bluuebunny/crossref_metadata_2025 huggingface dataset:
A critical assessment of comparative molecular modeling of tertiary structures of proteins*
Authors: Mosimann Steven , Meleshko Ron , James Michael N. G.
Published: May 2005

In spite of the tremendous increase in the rate at which protein structures are being determined, there is still an enormous gap between the numbers of known DNA‐derived sequences and the numbers of three‐dimensional structures. In order to shed light on the biological functions of the molecules, researchers often resort to comparative molecular modeling. Earlier work has shown that when the sequence alignment is in error, then the comparative model is guaranteed to be wrong. In addition, loops, the sites of insertions and deletions in families of homologous proteins, are exceedingly difficult to model. Thus, many of the current problems in comparative molecular modeling are minor versions of the global protein folding problem. In order to assess objectively the current state of comparative molecular modeling, 13 groups submitted blind predictions of seven different proteins of undisclosed tertiary structure. This assessment shows that where sequence identity between the target and the template structure is high (> 70%), comparative molecular modeling is highly successful. On the other hand, automated modeling techniques and sophisticated energy minimization methods fail to improve upon the starting structures when the sequence identity is low (∼30%). Based on these results it appears that insertions and deletions are still major problems. Successfully deducing the correct sequence alignment when the local similarity is low is still difficult. We suggest some minimal testing of submitted coordinates that should be required of authors before papers on comparative molecular modeling are accepted for publication in journals. © 1995 Wiley‐Liss, Inc.
Evaluation of comparative protein modeling by MODELLER
Authors: Šali Andrej , Potterton Liz , Yuan Feng , van Vlijmen Herman , Karplus Martin
Published: May 2005

We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non‐conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X‐ray structure of ≈ 1 Å, in large part because the templates are likely to be that similar to the X‐ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X‐ray crystallography structures of the same protein. © 1995 Wiley‐Liss, Inc.
Threading a database of protein cores
Authors: Madej Thomas , Gibrat Jean‐François , Bryant Stephen H.
Published: May 2005

We present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”1 The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then‐known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small “register shifts” of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures. Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the “cores” of known structures and errors arising from inherent limitations in the threading potential. It would appear from the results that successful substructure recognition depends most critically on accurate definition of the “fold” of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution. © 1995 Wiley‐Liss, Inc.
Progress in fold recognition
Authors: Flöckner Hannes , Braxenthaler Michael , Lackner Peter , Jaritz Markus , Ortner Maria , Sippl Manfred J.
Published: May 2005

The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition. © 1995 Wiley‐Liss, Inc.
Evaluation of current techniques for Ab initio protein structure prediction
Authors: Defay Tom , Cohen Fred E.
Published: May 2005

The results of a protein structure prediction contest are reviewed. Twelve different groups entered predictions on 14 proteins of known sequence whose structures had been determined but not yet disseminated to the scientific community. Thus, these represent true tests of the current state of structure prediction methodologies. From this work, it is clear that accurate tertiary structure prediction is not yet possible. However, protein fold and motif prediction are possible when the motif is recognizably similar to another known structure. Internal symmetry and the information inherent in an aligned family of homologous sequences facilitate predictive efforts. Novel folds remain a major challenge for prediction efforts. © 1995 Wiley‐Liss, Inc.
Toward understanding the structure and interactions of microtubules and motor proteins
Authors: Wade R. H. , Horowitz R. , Milligan R. A.
Published: May 2005

To obtain an overall three‐dimensional picture of the interaction between microtubules and the motor proteins of the kinesin family it will be necessary to take account of both atomic resolution structures obtained by X‐ray crystallography and medium resolution reconstructions obtained by electron cryomicroscopy. We examine the problems associated with obtaining the required structural information from electron micrographs of vitreous ice‐embedded microtubules decorated with motor domains. We find that the minus‐end directed motor, ncd, decorates microtubules with an 80 Å periodicity as for kinesin. Our theoretical analysis and experiments with ncd illustrate the difficulty in determining unambiguously the surface lattice organization by diffraction analysis of micrographs. 3D reconstructions of decorated microtubules are required to accurately locate the motor domains. Helical diffraction theory is not usually applicable because microtubules are cylindrical structures that rarely have complete helical symmetry. We propose using a back‐projection method based on the long pitch helices formed by individual protofilaments. Model reconstructions show that this approach is feasible. © 1995 Wiley‐Liss, Inc.
Binding geometry of α‐helices that recognize DNA
Authors: Suzuki Masashi , Gerstein Mark
Published: May 2005

