Vacuum-ultraviolet photoionization and mass spectrometric characterization of lignin monomers coniferyl and sinapyl alcohols

The fragmentation mechanisms of monolignols under various energetic processes are studied with jet-cooled thermal desorption molecular beam (TDMB) mass spectrometry (MS), 25 keV Bi(3)(+) secondary ion MS (SIMS), synchrotron vacuum-ultraviolet secondary neutral MS (VUV-SNMS) and theoretical methods. Experimental and calculated appearance energies of fragments observed in TDMB MS indicate that the coniferyl alcohol photoionization mass spectra contain the molecular parent and several dissociative photoionization products. Similar results obtained for sinapyl alcohol are also discussed briefly. Ionization energies of 7.60 eV ± 0.05 eV for coniferyl alcohol and <7.4 eV for both sinapyl and dihydrosinapyl alcohols are determined. The positive ion SIMS spectrum of coniferyl alcohol shares few characteristic peaks (m/z = 137 and 151) with the TDMB mass spectra, shows extensive fragmentation, and does not exhibit clear molecular parent signals. VUV-SNMS spectra, on the other hand, are dominated by the parent ion and main fragments also present in the TDMB spectra. Molecular fragmentation in VUV-SNMS spectra can be reduced by increasing the extraction delay time. Some features resembling the SIMS spectra are also observed in the desorbed neutral products. The monolignol VUV-SNMS peaks shared with the TDMB mass spectra suggest that dissociative photoionization of ion-sputtered neutral molecules predominate in the VUV-SNMS mass spectra, despite the extra internal energy imparted in the initial ion impact. The potential applications of these results to imaging MS of biomolecules are discussed.     

Emission of secondary ions from osmium under oxygen and the nitrogen oxides N2O, NO and NO2

Summary Small briquettes compressed of high-purity Os powder were bombarded by primary Ar⁺ ions for moderate dynamic SIMS conditions. Secondary ion mass spectra were observed for positive ions which were produced under residual gas and under O₂, N₂O, NO, NO₂. For the different reactant gases these spectra were found rather similar, indicating that the nitrogen oxides mainly act as sources of reactive oxygen. But also some individual secondary ions containing nitrogen or NO are emitted from the target surface which, at least in the case of N₂O and NO₂, give some evidence of partial adsorptive fragmentation of the respective reactant gas molecules.     

Fragmentation dynamics of methane by few-cycle femtosecond laser pulses

The fragmentation pattern of CH4 was experimentally studied at an intensity of approximately 10(14) W/cm2 with laser durations varying from 8 to 110 fs. When the laser duration was 8 fs, only the primarily fragmental CH3+ ion was observed in addition to the parent CH4+ ion. When the laser duration was 30 fs, small fragmental CH2+ and H+ ions appeared. When the laser duration was 110 fs, some doubly charged ions were also observed in addition to the abundant singly charged ions. The large mass spectra difference demonstrated that the pulse duration had a strong effect on the fragmentation of the parent ion produced in the single ionization. The effect of laser intensity on the fragmentation of CH4+ was also studied for few-cycle femtosecond laser pulses. The results demonstrated that the first-return recollision between the rescattered electron and the parent ion played a significant role in the fragmentation dynamics of the parent ion. Depending on the ion-electron impact energy, the recollision excited the parent ion to a dissociated state or doubly charged state. The experimentally observed singly charged fragmental ions resulted from the recollision-induced dissociation of CH4+ or the Coulomb explosion of CH(4)2+.     

Time of flight secondary ion mass spectrometric determination of molecular weight distributions of low polydispersity poly(dimethyl siloxane) with polyatomic primary ions

This work reports a comparison of oligomer and fragment ion intensities resulting from primary ion bombardment with several primary ion sources (Bi_n⁺, C₆₀⁺, and Cs⁺) at various energies in secondary ion mass spectrometry (SIMS). Although the use of polyatomic primary ions are of great interest due to increased secondary ion efficiency and yield, we demonstrate that monatomic primary ions result in increased oligomer ion yield for polymers prepared as submonolayer films on silver substrates. The enhancement of oligomer secondary ion yield with monatomic ions is evidence that monatomic primary ions have a shallower sampling depth than polyatomic ions, resulting from a collision cascade that is less energetic at the sample surface. The results are also consistent with a lower degree of fragmentation of the resultant secondary ions, which is observed when evaluating the fragmentation data and the spectral data.     

