bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal search: A computer program that helps design tetrahedral metal‐binding sites
Authors: Clarke Neil D. , Yuan Shao‐Min
Published: May 2005

We describe a computer program (Metal Search) that helps design tetrahedrally coordinated metal binding sites in proteins of known structure. The program takes as input the backbone coordinates of a protein and outputs lists of four residues that might form tetrahedral sites if wild‐type amino acids were replaced by cysteine or histidine. The program also outputs the side chain dihedral angles of the amino acids and the coordinates of the predicted metal ion. The only function evaluated by Metal Search is the ability of side chains to meet simple geometric criteria for formation of a tetrahedral site, but these criteria are sufficient to produce a manageably small list that can then be evaluated by other means. The program has been used in the introduction of zinc binding sites in the designed four‐helix bundle protein α 4 and in the B1 domain of streptococcal protein G, and in both cases the tetrahedral coordination of a bound metal ion has been confirmed1 (Klemba, M., Gardner, K. H., Marino, S., Clarke, N. D., and Regan, L., Nature: Structural Biology 2:368–373, 1995). © 1995 Wiley‐Liss, Inc.
A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase
Authors: Jedrzejas Marek J. , Singh Sangeeta , Brouillette Wayne J. , Air Gillian M. , Luo Ming
Published: May 2005

Neuraminidase (NA) is one of the two major surface antigens of influenza virus. It plays an indispensable role in the release and spread of progeny virus particles during infection. NA inhibitors reduce virus infection in animals. To improve the clinical efficacy of NA inhibitors, we have begun the design of non‐carbohydrate inhibitors based on the active site structure of NA. The approach is an iterative process of ligand modeling and electrostatic calculations followed by chemical synthesis of compounds, biological testing, and NA‐inhibitor complex structure determination by X‐ray crystallography. A strategy has been developed to calculate Ki for newly designed inhibitors. The calculations using the DelPhi program were performed for carbohydrate inhibitors and three preliminary benzoic acid inhibitors of neuraminidase (BANA) that have been synthesized and shown to bind to the active site of NA in the crystal structure. The calculated Kis of these inhibitors have an enlightening agreement with their in vitro biological activities. This demonstrates that the calculations produce informative results on the affinity of modeled inhibitors. GRID maps were also calculated and several pockets were identified for accepting possible new ligands. The calculated Kis for newly designed ligands suggest that these potential compounds will have high inhibitory activities. © 1995 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray analysis of PepX, an X‐prolyl dipeptidyl aminopeptidase from Lactococcus lactis
Authors: Chich Jean‐François , Rigolet Pascal , Nardi Michèle , Gripon Jean‐Claude , Ribadeau‐Dumas Bruno , Brunie Simone
Published: May 2005

The X‐prolyl dipeptidyl aminopeptidase PepX, a serine peptidase isolated originally from Lactococcus lactis subsp lactis NCDO 763, was cloned and overproduced in Escherichia coli. The enzyme was isolated in its active form in two purification steps. Crystals of PepX were grown by the hanging drop vapor diffusion method using polyethyleneglycol 4000 as precipitant at pH 5.0. The crystals are orthorhombic with cell dimensions a = 92.8 Å, b = 102.6 Å, and c = 101.6 Å, space group P21212, and probably contain one monomer of 87.5 kDa in the asymmetric unit. The crystals, very stable under X‐rays, diffract to at least 2.2 Å and are suitable for high‐resolution structural analysis. © 1995 Wiley‐Liss, Inc.
Crystallization of intact monoclonal antibodies
Authors: Harris Lisa J. , Skaletsky Eileen , McPherson Alexander
Published: May 2005

Attempts were made to crystallize four monoclonal antibodies, one IgG2ak and three IgG1k. Using a PEG 3350 screen combined with detergents, and developed from our experiments with an IgG2ak antibody specific for canine lymphoma cells,1,2 crystals have now been obtained of two of these four immunoglobulins, an antiphenytoin and an antiphenobarbital antibody. A complex between the antiphenobarbital antibody and its drug antigen crystallized as well. The antibody for phenytoin has, to this point, produced only clustered microcrystals, marginally suitable for X‐ray analysis. Single crystals of the IgG1k antibody against phenobarbital, however, were characterized by X‐ray diffraction to be primitive monoclinic, with unit cell dimensions a = 67 Å, b = 193 Å, c = 74 Å, and β = 110°. These crystals have an entire IgG1k molecule as the asymmetric unit and they diffract to at least 3.2 Å resolution. © 1995 Wiley‐Liss, Inc.
Homology modeling by the ICM method
Authors: Cardozo Timothy , Totrov Maxim , Abagyan Ruben
Published: May 2005

Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three‐dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three‐dimensional structure, the modeling procedure consists of two subproblems: side‐chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the noncon‐served portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side‐chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low‐energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near‐native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed. © 1995 Wiley‐Liss, Inc.
The use of position‐specific rotamers in model building by homology
Authors: Chinea G. , Padron G. , Hooft R. W. W. , Sander C. , Vriend G.
Published: May 2005

