Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions

The beam-type and ion trap collision-induced dissociation (CID) behaviors of protonated bovine ubiquitin ions were studied for charge states ranging from +6 to +12 on a modified triple quadrupole/linear ion trap tandem mass spectrometer. Both beam-type CID and ion trap CID were conducted in a high-pressure linear ion trap, followed by proton-transfer ion/ion reactions to reduce the charge states of product ions mostly to +1. The product ions observed under each activation condition were predominantly b- and y-type ions. Fragmentation patterns showed a much stronger dependence on parent ion charge state with ion trap CID than with beam-type CID using nitrogen as the collision gas, with preferential cleavages C-terminal to aspartic acid at relatively low charge states, nonspecific fragmentation at moderate charge states, and favored cleavages N-terminal to proline residues at high charge states. In the beam-type CID case, extensive cleavage along the protein backbone was noted, which yielded richer sequence information (77% of backbone amide bond cleavages) than did ion trap CID (52% of backbone amide bond cleavages). Collision gas identity and collision energy were also evaluated in terms of their effects on the beam-type CID spectrum. The use of helium as collision gas, as opposed to nitrogen, resulted in CID behavior that was sensitive to changes in collision energy. At low collision energies, the beam-type CID data resembled the ion trap CID data with preferential cleavages predominant, while at high collision energies, nonspecific fragmentation was observed with increased contributions from sequential fragmentation.     

Quantum chemical study on nitroimidazole, polynitroimidazole and their methyl derivatives

The insensitive explosive candidates, nitroimidazoles, polynitroimidazoles and their methyl derivatives, are investigated using density functional theory (DFT). The homolytic bond dissociation energies (BDEs) corresponding to -NO2 group removal from carbon or nitrogen site on imidazole ring were calculated at B3P86/6-311G** level, and the weakest bond has been determined. Further, a correlation is developed between impact sensitivity h50 and the ratio (BDE/E) of the weakest bond BDE to the total energy E, and we extrapolate this relationship to predict the impact sensitivities for compounds where experiments are not available. It is found that most of the title compounds are insensitive towards impact stimuli with their h50 larger than 60.0cm. Heats of formation (HOFs) for the 21 title compounds at 298K in gas are also determined both at B3LYP/6-311G** and B3P86/6-311G** levels using isodesmic work reactions. The calculated BDEs and HOFs consistently indicate that C-nitro-substituted imdazole is more stable than the corresponding N-substituted one, and the introduction of methyl on C increases the stability whereas the methyl attached to N atom decreases the stability.     

Fragmentation pattern of gold clusters collided with xenon atoms

The dissociation channels of gold cluster ions Au_n⁺ (2 ≤ n ≤ 23) have been investigated via collision induced dissociation in a Penning trap. Excited odd cluster ions with n ≤ 15 decay by evaporation of dimers, all others decay by monomer evaporation. Information on the binding energies is deduced from these dissociation channels.     

Unbiased high-throughput screening of reactive metabolites on the linear ion trap mass spectrometer using polarity switch and mass tag triggered data-dependent acquisition

Constant neutral loss (CNL) and precursor ion (PI) scan have been widely used for the in vitro screening of glutathione conjugates derived from reactive metabolites, but these two methods are only applicable to triple quadrupole or hybrid triple quadrupole mass spectrometers. Additionally, the success of CNL and PI scanning largely depends on structure and CID fragmentation pathways of GSH conjugates. In the present study, a highly efficient methodology has been developed as an alternative approach for high-throughput screening and structural characterization of reactive metabolites using the linear ion trap mass spectrometer. In microsomal incubations, a mixture of glutathione [GSH, gamma-glutamyl-cystein-glycin] and the stable-isotope labeled compound [GSX, gamma-glutamyl-cystein-glycin-(13)C2-(15)N] was used to trap reactive metabolites, resulting in formation of both labeled and unlabeled conjugates at a given isotopic ratio. A mass difference of 3.0 Da between the natural and labeled GSH conjugate (mass tag) at a fixed isotopic ratio constitutes a unique mass pattern that can selectively trigger the data-dependent MS(2) scan of both isotopic partner ions, respectively. In order to eliminate the response bias of GSH adducts in the positive and negative mode, a polarity switch is executed between the mass tag-triggered data dependent MS(2) scan, and thus ESI- and ESI+ MS(2) spectra of both labeled and nonlabeled GSH conjugates are obtained in a single LC-MS run. Unambiguous identification of glutathione adducts was readily achieved with great confidence by MS(2) spectra of both labeled and unlabeled conjugates. Reliability of this method was vigorously validated using several model compounds that are known to form reactive metabolites. This approach is not based on the appearance of a particular product ion such as MH(+) - 129 and anion at m/z 272, whose formation can be structure-dependent and sensitive to the collision energy level; therefore, the present method can be suitable for unbiased screening of any reactive metabolites, regardless of their CID fragmentation pathways. Additionally, this methodology can potentially be applied to triple quadrupole or hybrid triple quadrupole mass spectrometers.     

