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Sample records for collision-induced dissociation fragmentation

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions

    NASA Astrophysics Data System (ADS)

    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: AAAAH AA-NH2 (where " A" denotes carbon thirteen (13C1) 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Gas-phase separations of protein and peptide ion fragments generated by collision-induced dissociation in an ion trap.

    PubMed

    Badman, Ethan R; Myung, S; Clemmer, David E

    2002-10-01

    Ion mobility/time-of-flight mass spectrometry techniques have been used to examine distributions of fragment ions generated by collision-induced dissociation (CID) in a quadrupole ion trap. The mobility-based separation step prior to mass-to-charge (m/z) analysis reduces spectral congestion and provides information that complements m/z-based assignments of peaks. The approach is demonstrated by examining fragmentation patterns of insulin chain B (a 30-residue peptide), and ubiquitin (a protein containing 76 amino acids). Some fragments of ubiquitin show evidence for multiple stable conformations.

  13. 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.

  14. Predicting collision-induced dissociation mass spectra: understanding the role of the mobile proton in small molecule fragmentation.

    PubMed

    Wright, Patricia; Alex, Alexander; Pullen, Frank

    2016-05-15

    Intramolecular proton migration has been reported to be required for fragmentation by collision-induced dissociation (CID). If the collision energy is required to provide energy for proton movement to a ‘dissociative’ site, it may be possible to predict the optimal collision energy for fragmentation using quantum computational chemistry software. A greater understanding of the mechanism(s) of proton migration is necessary. The product ion spectra of seven compounds were obtained at collision energies stepped in the range from 5 to 50 eV, with precursor ions being generated in positive ion mode by both atmospheric pressure chemical ionization (APCI) and electrospray ionisation (ESI) (using an ESCi ionisation source with or without corona discharge, respectively). The products ions observed at each collision energy were assessed in terms of structure to ascertain if they were formed as a result of protonation at the initial ionisation site or if the proton had migrated to a dissociative site. Proton migration was shown to be independent of collision energy, stability of the protonated molecule and the distance that the proton moved. Therefore, proton migration is not a barrier to fragmentation as the proton appears to be fully mobile at 5 eV. As proton migration is independent of collision energy for these compounds, whereas fragmentation is energy dependent, protonation at the dissociative site alone is not sufficient to cause bond cleavage. The role of collision energy in bond cleavage may be to increase the vibrational energy of the bond and/or increase the rate of bond cleavage such that it occurs within the residence time of the ion within the collision cell rather than to supply the energy for proton migration. Therefore, quantum chemistry alone cannot predict the collision energies appropriate for fragmentation on the basis of modelling proton movements.

  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. 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.

  17. 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.

  18. High-energy collision-induced dissociation by MALDI TOF/TOF causes charge-remote fragmentation of steroid sulfates.

    PubMed

    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.

  19. Collision-Induced Dissociation Fragmentation Inside Disulfide C-Terminal Loops of Natural Non-Tryptic Peptides

    NASA Astrophysics Data System (ADS)

    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.

  20. 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.

  1. Differential mobility spectrometry combined with multiple ion monitoring for bioanalysis of disulfide-bonded peptides with inefficient collision-induced dissociation fragmentation.

    PubMed

    Xia, Yuan-Qing; Ciccimaro, Eugene; Zheng, Naiyu; Zhu, Mingshe

    2017-01-01

    It is challenging to develop a multiple reaction monitoring (MRM) method for some disulfide-bonded peptides with inefficient collision-induced dissociation fragmentation. This study describes a new methodology using differential mobility spectrometry (DMS) combined with multiple ion monitoring (MIM) to enhance bioanalytical sensitivity for sunflower trypsin inhibitor. By combining DMS with MIM to monitor the intact precursor ion in Q1 and Q3 MS analyzers, a lower limit of quantitation at 0.125 ng/ml was achieved to quantify sunflower trypsin inhibitor in rat plasma, representing a 40-fold sensitivity improvement over MIM without DMS. DMS coupled with MIM method provides triple quadrupole MS users an effective means to overcome challenges in analyzing disulfide-bonded peptides or other analytes that do not have useful collision-induced dissociation fragment ions for MRM analysis.

  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. Collision-induced dissociation of aflatoxins.

    PubMed

    Tóth, Katalin; Nagy, Lajos; Mándi, Attila; Kuki, Ákos; Mézes, Miklós; Zsuga, Miklós; Kéki, Sándor

    2013-02-28

    The aflatoxin mycotoxins are particularly hazardous to health when present in food. Therefore, from an analytical point of view, knowledge of their mass spectrometric properties is essential. The aim of the present study was to describe the collision-induced dissociation behavior of the four most common aflatoxins: B1, B2, G1 and G2. Protonated aflatoxins were produced using atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) combined with high-performance liquid chromatography (HPLC). For the tandem mass spectrometry (MS/MS) experiments nitrogen was used as the collision gas and the collision energies were varied in the range of 9-44 eV (in the laboratory frame). The major APCI-MS/MS fragmentations of protonated aflatoxins occurred at 30 eV collision energy. The main fragmentation channels were found to be the losses of a series of carbon monoxide molecules and loss of a methyl radical, leading to the formation of radical-type product ions. In addition, if the aflatoxin molecule contained an ether- or lactone-oxygen atom linked to a saturated carbon atom, loss of a water molecule was observed from the [M + H](+) ion, especially in the case of aflatoxins G1 and G2. A relatively small modification in the structure of aflatoxins dramatically altered the fragmentation pathways and this was particularly true for aflatoxins B1 and B2. Due to the presence of a C = C double bond connected to the ether group in aflatoxin B1 no elimination of water was observed but, instead, formation of radical-type product ions occurred. Fragmentation of protonated aflatoxin B1 yielded the most abundant radical-type cations. Copyright © 2013 John Wiley & Sons, Ltd.

  4. 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.

  5. 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.

  6. Collision induced dissociation of titanium-carbon cluster cations

    NASA Astrophysics Data System (ADS)

    Kerns, K. P.; Guo, B. C.; Deng, H. T.; Castleman, A. W., Jr.

    1994-11-01

    Titanium-carbon clusters are investigated by collision induced dissociation (CID) using our newly designed triple quadrupole mass spectrometer coupled with a laser vaporization source. Their fragmentation patterns are determined under various collision conditions. It is observed that the Met-Car Ti8C+12 mainly loses a neutral metal atom in the primary dissociation step and several metal atoms in sequential dissociation processes. The dissociation threshold of the Met-Car Ti8C+12 is estimated to be about 9 eV. In addition, several of the larger TixC+y cluster ions, including those containing nine or ten metal atoms, are found to fragment directly to Ti8C+12 during single step dissociation. Product channels for dissociation of Ti9C+12 establishes the ionization potential for Ti8C12 to be equal to, or less than the IP of the titanium atom.

  7. 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.

  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. 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.

  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. 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.

  12. Shattering transitions in collision-induced fragmentation

    NASA Astrophysics Data System (ADS)

    Krapivsky, P. L.; Ben-Naim, E.

    2003-08-01

    We investigate the kinetics of nonlinear collision-induced fragmentation. We obtain the fragment mass distribution analytically by utilizing its traveling wave behavior. The system undergoes a shattering transition in which a finite fraction of the mass is lost to infinitesimal fragments (dust). The nature of the shattering transition depends on the fragmentation process. When the larger of the two colliding fragments splits, the transition is discontinuous and the entire mass is transformed into dust at the transition point. When the smaller fragment splits, the transition is continuous with the dust gaining mass steadily on the account of the fragments. At the transition point, the fragment mass distribution diverges algebraically for small masses, c(m)˜m-α, with α=1.201 91… .

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Infrared and collision-induced fragmentation of iron ethoxide cations

    NASA Astrophysics Data System (ADS)

    Kirkwood, D. A.; Stace, A. J.

    1997-12-01

    The multi-photon infrared photo-dissociation (MPD) of iron ethoxide cations of the general form Fe+(EtOH)m(EtO)n has been studied in an ion trap using a line tuneable CO2 laser. The ions exhibit very characteristic infrared absorption profiles which are shown to be quite different from those recorded for Fe+(EtOH)n cluster ions. From a comparison with solid state data, it is suggested that the mode responsible for absorption is a C---O stretch in the ethoxide group. To complement the interpretation of the MPD data, the collision-induced dissociation (CID) of the same series of ions was promoted by the application of a tickle voltage to the end caps of the ion trap. Both MPD and CID generate the same fragment ions, but the relative intensities are different. A detailed study of Fe+(EtOH)(EtO) using isotopes reveals fragmentation pathways leading primarily to the loss of H2, CH2O and CH3CHO, all of which can be accounted for via a series of insertion and radical transfer steps. Central to many of the reactions is an initial insertion step which results in the formation of HFe+(EtO)2.

  2. IONIZATION AND COLLISION INDUCED DISSOCIATION OF STEROID BIS-GLUCURONIDES.

    PubMed

    Esquivel, Argitxu; Matabosch, Xavier; Kotronoulas, Aristotelis; Balcells, Georgina; Joglar, Jesús; Ventura, Rosa

    2017-07-21

    Studies on steroid metabolism are of utmost importance to improve the detection capabilities of anabolic androgenic steroids (AAS) misuse in sports drug testing. In humans, glucuronoconjugates are the most abundant phase II metabolites of AAS. Bis-glucuronidation is a reaction where two separated functional groups on the same molecule are conjugated with glucuronic acid. These metabolites have not been studied in depth for steroids and could be interesting markers for doping control. The aim of the present work was to study the ionization and collision induced dissociation of steroid bis-glucuronides to be able to develop mass spectrometric analytical strategies for their detection in urine samples after AAS administration. Since steroid bis-glucuronides are not commercially available, nineteen of them were qualitatively synthesized to study their mass spectrometric behavior. Bis-glucuronides ionized as [M+NH4 ](+) in positive mode, and as [M-H](-) and [M-2H](2-) in negative mode. The most specific product ions of steroid bis-glucuronides in positive mode resulted from the neutral losses of 387 and 405 Da (corresponding to [M+NH4 -NH3 -2gluc-H2 O](+) and [M+NH4 -NH3 -2gluc-2H2 O](+) , respectively, being 'gluc' a dehydrated glucuronide moiety) and, in negative mode, the fragmentation of [M-2H](2-) showed ion losses of m/z 175 and 75 (gluc(-) and HOCH2 CO2(-) , respectively). Based on the common behavior, a selected reaction monitoring method was developed to detect bis-glucuronide metabolites in urine samples. As a proof of concept, urines obtained after administration of norandrostenediol were studied, and a bis-glucuronide metabolite was detected in those urines. The results demonstrate the usefulness of the analytical strategy to detect bis-glucuronide metabolites in urine samples, and the formation of these metabolites after administration of AAS. This article is protected by copyright. All rights reserved.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Final report. Surface-induced dissociation versus collision-induced dissociation

    SciTech Connect

    Futrell, Jean H.

    2001-04-19

    A 7-Tesla Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer was modified to insert a surface inside the cell for ion-surface collisions leading to the dissociation of impacting ions. Modifications were made to the software/hardware to collide the ions brought into the cell and trap the resulting fragment and undissociated primary ions inside the cell. The trapping plates were also ramped to determine kinetic energy distributions of these ions. The surface-induced dissociation (SID) of benzene and chromium hexacarbonyl ions was first studied as test cases for the instrument. Then a systematic study of the SID of small protonated peptides formed by electrospray ionization was begun. A series of small alanine(A)-containing peptides, viz., AA, AAA, AAAA, AAAAA, and PAAAA were used in the study. In the absence of any direct comparisons of the SID processes with the commonly used technique of tandem mass spectrometry of collision-induced dissociations (CID) via collisions with a neutral gas, a comparative study of CID and SID using the same protonated peptides was made. Since multiple collisions are often used to enhance dissociation efficiency in CID, the CID was performed under single as well as multiple collisional activation conditions. Both on-resonance and sustained off-resonance irradiation excitation were used for CID experiments. Kinetic energy of the ions was varied by changing peak-to-peak voltage applied to the excitation plates. Results are shown in a series of graphs, and a simple theoretical model is presented. This direct comparison of the two activation techniques on the same instrument provided insights into the similarities and differences between these two. The results suggest that internal energy distributions of ions activated by ion-surface collision and multiple collision ion-gaseous neutral collisions are quite comparable. The results also suggest that, in ion-surface collisions, the ion collides with only a small fraction of th

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

    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. Graphical Abstract ᅟ.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

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

    PubMed

    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. Graphical Abstract ᅟ.

  17. 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.

  18. 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).

  19. 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.

  20. 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.

  1. Vibrational relaxation and collision-induced dissociation of xenon fluoride by neon

    SciTech Connect

    Wilkins, R.L.

    1989-03-01

    Rate coefficients were calculated for vibrational relaxation and collision induced dissociation of ground-state xenon fluoride in neon at temperatures between 300 and 1000 K for each of nine vibrational levels. These coefficients were calculated using a pairwise additive potential energy surface, which consists, of a Morse function for the XeF interaction and Lennard-Jones functions for the NeXe and NeF interactions. Rate coefficients are provided for temperature and v-dependences. The vibrational relaxation and dissociation processes occur by multiquanta transitions. Dissociation can take place from all v-levels, provided that the internal energy of the XeF molecule is close to the rotationless dissociation limit. The order of increase effectiveness of the various forms of energy in promoting dissociation in XeF was found to be translation-rotation-vibration. At room temperature, neon atoms were more efficient than helium atoms in the dissociation processes.

  2. 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.

  3. 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).

  4. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay.

    PubMed

    Bashir, Sajid; Giannakopulos, Anastassios E; Derrick, Peter J; Critchley, Peter; Bottrill, Andrew; Padley, Henry J

    2004-01-01

    In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.

  5. Target Gas Effects on Collision-Induced Dissociation of Peptides in a Tandem Four-Sector Mass Spectrometer.

    DTIC Science & Technology

    1991-05-01

    regulator to the metering valve at the collision cell was thoroughly evacuated and then purged three times before each experiment by introducing small amounts...Thesis; Aug 89 - May 91 4. TIfLE AND S.BTiTLE S. FUNDING NUMBERS Target Gas Effects on Collision-Induced Dissociation of Peptides in a Tandem Four...intensities of ihe undecapeptide physalaemin during collision-induced dissociation (CID) has been determined to be target mass dependent. The data

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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%.

  11. 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.

  12. Collision-Induced Dissociation and Theoretical Studies of Ag+(methanol)(n) , n= 1 - 4

    SciTech Connect

    Koizumi, Hideya; Larsen, Melissa; Armentrout, Peter B.; Feller, David F. )

    2003-04-24

    Collision-induced dissociations of the Ag+(methanol)n complexes for n= 1 - 4 are studied using kinetic energy dependent guided ion beam tandem mass spectrometry. In all cases, the primary products are endothermic loss of an intact neutral ligand from the complex. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-molecule collisions, internal energy of the complexes, and unimolecular decay rates. These values are compared with theoretical values obtained using high level ab initio calculations. Generally good agreement is found except for the third ligand. The nature of the bonding in these complexes and their BDEs are examined in detail. Although the effect is not as dramatic as in singly or doubly ligated copper complexes, 5s-4ds hybridization found in the Ag+(methanol)n complexes, n= 1 and 2, enhances the BDEs.

  13. 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.

  14. 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.

  15. Mechanistic Investigation of Phosphate Ester Bond Cleavages of Glycylphosphoserinyltryptophan Radical Cations under Low-Energy Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Quan, Quan; Hao, Qiang; Song, Tao; Siu, Chi-Kit; Chu, Ivan K.

    2013-04-01

    Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G p SW]•+) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G• p SW]+). The dissociation of [G• p SW]+ is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H]•+/y1 + pair as the minor products. In contrast, for [G p SW]•+, competitive cleavages along the peptide backbone, such as the formation of [G p SW - CO2]•+ and the [c2 + 2H]+/[z1 - H]•+ pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G• p SW]+ and [G p SW]•+ and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G• p SW]+ results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G p SW]•+.

  16. 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.

  17. 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.

  18. 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.

  19. Electron Transfer Reagent Anion Formation via Electrospray Ionization and Collision-induced Dissociation

    PubMed Central

    Huang, Teng-Yi; Emory, Joshua F.; O’Hair, Richard A.J.; McLuckey, Scott A.

    2011-01-01

    A strategy is described and demonstrated for the formation of reagent anions via electrospray ionization (ESI) for electron transfer dissociation (ETD). To circumvent difficulties associated with formation of high mass-to-charge ratio (m/z) reagent anions, it is desirable to form ETD reagents via means other than those that require reagent molecule vaporization. ESI is a candidate method but anions that are generally generated efficiently by ESI tend to react with multiply protonated polypeptides via proton transfer. The strategy described herein involves the use of a precursor reagent molecule that ionizes efficiently via electrospray ionization and that can subsequently be converted to an ETD reagent via gas-phase dissociation. The approach is demonstrated with arene carboxylic acids that yield strong signals associated with the deprotonated molecule and that subsequently undergo collision-induced dissociation (CID) by loss of CO2. In the present work, triply protonated KGAILKGAILR served as a test substrate for the CID product ions to give rise to ETD. Several precursor molecules were shown to be capable of generating ETD reagents via ESI followed by CID. These included 9-anthracenecarboxylic acid, 2-fluoro-5-iodobenzoic acid, and 2-(fluoranthene-8-carbonyl)-benzoic acid. The latter molecule has the most attractive set of characteristics as a precursor for a relatively high m/z ratio ETD reagent. PMID:17073403

  20. 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.

  1. Collision induced dissociation study of azobenzene and its derivatives: computational and experimental results

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    2015-03-01

    Experimental and computational investigation have been performed in order to study the bond dissociation energy of azobenzene and its derivatives using collision induced dissociation method as well as other energy and structural characteristics. The results have been verified by comparing with results obtained from computational quantum chemistry. We used different density functional methods as well as the Möller-Plesset perturbation theory and the coupled cluster methods to explore geometric, electronic and the spectral properties of the sample molecules. Geometries were calculated and optimized using the 6-311 + + G(2d,2p) basis set and the B3LYP level of theory and these optimized structures have been subjected to the frequency calculations to obtain thermochemical properties by means of different density functional, Möller-Plesset, and coupled cluster theories to obtain a high accuracy estimation of the bond dissociation energy value. The results from experiments and the results obtained from computational thermochemistry are in close agreement. Physics and Astronomy Department

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

    PubMed

    McNary, Christopher P; Armentrout, P B

    2016-12-07

    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.

  3. 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.

  4. 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.

  5. 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. Copyright 2009 John Wiley & Sons, Ltd.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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. © 2016 Wiley Periodicals, Inc.

  13. Electrospray ionization collision-induced dissociation tandem mass spectrometry of amoxicillin and ampicillin and their degradation products.

    PubMed

    Frański, Rafał; Czerniel, Joanna; Kowalska, Marta; Frańska, Magdalena

    2014-04-15

    Detailed analysis of the literature results on the electrospray ionization mass spectrometry (ESI-MS) fragmentation of amoxicillin and ampicillin, and their comparison with our results, have revealed some incorrect suggestions or incomplete interpretations of mass spectra of these compounds. Therefore, this paper contains a comprehensive discussion devoted to the ESI-MS/MS of ampicillin and amoxicillin as well as their degradation products, namely products of hydrolysis and methanolysis. Electrospray ionization collision-induced dissociation tandem mass (ESI-CID-MS/MS) spectra and accurate mass measurements were made on a quadrupole time-of-flight (Q-tof) mass spectrometer. Hydrolysis of the antibiotics was performed by heating, for a few hours, their aqueous solutions adjusted to pH 10. Methanolysis of the antibiotics was performed by heating their methanol solutions for a few minutes. Additionally, mass spectra of isotope-labeled compounds were also obtained. A number of fragment ions, previously wrongly interpreted or not interpreted, have been rationalized. For example, formation of an abundant fragment at m/z 208 originating from the protonated amoxicillin molecule (ion [Amox + H](+)) was previously rationalized as a result of breaking of two bonds of the β-lactam ring. We found that this fragment ion had to be formed by the loss of ammonia and breaking of three bonds of the bicyclic system. The discussion presented enables a better understanding of the MS decompositions of amoxicillin and ampicillin as well as their degradation products. MS decomposition is used for the determinations of these compounds, when the so-called multiple-reaction monitoring is applied during liquid chromatography (LC)/ESI-MS analysis. Thus, better understanding of MS decompositions of the above compounds seems to be important. Copyright © 2014 John Wiley & Sons, Ltd.

  14. Gas chromatography/chemical ionization triple quadrupole mass spectrometry analysis of anabolic steroids: ionization and collision-induced dissociation behavior.

    PubMed

    Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

    2016-02-28

    The detection of new anabolic steroid metabolites and new designer steroids is a challenging task in doping analysis. Switching from electron ionization gas chromatography triple quadrupole mass spectrometry (GC/EI-MS/MS) to chemical ionization (CI) has proven to be an efficient way to increase the sensitivity of GC/MS/MS analyses and facilitate the detection of anabolic steroids. CI also extends the possibilities of GC/MS/MS analyses as the molecular ion is retained in its protonated form due to the softer ionization. In EI it can be difficult to find previously unknown but expected metabolites due to the low abundance or absence of the molecular ion and the extensive (and to a large extent unpredictable) fragmentation. The main aim of this work was to study the CI and collision-induced dissociation (CID) behavior of a large number of anabolic androgenic steroids (AAS) as their trimethylsilyl derivatives in order to determine correlations between structures and CID fragmentation. Clarification of these correlations is needed for the elucidation of structures of unknown steroids and new metabolites. The ionization and CID behavior of 65 AAS have been studied using GC/CI-MS/MS with ammonia as the reagent gas. Glucuronidated AAS reference standards were first hydrolyzed to obtain their free forms. Afterwards, all the standards were derivatized to their trimethylsilyl forms. Full scan and product ion scan analyses were used to examine the ionization and CID behavior. Full scan and product ion scan analyses revealed clear correlations between AAS structure and the obtained mass spectra. These correlations were confirmed by analysis of multiple hydroxylated, methylated, chlorinated and deuterated analogs. AAS have been divided into three groups according to their ionization behavior and into seven groups according to their CID behavior. Correlations between fragmentation and structure were revealed and fragmentation pathways were postulated. Copyright © 2016 John Wiley

  15. 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

  16. 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.

  17. 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.

  18. Three-body collision contributions to recombination and collision-induced dissociation. 1: Cross sections

    SciTech Connect

    Pack, R.T.; Walker, R.B.; Kendrick, B.K.

    1998-04-10

    Atomic and molecular recombination and collision-induced dissociation (CID) reactions comprise two of the most fundamental types of chemical reactions. They are important in all gas phase chemistry; for example, about half of the 196 reactions identified as important in combustion chemistry are recombination or CID reactions. Many of the current chemical kinetics textbooks and kinetics papers treat atomic and molecular recombination and CID as occurring only via sequences of two-body collisions. Actually, there is considerable evidence from experiment and classical trajectory calculations for contributions by true three-body collisions to the recombination of atomic and diatomic radicals, and that evidence is reviewed. Then, an approximate quantum method treating both two-body and three-body collisions simultaneously and on equal footing is used to calculate cross sections for the reaction Ne{sub 2} + H {rightleftharpoons} Ne + Ne + H. The results provide clear quantum evidence that direct three-body collisions do contribute significantly to recombination and CID.

  19. 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.

  20. Effects of transition metal ion coordination on the collision-induced dissociation of polyalanines.

    PubMed

    Watson, Heather M; Vincent, John B; Cassady, Carolyn J

    2011-11-01

    Transition metal-polyalanine complexes were analyzed in a high-capacity quadrupole ion trap after electrospray ionization. Polyalanines have no polar amino acid side chains to coordinate metal ions, thus allowing the effects metal ion interaction with the peptide backbone to be explored. Positive mode mass spectra produced from peptides mixed with salts of the first row transition metals Cr(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(I), and Cu(II) yield singly and doubly charged metallated ions. These precursor ions undergo collision-induced dissociation (CID) to give almost exclusively metallated N-terminal product ions whose types and relative abundances depend on the identity of the transition metal. For example, Cr(III)-cationized peptides yield CID spectra that are complex and have several neutral losses, whereas Fe(III)-cationized peptides dissociate to give intense non-metallated products. The addition of Cu(II) shows the most promise for sequencing. Spectra obtained from the CID of singly and doubly charged Cu-heptaalanine ions, [M + Cu - H](+) and [M + Cu](2+) , are complimentary and together provide cleavage at every residue and no neutral losses. (This contrasts with [M + H](+) of heptaalanine, where CID does not provide backbone ions to sequence the first three residues.) Transition metal cationization produces abundant metallated a-ions by CID, unlike protonated peptides that produce primarily b- and y-ions. The prominence of metallated a-ions is interesting because they do not always form from b-ions. Tandem mass spectrometry on metallated (Met = metal) a- and b-ions indicate that [b(n)  + Met - H](2+) lose CO to form [a(n)  + Met - H](2+), mimicking protonated structures. In contrast, [a(n)  + Met - H](2+) eliminate an amino acid residue to form [a(n-1)  + Met - H](2+), which may be useful in sequencing. Copyright © 2011 John Wiley & Sons, Ltd.

  1. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

    PubMed Central

    Brown, Robert; Stuart, Scott A.; Houel, Stephane; Ahn, Natalie G.; Old, William M.

    2015-01-01

    Collision-induced dissociation (CID) remains the predominant mass spectrometry based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust non-parametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably due to steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss. PMID:25851653

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. 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.

  7. Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

    PubMed

    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 VxOyCl(n-) 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 VxOyCl(n-) 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

    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. Graphical Abstract ᅟ.

  17. 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.

  18. Collision-induced dissociation of the A + 2 isotope ion facilitates glucosinolates structure elucidation by electrospray ionization-tandem mass spectrometry with a linear quadrupole ion trap.