In this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how to avoid the combinatorial explosion that results from the combination of many residues for which multiple good rotamers are predicted? We attempt to solve these problems by choosing position‐specific rather than generalized rotamers and by sorting the residues that have to be modelled as a function of their freedom in rotamer space. The practical advantages of our method are the quality of the models for cases of high backbone similarity, the small amount of human intervention needed, and the fact that the method automatically estimates the reliability with which each residue has been modeled. Other methods described in this issue are probably more suitable if large backbone rearrangements or loop insertions and deletions need to be modeled. © 1995 Wiley‐Liss, Inc.
Analysis of six protein structures predicted by comparative modeling techniques
Authors: Harrison Robert W. , Chatterjee Devjani , Weber Irene T.
Published: May 2005

The protein structures of six comparative modeling targets were predicted in a procedure that relied on improved energy minimization, without empirical rules, to position all new atoms. The structures of human nucleoside diphosphate kinase NM23‐H2, HPr from Mycoplasma capricolum, 2Fe‐2S ferredoxin from Haloarcula marismortui, eosinophil‐derived neurotoxin (EDN), mouse cellular retinoic acid protein I (CRABP1), and P450eryf were predicted with root mean square deviations on Cα atoms of 0.69, 0.73, 1.11, 1.48, 1.69, and 1.73 Å, respectively, compared to the target crystal structures. These differences increased as the sequence similarity between the target and parent proteins decreased from about 60 to 20% identity. More residues were predicted than form the common region shared by the two crystal structures. In most cases insertions or deletions between the target and the related protein of known structure were not correctly positioned. One two residue insertion in CRABP1 was predicted in the correct conformation, while a nine residue insertion in EDN was predicted in the correct spatial region, although not in the correct conformation. The positions of common cofactors and their binding sites were predicted correctly, even when overall sequence similarity was low. © 1995 Wiley‐Liss, Inc.
Docking of a human rhinovirus neutralizing antibody onto the viral capsid
Authors: Tormo José , Centeno Nuria B. , Fontana Emilia , Bubendorfer Thomas , Fita Ignacio , Blaas Dieter
Published: May 2005

The structure of the complex between the Fab fragment of a human rhinovirus serotype 2 (HRV2) neutralizing antibody (8F5) and a cross‐reactive synthetic peptide derived from the viral capsid protein VP2 has been recently determined by crystallographic methods.1 The conformation adopted by the peptide was very similar to and could be superimposed onto the corresponding region of the viral protein VP2 of human rhinovirus 1A (HRV1A) whose three‐dimensional structure is known.2 The structure of the Fab fragment determined in the complex was docked onto the viral capsid using the superimposition transformation found for the peptide. In the resulting model the Fab protrudes almost radially to about 60 Å from the surface of the virion without any major steric problem. The Fab fragment was then placed on each one of the 60 equivalent epitopes using the T = 1 icosahedral symmetry of the virus. The closest pairs of Fab fragments are related by viral 2‐fold axes and run almost parallel to each other without clashing. These axes of symmetry from the viral particle could thus be coincident with the dyad axes of the antibodies. Furthermore, comparison of the three‐dimensional structure of the Fab/peptide complex with the structure of the Fab fragment alone3 indicates that the flexibility of the antibody's elbow would facilitate bivalent attachment to the same viral particle. In accordance with the docking results, experimental determination of the stoichiometry of binding yielded a ratio of 30 IgG molecules per virion also suggesting bivalent attachment of antibody 8F5 onto the viral particle. The neutralization of viral infectivity, being neither aggregation (this paper) nor inhibition of receptor binding,4 might be mainly achieved by reducing viral spread from cell to cell and/or inhibition of uncoating. © 1995 Wiley‐Liss, Inc.
Crystallographic structure of metal‐free concanavalin A at 2.5 Å resolution
Authors: Bouckaert Julie , Loris Remy , Poortmans Freddy , Wyns Lode
Published: May 2005

The three‐dimensional structure of demetallized concanavalin A has been determined at 2.5 Å resolution and refined to a crystallographic R‐factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site. Large structural differences between the native and the metal‐free lectin are observed in the metal‐binding region and consequently for the residues involved in the specific binding of saccharides. The demetallization invokes a series of conformational changes in the protein backbone, apparently initiated mainly by the loss of the calcium ion. Most of the Mn2+ ligands retain their position, but the Ca2+ binding site is destroyed. The Ala207‐Asp208 peptide bond, in the β‐strand neighboring the metal‐binding sites, undergoes a cis to trans isomerization. The cis conformation for this bond is a highly conserved feature among the leguminous lectins and is critically maintained by the Ca2+ ion in metal‐bound concanavalin A. A further and major change adjacent to the isomerized bond is an expansion of the loop containing the monosaccharide ligand residues Leu99 and Tyr100. The dispersion of the ligand residues for the monosaccharide binding site (Asn14, Agr228, Asp208, Leu99, and Tyr100) in metalfree concanavalin A abolishes the lectin's ability to bind saccharides. Since the quaternary structure of legume lectins is essential to their biological role, the tetramer formation was analyzed. In the crystal (pH 5), the metal‐free concanavalin A dimers associate into a tetramer that is similar to the native one, but with a drastically reduced number of inter‐dimer interactions. This explains the tetramer dissociation into dimers below pH values of 6.5. © 1995 Wiley‐Liss, Inc.
Protein–protein interaction at crystal contacts
Authors: Janin Joel , Rodier Francis
Published: May 2005