Many transcription factors have an α‐helix that binds to DNA bases in a specific fashion. The DNA‐binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call α. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for α. © 1995 Wiley‐Liss, Inc.
Fermenter production of an artificial fab fragment, rationally designed for the antigen cystatin, and its optimized crystallization through constant domain shuffling
Authors: Schiweck Wolfram , Skerra Arne
Published: May 2005

The synthetic antibody model “M41” was rationally designed with a binding site complementary to chicken egg white cystatin as the prescribed antigen. In order to permit comparison between the computer model and an experimental three‐dimensional structure of the artificial protein, its X‐ray crystallographic analysis was pursued. For this purpose, M41 was expressed as a recombinant Fab fragment in E. coli by medium cell density fermentation employing the tightly regulated tetracycline promoter. The Fab fragment was efficiently purified via a His‐6 tail fused to its heavy chain and immobilized metal affinity chromatography. To raise the chances for the productive formation of crystal packing contacts, three versions of the Fab fragment were generated with differing constant domains. One of these, the variant with murine CK and CH1γ1 domains, was successfully crystallized by microseeding in a sitting drop. The orthorhombic crystals exhibited symmetry of the space group P212121 with unit cell dimensions a = 104.7 Å, b = 113.9 Å, c = 98.8 Å and diffracted X‐rays to a nominal resolution of 2.5 Å. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray crystallographic analysis of ImmE7 protein of colicin E7
Authors: Ku Wen‐Yen , Wang Ching‐Shao , Chen Chieh‐Yen , Chak Kin‐Fu , Safo Martin K. , Yuan Hanna S.
Published: May 2005

The ImmE7 protein, which can bind specifically to the DNase colicin E7 and neutralize its bactericidal activity, has been purified and crystallized in two different crystal forms by vapor diffusion method. The orthorhombic crystals belong to space group I222 or I212121 and have unit cell dimensions a = 75.1 Å, b = 50.5 Å, and c = 45.4 Å. The second form is monoclinic space group P21 with ceil dimensions a = 29.3 Å, b = 102.7 Å, c = 53.0 Å and β = 91.5°. The orthorhombic crystals diffract to 1.8 Å resolution, and are suitable for high‐resolution X‐ray analysis. © 1995 Wiley‐Liss, Inc.
Crystallization and X‐ray analysis of a single fab binding domain from protein L of Peptostreptococcus magnus
Authors: Sohi Maninder K. , Wan Tommy , Sutton Brian J. , Atkinson Tony , Atkinson Max A. , Murphy Jonathan P. , Bottomley Stephen P. , Gore Michael G.
Published: May 2005

Protein L is a multi domain cell wall constituent of certain strains of Peptostreptococcus magnus which binds to the variable domain of immunoglobulin κ‐light chains. A single immunoglobulin‐binding domain of Mr = 9000 from this protein has been isolated and crystallized. The crystals are of space group P42212, with cell dimensions a = b = 66.9 Å, c = 68.3 Å, and diffract to at least 2.2 Å resolution. The asymmetric unit of the crystal contains two molecules of the protein L domain, related by a noncrystallographic 2‐fold axis, as revealed by a self‐rotation function calculated with native diffraction data. © 1995 Wiley‐Liss, Inc.
Microstructural modification of nc‐Si/SiOx films during plasma‐enhanced chemical vapor deposition
Authors: Zhang X. W.
Published: May 2005