    PubMed

    Cataldi, Tommaso R I; Lelario, Filomena; Orlando, Donatella; Bufo, Sabino A

    2010-07-01

    An approach is presented that can be of general applicability for structural elucidation of naturally occurring glucosinolates (GLSs) in crude plant extracts based on the fragmentation of isotopic A and A + 2 peaks. The most important fragmentation pathways were studied by tandem mass spectrometry (MS(n), n = 2, 3) using a linear quadrupole ion trap (LTQ) upon GLSs separation by optimized reversed-phase liquid chromatography (RPLC) and electrospray ionization (ESI) in negative ion mode. As the LTQ MS analyzer ensures high sensitivity and linearity, the fragmentation behavior under collision induced dissociation (CID) of the isotopic peaks A and A + 2 as precursor ions was carefully examined. All GLSs (R-C(7)H(11)O(9)NS(2)(-)) share a common structure with at least two sulfur atoms and significant isotopic abundance of (34)S. Thus, dissociation of the +2 Da isotopomeric ions results in several fragment ion doublets containing a combination of (32)S and (34)S. Accordingly, their relative abundances allow one to speed up the structural recognition of GLSs with great confidence, as it produces more structurally informative ions than conventional tandem MS performed on A ions. This approach has been validated on known GLSs bearing two, three, four, and six sulfur atoms by comparing expected and measured isotopic peak abundance ratios (I(A)/I(A)(+2)). Both group- and compound-specific fragments were observed; the predominant pathway of fragmentation of GLSs gives rise to species having the following m/z values, [M - SO(3) - H](-), [M - 196 - H](-), [M - 178 - H](-), and [M - 162 - H](-) after H rearrangement from the R- side chain. The present strategy was successfully applied to extracts of rocket salad leaves (Eruca sativa L.), which was sufficient for the chemical identification of a not already known 6-methylsulfonyl-3-oxohexyl-GLS, a long-chain-length aliphatic glucosinolate, which contains three sulfurs and exhibits a deprotonated molecular ion at m/z 494.1.

  19. 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.

  20. 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.

  1. Linkage Determination of Linear Oligosaccharides by MSn (n > 2) Collision-Induced Dissociation of Z1 Ions in the Negative Ion Mode

    NASA Astrophysics Data System (ADS)

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2013-12-01

    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 (MSn, n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides 18O-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. MS3 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 MSn 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.

  2. 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.

  3. 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.

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

    SciTech Connect

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

    2013-07-02

    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

  5. 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.

  6. 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.

  7. Collision-induced dissociation of II-VI semiconductor nanocrystal precursors, Cd2+ and Zn2+ complexes with trioctylphosphine oxide, sulfide, and selenide.

    PubMed

    Min, Won Ja; Jung, Sunghan; Lim, Sung Jun; Kim, Yongwook; Shin, Seung Koo

    2009-09-03

    The metal (M = Cd2+ and Zn2+) complexes with trioctylphosphine chalcogenide (TOPE, E = O, S, and Se) are prepared by electrospray ionization, and their relative stabilities and intramolecular reactions are studied by collision-induced dissociation (CID) with Xe under single collision conditions. These metal-TOPE complexes are considered as molecular precursors for the colloidal synthesis of II-VI compound semiconductor nanocrystals employing TOPO as a metal-coordinating solvent and TOPS or TOPSe as a chalcogen precursor. Of the various [M + nTOPE]2+ (n = 2-7) ions generated by ESI, the n = 2-4 complexes are characterized by CID as a function of collision energy. The collision energy at 50% dissociation (E50%) is determined from the cracking curve and the relative stabilities of the complexes are established. Between the two metal ions, the zinc-TOPE complexes are more stable than the cadmium-TOPE complexes when n = 2-3, whereas their stabilities are reversed when n = 4. Of the TOPE, TOPO binds most strongly to the metal ion, while TOPSe does most weakly. Upon CID, loss of TOPE occurs exclusively from the tetra-TOPE complexes, while extensive fragmentation of TOPE takes place from the di-TOPE complexes, showing the signature of the metal chacogenide formation. The nucleation of nanocrystals appears to begin with cracking of [M + 2TOPE]2+ (E = S and Se).

  8. A Comparison of the Effects of Amide and Acid Groups at the C-Terminus on the Collision-Induced Dissociation of Deprotonated Peptides

    NASA Astrophysics Data System (ADS)

    Bokatzian-Johnson, Samantha S.; Stover, Michele L.; Dixon, David A.; Cassady, Carolyn J.

    2012-09-01

    The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic cm-2 - product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of cm-3 -; however, this is not generally as pronounced as cm-2 - production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH2) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of cm-2 - and a 6-membered ring diketopiperazine neutral requires >31.6 kcal/mol, which is 26.1 kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications.

  9. 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.

  10. 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.

  11. How Hot are Your Ions Really? A Threshold Collision-Induced Dissociation Study of Substituted Benzylpyridinium "Thermometer" Ions

    NASA Astrophysics Data System (ADS)

    Carpenter, John E.; McNary, Christopher P.; Furin, April; Sweeney, Andrew F.; Armentrout, P. B.

    2017-05-01

    The first absolute experimental bond dissociation energies (BDEs) for the main heterolytic bond cleavages of four benzylpyridinium "thermometer" ions are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. In this experiment, substituted benzylpyridinium ions are introduced into the apparatus using an electrospray ionization source, thermalized, and collided with Xe at varied kinetic energies to determine absolute cross-sections for these reactions. Various effects are accounted for, including kinetic shifts, multiple collisions, and internal and kinetic energy distributions. These experimentally measured 0 K BDEs are compared with computationally predicted values at the B3LYP-GD3BJ, M06-GD3, and MP2(full) levels of theory with a 6-311+G(2d,2p) basis set using vibrational frequencies and geometries determined at the B3LYP/6-311+G(d,p) level. Additional dissociation pathways are observed for nitrobenzylpyridinium experimentally and investigated using these same levels of theory. Experimental BDEs are also compared against values in the literature at the AM1, HF, B3LYP, B3P86, and CCSD(T) levels of theory. Of the calculated values obtained in this work, the MP2(full) level of theory with counterpoise corrections best reproduces the experimental results, as do the similar literature CCSD(T) values. Lastly, the survival yield method is used to determine the characteristic temperature (Tchar) of the electrospray source prior to the thermalization region and to confirm efficient thermalization.

  12. 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.

  13. Matrix-Assisted Laser Desorption/Ionisation - High-Energy Collision-Induced Dissociation of Steroids: Analysis of Oxysterols in Rat Brain

    PubMed Central

    Wang, Yuqin; Hornshaw, Martin; Alvelius, Gunvor; Bodin, Karl; Liu, Suya; Sjövall, Jan; Griffiths, William J.

    2008-01-01

    Neutral steroids have traditionally been analysed by gas chromatography – mass spectrometry (GC-MS) after necessary derivatisation reactions. However, GC-MS is unsuitable for the analysis of many conjugated steroids and those with unsuspected functional groups. Here we describe an alternative analytical method specifically designed for the analysis of oxosteroids and those with a 3β-hydroxy-Δ5 or 5α-hydrogen-3β-hydroxy structure. Steroids were derivatised with Girard P (GP) hydrazine to give GP hydrazones which are charged species and readily analysed by matrix-assisted laser desorption/ionization mass spectrometry. The resulting [M]+ ions were then subjected to high-energy collision-induced dissociation on a tandem time-of-flight instrument. The product-ion spectra give structurally informative fragment-ion patterns. The sensitivity of the analytical method is such that steroids structures can be determined from low pg (low fmole) amounts of sample. The utility of the method has been demonstrated by the analysis of oxysterols extracted from rat brain. PMID:16383324

  14. 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.

  15. 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.

  16. Enhancing structural characterisation of glucuronidated O-linked glycans using negative mode ion trap higher energy collision-induced dissociation mass spectrometry.

    PubMed

    Ashwood, Christopher; Abrahams, Jodie L; Nevalainen, Helena; Packer, Nicolle H

    2017-05-30

    High protein production and secretion with eukaryotic glycosylation machinery make T. reesei RUT-C30 a suitable expression host for recombinant proteins. The N-glycosylation of secreted proteins of RUT-C30 is known to vary depending on culture nutrients but O-glycosylation has been less extensively studied. O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. O-Glycans were analysed in negative ion mode by electrospray ionisation linear ion trap mass spectrometry and glycopeptides in positive ion mode by electrospray ionisation hybrid quadrupole-orbitrap mass spectrometry. Tandem mass spectrometry was used on O-glycans and glycopeptides including ion trap higher energy collision-induced dissociation (tHCD) to detect glycan fragments not detectable with standard ion trap fragmentation. tHCD allowed targeted MS(3) experiments to be performed on structures containing hexuronic acid, which was not possible with ion trap CID, validating this novel O-glycan composition. Positive mode C18-LC/ESI-MS/MS was used to identify and characterise glycopeptides found to be modified with this class of O-glycans, identifying cellobiohydrolase I as a carrier of these novel O-glycans. Negative mode ion trap higher energy collision-induced dissociation allowed detection and targeted MS(3) experiments to be performed on the hexuronic acid substituent of O-glycan structures, which was not possible with ion trap CID, validating the novel O-glycan composition to include hexuronic acid. Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. These are the first reported O-glycans to contain acidic sugars in fungi and they could have significant implications for cellobiohydrolase I structure and activity as well as the activity of recombinant proteins expressed in this host system

  17. 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.

  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 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

  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

    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.

  20. 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.

  1. Energy-resolved collision-induced dissociation pathways of model N-linked glycopeptides: implications for capturing glycan connectivity and peptide sequence in a single experiment.

    PubMed

    Kolli, Venkata; Dodds, Eric D

    2014-05-07

    Tandem mass spectrometry (MS/MS) of glycopeptides stands among the principal analytical approaches for assessing protein glycosylation in a site-specific manner. The aims of such experiments are often to determine the monosaccharide connectivity of the glycan, the amino acid sequence of the peptide, and the site of glycan attachment. This level of detail is often difficult to achieve using any single ion dissociation method; however, precedent does exist for use of collision-induced dissociation (CID) to establish either the connectivity of the oligosaccharide or the sequence of the polypeptide depending upon the applied collision energy. Unfortunately, the relative energy requirements for glycan and peptide cleavage have not been thoroughly characterized with respect to specific physicochemical characteristics of the precursor ions. This report describes case studies on the energy-resolved CID pathways of model tryptic glycopeptides derived from Erythrina cristagalli lectin and bovine ribonuclease B. While glycopeptide ions having disparate physical and chemical characteristics shared strikingly similar qualitative responses to increasing vibrational energy deposition, the absolute collision energies at which either glycan or peptide fragmentations were accessed varied substantially among the precursor ions examined. Nevertheless, these data suggest that the energy requirements for peptide and glycan cleavage may be somewhat predictable based on characteristics of the precursor ion. The practical usefulness of these observations was demonstrated through implementation of online collision energy modulation such that both glycan and peptide fragmentation were captured in the same spectrum, providing near-exhaustive glycopeptide characterization in a single experiment. Overall, these results highlight the potential to further extend the capabilities of CID in the context of glycoproteomics.

  2. 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.

  3. How Hot are Your Ions Really? A Threshold Collision-Induced Dissociation Study of Substituted Benzylpyridinium "Thermometer" Ions

    NASA Astrophysics Data System (ADS)

    Carpenter, John E.; McNary, Christopher P.; Furin, April; Sweeney, Andrew F.; Armentrout, P. B.

    2017-09-01

    The first absolute experimental bond dissociation energies (BDEs) for the main heterolytic bond cleavages of four benzylpyridinium "thermometer" ions are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. In this experiment, substituted benzylpyridinium ions are introduced into the apparatus using an electrospray ionization source, thermalized, and collided with Xe at varied kinetic energies to determine absolute cross-sections for these reactions. Various effects are accounted for, including kinetic shifts, multiple collisions, and internal and kinetic energy distributions. These experimentally measured 0 K BDEs are compared with computationally predicted values at the B3LYP-GD3BJ, M06-GD3, and MP2(full) levels of theory with a 6-311+G(2d,2p) basis set using vibrational frequencies and geometries determined at the B3LYP/6-311+G(d,p) level. Additional dissociation pathways are observed for nitrobenzylpyridinium experimentally and investigated using these same levels of theory. Experimental BDEs are also compared against values in the literature at the AM1, HF, B3LYP, B3P86, and CCSD(T) levels of theory. Of the calculated values obtained in this work, the MP2(full) level of theory with counterpoise corrections best reproduces the experimental results, as do the similar literature CCSD(T) values. Lastly, the survival yield method is used to determine the characteristic temperature (Tchar) of the electrospray source prior to the thermalization region and to confirm efficient thermalization. [Figure not available: see fulltext.

  4. State to state collision induced dissociation and gas/surface interactions

    NASA Astrophysics Data System (ADS)

    Wittig, Curt; Reisler, Hanna

    1989-03-01

    The main thrust of our contract was directed towards the study of gas surface interactions and the complementary collisionless photodissociation processes. The initial experiments were concerned with NO scattering from an insulating MgO(100) single crystal surfaces, and the preliminary results were published in Chem. Phys. Lett. Experiments are being conducted in which molecules with high kinetic energy are dissociated and/or ionized upon impact on surfaces. The preliminary results, which are first of their kind since they involve state-resolved detection of the dissociation products, were accepted as a Communication in the Journal of Chemical Physics. In parallel with these new experiments, studies were continued in the photophysics and photodissociation dynamics of molecules which are suitable candidates for the beam/surface and beam/beam experiments. These include detailed studies of the photodissociation dynamics of such molecules as nitrosyl cyanide, nitrosyl chloride, t-BuNO and n- and iso-nitrosopropane.

  5. 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.

  6. 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.

  7. 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.

  8. Probing lysine acetylation with a modification-specific marker ion using high-performance liquid chromatography/electrospray-mass spectrometry with collision-induced dissociation.

    PubMed

    Kim, Jin Young; Kim, Kyoung Wook; Kwon, Ho Jeong; Lee, Dai Woon; Yoo, Jong Shin

    2002-11-01

    Posttranslational acetylation of proteins regulates many diverse functions, including DNA recognition, protein-protein interaction, and protein stability. The identification of enzymes that regulate protein acetylation has revealed broader use of this modification than was previously suspected. In this study, we describe a method for identifying protein acetylation at lysine residues by analysis of digested protein using HPLC/ESI-MS with a new modification-specific marker ion. Collision-induced dissociation with capillary or nano-LC/ESI-TOF-MS was used to obtain a fragment ion useful as a marker for acetylated lysine. Although the acetylated lysine immonium ion at m/z 143.1 has been used as a marker ion for detecting acetylated lysine, it can be confused with internal fragment ion in some peptides, producing false positive results. We have found a novel marker ion at m/z 126.1, which is a further fragment ion induced by the loss of NH3 from the acetylated lysine immonium ions at m/z 143.1. This novel marker ion was found to be more specific and approximately 9 times more sensitive than the immonium ion at m/z 143.1. In addition, no interfering ions for acetylated peptides were found in the extracted ion chromatogram at m/z 126.1. The utility of this method was demonstrated with acetylated cytochrome c as a model compound. After the modification was probed by the new marker ion, the acetylated lysine site was determined by the CID-MS spectrum. This method was applied to identify histone H4 acetylation in HeLa cells treated with trichostatin A. Three protein bands separated by acid-urea-Triton gel electrophoresis were confirmed as tetra, tri, and diacetylated histone H4 at lysines 5, 8, 12, and 16. This method may be useful for assaying for lysine acetylation, which is an important regulatory process for a range of biological functions.

  9. Characterization of alpha- and gamma-glutamyl dipeptides by negative ion collision-induced dissociation.

    PubMed

    Harrison, Alex G

    2004-02-01

    The low-energy CID mass spectra of the [M-H](-) ions of a variety of dipeptides containing glutamic acid have been obtained using cone-voltage collisional activation. Dipeptides with the gamma-linkage, H-Glu(Xxx-OH)-OH, are readily distinguished from those with the alpha-linkage, H-Glu-Xxx-OH, by the much more prominent elimination of H-Xxx-OH from the [M-H](-) ions of the former isomers, resulting in formation of m/z 128, presumably deprotonated pyroglutamic acid. Dipeptides with the reverse linkage, H-Xxx-Glu-OH, show distinctive fragmentation reactions of the [M-H](-) ions including enhanced elimination of CO(2) and formation of deprotonated glutamic acid. Exchange of the labile hydrogens for deuterium has shown that there is considerable interchange of C-bonded hydrogens with labile (N- and O-bonded) hydrogens prior to most fragmentation reactions. All dipeptides show loss of H(2)O from [M-H](-). MS(3) studies show that the [M-H-H(2)O](-) ion derived from H-Glu-Gly-OH has the structure of deprotonated pyroglutamylglycine while the [M-H-H(2)O](-) ions derived from H-Glu(Gly-OH)-OH and H-Gly-Glu-OH show a different fragmentation behaviour indicating distinct structures for the fragment ions. Copyright 2004 John Wiley & Sons, Ltd.

  10. 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.

  11. THE IMPLANTATION AND INTERACTIONS OF O{sup +} IN TITAN'S ATMOSPHERE: LABORATORY MEASUREMENTS OF COLLISION-INDUCED DISSOCIATION OF N{sub 2} AND MODELING OF POSITIVE ION FORMATION

    SciTech Connect

    Shah, M. B.; Latimer, C. J.; Montenegro, E. C.; Tucker, O. J.; Johnson, R. E.; Smith, H. T.

    2009-10-01

    Energetic oxygen ions are an important component of the plasma incident onto Titan's atmosphere. Therefore, we report measurements of electron capture and ionization collisions of N{sub 2} with incident O{sup +} over the energy range 10-100 keV. Using time of flight coincidence counting techniques we also measured the collision-induced dissociation of N{sub 2} following ionization and electron capture. The electron capture and ionization cross sections were found to have comparable magnitudes. Capture collisions are dominated by non-dissociative processes with the dissociative processes providing contributions that are only slightly smaller. In contrast, ionization is entirely dominated by the dissociative processes. The energy distributions of the N{sup +} and N atom fragments ejected by 20, 50, and 100 keV incident O{sup +} projectiles have also been determined. These fragments carry considerable amounts of energy and if produce in the exobase region can readily escape. The cross sections measured here have been used with Cassini energetic ion and atmospheric density data to determine the ionization by and neutralization of energetic O{sup +} penetrating Titan's N{sub 2} rich atmosphere. Neutralization by charge exchange is found not to occur efficiently above Titan's exobase, so energetic particles with large gyroradii penetrate the atmosphere primarily as ions. When the energetic O{sup +} flux is large, we also show it is an important source of ionization and heating at depth into Titan's atmosphere and the fragments contribute to the net atmospheric loss rate.

  12. 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.

  13. 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.

  14. 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

  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. Cluster ions of diquat and paraquat in electrospray ionization mass spectra and their collision-induced dissociation spectra.

    PubMed

    Milman, Boris L

    2003-01-01

    Cluster ions such as [Cat+X+nM](+) (n = 0-4); [Cat-H+nM](+) (n = 1-3); and [2(Cat-H)+X+nM](+) (n = 0-2), where Cat, X, and M are the dication, anion, and neutral salt (CatX(2)), respectively, are observed in electrospray ionization (ESI) mass spectrometry of relatively concentrated solutions of diquat and paraquat. Collision-induced dissociation (CID) reactions of the clusters were observed by tandem mass spectrometry (MS/MS), including deprotonation to form [Cat-H](+), one-electron reduction of the dication to form Cat(+.), demethylation of the paraquat cation to form [Cat-CH(3)](+), and loss of neutral salt to produce smaller clusters. The difference in acidity and reduction power between diquat and paraquat, evaluated by thermodynamical estimates, can rationalize the different fractional yields of even-electron ([Cat-H](+) and its clusters) and odd-electron (mostly Cat(+)) ions in ESI mass spectra of these pesticides. The [Cat+n. Solv](2+) doubly charged cluster ions, where n

  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. 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.

  19. Structural characterization of flavonol di-O-glycosides from Farsetia aegyptia by electrospray ionization and collision-induced dissociation mass spectrometry.

    PubMed

    Shahat, Abdelaaty A; Cuyckens, Filip; Wang, Wu; Abdel-Shafeek, Khaled A; Husseiny, Husseiny A; Apers, Sandra; Van Miert, Sabine; Pieters, Luc; Vlietinck, Arnold J; Claeys, Magda

    2005-01-01

    This study reports the application of mass spectrometric methods to characterize unknown flavonoids of the herb Farsetia aegyptia Turra (Crucifereae). High-performance liquid chromatography was performed in combination with UV-photodiode array detection (LC/UV-DAD) and electrospray ionization mass spectrometry (LC/ESI-MS) in both positive and negative ion modes. Collision-induced dissociation (CID) mass spectral data were obtained off-line by nanospray (nano-ESI) analysis, which provided a wealth of information and led to the structural proposal of the flavonol di-O-glycosides present in the herb extract. In addition to the mass spectral data, we also report NMR data for the major compound which allowed the completion of its structural elucidation. The Farsetia aegyptia Turra herb extract was found to contain three flavonol di-O-glycosides containing a monosaccharidic residue linked to the 3-O position and a disaccharidic residue linked to the 7-O position; the major compound was characterized as the new flavonoid, isorhamnetin 3-O-alpha-L-arabinoside 7-O-[beta-D-glucosyl-1 --> 2]-alpha(L)rhamnoside. Different types of CID spectra, i.e., low-energy [M+H]+, [M+Na]+ and [M--H]- spectra as well as high-energy [M+Na]+ spectra, were evaluated with respect to their utility to locate the O-linked saccharidic residues in flavonol di-O-glycosides and to determine the sequence in the disaccharidic part. In agreement with previously published data, the 3-O-glycosyl residue was more readily lost from the protonated molecule than the 7-O-glycosyl residue. The opposite behavior was noted for the fragmentation of the deprotonated and sodiated molecules. Radical ions were observed in the high-energy [M+Na]+ CID spectra which provided supporting information on the glycosylation positions. (c) 2005 John Wiley & Sons, Ltd.

  20. Simultaneous Quantification of Free Cholesterol, Cholesteryl Esters, and Triglycerides without Ester Hydrolysis by UHPLC Separation and In-Source Collision Induced Dissociation Coupled MS/MS

    NASA Astrophysics Data System (ADS)

    Gardner, Michael S.; McWilliams, Lisa G.; Jones, Jeffrey I.; Kuklenyik, Zsuzsanna; Pirkle, James L.; Barr, John R.

    2017-08-01

    We demonstrate the application of in-source nitrogen collision-induced dissociation (CID) that eliminates the need for ester hydrolysis before simultaneous analysis of esterified cholesterol (EC) and triglycerides (TG) along with free cholesterol (FC) from human serum, using normal phase liquid chromatography (LC) coupled to atmospheric pressure chemical ionization (APCI) tandem mass spectrometry (MS/MS). The analysis requires only 50 μL of 1:100 dilute serum with a high-throughput, precipitation/evaporation/extraction protocol in one pot. Known representative mixtures of EC and TG species were used as calibrators with stable isotope labeled analogs as internal standards. The APCI MS source was operated with nitrogen source gas. Reproducible in-source CID was achieved with the use of optimal cone voltage (declustering potential), generating FC, EC, and TG lipid class-specific precursor fragment ions for multiple reaction monitoring (MRM). Using a representative mixture of purified FC, CE, and TG species as calibrators, the method accuracy was assessed with analysis of five inter-laboratory standardization materials, showing -10% bias for Total-C and -3% for Total-TG. Repeated duplicate analysis of a quality control pool showed intra-day and inter-day variation of 5% and 5.8% for FC, 5.2% and 8.5% for Total-C, and 4.1% and 7.7% for Total-TG. The applicability of the method was demonstrated on 32 serum samples and corresponding lipoprotein sub-fractions collected from normolipidemic, hypercholesterolemic, hypertriglyceridemic, and hyperlipidemic donors. The results show that in-source CID coupled with isotope dilution UHPLC-MS/MS is a viable high precision approach for translational research studies where samples are substantially diluted or the amounts of archived samples are limited. [Figure not available: see fulltext.

  1. 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., fragmentation, can be characterized by the CID-MS2 step. A more targeted approach can then be followed in subsequent LC-MS runs to obtain additional information, if needed. Overall, the recently introduced ETD not only provides useful structural information, but also

  2. 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.

  3. Collision-induced dissociation studies of Fe(m)O(n) (+) : Bond energies in small iron oxide cluster cations, Fe(m)O(n) (+) (m=1-3, n=1-6).

    PubMed

    Li, Ming; Liu, Shu-Rong; Armentrout, P B

    2009-10-14

    A variety of iron oxide cluster cations is synthesized in a laser vaporization ion source. The kinetic energy dependence of the collision-induced dissociation (CID) of mass selected Fe(m)O(n) (+) (m=1-3, n=1-6) clusters with Xe is studied in this work using a guided ion beam tandem mass spectrometer. Examination of the general dissociation behavior over a broad collision energy range (0-15 eV) shows that iron oxide clusters can dissociate via evaporation of neutral Fe and O atoms as well as fission by loss of neutral O(2), FeO, FeO(2), Fe(2)O(2), and Fe(2)O(3) fragments. Such fission pathways, which are not observed in the CID studies of pure Fe cluster cations and most other pure transition metal cluster cations, result from the strong iron oxygen bonds. In general, the predominant dissociation pathways are found to correlate with the oxidation state of the iron in the cluster. Thresholds for loss of neutral Fe, O, O(2), FeO, FeO(2), Fe(2)O(2), and Fe(2)O(3) from various iron oxide cluster cations are quantitatively determined. These values are used to determine bond energies and heats of formation for both neutral and cationic iron oxide clusters in this size range.

  4. 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.

  5. Dissociation and Memory Fragmentation in Posttraumatic Stress Disorder: An Evaluation of the Dissociative Encoding Hypothesis

    PubMed Central

    Bedard-Gilligan, Michele; Zoellner, Lori A.

    2012-01-01

    Several prominent theories of posttraumatic stress disorder (PTSD) posit that peritraumatic dissociation results in insufficient encoding of the trauma memory and that persistent dissociation prevents memory elaboration, resulting in memory fragmentation and PTSD. In this review, we summarize the empirical literature on peritraumatic and trait dissociation and trauma narrative fragmentation as measured by meta-memory and rater/objective coding. Across 16 studies to date, the association between dissociation and fragmentation was most prominent when examining peritraumatic dissociation and patient's own ratings of memory fragmentation. This relationship did not hold when examining trait dissociation or rater-coded or computer-generated measures of fragmentation. Thus, initial evidence points more toward a strong self-reported association between constructs that is not supported on more objective fragmentation coding. Measurement overlap, construct ambiguity, and exclusion of potential confounds may underlie lack of a strong association between dissociation and objective-rated fragmentation. PMID:22348400

  6. 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.

  7. 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)

    NASA Astrophysics Data System (ADS)

    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.

  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. Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]{sup 2+} gas phase unimolecular reactivity via chemical dynamics simulations

    SciTech Connect

    Spezia, Riccardo; Salpin, Jean-Yves; Cimas, Alvaro; Gaigeot, Marie-Pierre; Song, Kihyung; Hase, William L.

    2012-07-01

    In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)]{sup 2+}, in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar{sup +} [Ca(urea)]{sup 2+} collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex. (authors)

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

    PubMed

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

    2016-02-15

    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. 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. A CID spectrum of the P14 R1 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. 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 Mass Spectrometry published by John Wiley

  11. 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

  12. 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.