Stone-Wales Rearrangement as the Double Olefin-Carbene 1,2-CC Bond Shift. Denied Role of Triplet Biradicals

Stone-Wales rearrangement may be considered to consist of two contiguous steps of olefin-carbene 1,2-C-C bond shift. Computational study on this mechanism led to high activation energies comparable to the bond dissociation energies of C-C bonds in fullerenes and their precursors. the possibility of passing through triplet transition state is denied on computational grounds.     

Stone-Wales Rearrangement as the Double Olefin-Carbene 1,2-CC Bond Shift. Denied Role of Triplet Biradicals

Abstract

Stone-Wales rearrangement may be considered to consist of two contiguous steps of olefin-carbene 1,2-C-C bond shift. Computational study on this mechanism led to high activation energies comparable to the bond dissociation energies of C-C bonds in fullerenes and their precursors. the possibility of passing through triplet transition state is denied on computational grounds.     

Re-evaluation of the proton affinity of 18-crown-6 using competitive threshold collision-induced dissociation techniques

The proton affinity (PA) of 18-crown-6 (18C6) is determined using competitive threshold collision-induced dissociation (TCID) techniques. The PA of 18C6 is derived from four thermochemical cycles involving the relative thresholds for production of the protonated bases, H(+)(B), and protonated crown, H(+)(18C6), from the collision-induced dissociation (CID) of four proton bound heterodimers, (B)H(+)(18C6). The bases examined include glycine (Gly), alanine (Ala), imidazole (Imid), and 4-methylimidazole (4MeImid). In all cases, CID pathways for the loss of intact B and 18C6 are observed in competition. Loss of intact 18C6 is observed as the lowest-energy CID pathway for the (Imid)H(+)(18C6) and (4MeImid)H(+)(18C6) complexes. In contrast, loss of intact Gly and Ala is observed as the lowest-energy CID pathway for the (Gly)H(+)(18C6) and (Ala)H(+)(18C6) complexes, respectively. Excellent agreement between the measured and calculated (B)H(+)-18C6 and (18C6)H(+)-B bond dissociation energies (BDEs) is found with M06 theory, whereas B3LYP theory systematically underestimates these BDEs. On the basis of the relative TCID thresholds for the primary and competitive CID pathways, as well as the literature PAs of the bases, the PA of 18C6 is evaluated. The PA determined here for 18C6 exhibits excellent agreement with M06 and B3LYP theories, and very good agreement with the value reported by Meot-Ner determined using high pressure mass spectrometry (HPMS) techniques, suggesting that the PA of 18C6 reported in the NIST Webbook based on HPMS measurements by Kebarle and co-workers is overestimated.     

Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry

We modified and optimized a first generation quadrupole time-of-flight (Q-TOF) 1 to perform tandem mass spectrometry on macromolecular protein complexes. The modified instrument allows isolation and subsequent dissociation of high-mass protein complexes through collisions with argon molecules. The modifications of the Q-TOF 1 include the introduction of (1) a flow-restricting sleeve around the first hexapole ion bridge, (2) a low-frequency ion-selecting quadrupole, (3) a high-pressure hexapole collision cell, (4) high-transmission grids in the multicomponent ion lenses, and (5) a low repetition rate pusher. Using these modifications, we demonstrate the experimental isolation of ions up to 12 800 mass-to-charge units and detection of product ions up to 38 150 Da, enabling the investigation of the gas-phase stability, protein complex topology, and quaternary structure of protein complexes. Some of the data reveal a so-far unprecedented new mechanism in gas-phase dissociation of protein oligomers whereby a tetramer complex dissociates into two dimers. These data add to the current debate whether gas-phase structures of protein complexes do retain some of the structural features of the corresponding species in solution. The presented low-cost modifications on a Q-TOF 1 instrument are of interest to everyone working in the fields of macromolecular mass spectrometry and more generic structural biology.     

