bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystallization, characterization, and preliminary crystallographic studies of mitochondrial carbamoyl phosphate synthetase I ofRana catesbeiana
Authors: Marina Alberto , Bravo Jerónimo , Fita Ignacio , Rubio Vicente
Published: May 2005

Carbamoyl phosphate synthetase I (ammonia; E C 6.3.4.16) was purified from the liver ofRana catesbeiana(bullfrog). Crystals of the protein have been obtained at 22°C by the hanging drop vapor diffusion technique, with polyethylene glycol as precipitant. Tetragonal crystals of about 0.3 × 0.3 × 0.7 mm diffract at room temperature to at least 3.5 Å using a conventional source and are stable to X‐radiation for about 12 h. Therefore, these crystals are suitablefor high resolution studies. The space group isP41212 (or its enantiomorphP43212), with unit cell dimensionsa=b= 291.6 Å andc= 189.4 Å. Density packing considerations areconsistent with the presence of 4‐6 monomers (Mrof the monomer, 160,000) in the asymmetric unit. Amino‐terminal sequence of the enzyme and of a chymotryptic fragment of 73.7 kDa containing the COOH‐terminus has been obtained. The extensive sequence identity with rat and human carbamoyl phosphate synthetase I indicates the relevance for mammals of structural data obtained with the frog enzyme. © 1995 Wiley‐Liss, Inc.
Hard α‐keratin IF: A structural model lacking a head‐to‐tail molecular overlap but having hybrid features characteristic of both epidermal keratin and vimentin IF
Authors: Parry David A. D.
Published: May 2005

In intermediate filaments (IF) both epidermal keratin and vimentin molecules have been shown to have an eight residue head to‐tail overlap between the rod domains of similarly directed molecules. In the case of the epidermal keratins this region has also been shown to have particular structural/functional significance since it represents a hot‐spot for mutations in the four keratinopathies characterized to date. While there is good evidence that this head‐to‐tail overlap is present in IF containing Type III, IV, and V chains, as well as in the epidermal keratin IF (Ib/IIb), there are no data currently available for the hard α‐keratin IF (Ia/IIa). Using a variety of data derived from X‐ray diffraction and crosslinking studies, as well as theoretical modeling, it is now possible to demonstrate that the overlap region is not a feature of hard α‐keratin IF. Indeed, it is shown that there is a nine residue gap between consecutive parallel molecules in the IF. An explanation for this observation is presented in terms of compensating disulfide bonds that occur both within the IF, and between the IF and the matrix in which the IF are embedded. © 1995 Wiley‐Liss, Inc.
Consensus preferred hydration sites in six FKBP12‐drug complexes
Authors: Faerman Carlos H. , Karplus P. Andrew
Published: May 2005

A set of consens us hydration sites for the FK506‐FKBP12 complex are derived by comparing six FKBP12‐drug complexes. These hydration sites include a subset of the observed water molecules plus some sites that are occupied by neighboring protein atoms in the FK506‐FKBP12 crystal structure. Two hydration prediction algorithms, AUTO‐SOL and AQUARIUS2, showed significant increases in apparent efficacy using these consensus water sites, suggesting that our proposed set of consensus hydration sites is truly a better representation of the hydration properties of FKBP12 in solution. Predictably, the consensus hydration sites include all buried water molecules. Otherwise, the features of solvation sites included in the consensus list versus those discarded reveal no distinctive features that would allow them to be selected unambiguously without reference to multiple crystal forms. We suggest that analyses such as this one are a crucial prelude to any theoretical analysis aimed at understanding hydration properties. © 1995 Wiley‐Liss, Inc.
Zinc binding in proteins and solution: A simple but accurate nonbonded representation
Authors: Stote Roland H. , Karplus Martin
Published: May 2005

Force field parameters that use a combination of Lennard‐Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 β all‐atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer‐range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site. It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc‐containing systems. © 1995 Wiley‐Liss, Inc.
Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long‐time molecular dynamics simulations
Authors: Brunne R. M. , Berndt K. D. , Güntert P. , Wüthrich K. , van Gunsteren W. F.
Published: May 2005

Structural and dynamic properties of bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution are investigated using two molecular dynamics (MD) simulations: one of 1.4 ns length and one of 0.8 ns length in which atom‐atom distance bounds derived from NMR spectroscopy are included in the potential energy function to make the trajectory satisfy these experimental data more closely. The simulated properties of BPTI are compared with crystal and solution structures of BPTI, and found to be in agreement with the available experimental data. The best agreement with experiment was obtained when atom‐atom distance restraints were applied in a time‐averaged manner in the simulation. The polypeptide segments found to be most flexible in the MD simulations coincide closely with those showing differences between the crystal and solution structures of BPTI. © 1995 Wiley‐Liss, Inc.
Crystallization and X‐ray diffraction data of the cleaved form of plasminogen activator inhibitor‐1
Authors: Aertgeerts K. , De Bondt H. L. , De Ranter C. , Declerck P. J.
Published: May 2005

To characterize the structural requirements for the conformational flexibility in plasminogen activator inhibitor‐1 (Pal‐1) we have crystallized human PAI‐1, carrying a mutation which stabilizes PAI‐1 in its substrate form. Crystallization was performed by the hanging drop diffusion method at pH 8.5 in the presence of 19% (w/v) polyethyleneglycol 4000 as a precipitant. The crystals appear after 3 days at 23°C and belong to the monoclinic space group C2 with cell dimensions of a=151.8 Å, b=47.5 Å, c=62.7 Å, and β=113.9°, and one molecule in the asymmetric unit. The X‐ray diffraction data set contains data with a limiting resolution of 2.5 Å. Biochemical analysis of the redissolved crystals indicated that during the crystallization process, cleavage had occurred in the active site loop at the P1‐P1′ position. The availability of good‐quality crystals of the cleaved form of this serpin will allow its three‐dimensional structure to be solved and will provide detailed information on the structure‐function relationship in PAI‐1. © 1995 Wiley‐Liss, Inc.
Crystallization of a soluble, catalytically active form of Escherichia coli leader peptidase
Authors: Paetzel Mark , Chernaia Maia , Strynadka Natalie , Tschantz William , Cao Gnoqing , Dalbey Ross E. , James Michael N. G.
Published: May 2005