  13. 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.

  14. 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.

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

    PubMed

    Yang, Zhibo; Rodgers, M T

    2004-12-15

    The influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Bond dissociation energies of alkali metal ion-halouracil complexes, M+(XU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and XU = 5-fluorouracil, 5-chlorouracil, 6-chlorouracil, 5-bromouracil, and 5-iodouracil. The structures and theoretical bond dissociation energies of these complexes are determined from ab initio calculations. Theoretical calculations are also performed to examine the influence of halogenation on the acidities, proton affinities, and Watson-Crick base pairing energies. Halogenation of uracil is found to produce a decrease in the proton affinity, an increase in the alkali metal ion binding affinities, an increase in the acidity, and stabilization of the A::U base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Liquid chromatography coupled with ultraviolet absorbance detection, electrospray ionization, collision-induced dissociation and tandem mass spectrometry on a triple quadrupole for the on-line characterization of polyphenols and methylxanthines in green coffee beans.

    PubMed

    Alonso-Salces, Rosa Maria; Guillou, Claude; Berrueta, Luis A

    2009-02-01

    Liquid chromatography coupled with a photodiode array detector, electrospray ionization, collision-induced dissociation and tandem mass spectrometry (LC-DAD/ESI-CID-MS/MS) on a triple quadrupole (QqQ) has been used to detect and characterize polyphenols and methylxanthines in green coffee beans: three phenolic acids (caffeic acid, ferulic acid and dimethoxycinnamic acid), three isomeric caffeoylquinic acids (M(r) 354), three feruloylquinic acids (M(r) 368), one p-coumaroylquinic acid (M(r) 338), three dicaffeoylquinic acids (M(r) 516), three feruloyl-caffeoylquinic acids (M(r) 530), four p-coumaroyl-caffeoylquinic acids (M(r) 500), three diferuloylquinic acids (M(r) 544), six dimethoxycinnamoyl-caffeoylquinic acids (M(r) 544), three dimethoxycinnamoyl-feruloylquinic acids (M(r) 558), six cinnamoyl-amino acid conjugates, three cinnamoyl glycosides, and three methylxanthines (caffeine, theobromine and theophylline). Dimethoxycinnamic acid, three isomers of dimethoxycinnamoyl-caffeoylquinic acids and another three of dimethoxycinnamoyl-feruloylquinic acids, as well as the three cinnamoyl glycosides, had not previously been reported in coffee beans. Structures have been assigned on the basis of the complementary information obtained from UV-visible spectra, relative hydrophobicity, scan mode MS spectra, and fragmentation patterns in MS(2) spectra (both in the positive and negative ion modes) obtained using a QqQ at different collision energies. A structure diagnosis scheme is provided for the identification of different isomers of polyphenols and methylxanthines. Copyright 2009 John Wiley & Sons, Ltd.

  4. 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.

  5. Structural determination of cerebrosides isolated from Asterias amurensis starfish eggs using high-energy collision-induced dissociation of sodium-adducted molecules.

    PubMed

    Park, Taeseong; Park, Young Seung; Rho, Jung-Rae; Kim, Young Hwan

    2011-03-15

    Six cerebrosides were isolated from the eggs of the starfish Asterias amurensis using solvent extraction, silica gel column chromatography, and reversed-phase high-performance liquid chromatography. This study demonstrated that the structures of cerebrosides could be completely characterized, based on their sodium-adducted molecules, using fast atom bombardment (FAB) tandem mass spectrometry. The high-energy collision-induced dissociation of the sodium-adducted molecule, [M + Na](+), of each cerebroside molecular species generated abundant ions, providing information on the compositions of the 2-hydroxy fatty acids and long-chain sphingoid bases, as well as the sugar moiety polar head group. Each homologous ion series along the fatty acid and aliphatic chain of the sphingoid base was useful for locating the double-bond positions of both chains and the methyl branching position of the long-chain base. The N-fatty acyl portions were primarily long-chain saturated or monoenoic acids (C16 to C24) with an α-hydroxy group. The sphingoid long-chain base portions were aliphatic chains (C18 or C22) with two or three degrees of unsaturation and with or without methyl branching. Copyright © 2011 John Wiley & Sons, Ltd.

  6. 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.

  7. Quasiclassical trajectory study of energy transfer and collision-induced dissociation in hyperthermal Ar + CH4 and Ar + CF4 collisions.

    PubMed

    Troya, Diego

    2005-07-07

    We present a study of energy transfer in collisions of Ar with methane and perfluoromethane at hyperthermal energies (E(coll) = 4-10 eV). Quasiclassical trajectory calculations of Ar + CX(4) (X = H, F) collisions indicate that energy transfer from reagents' translation to internal modes of the alkane molecule is greatly enhanced by fluorination. The reasons for the enhancement of energy transfer upon fluorination are shown to emerge from a decrease in the hydrocarbon vibrational frequencies of the CX(4) molecule with increasing the mass of the X atom, and to an increase of the steepness of the Ar-CX(4) intermolecular potential. At high collision energies, we find that the cross section of Ar + CF(4) collisions in which the amount of energy transfer is larger than needed to break a C-F bond is at least 1 order of magnitude larger than the cross sections of Ar + CH(4) collisions producing CH(4) with energy above the dissociation limit. In addition, collision-induced dissociation is detected in short time scales in the case of the fluorinated species at E(coll) = 10 eV. These results suggest that the cross section for degradation of fluorinated hydrocarbon polymers under the action of nonreactive hyperthermal gas-phase species might be significantly larger than that of hydrogenated hydrocarbon polymers. We also illustrate a practical way to derive intramolecular potential energy surfaces for bond-breaking collisions by improving semiempirical Hamiltonians based on grids of high-quality ab initio calculations.

  8. 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.

  9. 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.

  10. Fragmentation pathways analysis for the gas phase dissociation of protonated carnosine-oxaliplatin complexes.

    PubMed

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

    2015-03-14

    Collision-induced dissociation (CID) experiments on the protonated carnosine-oxaliplatin complex, [Carnosine + OxPt + H](+) using several collision energies were shown to yield nine different fragment ions. Energy-resolved CID experiments on [Carnosine + OxPt + H](+) showed that the generation of the product ion [Carnosine - H + Pt(dach)](+) (where dach is 1,2-diaminocyclohexane) is the lowest energy process. At slightly higher collision energies, the loss of neutral carnosine from [Carnosine + OxPt + H](+) to produce [OxPt + H](+) was observed, followed by the loss of oxaliplatin from the same precursor ion to produce [Carnosine + H](+). At significantly higher energies, the ion [OxPt - CO2 + H](+) was shown to be formed, while the last two investigated ions [Carnosine + OxPt - CO2 + H](+) and [Carnosine - NH3 - H + Pt(dach)](+) did not attain any significant relative abundance. Density functional calculations at the B3LYP/LANL2DZ level were employed to probe the fragmentation mechanisms that account for all experimental data. The lowest free energy barriers for the generation of each of the ions [Carnosine - H + Pt(dach)](+), [OxPt + H](+), [Carnosine + H](+), [Carnosine + OxPt - CO2 + H](+) and [Carnosine - NH3 - H + Pt(dach)](+) from [Carnosine + OxPt + H](+) according to the fragmentation mechanisms offered here were calculated to be 31.9, 38.8, 49.3, 75.2, and 85.6 kcal mol(-1), respectively.

  11. 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.

  12. Dissociation and memory fragmentation in post-traumatic stress disorder: an evaluation of the dissociative encoding hypothesis.

    PubMed

    Bedard-Gilligan, Michele; Zoellner, Lori A

    2012-01-01

    Several prominent theories of post-traumatic stress disorder (PTSD) posit that peritraumatic dissociation results in insufficient encoding of the trauma memory and that persistent dissociation prevents memory elaboration, resulting in memory fragmentation and PTSD. In this review we summarise the empirical literature on peritraumatic and trait dissociation and trauma narrative fragmentation as measured by meta-memory and rater/objective coding. Across 16 studies to date, the association between dissociation and fragmentation was most prominent when examining peritraumatic dissociation and patient's own ratings of memory fragmentation. This relationship did not hold when examining trait dissociation or rater-coded or computer-generated measures of fragmentation. Thus initial evidence points more towards a strong self-reported association between constructs that is not supported on more objective fragmentation coding. Measurement overlap, construct ambiguity, and exclusion of potential confounds may underlie lack of a strong association between dissociation and objective-rated fragmentation.

  13. 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.

  14. 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.

  15. Collision-induced dissociation processes of protonated benzoic acid and related compounds: competitive generation of protonated carbon dioxide or protonated benzene.

    PubMed

    Xu, Sihang; Pavlov, Julius; Attygalle, Athula B

    2017-04-01

    Upon activation in the gas phase, protonated benzoic acid (m/z 123) undergoes fragmentation by several mechanisms. In addition to the predictable water loss followed by a CO loss, the m/z 123 ion more intriguingly eliminates a molecule of benzene to generate protonated carbon dioxide (H - O(+)  ═ C ≡ O, m/z 45), or a molecule of carbon dioxide to yield protonated benzene (m/z 79). Experimental evidence shows that the incipient proton ambulates during the fragmentation processes. For the CO2 or benzene loss, protonated benzoic acid transfers the charge-imparting proton initially to the ortho position and then to the ipso position to generate a transient species which dissociates to form an ion-neutral complex between benzene and protonated CO2 . The formation of the m/z 45 ion is not a phenomenon unique to benzoic acid: spectra from protonated isophthalic acid, terephthalic acid, trans-cinnamic acid and some aliphatic acids also displayed a peak for m/z 45. However, the m/z 45 peak is structurally diagnostic only for certain benzene polycarboxylic acids because the spectra of compounds with two carboxyl groups on adjacent ring carbons do not produce a peak at m/z 45. For the m/z 79 ion to be formed, an intramolecular reaction should take place in which protonated CO2 within the ion-neutral complex acts as the attacking electrophile to transfer a proton to benzene. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  16. 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.

  17. 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.

  18. 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.

  19. Electromagnetic Dissociation Cross Sections for High LET Fragments

    NASA Technical Reports Server (NTRS)

    Norbury, John

    2016-01-01

    Nuclear interaction cross sections are used in space radiation transport codes to calculate the probability of fragment emission in high energy nucleus-nucleus collisions. Strong interactions usually dominate in these collisions, but electromagnetic (EM) interactions can also sometimes be important. Strong interactions typically occur when the projectile nucleus hits a target nucleus, with a small impact parameter. For impact parameters larger than the sum of the nuclear radii, EM reactions dominate and the process is called electromagnetic dissociation (EMD) if one of the nuclei undergo fragmentation. Previous models of EMD have been used to calculate single proton (p) production, single neutron (n) production or light ion production, where a light ion is defined as an isotope of hydrogen (H) or helium (He), such as a deuteron (2H), a triton (3H), a helion (3He) or an alpha particle (4He). A new model is described which can also account for multiple nucleon production, such as 2p, 2n, 1p1n, 2p1n, 2p2n, etc. in addition to light ion production. Such processes are important to include for the following reasons. Consider, for example, the EMD reaction 56Fe + Al --> 52Cr + X + Al, for a 56Fe projectile impacting Al, which produces the high linear energy transfer (LET) fragment 52Cr. In this reaction, the most probable particles representing X are either 2p2n or 4He. Therefore, production of the high LET fragment 52Cr, must include the multiple nucleon production of 2p2n in addition to the light ion production of 4He. Previous models, such as the NUCFRG3 model, could only account for the 4He production process in this reaction and could not account for 2p2n. The new EMD model presented in this work accounts for both the light ion and multiple nucleon processes, and is therefore able to correctly account for the production of high LET products such as 52Cr. The model will be described and calculations will be presented that show the importance of light ion and multiple

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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. Copyright © 2016 John Wiley & Sons, Ltd.

  5. 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.

  6. Analyses of chlorogenic acids and related cinnamic acid derivatives from Nicotiana tabacum tissues with the aid of UPLC-QTOF-MS/MS based on the in-source collision-induced dissociation method.

    PubMed

    Ncube, Efficient N; Mhlongo, Msizi I; Piater, Lizelle A; Steenkamp, Paul A; Dubery, Ian A; Madala, Ntakadzeni E

    2014-01-01

    Chlorogenic acids (CGAs) are a class of phytochemicals that are formed as esters between different derivatives of cinnamic acid and quinic acid molecules. In plants, accumulation of these compounds has been linked to several physiological responses against various stress factors; however, biochemical synthesis differs from one plant to another. Although structurally simple, the analysis of CGA molecules with modern analytical platforms poses an analytical challenge. The objective of the study was to perform a comparison of the CGA profiles and related derivatives from differentiated tobacco leaf tissues and undifferentiated cell suspension cultures. Using an UHPLC-Q-TOF-MS/MS fingerprinting method based on the in-source collision induced dissociation (ISCID) approach, a total of 19 different metabolites with a cinnamic acid core moiety were identified. These metabolites were either present in both leaf tissue and cell suspension samples or in only one of the two plant systems. Profile differences point to underlying biochemical similarities or differences thereof. Using this method, the regio- and geometric-isomer profiles of chlorogenic acids of the two tissue types of Nicotiana tabacum were achieved. The method was also shown to be applicable for the detection of other related molecules containing a cinnamic acid core.

  7. 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.

  8. 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.

  9. 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 peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous

  10. 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

    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

    2011-02-01

    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 peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous

  11. Evidence for site-specific intra-ionic hydrogen/deuterium exchange in the low-energy collision-induced dissociation product ion spectra of protonated small molecules generated by electrospray ionisation.

    PubMed

    Holman, Stephen W; Wright, Patricia; Wells, Neil J; Langley, G John

    2010-04-01

    The experimental investigation of site-specific intra-ionic hydrogen/deuterium (H/D) exchange in the low-energy collision-induced dissociation (CID) product ion spectra of protonated small molecules generated by electrospray ionisation (ESI) is presented. The observation of intra-ionic H/D exchange in such ions under low-energy CID conditions has hitherto been rarely reported. The data suggest that the intra-ionic H/D exchange takes place in a site-specific manner between the ionising deuteron, localised at either a tertiary amine or a tertiary amine-N-oxide, and a gamma-hydrogen relative to the nitrogen atom. Nuclear magnetic resonance (NMR) spectroscopy measurements showed that no H/D exchange takes place in solution, indicating that the reaction occurs in the gas phase. The compounds analysed in this study suggested that electron-withdrawing groups bonded to the carbon atom bearing the gamma-hydrogen can preclude exchange. The effect of the electron-withdrawing group appears dependent upon its electronegativity, with lower chi value groups still allowing exchange to take place. However, the limited dataset available in this study prevented robust conclusions being drawn regarding the effect of the electron-withdrawing group. The observation of site-specific intra-ionic H/D exchange has application in the area of structural elucidation, where it could be used to introduce an isotopic label into the carbon skeleton of a molecule containing specific structural features. This could increase the throughput, and minimise the cost, of such studies due to the obviation of the need to produce a deuterium-labelled analogue by synthetic means. Copyright 2010 John Wiley & Sons, Ltd.

  12. Electromagnetic dissociation effects in galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Townsend, L. W.

    1986-01-01

    Methods for calculating cross sections for the breakup of galactic heavy ions by the Coulomb fields of the interacting nuclei are presented. By using the Weizsacker-Williams method of virtual quanta, estimates of electromagnetic dissociation cross sections for a variety of reactions applicable to galactic cosmic ray shielding studies are presented and compared with other predictions and with available experimental data.

  13. Affective Association: An Effective Intervention in Countering Fragmentation and Dissociation

    ERIC Educational Resources Information Center

    Hart, Carolyn

    2008-01-01

    This paper is concerned with the processes, both psychoanalytic and neuroscientific, involved in the undoing of dissociation in a 3-year-old, who was seen weekly over a nine month period. A neuroscientific and psychoanalytic developmental framework is used to follow a sequence of phenomena that emerged over the duration of relatively brief once…

  14. Affective Association: An Effective Intervention in Countering Fragmentation and Dissociation

    ERIC Educational Resources Information Center

    Hart, Carolyn

    2008-01-01

    This paper is concerned with the processes, both psychoanalytic and neuroscientific, involved in the undoing of dissociation in a 3-year-old, who was seen weekly over a nine month period. A neuroscientific and psychoanalytic developmental framework is used to follow a sequence of phenomena that emerged over the duration of relatively brief once…

  15. Fluorescence of dissociating fragments from supersonic jet-electron collisions

    NASA Astrophysics Data System (ADS)

    Blake, Thomas A.; Smilgys, Russell V.; Lobue, James M.; Schiffman, Aram P.; Novick, Stewart E.

    1985-05-01

    Supersonically cooled jets of nitrogen, methane, ethane, cyclopropane, and azomethane are crossed with collimated streams of electrons. The CH (B 2Σ - → X 2Π) spectra resulting from the electron-induced dissociation of CH 4, C 2H 6, and CH 2) 3 can be fit with rotation temperatures between 4000 and 6000 K for an electron energy of 100 eV. Flourescence spectra of N 2+ (B 2Σ w+ → X 2Π) from the dissociative ionization of azomethane yield a rotational temperature of =8×10 3 K; from ionization of molecular nitrogen the rotational temperature of B 2Σ w+ N 2+ is 45 K. Mechanisms for these various processes are discussed.

  16. Experimental and data analysis techniques for deducing collision-induced forces from photographic histories of engine rotor fragment impact/interaction with a containment ring

    NASA Technical Reports Server (NTRS)

    Yeghiayan, R. P.; Leech, J. W.; Witmer, E. A.

    1973-01-01

    An analysis method termed TEJ-JET is described whereby measured transient elastic and inelastic deformations of an engine-rotor fragment-impacted structural ring are analyzed to deduce the transient external forces experienced by that ring as a result of fragment impact and interaction with the ring. Although the theoretical feasibility of the TEJ-JET concept was established, its practical feasibility when utilizing experimental measurements of limited precision and accuracy remains to be established. The experimental equipment and the techniques (high-speed motion photography) employed to measure the transient deformations of fragment-impacted rings are described. Sources of error and data uncertainties are identified. Techniques employed to reduce data reading uncertainties and to correct the data for optical-distortion effects are discussed. These procedures, including spatial smoothing of the deformed ring shape by Fourier series and timewise smoothing by Gram polynomials, are applied illustratively to recent measurements involving the impact of a single T58 turbine rotor blade against an aluminum containment ring. Plausible predictions of the fragment-ring impact/interaction forces are obtained by one branch of this TEJ-JET method; however, a second branch of this method, which provides an independent estimate of these forces, remains to be evaluated.

  17. Fragmentation patterns of Chromophore-Tagged Peptides in Visible Laser Induced Dissociation.

    PubMed

    Garcia, Lény; Lemoine, Jérôme; Dugourd, Philippe; Girod, Marion

    2017-09-08

    Tandem mass spectrometry (MS/MS) is the pivotal tool for protein structural characterization and quantification. Identification relies on the fragmentation step of tryptic peptides in bottom-up strategy. Specificity of fragmentation can be obtained using laser induced dissociation (LID) in the visible range, after tagging of the targeted peptides with an adequate chromophore. Backbone fragmentation is required to obtain specific fragments and confident identification. We present herein a study of fragmentation patterns of chromophore-tagged peptides in LID, showing the potential of LID methodology to provide the maximum of fragments for further identification and quantification. 401 cysteine-containing tryptic peptides coming from the human proteome were derivatizated on the thiol group of cysteine with a Dabcyl maleimide chromophore, which has a high photo-absorption cross section at 473 nm. The derivatized peptides were then analyzed by LID at 473 nm on a Q Exactive instrument. LID spectra present a characteristic fragment at m/z 252.112 for all precursors. This product ion arises from the internal dissociation of the dabcyl chromophore. Several peptide-backbone fragment ions are also detected. Results show the quasi absence of fragmentation at the cysteine site. This indicates that part of the energy must be redistributed across the entire system despite excitation initially localized at the chromophore. Indeed, the fragmentation mainly occurs at 3 to 5 amino acids from the derivatized cysteine residue. LID of derivatized cysteine-containing peptides displays the initial fragmentation of the chromophore. As energy is redistributed all along the peptide sequence, fragmentation of the peptide backbone is also observed. Thus, LID of chromophore-tagged peptides produces adequate fragment ions, allowing both good sequence coverage for a greater confidence of identification, and a large choice of transitions for specific quantification. This article is protected by

  18. Excited ionic and neutral fragments produced by dissociation of the N2(+)* H band

    NASA Technical Reports Server (NTRS)

    Samson, James A. R.; Chung, Y.; Lee, E.-M.

    1991-01-01

    N I and N II fluorescent radiation was observed when N2 was irradiated by undispersed synchrotron radiation with an upper energy limit of approximately 200 eV. The excited fragments originate from dissociation of a band of excited ionic states of N2 lying between 34.7 and 44 eV.

  19. Excitations from dissociative fragments produced in H++H2O collisions

    NASA Astrophysics Data System (ADS)

    Monce, Michael N.; Pan, Sihui; Radeva, Nadezhda L.; Pepper, Jaime L.

    2009-01-01

    We report on photon emissions in the 200 800nm region resulting from collisions of 200keV protons with H2O . The most prominent features observed in the spectrum are the Balmer series of hydrogen and two OH molecular bands. Several less intense O+ as well as neutral O lines are also observed. The absolute photon emission cross sections of the major lines and bands were measured. The results indicate that a primary dissociation pathway involves the formation of H2O+ by removing a 1b2 electron. The unstable H2O+ ion further dissociates into H++OH or OH++H . The dominant presence of neutral hydrogen lines and O+ lines leads to the conclusion that the subsequent dissociation of OH+ into H+O+ prevails over the other possible dissociation pathway leading to H+ and neutral oxygen fragments.

  20. Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation.

    PubMed

    Durbin, Kenneth R; Skinner, Owen S; Fellers, Ryan T; Kelleher, Neil L

    2015-05-01

    Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

  1. Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation

    NASA Astrophysics Data System (ADS)

    Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T.; Kelleher, Neil L.

    2015-05-01

    Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

  2. Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation

    PubMed Central

    Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T.; Kelleher, Neil L.

    2015-01-01

    Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis. PMID:25716753

  3. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time- and Energy-Resolved Surface-Induced Dissociation Studies

    SciTech Connect

    Laskin, Julia

    2006-07-01

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM-based approach developed at the Environmental Molecular Sciences Laboratory (EMSL).

  4. Measurement of the velocity of neutral fragments by the "correlated ion and neutral time of flight" method combined with "velocity-map imaging"

    NASA Astrophysics Data System (ADS)

    Berthias, F.; Feketeová, L.; Della Negra, R.; Dupasquier, T.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Märk, T. D.

    2017-08-01

    In the challenging field of imaging molecular dynamics, a novel method has been developed and implemented that allows the measurement of the velocity of neutral fragments produced in collision induced dissociation experiments on an event-by-event basis. This has been made possible by combining a correlated ion and neutral time of flight method with a velocity map imaging technique. This new method relies on a multiparametric correlated detection of the neutral and charged fragments from collision induced dissociation on one single detector. Its implementation on the DIAM device (Device for irradiation of biomolecular clusters) (Dispositif d'Irradiation d'Agrégats bioMoléculaires) allowed us to measure the velocity distribution of water molecules evaporated from collision induced dissociation of mass- and energy-selected protonated water clusters.

  5. Fragmentation of polyatomic molecules by grazing incidence surface-induced dissociation (GI-SID).

    PubMed

    Wieghaus, A; Schmidt, L; Popova, A M; Komarov, V V; Jungclas, H

    1999-11-01

    The grazing incidence surface-induced dissociation (GI-SID) of n-hexadecylpyridinium and verapamil ions generated by fission fragment desorption was studied. These molecules show the effect of enhanced surface-induced dissociation at grazing incidence as it was observed in former experiments with metal organic ions. A liquid film of perfluorinated polyether is used as collision surface. Small hydrocarbon fragment ions predominate in the GI-SID spectra. Pyridine ions appear as specific fragment ions in the GI-SID spectrum of n-hexadecylpyridinium. The GI-SID conversion efficiency varies in the range 40-70%. The experimental results are discussed within the scope of a quantum mechanical model which is based on the accumulation of internal molecular energy by resonant excitation of collective vibrational states and energy transfer to a trap bond due to dipole-dipole interactions. In this context the GI-SID spectra of n-hexadecylpyridinium and verapamil ions are compared with the fragmentation occurring in regular (252)Cf plasma desorption mass spectrometry.

  6. Electron-impact dissociation of CH{sup +} ions: Measurement of C{sup +} fragment ions

    SciTech Connect

    Bannister, M.E.; Krause, H.F.; Vane, C.R.; Djuric, N.; Popovic, D.B.; Stepanovic, M.; Dunn, G.H.; Chung, Y.-S.; Smith, A.C.H.; Wallbank, B.

    2003-10-01

    Absolute cross sections for electron-impact dissociation of CH{sup +} producing C{sup +} fragment ions were measured in the 3-100 eV range using a crossed electron-ion beams technique with total uncertainties of about 10% near the cross-section peak. Although the measured energy dependence agrees well with two sets of storage ring measurements, the magnitude of the present results lies about 15-25 % below the other results at the cross-section peak near 40 eV. Below 10 eV, the present data tend to exceed the storage ring data, consistent with the presence of excited states in the CH{sup +} ion beam. For energies above 29 eV, the cross sections should also include contributions from dissociative ionization, though no clear onset of this channel is evident in any of the three sets of measured data.

  7. Kinetic-energy release of fragments from electron-impact dissociation of the molecular hydrogen ion and its isotopologues

    NASA Astrophysics Data System (ADS)

    Scarlett, Liam H.; Zammit, Mark C.; Fursa, Dmitry V.; Bray, Igor

    2017-08-01

    We calculate the kinetic-energy release distributions of fragments produced for electron-impact dissociation of the vibrationally excited molecular hydrogen ion H2 + and its isotopologues D2 + and T2 +. Here we apply the adiabatic-nuclei convergent close-coupling method and compare results with several different methods, including the δ approximation. Results are presented for a number of dissociative excitation transitions and dissociative ionization as a function of the initial vibrational state of the molecule. We confirm that the square root approximation is a good approximation for the adiabatic-nuclei kinetic-energy release cross sections of H2 +. Agreement with experiment, where available, is good.

