics.

  19. Large-scale Identification of Endogenous Secretory Peptides Using Electron Transfer Dissociation Mass Spectrometry*

    PubMed Central

    Sasaki, Kazuki; Osaki, Tsukasa; Minamino, Naoto

    2013-01-01

    Mass spectrometry-based unbiased analysis of the full complement of secretory peptides is expected to facilitate the identification of unknown biologically active peptides. However, tandem MS sequencing of endogenous peptides in their native form has proven difficult because they show size heterogeneity and contain multiple internal basic residues, the characteristics not found in peptide fragments produced by in vitro digestion. Endogenous peptides remain largely unexplored by electron transfer dissociation (ETD), despite its widespread use in bottom-up proteomics. We used ETD, in comparison to collision induced dissociation (CID), to identify endogenous peptides derived from secretory granules of a human endocrine cell line. For mass accuracy, both MS and tandem MS were analyzed on an Orbitrap. CID and ETD, performed in different LC-MS runs, resulted in the identification of 795 and 569 unique peptides (ranging from 1000 to 15000 Da), respectively, with an overlap of 397. Peptides larger than 3000 Da accounted for 54% in CID and 46% in ETD identifications. Although numerically outperformed by CID, ETD provided more extensive fragmentation, leading to the identification of peptides that are not reached by CID. This advantage was demonstrated in identifying a new antimicrobial peptide from neurosecretory protein VGF (non-acronymic), VGF[554–577]-NH2, or in differentiating nearly isobaric peptides (mass difference less than 2 ppm) that arise from alternatively spliced exons of the gastrin-releasing peptide gene. CID and ETD complemented each other to add to our knowledge of the proteolytic processing sites of proteins implicated in the regulated secretory pathway. An advantage of the use of both fragmentation methods was also noted in localization of phosphorylation sites. These findings point to the utility of ETD mass spectrometry in the global study of endogenous peptides, or peptidomics. PMID:23250050

  20. [Clinical Handling of Patients with Dissociative Disorders].

    PubMed

    Okano, Kenichiro

    2015-01-01

    This paper discusses the way informed psychiatrists are expected to handle dissociative patients in clinical situations, with a specific focus on dissociative identity disorders and dissociative fugue. On the initial interview with dissociative patients, information on their history of trauma and any nascent dissociative symptoms in their childhood should be carefully obtained. Their level of stress in their current life should also be assessed in order to understand their symptomatology, as well as to predict their future clinical course. A psychoeducational approach is crucial; it might be helpful to give information on dissociative disorder to these patients as well as their family members in order to promote their adherence to treatment. Regarding the symptomatology of dissociative disorders, detailed symptoms and the general clinical course are presented. It was stressed that dissociative identity disorder and dissociative fugue, the most high-profile dissociative disorders, are essentially different in their etiology and clinical presentation. Dissociative disorders are often confused with and misdiagnosed as psychotic disorders, such as schizophrenia. Other conditions considered in terms of the differential diagnosis include borderline personality disorder as well as temporal lobe epilepsy. Lastly, the therapeutic approach to dissociative identity disorder is discussed. Each dissociative identity should be understood as potentially representing some traumatically stressful event in the past. The therapist should be careful not to excessively promote the creation or elaboration of any dissociative identities. Three stages are proposed in the individual psychotherapeutic process. In the initial stage, a secure environment and stabilization of symptoms should be sought. The second stage consists of aiding the "host" personality to make use of other more adaptive coping skills in their life. The third stage involves coaching as well as continuous awareness of

  1. Dissociative experiences on ice--peritraumatic and trait dissociation during the cold pressor test.

    PubMed

    Giesbrecht, Timo; Smeets, Tom; Merckelbach, Harald

    2008-01-15

    The present study investigated the relationship between trait dissociation and peritraumatic dissociation during acute painful stimulation. In a sample of 70 undergraduate students, peritraumatic dissociation was induced by means of a cold pressor test, which basically consists of participants holding an arm in ice water for as long as possible. Results indicate that heightened trait dissociation scores were related to shorter durations that participants could sustain the task. However, trait dissociation was not associated with increases in acute dissociative symptoms (i.e., peritraumatic dissociation). These findings are in sharp contrast to the defensive function ascribed to both types of dissociation and also the commonly held assumption that peritraumatic and trait dissociation are intimately linked.

  2. Deuterium enrichment by selective photoinduced dissociation of a multihalogenated organic compound

    DOEpatents

    Marling, John B.; Herman, Irving P.