Quantum chemical study on 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and some of its constitutional isomers

Presently, certain isomeric compounds of NTO and their tautomers have been investigated by performing density functional theory (DFT) calculations at B3LYP/6-31G(d,p) and ROB3P86/6-311G(d,p) levels and also ab initio calculations at RHF/6-311G(d,p) level. The optimized geometries, vibrational frequencies, electronic structures and some thermodynamical values for the presently considered NTO isomers have been obtained in their ground states. Also, detonation performances were evaluated by the Kammlet-Jacobs equations, based on the calculated densities and heat of formation values. The homolytic bond dissociation energies (BDEs) (at ROB3P86/6-311G(d,p) level) of NNO(2) and CNO(2) for the molecules were calculated. Moreover, aromatic character of NTO and its isomers and tautomers were investigated by performing NICS calculations using the gauge invariant atomic orbital (GIAO) approach at the B3LYP/6-31G(d,p) and B3LYP/cc-pVDZ levels.     

Average Bond Dissociation Energies of Fullerene

Average carbon-carbon bond dissociation energy of buckminsterfullerene C₆₀ is estimated to be 106.87 kcal/mol by using experimentally determined thermochemical data. With a few assumptions this value was converted to the following bond-specific dissociation energies for fullerenes in general: 112.04 kcal/mol for 6/6 type bond, and 104.88 for 5/6 type. Similarly an average value of 60.34 kcal/mol was assigned to 5/5 type bond.     

Ion trap/ion mobility/quadrupole/time-of-flight mass spectrometry for peptide mixture analysis

An ion trap/ion mobility/quadrupole/time-of-flight mass spectrometer has been developed for the analysis of peptide mixtures. In this approach, a mixture of peptides is electrosprayed into the gas phase. The mixture of ions that is created is accumulated in an ion trap and periodically injected into a drift tube where ions separate according to differences in gas-phase ion mobilities. Upon exiting the drift tube, ions enter a quadrupole mass filter where a specific mass-to-charge (m/z) ratio can be selected prior to collisional activation in an octopole collision cell. Parent and fragment ions that exit the collision cell are analyzed using a reflectron geometry time-of-flight mass spectrometer. The overall configuration allows different species to be selected according to their mobilities and m/z ratios prior to collision-induced dissociation and final MS analysis. A key parameter in these studies is the pressure of the target gas in the collision cell. Above a critical pressure, the well-defined mobility separation degrades. The approach is demonstrated by examining a mixture of tryptic digest peptides of ubiquitin.     

Tandem mass spectrometry characteristics of silver-cationized polystyrenes: internal energy, size, and chain end versus backbone substituent effects

The Ag(+) adducts of polystyrene (PS) oligomers with different sizes (6-19 repeat units) and initiating (alpha) or terminating (omega) end groups mainly decompose via free radical chemistry pathways upon collisionally activated dissociation. This reactivity is observed for ions formed by matrix-assisted laser desorption/ionization as well as electrospray ionization. With end groups lacking weak bonds (robust end groups), dissociation starts with random homolytic C-C bond cleavages along the PS chain, which lead to primary and benzylic radical ions containing either of the chain ends. The primary radical ions mainly depolymerize by successive beta C-C bond scissions. For the benzylic radical ions, two major pathways are in competition, namely, depolymerization by successive beta C-C bond scissions and backbiting via 1,5-H rearrangement followed by beta C-C bond scissions. The extent of backbiting decreases with internal energy. With short PS chains, the primary radical ions also undergo backbiting involving 1,4- and 1,6-H rearrangements; however, this process becomes negligible with longer chains. If the polystyrene contains a labile substituent at a chain end, this substituent is eliminated easily and, thus, not contained in the majority of observed fragments. Changes in the PS backbone structure can have a dramatic effect on the resulting dissociation chemistry. This is demonstrated for poly(alpha-methylstyrene), in which backbiting is obstructed due to the lack of benzylic H atoms; instead, this backbone connectivity promotes 1,2-phenyl shifts in the primary radical ions formed after initial C-C bond homolyses as well as H atom transfers between the incipient primary and benzylic radicals emerging from these homolyses.     