  8. Studies of negative ions by collision-induced decomposition and hydrogen-deuterium exchange techniques.

    PubMed Central

    Hunt, D F; Sethi, S K; Shabanowitz, J

    1980-01-01

    Development of two new techniques for studying the gas phase chemistry of negative ions is reported. Collision induced dissociation (CID) of (M-1)- ions has been accomplished in a newly constructed triple stage quadrupole mass spectrometer. This instrument was assembled by adding two additional Finnigan quadrupole mass filters to a Finnigan Model 3200 CI mass spectrometer. Generation of (M-1)- ions is accomplished by allowing OH- and sample to react under CI conditions in the ion source. The first quadrupole mass filter, Q1, is then employed to selectively pass the (M-1)- ion into a second quadrupole filter containing argon or neon at 10(-3) torr. On collision with the inert gas the (M-1)- ions dissociate into fragments which are then mass analyzed in the third quadrupole filter, CID spectra of (M-1)- ions from twelve carbonyl compounds are presented in this paper. Ion molecule isotope exchange reactions in the CI ion source can be used to count the number of hydrogen atoms in many different chemical environments. Collisions between sample (M-1)- ions and deuterium-labeled reagent gases (ND3, D2O, EtOD) facilitate incorporation of deuterium into the negative ion if the basicities of the sample and reagent anions are similar. Thus it is possible to selectively incorporate deuterium into many organic samples by controlling the exothermicity of the acid base, ion-molecule chemistry. PMID:7428745

  9. Studies of negative ions by collision-induced decomposition and hydrogen-deuterium exchange techniques.

    PubMed

    Hunt, D F; Sethi, S K; Shabanowitz, J

    1980-06-01

    Development of two new techniques for studying the gas phase chemistry of negative ions is reported. Collision induced dissociation (CID) of (M-1)- ions has been accomplished in a newly constructed triple stage quadrupole mass spectrometer. This instrument was assembled by adding two additional Finnigan quadrupole mass filters to a Finnigan Model 3200 CI mass spectrometer. Generation of (M-1)- ions is accomplished by allowing OH- and sample to react under CI conditions in the ion source. The first quadrupole mass filter, Q1, is then employed to selectively pass the (M-1)- ion into a second quadrupole filter containing argon or neon at 10(-3) torr. On collision with the inert gas the (M-1)- ions dissociate into fragments which are then mass analyzed in the third quadrupole filter, CID spectra of (M-1)- ions from twelve carbonyl compounds are presented in this paper. Ion molecule isotope exchange reactions in the CI ion source can be used to count the number of hydrogen atoms in many different chemical environments. Collisions between sample (M-1)- ions and deuterium-labeled reagent gases (ND3, D2O, EtOD) facilitate incorporation of deuterium into the negative ion if the basicities of the sample and reagent anions are similar. Thus it is possible to selectively incorporate deuterium into many organic samples by controlling the exothermicity of the acid base, ion-molecule chemistry.

  10. Conformation changes and dissociation of Fc fragments of rabbit immunoglobulin G as a function of pH

    PubMed Central

    Charlwood, P. A.; Utsumi, S.

    1969-01-01

    1. The sedimentation coefficients of rabbit immunoglobulin G, four types of Fc fragments, univalent Fab and bivalent F(ab)2 fragments were measured as a function of pH. 2. In conjunction with molecular-weight determinations by sedimentation equilibrium, and with the behaviour on gel filtration, this enabled the state of association of the Fc fragments to be followed. 3. The type possessing an interchain disulphide bond, 1Fc fragment, changed extensively in structure, but not in molecular weight. 4. There was good correlation between the readiness to dissociate and the chain length of the shorter Fc fragments that do not contain the interchain covalent bond. 5. The increasing resistance to dissociation as the fragments became shorter ran parallel with the ability to resist enzymic attack. 6. The site of the strong association between component chains of Fc fragment is located in the C-terminal half. 7. The gel-filtration behaviour of the Fc fragments clearly confirms that the process is governed by the Stokes radius rather than molecular weight. 8. The ultracentrifugal results were used to estimate the separations of the hydrodynamic subunits in intact immunoglobulin G, and as a basis for a schematic structure. ImagesFig. 3. PMID:5801306

  11. Energetics and dynamics of fragmentation of protonated leucine enkephalin from time- and energy-resolved surface-induced dissociation studies.

    PubMed

    Laskin, Julia

    2006-07-13

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM-based approach developed in our laboratory. The following threshold energies and activation entropies were determined in this study: E(0) = 1.20 eV and DeltaS++ = -20 eu(1) (MH(+)-->b(5)); E(0) = 1.14 eV and DeltaS++ = -14.7 eu (MH(+)-->b(4)); E(0) = 1.42 eV and DeltaS++ = -2.5 eu (MH(+)-->b(3)); E(0) = 1.30 eV and DeltaS++ = -4.1 eu (MH(+)-->a(4)); E(0) = 1.37 eV and DeltaS++ = -5.2 eu (MH(+)-->y ions); E(0) = 1.50 eV and DeltaS++ = 1.6 eu (MH(+)-->internal fragments); E(0) = 1.62 eV and DeltaS++ = 5.2 eu (MH(+)-->F). Comparison with Arrhenius activation energies reported in the literature demonstrated for the first time the reversal of the order of activation energies as compared to threshold energies for dissociation.

  12. 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.

  13. 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.

  14. The Effect of the Secondary Structure on Dissociation of Peptide Radical Cations: Fragmentation of Angiotensin III and Its Analogues

    SciTech Connect

    Yang, Zhibo; Lam, Corey; Chu, Ivan K.; Laskin, Julia

    2008-09-28

    Fragmentation of protonated RVYIHPF and RVYIHPF-OMe and the corresponding radical cations was studied using time- and collision energy-resolved surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. Both the energetics and mechanisms of dissociation of even-electron and odd-electron angiotensin III ions are quite different. Protonated molecules are much more stable towards fragmentation than the corresponding radical cations. RRKM modeling of the experimental data suggests that this stability is largely attributed to differences in threshold energies for dissociation while activation entropies are very similar. Detailed analysis of the experimental data obtained for radical cations demonstrated the presence of two distinct structures separated by a high free-energy barrier. The two families of structures were ascribed to the canonical and zwitterionic forms of the radical cations produced in our experiments.

  15. Effect of Basic Residue on the Kinetics of Peptide Fragmentation Examined Using Surface-Induced Dissociation Combined with Resonant Ejection

    SciTech Connect

    Laskin, Julia

    2015-11-30

    In this work, resonant ejection coupled with surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer is used to examine fragmentation kinetics of two singly protonated hexapeptides, RYGGFL and KYGGFL, containing the basic arginine residue and less basic lysine residue at the N-terminus. The kinetics of individual reaction channels at different collision energies are probed by applying a short ejection pulse (1 ms) in resonance with the cyclotron frequency of a selected fragment ion and varying the delay time between ion-surface collision and resonant ejection while keeping total reaction delay time constant. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data provides accurate threshold energies and activation entropies of individual reaction channels. Substitution of arginine with less basic lysine has a pronounced effect on the observed fragmentation kinetics of several pathways, including the b2 ion formation, but has little or no effect on formation of the b5+H2O fragment ion. The combination of resonant ejection SID, time- and collision energy-resolved SID, and RRKM modeling of both types of experimental data provides a detailed mechanistic understanding of the primary dissociation pathways of complex gaseous ions.

  16. 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

  17. Dissociation Chemistry of Hydrogen-Deficient Radical Peptide Anions

    NASA Astrophysics Data System (ADS)

    Moore, Benjamin; Sun, Qingyu; Hsu, Julie C.; Lee, Albert H.; Yoo, Gene C.; Ly, Tony; Julian, Ryan R.

    2012-03-01

    The fragmentation chemistry of anionic deprotonated hydrogen-deficient radical peptides is investigated. Homolytic photodissociation of carbon-iodine bonds with 266 nm light is used to generate the radical species, which are subsequently subjected to collisional activation to induce further dissociation. The charges do not play a central role in the fragmentation chemistry; hence deprotonated peptides that fragment via radical directed dissociation do so via mechanisms which have been reported previously for protonated peptides. However, charge polarity does influence the overall fragmentation of the peptide. For example, the absence of mobile protons favors radical directed dissociation for singly deprotonated peptides. Similarly, a favorable dissociation mechanism initiated at the N-terminus is more notable for anionic peptides where the N-terminus is not protonated (which inhibits the mechanism). In addition, collisional activation of the anionic peptides containing carbon-iodine bonds leads to homolytic cleavage and generation of the radical species, which is not observed for protonated peptides presumably due to competition from lower energy dissociation channels. Finally, for multiply deprotonated radical peptides, electron detachment becomes a competitive channel both during the initial photoactivation and following subsequent collisional activation of the radical. Possible mechanisms that might account for this novel collision-induced electron detachment are discussed.

  18. 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

  19. Excited ionic and neutral fragments produced by dissociation of the N2(+)-asterisk H band

    NASA Technical Reports Server (NTRS)

    Samson, James A. R.; Chung, Y.; Lee, E.-M.

    1991-01-01

    Atomic fluorescence produced by dissociative photoionization of N2 was observed and identified in experiments where fluorescent radiation was produced by irradiating N2 gas with undispersed synchrotron radiation. The spectrum was detected with a multichannel plate electron multiplier. Evidence is presented that the H band of N2(+)-asterisk does predissociate into excited neutral and ionic atoms.

  20. New Approach for Studying Slow Fragmentation Kinetics in FT-ICR: Surface-Induced Dissociation Combined with Resonant Ejection

    SciTech Connect

    Laskin, Julia; Futrell, Jean H.

    2015-02-01

    We introduce a new approach for studying the kinetics of large ion fragmentation in the gas phase by coupling surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer with resonant ejection of selected fragment ions using a relatively short (5 ms) ejection pulse. The approach is demonstrated for singly protonated angiotensin III ions excited by collisions with a self-assembled monolayer of alkylthiol on gold (HSAM). The overall decomposition rate and rate constants of individual reaction channels are controlled by varying the kinetic energy of the precursor ion in a range of 65–95 eV. The kinetics of peptide fragmentation are probed by varying the delay time between resonant ejection and fragment ion detection at a constant total reaction time. RRKM modeling indicates that the shape of the kinetics plots is strongly affected by the shape and position of the energy deposition function (EDF) describing the internal energy distribution of the ion following ion-surface collision. Modeling of the kinetics data provides detailed information on the shape of the EDF and energy and entropy effects of individual reaction channels.

  1. 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.

  2. 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

  3. 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.

  4. Measuring fragmentation in dissociative identity disorder: the integration measure and relationship to switching and time in therapy.

    PubMed

    Barlow, M Rose; Chu, James A

    2014-01-01

    Some people with dissociative identity disorder (DID) have very little communication or awareness among the parts of their identity, while others experience a great deal of cooperation among alternate identities. Previous research on this topic has been sparse. Currently, there is no empirical measure of integration versus fragmentation in a person with DID. In this study, we report the development of such a measure. The goal of this study was to pilot the integration measure (IM) and to address its psychometric properties and relationships to other measures. The IM is the first standardized measure of integration in DID. Eleven women with DID participated in an experiment that included a variety of tasks. They filled out questionnaires about trauma and dissociation as well as the IM. They also provided verbal results about switching among alternate identities during the study sessions. Participants switched among identities an average of 5.8 times during the first session, and switching was highly correlated with trauma. Integration was related to switching, though this relationship may be non-linear. Integration was not related to time in psychotherapy. The IM provides a useful beginning to quantify and study integration and fragmentation in DID. Directions for future research are also discussed, including expanding the IM from this pilot. The IM may be useful in treatment settings to assess progress or change over time.

  5. Measuring fragmentation in dissociative identity disorder: the integration measure and relationship to switching and time in therapy

    PubMed Central

    Barlow, M. Rose; Chu, James A.

    2014-01-01

    Background Some people with dissociative identity disorder (DID) have very little communication or awareness among the parts of their identity, while others experience a great deal of cooperation among alternate identities. Previous research on this topic has been sparse. Currently, there is no empirical measure of integration versus fragmentation in a person with DID. In this study, we report the development of such a measure. Objective The goal of this study was to pilot the integration measure (IM) and to address its psychometric properties and relationships to other measures. The IM is the first standardized measure of integration in DID. Method Eleven women with DID participated in an experiment that included a variety of tasks. They filled out questionnaires about trauma and dissociation as well as the IM. They also provided verbal results about switching among alternate identities during the study sessions. Results Participants switched among identities an average of 5.8 times during the first session, and switching was highly correlated with trauma. Integration was related to switching, though this relationship may be non-linear. Integration was not related to time in psychotherapy. Conclusions The IM provides a useful beginning to quantify and study integration and fragmentation in DID. Directions for future research are also discussed, including expanding the IM from this pilot. The IM may be useful in treatment settings to assess progress or change over time. PMID:24396569

  6. Elucidation of the mass fragmentation pathways of tomatidine and β1-hydroxytomatine using orbitrap mass spectrometry.

    PubMed

    Caprioli, Giovanni; Cahill, Michael; Logrippo, Serena; James, Kevin

    2015-04-01

    Tomatoes, members of the Solanaceae plant family, produce biologically active secondary metabolites, including glycoalkaloids, which may have both adverse and beneficial biological effects. Using the linear ion trap (LIT) mass spectrometry, multi-stage collision induced dissociation (CID) experiments (MSn) were performed to elucidate characteristic fragmentation pathways of the glycoalkaloid, tomatidine and of β1-hydroxytomatine. High resolution with high accuracy mass analysis using an Orbitrap fourier transform MS with higher-energy collisional induced dissociation (HCD) was used to produce mass spectra data across a wide spectral range for confirmation of proposed ion structures and formulae.

  7. Combustion Pathways of the Alkylated Heteroaromatics: Bond Dissociation Enthalpies and Alkyl Group Fragmentations

    NASA Astrophysics Data System (ADS)

    Hayes, Carrigan J.; Hadad, Christopher M.

    2009-04-01

    The bond dissociation enthalpies (BDEs) of the alkyl groups of the alkyl-substituted heterocycles have been studied and compiled using DFT methodology, with the intent of modeling the larger heterocyclic functionalities found in coal. DFT results were calibrated against CBS-QB3 calculations, and qualitative trends were reproduced between these methods. Loss of hydrogen at the benzylic position provided the most favorable route to radical formation, for both the azabenzenes and five-membered heterocycles. The ethyl derivatives had lower BDE values than the methyl derivatives due to increased stabilization of the corresponding radicals. Calculated spin densities correlated well with bond dissociation enthalpies for these compounds, while geometric effects were minimal with respect to the heterocycles themselves. Temperature effects on the bond dissociation enthalpies were minor, ranging by about 5 kcal/mol from 298 to 2000 K; the free energies of reaction dropped significantly over the same range due to entropic effects. Monocyclic heteroaromatic rings were seen to replicate the chemistry of multicyclic heteroaromatic systems.

  8. Kinetic energies of fragment ions produced by dissociative photoionization of NO

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Angel, G. C.; Rstgi, O. P.

    1985-01-01

    The kinetic energies of ions produced by dissociative photoionization of NO have been measured at the discrete resonance lines of He (584A) and Ne (736A), and with undispersed synchrotron radiation. O sup + ions were identified with energies from 0 to approximately 0.5 eV and two groups of N sup + ions one with energy of 0.36 eV and another with energies between 0.9 and 1.5 eV, apparently produced by predissociation of the C sup 3 P 1 and B'1 sigma states respectively.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap.

    PubMed

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

    2009-11-01

    Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (approximately 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification.

  14. Efficient and scalable culture of single dissociated human pluripotent stem cells using recombinant E8 fragments of human laminin isoforms.

    PubMed

    Miyazaki, Takamichi; Kawase, Eihachiro

    2015-02-02

    This unit describes a protocol for efficient expansion of human pluripotent stem cells (hPSCs). A key feature of this method is subculture of hPSCs by single-cell dissociation passaging on substrates coated with recombinant E8 fragments of human laminin isoforms (LM-E8s). LM-E8s, provide superior adhesion over intact laminin isoforms and Matrigel. Single hPSCs seeded on LM-E8s show accelerated migration and rapid reconstruction of clusters, resulting in robust survival and proliferation. This protocol yields 200-fold more hPSCs than conventional subculture methods in 1 month of culture. Furthermore, this protocol can be easily adapted to most hPSC lines in combination with the use of various xeno-free, defined culture media, and large-scale expansion of hPSCs is easily achievable to facilitate the practical applications of hPSCs. Copyright © 2015 John Wiley & Sons, Inc.

  15. Restoring literary wholeness to the fragmented account of Antoine Despine's magnetic cure of Estelle L'Hardy's dissociative disorder.

    PubMed

    McKeown, Joanne M

    2007-10-01

    Dr. Charles-Humbert Antoine Despine's (1777-1852) De L'Emploi du magnétisme animal et des eaux minerales dans le traitement des maladies nerveuses, suivi d'une observation très curieuse de guérison de névropathie [A Study of the uses of animal magnetism in the treatment of disorders of the nervous system followed by a case of a highly unusual cure of neuropathy] (Paris: Germer, Baillière, 1840) is one of the earliest published, complete accounts of a successful cure with animal magnetism of a dissociative disorder. Despine's methodical and gentle treatment of more than 20 patients with multiple personalities repeatedly brought fusion to separation. His writing style displays a lack of order and unity that resembles the dissociative symptoms of his patients, but the monograph's sloppiness belies Despine's methodical approach to his work and his thoughtful handling of his patients. This paper explores these inconsistencies and how translators of the monograph act as literary therapists for his confused and fragmented account.

  16. 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.

  17. Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment

    SciTech Connect

    Kopyra, Janina; Abdoul-Carime, Hassan

    2015-05-07

    Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T − H){sup −} produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10{sup −19} cm{sup 2}. These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.

  18. Collision induced migration of adsorbates on surfaces

    NASA Astrophysics Data System (ADS)

    Romm, L.; Asscher, M.; Zeiri, Y.

    1999-06-01

    Collision induced migration (CIM) has been identified as a new surface phenomenon and has been studied for the first time using molecular dynamics simulations. The CIM process was represented by an energetic gas phase argon atom, striking an adsorbed nitrogen molecule on Ru(001). The efficiency of CIM was investigated as a function of the collider initial kinetic energy and angle of incidence. It was found that at low coverages an adsorbed molecule can migrate more than 150 Å following collisions at high energies and grazing angles of incidence. As coverage increases, inter-adsorbate collisions result in significant reduction of migration distances. At high energies, the competing process of collision induced desorption becomes dominant, leaving behind molecules which migrate shorter distances. These competing channels lead to a collision energy for which CIM is maximized. For the N2/Ru system, the CIM process is most effective near collider energy of 2.0 eV. This new surface phenomenon of CIM has to be considered for better understanding the full range of surface processes which govern industrial high pressure catalysis. At the tail of the thermal kinetic energy distribution, energetic colliders from the gas phase lead to CIM and generate high energy inter-adsorbate collisions, sometimes discussed in terms of "hot-particle" chemistry.

  19. Combining Higher-Energy Collision Dissociation and Electron-Transfer/Higher-Energy Collision Dissociation Fragmentation in a Product-Dependent Manner Confidently Assigns Proteomewide ADP-Ribose Acceptor Sites.

    PubMed

    Bilan, Vera; Leutert, Mario; Nanni, Paolo; Panse, Christian; Hottiger, Michael O

    2017-02-07

    Protein adenosine diphosphate (ADP)-ribosylation is a physiologically and pathologically important post-translational modification. Recent technological advances have improved analysis of this complex modification and have led to the discovery of hundreds of ADP-ribosylated proteins in both cultured cells and mouse tissues. Nevertheless, accurate assignment of the ADP-ribose acceptor site(s) within the modified proteins identified has remained a challenging task. This is mainly due to poor fragmentation of modified peptides. Here, using an Orbitrap Fusion Tribrid mass spectrometer, we present an optimized methodology that not only drastically improves the overall localization scores for ADP-ribosylation acceptor sites but also boosts ADP-ribosylated peptide identifications. First, we systematically compared the efficacy of higher-energy collision dissociation (HCD), electron-transfer dissociation with supplemental collisional activation (ETcaD), and electron-transfer/higher-energy collision dissociation (EThcD) fragmentation methods when determining ADP-ribose acceptor sites within complex cellular samples. We then tested the combination of HCD and EThcD fragmentation, which were employed in a product-dependent manner, and the unique fragmentation properties of the ADP-ribose moiety were used to trigger targeted fragmentation of only the modified peptides. The best results were obtained with a workflow that included initial fast, high-energy HCD (Orbitrap, FT) scans, which produced intense ADP-ribose fragmentation ions. These potentially ADP-ribosylated precursors were then selected and analyzed via subsequent high-resolution HCD and EThcD fragmentation. Using these resulting high-quality spectra, we identified a xxxxxxKSxxxxx modification motif where lysine can serve as an ADP-ribose acceptor site. Due to the appearance of serine within this motif and its close presence to the lysine, further analysis revealed that serine serves as a new ADP-ribose acceptor site

  20. 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.

  1. Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: focus on triglyceride detection and characterization.

    PubMed

    Bird, Susan S; Marur, Vasant R; Sniatynski, Matthew J; Greenberg, Heather K; Kristal, Bruce S

    2011-09-01

    There is a growing need both clinically and experimentally to improve the characterization of blood lipids. A liquid chromatography-mass spectrometry (LC-MS) method, developed for the qualitative and semiquantitative detection of lipids in biological samples and previously validated in mitochondrial samples, was now evaluated for the profiling of serum lipids. Data were acquired using high-resolution, full scan MS and high-energy, collisional dissociation (HCD), all ion fragmentation. The method was designed for efficient separation and detection in both positive and negative ionization mode and evaluated using standards spanning seven lipid classes. Platform performance, related to the identification and characterization of serum triglycerides (TGs), was assessed using extracted ion chromatograms with mass tolerance windows of 5 ppm or less from full scan exact mass measurements determined using SIEVE nondifferential LC-MS analysis software. The platform showed retention time coefficients of variation (CV) of <0.3%, mass accuracy values of <2 ppm error, and peak area CV of <13%, with the majority of that error coming from sample preparation and extraction rather than the LC-MS analysis, and linearity was shown to be over 4 orders of magnitude (r(2) = 0.999) for the standard TG (15:0)(3) spiked into serum. Instrument mass accuracy and precision were critical to the identification of unknown TG species, in part because these parameters enabled us to reduce false positives. In addition to detection and relative quantitation of TGs in serum, TG structures were characterized through the use of alternating HCD scans at different energies to produce diagnostic fragmentations on all ions in the analysis. The lipidomics method was applied to serum samples from 192 rats maintained on diets differing in macronutrient composition. The analysis identified 86 TG species with 81 unique masses that varied over 3.5 orders of magnitude and showed diet-dependency, consistent with

  2. 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.

  3. 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.

  4. 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.

  5. Gas-Surface Interactions Near Dissociation Threshold

    DTIC Science & Technology

    1992-03-26

    irtcJE "Gas-Surface Interactions Near Dissociation Threshold" AFOS-R-39-0057 University of Southern California MQ 4ME Department of Chemistry A U-Oj...the study collision-induced dissociation (cm)) of hyperthermal molecules on insulators (MgO), semiconductors (GaAs) and metals (Ag). Supersonic beams of... dissociation threshold at high surface temperature. The yield depends on the stiffness of the surface. The NO distributions are similar to those

  6. Effects of molecular rotation after ionization and prior to fragmentation on observed recoil-frame photoelectron angular distributions in the dissociative photoionization of nonlinear molecules

    NASA Astrophysics Data System (ADS)

    López-Domínguez, Jesús A.; Lucchese, Robert R.

    2016-03-01

    Experimental angle-resolved photoelectron-photoion coincidence experiments measure photoelectron angular distributions (PADs) in dissociative photoionization (DPI) in the reference frame provided by the momenta of the emitted heavy fragments. By extension of the nomenclature used with DPI of diatomic molecules, we refer to such a PAD as a recoil-frame PAD (RFPAD). When the dissociation is fast compared to molecular rotational and bending motions, the emission directions of the heavy fragments can be used to determine the orientation of the bonds that are broken in the DPI at the time of the ionization, which is known as the axial-recoil approximation (ARA). When the ARA is valid, the RFPADs correspond to molecular-frame photoelectron angular distributions (MFPADs) when the momenta of a sufficient number of the heavy fragments are determined. When only two fragments are formed, the experiment cannot measure the orientation of the fragments about the recoil axes so that the resulting measured PAD is an azimuthally averaged RFPAD (AA-RFPAD). In this study we consider how the breakdown of the ARA due to rotation will modify the observed RFPADs for DPI processes in nonlinear molecules for ionization by light of arbitrary polarization. This model is applied to the core C 1 s DPI of CH4, with the results compared to experimental measurements and previous theoretical calculations done within the ARA. The published results indicate that there is a breakdown in the ARA for two-fragment events where the heavy-fragment kinetic energy release was less than 9 eV. Including the breakdown of the ARA due to rotation in our calculations gives very good agreement with the experimental AA-RFPAD, leading to an estimate of upper bounds on the predissociative lifetimes as a function of the kinetic energy release of the intermediate ion states formed in the DPI process.

  7. Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

    NASA Astrophysics Data System (ADS)

    Medzihradszky, Katalin F.; Bohlen, Christopher J.

    2012-05-01

    A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

  8. Partial de novo sequencing and unusual CID fragmentation of a 7 kDa, disulfide-bridged toxin

    PubMed Central

    Medzihradszky, Katalin F.; Bohlen, Christopher J.

    2015-01-01

    A 7 kDa toxin isolated from the venom of the Texas coral snake (Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed. PMID:22351294

  9. 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.

  10. 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.

  11. 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

  12. DISSOCIATION OF B2H6 AND ADSORPTION OF THE FRAGMENTS OF B2H6 ON THE STEPPED Ge(100) SURFACE

    NASA Astrophysics Data System (ADS)

    Türkmenoğlu, Mustafa; Katircioğlu, Şenay

    2012-06-01

    In this work, the p-type doping of the SA type stepped Ge(100) surface by a diborane (B2H6) gas flow has been simulated by the possible dissociation and adsorption models. The most probable dissociation model of B2H6 and adsorption models of the fragments of B2H6 on the stepped Ge(100) surface have been determined by the local minimum total energy and/or binding energy calculations based on the Density functional (B3LYP/6-3g) and Hartree-Fock (HF/STO-3g) theories, respectively. The present calculations have shown that, the step region (for both up and down terraces) of the stepped Ge(100) surface has the most attractive sites for BH3 molecules determined to be the first dissociation fragments of B2H6 by an external energy of 1.3 eV. It has been found that, at the first step of the adsorption, BH3 can dissociate to BH2 and BH fragments on the stepped Ge(100) surface. While BH3 and BH2 products prefer to be attached to a single surface Ge atom, BH is bridged between two adjacent surface Ge atoms. According to the present optimization calculations, the p-type doping process of the stepped Ge(100) surface has started with the adsorption of BH3 on the electron deficient site (buckled down) of the Ge dimer bond close to the step edge and ended with the substitutional occupation of the Ge site in the layers of the surface by B atom. The beginning of the p-type doping of the stepped Ge(100) surface has been illustrated by the electronic states of B appeared in the optical energy gap of Ge very close to the edge of the HOMO.