Packing contacts are crystal artifacts, yet they make use of the same forces that govern specific recognition in protein‐protein complexes and oligomeric proteins. They provide examples of a nonspecific protein‐protein interaction which can be compared to biologically relevant ones. We evaluate the number and size of pairwise interfaces in 152 crystal forms where the asymmetric unit contains a monomeric protein. In those crystal forms that have no element of 2‐fold symmetry, we find that molecules form 8 to 10 pairwise interfaces. The total area of the surface buried on each molecule is large, up to 4400 Å2. Pairwise interfaces bury 200–1200 Å2, like interfaces generated at random in a computer simulation, and less than interfaces in protease‐inhibitor or antigen‐antibody complexes, which bury 1500 Å2 or more. Thus, specific contacts occurring in such complexes extend over a larger surface than nonspecific ones. In crystal forms with 2‐fold symmetry, pairwise interfaces are fewer and larger on average than in the absence of 2‐fold symmetry. Some bury 1500–2500 Å2, like interfaces in oligomeric proteins, and create “crystal oligomers” which may have formed in the solution before crystallizing. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei
Authors: Knapp Stefan , Rüdiger Andrea , Antranikian Garabed , Jorgensen Per L. , Ladenstein Rudolf
Published: May 2005

The thermostable amylopullulanase from Pyrococcus woesei was crystallized. Crystals, suitable for a crystallographic analysis up to a size of 0.6 mm in their longest dimension, have been obtained by the vapor diffusion method in a solution containing polyethyleneglycol 4000 (PEG 4000), isopropanol, and Tris/Cl− buffer pH 7.5. Crystals grown under these conditions form hexagonal rods and diffract to a maximum resolution of 3 Å. The crystals belong to the trigonal lattice type with the spacegroup P3121 or P3221, respectively, have the cell dimensions a = b = 96.8 Å, c = 196.2 Å, α = β = 90°,γ = 120°. The crystals have a theoretical packing density of 2.7 Å3/Da, assuming one molecule with a molecular weight of 88.8 kDa in the asymmetric unit. Furthermore the self‐rotation analysis of the dataset revealed only crystallographic symmetries. The merged native data of two crystals resulted in a 88% complete dataset. © 1995 Wiley‐Liss, Inc.
Stereochemistry and the mass spectra of some 1,3‐ and 3,1‐perhydrobenzoxazines
Authors: Pihlaja Kalevi , Vainiotalo Pirjo , Fülöp Ference , Bernáth Gábor
Published: May 2005

cis‐Anellated 3‐methyl‐ (1) and cis (2)‐ and trans (3)‐anellated 2,3‐dimethyl‐1,3‐perhydrobenzoxazines and the corresponding 3,1‐perhydrobenzoxazines (4, 5a, 5b, and 6, respectively) have been prepared and their configurations assigned with 1H NMR spectroscopy. The electron‐impact induced fragmentations differentiate clearly the two sets of isomers since only the [MH]+ and [MMe]+ ions from 1–3 exhibit an appreciable retro Diels‐Alder reaction giving rise to the ions m/z 72 and/or m/z 86. Besides the main reaction, elimination of methyl radical, isomers 5a, 5b and 6 also eliminate C3H and C2H3O− forming the ions [C7H12NO]+ and [C8H16N]+, at m/z 126. The formation of the former is most favourable for 5a, 5b both for reasons of chemical composition and stereochemistry. The ion C6H10NO+ at m/z 112 represents the base peak of compound 4, i.e., a methyl group at the 2‐position is a better leaving group than a hydrogen atom and the ring nitrogen assists the α ‐cleavage of the cyclohexane ring in this case. Even the mass spectra of the isomeric cis‐ and trans‐annellated forms (2 vs 3 and 5a, 5b vs 6) can be distinguished from each other on the basis of some intensity differences caused by stereochemical effects. However, the two epimeric cis forms 5a and 5b gave indistinguishable spectra. The characteristic decompositions have been verified by low resolution, high resolution, metastable and collision‐induced dissociation techniques. The compounds studied could not be differentiated based on their ammonia or isobutane chemical‐ionization spectra.
Application of continuous‐flow liquid chromatography/fast‐atom bombardment mass spectrometry to the analysis of diagnostic acylcarnitines in human urine
Authors: Norwood Daniel L. , Kodo Naoki , Millington David S. , Gaskell S. J.
Published: May 2005

Acylcarnitine profiles of diagnostic value were generated from the equivalent of 0.1 μL of raw urine using the continuous‐flow liquid chromatography/fast‐atom bombardment mass spectrometry (LC/FAB‐MS) interface for sample introduction. Further analysis was accomplished by gradient LC/MS using a commercially available packed fused‐silica microbore column.
Combined supercritical‐fluid chromatography/mass spectrometry in the analysis of diuron in plasma using on‐line phase‐system switching
Authors: Niessen W. M. A. , de Kraa M. A. G. , Verheij E. R. , Bergers P. J. M. , La Vos G. F. , Tjaden U. R. , van der Greef J.
Published: May 2005

On‐line sample pretreatment by means of the phase‐system switching approach is an interesting technique for the analysis of aqueous samples, e.g., plasma, by means of supercritical‐fluid chromatography. In order to analyse plasma samples the following analytical procedure is used. The plasma sample is injected on to a short precolumn, which is washed with water and subsequently dried with nitrogen. Next, the solutes are desorbed with the supercritical mobile phase, analysed with packed‐column supercritical‐fluid chromatography and detected with either a UV detector or a mass spectrometer, equipped with a moving‐belt interface. The herbicide diuron is selected as a test compound to study the feasibility of this approach. Using a selective detector the procedure is sufficiently sensitive to detect diuron in plasma, but not appropriate to detect the diuron metabolites in a post‐mortem plasma sample. These have been identified with liquid chromatography/mass spectrometry. The detection limit of diuron in plasma using the procedure described is about 30 ng/mL.
Mass spectrometry of sulphur‐containing compounds. 3. The behaviour of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides
Authors: Traldi P. , Bravo P. , Resnati G. , Bortolini O.
Published: May 2005