Negative-mode MALDI-TOF/TOF-MS of oligosaccharides labeled with 2-aminobenzamide

MALDI-TOF-MS of 2-aminobenzamide-labeled N-glycans was shown to allow the analysis of sodium adducts and proton adducts in the positive-ion mode as well as deprotonated species in the negative-ion mode from a single preparation spot, using N-glycans of adult worms of the human parasite Schistosoma mansoni as model substances. Fragment ion analysis of these species was performed by MALDI-TOF/TOF-MS. With laser-induced dissociation, sodium adducts and proton adducts mainly showed cleavage of glycosidic linkages. High-energy collision-induced dissociation of sodium adducts resulted in extensive cross-ring cleavages and provided information on linkage positions. Of particular value were the negative-mode MALDI-TOF/TOF-MS analyses of the deprotonated N-glycans, which featured (1) various ring fragmentations giving linkage information, (2) extensive (1,3)A cross-ring cleavage of mannoses carrying an antenna readily revealing the composition of the antenna, (3) D as well as [D-18]- ions providing specifically the composition of the 6-antenna, and (4) pronounced stability of fucose linkages resulting in detailed information on fucosylation positions. The outlined approach thus allows the acquisition of both heCID MS/MS spectra of sodium adducts and LID MS/MS spectra of deprotonated species from a 2-aminobenzamide-labeled N-glycan prepared in 6-aza-2-thiothymine, resulting in a wealth of structural information.     

Thermally assisted collision-induced dissociation in a quadrupole ion trap mass spectrometer

Thermally assisted collision-induced dissociation (TA-CID) provides increased dissociation in comparison with CID performed at ambient temperature in a quadrupole ion trap mass spectrometer. Heating the bath/collision gas during CID increases the initial internal energy of the ions and reduces the collisional cooling rate. Thus, using the same CID parameters, the parent ion can be activated to higher levels of internal energy, increasing the efficiency of dissociation and the number of dissociation pathways. The increase in the number of dissociation pathways can provide additional structural information. A consequence of the increase in initial internal energy is the ability to use less power to effect collisional activation. This allows lower q(z) values to be used and, thus, a greater mass range of product ions to be observed. TA-CID alleviates the problems associated with traditional CID and results in more available information than traditional CID.     

Infrared multiphoton dissociation for enhanced de novo sequence interpretation of N-terminal sulfonated peptides in a quadrupole ion trap

Infrared multiphoton dissociation (IRMPD) of N-terminal sulfonated peptides improves de novo sequencing capabilities in a quadrupole ion trap mass spectrometer. Not only does IRMPD promote highly efficient dissociation of the N-terminal sulfonated peptides but also the entire series of y ions down to the y(1) fragment may be detected due to alleviation of the low-mass cutoff problem associated with conventional collisional activated dissociation (CAD) methods in a quadrupole ion trap. Commercial de novo sequencing software was applied for the interpretation of CAD and IRMPD MS/MS spectra collected for seven unmodified peptides and the corresponding N-terminal sulfonated species. In most cases, the additional information obtained by N-terminal sulfonation in combination with IRMPD provided significant improvements in sequence identification. The software sequence tag results were combined with a commercial database searching algorithm to interpret sequence information of a tryptic digest on alpha-casein s1. Energy-variable CAD studies confirmed a 30-40% reduction in the critical energies of the N-terminal sulfonated peptides relative to unmodified peptides. This reduction in dissociation energy facilitates IRMPD in a quadrupole ion trap.     

Identification of anomeric configuration of underivatized reducing glucopyranosyl-glucose disaccharides by tandem mass spectrometry and multivariate analysis

The possibility of discrimination of the anomeric configuration (alpha or beta) of underivatized reducing glucopyranosyl-glucose disaccharides, using a hybrid mass spectrometer Q-TOF 2 (Micromass), a linear ion trap LXQ (Thermo), and a triple quadrupole Quattro (Micromass) with an electrospray source (ESI) was investigated. Differences observed in the relative abundances of specific product ions obtained from collisionally induced dissociation of the [M + Li]+ adducts were statistically analyzed, and discriminant analysis was performed. MANOVA has shown that anomeric configuration has influence on the combined dependent variables (relative abundances of m/z product ions) in all the three mass spectrometers used (Q-TOF 2, LIT, and QqQ). Discriminant analysis has shown that, in all instruments, it is possible to discriminate anomeric configurations and to build a diagnostic model. These diagnostic differences are even more relevant considering that no derivatization procedures are needed for obtaining this structural information. The Q-TOF 2 instrument has been shown to give data that allowed us to build a model with better discriminant power (Wilks' lambda value of 0.014) followed by the QqQ instrument (Wilks' lambda value of 0.029) and the LIT instrument (Wilks' lambda value of 0.037).     