  13. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time-and Energy-Resolved Surface-Induced Dissociation Studies

    SciTech Connect

    Laskin, Julia

    2006-07-13

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM based approach developed in our laboratory. The following threshold energies and activation entropies were determined in this study: E0=1.20 eV and ΔS‡=-20 e.u.1 (MH+→b5); E0=1.14 eV and ΔS‡=-14.7 e.u. (MH+→b4); E0=1.42 eV and ΔS‡=-2.5 e.u. (MH+→b3); E0=1.30 eV and ΔS‡=-4.1 e.u. (MH+→a4); E0=1.37 eV and ΔS‡=-5.2 e.u. (MH+→y ions); E0=1.50 eV and ΔS‡=1.6 e.u. (MH+→internal fragments); E0=1.62 eV and S‡=5.2 e.u. (MH+→F). Comparison with Arrhenius activation energies reported in the literature demonstrated for the first time the reversal of the order of activation energies as compared to threshold energies for dissociation.

  14. Negative ion fragmentations of deprotonated heterocycles. The isothiazole, thiazole, isoxazole, and oxazole ring systems

    NASA Astrophysics Data System (ADS)

    Adams, Gregory W.; Bowie, John H.; Hayes, Roger N.

    1992-05-01

    The major collision-induced dissociations of deprotonated isothiazole occur from the 5-anion, while deprotonated thiazole fragments almost equally through the 2- and 5-anions. Both 5-anions fragment by a simple retro cleavage yielding HC2S- and HCN. The 5-anion of isothiazole and the 2-anion of thiazole also rearrange to the common intermediate -SCH=CHCN which decomposes by losses of H2, HCN and H2S. There is no evidence for direct interconversion of isothiazole and thiazole anions. The spectra of deprotonated methylisothiazoles are complex, but the major fragmentations are of ring deprotonated ions and are generally analogous to the parent systems. The fragmentation behaviour of deprotonated isoxazole and oxazole is analogous to that of the isothiazole and thiazole systems.

  15. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

    PubMed Central

    Vaniya, Arpana

    2015-01-01

    Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations. PMID:26213431

  16. Peptide identification by tandem mass spectrometry with alternate fragmentation modes.

    PubMed

    Guthals, Adrian; Bandeira, Nuno

    2012-09-01

    The high-throughput nature of proteomics mass spectrometry is enabled by a productive combination of data acquisition protocols and the computational tools used to interpret the resulting spectra. One of the key components in mainstream protocols is the generation of tandem mass (MS/MS) spectra by peptide fragmentation using collision induced dissociation, the approach currently used in the large majority of proteomics experiments to routinely identify hundreds to thousands of proteins from single mass spectrometry runs. Complementary to these, alternative peptide fragmentation methods such as electron capture/transfer dissociation and higher-energy collision dissociation have consistently achieved significant improvements in the identification of certain classes of peptides, proteins, and post-translational modifications. Recognizing these advantages, mass spectrometry instruments now conveniently support fine-tuned methods that automatically alternate between peptide fragmentation modes for either different types of peptides or for acquisition of multiple MS/MS spectra from each peptide. But although these developments have the potential to substantially improve peptide identification, their routine application requires corresponding adjustments to the software tools and procedures used for automated downstream processing. This review discusses the computational implications of alternative and alternate modes of MS/MS peptide fragmentation and addresses some practical aspects of using such protocols for identification of peptides and post-translational modifications.

  17. 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.

  18. 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.

  19. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

    NASA Astrophysics Data System (ADS)

    DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

    2016-12-01

    Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

  20. Travelling-wave ion mobility and negative ion fragmentation of high mannose N-glycans

    PubMed Central

    Harvey, David J.; Scarff, Charlotte A.; Edgeworth, Matthew; Struwe, Weston B.; Pagel, Kevin; Thalassinos, Konstantinos; Crispin, Max; Scrivens, Jim

    2016-01-01

    The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility-mass spectrometry (TW IM-MS)for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation (CID) gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers were being separated. Collision cross sections (CCSs) of the isomers in positive and negative fragmentation mode were estimated from TW IM-MS data using dextran glycans as calibrant. More complete CCS data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross sectional data, details of the negative ion collision-induced dissociation (CID) spectra of all resolved isomers are discussed. PMID:26956389

  1. Activation Energies of Fragmentations of Disaccharides by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kuki, Ákos; Nagy, Lajos; Szabó, Katalin E.; Antal, Borbála; Zsuga, Miklós; Kéki, Sándor

    2014-03-01

    A simple multiple collision model for collision induced dissociation (CID) in quadrupole was applied for the estimation of the activation energy (Eo) of the fragmentation processes for lithiated and trifluoroacetated disaccharides, such as maltose, cellobiose, isomaltose, gentiobiose, and trehalose. The internal energy-dependent rate constants k(Eint) were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) or the Rice-Ramsperger-Kassel (RRK) theory. The Eo values were estimated by fitting the calculated survival yield (SY) curves to the experimental ones. The calculated Eo values of the fragmentation processes for lithiated disaccharides were in the range of 1.4-1.7 eV, and were found to increase in the order trehalose < maltose < isomaltose < cellobiose < gentiobiose.

  2. Negative Ion CID Fragmentation of O-linked Oligosaccharide Aldoses—Charge Induced and Charge Remote Fragmentation

    NASA Astrophysics Data System (ADS)

    Doohan, Roisin A.; Hayes, Catherine A.; Harhen, Brendan; Karlsson, Niclas Göran

    2011-06-01

    Collision induced dissociation (CID) fragmentation was compared between reducing and reduced sulfated, sialylated, and neutral O-linked oligosaccharides. It was found that fragmentation of the [M - H]- ions of aldoses with acidic residues gave unique Z-fragmentation of the reducing end GalNAc containing the acidic C-6 branch, where the entire C-3 branch was lost. This fragmentation pathway, which is not seen in the alditols, showed that the process involved charge remote fragmentation catalyzed by a reducing end acidic anomeric proton. With structures containing sialic acid on both the C-3 and C-6 branch, the [M - H]- ions were dominated by the loss of sialic acid. This fragmentation pathway was also pronounced in the [M - 2H]2- ions revealing both the C-6 Z-fragment plus its complementary C-3 C-fragment in addition to glycosidic and cross ring fragmentation. This generation of the Z/C-fragment pairs from GalNAc showed that the charges were not participating in their generation. Fragmentation of neutral aldoses showed pronounced Z-fragmentation believed to be generated by proton migration from the C-6 branch to the negatively charged GalNAc residue followed by charge remote fragmentation similar to the acidic oligosaccharides. In addition, A-type fragments generated by charge induced fragmentation of neutral oligosaccharides were observed when the charge migrated from C-1 of the GalNAc to the GlcNAc residue followed by rearrangement to accommodate the 0,2A-fragmentation. LC-MS also showed that O-linked aldoses existed as interchangeable α/β pyranose anomers, in addition to a third isomer (25% of the total free aldose) believed to be the furanose form.

  3. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    PubMed Central

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2012-01-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO2− anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO2− rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples. PMID:21953257

  4. Unusual Fragmentation Pathways in Collagen Glycopeptides

    NASA Astrophysics Data System (ADS)

    Perdivara, Irina; Perera, Lalith; Sricholpech, Marnisa; Terajima, Masahiko; Pleshko, Nancy; Yamauchi, Mitsuo; Tomer, Kenneth B.

    2013-07-01

    Collagens are the most abundant glycoproteins in the body. One characteristic of this protein family is that the amino acid sequence consists of repeats of three amino acids -(X—Y—Gly)n. Within this motif, the Y residue is often 4-hydroxyproline (HyP) or 5-hydroxylysine (HyK). Glycosylation in collagen occurs at the 5-OH group in HyK in the form of two glycosides, galactosylhydroxylysine (Gal-HyK) and glucosyl galactosylhydroxylysine (GlcGal-HyK). In collision induced dissociation (CID), collagen tryptic glycopeptides exhibit unexpected gas-phase dissociation behavior compared to typical N- and O-linked glycopeptides (i.e., in addition to glycosidic bond cleavages, extensive cleavages of the amide bonds are observed). The Gal- or GlcGal- glycan modifications are largely retained on the fragment ions. These features enable unambiguous determination of the amino acid sequence of collagen glycopeptides and the location of the glycosylation site. This dissociation pattern was consistent for all analyzed collagen glycopeptides, regardless of their length or amino acid composition, collagen type or tissue. The two fragmentation pathways—amide bond and glycosidic bond cleavage—are highly competitive in collagen tryptic glycopeptides. The number of ionizing protons relative to the number of basic sites (i.e., Arg, Lys, HyK, and N-terminus) is a major driving force of the fragmentation. We present here our experimental results and employ quantum mechanics calculations to understand the factors enhancing the labile character of the amide bonds and the stability of hydroxylysine glycosides in gas phase dissociation of collagen glycopeptides.

  5. Unusual fragmentation pathways in collagen glycopeptides

    PubMed Central

    Perdivara, Irina; Perera, Lalith; Sricholpech, Marnisa; Terajima, Masahiko; Pleshko, Nancy; Yamauchi, Mitsuo; Tomer, Kenneth B.

    2013-01-01

    Collagens are the most abundant glycoproteins in the body. One characteristic of this protein family is that the amino acid sequence consists of repeats of three amino acids –(X—Y—Gly)n. Within this motif, the Y residue is often 4-hydroxyproline (HyP) or 5-hydroxylysine (HyK). Glycosylation in collagen occurs at the 5-OH group in HyK in the form of two glycosides, galactosylhydroxylysine (Gal-HyK) and glucosyl galactosylhydroxylysine (GlcGal-HyK). In collision induced dissociation (CID), collagen tryptic glycopeptides exhibit unexpected gas-phase dissociation behavior compared to typical N- and O-linked glycopeptides, i.e. in addition to glycosidic bond cleavages, extensive cleavages of the amide bonds are observed. The Gal- or GlcGal- glycan modifications are largely retained on the fragment ions. These features enable unambiguous determination of the amino acid sequence of collagen glycopeptides and the location of the glycosylation site. This dissociation pattern was consistent for all analyzed collagen glycopeptides, regardless of their length or amino acid composition, collagen type or tissue. The two fragmentation pathways – amide bond and glycosidic bond cleavage – are highly competitive in collagen tryptic glycopeptides. The number of ionizing protons relative to the number of basic sites (i.e. Arg, Lys, HyK and N-terminus) is a major driving force of the fragmentation. We present here our experimental results and employ quantum mechanics calculations, to understand the factors enhancing the labile character of the amide bonds and the stability of hydroxylysine glycosides in gas phase dissociation of collagen glycopeptides. PMID:23633013

  6. Elucidating the sequence of intact bioactive peptides by using electron capture dissociation and hot electron capture dissociation in a linear radio-frequency quadrupole ion trap.

    PubMed

    Satake, Hiroyuki; Manri, Naomi; Kaneko, Akihito; Hirabayashi, Atsumu; Hasegawa, Hideki; Hashimoto, Yuichiro; Baba, Takashi; Sakamoto, Takeshi; Masuda, Katsuyoshi

    2013-12-15

    Electron capture dissociation (ECD) is useful tool for sequencing of peptides and proteins with post-translational modifications. To increase the sequence coverage for peptides and proteins, it is important to develop ECD device with high fragmentation efficiency. Sequence analysis of intact undigested bioactive peptides (3000-5000 Da) was performed by use of electron capture dissociation (rf-ECD) and collision-induced dissociation (CID) in a linear radio-frequency quadrupole ion trap that was coupled to a time-of-flight mass spectrometer. We applied rf-ECD, hot rf-ECD (rf-ECD with high electron energy), and CID for intact bioactive peptide ions of various charge states and evaluated the sequence coverage of their fragment spectra. Hot rf-ECD produced a higher number of c- and z-type fragment ions of modified peptide ions as electron energy increased in lower charged peptide ions, and sequence coverage greater than 80% was obtained compared with the CID case (40-80%). The result indicates that intact bioactive modified peptides (Ghrelin, ANP) were correctly identified by use of hot rf-ECD. Copyright © 2013 John Wiley & Sons, Ltd.

  7. Ultrashort-laser-pulse-mediated asymmetry in the branching of dissociated fragments of HD+: Effects of a weak third pulse and carrier envelope phase of the dissociating pulse

    NASA Astrophysics Data System (ADS)

    Chatterjee, Souvik; Bhattacharyya, S. S.

    2013-08-01

    We have numerically explored the possibility of controlling the branching ratio of the two distinguishable photodissociation products of HD+ (neutral D and neutral H) in an ultrashort laser field. In our multipulse scheme, a bound vibrational wave packet is generated in the ground electronic state of HD+ by vertical ionization from the ground state of HD. The control pulse acts on this wave packet at different time delays after the wave-packet generation is completed. It was found that, for a broad range of delay times between the pump pulse and the control pulse, any possible asymmetry in the branching ratio disappears due to the nonadiabatic coupling effects present in HD+. A third pulse, termed the driving pulse, with a relatively longer duration and a much weaker field strength, is introduced to counterbalance the nonadiabatic effects relevant for this heteronuclear system and to guide the dissociative reaction to a specific product channel. In fact, we have shown that the application of the driving pulse reproduces the branching-ratio pattern obtained on variation in the interpulse delay time between the pump pulse and the control pulse in the absence of the nonadiabatic coupling effects. The role of both the delay time between the pump pulse and the control pulse as well as the carrier envelope phase effects of the optical field of the control laser on the branching ratios in the two reaction channels were studied. The robustness of the driving pulse mediated asymmetry control, and any possible introduction of asymmetry by the driving pulse itself were also investigated.

  8. Angular and energy distribution of fragment ions in dissociative double photoionization of acetylene molecules at 39 eV

    SciTech Connect

    Alagia, M.; Callegari, C.; Richter, R.; Candori, P.; Falcinelli, S.; Vecchiocattivi, F.; Pirani, F.; Stranges, S.

    2012-05-28

    The two-body dissociation reactions of the dication, C{sub 2}H{sub 2}{sup 2+}, produced by 39.0 eV double photoionization of acetylene molecules, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The results provide the kinetic energy and angular distributions of product ions. The analysis of the results indicates that the dissociation leading to C{sub 2}H{sup +}+H{sup +} products occurs through a metastable dication with a lifetime of 108 {+-} 22 ns, and a kinetic energy release (KER) distribution exhibiting a maximum at {approx}4.3 eV with a full width at half maximum (FWHM) of about 60%. The reaction leading to CH{sub 2}{sup +}+C{sup +} occurs in a time shorter than the typical rotational period of the acetylene molecules (of the order of 10{sup -12} s). The KER distribution of product ions for this reaction, exhibits a maximum at {approx}4.5 eV with a FWHM of about 28%. The symmetric dissociation, leading to CH{sup +} + CH{sup +}, exhibits a KER distribution with a maximum at {approx}5.2 eV with a FWHM of 44%. For the first two reactions the angular distributions of ion products also indicate that the double photoionization of acetylene occurs when the neutral molecule is mainly oriented perpendicularly to the light polarization vector.

  9. 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.

  10. 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.

  11. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    SciTech Connect

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

  12. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  13. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    PubMed Central

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel C.; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-01-01

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification. PMID:23499924

  14. EVALUATION OF THE EXPERIMENTAL PARAMETERS WHICH CONTROL ELECTRON DETACHMENT DISSOCIATION, AND THEIR EFFECT ON THE FRAGMENTATION EFFICIENCY OF GLYCOSAMINOGLYCAN CARBOHYDRATES

    PubMed Central

    Leach, Franklin E.; Wolff, Jeremy J.; Laremore, Tatiana N.; Linhardt, Robert J.; Amster, I. Jonathan

    2008-01-01

    The efficiency of conversion of precursor ions to observable products for electron detachment dissociation (EDD) was measured as a function of the key experimental parameters to determine their optimal values for the Fourier transform mass spectrometry analysis of anionic glycosaminoglycan carbohydrates. These parameters include electron current, electron energy, dispenser cathode heater current, electron beam duration, charge state of the precursor ion, oligomer length, and precursor ion number accumulated in an external radio frequency multipole trap. Precursor conversion is most efficient at an electron current of 15 µA, and decreases at higher and lower values. The conversion of precursor to product ions increases in efficiency as the electron pulse duration is increased. Together, these data suggest that a radially repulsive electric field is produced between the electron beam and negative ions during EDD which causes the reaction cross section to decrease at higher values of electron current (>15 µA). Elevating the heater current of the dispenser cathode increases the electron flux, but also causes ion activation, presumably by blackbody infrared irradiation. An electronic circuit is described that allows the electron current produced by the dispenser cathode to be measured during an EDD or electron capture dissociation (ECD) experiment. PMID:19802340

  15. 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.

  16. Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring*

    PubMed Central

    Baker, Peter R.; Medzihradszky, Katalin F.; Chalkley, Robert J.

    2010-01-01

    The use of electron transfer dissociation (ETD) fragmentation for analysis of peptides eluting in liquid chromatography tandem mass spectrometry experiments is increasingly common and can allow identification of many peptides and proteins in complex mixtures. Peptide identification is performed through the use of search engines that attempt to match spectra to peptides from proteins in a database. However, software for the analysis of ETD fragmentation data is currently less developed than equivalent algorithms for the analysis of the more ubiquitous collision-induced dissociation fragmentation spectra. In this study, a new scoring system was developed for analysis of peptide ETD fragmentation data that varies the ion type weighting depending on the precursor ion charge state and peptide sequence. This new scoring regime was applied to the analysis of data from previously published results where four search engines (Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), Spectrum Mill, and X!Tandem) were compared (Kandasamy, K., Pandey, A., and Molina, H. (2009) Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal. Chem. 81, 7170–7180). Protein Prospector identified 80% more spectra at a 1% false discovery rate than the most successful alternative searching engine in this previous publication. These results suggest that other search engines would benefit from the application of similar rules. PMID:20513802

  17. Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments

    NASA Astrophysics Data System (ADS)

    Zaccone, A.; Terentjev, I.; Herling, T. W.; Knowles, T. P. J.; Aleksandrova, A.; Terentjev, E. M.

    2016-09-01

    While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k- and establish the law koff/k- = exp[(ɛ‖ - ɛ⊥)/kBT] = exp[0.5ɛ/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments.

  18. Lipidomics profiling by high-resolution LC-MS and high-energy collisional dissociation fragmentation: focus on characterization of mitochondrial cardiolipins and monolysocardiolipins.

    PubMed

    Bird, Susan S; Marur, Vasant R; Sniatynski, Matthew J; Greenberg, Heather K; Kristal, Bruce S

    2011-02-01

    A liquid chromatography-mass spectrometry (LC-MS) method was used for separation of lipid classes as well as both qualitative and semiquantitative detection of individual lipids in biological samples. Data were acquired using high-resolution full-scan MS and high-energy collisional dissociation (HCD) all ion fragmentation. The method was evaluated for efficient separation and detection in both positive and negative ionization mode using standards spanning six lipid classes. Platform linearity and robustness, related to the mitochondrial lipid cardiolipin (CL), were assessed using extracted ion chromatograms with mass tolerance windows of 5 ppm or less from full scan exact mass measurements. The platform CL limit of detection was determined to be 5 pmol (0.9 μM) on the column, with mass accuracy <1.5 ppm, retention time coefficients of variation (CV) < 0.5%, and area CV < 13%. This mass accuracy was critical to the identification of unknown CL species in mitochondria samples, through the elimination of false positives. In addition to detection and relative quantitation of CL species in mitochondria, CL structures were characterized through the use of alternating HCD scans at different energies to produce diagnostic fragmentations on all ions in the analysis. The developed lipid profiling method was applied to mitochondrial samples from an animal study related to the linkages between diet, mitochondrial function, and disease. The analysis identified 28 unique CL species and two monolysocardiolipin species that are often associated with mitochondrial stress and dysfunction.

  19. 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.

  20. Differential Fragmentation of Mobility-Selected Glycans via Ultraviolet Photodissociation and Ion Mobility-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Morrison, Kelsey A.; Clowers, Brian H.

    2017-06-01

    The alternative dissociation pathways initiated by ultraviolet photodissociation (UVPD) compared with collision-induced dissociation (CID) may provide useful diagnostic fragments for biomolecule identification, including glycans. However, underivatized glycans do not commonly demonstrate strong UV absorbance, resulting in low fragmentation yields for UVPD spectra. In contrast to UVPD experiments that leverage covalent modification of glycans, we detail the capacity of metal adduction to yield comparatively rich UVPD fragmentation patterns and enhance separation factors for an isomeric glycan set in a drift tube ion mobility system. Ion mobility and UVPD-MS spectra for two N-acetyl glycan isomers were examined, each adducted with sodium or cobalt cations, with the latter providing fragment yield gains of an order of magnitude versus sodium adducts. Furthermore, our glycan analysis incorporated front-end ion mobility separation such that the structural glycan isomers could still be identified even as a mixture and not simply composite spectra of isomeric standards. Cobalt adduction proved influential in the glycan separation by yielding an isomer resolution of 0.78 when analyzed simultaneously versus no discernable separation obtained with the sodium adducts. It is the combined enhancement of both isomeric drift time separation and isomer distinction with improved UVPD fragment ion yields that further bolster multivalent metal adduction for advancing glycan IM-MS experiments. [Figure not available: see fulltext.

  1. 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.

  2. 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.

  3. 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.

  4. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine

    PubMed Central

    Bythell, Benjamin J.; Csonka, István P.; Suhai, Sándor; Barofsky, Douglas F.; Paizs, Béla

    2010-01-01

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc., 2009, 131, 14057–14065.). In addition to these findings we also report on the mechanisms for the formation of the b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion. PMID:20973555

  5. Formation of peptide radical ions through dissociative electron transfer in ternary metal-ligand-peptide complexes.

    PubMed

    Chu, Ivan K; Laskin, Julia

    2011-01-01

    The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals, including the canonical radical cations, M(+•), radical dications, [M+H](2+•), radical anions, [M-2H](-•) and phosphorylated radical cations. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side-chain losses from the radical ions. Subsequent fragmentation of these species provides information regarding the role of charge and location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT) and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities and the energetics and dynamics of fragmentation of these complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.

  6. Fragmentation of 3-hydroxyflavone; a computational and mass spectrometric study.

    PubMed

    Lewars, Errol G; March, Raymond E

    2007-01-01

    In a recent study of the collision-induced dissociation of protonated and deprotonated molecules of 3-, 5-, 6-, 7-, 2'-, 3'- and 4'-hydroxyflavone, it was observed that the ratio, gamma, of the propensities for cross-ring cleavage (CRC) to ring opening (RO) varied by a factor of 660, i.e., from 0.014:1 (for deprotonated 3-hydroxyflavone) to 9.27:1 (for deprotonated 5-hydroxyflavone). An explanation for the variation of gamma was presented in terms of experimental NMR (13)C and (1)H spectra modified by computation. Deprotonated 3-hydroxyflavone exhibited the highest ion signal intensity for fragmentation following RO relative to that for CRC in that gamma = 0.014:1. Because no chemical computations of the fragmentation of protonated and deprotonated monohydroxyflavone molecules have been carried out thus far, the basis on which fragmentation mechanisms for deprotonated 3-hydroxyflavone have been proposed is principally chemical intuition. The energy states of product ions formed in the fragmentation of deprotonated 3-hydroxyflavone molecules were computed by the CBS-4M method implemented in Gaussian 03. The overly demanding calculations needed to handle diradicals reliably and directly were circumvented by a process in which each of the bond-breaking reactions was approximated by a process that gave two monoradicals. Bond energies were calculated, with one exception, from the approximation reactions as the energy of products minus the energy of reactants.

  7. Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bhawal, Ruchika P.; Shahinuzzaman, A. D. A.; Chowdhury, Saiful M.

    2017-04-01

    Farnesylation and geranylgeranylation are the two types of prenyl modification of proteins. Prenylated peptides are highly hydrophobic and their abundances in biological samples are low. In this report, we studied the oxidized prenylated peptides by electrospray ionization mass spectrometry and identified them by collision-induced dissociation (CID) and electron-transfer dissociation (ETD) tandem mass spectrometry. Modified prenyl peptides were generated utilizing strong and low strength oxidizing agents to selectively oxidize and epoxidize cysteine sulfur and prenyl side chain. We selected three peptides with prenyl motifs and synthesized their prenylated versions. The detailed characteristic fragmentations of oxidized and epoxidized farnesylated and geranylgeranylated peptides were studied side by side with two popular fragmentation techniques. CID and ETD mass spectrometry clearly distinguished the modified version of these peptides. ETD mass spectrometry provided sequence information of the highly labile modified prenyl peptides and showed different characteristic fragmentations compared with CID. A detailed fragmentation of modified geranylgeranylated peptides was compared by CID and ETD mass spectrometry for the first time.

  8. Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry.

    PubMed

    Bhawal, Ruchika P; Shahinuzzaman, A D A; Chowdhury, Saiful M

    2017-04-01

    Farnesylation and geranylgeranylation are the two types of prenyl modification of proteins. Prenylated peptides are highly hydrophobic and their abundances in biological samples are low. In this report, we studied the oxidized prenylated peptides by electrospray ionization mass spectrometry and identified them by collision-induced dissociation (CID) and electron-transfer dissociation (ETD) tandem mass spectrometry. Modified prenyl peptides were generated utilizing strong and low strength oxidizing agents to selectively oxidize and epoxidize cysteine sulfur and prenyl side chain. We selected three peptides with prenyl motifs and synthesized their prenylated versions. The detailed characteristic fragmentations of oxidized and epoxidized farnesylated and geranylgeranylated peptides were studied side by side with two popular fragmentation techniques. CID and ETD mass spectrometry clearly distinguished the modified version of these peptides. ETD mass spectrometry provided sequence information of the highly labile modified prenyl peptides and showed different characteristic fragmentations compared with CID. A detailed fragmentation of modified geranylgeranylated peptides was compared by CID and ETD mass spectrometry for the first time. Graphical Abstract ᅟ.

  9. Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bhawal, Ruchika P.; Shahinuzzaman, A. D. A.; Chowdhury, Saiful M.