The electron ionization and chemical ionization mass spectrometry of some diastereomeric β‐hydroxy‐γ‐fluoro alkyl aryl sulphoxides is described and the mechanisms of the common fragmentation patterns are discussed with the aid of linked scans at constant B/E and at constant B2/E, mass‐analysed ion kinetic energy spectra and labelling experiments.
Collision‐induced dissociations of peptide ions 2. Remote charge‐site fragmentations in a tandem, hybrid mass spectrometer
Authors: Alexander A. J. , Thibault P. , Boyd R. K.
Published: May 2005

Collision‐induced dissociation of peptide ions yields „sequence”︁ ions arising from dissociations of the peptide backbone. Recently, Biemann and his collaborators have elucidated fragment ions involving cleavage of all or part of the side‐chains, and have characterized them as remote‐site fragmentations of the type investigated for other molecular species by Gross et al. The present work reports results of experiments conducted using a tandem, hybrid mass spectrometer, and devoted to investigating whether remote‐site fragmentations (including side‐chain cleavages for peptide ions) can be observed for collision energies substantially lower than the keV range used previously. It was found that (laboratory‐frame) collision energies of at least 200 eV, and preferably greater, are required for the formation of such fragments. At collision energies in this range the transmission efficiency of the qQ assembly is much lower than for the more usual range of a few tens of eV; this drop in transmission efficiency becomes increasingly severe with increasing mass of the precursor.
Mass range extension in a quadrupole ion‐trap mass spectrometer
Authors: Kaiser Raymond E. , Cooks R. Graham , Moss James , Hemberger Phillip H.
Published: May 2005

A quadrupole ion‐trap mass spectrometer having half the dimensions of the commercial ion‐trap instrument has been built. When operated in the mass‐selective instability mode using the commercial electronics and data system and the standard vacuum system, it yields a mass range of > 2500 Da. This represents achievement of the expected fourfold increase in mass range upon halving the trap radius (to 0.5 cm). The sensitivity of the miniature trap is comparable to that of the commercial ion‐trap; however, resolution is inferior, partly due to the high mass‐scan rate. The effects of using relatively high pressures of helium as a buffer gas are discussed in relation to improving sensitivity and resolution. The use of the high‐mass ion‐trap as a device for studying biomolecules is discussed and methods of extending the mass range even further are suggested.
Fast‐atom bombardment and thermospray mass spectrometry for the characterization of two glucuronide metabolites of methapyrilene
Authors: Lay J. O. , Getek T. A. , Kelly D. W. , Slikker W. , Korfmacher W. A.
Published: May 2005

Two conjugated metabolites of methapyrilene hydrochloride isolated from mouse‐hepatocytes were examined by mass spectrometry using fast‐atom bombardment (FAB) and thermospray ionization. The major metabolite, methapyrilene glucuronide, was identified based on a prominent peak due to the protonated molecule as well as the loss of the dimethylamine and sugar moieties. Identification of the second metabolite was complicated by large signals associated with the biological sample matrix. The complementary nature of the fragmentation observed in the mass spectra using FAB and thermospray ionization allowed this metabolite to be identified as the desmethylmethapyrilene glucuronide. The fragmentation observed using FAB ionization was not greatly affected by the presence of the glucuronide moiety. While loss of the sugar moiety indicated a glucuronide, additional fragmentation confirmed the presence of the underlying ethylenediamine substructure which is characteristic of this class of antihistamines.
Mass spectrometric indication of double‐bond position in dodecenyl acetates based on a fuzzy classification
Authors: Horiike Michio , Gu Yuan , Hirano Chisato
Published: May 2005

Ten positional isomers of dodecenyl acetate were analyzed by conventional combined gas chromatography/electron ionization mass spectrometry. The relative intensities of some predominant fragments in the isomers examined varied with the double‐bond position in the chain. The mass spectra were interpreted in terms of the standard parameters, similarity coefficients, clustering weight and clustering coefficients. The original double‐bond position in the acetates was located unambiguously.
Ion‐spray mass spectrometry of marine neurotoxins
Authors: Quilliam Michael A. , Thomson Bruce A. , Scott George J. , Siu K. W. Michael
Published: May 2005

Ion‐spray mass spectrometry was investigated for the analysis of three marine neurotoxins: domoic acid, saxitoxin and tetrodotoxin. All three compounds gave positive‐ion spectra with abundant ions of protonated molecules and no significant fragmentation. Domoic acid gave a negative‐ion spectrum with a strong [M–H]−ion. Tandem mass spectrometry provided useful fragment‐ion spectra for all compounds. Detection limits for flow injection analyses with selected‐ion monitoring were determined to be 30 pg for saxitoxin, 100 pg for domoic acid and 200 pg for tetrodotoxin. Combining liquid chromatography with ion‐spray mass spectrometry allowed the determination of domoic acid and some of its isomers in toxic shellfish tissue extracts.
The oxyisocyanate [ONCO]− and amidoisocyanate [HNNCO]− negative ions
Authors: Waugh Russell J. , Eichinger Peter C. H. , O'Hair Richard A. J. , Sheldon John C. , Bowie John H. , Hayes Roger N.
Published: May 2005