Leader peptidase, a novel serine protease in Escherichia coli, catalyzes the cleavage of the amino‐terminal leader sequences from exported proteins. It is an integral membrane protein containing two transmembrane segments with its carboxy‐terminal catalytic domain residing in the periplasmic space. Here, we report a procedure for the purification and the crystallization of a soluble non‐membrane‐bound form of leader peptidase (Δ2‐75). Crystals were obtained by the sitting‐drop vapor diffusion technique using ammonium dihydrogen phosphate as the precipitant. Interestingly, we have found that the presence of the detergent Triton X‐100 is required to obtain crystals sufficiently large for X‐ray analysis. The crystals belong to the tetragonal space group P42212, with unit cell dimensions of a = b = 115 Å and c = 100 Å, and contain 2 molecules per asymmetric unit. This is the first report of the crystallization of a leader (or signal) peptidase. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic analysis of recombinant abrin‐a A‐chain with ribosome inactivating Activity
Authors: Kohno Tetsuya , Senda Toshiya , Narumi Hideki , Kimura Shigenobu , Mitsui Yukio
Published: May 2005

Crystals have been obtained for a recombinant abrin‐a A‐chain produced by E. coli. The crystals were grown using PEG6000 as the precipitating agent. The crystals belong to an orthrhombic space group P 212121 and diffract to 1.7 Å. © 1995 Wiley‐Liss, Inc.
Perfect temperature for protein structure prediction and folding
Authors: Finkelstein Alexei V. , Gutin Alexander M. , Badretdinov Azat Ya.
Published: May 2005

We have investigated the influence of the “noise” of inevitable errors in energetic parameters on‐protein structure prediction. Because of this noise, only a part of all the interactions operating in a protein chain can be taken into account, and therefore a search for the energy minimum becomes inadequate for protein structure prediction. One can rather rely on statistical mechanics: a calculation carried out at a temperature T* somewhat below that of protein melting gives the best possible, though always approximate prediction. The early stages of protein folding also “take into account” only a part of all the interactions; consequently, the same temperature T* is favorable for the self‐organization of native‐like intermediates in protein folding. © 1995 Wiley‐Liss, Inc.
Kinetic folding and unfolding of staphylococcal nuclease and its six mutants studied by stopped‐flow circular dichroism
Authors: Kalnin Nikolay N. , Kuwajima Kunihiro
Published: May 2005

Kinetics of refolding and unfolding of staphylococcal nuclease and its six mutants, each carrying single or double amino acid substitutions, are studied by stopped‐flow circular dichroism measurements. A transient kinetic intermediate formed within 10 ms after refolding starts possesses a substantial part of the N‐domain core β‐structure, whereas helices are formed at the later stages. The structure of the kinetic intermediate is less organized than the structure that is known to be formed by a nuclease 1‐136 fragment. Only the refolding kinetics are affected by the mutations in all the mutants except two in which the mutations have changed the native structure. From this result and also from the locations of the mutation sites, the major N‐terminal domain of the nuclease in the transition state of folding has a structure nearly identical to the native one. On the other hand, the minor C‐terminal domain has previously been shown to be still disorganized in the transition state. The effects of the amino acid substitutions on the stability of the native and the transition states are in good agreement with the changes in the hydration free energy, expected for the corresponding amino acid replacements in the unfolded polypeptide. Since side chains of all the mutated residues are not accessible to solvent in the native structure, the result suggests that it is the unfolded state that is mainly affected by the mutations. © 1995 Wiley‐Liss, Inc.
Purification, characterization, crystallization, and preliminary X‐ray results from Paracoccus denitrificans porin
Authors: Hirsch Andreas , Wacker Thomas , Weckesser Jürgen , Diederichs Kay , Welte Wolfram
Published: May 2005

The porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with β‐d‐octylglucopyra‐noside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 Å, b = 193.8 Å, c = 100.5 Å and β = 129.2°. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with α = 89.7 Å, b = 98.8 Å, c = 112.5 Å, b = 112.5Å, β = 101.8°, γ = 106.7° (2 trimers per asymmetric unit). Both crystal forms diffract to 3 Å. © 1995 Wiley‐Liss, Inc.
Crystallization of a membrane pore‐forming protein with mosquitocidal activity from Bacillus thuringiensis subspecies kyushuensis
Authors: Li Jade , Koni Pandelakis A. , Ellar David J.
Published: May 2005

CytB, a membrane pore‐forming toxin from Bacillus thuringiensis subspecies kyushuensis, is specifically toxic to dipteran insect larvae but broadly cytolytic in vitro. It has been purified in the protoxin form from a recombinant Escherichia coli source and crystals have been obtained which diffract X‐rays to at least 2.6 Å resolution. The tendency for CytB to aggregate in solution was overcome by including 50 mM of urea or 8 mM of ethanolamine during crystallization. Mutants designed to add or subtract single cysteine residues for the purpose of heavy atom derivative preparation were similarly purified and crystallized. The crystals are hexagonal bipyramids. They belong to space group P6122 (or P6522) with lattice constants a = b = 67.34 Å, c = 170.96 Å, and contain one molecule of the CytB protoxin (MW 29235) per asymmetric unit and 27% solvent by volume. © 1995 Wiley‐Liss, Inc.
Assessment of a protein fold recognition method that takes into account four physicochemical properties: Side‐chain packing, solvation, hydrogen‐bonding, and local conformation
Authors: Matsuo Yo , Nishikawa Ken
Published: May 2005