    2016-10-01

    Farnesylation and geranylgeranylation are the two types of prenyl modification of proteins. Prenylated peptides are highly hydrophobic and their abundances in biological samples are low. In this report, we studied the oxidized prenylated peptides by electrospray ionization mass spectrometry and identified them by collision-induced dissociation (CID) and electron-transfer dissociation (ETD) tandem mass spectrometry. Modified prenyl peptides were generated utilizing strong and low strength oxidizing agents to selectively oxidize and epoxidize cysteine sulfur and prenyl side chain. We selected three peptides with prenyl motifs and synthesized their prenylated versions. The detailed characteristic fragmentations of oxidized and epoxidized farnesylated and geranylgeranylated peptides were studied side by side with two popular fragmentation techniques. CID and ETD mass spectrometry clearly distinguished the modified version of these peptides. ETD mass spectrometry provided sequence information of the highly labile modified prenyl peptides and showed different characteristic fragmentations compared with CID. A detailed fragmentation of modified geranylgeranylated peptides was compared by CID and ETD mass spectrometry for the first time.

  10. Fragmentation of alpha-Radical Cations of Arginine-Containing Peptides

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Ng, Dominic C.; Chu, Ivan K.

    2010-04-01

    Fragmentation pathways of peptide radical cations, M+, with well-defined initial location of the radical site were explored using collision-induced dissociation (CID) experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes [salen = N,N´-ethylenebis (salicylideneaminato)]. Subsequent hydrogen abstraction from the -carbon of the side chain followed by Ca-C bond cleavage results in the loss of a neutral side chain and formation of an a-radical cation with the radical site localized on the a-carbon of the backbone. Similar CID spectra dominated by radical-driven dissociation products were obtained for a number of a-radicals when the basic arginine side chain was present in the sequence. In contrast, proton-driven fragmentation dominates CID spectra of a-radicals produced via the loss of the arginine side chain. Our results suggest that in most cases radical migration precedes fragmentation of large peptide radical cations.

  11. 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.

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

    DOE PAGES

    Barnat, E. V.; Fierro, A.

    2017-03-07

    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 emore » cm-3. Lastly, 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.« less

  13. 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.

  14. 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.

  15. 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.

  16. Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence

    NASA Astrophysics Data System (ADS)

    Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

    2014-06-01

    Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., 2,4AR, 2,4AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + 0,2X0-H]- and [peptide-NH3-H]-). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36]-, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

  17. 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.

  18. Study of the dissociation of a charge-reduced phosphopeptide formed by electron transfer from an alkali metal target.

    PubMed

    Hayakawa, Shigeo; Hashimoto, Mami; Nagao, Hirofumi; Awazu, Kunio; Toyoda, Michisato; Ichihara, Toshio; Shigeri, Yasushi

    2008-01-01

    Doubly protonated phosphopeptide (YGGMHRQET(p)VDC) ions obtained by electrospray ionization were collided with Xe and Cs targets to give singly and doubly charged positive ions via collision-induced dissociation (CID). The resulting ions were analyzed and detected by using an electrostatic analyzer (ESA). Whereas doubly charged fragment ions resulting from collisionally activated dissociation (CAD) were dominant in the CID spectrum with the Xe target, singly charged fragment ions resulting from electron transfer dissociation (ETD) were dominant in the CID spectrum with the Cs target. The most intense peak resulting from ETD was estimated to be associated with the charge-reduced ion with H2 lost from the precursor. Five c-type fragment ions with amino acid residues detached consecutively from the C-terminal were clearly observed without a loss of the phosphate group. These ions must be formed by N--Calpha bond cleavage, in a manner similar to the cases of electron capture dissociation (ECD) and ETD from negative ions. Although the accuracy in m/z of the CID spectra was about +/-1 Th because of the mass analysis using the ESA, it is supposed from the m/z values of the c-type ions that these ions were accompanied by the loss of a hydrogen atom. Four z-type (or y--NH3, or y--H2O) ions analogously detached consecutively from the N-terminal were also observed. The fragmentation processes took place within the time scale of 4.5 micros in the high-energy collision. The present results demonstrated that high-energy ETD with the alkali metal target allowed determination of the position of phosphorylation and the amino acid sequence of post-translational peptides.

  19. 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.

  20. 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

  1. 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.

  2. Laser photo-induced dissociation using tandem time-of-flight mass spectrometry

    PubMed

    Quiniou; Yates; Langridge-Smith

    2000-01-01

    A novel tandem time-of-flight (TOF) mass spectrometer has been developed for studying the photo-induced dissociation of large molecules and elemental clusters. It consists of a linear first stage TOF analyser for primary mass separation and precursor ion selection, and a second orthogonal reflecting field TOF analyser for product ion analysis. The instrument is equipped with a large volume throughput molecular beam source chamber allowing the production of jet-cooled molecules and molecular clusters, as well as elemental clusters, using either a pulsed laser vaporisation source (LVS) or a pulsed are cluster ion source (PACIS). A second differentially pumped chamber can be used with effusive sources, or for infrared laser desorption of large molecules, followed by laser ionisation. These primary ions can then be irradiated with a second, high energy laser to induce photodissociation. Detailed information about the fragmentation mechanisms can be deduced from the product ion mass spectra. Preliminary results on the photo-induced dissociation (PID) of the molecule ion of aniline at 266 nm are presented. In this case the molecule ions were generated via two-photon laser ionisation at 266 nm using an effusive source. Results for the collision-induced dissociation (CID) of the aniline molecule ion, using a commercial mass spectrometer equipped with an atmospheric pressure electrospray ionisation interface, are also presented. Copyright 2000 John Wiley & Sons, Ltd.

  3. 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.

  4. Observation of an unusually facile fragmentation pathway of gas-phase peptide ions: a study on the gas-phase fragmentation mechanism and energetics of tryptic peptides modified with 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC) and their 18-crown-6 complexes.

    PubMed

    Shin, Joong-Won; Lee, Yong Ho; Hwang, Sungu; Lee, Sang-Won

    2007-03-01

    Various peptide modifications have been explored recently to facilitate the acquisition of sequence information. N-terminal sulfonation is an interesting modification because it allows unambiguous de novo sequencing of peptides, especially in conjunction with MALDI-PSD-TOF analysis; such modified peptide ions undergo fragmentation at energies lower than those required conventionally for unmodified peptide ions. In this study, we systematically investigated the fragmentation mechanisms of N-terminal sulfonated peptide ions prepared using two different N-terminal sulfonation reagents: 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC). Collision-induced dissociation (CID) of the SPC-modified peptide ions produced a set of y-series ions that were more evenly distributed relative to those observed for the SPITC-modified peptides; y(n-1) ion peaks were consistently and significantly larger than the signals of the other y-ions. We experimentally investigated the differences between the dissociation energies of the SPITC- and SPC-modified peptide ions by comparing the MS/MS spectra of the complexes formed between the crown ether 18-crown-6 (CE) and the modified peptides. Upon CID, the complexes formed between 18-crown-6 ether and the protonated amino groups of C-terminal lysine residues underwent either peptide backbone fragmentation or complex dissociation. Although the crown ether complexes of the unmodified ([M + CE + 2H]2+) and SPC-modified ([M* + CE + 2H]2+) peptides underwent predominantly noncovalent complex dissociation upon CID, the low-energy dissociations of the crown ether complexes of the SPITC-modified peptides ([M' + CE + 2H]2+) unexpectedly resulted in peptide backbone fragmentations, along with a degree of complex dissociation. We performed quantum mechanical calculations to address the energetics of fragmentations observed for the modified peptides. Copyright 2007 John Wiley & Sons, Ltd.

  5. Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap.

    PubMed

    Wassermann, Tobias N; Boyarkin, Oleg V; Paizs, Béla; Rizzo, Thomas R

    2012-06-01

    We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.

  6. 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.

  7. 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.

  8. 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.

  9. Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines.

    PubMed

    van der Hooft, Justin J J; Ridder, Lars; Barrett, Michael P; Burgess, Karl E V

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context of

  10. Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines

    PubMed Central

    van der Hooft, Justin J. J.; Ridder, Lars; Barrett, Michael P.; Burgess, Karl E. V.

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context

  11. Fragmentation dynamics of meso-tetraphenyl iron (III) porphyrin chloride dication under energy control.

    PubMed

    Li, B; Allouche, A R; Bernard, J; Brédy, R; Qian, D B; Ma, X; Martin, S; Chen, L

    2017-03-28

    Meso-tetraphenyl iron (III) porphyrin chloride dications (FeTPPCl(2+))(*) were prepared in collisions with F(+) and H(+) at 3 keV. The dominant fragmentation channels were observed to involve the loss of the Cl atom and the successive loss of neutral phenyl groups for both collisional systems. The mass spectra in correlation with the deposited excitation energy distributions of the parent ions for the main fragmentation channels were measured by using the collision induced dissociation under energy control method. The global excitation energy distribution was found to be shifted to lower energies in collisions with H(+) compared to collisions with F(+) showing a noteworthy change of the excitation energy window using different projectile ions. Partial excitation energy distributions of the parent ions FeTPPCl(2+) were obtained for each fragmentation group. In a theoretical work, we have calculated the dissociation energies for the loss of one and two phenyl groups, including phenyl and (phenyl ± H). The energy barrier for the hydrogen atom transfer during the loss of (phenyl-H) has been also calculated. The measured energy difference for the successive loss of two phenyl groups was compared with the theoretical values.

  12. Fragmentation dynamics of meso-tetraphenyl iron (III) porphyrin chloride dication under energy control

    NASA Astrophysics Data System (ADS)

    Li, B.; Allouche, A. R.; Bernard, J.; Brédy, R.; Qian, D. B.; Ma, X.; Martin, S.; Chen, L.

    2017-03-01

    Meso-tetraphenyl iron (III) porphyrin chloride dications (FeTPPCl2+)* were prepared in collisions with F+ and H+ at 3 keV. The dominant fragmentation channels were observed to involve the loss of the Cl atom and the successive loss of neutral phenyl groups for both collisional systems. The mass spectra in correlation with the deposited excitation energy distributions of the parent ions for the main fragmentation channels were measured by using the collision induced dissociation under energy control method. The global excitation energy distribution was found to be shifted to lower energies in collisions with H+ compared to collisions with F+ showing a noteworthy change of the excitation energy window using different projectile ions. Partial excitation energy distributions of the parent ions FeTPPCl2+ were obtained for each fragmentation group. In a theoretical work, we have calculated the dissociation energies for the loss of one and two phenyl groups, including phenyl and (phenyl ± H). The energy barrier for the hydrogen atom transfer during the loss of (phenyl-H) has been also calculated. The measured energy difference for the successive loss of two phenyl groups was compared with the theoretical values.

  13. Electrospray ionization mass spectrometric studies on the characteristic fragmentation of Asp/cyclen conjugates.

    PubMed

    Ma, Chunying; Li, Chao; Luan, Xingrong; Zhang, Jin; Qiao, Renzhong; Zhao, Yufen

    2014-03-30

    Differentiation and structural characterization of Asp/cyclen conjugates by electrospray ionization tandem mass spectrometry (ESI-MS(n)) are significantly important for their biomedical application. Hence, the present study is conducted. The fragmentations of Asp/cyclen conjugates generated by positive ion mode electrospray ionization were examined here by low-energy collision-induced dissociation (CID). ESI-MS(n) spectra of cyclen were acquired to confirm cyclen contraction products derived from the studied compounds. The fragments derived from the Asp/cyclen conjugates were proved by deuterium-exchange experiments. Asp/cyclen conjugates displayed characteristic dissociation pathways, including cleavages of amide bonds, loss of NH3 and cyclen contraction pathways. It was observed that cleavages of C-terminal amide bonds generated b2 and b2  + H2O ions from the protonated CyclenAspAspAsp and a b1  + H2O ion from the protonated CyclenAspAsp. In addition, various cyclen contraction products were also observed. In ESI-MS(n) spectra of studied compounds, fragments of bn-1  + H2O or cyclic anhydride were generated due to facile mobilization of C-terminal or side-chain COOH protons. In addition, the cyclen contraction products were detected. These results might provide sufficient information for the identification of Asp/cyclen conjugates by mass spectrometry. Copyright © 2014 John Wiley & Sons, Ltd.

  14. 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.

  15. Review: Formation of Peptide Radical Ions Through Dissociative Electron Transfer in Ternary Metal-Ligand-Peptide Complexes

    SciTech Connect

    Chu, Ivan K.; Laskin, Julia

    2011-12-31

    The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals including the canonical radical cations, M{sup +{sm_bullet}}, radical dications, [M{sup +}H]{sup 2+{sm_bullet}}, radical anions, [M-2H]{sup -{sm_bullet}}. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side chain losses from the radical ions. Subsequent fragmentation of these species provides information on the role of charge and the location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT), and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities, and the energetics and dynamics of fragmentation of such complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.

  16. 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.

  17. Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra.

    PubMed

    Yagüe, Jesús; Paradela, Alberto; Ramos, Manuel; Ogueta, Samuel; Marina, Anabel; Barahona, Fernando; López de Castro, José A; Vázquez, Jesús

    2003-03-15

    The emergence of proteomics has placed great interest in the understanding of the mechanisms of MS/MS fragmentation of peptides under low-energy collision-induced dissociation. In this work, we describe the presence of anomalous fragments, which correspond to neutral loss elimination of internal amino acids from ions of the b series in quadrupole ion trap MS/MS spectra from naturally occurring peptides. Internal amino acid elimination occurred preferentially with aliphatic amino acids. The phenomenon was more apparent when doubly charged precursors were fragmented and was inhibited when peptides were N-acetylated at the N-terminus. Fragmentation of isomeric peptides where some internal amino acids were relocated in N-terminal position produced MSn spectra indistinguishable from those of the original peptides, indicating that some b ions underwent a structural rearrangement process. Formation of anomalous fragments required a minimum activation time. Our data are consistent with a nucleophile attack of the N-terminal nitrogen over the electrophilic carbonyl carbon at one peptide bond, forming a cyclic b ion intermediate that, by reopening at preferential sites, exposes internal amino acids to the C-terminal side.

  18. A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation

    NASA Astrophysics Data System (ADS)

    DeGraan-Weber, Nick; Ward, Sarah A.; Reilly, James P.

    2017-09-01

    Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. [Figure not available: see fulltext.

  19. Dissociative Disorders

    MedlinePlus

    ... last minutes, hours, or rarely, months or years. Dissociative identity disorder. Formerly known as multiple personality disorder, this disorder ... each identity is with the others. People with dissociative identity disorder typically also have dissociative amnesia and often have ...

  20. Angular and energy distributions of fragment ions in dissociative double photoionization of acetylene molecules in the 31.9-50.0 eV photon energy range

    NASA Astrophysics Data System (ADS)

    Falcinelli, Stefano; Alagia, Michele; Farrar, James M.; Kalogerakis, Konstantinos S.; Pirani, Fernando; Richter, Robert; Schio, Luca; Stranges, Stefano; Rosi, Marzio; Vecchiocattivi, Franco

    2016-09-01

    The two-body dissociation reactions of the dication C2H2+2, initiated via double ionization of acetylene molecules by photons in the energy range 31.9-50.0 eV, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The angular distributions and kinetic energy of product ions, measured in the 31.9-50.0 eV energy range, exhibit significant differences for the three leading dissociation reactions with respect to a previous investigation carried out at a fixed energy of 39.0 eV, providing thus new information on the dynamical evolution of the system. The analysis of the results indicates that such dissociation reactions occur with a different mechanism. In particular, the symmetric dissociation in two CH+ ions is characterized by different dynamics, and the anisotropy of the angular distribution of ionic products increases with photon energy in a more pronounced way than the other two reactions. Moreover, the kinetic energy distribution of the symmetric dissociation reaction exhibits several components that change with photon energy. The new experimental findings cast light on the microscopic evolution of the system and can provide a laboratory reference for new theoretical calculations on specific features of the multidimensional potential energy surface, namely, the structure, energy and symmetry of dication states, the electronic state of dissociation products, energy barriers and their dependence on the geometry of the intermediate state.

  1. Electron ionization mass spectrometry fragmentation pathways of trimethylsilyl derivatives of isomeric allylic alcohols derived from HBI alkene oxidation.

    PubMed

    Rontani, Jean-François; Belt, Simon T; Brown, Thomas A; Aubert, Claude

    2014-09-15

    C25 tri-unsaturated highly branched isoprenoid (HBI) alkenes are produced by a number of marine diatoms around the world yet are very easily oxidized during senescence to yield several isomeric allylic 9-hydroperoxides. Elucidation of the electron ionization mass spectrometry (EIMS) fragmentation pathways of the trimethylsilyl (TMS) derivatives of the alcohols (obtained by reduction of the corresponding 9-hydroperoxides) is essential for their characterization and quantification in natural samples. EIMS fragmentation pathways of TMS derivatives of isomeric allylic alcohols resulting from NaBH4 reduction of photo- and autoxidation products of HBI alkenes were investigated. These pathways were deduced by: (i) low-energy collision-induced dissociation gas chromatography/tandem mass spectrometry (CID-GC/MS/MS) and (ii) deuterium labelling. CID-MS/MS analyses and deuterium labelling allowed us to elucidate EIMS fragmentations of TMS derivatives of several isomeric allylic alcohols resulting from NaBH4 reduction of HBI alkene oxidation products and to propose some specific fragment ions for differentiating individual isomers. As an application of some of the described fragmentations, these oxidized compounds in phytoplanktonic cells collected from the Antarctic were characterized and quantified in multiple reaction monitoring (MRM) mode. EIMS fragmentations of TMS derivatives of several isomeric allylic alcohols resulting from NaBH4 reduction of HBI alkene oxidation products are shown to be strongly dependent on the position and configuration of double bonds, allowing simple, yet robust differentiation of individual isomers in natural samples. Copyright © 2014 John Wiley & Sons, Ltd.

  2. 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.

  3. The fragmentation dynamics of small Cs(CsI)n+ cluster ions under low-energy multiple collision conditions

    NASA Astrophysics Data System (ADS)

    Herzschuh, Rainer; Drewello, Thomas

    2004-04-01

    The collision-induced dissociations of small caesium iodide cluster ions of the type Cs(CsI)n+ where n=3-7, have been investigated under low-energy multiple collision conditions. The collisions were performed in the rf-only quadrupole of a BEqQ hybrid mass spectrometer. Breakdown graphs of selected parent ions were obtained by varying the laboratory collision energy in the range of 0-400 eV. The fragmentation dynamic established under these conditions provides a link between the well-known decay behaviour occurring unimolecularly and the dissociations following high energy (keV) collisional activation. Of particular interest is the observation that the energy-dependent dissociation pattern supplies support for the occurrence of one-step fission reactions, featuring the evaporation of presumably intact (CsI)n neutrals as opposed to a sequential decay via nCsI losses. The breakdown graphs thus provide a valuable tool to enhance insight into the fragmentation mechanism of these clusters.

  4. 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.

  5. Collision induced desorption of N2 from Ru(001)

    NASA Astrophysics Data System (ADS)

    Romm, L.; Zeiri, Y.; Asscher, M.

    1998-05-01

    The dynamics of collision-induced desorption (CID) of N2 from Ru(001) exposed to hyperthermal rare gas colliders generated in a supersonic atomic beam source have been studied. Low coverage of 0.01 ML 15N2 at crystal temperature of 96 K was chosen to represent a CID process of a practically isolated molecule, neglecting the effect of lateral N2-N2 interactions. The cross sections for CID of nitrogen molecules, σdes(Ei,θi), as a function of the kinetic energy and angle of incidence of Ar and Kr colliders have been measured. It was found that σdes(Ei,θi=0°) changes monotonically in the range 0-25 Å2 for beam energy in the range of 0.5-5.5 eV and is insensitive to the type of collider (Ar, Kr) as well as to the adsorbate isotope (14N2,15N2). The threshold energy for desorption has been determined to be 0.50±0.10 eV, which is twice the binding energy of N2 to Ru(001). The cross section for CID at a fixed collider's energy rises approximately four times as the incidence angle θi increases from 0° to 70° relative to the surface normal. Neither normal nor total energy scaling of the cross section could describe the results. The σdes(θi) scales reasonably well, however, with the tangential energy of the collider for angles above 30°. Classical molecular dynamics simulations were performed to gain better understanding of the CID process. Threshold energy and angular dependence of the cross section were reproduced very well. The predominant CID mechanism was concluded to originate from a direct rare gas-nitrogen collision, in which impulsive-bending and the motion along the surface are coupled to the adsorbate motion which leads to desorption.

  6. Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides

    PubMed Central

    2016-01-01

    Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods and two combinations: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), ETciD, and EThcD. Trypsin-digested, SDA-cross-linked human serum albumin (HSA) served as a test sample, yielding over all methods and in triplicate analysis in total 2602 matched PSMs and 1390 linked residue pairs at 5% false discovery rate, as confirmed by the crystal structure. HCD wins in number of matched peptide-spectrum-matches (958 PSMs) and identified links (446). CID is most complementary, increasing the number of identified links by 13% (58 links). HCD wins together with EThcD in cross-link site calling precision, with approximately 62% of sites having adjacent backbone cleavages that unambiguously locate the link in both peptides, without assuming any cross-linker preference for amino acids. Overall quality of spectra, as judged by sequence coverage of both peptides, is best for EThcD for the majority of peptides. Sequence coverage might be of particular importance for complex samples, for which we propose a data dependent decision tree, else HCD is the method of choice. The mass spectrometric raw data has been deposited in PRIDE (PXD003737). PMID:27454319

  7. 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.

  8. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    USDA-ARS?s Scientific Manuscript database

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. For phytochem...

  9. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    USDA-ARS?s Scientific Manuscript database

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. However, th...

  10. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    USDA-ARS?s Scientific Manuscript database

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Enrichment and Analysis of Non-enzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron Transfer Dissociation Mass Spectrometry

    PubMed Central

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W. C.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    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. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus. PMID:17488106

  16. Competition of charge- versus radical-directed fragmentation of gas-phase protonated cysteine sulfinyl radicals.

    PubMed

    Love, Chasity B; Tan, Lei; Francisco, Joseph S; Xia, Yu

    2013-04-24

    The fragmentation behavior of various cysteine sulfinyl ions (intact, N-acetylated, and O-methylated), new members of the gas-phase amino acid radical ion family, was investigated by low-energy collision-induced dissociation (CID). The dominant fragmentation channel for the protonated cysteine sulfinyl radicals ((SO•)Cys) was the radical-directed Cα-Cβ homolytic cleavage, resulting in the formation of glycyl radical ions and loss of CH2SO. This channel, however, was not observed for protonated N-acetylated cysteine sulfinyl radicals (Ac-(SO•)Cys); instead, charge-directed H2O loss followed immediately by SH loss prevailed. Counterintuitively, the H2O loss did not derive from the carboxyl group but involved the sulfinyl oxygen, a proton, and a Cβ hydrogen atom. Theoretical calculations suggested that N-acetylation significantly increases the barrier (~14 kcal mol(-1)) for the radical-directed fragmentation channel because of its reduced capability to stabilize the thus-formed glycyl radical ions via the captodative effect. N-Acetylation also assists in moving the proton to the sulfinyl site, which reduces the barrier for H2O loss. Our studies demonstrate that for cysteine sulfinyl radical ions, the stability of the product ions (glycyl radical ions) and the location of the charge (proton) can significantly modulate the competition between radical- and charge-directed fragmentation.

  17. Fragmentation studies and electrospray ionization mass spectrometry of lapachol: protonated, deprotonated and cationized species.

    PubMed

    Vessecchi, Ricardo; Emery, Flavio S; Galembeck, Sérgio E; Lopes, Norberto P

    2010-07-30

    Electrospray ionization mass spectrometric analysis of lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) was accomplished in order to elucidate the gas-phase dissociation reactions of this important biologically active natural product. The occurrence of protonated and cationized species in the positive mode and of deprotonated species in the negative mode was explored by means of collision-induced dissociation (CID) experiments. For the protonated molecule, the H(2)O and C(4)H(8) losses occur by two competitive channels. For the deprotonated molecule, the even-electron rule is not conserved, and the radicalar species are eliminated by formation of distonic anions. The fragmentation mechanism for each ion was suggested on the basis of computational thermochemistry. Atomic charges, relative energies, and frontier orbitals were employed aiming at a better understanding of the gas-phase reactivity of lapachol. Potential energy surfaces for fragmentation reactions were obtained by the B3LYP/6-31+G(d,p) model.

  18. Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Kjeldsen, Frank; Haselmann, Kim F; Sørensen, Esben S; Zubarev, Roman A

    2003-03-15

    In hot electron capture dissociation (HECD), multiply protonated polypeptides fragment upon capturing approximately 11-eV electrons. The excess of energy upon the primary c, z* cleavage induces secondary fragmentation in z* fragments. The resultant w ions allow one to distinguish between the isomeric Ile and Leu residues. The analytical utility of HECD is evaluated using tryptic peptides from the bovine milk protein PP3 containing totally 135 amino acid residues. Using a formal procedure for Ile/Leu (Xle) residue assignment, the identities of 20 out of 25 Xle residues (80%) were determined. The identity of an additional two residues could be correctly guessed from the absence of the alternative w ions, and only two residues, for which neither expected nor alternative w ions were observed, remained unassigned. Reinspection of conventional ECD spectra also revealed the presence of Xle w ions, although at lower abundances, with 44% of all Xle residues distinguished. Using a dispenser cathode as an electron source, identification of four out of five Xle residues in a 2.7-kDa peptide was possible with one acquisition 2 s long, with identification of all five residues by averaging of five such acquisitions. Unlike the case of high-energy collision-induced dissociation, no d ions were observed in the HECD of tryptic peptides.

  19. 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/.

  20. 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.

  1. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. A fragmentation study of kaempferol using electrospray quadrupole time-of-flight mass spectrometry at high mass resolution

    NASA Astrophysics Data System (ADS)

    March, Raymond E.; Miao, Xiu-Sheng

    2004-02-01

    A mass spectrometric method based on the combined use of electrospray ionization, collision-induced dissociation and tandem mass spectrometry at high mass resolution has been applied to an investigation of the structural characterization of protonated and deprotonated kaempferol (3,5,7,4'-tetrahydroxyflavone). Low-energy product ion mass spectra of [M+H]+ ions showed simple fragmentations of the C ring that permitted characterization of the substituents in the A and B rings. In addition, four rearrangement reactions accompanied by losses of C2H2O, CHO[radical sign], CO, and H2O were observed. Low-energy product ion mass spectra of [M-H]- ions showed only four rearrangement reactions accompanied by losses of OH[radical sign], CO, CH2O, and C2H2O. The use of elevated cone voltages permitted observation of product ion mass spectra of selected primary and secondary fragment ions so that each fragment ion reported was observed as a direct product of its immediate precursor ion. Product ion mass spectra examined at high mass resolution allowed unambiguous determination of the elemental composition of fragment ions and resolution of two pairs of isobars. Fragmentation mechanisms and ion structures have been proposed.

  3. 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.

  4. 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).