Ab initio calculations indicate that the ion [ONCO]− is linear, whereas [HNNCO]− is effectively coplanar. The ions may be formed by collisional activation of deprotonated hydroxy and aminocarbamates. The characteristic fragmentations of [ONCO]− and [HNNOO]− are losses of O and NH respectively.
Influence of metal ions on the acquisition and quality of 252Cf plasma‐desorption mass spectra
Authors: Deprun Claude , Szabó Ladislas
Published: May 2005

The presence of a few mol per cent of Ca2+ ions considerably modified the 252Cf plasma‐desorption mass spectrum of a phosphorylated glycolipid. In the negative‐ion mode, increasing amounts of Ca2+ caused gradual disappearance of the spectrum; it was quenched at the molar ratio 3 Ca2+/4 glycolipid. Clusters as big as 5500 were observed at certain ratios of Ca2+/glycolipid. Similar, but less pronounced effects were seen in the positive‐ion mode.
Charge separation of triply charged ions
Authors: Hagan D. A. , Eland J. H. D.
Published: May 2005

Formation of multiply charged ions is shown to contribute a significant fraction of the total ionization by high energy electrons, and multiple ionization is almost always followed by charge‐separation reactions. Triple ionization and subsequent dissociations can be well characterized by the electron‐three ion coincidence technique. Results obtained using this new technique are compared with computer simulations of the dissociations of OCS3+ and SO3+2, and the initial momenta and relátive angles of all three fragments are thereby determined. Triply charged benzene ions are shown to undergo many competing charge‐separation reactions.
Determination of appearance energy for ions formed in the gaseous phase over alkali iodide and rare earth iodide systems
Authors: Popovič A. , Muhič S. , Marsel J. , Ajtony Zs. , Bencze L. , Kaposi O. , Zmbov K. F.
Published: May 2005

Knudsen cell mass spectrometric measurements are reported on the composition of vapour over solid and fused NaI, CsI, HoI3, DyI3, (NaI + HoI3), (NaI + DyI3, (CsI + HoI3) and (CsI + DyI3 systems. For the determination of evaporation thermodynamics, the assignment of the essential ions to their neutral precursors was carried out by determining ionization efficiency curves. Due to the spread in electron energy, the linear extrapolation and vanishing current methods, which are generally used in high temperature mass spectrometry for evaluation of efficiency curves, could be used with limitations only. The analytical energy‐distribution difference method was used to determine the fine structure of the ionization efficiency curves. The method uncovered relationships between the detected ions and neutral vapour‐phase species, and served to determine thermodynamic data with improved precision.
Mass spectrometry of some carbamoyl‐ and thiocarbamoylcyclohexanones
Authors: Srzić D.
Published: May 2005

The fragmentation of some carbamoyl‐ and thiocarbamoylcyclohexanones under electron ionization has been investigated by means of high‐ and low‐resolution mass spectrometry and deuterium labelling. Some characteristic fragmentation processes observed in the mass spectra of thiocarbamoylcyclohexanones indicate that both keto and enol forms of their molecular ions exist in the gas phase. The fragmentation data for carbamoylcyclohexanone show that the keto form is largely predominant in the keto‐enol tautomeric equilibrium.
Kinetic energy release in metastable‐ion fragmentations
Authors: Burgers Peter C. , Holmes John L.
Published: May 2005

The average kinetic energy, (〈T〉), released in a number of well known metastable‐ion decompositions (reaction‐time 10−5‐10−6s−1) has been related to the excess energy in the fragmenting ion (E). It was observed that for small values of E (< 1 eV) the fraction of energy released, 〈T〉/E, increases rapidly as E decreases, as predicted by statistical theory.
Philanthotoxins. A mass spectrometric investigation
Authors: Kenny Peter T. M. , Goodnow Jr Robert A , Konno Katsuhiro , Nakanishi Koji
Published: May 2005

A method employing liquid secondary‐ion mass spectrometry (SIMS) in conjunction with metastable‐ion measurements (linked scanning at constant B/E) to obtain sequence‐specific information for three synthetic polyamine isomers was developed. The normal liquid SIMS spectra gave molecular weight information, but important sequence ions were of low intensity or obscured by the background. The metastable‐ion spectra contained important fragment ions in particular due to cleavage along the polyamine chain. One of the three synthetic isomers was identical with a toxin present in the venom of the digger wasp. In conjunction with nuclear magnetic resonance spectroscopic studies, this should be a powerful method for the structural characterization of other closely related toxins present in the venom of this wasp.
Fourier transform ion cyclotron resonance study of the gas‐phase reaction of the yttrium ion with silane
Authors: Decouzon M. , Gal J‐F. , Géribaldi S. , Rouillard M. , Sturla J‐M. , Bouchoux G.
Published: May 2005

Preliminary results obtained with a home‐made Fourier transform ion cyclotron resonance mass spectrometer on the sequential clustering reactions of silane using yttrium cation activation are reported. [YSinH2n]+ and [YSinH2n − 2]+ ions are formed. So far, we have observed these ions up to n = 7, and a sequential clustering mechanism is proposed. The ion structures are characterized by collision‐induced dissociation, and kinetic measurements to determine the formation and decay rates of each ion are performed.
The formation of cyclopentadienone ions. An internal oxidation process
Authors: Maquestiau A. , Flammang R. , Govaert Y. , Chen L. Z. , Longevialle P.
Published: May 2005

