Mass Spectrum Pattern Research Articles

Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra

A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.

Quantum Chemical Studies of Neutral and Ionized DyX, DyX2, and DyX3 Species (X = F, Cl, Br, I) and the Implications for the Mass Spectra of Gaseous DyX3

AbstractThe mass spectrum pattern of DyF3(g) and the appearance potentials for identified ions were measured and compared with the respective data obtained previously for DyCl3, DyBr3, and DyI3. The structural parameters, total energies, and vibrational frequencies of DyX3, DyX2, and DyX (X = F, Cl, Br, I) neutral and single ionized species were determined by quantum‐chemical studies. The theoretical appearance potentials of different ions, calculated from energies of gaseous species, are in the good agreement with the experimental data. Fragmentation energies of the DyXn+ ion, where n = 1, 2, 3, were computed and compared with the mass spectra patterns of the respective vapour species. A theoretical electron population analysis indicates the involvement of the s and f valence electrons of Dy in the bond formation as well as in the ionization processes. The σ‐back donation from halogen atoms to the dysprosium center partially compensates the electron density loss. The ionization strengthens the bonding in the DyX and DyX2 molecules. The ionization of DyX3 destroys the C3v symmetrical structure due to the Jahn−Teller effect. Contrary to the other studied systems, the open shell character of DyX3+ arises not only from unpaired electrons of dysprosium but also from electron density on halogen atoms. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Comparison of Surface Organic Compound Mass Spectrum Patterns by LD-TOFMS for Megalopolis Atmospheric Particles and Diesel Exhaust Particles (DEP)

PM2.5 and PM10 samples for megalopolis atmospheric particles were collected at Shinjuku, Tokyo in December 1998–January 1999 and August 1999, for two weeks both in winter and summer, with a 24 hr sampling interval. Sampling of PM2.5 and PM10 in diesel exhaust particles (DEP) was carried out using an automobile exhaust testing system, with a diesel truck placed on a chassis dynamometer. Sampling conditions included idling, constant speed of 40 km hr-1, M-15 test pattern and 60%-revolution/40%-load of maximum power. Mass spectrums of organic compounds adhering to the surface of the PM2.5 and PM10 samples were analyzed by laser desorption time-of-flight mass spectrometry (LD-TOFMS, analytical mass range: m/z 1–m/z 380 000). LD-TOFMS analysis of those samples revealed consistently the detection of low-mass organic compounds up to m/z 800. For the megalopolis atmospheric particles, the mass spectrum pattern of wintertime samples was almost the same as that of the summertime samples for both PM2.5 and PM10. The major peak was m/z 177, and the minor peaks were m/z 84, 94, 101, 163, 189 and 235. The mass spectrum pattern of DEP was the same for all samples under all test conditions. The major peak was m/z 101, and other detected peaks were small.

Surface-induced reactions anddissociations of small acetone, acetonitrile and ethanolcluster ions: competitive chemical reactions, dissociationmechanisms and determination of dissociation energy

Using a recently commissioned tandem mass spectrometer system,BESTOF, we have carried out systematic investigations (usingalso deuterated molecules) on the interaction of variousmolecular cluster ions (including stoichiometric acetone andacetonitrile cluster ions and protonated ethanol cluster ions) with a hydrocarbon-covered stainless steel surface. Besidesobserving competitive chemical reactions for the stoichiometriccluster ions driven by the energy transfer in the surfacecollision (intra-cluster reactions versus surfaceH-atom pick-up reactions), we were able to see clearevidence that unimolecular dissociation kinetics determines theproduction of the observed decay patterns in collision energy-resolved mass spectra (CERMS). From characteristic shifts inthese CERMS we can deduce corresponding binding energies, i.e.,{D}((CD3CN)2+ - CD3CN) = 0.66 eV, {D}((C2H5OH)2H+ - C2H5OH) = 0.95 eV, and forthe protonated dimer {D}((C2H5OH)H+ - C2H5OH) = 1.6 eV. Thefirst value is in good agreement with values currently calculated using the B3LYP (Becke-Lee-Yang-Parr) density functional and the 6-311G(d, p) basisset, the latter values are in good agreement with valuesderived earlier from thermochemical data. Moreover, in the case of the protonated ethanol cluster ion, itis possible to arrive at a single (universal) breakdown graphfor the trimer composed of data derived from monomer, dimer andtrimer CERMS. This can be achieved by renormalizing the energyscale in the CERMS for themonomer, dimer and trimer ions (taking into account the conversion from translational to internal energy and assumingthat the clusters behave like a statistical ensemble with thecorresponding degrees of freedom).