A protein fold recognition method was tested by the blind prediction of the structures of a set of proteins. The method evaluates the compatibility of an amino acid sequence with a three‐dimensional structure using the four evaluation functions: side‐chain packing, solvation, hydrogen‐bonding, and local conformation functions. The structures of 14 proteins containing 19 sequences were predicted. The predictions were compared with the experimental structures. The experimental results showed that 9 of the 19 target sequences have known folds or portions of known folds. Among them, the folds of Klebsiella aerogenes urease β subunit (KAUB) and pyruvate phosphate dikinase domain 4 (PPDK4) were successfully recognized; our method predicted that KAUB and PPDK4 would adopt the folds of macromomycin (Ig‐fold) and phosphoribosylanthra‐nilate isomerase:indoleglycerol‐phosphate synthase (TIM barrel), respectively, and the experimental structure revealed that they actually adopt the predicted folds. The predictions for the other targets were not successful, but they often gave secondary structural patterns similar to those of the experimental structures. © 1995 Wiley‐Liss, Inc.
Fold recognition and ab initio structure predictions using hidden markov models and β‐strand pair potentials
Authors: Hubbard Tim J. , Park J.
Published: May 2005

Protein structure predictions were submitted for 9 of the target sequences in the competition that ran during 1994. Targets sequences were selected that had no known homology with any sequence of known structure and were members of a reasonably sized family of related but divergent sequences. The objective was either to recognize a compatible fold for the target sequence in the database of known structures or to predict ab initio its rough 3D topology. The main tools used were Hidden Markov models (HMM) for fold recognition, a β‐ strand pair potential to predict β‐sheet topology, and the PHD server for secondary structure prediction. Compatible folds were correctly identified in a number of cases and the β‐strand pair potential was shown to be a useful tool for ab initio topology prediction. © 1995 Wiley‐Liss, Inc.
Crystallization of the complex of human IFN‐γ and the extracellular domain of the IFN‐γ receptor
Authors: Chiène Christiane , Fountoulakis Michael , Döbeli Heinz , D'Arcy Brigitte , Winkler Fritz , D'Arcy Allan
Published: May 2005

A complex of human interferon‐γ (IFN‐ γ) with the soluble extracellular domain of the IFN‐ γ receptor α‐chain (IFN‐γ‐R) has been crystallised. Crystals of the complex were grown using PEG 4000 as the precipitating agent in the presence of β‐octyl glucoside. The receptor‐ligand complex crystallizes in a monoclinic space group and diffracts to about 3.0 Å resolution. Isomorphous crystals have been obtained with complex containing selenomethionine and cysteine mutants of IFN‐γ, which may facilitate the ongoing X‐ray structure determination. © 1995 Wiley‐Liss, Inc.
Reaction‐induced mass discrimination in XQQ instruments. Absolute cross‐sections for N + SF6 → N2 + SF (x=1–5)
Authors: Martinez Richard I. , Ganguli B. , Boyd R. K.
Published: May 2005

Dynamically‐correct branching ratios can be measured in a XQQ tandem mass spectrometer (MS/MS) under single‐collision conditions when the key MS/MS parameters are properly selected to correct for reaction‐induced mass discrimination within the RF‐only quadrupole mass filter (Q2). The energy dependence of the cross‐section, σ(E), for the reaction N + SF6 → N2+SFx+ (x = 1–5) was measured in the NBS triple quadrupole (QQQ) tandem mass spectrometer. For P≃0.02–0.13 mTorr and E ≃ 5–60 eV (Lab) [the range of collision energies used for collisionally activated dissociation (CAD)], identical σ(E) were measured from both the rate of reactant ion decay and the rate of product ion formation. Therefore, these σ values are substantially free from kinetic interferences (i.e., no back reactions, no impurity reactions, no scattering losses, minimal fringing fields, no mass discrimination, well‐defined gas target, etc.). Moreover, there is probably no significant systematic error in our measurements of the absolute σ values for N + SF6 → N2+SF (x = 1–5) because the σ values we measured with this same technique for Ne +˙+ Ne → Ne+Ne+˙, Ar+˙ + Ar → Ar+Ar+˙, and Ar+˙+N2 → Ar+N agreed well with literature values obtained with several well‐established techniques.
Obtaining structural information of perfluoro‐1,3‐dimethyladamantane from collisionally activated decomposition mass spectra
Authors: Huang Sunkwei , Klein David H. , Adcock James L. , Gross Michael L.
Published: May 2005

Cyclic, high molecular weight perfluorocarbons (PFC's) are very electronegative, and can be detected by methane negative ion chemical ionization (NICI); however only molecular ions are detected. Electron ionization (EI) of PFC's, on the other hand, yields little or no molecular ion but very intense low mass fragment ions such as CF (m/z 69), C3F (m/z 131) and C4F (m/z 181), which are not structurally characteristic. High‐energy collisionally activated decomposition (CAD) of positive, molecular ions of perfluoro‐1,3‐dimethyladamantane yields important structural information by providing more intense high mass fragment ions. Fragments of the following formulae and abundances (in brackets): C5F (100), C11F (73), C7F (67), C8F (43), C4F (26), C7F (18), and CF (14) are detected by this method.
An experimental investigation of the possibility of developing a database for tandem mass spectrometry using xqq instruments
Authors: Dheandhanoo Seksan , Boyd R. K.
Published: May 2005