Nanocrystalline‐silicon embedded silicon oxide films are prepared by plasma‐enhanced chemical vapor deposition (PECVD) at 300 °C without post‐heat treatment. Measurements of XPS, IR, XRD, and HREM are performed. Microstructural modifications are found occurring throughout the film deposition. The silica network with a high oxide state is suggested to be formed directly under the abduction of the former deposited layer, rather than processing repeatedly from the original low‐oxide state of silica. Nanocrystalline silicon particles with a size of 6–10 nm are embedded in the SiOx film matrix, indicating the potential application in Si‐based optoelectronic integrity. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A time‐of‐flight mass analyzer with high resolving power
Authors: Grix R. , Kutscher R. , Li G. , Grüner U. , Wollnik H. , Matsuda H.
Published: May 2005

It is shown that time‐of‐flight mass analyzers are capable of reaching high mass resolving powers as compared to sector field instruments. By combining a new electron‐impact ion source with an optimized grid‐free ion mirror, mass resolving powers m/Δm of about 20000 are reached.
Cytidylate cyclase activity: Identification of cytidine 3′,5′‐cyclic monophosphate and four novel cytidine cyclic phosphates as biosynthetic products from cytidine triphosphate
Authors: Newton R. P. , Hakeem N. A. , Salvage B. J. , Wassenaar G. , Kingston E. E.
Published: May 2005

Identification of cytidine 3′,5′‐cyclic monophosphate (cyclic CMP) as one of the products resulting from the incubation of dialysed cell‐free preparations from rat brain, liver and kidney with cytidine 5′‐triphosphate (CTP) is described. The non‐acidic precipitable products after incubation of the tissue preparations with unlabelled, with 14C‐single labelled, and with 14C‐ and 32P‐dual labelled CTP were examined by thin‐layer chromatography and high‐pressure liquid chromatography, isotopic ratio determination, UV absorbance spectrophotometry, selective hydrolysis with nucleotidase, phosphodiesterase and acid, and by fast atom bombardment mass spectrometry with mass‐analysed ion kinetic energy spectrum scanning. In addition to cyclic CMP and unchanged CTP, the products of the reaction were found to include cytidine monophosphate (CMP) and cytidine diphosphate (CDP) together with four novel cytidine compounds identified as cytidine 3′,5′‐cyclic pyrophosphate, cytidine 2′‐monosphosphate 3′,5′‐cyclic monophosphate, cytidine 2′‐O‐aspartyl‐3′,5′‐cyclic monophosphate and cytidine 2′‐O‐glutamyl‐3′,5′‐cyclic monosphate. The evidence presented constitutes conclusive proof of the natural occurrence of cytidylate cyclase activity; the four novel cytidine cyclic phosphates described provide a feasible explanation of the discrepancies in previous reports which have led to the controversy which exists concerning the existence of cytidylate cyclase activity.
Identification of C4H9O+ isomers by collisional activation mass spectrometry
Authors: Maquestiau André , Beugnies Didier , Flammang Robert , Houriet Raymond , Bouchoux Guy
Published: May 2005

C4H9O+ ions have been produced in the high pressure ion source of a triple sector mass spectrometer either by protonation of C4H8O isomers using methane as the reagent gas, or by methylation of C3H6O isomers using iodomethane or chloromethane as reagent gas. The collisional activation spectra of these mass selected C4H9O+ ions (m/z 73) allow the identification of several stable isomers in the gas phase.
Differentiation of methyl substituted fluorenes, anthracenes and benz[a]anthracenes using surface‐catalyzed oxidation reactions and negative ion chemical ionization mass spectrometry
Authors: Stemmler Elizabeth A. , Buchanan Michelle V. , Marshall Alan G.
Published: May 2005

Methyl‐substituted polycyclic aromatic hydrocarbons (PAH) are shown to undergo surface‐catalyzed reactions with oxygen. These reactions generate oxidized products, which include aldehydes, quinones, and anhydrides. The products dominate the O2/N2 negative ion chemical ionization (NICI) mass spectra of methyl‐PAH when the ion source temperature is elevated to 300°C. The NICI mass spectra of methyl‐PAH measured under these conditions show ions that can be used to distinguish the position of methyl groups substituted on fluorene, anthracene, and benz[a]anthracene isomers.
The determination of protein, oligonucleotide and peptide molecular weights by ion‐spray mass spectrometry
Authors: Covey Thomas R. , Bonner Ronald F. , Shushan Bori I. , Henion Jack , Boyd R. K.
Published: May 2005