  5. Differentiation of complex lipid isomers by radical-directed dissociation mass spectrometry.

    PubMed

    Pham, Huong T; Ly, Tony; Trevitt, Adam J; Mitchell, Todd W; Blanksby, Stephen J

    2012-09-04

    Contemporary lipidomics protocols are dependent on conventional tandem mass spectrometry for lipid identification. This approach is extremely powerful for determining lipid class and identifying the number of carbons and the degree of unsaturation of any acyl-chain substituents. Such analyses are however, blind to isomeric variants arising from different carbon-carbon bonding motifs within these chains including double bond position, chain branching, and cyclic structures. This limitation arises from the fact that conventional, low energy collision-induced dissociation of even-electron lipid ions does not give rise to product ions from intrachain fragmentation of the fatty acyl moieties. To overcome this limitation, we have applied radical-directed dissociation (RDD) to the study of lipids for the first time. In this approach, bifunctional molecules that contain a photocaged radical initiator and a lipid-adducting group, such as 4-iodoaniline and 4-iodobenzoic acid, are used to form noncovalent complexes (i.e., adduct ions) with a lipid during electrospray ionization. Laser irradiation of these complexes at UV wavelengths (266 nm) cleaves the carbon-iodine bond to liberate a highly reactive phenyl radical. Subsequent activation of the nascent radical ions results in RDD with significant intrachain fragmentation of acyl moieties. This approach provides diagnostic fragments that are associated with the double bond position and the positions of chain-branching in glycerophospholipids, sphingomyelins and triacylglycerols and thus can be used to differentiate isomeric lipids differing only in such motifs. RDD is demonstrated for well-defined lipid standards and also reveals lipid structural diversity in olive oil and human very-low density lipoprotein.

  6. 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

  7. 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.

  8. 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.

  9. 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 ...

  10. Fragmentation of peptide radical cations containing a tyrosine or tryptophan residue: structural features that favor formation of [x(n-1) + H]˙⁺ and [z(n-1) + H]˙⁺ ions.

    PubMed

    Mädler, Stefanie; Lau, Justin Kai-Chi; Williams, Declan; Wang, Yating; Saminathan, Irine S; Zhao, Junfang; Siu, K W Michael; Hopkinson, Alan C

    2014-06-12

    Peptide radical cations A(n)Y(•+) (where n = 3, 4, or 5) and A5W(•+) have been generated by collision-induced dissociation (CID) of [Cu(II)(tpy)(peptide)](•2+) complexes. Apart from the charge-driven fragmentation at the N-Cα bond of the hetero residue producing either [c + 2H](+) or [z - H](•+) ions and radical-driven fragmentation at the Cα-C bond to give a(+) ions, unusual product ions [x + H](•+) and [z + H](•+) are abundant in the CID spectra of the peptides with the hetero residue in the second or third position of the chain. The formation of these ions requires that both the charge and radical be located on the peptide backbone. Energy-resolved spectra established that the [z + H](•+) ion can be produced either directly from the peptide radical cation or via the fragment ion [x + H](•+). Additionally, backbone dissociation by loss of the C-terminal amino acid giving [b(n-1) - H](•+) increases in abundance with the length of the peptides. Mechanisms by which peptide radical cations dissociate have been modeled using density functional theory (B3LYP/6-31++G** level) on tetrapeptides AYAG(•+), AAYG(•+), and AWAG(•+).

  11. Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

    PubMed

    Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

    2013-02-01

    Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated.

  12. Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry.

    PubMed

    Snijders, Ambrosius P L; Hung, Ming-Lung; Wilson, Stuart A; Dickman, Mark J

    2010-01-01

    Arginine and lysine methylation are widespread protein post-translational modifications. Peptides containing these modifications are difficult to retain using traditional reversed-phase liquid chromatography because they are intrinsically basic/hydrophilic and often fragment poorly during collision induced fragmentation (CID). Therefore, they are difficult to analyze using standard proteomic workflows. To overcome these caveats, we performed peptide separations at neutral pH, resulting in increased retention of the hydrophilic/basic methylated peptides before identification using MS/MS. Alternatively trifluoroacetic acid (TFA) was used for increased trapping of methylated peptides. Electron-transfer dissociation (ETD) mass spectrometry was then used to identify and characterize methylated residues. In contrast to previous reports utilizing ETD for arginine methylation, we observed significant amount of side-chain fragmentation. Using heavy methyl stable isotope labeling with amino acids in cell culture it was shown that, similar to CID, a loss of monomethylamine or dimethylamine from the arginine methylated side-chain during ETD can be used as a diagnostic to determine the type of arginine methylation. CID of lysine methylated peptides does not lead to significant neutral losses, but ETD is still beneficial because of the high charge states of such peptides. The developed LC MS/MS methods were successfully applied to tryptic digests of a number of methylated proteins, including splicing factor proline-glutamine-rich protein (SFPQ), RNA and export factor-binding protein 2 (REF2-I) and Sul7D, demonstrating significant advantages over traditional LC MS/MS approaches.

  13. Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

    NASA Astrophysics Data System (ADS)

    Koolen, Hector H. F.; Gomes, Alexandre F.; Schwab, Nicolas V.; Eberlin, Marcos N.; Gozzo, Fabio C.

    2014-07-01

    Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

  14. Classical line shapes based on analytical solutions of bimolecular trajectories in collision induced emission. II. Reactive collisions

    NASA Astrophysics Data System (ADS)

    Reguera, David; Rawlings, Philip K.; Birnbaum, George

    2013-06-01

    The classical theory of collision induced emission (CIE) from pairs of dissimilar rare gas atoms was developed in Paper I [D. Reguera and G. Birnbaum, J. Chem. Phys. 125, 184304 (2006)], 10.1063/1.2371097 from a knowledge of the straight line collision trajectory and the assumption that the magnitude of the dipole could be represented by an exponential function of the inter-nuclear distance. This theory is extended here to deal with other functional forms of the induced dipole as revealed by ab initio calculations. Accurate analytical expression for the CIE can be obtained by least square fitting of the ab initio values of the dipole as a function of inter-atomic separation using a sum of exponentials and then proceeding as in Paper I. However, we also show how the multi-exponential fit can be replaced by a simpler fit using only two analytic functions. Our analysis is applied to the polar molecules HF and HBr. Unlike the rare gas atoms considered previously, these atomic pairs form stable bound diatomic molecules. We show that, interestingly, the spectra of these reactive molecules are characterized by the presence of multiple peaks. We also discuss the CIE arising from half collisions in excited electronic states, which in principle could be probed in photo-dissociation experiments.

  15. Investigation of fragmentation pattern of bis(trimethylsilyl) ester of 3-mercaptopropionic acid

    NASA Astrophysics Data System (ADS)

    Potapov, Alexey I.; Vorontsov, Alexandre V.

    2004-07-01

    The routes of fragmentation of the parent molecule resulting from electron impact ionization have been studied in a quadrupole ion trap using collision induced dissociation (CID) of fragments. Fragmentation of the parent molecular ion m/z 250 results in major ions 235, 178, 163, 135, 129, 75, 73, and 55. While some fragments are easily assigned according to literature--m/z 235 to [M - CH3]+, m/z 73 to [Si(CH3)3]+, m/z 75 to [Si(CH3)2OH]+, and m/z 55 to [CH2CHCO]+--other ions required CID to obtain their structure. Fragment m/z 178 was found to emerge from breaking of Si---S bond and hydrogen rearrangement in the molecular ion. Fragment m/z 163 is formed by elimination of CH3 group from ion m/z 178. Elimination of H2S from ion m/z 163 leads to formation of the ion m/z 129. Another route is elimination of molecule CO from ion m/z 163 to form ion m/z 135. Fragmentation of ion m/z 129 by elimination of neutral molecule CO2 leads to emerging of ion m/z 85. For supporting the assumed structure of ions m/z 178, 163, 135, quantum chemical calculations were performed using methods PM3 and DFT. The calculations demonstrated that these ions have TMS group attached to the carboxyl group. The stability of the ions is associated with forming cyclic structures containing new bonds S---O (m/z 178), O---Si (m/z 163) and S---Si (m/z 129). Molecular dynamics calculations confirmed that these structures are the most stable conformations of the ions.

  16. Mass spectrometry of oligosaccharides by chloride-attachment reactions: the origin of fragment loss.

    PubMed

    Promé, D; Promé, J C; Puzo, G; Aurelle, H

    1985-07-01

    The direct exposure, negative chemical ionisation, chloride-attachment mass spectrometry of trehalose and sucrose gave abundant chloride-attached molecular ions. The same feature was observed when these sugars were subjected to fast-atom bombardment (f.a.b.) in a glycerol matrix containing ammonium chloride. No characteristic fragment ion was found when trehalose was analysed by either method. In contrast, sucrose gave intense chloride-containing fragments, arising by glycosidic cleavage, when analysed by the first method, whereas such cleavage was not detectable by f.a.b.-ammonium chloride analysis. However, the mass-analysed ion kinetic energy (m.i.k.e.) spectra of the (M + Cl)- ions from either trehalose and sucrose, generated under f.a.b.-ammonium chloride conditions, showed glycosidic cleavage reactions in addition to a large loss of HCl. These cleavage reactions might be attributed to SN2-like reactions on the acetal carbon atom and to base-induced eliminations, and they were enhanced by collision-induced dissociations. However, the relative abundance of such glycosidic cleavages from the ionic state would be too weak to explain the presence of the large chloride-containing fragments in the direct exposure spectra of sucrose. Thus, these ions were mainly produced by a thermal cleavage followed by chloride-attachment reactions.

  17. Fragmentation of benzylpyridinium "thermometer" ions and its effect on the accuracy of internal energy calibration.

    PubMed

    Barylyuk, Konstantin V; Chingin, Konstantin; Balabin, Roman M; Zenobi, Renato

    2010-01-01

    Electrospray ionization mass spectrometry (ESI-MS) is a powerful analytical method to study biomolecules and noncovalent complexes. The prerequisite for their intact observation is soft ionization. In ESI, the internal energy of ions is primarily influenced by collisional activation in the source. The survival yield method is frequently used to probe the energy deposition in ions during the electrospray process. In the present work, we investigate the fragmentation pathways of para-substituted benzylpyridinium ions, the most widely used "thermometer ions" in the survival yield method. In addition to the C-N bond cleavage, alternative fragmentation channels were found for the compounds studied. We consider these pathways to result from intramolecular rearrangements. The effect of these additional fragments on the accuracy of the internal energy calibration is estimated for both collision-cell and in-source collision-induced dissociation (CID). Altogether, results presented suggest that a correction of the energy scale is necessary for the method based on benzylpyridinium ions to precisely quantify ion internal energies. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

  18. Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

    NASA Astrophysics Data System (ADS)

    Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

    2006-07-01

    Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

  19. Structurally intact (78-kDa) forms of maternal lactoferrin purified from urine of preterm infants fed human milk: identification of a trypsin-like proteolytic cleavage event in vivo that does not result in fragment dissociation.

    PubMed Central

    Hutchens, T W; Henry, J F; Yip, T T

    1991-01-01

    Two forms of lactoferrin, an intact lactoferrin and a "nicked" but apparently intact (i.e., 78-kDa) form, have been isolated from the urine of preterm infants fed human milk. These two forms of lactoferrin, demonstrated to be entirely of maternal origin, were copurified using affinity columns of immobilized single-stranded DNA-agarose. The relative concentrations of the intact lactoferrin and the "nicked" lactoferrin were determined after denaturation and separation by reverse-phase HPLC. N-terminal sequence analyses showed that the intact 78-kDa form had lost two residues from its N terminus. The nicked 78-kDa form was composed of only two fragments; one fragment was identified as the N terminus of the N-lobe (residues 3-283). The other fragment started with Ser-284 and included the alpha-helical structures at the C terminus of the N-lobe, as well as the entire C-lobe. Although no disulfide bonds connect these two fragments, they were tightly associated in vivo and were not separated in vitro except under denaturing conditions. Limited in vitro digestion of human milk lactoferrin with trypsin produced a nicked, but stable (78-kDa), form of DNA-binding lactoferrin nearly indistinguishable from the isolated urinary lactoferrin, except for the absence of one additional arginine residue at the N terminus of the N-lobe. Residues involved in the stable molecular interaction between fragments were evaluated using data obtained from the high-resolution crystal structure of hololactoferrin. Two features, entirely within the N-lobe, account for the lack of fragment dissociation after cleavage at residue 283 in vivo: an extensive interface at the hinge region behind the iron-binding cleft and an "anchor" sequence traversing the remainder of the N-lobe at 90 degrees relative to the fragment interface. These results document the remarkably limited degradation of absorbed lactoferrin in vivo and suggest that iron-binding activity, receptor-binding properties, and postulated

  20. Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides.

    PubMed

    Banerjee, Raja; Sudarslal, S; Ranganayaki, R S; Raghothama, S

    2011-09-21

    Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

  1. Proteome analysis of Sorangium cellulosum employing 2D-HPLC-MS/MS and improved database searching strategies for CID and ETD fragment spectra.

    PubMed

    Leinenbach, Andreas; Hartmer, Ralf; Lubeck, Markus; Kneissl, Benny; Elnakady, Yasser A; Baessmann, Carsten; Müller, Rolf; Huber, Christian G

    2009-09-01

    Shotgun proteome analysis of the myxobacterial model strain for secondary metabolite biosynthesis Sorangium cellulosum was performed employing off-line two-dimensional high-pH reversed-phase HPLC x low-pH ion-pair reversed-phase HPLC and dual tandem mass spectrometry with collision-induced dissociation (CID) and electron transfer dissociation (ETD) as complementary fragmentation techniques. Peptide identification using database searching was optimized for ETD fragment spectra to obtain the maximum number of identifications at equivalent false discovery rates (1.0%) in the evaluation of both fragmentation techniques. In the database search of the CID MS/MS data, the mass tolerance was set to the well-established 0.3 Da window, whereas for ETD data, it was widened to 1.1 Da to account for hydrogen-rearrangement in the radical-intermediate of the peptide precursor ion. To achieve a false discovery rate comparable to the CID results, we increased the significance threshold for peptide identification to 0.001 for the ETD data. The ETD based analysis yielded about 74% of all peptides and about 78% of all proteins compared to the CID-method. In the combined data set, 952 proteins of S. cellulosum were confidently identified by at least two peptides per protein, facilitating the study of the function of regulatory proteins in the social myxobacteria and their role in secondary metabolism.

  2. Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools.

    PubMed

    Barlow, Christopher K; O'Hair, Richard A J

    2008-10-01

    This tutorial provides an overview of the evolution of some of the key concepts in the gas-phase fragmentation of different classes of peptide ions under various conditions [e.g. collision-induced dissociation (CID) and electron transfer dissociation (ETD)], and then demonstrates how these concepts can be used to develop new methods. For example, an understanding of the role of the mobile proton and neighboring group interactions in the fragmentation reactions of protonated peptides has led to the design of the 'SELECT' method. For ETD, a model based on the Landau-Zener theory reveals the role of both thermodynamic and geometric effects in the electron transfer from polyatomic reagent anions to multiply protonated peptides, and this predictive model has facilitated the design of a new strategy to form ETD reagent anions from precursors generated via ESI. Finally, two promising, emerging areas of gas-phase ion chemistry of peptides are also described: (1) the design of new gas-phase radical chemistry to probe peptide structure, and (2) selective cleavage of disulfide bonds of peptides in the gas phase via various physicochemical approaches.

  3. THE DISSOCIATIVE TURN IN PSYCHOANALYSIS.

    PubMed

    Itzkowitz, Sheldon

    2015-06-01

    In his response to the Roundtable Discussions on what is effective in psychoanalytic psychotherapy, the author focuses on the renewed interest in the concept of dissociation that began to emerge toward the end of the 20th century. A contemporary psychoanalytic position informed by the impact of developmental trauma has led to an understanding of and interest in the dissociative mind. The actuality of trauma during infancy and early childhood is recognized as a key factor leading to the emergence of dissociative processes, the potential dissociative structuring of the mind, and mind being characterized by multiple, discontinuous, centers of consciousness. The therapeutic goal in the psychoanalytic work with fragmented patients is to establish communication and understanding between the dissociated self-states. The author offers two brief clinical examples of working with dissociated self-states.

  4. 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.

  5. Fragmentation analysis of water-soluble atmospheric organic matter using ultrahigh-resolution FT-ICR mass spectrometry.

    PubMed

    Leclair, Jeffrey P; Collett, Jeffrey L; Mazzoleni, Lynn R

    2012-04-17

    Isolated water-soluble atmospheric organic matter (AOM) analytes extracted from radiation fogwater samples were analyzed using collision induced dissociation with ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Tandem mass analysis was performed on several mass ranges between 100 and 400 Da to characterize the functional groups of AOM species. Compounds containing nitrogen and/or sulfur were targeted because of the high number of oxygen atoms contained in their molecular formulas. Due to the large number of isobaric ions in the precursor isolation ranges, large numbers of product ions resulted from collision induced dissociation. Common neutral losses were assigned by matching the molecular formulas of the expected product ions with the detected product ions within the appropriate mass spectra. Since polar functional groups are expected to affect the hygroscopic properties of aerosols, the losses of H(2)O, CO(2), CH(3)OH, HNO(3), CH(3)NO(3), SO(3), SO(4) and combinations of these were specifically targeted. Among the 421 compounds studied, the most frequently observed neutral losses were CO(2) (54%), H(2)O (43%) and CH(3)OH (40%). HNO(3) losses were observed for 63% of the studied nitrogen containing compounds and 33% of the studied compounds containing both nitrogen and sulfur. SO(3) losses were observed for 85% of the studied sulfur containing compounds and 42% of studied compounds containing both nitrogen and sulfur. A number of molecular formulas matching those of monoterpene ozonolysis SOA were observed; they include organonitrates, organosulfates, and nitroxy-organosulfates. Overall, the results of fragmentation analysis of 400+ individual molecular precursors elucidate the complexity and multifunctional nature of the isolated water-soluble AOM.

  6. Gas-Phase Fragmentation Pathways of Mixed-Addenda Keggin Anions: PMo12-nWnO403- (n = 0-12)

    SciTech Connect

    Gunaratne, Kalupathirannehelage Don D.; Prabhakaran, Venkateshkumar; Johnson, Grant E.; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo12-nWnO403- (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed POMs examined in this study. CID of molybdenum-rich anions, PMo12- nWnO403- (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and twenty-two oxygen atoms (M7O222-) and its complementary singly charged PM5O18- ion, while the Lindqvist anion, (M6O192-) and its complementary PM6O21- ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo12-nWnO403- (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms may be attributed to the higher stability of tungsten-rich anions towards isomerization. We find that the observed distribution of Mo and W atoms in the major M6O192- and M7O222- fragment ions is different from that predicted by a random distribution indicating substantial segregation of the addenda metal atoms in the POMs. Electron detachment from the triply charged precursor anion resulting in formation of doubly charged anions is observed. This is a dominant dissociation pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and electron detachment pathways of POM anions.

  7. 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.

  8. Mechanisms of fragmentation of cationic peptide ions

    NASA Astrophysics Data System (ADS)

    Zhao, Hong; Adams, Jeanette

    1993-06-01

    Fragmentation mechanisms for formation of several commonly occurring product ions in high-energy collision-induced induced decomposition spectra of either (M + Cat2+ - H)+ ions of peptides cationized with alkaline earth metal ions, (M + Ca+)+ ions cationized with alkali metal ions, or (M + H)+ ions are evaluated by using deuterium-labelled peptides. The different sources of hydrogen transferred in the reactions are identified. Our study supports some previously proposed mechanisms but also provides evidence for others.

  9. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. 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.

  11. 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.

  12. Bond breaking in a Morse chain under tension: Fragmentation patterns, higher index saddles, and bond healing

    NASA Astrophysics Data System (ADS)

    Mauguière, F. A. L.; Collins, P.; Ezra, G. S.; Wiggins, S.

    2013-04-01

    We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices), and energy of all equilibria for the general n-particle chain, and have highlighted the importance of saddle points with index >1. We show that for an n = 2-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectories passing through a neighborhood of the saddle point using the values of the integrals associated with the normal form. We also generalize our definition of the dividing surface and define an extended dividing surface (EDS), which is used to sample and classify all trajectories that pass through a phase space neighborhood of the index 2 saddle at total energies less than that of the saddle. Classical trajectory simulations are used to study fragmentation patterns for the n = 2 chain under tension. That is, we investigate the relative probability for breaking one bond versus concerted fission of several (two, in this case) bonds. Initial conditions for trajectories are obtained by sampling the EDS at constant energy. We sample trajectories at fixed energies both above and below the energy of the saddle. The fate of trajectories (single versus multiple bond breakage) is explored as a function of the location of the initial condition on the EDS, and a connection made to the work of Chesnavich on collision-induced dissociation. A significant finding is that we can readily identify trajectories that exhibit bond healing. Such trajectories pass outside the nominal (index 1) transition state for single bond dissociation, but return to the potential well region, possibly several times, before ultimately dissociating.

  13. Identification of disulfide bonds in wheat gluten proteins by means of mass spectrometry/electron transfer dissociation.

    PubMed

    Lutz, Elena; Wieser, Herbert; Koehler, Peter

    2012-04-11

    Disulfide bonds within gluten proteins play a key role in the breadmaking performance of wheat flour. In the present study, disulfide bonds of wheat gluten proteins were identified by using a new liquid chromatography-mass spectrometry (LC-MS) technique with alternating electron transfer dissociation (ETD)/collision-induced dissociation (CID). Wheat flour was partially hydrolyzed with thermolysin (pH 6.5, 37 °C, 16 h), and the digest was subjected to LC-MS with alternating ETD/CID fragmentation. Whereas CID provided peptide fragments with intact disulfide bonds, cleavage of disulfide bonds was preferred over peptide backbone fragmentations in ETD. The simultaneous observation of disulfide-linked and disulfide-cleaved peptide ions in the mass spectra not only provided distinct interpretation with high confidence but also simplified the conventional approach for determination of disulfide bonds, which often requires two separate experiments with and without chemical reduction. By application of the new method 14 cystine peptides were identified. Eight peptides confirmed previously established disulfide bonds within gluten proteins, and the other six cystine peptides were identified for the first time. One of the newly identified cystine peptides represented a "head-to-tail" cross-link between high molecular weight glutenin subunits. This type of cross-link, which has been postulated as an integral part of glutenin models published previously, has now been proven experimentally for the first time. From the six remaining cystine peptides interchain disulfide bonds between α-gliadins, γ-gliadins, and low molecular weight glutenin subunits were established.

  14. Fragmentation Pathways in the Uracil Radical Cation

    SciTech Connect

    Zhou, Congyi; Matsika, Spiridoula; Kotur, Marija; Weinacht, Thomas C.

    2012-08-24

    We investigate pathways for fragmentation in the uracil radical cation using ab initio electronic structure calculations. We focus on the main fragments produced in pump–probe dissociative ionization experiments. These are fragments with mass to charge ratios (m/z) of 69, 28, 41, and 42. Barriers to dissociation along the ground ionic surface are reported, which provide an estimate of the energetic requirements for the production of the main fragments. Finally, direct and sequential fragmentation mechanisms have been analyzed, and it is concluded that sequential fragmentation after production of fragment with m/z 69 is the dominant mechanism for the production of the smaller fragments.

  15. 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.

  16. Density Functional Theory and Mass Spectrometry of Phthalate Fragmentations Mechanisms: Modeling Hyperconjugated Carbocation and Radical Cation Complexes with Neutral Molecules

    NASA Astrophysics Data System (ADS)

    Jeilani, Yassin A.; Cardelino, Beatriz H.; Ibeanusi, Victor M.

    2011-11-01

    This is the first ab initio study of the energetics of the fragmentation mechanisms of phthalate, by mass spectrometry, leading to protonated phthalic anhydride ( m/z 149). Phthalates fragment by two major pathways; namely, the McLafferty + 1 rearrangement and the loss of alkoxy. Both pathways involve a carbonyl oxygen attack to the ortho-carbonyl carbon leading to structures with tetrahedral carbon intermediates that eventually give m/z 149. These pathways were studied by collision induced dissociation (CID) using triple quadrupole mass spectrometry. The proposed McLafferty + 1 pathway proceeds through a distonic M•+, leading to the loss of an allylic-stabilized alkene radical. The McLafferty rearrangement step proceeds through a six-membered ring transition state with a small activation energy ranging 0.4-6.2 kcal/mol; the transfer of a second H from the distonic ion of the rearrangement step proceeds through a radical cation molecule complex. Based on quantum chemical modeling of the cation molecule complexes, two kinds of cation molecule complexes were identified as radical cation molecule complex and hyperconjugated cation molecule complex. This distinction is based on the cation and simplifies future modeling of similar complexes. Optimization of important fragments in these pathways showed cyclized and hydrogen-bonded structures to be favored. An exception was the optimized structure of the protonated phthalic anhydride ( m/z 149) that showed a structure with an open anhydride ring.

  17. 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.

  18. Dissociation dynamics of methanol clusters following multiphoton ionization

    SciTech Connect

    Morgan, S.; Castleman, A.W. Jr. )

    1989-06-01

    Following multiphoton ionization (MPI), neutral methanol clusters are found to undergo a well-known ion-molecule reaction which leads to the production of protonated clusters. Evaporative dissociation rates of the cluster ions are measured for sizes ranging from the dimer to the 21-mer following MPI. There is a general trend of the rates decreasing with time after the initial ionization event in accordance with the evaporative ensemble model. Rates measured at long times after ionization display a consistent trend of increasing with cluster size. These findings are shown to be in accord with statistical considerations of evaporative unimolecular dissociation. Collision-induced-dissociation cross sections are found to generally increase with size; the finding of a local minimum in the value for H{sup +}(CH{sub 3}OH){sub 3} is in agreement with predictions of its structure. Finally, through a combination of unimolecular evaporative and collision-induced-dissociation processes, as many as five methanol monomers are found to be lost from a cluster as small as H{sup +} (CH{sub 3}OH){sub 7}.

  19. 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.

  20. 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.

  1. Hydrogen broadening and collision-induced line shifts of methane at 4200/cm

    NASA Technical Reports Server (NTRS)

    Margolis, Jack S.

    1993-01-01

    Many of the lines of the nu1 + nu4 and nu3 + nu4 bands of methane in the vicinity of 4200/cm have been assigned and are reported in the HITRAN data-base which is commonly used for atmospheric transmission calculations in the IR. The collision-induced broadening coefficients of hydrogen for more than 200 of these lines are reported. Also, by using the water-vapor lines which occur in the spectra as calibration marks, the frequencies of the broadened lines are determined. This permitted the collision-induced line shifts to be measured for lines sufficiently isolated from interfering blends: all of the shifts which could be reliably determined in this way were negative.