The NBS round‐robin protocol for testing the performance of XQQ tandem mass spectrometers (R.I. Martinez, Rapid Commun. Mass. Spectrom. 2, 8 (1988)) has been evaluated using a QQQ instrument which is significantly different in both the size of the quadrupole rods and the design from that used in the NBS work. The NBS experimental cross‐sections for the Ar+./Ar charge‐transfer reactions were used to provide a calibration of target thickness in the present apparatus. The present experimental value of the reaction cross‐section for the N2+./SF6 system is 60 ± 3 Å2 at the center‐of‐mass collision energy of 4.4 eV, in excellent agreement with the NBS literature value (55 Å2). This result supports the view that a library of collisionally activated dissociation spectra is feasible provided that the instruments used are of dynamically correct design.
Negative ion mass spectrometry of silylated cytokinins
Authors: Hocart Charles H. , Schlunegger Urs P.
Published: May 2005

The negative ion mass spectra or trimethylsilylzeatin riboside and t‐butyldimethylsilylzeatin, generated using either ammonia or 10% CO2/Ar as reagent gas, are described. Optimal yields of [M‐H]− ions were obtained with a source pressure of 5 Pa in the electron ionization source of a ZAB‐2F mass spectrometer, compared with 15 Pa to generate [M+H]+ in the chemical ionization mode. At 15 Pa no negative ions could be observed.
Fast‐atom bombardment tandem mass spectrometry of phosphohydroxylysine and related phosphohydroxy amino acids
Authors: Kulik W. , Heerma W. , Dorland L. , de Bree P. K. , Duran M.
Published: May 2005

Phosphohydroxylysine a compound found in the urine of two patients with a possible inborn error of hydroxylysine metabolism, and related phosphohydroxycompounds were investigated with fast‐atom bombardment tandem mass spectrometry techniques. This resulted in a reliable and quick identification method for phospho amino acids in general.
Isomerization of proton‐bound alcohol dimers
Authors: Audier H. E. , Monteiro C. , Mourgues P. , Robin D.
Published: May 2005

Proton‐bound dimers [ROH… \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm H}\limits^ + $\end{document}… HOR] have been studied under chemical ionization conditions. The structures of the fragment ions and the behaviour of variously deuterated ions when R = iC3H7 lead to a proposed fragmentation pathway.
Characterization of high molecular weight macrocycles by desorption chemical ionization mass spectrometry
Authors: Guglielmetti Gianfranco , Dalcanale Enrico , Bonsignore Stefanio , Vincenti Marco , Busch K. L.
Published: May 2005

A series of multi‐armed macrocycles with molecular weights up to 4400 Da was studied by desorption chemical ionization. Both negative‐ and positive‐ion spectra exhibited excellent signal‐to‐noise ratio, despite the limited amount of material sampled (0.1–1 pmol). The molecular ions generally represent the base peaks of the spectra, but the extent of fragmentation increases as the source temperature is raised.
Direct analysis of drugs by continuous‐flow fast‐atom bombardment and tandem mass spectrometry
Authors: Seifert William E. , Ballatore Annie , Caprioli Richard M. , Boyd R. K.
Published: May 2005

The techniques of continuous‐flow fast‐atom bombardment (CF‐FAB) and tandem mass spectrometry (MS/MS) are combined and applied to the analysis of small molecular mass drugs (mol.wt < 500 Da). The approach involves the interfacing of a CF‐FAB inlet with a triple‐stage quadrupole mass spectrometer, enabling the acquisition of collision‐activated decomposition mass spectra of the drugs after FAB ionization. The relationship between a stable sample surface on the CF‐FAB probe tip and the quality of the mass spectrum is discussed, as are practical methods for obtaining and maintaining surface stability. CF‐FAB MS/MS spectra for several drugs are presented, including penicillin G, phentolamine, cocaine and benzoylecgonine. Minimum detection limits range from 50–500 pg injected, depending on the compound. The reproducibility of the integrated areas of peaks from repetitive injections is approximately five per cent. Data are also presented for the direct CF–FAB MS/MS analysis of cocaine and benzoylecgonine in spiked urine samples.
Oligopeptide sequence analysis by collision‐activated dissociation of multiply charged ions
Authors: Hunt Donald F. , Zhu Nian‐Zhou , Shabanowitz Jeffrey , Cooks R. G.
Published: May 2005

Collision‐activated dissociation of an [M + 2H]2+ ion from a tryptic peptide of molecular weight 2315.3 provides sets of overlapping fragments that allow the amino acid sequence of this peptide to be determined on a triple quadrupole mass spectrometer having a mass range of 1800 Da.
Experimental determination of the double‐ionization energies of the trihalomethanes CF2ClH and CFCl2H
Authors: Griffiths W. J. , Harris F. M.
Published: May 2005

The double‐ionization energies of CF2ClH and CFCl2H have been measured by double‐charge‐transfer spectro‐scopy and are 33.1±0.5 eV and 30.3±0.5 eV, respectively. These values are smaller than the double‐ionization energy of CF3H and larger than the double‐ionization energy of CCl3H and thus exhibit the expected decrease as the fluorine atoms are replaced successively by chlorine atoms. This trend reflects a similar trend in the singleionization energies since for all the molecules the ratio of double‐ to single‐ionization energy lies between 2.5 and 2.6.
Determination of lovastatin acid in serum by gas chromatography/mass spectrometry
Authors: Wang‐Iverson David , Ivashkiv Eugene , Jemal Mohammed , Cohen Allen I.
Published: May 2005