Multi-charged Oligonucleotide Ion Formation in Sonic Spray Ionization

An oligonucleotide tends to release hydrogen atoms from a phosphoric acid group and to form negative ions that can be detected by mass spectrometry. Usually, with a solution-spray based ionization technique, the negative ions are present in different charge states. Ion formation for the nucleotide is quite complicated and is easily influenced by matrix and other constituents in a sample solution, as well as by the operating parameters for a mass spectrometer. In this work, we studied oligonucleotide ion formation by using an ion trap mass spectrometer combined with a sonic spray ionization (SSI) source. An oligonucleotide with 20 bases was measured. Effects from contaminants and parameters affecting the ion production, such as a high voltage applied to the ionization source and sample solution-flow rate, were investigated. Our results showed that an ion with about one charge for every three bases was most abundant. However, the signal intensity and the mass spectrum pattern were sensitive to the matrix and operating parameters. One of the reasons for such sensitivity is that there are various ion states for an oligonucleotide. Any change in the matrix or an operating parameter may shift the balances between the ion states. Adding Tris, or (hydroxymethyl)aminomethane, enhanced the signal intensity of the oligonucleotide and promoted formation of the oligonucleotide ion with higher charges, while adding acetic acid favored the ions with lower charges, compared with that obtained in the medium without adding Tris and acetic acid. The effects on charged droplets and chemical enhancement were investigated. The mechanism for oligonucleotide ion formation is discussed.

Using stable-isotope-labeled proteins for hydrogen exchange studies in complex mixtures.

The use of mass spectrometry to measure hydrogen exchange rates for individual proteins in complex mixtures is described. Incorporation of stable-isotope-labeled (SIL) amino acids into a protein of interest during overexpression in bacteria produced distinctive isotope patterns in mass spectra of peptic peptides from the labeled protein. The isotope pattern was used as a signature for peptides originating from the SIL protein. In addition, stable-isotope labeling simplified identification of the peptic peptides by providing partial amino acid composition information. Despite the complex isotope patterns associated with SIL peptides, hydrogen exchange rates could still be measured for peptides from SIL protein and were found to be the same as exchange rates for unlabeled protein. Hydrogen exchange in a single protein of interest was measured in a complex mixture of proteins, a bacterial cell lysate. This methodology, which includes easy recognition of peptic peptides from the protein(s) of interest during hydrogen exchange studies in heterogeneous systems, will permit analysis of structural properties and dynamics of large protein complexes and complex protein systems.

Supersymmetry and finite radiative electroweak breaking from an extra dimension

A five dimensional N=1 supersymmetric theory compactified on the orbifold $S^1/\mathbb{Z}_2$ is constructed. Gauge fields and $SU(2)_L$ singlets propagate in the bulk ($U$-states) while $SU(2)_L$ doublets are localized at an orbifold fixed point brane ($T$-states). Zero bulk modes and localized states constitute the MSSM and massive modes are arranged into N=2 supermultiplets. Superpotential interactions on the brane are of the type $UTT$. Supersymmetry is broken in the bulk by a Scherk-Schwarz mechanism using the $U(1)_R$ global $R$-symmetry. A radiative finite electroweak breaking is triggered by the top-quark/squark multiplet $\mathbb{T}$ propagating in the bulk. The compactification radius $R$ is fixed by the minimization conditions and constrained to be $1/R \simlt 10-15$ TeV. It is also constrained by precision electroweak measurements to be $1/R \simgt 4$ TeV. The pattern of supersymmetric mass spectrum is well defined. In particular, the lightest supersymmetric particle is the sneutrino and the next to lightest supersymmetric particle the charged slepton, with a squared-mass difference $\sim M_Z^2$. The theory couplings, gauge and Yukawa, remain perturbative up to scales $E$ given, at one-loop, by $ER \simlt 30-40$. Finally, LEP searches on the MSSM Higgs sector imply an absolute lower bound on the SM-like Higgs mass, around 145 GeV in the one-loop approximation.

Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds

Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds

Fragmentation patterns in the electron impact mass spectra of 1,3,5-triazin-2-one derivatives

Fragmentation patterns in the electron impact (EI) mass spectra of a series of 5-substituted 1,3,5- triazin-2-ones, prepared from the reaction of dimethylolurea with selected primary amines, have been elucidated using a combination of high-resolution, comparative low-resolution and metastable peak analysis. In addition to characteristic fragmentations, in which the triazine nucleus remains intact, the 5-substituted 1,3,5-triazin-2-ones appear to exhibit a series of extrusion/ring-contraction processes, resulting in the formation of 3- and 4-membered ring fragments. Resonance-stabilised even-electron ions, arising, in each case, from loss of a hydrogen atom from the molecular ion, are considered pivotal in the formation of these heterocyclic fragments.