  2. Application of ESI/MS, CID/MS and tandem MS/MS to the fragmentation study of eriodictyol 7-O-glucosyl-(1-->2)-glucoside and luteolin 7-O-glucosyl-(1-->2)-glucoside

    NASA Astrophysics Data System (ADS)

    Es-Safi, Nour-Eddine; Kerhoas, Lucien; Einhorn, Jacques; Ducrot, Paul-Henri

    2005-12-01

    A mass spectrometric method based on the combined use of positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry has been applied to the structural characterization of the eriodictyol 7-O-glucosyl-(1-->2)-glucoside and luteolin 7-O-glucosyl-(1-->2)-glucoside. The low-energy product ion mass spectrum of [M + H]+ and [M - H]- ions showed extensive fragmentation of the diglucose moiety, loss of the glycan residue, and fragmentation of the aglycon units that permit characterization of the interglycosidic linkage and the substituents in the A- and B-rings. Both glycosides were shown to yield the 0,2X00,2X1 ion which can be considered as characteristic of the 1-->2 interglycosidic linkage in the glucoglucoside adducts, since it can not be formed in the case of other interglycosidic types. In the case of the eriodictyol diglucoside the 1, 3 fragmentation of the C-ring was observed before those involving the carbohydrates thus allowing the position determination of the diglucoside moiety on the A-ring. In the negative ion mode only the luteolin diglucoside was shown to undergo collision-induced homolytic and heterolytic cleavages of the O-glycosidic bond producing the aglycone radical-anion [Y0-H]-- and Y0- product ions, while this was not observed in the case of eriodictyol glycoside. CID MS/MS analysis of the sodiated molecules gave complementary informations for the structural characterization of the studied compounds. The B2+ fragment which is useful for establishing that the terminal carbohydrate unit is linked to another carbohydrate and not directly to the aglycone was obtained as base peak. This result is of analytical value for the differentiation of O-diglycosyl and di-O-glycosyl flavonoids.

  3. Fragmentation of protonated 2-(2-phenylethyl)chromones from agarwood: the diagnostic role of ion/neutral complexes as reactive intermediates.

    PubMed

    Yang, Delan; Xia, Bing; Jiang, Yan; Mei, Wenli; Kuck, Dietmar

    2015-01-01

    A positive-ion electrospray ionisation collision-induced dissociation mass spectrometric study on the fragmentation of the [M + H](+) ions of 2-(2-phenylethyl)chromone and a set of nine hydroxyl- and/or methoxy-substituted derivatives has revealed a highly prominent fragmentation channel, the loss of benzoquinomethanes or a benzaldehyde, respectively, as a diagnostic feature for 2-(2-phenylethyl)chromones that bear a hydroxyl group at the para- (4'-), ortho- (2'-) and/or benzylic (α-) position of the phenylethyl residue. Derivatives that bear only a meta- (3'-) hydroxyl group do not undergo this elimination. The intermediacy of ion/neutral complexes (INCs) is invoked to explain this fragmentation, which involves the remarkable intra-complex proton or hydrogen atom transfer from the remote 4'-OH (or the 2'- or α-OH) functionalities. Density functional theory (B3LYP/6-31G(d)) calculations confirm the energetic preference for these elimination channels and agree with the limited thermochemical data known for para- and ortho- benzoquinomethanes. The INC-mediated losses of the benzaldehydes from the [M + H](+) ions of the α-hydroxy-substituted 2-(2-phenylethyl)chromones correspond to a particularly facile (vinylogous) Grob fragmentation. The study may be viewed as a telling example of the diagnostic role of ion/neutral complexes as intermediates for the structural assignment of constitutional isomers by mass spectrometry.

  4. Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry.

    PubMed

    Hosseini, Seyed Esmaeil; Saeidian, Hamid; Amozadeh, Ali; Naseri, Mohammad Taghi; Babri, Mehran

    2016-12-30

    For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O-alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes. O-Alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS-inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision-induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction. The EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC-related chemicals during on-site inspection and/or off-site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

    PubMed

    Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

    2013-09-24

    Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale.

  10. Formation, isomerization, and dissociation of ε- and α-carbon-centered tyrosylglycylglycine radical cations.

    PubMed

    Lai, Cheuk-Kuen; Mu, Xiaoyan; Hao, Qiang; Hopkinson, Alan C; Chu, Ivan K

    2014-11-28

    The fragmentation products of the ε-carbon-centered radical cations [Y(ε)˙LG](+) and [Y(ε)˙GL](+), made by 266 nm laser photolysis of protonated 3-iodotyrosine-containing peptides, are substantially different from those of their π-centered isomers [Y(π)˙LG](+) and [Y(π)˙GL](+), made by dissociative electron transfer from ternary metal-ligand-peptide complexes. For leucine-containing peptides the major pathway for the ε-carbon-centered radical cations is loss of the side chain of the leucine residue forming [YG(α)˙G](+) and [YGG(α)˙](+), whereas for the π-radicals it is the side chain of the tyrosine residue that is lost, giving [G(α)˙LG](+) and [G(α)˙GL](+). The fragmentations of the product ions [YG(α)˙G](+) and [YGG(α)˙](+) are compared with those of the isomeric [Y(ε)˙GG](+) and [Y(π)˙GG](+) ions. The collision-induced spectra of ions [Y(ε)˙GG](+) and [YGG(α)˙](+) are identical, showing that interconversion occurs prior to dissociation. For ions [Y(ε)˙GG](+), [Y(π)˙GG](+) and [YG(α)˙G](+) the dissociation products are all distinctly different, indicating that dissociation occurs more readily than isomerization. Density functional theory calculations at B3LYP/6-31++G(d,p) gave the relative enthalpies (in kcal mol(-1) at 0 K) of the five isomers to be [Y(ε)˙GG](+) 0, [Y(π)˙GG](+) -23.7, [YGG(α)˙](+) -28.7, [YG(α)˙G](+) -31.0 and [Y(α)˙GG](+) -38.5. Migration of an α-C-H atom from the terminal glycine residue to the ε-carbon-centered radical in the tyrosine residue, a 1-11 hydrogen atom shift, has a low barrier, 15.5 kcal mol(-1) above [Y(ε)˙GG](+). By comparison, isomerization of [Y(ε)˙GG](+) to [YG(α)˙G](+) by a 1-8 hydrogen atom migration from the α-C-H atom of the central glycine residue has a much higher barrier (50.6 kcal mol(-1)); similarly conversion of [Y(ε)˙GG](+) into [Y(π)˙GG](+) has a higher energy (24.4 kcal mol(-1)).

  11. N-Protonated Isomers and Coulombic Barriers to Dissociation of Doubly Protonated Ala8Arg

    NASA Astrophysics Data System (ADS)

    Haeffner, Fredrik; Irikura, Karl K.

    2017-10-01

    Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala n ( n = 3-11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated Ala8Arg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N9. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions. [Figure not available: see fulltext.

  12. N-Protonated Isomers and Coulombic Barriers to Dissociation of Doubly Protonated Ala8Arg

    NASA Astrophysics Data System (ADS)

    Haeffner, Fredrik; Irikura, Karl K.

    2017-07-01

    Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala n (n = 3-11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated Ala8Arg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N9. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions.

  13. 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.

  14. Gas-Phase Fragmentation Pathways of Mixed Addenda Keggin Anions: PMo12-nWnO40 3- (n = 0-12)

    NASA Astrophysics Data System (ADS)

    Gunaratne, K. Don D.; Prabhakaran, Venkateshkumar; Johnson, Grant E.; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo12-nWnO40 3- (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed addenda POMs examined in this study. CID of molybdenum-rich anions, PMo12-nWnO40 3- (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and 22 oxygen atoms (M7O22 2-) and its complementary singly charged PM5O18 - ion. In comparison, the doubly charged Lindqvist anion, (M6O19 2-) and its complementary singly charged PM6O21 - ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo12-nWnO40 3- (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms in the POM may be attributed to the higher barrier of tungsten-rich anions towards isomerization. We present evidence that the observed distribution of Mo and W atoms in the major M6O19 2- and M7O22 2- fragment ions is different from that predicted by a random distribution, indicating substantial segregation of the addenda metal atoms in the POMs. Charge reduction of the triply charged precursor anion resulting in formation of doubly charged anions is also observed. This is a dominant pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and charge loss pathways in CID of POM anions.

  15. 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.

  16. 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.

  17. Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra.

    PubMed

    Sun, Rui-Xiang; Dong, Meng-Qiu; Song, Chun-Qing; Chi, Hao; Yang, Bing; Xiu, Li-Yun; Tao, Li; Jing, Zhi-Yi; Liu, Chao; Wang, Le-Heng; Fu, Yan; He, Si-Min

    2010-12-03

    In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis of intact proteins. However, peptide identification rates from ETD spectra compare poorly with those from collision induced dissociation (CID) spectra, especially for doubly charged precursors. This is in part due to an insufficient understanding of the characteristics of ETD and consequently a failure of database search engines to make use of the rich information contained in the ETD spectra. In this study, we statistically characterized ETD fragmentation patterns from a collection of 461 440 spectra and subsequently implemented our findings into pFind, a database search engine developed earlier for CID data. From ETD spectra of doubly charged precursors, pFind 2.1 identified 63-122% more unique peptides than Mascot 2.2 under the same 1% false discovery rate. For higher charged peptides as well as phosphopeptides, pFind 2.1 also consistently obtained more identifications. Of the features built into pFind 2.1, the following two greatly enhanced its performance: (1) refined automatic detection and removal of high-intensity peaks belonging to the precursor, charge-reduced precursor, or related neutral loss species, whose presence often set spectral matching askew; (2) a thorough consideration of hydrogen-rearranged fragment ions such as z + H and c - H for peptide precursors of different charge states. Our study has revealed that different charge states of precursors result in different hydrogen rearrangement patterns. For a fragment ion, its propensity of gaining or losing a hydrogen depends on (1) the ion type (c or z) and (2) the size of the fragment relative to the precursor, and both dependencies are affected by (3) the charge state of the precursor. In addition, we discovered ETD characteristics that are unique for certain types of amino acids (AAs), such as a prominent

  18. In-source fragmentation technique for the production of thermalized ions.

    PubMed

    Carl, Damon R; Moision, Robert M; Armentrout, P B

    2009-12-01

    Our electrospray ionization-ion funnel-rf hexapole (ESI-IF-6P) source is designed to produce ions for threshold collision-induced dissociation (TCID) studies in a guided ion beam mass spectrometer. This ion source forms an initial distribution of Ca2+(H2O)x ions where x is 6-9. A new in-source fragmentation technique within the hexapole ion guide of the source is described, which is easy to implement and of modest machining and electrical costs, and is able to generate smaller Ca2+(H2O)x complexes, where x = 2-5. Fragmentation is achieved by biasing an assembly of six 0.25 in. long electrodes that are inserted between the hexapole rods. The assembly is positioned in the high-pressure region of the source such that newly formed Ca2+(H2O)x ions undergo enough collisions to become thermalized, as verified by TCID studies. From the initial distribution of ions, fragmentation proceeds along the lowest energy pathway, which corresponds to sequential water loss for most complexes. However, the Ca2+(H2O) complex cannot be formed using this method because charge separation into CaOH+ and H3O+ becomes the lowest energy pathway from the Ca2+(H2O)2 complex. Therefore, this fragmentation technique can be used to identify the critical size complex for M2+(H2O)x systems, which we define as the complex size (x) at which charge separation becomes a lower energy pathway compared with simple ligand loss.

  19. Exploring rearrangements along the fragmentation pathways of diuron anion: A combined experimental and computational investigation

    NASA Astrophysics Data System (ADS)

    Kanawati, Basem; Harir, Mourad; Schmitt-Kopplin, Philippe

    2009-12-01

    Diuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea), a common herbicide from phenyl urea class, was investigated by studying the formation of several negative ions [M-H]- in the gas phase and the fragmentation behaviour of the thermodynamically most probably formed isomeric anions upon linear ion acceleration/collision experiments. The collision induced dissociation experiments (CID) were carried out in a hexapole-quadrupole-hexapole hybrid system coupled to 12 T magnet with infinity ICR cell for high resolution measurements. Two distinctive main pathways were observed in the MS/MS spectrum. Sustained off-resonance irradiation (SORI) experiments inside the ICR cell reinforce the fragmentation channels obtained from linear ion acceleration experiments. The fragmentation pathways were also completely investigated by the use of B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) level of theory. Elimination of dimethylamine takes place in a two-step process, by which two successive 1,3 proton shifts occur. The second 1,3 proton shift is concerted with the departure of dimethylamine. The driving force for the (CH3)2NH elimination is the formation of isocyanate group. The formed primary product ion can further decompose to release HCl through a new transition state. A stable new aromatic product ion is formed with 10[pi] electrons. Loss of C3H5NO neutral from another anionic isomer of the precursor ion was also observed and is characteristic for the amide terminal of the diamide functional group. A concerted mechanism is proposed, by which N-C bond breakage and cyclization of the eliminated neutral fragment C3H5NO takes place simultaneously to form 1-methyl-aziridin-2-one.

  20. Evidence of molecular fragmentation inside the charged droplets produced by electrospray process.

    PubMed

    Banerjee, Shibdas; Prakash, Halan; Mazumdar, Shyamalava

    2011-10-01

    The behavior of the analyte molecules inside the neutral core of the charged droplet produced by the electrospray (ES) process is not unambiguously known to date. We have identified interesting molecular transformations of two suitably chosen analytes inside the ES droplets. The highly stable Ni(II) complex of 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane (1) that consists of a positive charge at the metal center, and the allyl pendant armed tertiary amine containing macrocycle 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetraallyl-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-diene (M(4p)) have been studied by ESI mass spectrometry as the model analytes. We have shown that these two molecules are not representatively transferred from solution to gas phase by ESI; rather, they undergo fragmentation inside the charged droplets. The results indicated that a charged analyte such as 1 was possibly unstable inside the neutral core of the ES droplet and undergoes fragmentation due to the Coulombic repulsion imparted by the surface protons. Brownian motion of the neutral analyte such as M(4p) inside the droplet, on the other hand, may lead to proton attachment on interaction with the charged surface causing destabilization that leads to fragmentation of M(4p) and release of resonance stabilized allyl cations from the core of the droplet. Detailed solvent dependence and collision-induced dissociation (CID) studies provided compelling evidences that the fragmentation of the analytes indeed occurs inside the charged ES droplets. A viable model of molecular transformations inside the ES droplet was proposed based on these results to rationalize the behavior of the analyte molecules inside the charged ES droplets.

  1. Multiple-vehicle collision induced by lane changing in traffic flow

    NASA Astrophysics Data System (ADS)

    Nagatani, Takashi; Yonekura, Shoichi

    2014-06-01

    We study the multiple-vehicle collision when a vehicle changes from the first lane to the second lane on a two-lane highway. If a vehicle with high (low) speed on the first lane enters into the second lane, it may crash into the forward (rear) vehicle on the second lane and the crash may induce more collisions. We investigate whether or not the incoming vehicle induces the multiple-vehicle collision. The number of collisions depends on the initial velocity, the initial density, the incoming velocity, the incoming headway, the sensitivity, and the relative velocity. We derive the region map for the multiple-vehicle collision induced by lane changing.

  2. 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

  3. 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.

  4. 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.

  5. Selective and Nonselective Cleavages in Positive and Negative CID of the Fragments Generated from In-Source Decay of Intact Proteins in MALDI-MS

    NASA Astrophysics Data System (ADS)

    Takayama, Mitsuo; Sekiya, Sadanori; Iimuro, Ryunosuke; Iwamoto, Shinichi; Tanaka, Koichi

    2014-01-01

    Selective and nonselective cleavages in ion trap low-energy collision-induced dissociation (CID) experiments of the fragments generated from in-source decay (ISD) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) of intact proteins are described in both positive and negative ion modes. The MALDI-ISD spectra of the proteins demonstrate common, discontinuous, abundant c- and z'-ions originating from cleavage at the N-Cα bond of Xxx-Asp/Asn and Gly-Xxx residues in both positive- and negative-ion modes. The positive ion CID of the c- and z'-ions resulted in product ions originating from selective cleavage at Asp-Xxx, Glu-Xxx and Cys-Xxx residues. Nonselective cleavage product ions rationalized by the mechanism of a "mobile proton" are also observed in positive ion CID spectra. Negative ion CID of the ISD fragments results in complex product ions accompanied by the loss of neutrals from b-, c-, and y-ions. The most characteristic feature of negative ion CID is selective cleavage of the peptide bonds of acidic residues, Xxx-Asp/Glu/Cys. A definite influence of α-helix on the CID product ions was not obtained. However, the results from positive ion and negative ion CID of the MALDI-ISD fragments that may have long α-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions.

  6. Selective and nonselective cleavages in positive and negative CID of the fragments generated from in-source decay of intact proteins in MALDI-MS.

    PubMed

    Takayama, Mitsuo; Sekiya, Sadanori; Iimuro, Ryunosuke; Iwamoto, Shinichi; Tanaka, Koichi

    2014-01-01

    Selective and nonselective cleavages in ion trap low-energy collision-induced dissociation (CID) experiments of the fragments generated from in-source decay (ISD) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) of intact proteins are described in both positive and negative ion modes. The MALDI-ISD spectra of the proteins demonstrate common, discontinuous, abundant c- and z'-ions originating from cleavage at the N-Cα bond of Xxx-Asp/Asn and Gly-Xxx residues in both positive- and negative-ion modes. The positive ion CID of the c- and z'-ions resulted in product ions originating from selective cleavage at Asp-Xxx, Glu-Xxx and Cys-Xxx residues. Nonselective cleavage product ions rationalized by the mechanism of a "mobile proton" are also observed in positive ion CID spectra. Negative ion CID of the ISD fragments results in complex product ions accompanied by the loss of neutrals from b-, c-, and y-ions. The most characteristic feature of negative ion CID is selective cleavage of the peptide bonds of acidic residues, Xxx-Asp/Glu/Cys. A definite influence of α-helix on the CID product ions was not obtained. However, the results from positive ion and negative ion CID of the MALDI-ISD fragments that may have long α-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions.

  7. Host-guest chemistry in the gas phase: selected fragmentations of CB[6]-peptide complexes at lysine residues and its utility to probe the structures of small proteins.

    PubMed

    Heo, Sung Woo; Choi, Tae Su; Park, Kyung Man; Ko, Young Ho; Kim, Seung Bin; Kim, Kimoon; Kim, Hugh I

    2011-10-15

    The gas phase host-guest chemistry between cucurbit[6]uril (CB[6]) and peptide is investigated using electrospray ionization mass spectrometry (ESI-MS). CB[6] exhibits a high preference to interacting with a Lys residue in a peptide forming a CB[6]-peptide complex. Collisionally activated CB[6] complexes of peptides yield a common highly selective fragment product at m/z 549.2, corresponding to the doubly charged CB[6] complex of 5-iminiopentylammonium (5IPA). The process involves the formation of an internal iminium ion, which results from further fragments to an a-type ion from a y-type ion, and the resulting 5IPA ion threads through CB[6]. Numerous peptides are investigated to test the generality of the observed unique host-guest chemistry of CB[6]. Its potential utility in probing protein structures is demonstrated using CB[6] complexes of ubiquitin. Low-energy collision induced dissociation yields CB[6] complex fragments, and further MS(n) spectra reveal details of the CB[6] binding sites, which allow us to deduce the protein structure in the solution phase. The mechanisms and energetics of the observed reactions are evaluated using density functional theory calculations.

  8. Investigation of the electrochemical oxidation products of zotepine and their fragmentation using on-line electrochemistry/electrospray ionization mass spectrometry.

    PubMed

    Nozaki, Kazuyoshi; Kitagawa, Hiroshi; Kimura, Sumihisa; Kagayama, Akira; Arakawa, Ryuichi

    2006-05-01

    When zotepine, an antipsychotic drug, was electrochemically oxidized using electrospray ionization mass spectrometry (ESI-MS) coupled with a microflow electrolytic cell, [M + 16 + H]+ (m/z 348), [M-H]+ (m/z 330) and [M-14 + H]+ (m/z 318) were observed as electrochemical oxidation product ions (M represents the zotepine molecule). Although a major fragment ion that was derived from the dimethyl aminoethyl moiety was observed only at m/z 72 in the collision-induced dissociation (CID) spectrum of zotepine, new fragments such as m/z 315 and 286 ions could be generated in the CID spectrum by combining electrochemical oxidation and CID. Since these fragments were relatively specific with high ion strength, it was thought that they would be useful for developing a sensitive LC-MS/MS assay. The S-oxide and N-demethylated products were detected by electrolysis assuring that a portion of P450 metabolites of zotepine could be mimicked by the electrochemistry/electrospray ionization mass spectrometry (EC/ESI-MS) system.

  9. Identification of Anthropogenic Compounds in Urban Environments and Evaluation of Automated Methods for Reading Fragmentation-A Case of River Water.

    PubMed

    Yamamoto, Atsushi; Matsumoto, Naoko; Kawasaki, Hideya; Arakawa, Ryuichi

    2016-01-01

    A workflow based on liquid chromatography/high-resolution mass spectrometry (LC/HR-MS) was applied for the identification of compounds in urban environments. Substances extracted by solid-phase extraction from river water were wholly analyzed by LC/HR-MS without any purification. Fragmentation in collision-induced dissociation was manually studied for the 20 most intense ions in positive- and negative-ion electrospray ionization with accurate mass determination at a resolution of 100,000. Sixteen anthropogenic compounds in the extract were identified and confirmed using standard reference reagents. These compounds consisted of pharmaceuticals, surfactants, flame retardants, and industrial intermediates. The majority of the compounds are common in our daily life. In the identification process, two automated methods, MAGMa and MetFrag/MetFusion, for reading fragmentation were evaluated for the sixteen compounds. Although automated methods could be used to retrieve the correct molecular structures in most cases, they could not always be promoted to the top rank. Automated methods have yet to be a complete solution for identifying chemical compounds, but will considerably reduce the burden for humans in reading fragmentation.

  10. Simultaneous ESI-APCI+ ionization and fragmentation pathways for nine benzodiazepines and zolpidem using single quadrupole LC-MS.

    PubMed

    Galaon, Toma; Vacaresteanu, Catalina; Anghel, Dan-Florin; David, Victor

    2014-05-01

    Nine important 1,4-benzodiazepines and zolpidem were characterized by liquid chromatography-mass spectrometry using a multimode ionization source able to generate ions using both electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), and a single quadrupole mass analyzer. An optimum chromatographic separation was applied for all target compounds in less than 8 minutes using a Zorbax Eclipse Plus column (100 × 4.6 mm, 3.5 µm) kept at 35°C and a 0.3% HCOOH/ACN/IPA (61:34:5) mobile phase pumped at 1 ml/min. Optimization of LC-MS method generated low limit of quantitation (LOQ) values situated in the range 0.3-20.5 ng/ml. Comparison between differences in method sensitivity, under specified chromatographic conditions, when using ESI-only, APCI-only, and simultaneous ESI-APCI ionization with such a multimode source was discussed. Mixed ESI-APCI(+) mode proved to be the most sensitive ionization generating an average 35% detector response increase compared to ESI-only ionization and 350% detector response increase with respect to APCI-only ionization. Characterization of the nine benzodiazepines and zolpidem concerning their MS fragmentation pathway following 'in-source' collision-induced dissociation is discussed in detail and some general trends regarding these fragmentations are set.

  11. Discovery and mechanistic studies of facile N-terminal Cα-C bond cleavages in the dissociation of tyrosine-containing peptide radical cations.

    PubMed

    Mu, Xiaoyan; Song, Tao; Xu, Minjie; Lai, Cheuk-Kuen; Siu, Chi-Kit; Laskin, Julia; Chu, Ivan K

    2014-04-24

    Fascinating N-terminal Cα-C bond cleavages in a series of nonbasic tyrosine-containing peptide radical cations have been observed under low-energy collision-induced dissociation (CID), leading to the generation of rarely observed x-type radical fragments, with significant abundances. CID experiments of the radical cations of the alanyltyrosylglycine tripeptide and its analogues suggested that the N-terminal Cα-C bond cleavage, yielding its [x2 + H](•+) radical cation, does not involve an N-terminal α-carbon-centered radical. Theoretical examination of a prototypical radical cation of the alanyltyrosine dipeptide, using density functional theory calculations, suggested that direct N-terminal Cα-C bond cleavage could produce an ion-molecule complex formed between the incipient a1(+) and x1(•) fragments. Subsequent proton transfer from the iminium nitrogen atom in a1(+) to the acyl carbon atom in x1(•) results in the observable [x1 + H](•+). The barriers against this novel Cα-C bond cleavage and the competitive N-Cα bond cleavage, forming the complementary [c1 + 2H](+)/[z1 - H](•+) ion pair, are similar (ca. 16 kcal mol(-1)). Rice-Ramsperger-Kassel-Marcus modeling revealed that [x1 + H](•+) and [c1 + 2H](+) species are formed with comparable rates, in agreement with energy-resolved CID experiments for [AY](•+).

  12. Multistage fragmentation of ion trap mass spectrometry system and pseudo-MS3 of triple quadrupole mass spectrometry characterize certain (E)-3-(dimethylamino)-1-arylprop-2-en-1-ones: a comparative study.

    PubMed

    Abdelhameed, Ali S; Kadi, Adnan A; Abdel-Aziz, Hatem A; Angawi, Rihab F; Attwa, Mohamed W; Al-Rashood, Khalid A

    2014-01-01

    A new approach was recently introduced to improve the structure elucidation power of tandem mass spectrometry simulating the MS(3) of ion trap mass spectrometry system overcoming the different drawbacks of the latter. The fact that collision induced dissociation in the triple quadrupole mass spectrometer system provides richer fragment ions compared to those achieved in the ion trap mass spectrometer system utilizing resonance excitation. Moreover, extracting comprehensive spectra in the ion trap needs multistage fragmentation, whereas similar fragment ions may be acquired from one stage product ion scan using the triple quadrupole mass spectrometer. The new strategy was proven to enhance the qualitative performance of tandem mass spectrometry for structural elucidation of different chemical entities. In the current study we are endeavoring to prove our hypothesis of the efficiency of the new pseudo-MS(3) technique via its comparison with the MS(3) mode of ion trap mass spectrometry system. Ten pharmacologically and synthetically important (E)-3-(dimethylamino)-1-arylprop-2-en-1-ones (enaminones 4a-j) were chosen as model compounds for this study. This strategy permitted rigorous identification of all fragment ions using triple quadrupole mass spectrometer with sufficient specificity. It can be used to elucidate structures of different unknown components. The data presented in this paper provide clear evidence that our new pseudo-MS(3) may simulate the MS(3) of ion trap spectrometry system.

  13. 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.