The acid form of lovastatin, an HMG‐CoA reductase inhibitor, was analyzed by gas chromatography/negativeion chemical ionization mass spectrometry after derivatization with pentafluorobenzyl bromide and bis‐(trimethylsilyl)trifluoroacetamide (BSTFA). Mass spectrometry of this derivative produced a dominant [M–181]− ion under chemical ionization conditions using ammonia as the reagent gas. The limit of detection was approximately 2 pg injected on column.
Quantitation by fast‐atom bombardment/mass‐analysed ion kinetic energy spectrometry: Kinetic analysis of cyclic nucleotide phosphodiesterase activity
Authors: Newton R. P. , Walton T. J. , Brenton A. G. , Kingston E. E. , Harris F. M.
Published: May 2005

Quantitation of cyclic nucleotide phosphodiesterase activity by means of fast‐atom bombardment (FAB) mass spectrometry with mass‐analysed ion kinetic energy (MIKE) spectrum scanning is described. Characteristic peaks of the substrate, cyclic AMP, and product, AMP, were identified in positive‐ion FAB mass spectra and MIKE scans of the protonated molecules. By spiking enzyme incubates with known quantities of cyclic AMP and AMP and measuring peak heights in the MIKE spectra of both spiked and unspiked samples, the concentrations of cyclic AMP and AMP in solution at the end of a series of enzyme incubations have been estimated. From the data obtained the Km and Vmax of the enzymes were calculated as 181 μM and 28.6 nmol/min respectively, showing excellent agreement with values of the Michaelis constant, Km=205 μM and the maximum velocity Vmax=33.2 nmol/min obtained by radioactive assay.
Compensation for non‐normal ejection of large molecular ions in plasma‐desorption mass spectrometry
Authors: Jonsson G. , Hedin A. , Håkansson Per , Sundqvist B. U. R. , Bennich H. , Roepstorff P.
Published: May 2005

By introducing an Einzel lens in the field‐free region of a straight time‐of‐flight mass spectrometer, secondary ions of large mass can be detected more efficiently in plasma‐desorption mass spectrometry. This procedure compensates for the large radial velocities of large molecular ions recently observed experimentally. It is shown that large molecular ions like those of lysozyme can now be detected more efficiently, and larger molecular ions than observed before in plasma‐desorption mass spectrometry (like those of bovine ovalbumin, mol. wt 45 000) can now be studied.
Negative‐ion mass spectrometry of substituted adenine bases and adenosine nucleosides
Authors: Hocart Charles H. , Schlunegger Urs P.
Published: May 2005

The negative‐ion chemical ionization (ammonia, 5 Pa source pressure) mass spectra of a series of substituted adenine bases, adenosine nucleosides, and the trimethylsilyl derivatives of the nucleosides are described. Selected ions from these spectra were subject to collisionally activated dissociation with mass‐analysed ion kinetic energy (CAD/MIKE) analysis of the products and the spectra assessed for information content. In addition to observing strong peaks due to quasimolecular ions and heterocyclic‐base ions, it proved possible to differentiate between 2′‐, 3′‐ and 5′‐deoxy and between 2′‐ and 3′‐O‐methyl isomers. The negative‐ion chemical ionization spectra of four methyladenines are essentially identical, but could be clearly distinguished from each other by CAD/MIKE analysis.
Electrospray on magnetic instruments
Authors: Allen Mark H. , Lewis Ivor A. S.
Published: May 2005

The mass spectra of a number of compounds have been measured using a novel electrospray interface to magnetic sector instruments. The performance of the interface, combined here with both single‐ and double‐focusing spectrometers, is compared with existing interfaces to quadrupole instruments.
Competitive isomerization processes of 5‐methyl‐2‐hexanone radical cations
Authors: Audier H. E. , Denhez J. P. , Mourgues P.
Published: May 2005

Labelled derivatives of the 5‐methyl‐2‐hexanone radical cation have permitted the elucidation of the origin of the main fragment ion [MC2H5]+ and the characterization of different rearrangement processes.
Experimental determination of the single‐ionization energies of two environmentally important free radicals, CF2Cl˙ and CFCl2˙
Authors: Griffiths W. J. , Harris F. M. , Barton J. D.
Published: May 2005

The single‐ionization energies of the free radicals CF2Cl˙ and CFCI2˙ have been measured by double‐charge‐transfer spectroscopy. The values obtained were 9.0 ± 0.5 eV and 8.5 ± 0.5 eV for CF2Cl˙ and CFCl2˙, respectively.
Fast‐atom bombardment mass spectrometry of conjugated benzo(a)pyrene metabolites
Authors: Greaves J. , Bieri R. H.
Published: May 2005

Fast‐atom bombardment mass spectrometry has been used to obtain spectra of conjugated benzo(a)pyrene (bap) metabolites using a 1:1, glycerol+thioglycerol matrix. bap Glucuronides give positive‐and negative‐ion spectra with peaks due to [M + H]+ and [M − H]− ions and a Major fragment peak (base peak) at [bapOH]+ and [bapO]−. bap Sulfates (sodium salts) give similar negative‐ion spectra with [M − Na]− and [bapO]− peaks, but the positive‐ion spectra are dominated by sodium and glycerol adducts of the bap sulfates.
Characterization of impurities in a synthetic renin substrate peptide by fast‐atom bombardment mass spectrometry and hybrid tandem mass spectrometry
Authors: Mathews W. Rodney , Runge Thomas A. , Haroldsen Peter E. , Gaskell Simon J. , Tomer K. B.
Published: May 2005