Usefulness of MALDUTOF mass spectrometry of immunoprecipitated serum variant transthyretin in the diagnosis of familial amyloid polyneuropathy

A matrix-assisted laser desorption ionization/time-of flight (MALDI/TOF) mass spectrometry (MS) system was used io detect variant transthyretin (TTR) in immunoprecipitated serum TTR molecules obtained from 6 patients with familial amyloid polyneuropathy (FAP) who were already proven not to have ATTR Val 30Met. This simple and quick method showed six different patterns of mass spectra of TTR-related immunoprecipitates from these patients, and in each patient the clearly identified characteristic doublet-shaped ion peaks consisted of normal and variant TTR apart from each other peak with a mass difference between them. DNA sequencing confirmed that the patterns of variant TTR corresponded respectively to ATTR Val30Leu, ATTR Phe33Val, ATTR Asp38Ala, ATTR Ser50Arg, ATTR Ala97Gly and ATTR Ala97Ser. ATTR Asp38Ala and ATTR Ala97Ser are previously unknown variants of TTR leading to the development of FAP. ATTR Phe33Val was found in a Chinese FAP patient and ATTR Ala97Ser in a Taiwanese. Serum analysis using immunoprecipitation and MALDI/TOF MS system can provide useful information when investigating FAP patients with diverse types of variant TTR.

Excited baryon phenomenology from large-NcQCD

We present a phenomenological analysis of the strong couplings of the negative-parity $L=1$ baryons from the perspective of the large-${N}_{c}$ expansion. In the large-${N}_{c}$ limit the mass spectrum and mixing pattern of these states are constrained in a very specific way. The mixing angles are completely determined in this limit, with predictions in good agreement with experiment. In the combined large-${N}_{c}$ and SU(3) limits the pion couplings of the five negative-parity octets to the ground state baryons are given in terms of only 3 independent couplings. The large-${N}_{c}$ predictions for the ratios of strong couplings are tested against experimental data.

Quasi Yukawa fixed point due to decoupling of SUSY particles

We study effects of SUSY particle decouplings on a quasi fixed point (QFP) of Yukawa coupling. From renormalization group analysis it is shown that if the SUSY breaking scale M s is large (≳ 1 TeV), effects of decoupling of Higgsinos and squarks raise the top Yukawa QFP. This tendency is enhanced in most cases of non-universal SUSY breaking. For the case of M s ≲ 1 TeV, the decoupling of gluinos lowers m t QFP. We checked some parameter dependencies for the top Yukawa QFP. The bottom-top Yukawa unified case is also studied. When top quark mass is measured more precisely, some patterns of soft mass spectra could be excluded if a rather large initial top Yukawa coupling is realized by the underlying theory.

Fast Atom Bombardment Mass Spectrometry:Ionization Mechanism.

Some ideas have been presented to understand ion formation under matrix fast atom bombardment (FAB) conditions. A state of hydrogen-bonding hydrophilic solvation, named “quasi-preformed state”, has been introduced to explain the ion formation reflecting condensed-phase, and the both “quasi-preformed state” and a state of “preformed ion” have been defined on the basis of the Bjerrum's proposition for ion-pairs in solution. Some examples of preformed ion have been described. The extents of electronic excitation leading to the formation of molecular ions M+·, under matrix FAB conditions, have been examined by detecting FAB-induced fluorescence from a thin layer of alkali-halides (LiCl, NaCl, KCl, and CsCl), and by using some compounds of which ionization energies are known. The results obtained indicate that matrix FAB conditions are sufficient in energy for M+· formation (by about 10 eV electronic excitation) and are insufficient for M2+ formation (by about 20 eV electronic excitation). The mechanisms of the formation of various ions, [M+H]+, [M+Na]+, [M-H]+, M+·, M-·, and [M-H]-, under matrix FAB conditions have been described. A model for FAB ionization, named “cavity” model, has been introduced to deal quantitatively with the rate of ion formation or ion yields from matrix surface. The “cavity” model requires that the ion formation occurs in both processes, i) the collision cascade reflecting condensed-phase and ii) the ion/molecule reactions reflecting gas-phase. The influence of fast atom species (He, Ar, and Xe) on the ion yields which may directly relate to the size of cavity or crater has been examined by comparing with the spectral patterns in the gas-phase FAB mass spectra of m-nitrobenzyl alcohol. It has been roughly estimated that a “cavity” formed with Ar or Xe beam contains several 100 molecules.