1‐(2‐nitrophenyl)benzotriazole loses nitrogen upon electron ionization. This reaction is followed by a Wolff‐type ring contraction to give cyclopentadienylidene methanimine ions which undergo an internal oxidation process producing ionized cyclopentadienone.
Plasma‐desorption mass spectrometry of intact enzymes and proenzymes
Authors: Lacey M. P. , Keough T. , Chait B. T.
Published: May 2005

The plasma desorption (PD) mass spectra of several enzymes and proenzymes are reported. Chymotrypsin and chymotrypsinogen both yield usable PD mass spectra; however, the single‐chain chymotrypsinogen exhibits better sensitivity and less fragmentation than the multi‐chain chymotrypsin. Porcine pepsinogen contains 11 more basic residues (lysine and arginine) than porcine pepsin, but this does not lead to an increase in positive ion response. In fact, the additional basic residues may hinder response by increasing the strength of the interaction between the protein and the nitrocellulose surface. A series of subtilisins showed comparable PD mass spectrometric, response despite the fact that they differ considerably in primary sequence. Finally, PD mass spectrometry was used to correct the previously reported mass of a heat‐stable protease, a value that we found to be in error by almost 5000 Da.
Translational energy release and stereochemistry of steroids. 14. Epimeric dihydroxy steroids of the androstane series
Authors: Zaretskii Z. V. I. , Ghosh D. , Brenton A. G. , Beynon J. H.
Published: May 2005

The stereochemistry of dihydroxy steroids, both the mode of the A/B ring junctions and the configuration of OH groups, may be determined from translational energy (T50%) measurements for the loss of a CH3 radical, from the ratios of metastable‐ion peak heights to those of the main beam (determined for the dehydration reactions), and by comparing unimolecular and collision‐induced, mass‐analysed ion kinetic energy spectra of the new main beam of [M H2O]+˙ ions (i.e. those formed via dehydration of metastable molecular ions of epimeric hydroxy steroids in the first field‐free region of a double‐focusing mass spectrometer).
Gas chromatography/negative‐ion chemical ionization mass spectrometry of tertiary amines following Hofmann degradation. Application to the characterization of Loperamide
Authors: Leis Hans Jörg
Published: May 2005

A method for negative‐ion chemical ionization mass spectrometry of tertiary amines with special reference to the antidiarrhoeal Loperamide is presented. The method involves quaternization by reaction with pentafluorobenzyl bromide, conversion to the hydroxide base with silver oxide; subsequent Hofmann degradation occurs in the hot injector of the gas chromatograph. The method shows greater sensitivity than more orthodox Hofmann degradation reactions.
Three stable (PhenylC7H) isomers
Authors: Stone David J. M. , Eichinger Peter C. H. , Bowie John H.
Published: May 2005

Stable PhC7H isomers may be formed by deprotonation of diphenylmethane, phenylcycloheptatriene and 7‐phenylnorbornadiene. Each species has a characteristic fragmentation pattern—the elucidation of which is aided by deuterium‐labelling studies. There is no evidence of interconversion of the three species.
Metastable ions arising from pseudomolecular [M  H]− ions produced by fast‐atom bombardment negative‐ion mass spectrometry of ecdysteroids
Authors: Evershed Richard P. , Prescott Mark C. , Kabbouh Mohamed , Rees Huw H.
Published: May 2005

Metastable ions arising from pseudomolecular [M  H]− ions produced by fast‐atom bombardment negative‐ion mass spectrometry of a range of free ecdysteroids, ecdysteroid conjugates and polar metabolites were investigated by means of linked scanning at constant B/E. Free ecdysteroids displayed daughter‐ion spectra which allow 20‐hydroxyecdysteroids and ecdysteroids lacking C‐20 hydroxylation to be readily distinguished. The ejection of acetic acid from acetylated ecdysteroids was also readily detectable. Characteristic metastable‐ion decomposition of ecdysteroid acids was not observed, presumably as a result of charge localization. High‐mass daughter ions were also lacking in the case of phosphate conjugates.
Laser desorption/fourier transform mass spectrometry of organometallic complexes
Authors: Bjarnason Asgeir
Published: May 2005

A study of the analytical potential of laser desorption Fourier transform mass spectrometry for the mass spectral analysis of complexes is reported. Two platinum complexes, which are also organometallic, were successfully analyzed using this technique. Previous attempts using fast‐atom bombardment mass spectrometry had not yielded any useful information for these compounds. Two complexes of a different nature, 1,3‐bis(diphenylphosphino)propanenickel(II) chloride and N,N′ ‐bis(salicylidene)dianilinocobalt(II) were also analyzed to further evaluate this technique.
Measurement of unimolecular decay in peptides of masses greater than 1200 units by a reflecting time‐of‐flight mass spectrometer
Authors: Tang X. , Ens W. , Mayer F. , Standing K. G. , Westmore J. B. , Boyd R. K.
Published: May 2005