Fast‐atom bombardment mass spectrometry of a synthetic renin substrate decapeptide (Pro‐His‐Pro‐Phe‐His‐Leu‐Val‐Ile‐His‐D‐Lys) indicated the presence of several of side‐products, including a component 12 Da higher in mass. Low‐energy collisionally activated decomposition analyses were performed using a hybrid tanden, instrument and demonstrated that the heavier side product had two components, in which the structural modification was either at the N‐ or the C‐terminus. Additional analyses of the N‐acetyl derivative indicated that for each component the strucutrual modification blcoked a site of N‐acetylation. It is suggested that the formation of these side products is attributable to the generation of formaldehyde, during removal of the histidine protecting group (benzyloxymethyl), which reacts with the N‐terminus of the peptide to give an imidazolidinone structure or with the D‐lysine ε‐amine group to yield an imine. While the precise genesis of the side‐products remains speculative, it is clear that the combined strategy of derivatization and tandem mass spectrometry has allowed structural conclusions concerning individual components of an isobaric mixture.
Ion chemistry of the methylcarbonate anion
Authors: Hayes Roger N. , Waugh Russell J. , Bowie John H.
Published: May 2005

The ion MeOCO fragments upon collisional activation by competitive losses of Me, CH2 and CO2. The loss of formaldehyde involves hydride‐ion transfer to form HCO. MeOCO reacts as a methoxyl‐ion donor in a characteristic reaction with sulphur dioxide, i.e. MeOCO + SO2→ MeOSO+ CO2.
Tandem mass spectrometry of mirex
Authors: Cairns Thomas , Siegmund Emil G.
Published: May 2005

Product‐ion spectra derived from the major fragment ions of the polychloro‐cyclobutapentalene pesticide, Mirex, under ammonia chemical ionization have indicated that previous conclusions of a nucleophilic gas‐phase reaction with neutral ammonia were incorrect.
Rapid analysis of a peptide by fast‐atom bombardment mass spectrometry after polyacrylamide gel electrophoresis
Authors: Camilleri P. , Haskins N. J. , Hill A. J.
Published: May 2005

Gel electrophoresis has been a powerful technique for the separation of peptides and proteins for many years. After electrophoresis separation on a polyacrylamide gel, the peptide bradykinin was localized using Coomassie Blue as a staining dye. Excess dye was removed by washing the gel with water, For mass spectrometric analysis, bands containing the peptide were crushed, extracted with acetic acid and the eluent applied to the fast‐atom bombardment probe. Under these conditions the protonated molecule of bradykinin was clearly observed. Also apparent were sequence ions at about the same intensity observed from authentic bradykinin.
Pulsed extraction field for neutralization of sample charging in secondary‐ion mass spectrometry
Authors: Appelhans A. D. , Dahl D. A. , Delmore J. E.
Published: May 2005

A new technique for inhibiting the build‐up of surface charge on electrically non‐conducting samples in secondary‐ion mass spectrometry (SIMS) when using a negative‐ion or neutral primary beam is described. The technique, which involves alternately extracting positive and negative particles from the sample by rapidly reversing the polarity of the secondary‐ion extraction voltage, is non‐intrusive and applicable to all materials. A static SIMS instrument utilizing a negative‐ion and neutral molecular primary beam has been modified to demonstrate the technique.
Application of liquid chromatography/thermospray mass spectrometry to studies on the formation of glutathione and cysteine conjugates from monomethylcarbamate metabolites of bambuterol
Authors: Rashed Mohamed S. , Pearson Paul G. , Han Deog‐Hwa , Baillie Thomas A.
Published: May 2005

Liquid chromatography/thermospray mass spectrometry (LC/TSP‐MS) has been used to identify and study the rates of formation of S‐(N‐methylcarbamoyl) cysteine and S‐(N‐methylcarbamoyl)glutathione as products of the in vitro reaction of cysteine and glutathione, respectively, with two monomethylcarbamate metabolites of the bronchodilator pro‐drug bambuterol. The conjugates of interest afforded MH+ species and yielded abundant structurally informative fragment ions which were employed in the development of quantitative, selected‐ion monitoring assays. It is concluded that LC/TSP‐MS represents a rapid and convenient approach to the direct aqueous‐phase analysis of the class of S‐(N‐alkylcarbamoyl) conjugates of cysteine and glutathione.
Low‐energy collisional activation spectra of – O‐ and N‐epoxypropyltrahydroacridines
Authors: Madhusudanan K. P. , Asthana Pratibha , Rastogi Shri Nivas
Published: May 2005

A study of the low‐energy collisional activation (CA) spectra of O‐ and N‐epoxypropyltetrahydroacridines has revealed that the two isomers show characteristic differences in their spectra. The CA spectra of the M+ [MH], MH+ [M + C2H5]+ and [M + C3H5]+ ions are discussed.
Charge‐inversion reactions of CF+ and CCI+ ions
Authors: Griffiths W. J. , Harris F. M. , Barton J. D.
Published: May 2005

Double‐charge‐transfer spectroscopy has been used to confirm that CF+ and CCI+ can exist for times greater than several μs in electronically excited states. From the spectra obtained it was shown that those states are 4.7 ± 0.7eV and 3.3 ± 0.5eV above the ground states for CF+ and CCI+, respectively. The experimental technique is quite sensitive to the detection of long‐lived excited states and it is shown for CCI+ that the relative populations of the excited and ground states are markedly different when CFCI3 and CF2ClCFCI2 are used as the precursor molecules in the dissociative‐ionization process.
The effect of surface activity on quantification of linear alkylbenzenesulfonates by fast‐atom bombardment mass spectrometry
Authors: Wernery J. David , Peake David A.
Published: May 2005