Oxidation of Dimethylselenide by .delta.-MnO2: Oxidation Product and Factors Affecting Oxidation Rate

Volatile dimethylselenide (DMSe) was transformed to a nonvolatile Se compound in a δ-Mn0 2 suspension. The nonvolatile product was a single compound identified as dimethylselenoxide based on its mass spectra pattern. After 24 h, 100% of the DMSe added to a δ-MnO 2 suspension was converted to nonpurgable Se as opposed to 20%, 18%, and 4% conversion for chromate, permanganate, and the filtrate from the suspension, respectively. Manganese was found in solution after reaction. These results imply that the reaction between manganese oxide and DMSe was a heterogeneous redox reaction involving solid phase δ-MnD 2 and solution phase DMSe. Oxidation of DMSe to dimethylselenoxide [OSe(CH 3 ) 2 ] by a δ-MnO 2 suspension appears to be first order with respect to δ-MnO 2 , to DMSe, and to hydrogen ion with an overall rate law of d[OSe(CH 3 ) 2 ]/dt = 95 M -2 min -1 [MnO 2 ] 1 [DMSe] 1 [H + ] 1 for the MnD 2 concentration range of 0.89 x 10 -3 - 2.46 x 10 -3 M, the DMSe concentration range of 3.9 x 10 -7 - 15.5 x 10 -7 M Se, and a hydrogen ion concentation range of 7.4 x 10 -6 - 9.5 x 10 -8 M. A general surface site adsorption model is consistent with this rate equation if the uncharged OMnOH is the surface adsorption site. DMSe acts as a Lewis base, and the manganese oxide surface acts as a Lewis acid. DMSe adsorption to OMnOH can be viewed as a Lewis acid/base complex between the largely p orbitals of the DMSe lone pair and the unoccupied e g orbitals on manganese oxide. For such a complex, frontier molecular orbital theory predicts electron transfer to occur via an inner-sphere complex between the DMSe and the manganese oxide.

Wear and Degradation Characteristics of Perfluoroalkylpolyethers (PFPEs) in High Vacuum©

Wear and degradation as exhibited by degassing of three commercially available perfluoroalkylpolyethers, A, straight chain with acetal linkage (OCF2CF2)p(OCF2)q;B, straight chain without acetal linkage (CF2CF2CF2O)n; C, branched chain (CFCF3CF2O)m, were evaluated at 0.025 mis under 1 to 300 N at 10−5 Pa in a four-ball configuration using 440C and Si3N4 balls, Φ:6.35 mm, as test specimens. A quadrupole mass spectrometer having a mass range of 1 to 200 amu was employed to analyze gaseous products released from the sliding surfaces. Disregarding the gas released, Oil C showed slightly better wear characteristics than B, but far better than A when tested with a 440C ball on 440C balls. Taking gas evolution into account, Oil B carried the highest load; the initial degassing was detected at the Hertzian pressure of 1 GPa for A, 2 GPa for B, and 1.75 GPa for C when using 440C balls, and at 1.5 GPa for A and 2.75 GPa for C when using Si3N4 balls. Oil B evaluated with Si3N4 balls did not evolve gases even at 2.75 GPa. The initial outgassing load of sliding pairs of a Si3N4 ball against 440C balls and vice versa was closer to that of a 440C ball on 440C balls than to a Si3N4 ball on Si3N4 balls. Mass spectra patterns obtained from experiments with a Si3N4 ball on Si3N4 balls were similar to those from experiments with a 440C ball on 440C balls. Oil A released more CFO+ (m/e = 47) and CF2O+ (m/e = 66) than Oil B or C, which could originate from the acetal linkage of its molecular structure as shown by Mori and Morales (1).

Determination of isotope cluster patterns in mass spectra of GC-MS analyses by a chemometric detector

The computer program ISODET recognizes isotope cluster patterns in the mass spectra of the GC-MS analysis of atoms of chlorine, bromine, sulphur and chlorine/bromine combinations. The decision parameters used in the algorithm of the method were calculated by treating 2, 535 mass spectra from the NBS database. The result of the analysis is a graphic output (isotope cluster chromatograms) and tabulated output. The applicability and the reliability of the isotope detector and the mode of using the input program parameters are discussed. The reliability of the correct recognition of isotope clusters evaluated by means of the spectra from the NBS database was 92% for chlorinated and brominated compounds but only 51%, for sulphur containing compounds.