Daughter ions from decomposition of [M + H]+ parent ions have been observed in a time‐of‐flight mass spectrometer fitted with an ion mirror. Unit mass resolution is obtained for parent ions of masses up to several thousand u when the mirror voltage is set at a value determined by the usual velocity‐focusing criterion for parent ions. Under this condition the daughter‐ion resolution in the low‐mass range suffers. Considerable improvement is obtained when the daughter‐ion spectrum is examined in several segments, with the mirror voltage optimized for each segment. The daughter‐ion spectrum from decay of metastable [M + H]+ parent ions in Substance P is measured using this technique. Reasons are suggested for differences between the spectrum obtained and a spectrum for the same compound recently obtained using a tandem double‐focusing instrument.
The intramolecular migration of a trimethylsilyl group located α to a sulfone in substituted cyclohexyl systems
Authors: Wood K. V. , Rothwell A. P. , Anderson M. B. , Fuchs P. L.
Published: May 2005

The intramolecular migration of a trimethylsilyl moiety α to a sulfone group of some modified cylcohexyl ring systems is investigated. The large difference in the relative abundance of this rearrangement ion for similar compounds is related to the stability of the protonated species.
Capillary‐zone electrophoresis with fraction collection for desorption mass spectrometry
Authors: Takigiku Ray , Keough T. , Lacey M. P. , Schneider R. E.
Published: May 2005

A simple method for off‐line coupling of desorption mass spectrometry and capillary‐zone electrophoresis (CZE) is described. Use of a “porous glass joint”, near the cathodic end of the CZE column, facilitates fraction collection in a manner similar to that used with liquid chromatography. This method allows independent optimization of both the CZE and mass spectrometry parts of the experiment. It is directly applicable to a number of desorption mass spectrometry methods (including plasma desorption (PD) and UV laser desorption (LD)). In the present study, PD mass spectrometry was used for eluant characterization. The fraction collection procedure is described, as is mass transfer through the porous glass joint. Detection limits are discussed and the approach is illustrated by analysis of a simple mixture of bradykinin derivatives. Finally, a brief comparison to current on‐line CZE/mass spectrometric methods is presented.
Influence of sequence on the fragmentation of serine‐ and threonine‐containing peptides in 252Cf‐plasma desorption mass spectrometry
Authors: Lam‐Thanh Hung , Deprun Claude , Le Beyec Yvon
Published: May 2005

The molecular weights of four linear synthetic peptides, fragments of a snake α‐neurotoxin, were measured by 252Cf‐plasma desorption mass spectrometry. The fragmentation phenomenon observed at the level of serine and/or threonine residue with a concomitant ion/fragment association is reported for a group of two peptides (B and D) in contrast with the group (A and C) in spite of the high ratio of serine and threonine, namely peptide A. The propensity for specific fragmentation of peptide D seems to be correlated to the repetitive sequence, (Gly‐Ser)2. Finally, based on the m/z of the daughter‐ions measured, we propose an overall mechanism as an N→O acyl shift analogous to that observed for serine‐ and threonine‐ containing peptides in solution chemistry.
Translational energy release and stereochemistry of steroids 15. Reaction conformations of metastable molecular ions in stereoisomers of 3‐hydroxy steroids
Authors: Zaretskii Z V I , Ghosh D , Brenton A G , Beynon J H
Published: May 2005

The reaction conformations of the metastable molecular ions of the 3‐hydroxy steroids were characterized using translational energy (T50%) release values and the ratios of metastable‐ion peak heights to those of the main beams determined for the M+· → [M‐H2O]+· reactions.
Types of quasimolecular ions in thermospray ionization
Authors: Maeder H.
Published: May 2005

Thermospray mass spectra are usually dominated by [M + H]+ and [M + NH4]+ quasimolecular ions. Several years' work with various classes of compounds using the technique of liquid chromatography/thermospray ionization mass spectrometry has given us the opportunity of observing further adduct ions of lower intensity. Knowledge about these ions facilitates interpretation of thermospray spectra, enables the analysis of peak purity and gives additional confirmation of correct molecular weight assignment.
Mass spectral fragmentations of ionized alkylperhydro‐1,3‐oxazines
Authors: Vainiotalo Pirjo , Romppanen Tuula , Mälkönen Pentti J.
Published: May 2005

The mass spectral fragmentations of perhydro‐1,3‐oxazine and twelve of its alkyl derivatives were studied by metastable‐ion analysis and exact mass measurement. The role of the nitrogen atom was dominant in these fragmentations. Almost all the primary decompositions of the molecular ions started as α‐cleavage reactions with respect to the nitrogen atom, leading to the loss of a substituent from an adjacent carbon or to a ring‐cleavage reaction. Preference for the ring‐cleavage reaction was increased by a substituent at position 2. Some rearrangement reactions were observed as well. The expulsion of C2H3O˙ from the molecular ion was particularly favoured for the 3‐methyl substituted compounds. In this elimination, ring carbons 5 and 6 were lost simultaneously with a hydrogen atom transfer to the nitrogen atom.
Fragment pathway analysis using automated tandem mass spectrometry on an ion‐trap mass spectrometer
Authors: Pannell L. K. , Quan‐long Pu , Mason R. T. , Fales H. M.
Published: May 2005

A “key‐sequence” procedure is presented for the automated tandem mass spectrometric analysis of compounds on a Finnigan ion‐trap mass spectrometer. This allows fragmentation pathways of a range of masses or even a complete spectrum to be prepared automatically, obviating the tiresome preparation and optimization of individual scan‐editor files. The procedure is limited by the speed of the driving computer; an “IBM‐AT”, for example, permits more than 10 mass units to be scanned per minute. It is calibrated with perfluorotributylamine and methyl stearate is used to demonstrate its results. The Finnigan ion‐trap “programming option” is necessary for implementation of the procedure.
Peptide sequencing with electrospray ionization on a magnetic sector mass spectrometer
Authors: Meng C. K. , McEwen C. N. , Larsen B. S.
Published: May 2005