The effect of surface activity differences of sodium alkybenzene sulfonate homologs on quantification by fast‐atom bombardment mass spectrometry is investigated. By using three stable‐isotope internal standards to bracket the chainlength distribution, accurate quantification of surfactant mixtures is achieved. With a single deuterated internal standard, skewing of the distribution occurs. The magnitude of the skewing depends on the concentration of the sample and signal‐averaging time. The use of model mixtures of pure surfactants and analysis of commercial surfactant mixtures is demonstrated.
Preliminary studies on ion chromatography/fast‐atom bombardment mass spectrometry for the characterization of various ionic compounds
Authors: Al‐Omair Ali S. , Todd John F. J.
Published: May 2005

An ion chromatography/mass spectrometry system which makes use of a continuous‐flow fast‐atom bombardment probe, has been constructed and evaluated. Examples are given of applications to the analysis of inorganic anions (ion‐exchange chromatography), water soluble vitamins (ion‐pair chromatography) and glucose derivatives (ion‐excluson chromatography).
A deceleration lens system for hybrid mass spectrometers
Authors: Suter M. J.‐F. , Stepnowski R. M. , Schlunegger U. P.
Published: May 2005

A simple and efficient deceleration system for the coupling of magnetic and electric sector instruments to quadrupole analyzers is described. The trasnsmission efficiency of the system appears to be at least 80% or better as the ions are decelerated from 3 ke V to 30 eV (a deceleration factor of 1:100). No mass discrimination was observed in the range up to mass 1000.
Retro Diels‐Alder rearrangement in 4‐hydroxy‐2‐acylcyclohexane‐1,3‐diones
Authors: Mudd A.
Published: May 2005

High mass ions at even m/z values in the spectra of 4‐hydroxy‐2‐acylcyclohexane‐1,3‐diones are due to retro Diels‐Alder rearrangement. Evidence for the position of the enolic double bond in unsymmetrical 2‐acylcyclohexane‐1,3‐diones is adduced.
On‐line liquid chromatography/fast‐atom bombardment of protein tryptic digests
Authors: Bell David J , Brightwell Malcolm D. , Neville William A. , West Andrew
Published: May 2005

The assignment of the peptides in the chromatographic separation of tryptic peptides from a large protein was investigated by liquid chromatography/fast‐atom bombardment mass spectrometry (LC/FABMS). Methodical interfacing of the instrumentation was required to maintain the resolution of the 70 peptides in the mixture whilst gaining maximum fast‐atom bombardment sensitivity. The reconstructed ion current showed excellent correlation with ultra violet detection, illustrating that chromatographic resolution was indeed preserved. Results allowed the determination of retention times of peptides by plotting the mass chromatograms of the expected materials from the acquired spectra. It was also found that spectrum‐averaging and background subtraction could yield considerable sequence information from the LC/FAB spectra of peptides, acquired using a two‐sector instrument.
Characterization of isomeric pyranocoumarins by collision‐induced tandem mass spectrometry
Authors: Kiremire B. T. , Chiarello D. , Traldi P. , Vettori U. , Guiotto A. , Rodighiero P.
Published: May 2005

Three variously annulated isomeric pyranocoumarins 1, 2 and 3 have been examined using electron ionization and collisional mass spectroscopy. All the spectra showed diagnostic fragments that allowed characterization of the isomers. The best results were obtained using daughter‐ion spectra of selected parent ions.
Secondary‐ion mass spectrometry of particle beams
Authors: Sanders Phillip E.
Published: May 2005

A particle beam liquid chromatography/mass spectrometry interface has been developed which interfaces to a liquid secondary‐ion mass spectrometry ion source. High flow rates (e.g., 0.5–2.0 mL/min) have been achieved with sensitive performance. Matrix compounds were added through the particle‐beam interface. A cesium ion gun is used as the source of the primary ions.
Unimolecular chemistry of the 4‐hexen‐3‐one radical cation
Authors: Bouchoux G. , Djazi F. , Jaudon P. , Lefevre O.
Published: May 2005

Ionized 4‐hexen‐3‐one, fragments by losing CH˙3, CO, C2H4 and C2H˙5. The former process, which is found to dominate dissociations of metastable molecular ions proceeds via the cyclized enol cation CH3ĊHCH2CH2C(OH) = CH+. Use of deuterium labelling and relevant thermochemical data allow the determination of the various reaction mechanisms.
The use of 2‐hydroxyethyl disulphide as a matrix in liquid secondary‐ion mass spectrometry
Authors: Kenny Peter T. M.
Published: May 2005

Several novel applications of 2‐hydroxyethyl disulphide as a matrix material in liquid secondary‐ion mass spectrometry are presented. This matrix is superior to the conventional glycerol matrix for the analysis of peptides with hydrophobic residues. It was found to be an excellent matrix for the analysis of a wide range of other compounds. It is chemically inert, enhances the formation of [M + Na]+ and [M + K]+ adducts and gives few ions above m/z 300.
Computer‐aided interpretation of mass spectra by a combination of library search with principal component analysis
Authors: Varmuza K. , Werther W. , Henneberg D. , Weimann B.
Published: May 2005

The mass spectral set comprising the “hitlist” of a library search for spectra similar to that of an unknown is investigated by exploratory data analysis. Principal‐component mapping is used to present the “hitlist” as a two‐dimensional plot which allows an interactive classification of the unknown and the recognition of erroneous library spectra.
The loss of amine from low internal energy ions of aminosteroid stereoisomers
Authors: Mollova Nevena , Longevialle Pierre , Bouchoux Guy
Published: May 2005