Electrospray ionization and collision induced dissociation mass spectrometry of primary fatty acid amides

Primary fatty acid amides are a group of bioactive lipids that have been linked with a variety of biological processes such as sleep regulation and modulation of monoaminergic systems. As novel forms of these molecules continue to be discovered, more emphasis will be placed on selective, trace detection. Currently, there is no published experimental determination of collision induced dissociation of PFAMs. A select group of PFAM standards, 12 to 22 length carbon chains, were directly infused into an electrospray ionization source Quadrupole Time of Flight Mass Spectrometer. All standards were monitored in positive mode using the [M + H](+) peak. Mass Hunter Qualitative Analysis software was used to calculate empirical formulas of the product ions. All PFAMs showed losses of 14 m/z indicative of an acyl chain, while the monounsaturated group displayed neutral losses corresponding to H(2)O and NH(3). The resulting spectra were used to propose fragmentation mechanisms. Isotopically labeled PFAMs were used to validate the proposed mechanisms. Patterns of saturated versus unsaturated standards were distinctive, allowing for simple differentiation. This determination will allow for fast, qualitative identification of PFAMs. Additionally, it will provide a method development tool for selection of unique product ions when analyzed in multiple reaction monitoring mode.     

Tandem time-of-flight mass spectrometry with a curved field reflectron

The unique focusing properties of the curved-field reflectron provide a simple solution to the problem of compensating for the broad range of energies of product ions produced postsource in a time-of-flight mass spectrometer. This has been shown previously for the technique known as postsource decay, but in this report we demonstrate its use for tandem time-of-flight mass spectrometry using a high-performance MALDI time-of-flight instrument modified by the addition of a collision chamber to enable the recording of mass-selected product ions formed by collision-induced dissociation (CID). In particular, the curved-field reflectron enables the use of the full 20-keV kinetic energy provided by the ion source extraction voltage as the collision energy in the laboratory frame and obviates the need to reaccelerate the product ions, using a second "source" or "lift" cell. Results are presented for the collision-induced dissociation of fullerenes over a range of collision gas pressures and precursor ion attenuation. In addition, CID tandem mass spectra are obtained for several peptides.     

CL-20二氟氨基衍生物结构与性能的DFT研究

设计了CL-20的—NF_2衍生物,应用密度泛函理论(DFT)B3LYP/6-31G**方法进行了理论研究。设计等键反应,计算了气态生成焓,进而预测了固态生成焓;应用Politzer校正方法计算了晶体密度(ρ);由K-J方程估算爆热(Q)、爆速(D)和爆压(p),讨论了取代基对生成焓(HOF)、ρ、Q、D和p的影响;由键解离能(BDE)和落锤高度(h50)评价感度,并探讨了可能的热解引发机理。综合考虑爆轰性能与稳定性两方面因素,大多数CL-20的—NF_2衍生物为潜在的高能量密度材料,值得进一步研究。     

Surface-induced dissociation of protonated peptides: implications of initial kinetic energy spread.

Surface-induced dissociation (SID) has been used to produce daughter ion spectra of small protonated peptides generated by fast atom bombardment (FAB). The relative abundances of daughter ions depends critically upon the energy of the ion/surface collision. A wide array of decomposition processes may be observed using ELAB collision energies in the range 10-20 eV. At approximately 13-eV collision energy, the variety of decomposition processes is maximized for the small peptides studied; hence, maximum structural information may be deduced. Collisionally-activated dissociations (CAD) using argon gas and the identical protonated peptides could not produce as large an array of daughter ions in a constant condition experiment. An apparent contradiction is thereby posed because SID is known to produce a narrow distribution of ion internal energies relative to CAD. This apparent contradiction is resolved by considering the rather large kinetic energy spread of ions leaving the FAB source. For the SID process, this large initial kinetic energy distribution is converted into a significantly wider spread in center-of-mass collision energy, leading to a broader variety of decomposition processes (high and low energy) compared to CAD.