Sequence information is obtained by in‐source fragmentation of electrospray‐generated peptide ions. The complete sequences of leucine enkephalin, angiotensin I, and renin substrate are determined from their fragment ions and consume only low picomole amounts of material. The method involves collision‐induced fragmentation of singly and multiply charged molecular ions in the electrospray ion source and does not involve tandem mass spectrometric instrumentation. The charge on the fragment ions is determined by the spacing of the isotope peaks.
Mass spectrometric investigation of the thermal decomposition of lithium fluoroborate
Authors: Veljković Miomir , Ya. Borshcevskii Adrey , Nešković Olivera , Miletić Miodrag , Golobočanin Dušan , Vaisberg Victorya E. , Zmbov Kiro F.
Published: May 2005

Evaporation of crystalline LiBF4 was studied by Knudsen‐cell mass spectrometry in the temperature range 70–140°C. Only BF3 molecules were identified in the saturated vapour. The temperature dependence of BF3 pressure was measured and ΔrH°374 = 105.4 ± 9.6 kJ mol−1 for the reaction LiBF4(c) = LiF(c) + BF3(g) was obtained from the second‐law analysis. The corresponding heat of formation ΔfH° (LiBF4, c, 374) = −1856.4 ± 10.5 kJ mol−1 was evaluated and compared with Literature data.
Singlet/Triplet excitation (X1∑+→a3IIr) of CO by N+ and O+˙
Authors: Lee A. R. , Enos C. S. , Brenton A. G.
Published: May 2005

Vibrational excitation of CO by N+ and O+˙ is investigated by means of high‐resolution translational energy spectroscopy. The spectra display unusual features which are discussed in relation to the Wigner spinconservation rule. Reaction channels involving CO (X1Σ+→a3Πr) are prominently featured.
The gas phase benzilic acid rearrangement
Authors: Hayes Roger N. , Eichinger Peter C. H. , Bowie John H.
Published: May 2005

Reaction of benzil with HO− in the chemical ionization source of a triple‐analyser mass spectrometer forms a [benzl + HO−] ion. This ion, upon collisional activation, gives a mass spectrum identical to that obtained from deprotonated benzilic acid under the same experimental conditions.
Analysis of multi‐domain cellulolytic enzymes by UV‐laser induced desorption mass spectrometry
Authors: Perera I. K. , Uzcategui E. , Håkansson P. , Brinkmalm G. , Pettersson G. , Johansson G. , Sundqvist B. U. R.
Published: May 2005

This paper reports the application of matrix‐assisted UV‐laser induced desorption (LID) mass spectrometry for the analysis of some extracellular multi‐domain cellulolytic enzymes, in the molecular weight range 5000–90 000 u, produced by the fungi Phanerochaete chrysosporium and Trichoderma reesei. A high sensitivity (1–10pmol of protein), has been attained in obtaining the mass spectra of these highly glycosylated enzymes and some of their peptides, with carbohydrate content in the 10–40% range. The desorption of samples containing the enzymes mixed with a protein having an accurately known molecular weight—an internal calibrant—is also demonstrated. Spectra from complete enzymes and their functional domains are presented to explore the possibilities of employing LID for obtaining structural information.
Fast‐Atom bombardment mass spectrometry and collisional spectroscopy in the structural characterization of underivatized 1,4‐benzodiazepines
Authors: Ghezzo E. , Traldi P. , Minghetti G. , Cinellu M. A. , Bandini A. L. , Banditelli G. , Zecca L.
Published: May 2005

Fast‐atom bombardment (FAB) mass spectrometry linked with collision spectroscopy has been employed for the structural characterization of eight underivatized 1,4‐benzodiazepines. Both positive‐ and negative‐ion FAB led, in all cases examined, to the production of abundant molecular species. Collision experiments performed on such ions gave rise to the identification of diagnostic fragment ions, that could be related to the original structure.
Artifacts in four‐sector tandem mass spectrometry
Authors: Falick A. M. , Medzihradszky Katalin F. , Walls F. C.
Published: May 2005

Several types of artifacts were shown to be present in 4‐sector tandem collision‐induced dissociation (CID) mass spectra. In CID spectra of protonated peptides produced by liquid secondary‐ion mass spectrometry (LSIMS), peaks corresponding to successive losses of matrix molecules from the precursor ion were observed. In addition, peaks corresponding to MH+ ions of smaller peptides that were also present in the sample/matrix mixture in greater abundance than the selected precursor ion were observed. Both of these types of artifact peaks were shown to originate from the ‘peak‐at‐every‐mass’ chemical noise at the same nominal mass as that selected by the first 2 sectors (MS1). These noise ions are transmitted through to the collision cell and produce fragments that are analysed and detected in the next 2 sectors (MS2). A second, unrelated, kind of artifact was found to be due to decompositions in the second field‐free region of MS2 in an EBEB geometry machine. These artifacts, which are detectable over only a very limited mass range when using a conventional single‐point detector, can be present over a much greater mass range when an array detector is used and when the collision cell is floated above ground potential. A clear understanding of the origins of all peaks in a CID spectrum is important in order to have a firm foundation for interpretation, manual or computer‐aided, of the spectra of unknown compounds.