D‐labelling experiments show that the extent of hydrogen‐atom exchanges accompanying the loss of amine from ionized aminosteroids of low internal energy depends on structure and also, in a few cases, on the configuration of the amine function. Mechanisms are proposed.
Identification of 2‐(2′‐octenyl) succinic acid in urine
Authors: Giordano Giuseppe , McMurray Walter J. , Previs Stephen F. , Welch Roy D. , Rinaldo Piero
Published: May 2005

2‐(2′‐octenyl)succinic acid has been identified in urine samples from children investigated for a possible inherited metabolic disease. Its structural identification has been achieved by gas chromatography/mass spectrometry using both electron ionization and chemical ionization and by tandem mass spectrometry (MS/MS) using fast‐atom bombardment and high‐resolution electron‐ionization analyses of the molecular ion in a complex biological matrix. The localization of the double bond was obtained by interpretation of a unexpected rearrangement reaction occurring after dimethyl disulfide derivatization.
Sequence‐informative fragmentation of peptides up to a molecular weight of 4.6 kDa in plasma‐desorption mass spectrometry
Authors: Vorst H. J. , van Tilborg M. W. E. M. , van Veelen P. A. , Tjaden U. R. , van der Greef J.
Published: May 2005

The potential of plasma‐desorption mass spectrometry (PDMS) in peptide sequencing is investigated. This paper shows that PDMS spectra recorded for longer times and using larger amounts of peptide than used for obtaining molecular weight information, provides sequence information on peptides of up to 4.5 kDa molecular weight. This approach strongly enhances the utility of PDMS for validation of the sequence of recombinant peptides.
Observation of isolated electronic states in the collision‐induced dissociation of nitromethane ions
Authors: Qian Kuangnan , Shukla Anil , Futrell Jean
Published: May 2005

Collision‐induced dissociation of nitromethane molecular ions to NO+ and NO has been studied at 19 eV center‐of‐mass collision energy using a crossed‐beam tandem mass spectrometer. Center‐of‐mass velocity contour maps for the two dissociation processes are distinctly different; NO has its intensity maximum at 7 degrees with energy transfer endothermicities of 1.8 eV while NO+ has intensity maxima at zero and 8 degrees with energy transfer endothermicities of 0.3 and 5.5 eV, respectively. The observation of two distinct peaks in the NO+ contour map clearly demonstrates that nitromethane ions excited to 5.5 eV internal energy do not dissociate from the ground state potential surface. Dissociation is faster than intramolecular relaxation, in contradiction to the fundamental postulate of statistical theories (RRKM, QET) for unimolecular dissociation.
Evidence for distinction of cis and trans isomers of mono‐unsaturated fatty acids by fast‐atom bombardment tandem mass spectrometric analysis
Authors: Jensen Nancy , Lam Kai , Cody Robert B. , Tamura Jun
Published: May 2005

Fast‐atom bombardment tandem mass spectrometry negative‐ion analysis of the [MH]− ions of the cis and trans isomer pairs of 9‐hexadecenoic and 9‐octadecenoic acid with a four sector mass spectrometer, reveals distinctions between the cis and trans isomers of each pair. The definitive fragmentation is at the bond allylic to the double bond in the distal position on the chain. Fragmentation at this site involves both remote‐charge‐site fragmentation and a cleavage fragmentation.
Matrix‐assisted laser desorption of peptides in transmission geometry
Authors: Vertes Akos , Balazs Laszlo , Gijbels Renaat
Published: May 2005

The possibility of performing matrix‐assisted laser desorption experiments in transmission geometry is demonstrated for two neuropeptides (substance P and bombesin), for six analogs of the melanocyte‐stimulating hormone (MSH) core and for coliagenase enzyme substrates. Positive‐ and negative‐ion spectra of several peptides are produced without the presence of a metallic substrate. Cationized quasi‐molecular ions are abundant in the positive spectra. Peak broadening in the high‐mass range can be the consequence of overlapping molecular and adduct ions. The presence of synthesis by‐products can be identified readily from the spectra. Ultimately, picogram detection limits are possible for important bioactive peptides and other large molecules. Because of the clearly demonstrated matrix‐assisted laser ionization in a homogeneous environment, metal substrate participation in the volatilization mechanism seems less likely.
Molecular weight determination of proteins from multiply charged ions using thermospray ionization mass spectrometry
Authors: Straub Kenneth , Chan Kelvin
Published: May 2005

Data are presented showing the use of thermospray ionization to generate multiply charged ions for a number of proteins over the molecular weight range 5000–30000. These measurements were carried out on an unmodified, commercially available thermospray ion source. Between +3 and +19 charges were observed for a series of model proteins. Data can be obtained on as little as 100 pmol of sample. The accuracy and precision of the molecular weight determinations for these proteins is similar to those previously reported for these samples using electrospray or ionspray ionization. The formation of multiply charged ions from proteins via thermospray ionization occurs over a wide range of aqueous/organic solvent compositions, facilitating its interfacing with high‐performance liquid chromatography using conventional diameter columns.
Matrix‐assisted infrared‐laser (2.94 μm) desorption/ionization mass spectrometry of large biomolecules
Authors: Overberg A. , Karas M. , Bahr U. , Kaufmann R. , Hillenkamp F.
Published: May 2005

The matrix‐assisted desorption/ionization of large biomolecules with a wavelength of 2.94 μm in the infrared is reported. A mechanically Q‐switched Erbium‐YAG laser with a pulse width of ca. 200 ns was used for the experiments. A large variety of matrices have been used successfully, among them all matrices found useful for ultraviolet desorption and, in addition, carboxylic acids, glycerol and urea. Desorption of molecules at this wavelength and caffeic acid as a matrix results in ions with up to 13 charges per ion.