Collision induced decomposition of peptides. Choice of collision parameters

Collision-induced dissociation product ion spectra of a series of doubly charged tryptic peptide ions produced by electrospray ionization were obtained by triple-quadrupole tandem mass spectrometry. The sequence information content of the product ion spectra was explored as a function of collision energy and collision-cell gas pressure for parent ions with molecular masses ranging from 300 to 2000 u. The energy range (at a given pressure) in which the degree of fragmentation is acceptable was found to be narrow for parent ions of a given mass, and the optimal collision energy was observed to exhibit a strong linear correlation with parent ion mass. This observed correlation opens the way for on-line software-controled selection of optimal mass spectrometric conditions in the enzymatic digestion-liquid chromatography-tandem mass spectrometric strategy of amino acid sequencing of proteins.     

Soft-landing of peptides onto self-assembled monolayer surfaces

Mass-selected peptide ions produced by electrospray ionization were deposited as ions by soft-landing (SL) onto fluorinated and hydrogenated self-assembled monolayer (FSAM and HSAM) surfaces using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially designed for studying collisions of large ions with surfaces. Analysis of modified surfaces was performed in situ by combining 2 keV Cs(+) secondary ion mass spectrometry with FT-ICR detection of the sputtered ions (FT-ICR-SIMS). Similar SIMS spectra obtained following SL at different collision energies indicate that peptide fragmentation occurred in the analysis step (SIMS) rather than during ion deposition. The effect of the surface on SL was studied by comparing the efficiencies of SL on gold, FSAM, HSAM, and COOH-terminated SAM surfaces. It was found that FSAM surfaces are more efficient in retaining ions than their HSAM analogues, consistent with their larger polarizability. The efficiency of soft-landing of different peptides on the FSAM surface increases with the charge state of the ion, also consistent with an ion-polarizable molecule model for the initial stage of soft-landing on SAM surfaces. The gradual decrease of peptide ion deposition efficiency with an increase in collision energy found experimentally was quantitatively rationalized using the hard-cube model.     

Differences between the internal energy depositions induced by collisional activation and by electron transfer of W(CO)6(2+) ions on collision with Ar and K targets

Doubly charged tungsten hexacarbonyl W(CO)(6) (2+) ions were made to collide with Ar and K targets to give singly and doubly charged positive ions by collision-induced dissociation (CID). The resulting ions were analyzed and detected by using a spherical electrostatic analyzer. Whereas the doubly charged fragment ions resulting from collisional activation (CA) were dominant with the Ar target, singly charged fragment ions resulting from electron transfer were dominant with the K target. The internal energy deposition in collisionally activated dissociation (CAD) evaluated with the Ar target was broad and decreased with increasing internal energy. The predominant peaks observed with the K target were associated with singly charged W(CO)(2) (+) and W(CO)(3) (+) ions: these ions were not the result of CA, but arose from dissociation induced by electron transfer (DIET). The internal energy deposition resulting from the electron transfer was very narrow and centered at a particular energy, 7.8 eV below the energy level of the W(CO)(6) (2+) ion. This narrow internal energy distribution was explained in terms of electron transfer by Landau-Zener potential crossing at a separation of 5.9 x 10(-8) cm between a W(CO)(6) (2+) ion and a K atom, and the coulombic repulsion between singly charged ions in the exit channel. A large cross section of 1.1 x 10(-14) cm(2) was estimated for electron capture of the doubly charged W(CO)(6) (2+) ion from the alkali metal target, whose ionization energy is very low. The term "collision-induced dissociation," taken literally, includes all dissociation processes induced by collision, and therefore encompasses both CAD and DIET processes in the present work. Although the terms CID and CAD have been defined similarly, we would like to propose that they should not be used interchangeably, on the basis that there are differences in the observed ions and in their intensities with Ar and K targets.     

Determination of linkages of linear and branched oligosaccharides using closed-ring chromophore labeling and negative ion trap mass spectrometry

Linear as well as branched oligosaccharides were labeled with p-aminobenzoic ethyl ester (ABEE) using the glycosylamine closed-ring labeling approach and analyzed by negative-ion electrospray ionization mass spectrometry (ESI-MS). Linkage specific fragment ions of ABEE labeled linear oligosaccharides were proposed based on the MS2 and MS3 data for several ABEE labeled linear oligosaccharides with known linkage configurations. Fragmentation at the reducing end was similar to that observed for ABEE disaccharides whereas the fragmentation pattern not involving the reducing end was similar to underivatized disaccharides. Based on these ions, all the linkages of linear oligosaccharides could be unambiguously determined. The fragmentation pattern at the branched sugar was in general not quite the same as the linear one. However, many linkage specific fragment ions were also observed for linkages at the branched sugar. These ions along with the ions proposed for linear oligosaccharides were found to be quite useful for the determination of all the linkages of branched oligosaccharides.     