Application of secondary ion mass spectrometry (SIMS) for the analysis of asbestos fibers

Secondary ion mass spectrometry (SIMS) was applied for the analysis of asbestos fibers. It was possible to identify the asbestos fibers by the pattern of the positive secondary ion mass spectrum. The image of the asbestos fibers was measurable by use of any major positive secondary ions. The smallest size of detectable asbestos fiber was about 5 and 1 μm in length and diameter, respectively. Using a fast atom bombardment (FAB) source instead of primary ion beam, asbestos fibers collected on a membrane filter were easily detected without any pretreatment.

A study of the photodecomposition of different polychlorinated biphenyls by surface modified titanium (iv) oxide particles

Abstract We report the photosensitization of titanium (IV) oxide (TiO2) particles by zinc tetraphenylporphyrin (ZnTPP) bound to polyvinylpyridine (PVP). The resulting composite ZnTPP/PVP/TiO2 when used as a photocatalyst for the degradation of polychlorinated biphenyls (PCB's) in a mixed phase of hexanes and water is shown to be more efficient than TiO2 alone. The dechlorination monitored by a gas Chromatograph interfaced with a mass spectrometer (GC/MS) shows the loss of one chlorine as determined by one observable intermediate and by its mass spectrum pattern. Although further dechlorination could not unambiguously be accounted for by GC/MS, a test of the aqueous phase with AgNO3 indicated an approximate stoichiometric release of chloride ions. These observations suggest a fast dechlorination subsequent to the loss of the first chlorine.

Pyrolysis - Field lonization Mass Spectrometry - A New Method for Direct, Rapid Characterization of Tobacco

Abstract For the first time, pyrolysis - field ionization (Py-FI) mass spectra of the tobacco blends of three different cigarette brands have been recorded in the mass range up to 1000 mass units and evaluated by operational fingerprinting techniques. Due to the high reproducibility of the applied methods, all three tobacco blends could be differentiated clearly with several univariate or multivariate statistical methods. Feature scaling with Fisher ratios revealed that the signal at m/z 93, mainly due to aniline, is the most suited to distinguishing the tobacco blends analysed. Principal component analysis showed the variety of pyrolytic reactions during the thermal decomposition of tobacco in high vacuum. It revealed that, in addition to aniline, lignin-related signals can also be used for a clear differentiation. From the whole pattern of Py-FI mass spectrum, nearest-neighbour relationships are visualized by the non-linear mapping technique and further classification of tobacco blends is obtained by hierarchical cluster analysis. A thorough chemical interpretation of the data obtained should give new insights into the structure of tobacco and its pyrolytic decomposition. Pyrolysis - soft ionization mass spectrometry in combination with pattern recognition techniques appears to provide a useful tool for future investigations connected with the quality control of commercial tobacco products.

Electron-impact fragmentation of mono- and diacylhydrazines of fluorocarboxylic acids

The mechanism of electron-impact dissociative ionization of mono- (I) and diacylhydrazines (II) of fluorocarboxylic acids RC(O)NHNHR 1 (I) and RC(O)NHNR 1C(O)R (II) with RCH 3, CH 2F, CHF 2, CF 3, C 2F 5, C 3F 7, C 4F 9, C 6F 13; R 1H, CH 3, C 2H 5, C 3H 7, iC 3H 7, C 9H 19, C 6H 5 has been studied. The fragmentation of (I) with R 1H involves direct cleavage of C(O)C and C(O)N bonds. The accumulation of fluorines in the molecule increases the portion of dissociates at the C(O)C bond and, starting from R 1C 2F 5, no fragmentation at the C(O)N bond occurs. When an alkyl group is introduced into the hydrozine fragment some arrangements involving NN bond cleavage become prevailing processes. Elongation of perfluoroalkyl groups does not affect much the molecular ion fragmentation, the mass spectra pattern being dependent on only the size and character of the substituent R 1 attached to the nitrogen atom. The fragmentation of fluorine-containing diacylhydrazines (II) proceeds analogously to that of (I) with R 1H, independently of substituent R 1. The major contribution to the total ion current is from ions generated by dissociation of the perfluoroacyl fragment. The main trends in dissociation of parent ions and fragments have been considered and compared with fragmentation of some non-fluorinated analogs. Some mechanisms for the rearrangement processes have been suggested.