    1981-01-01

    A method for deuterium enrichment by photoinduced dissociation which uses as the deuterium source a multihalogenated organic compound selected from the group consisting of a dihalomethane, a trihalomethane, a 1,2-dihaloethene, a trihaloethene, a tetrahaloethane and a pentahaloethane. The multihalogenated organic compound is subjected to intense infrared radiation at a preselected wavelength to selectively excite and thereby induce dissociation of substantially only those molecules containing deuterium to provide a deuterium enriched dissociation product. The deuterium enriched product may be combusted with oxygen to provide deuterium enriched water. The deuterium depleted undissociated molecules may be redeuterated by treatment with a deuterium source such as water.

  3. Characterization of 4-hydroxy-2-nonenal-modified peptides by liquid chromatography-tandem mass spectrometry using data-dependent acquisition: neutral loss-driven MS3 versus neutral loss-driven electron capture dissociation.

    PubMed

    Rauniyar, Navin; Stevens, Stanley M; Prokai-Tatrai, Katalin; Prokai, Laszlo

    2009-01-15

    Reactive oxygen species generated during oxidative stress can lead to unfavorable cellular consequences, predominantly due to formation of 4-hydroxy-2-nonenal (HNE) during lipid peroxidation. Data-dependent and neutral loss (NL)-driven MS(3) acquisition have been reported for the identification of HNE adducts by mass spectrometry-based proteomics. However, the limitation associated with this method is the ambiguity in correct assignment of the HNE modification site when more than one candidate site is present as MS(3) is triggered on the neutral loss ion. We introduce NL-triggered electron capture dissociation tandem mass spectrometry (NL-ECD-MS/MS) for the characterization of HNE-modification sites in peptides. With this method performed using a hybrid linear ion trap-Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, ECD in the FTICR unit of the instrument is initiated on precursor ions of peptides showing the neutral loss of 156 Da corresponding to an HNE molecule in the prescan acquired via collision-induced dissociation tandem mass spectrometry in the linear ion trap. In addition to manifold advantages associated with the ECD method of backbone fragmentation, including extensive sequence fragments, ECD tends to retain the HNE group during MS/MS of the precursor ion, facilitating the correct localization of the modification site. The results also suggest that predisposition of a peptide molecular ion to lose HNE during collision-induced dissociation-based fragmentation is independent of its charge state (2+ or 3+). In addition, we have demonstrated that coupling of solid-phase enrichment of HNE-modified peptides facilitates the detection of this posttranslational modification by NL-driven strategies for low-abundance proteins that are susceptible to substoichiometric carbonylation during oxidative stress.

  4. Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics.

    PubMed

    Tsiatsiani, Liana; Giansanti, Piero; Scheltema, Richard A; van den Toorn, Henk; Overall, Christopher M; Altelaar, A F Maarten; Heck, Albert J R

    2017-02-03

    A key step in shotgun proteomics is the digestion of proteins into peptides amenable for mass spectrometry. Tryptic peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) because the fragmentation rules are well-understood. Here, we investigate LysargiNase, a perfect trypsin mirror protease, because it cleaves equally specific at arginine and lysine residues, albeit at the N-terminal end. LysargiNase peptides are therefore practically tryptic-like in length and sequence except that following ESI, the two protons are now both positioned at the N-terminus. Here, we compare side-by-side the chromatographic separation properties, gas-phase fragmentation characteristics, and (phospho)proteome sequence coverage of tryptic (i.e., (X)nK/R) and LysargiNase (i.e., K/R(X)n) peptides using primarily electron-transfer dissociation (ETD) and, for comparison, HCD. We find that tryptic and LysargiNase peptides fragment nearly as mirror images. For LysargiNase predominantly N-terminal peptide ions (c-ions (ETD) and b-ions (HCD)) are formed, whereas for trypsin, C-terminal fragment ions dominate (z-ions (ETD) and y-ions (HCD)) in a homologous mixture of complementary ions. Especially during ETD, LysargiNase peptides fragment into low-complexity but information-rich sequence ladders. Trypsin and LysargiNase chart distinct parts of the proteome, and therefore, the combined use of these enzymes will benefit a more in-depth and reliable analysis of (phospho)proteomes.

  5. Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni*

    PubMed Central

    Scott, Nichollas E.; Parker, Benjamin L.; Connolly, Angela M.; Paulech, Jana; Edwards, Alistair V. G.; Crossett, Ben; Falconer, Linda; Kolarich, Daniel; Djordjevic, Steven P.; Højrup, Peter; Packer, Nicolle H.; Larsen, Martin R.; Cordwell, Stuart J.

    2011-01-01

    Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that pep