Fragmentation of oligoribonucleotides from gas-phase ion-electron reactions

We have recently demonstrated that both electron capture dissociation (ECD) and electron detachment dissociation (EDD) can provide complementary sequence-specific cleavage of DNA compared with collision activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD). However, EDD is preferred because of more extensive fragmentation at higher sensitivity (due to its negative ion mode operation). Here, we extend the radical ion chemistry of these two gas-phase ion-electron reaction techniques to the characterization of RNA. Compared with DNA, rather limited information is currently available on the gas-phase fragmentation of RNA. We found that the ECD fragmentation patterns of the oligoribonucleotides A6, C6, and CGGGGC are nucleobase dependent, suggesting that cleavage proceeds following electron capture at the nucleobases. Only limited backbone cleavage was observed in ECD. EDD, on the other hand, provided complete sequence coverage for the RNAs A6, C6, G6, U6, CGGGGC, and GCAUAC. The EDD fragmentation patterns were different from those observed with CAD and IRMPD in that the dominant product ions correspond to d- and w-type ions rather than c- and y-type ions. The minimum differences between oligoribonucleotides suggest that EDD proceeds following direct electron detachment from the phosphate backbone.     

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

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.     

Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and <Emphasis Type="Italic">tert</Emphasis>-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer

Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes.     

Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions

Oxidation of cysteine residues to cysteic acids in C-terminal arginine-eontaining peptides (such as those derived by tryptic digestion of proteins) strongly promotes the formation of multiple members of the Y? series of fragment ions following low energy collision-activated decomposition (CAD) of the protonated peptides, Removal of the arginine residue abolishes the effect, which is also attenuated by conversion of the arginine to dimethylpyrim-idylornithine. The data indicate the importance of an intraionic interaction between the cysteic acid and arginine side-chains. Low energy CAD of peptides which include cysteic acid and histidine residues, also provides evidence for intraionic interactions. It is proposed that these findings are consistent with the general hypothesis that an increased heterogeneity (with respect to location of charge) of the protonated peptide precursor ion population is beneficial to the generation of a high yield of product ions via several charge-directed, low energy fragmentation pathways. Furthermore, these data emphasize the significance of gas-phase conformations of protonated peptides in determining fragmentation pathways.     

Electron Induced Dissociation of Singly Deprotonated Peptides

Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion–electron and ion–ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.     

Investigation of ionic liquids under Bi‐ion and Bi‐cluster ions bombardment by ToF‐SIMS

A systematic study of five different imidazolium‐based room temperature ionic liquids, 1‐butyl‐3‐methylimidazolium acetate, 1‐butyl‐3‐methylimidazolium nitrate, 1‐butyl‐3‐methylimidazolium iodide, 1‐butyl‐3‐methylimidazolium hexafluorophosphate and 1‐butyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide were carried out by means of time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) in positive and negative ion mode. The compounds were measured under Bi‐ion and Bi‐cluster ions (Bi_2–7⁺, Bi_{3, 5}²⁺) bombardment, and spectral information and general rules for the fragmentation pattern are presented. Evidence for hydrogen bonding, due to high molecular secondary cluster ions, could be found. Hydrogen bonding strength could be estimated by ToF‐SIMS via correlation of the anionic yield enhancement with solvent parameters. Copyright © 2010 John Wiley & Sons, Ltd.     

Comparative studies of SIMS and SNMS analyses during the build up of sputter equilibrium under oxygen and rare gas ion bombardment

Sputtering of solid surfaces by using a focused ion beam is the basis for secondary ion mass spectrometry (SIMS) and sputtered neutral mass spectrometry (SNMS). The ion bombardment initiates not only redistribution of sample atoms but also massive changes in the surface and near surface composition of the bombarded area due to the sputter process and implantation of the primary ions. Changes in the matrix-composition affects the secondary ion yields and therefore a steady state (sputter equilibrium) has to be reached before SIMS data can give quantifiable results. SNMS is much less affected by those yield effects and therefore a combination of SIMS and SNMS can establish a basis for interpretation of SIMS data before the steady state is reached. In order to determine the effects of primary ion incorporation, we applied different primary ion species successively to generate different equilibria. An oxygen ion beam oxidizes the sample surface and by using a rare gas primary ion (PI) this oxide can be removed and analyzed.     

Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS3 of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.     

Charge inversion mass spectrometry: dissociation of resonantly neutralized molecules

Charge inversion mass spectrometry is an MS/MS method in which the electric charge of the precursor ions is opposite to that of the secondary product ions. Charge inversion mass spectrometry is classified into four types depending on the electric charge and time scale of collisions. Charge inversion mass spectrometry using collisions with gaseous targets in the keV energy collision range has provided insights into the structures and reactions of ions and neutral molecules. The characteristics of charge inversion experiments are presented in terms of the reaction endothermicities and the cross sections and their dependence on the target species. In the case of rare-gas or simple molecular targets, double-electron transfer in one collision is effective to form positive ions from negative ions, while, in the case of alkali metal targets, successive single-electron transfers in two collisions is effective to form negative ions from positive ions. On the basis of the observed target-density dependence of the product ion intensity and thermochemical considerations for internal energy distribution using thermometer molecules, the charge inversion processes using alkali metal targets have been confirmed to occur by electron transfers in successive collisions and the dissociation processes are found to occur in energy-selected neutral species formed from near-resonant neutralization with alkali metal targets. While collisionally activated dissociation (CAD) is due to dissociation of activated ions with broad internal energy distributions, the charge inversion process using alkali metal targets is due to dissociation of energy-selected neutral species with narrow internal energy distributions. The charge inversion/alkali metal spectra provide clear differentiation of the isomeric cations of C(2)H(2), C(3)H(4) and dichlorobenzenes. The CAD spectra of these isomeric cations are similar.     

Structural studies on ceramides as lithiated adducts by low energy collisional-activated dissociation tandem mass spectrometry with electrospray ionization

We applied electrospray ionization (ESI) tandem quadrupole mass spectrometry to establish the fragmentation pathways of ceramides under low energy collisional-activated dissociation (CAD) by studying more than thirty compounds in nine subclasses. The product-ion spectra of the [M + Li]+ ions of ceramides contain abundant fragment ions that identify the fatty acyl substituent and the long-chain base (LCB) of the molecules, and thus, the structure of ceramides can be easily determined. Fragment ions specific to each ceramide subclasses are also observed. These feature ions permit differentiation among different ceramide subclasses. The ion series arising from the classical C-C bond cleavages that were reported in the fast-atom bombardment (FAB)-high energy tandem mass spectrometry is not observable; however, the product-ion spectra contain multiple fragment ions informative for structural characterization and isomer identification. We also investigated the tandem mass spectra of the fragment ions generated by in-source CAD (pseudo-MS3) and of the deuterium-labeling molecular species obtained by H/D exchange to support the ion structure assignments and the proposed fragmentation pathways that lead to the ion formation.     

Studies on sulfatides by quadrupole ion-trap mass spectrometry with electrospray ionization: Structural characterization and the fragmentation processes that include an unusual internal galactose residue loss and the classical charge-remote fragmentation

The structural characterization of sulfatides by collisional-activated dissociation (CAD) quadrupole ion-trap tandem mass spectrometric methods with electrospray ionization is described. When subjected to CAD in the negative-ion mode, the [M - H]- ions of sulfatides yield abundant structurally informative ions that permit unequivocal assignments of the long-chain base, and fatty acid constituent including the location of double bond. The identification of the position of the double bond on the fatty acyl substituent is based on the observation of the series of the ions arising from classical charge-remote fragmentation processes similar to those observed by high-energy CAD and by tandem quadrupole mass spectrometry. An unusual internal galactose residue loss due to a rearrangement process was also observed. The [M - H]- ions of sulfatides also dissociates to a ceramide anion, which undergoes consecutive fragmentation processes to yield ions informative for identification of the ceramide moiety and permits distinction the sulfatide with a sphingosine subclass from that with a sphinganine long-chain base subclass. The MS(2)-spectra of the sulfatide subclass with a sphingosine LCB and a alpha-hydroxy fatty acyl substituent (d18:1/hFA-sulfatide) are featured by the prominent ion sets of m/z 568, 550, 540, and 522, originated from a primary cleavage of the fatty acyl CO-CH(OH) bond, and are readily differentiable from those arising from the non-hydroxy sulfatide subclass (d18:1/nFA-sulfatide), in which the ion sets are of low abundance. The fragmentation pathways of sulfatides under low-energy CAD are proposed. The pathways are supported by the MS(2)- and MS(3)-spectra of various compounds, and of their H-D exchanged analogs.     

Static secondary ion mass spectrometry of organic plasma-deposited films created from stable isotope-labeled precursors. II. Mixtures of acetone and oxygen

A series of plasma-deposited films (PDFs), created by blending controlled ratios of acetone vapor and oxygen in the feed to the plasma reactor, were analyzed by static secondary ion mass spectrometry (SIMS). Examination of the quadrupole-based static SIMS fragmentation patterns of acetone–O₂ PDFs created from ¹³C-labeled acetone generally allowed the hydrocarbon secondary ions to be distinguished from oxygen-containing secondary ions. These results were compared with those obtained via high-mass resolution time-of-flight (TOF)-SIMS. The identified secondary ions were then assigned structural attributes, based on comparison of the static SIMS spectra of the acetone–O₂ PDFs with those of conventional hydrocarbon and oxygen-containing polymers. A preliminary investigation to unravel the mechanism of oxygen incorporation in the acetone–O₂ PDFs from the two plasma feed components was undertaken through the analysis of PDFs created from 1,2,3¹³C₃-acetone(¹⁶O) vapor and ¹⁸O₂ gas.