The mass spectra of several compounds with molecular weights in the 2500–20 000 Da range were obtained with a quadrupole mass spectrometer equipped with an atmospheric pressure ion source. Average molecular weight determinations of mellitin (2846.4 Da), a synthetic oligonucleotide (4262.8 Da), myoglobin (16 950.4 Da) and on the subunits of β‐lactoglobulin (18 277.1 Da) requiring as little as 1 pmol of material were achieved with accuracies and precisions of ± 1 Da. An ion‐spray interface was used to produce ions via the ion evaporation process, producing mass spectra containing a series of multiply‐charged molecular species. A simple method for calculating the molecular weight of unknown compounds from the spectra containing multiply‐charged ions is described.
A novel hybrid mass spectrometer
Authors: Suter M. J.‐ F. , Gfeller H. , Schlunegger U. P.
Published: May 2005

A new hybrid mass spectrometer of BEQiQu geometry (B, magnetic sector; E, Electric sector; Qi, quistor; Qu, quadrupole mass filter) is described. The high resolution stage (BE) is coupled to a quistor via a series of deceleration lenses, and this is followed by a mass‐analysing quadrupole. This configuration enables the storing of ions, investigation of their gas‐phase chemistry and the subsequent identification of the resulting fragment or product ions.
Precision and accuracy in XQQ measurements: A summary report of the National Institute of Standards and Technology/Environmental Protection Agency International Round Robin
Authors: Martinez Richard I.
Published: May 2005

We describe the kinetics‐based measurement protocol which was used for the National Institute of Standards and Technology/Environmental Protection Agency International Round Robin, and provide an interim summary report of the results. At least 50% of the QQQ instruments currently in the field potentially can provide a dynamically correct (i.e., instrument‐independent) representation of ion/molecule reactions.
Microdetermination of glucose content of plasma and its isotopic enrichment using capillary gas chromatography/ammonia chemical‐ionization mass spectrometry
Authors: Lepetit N. , Rocchiccioli F.
Published: May 2005

A new sensitive and precise method for the determination of the isotopic enrichment of [6, 6‐D2] ghicose and concentration of glucose in plasma microsamples (20 μL) has been developed. Glucose was extracted from plasma samples by anion‐cation column‐exchange with absolute ethanol, derivatized as 1,2:3,5‐bis(butylboronate)‐6‐acetyl‐α‐D‐glucofuranose, and analysed by capillary gas chromatography/ammonia chemical‐ionization mass spectrometry. This method gives a better reproducibility and precision (variation coefficient below 1%) than methods using isobutane chemical ionization.

Stable isotopes are being used increasingly to investigate energy metabolism in vivo. Recent work has involved the development of methodologies, especially mass spectrometry, to perform tracer experiments using the stable isotopes 2H, 13C, or 15N.1–4 Chemical‐ionization mass spectrometry is extensively used for the analysis of isotopically labelled amino acids.2–6

In neonates and chidren, „true”︁ glucose production can be measured by the continuous infusion of the stable isotopically labelled tracer 6,6‐dideutero‐glucose (6,6‐D2‐glucose), and analytical measurement is performed using gas chromatography/electron‐ionization mass spectrometry (GC/EIMS).7

Herein, we present a new, simple and sensitive method for the determination of the isotopic enrichment of [6,6‐D2]glucose and measurement of the concentration of glucose in plasma microsamples (20 μL), based on the use of capillary gas‐chromatography/ammonia chemical‐ionization mass spectrometry of 1,2:3,5‐bis(butylboronate)‐6‐acetyl‐α‐D‐glucofuranose.
Orthogonal‐acceleration time‐of‐flight mass spectrometer
Authors: Dawson J. H. J. , Guilhaus M.
Published: May 2005

A new time‐of‐flight mass analyser compatible with conventional continuous ionization methods is described. A mass resolution at m/z 2000 of m/Δm>2000 (50% valley) is predicted for the instrument which is presently being prototyped. Sensitivity advantages over scanning instruments are also predicted for this instrument.
Factors affecting the ultraviolet laser desorption of proteins
Authors: Beavis Ronald C. , Chait Brian T. , Standing K. G.
Published: May 2005

The production of high‐mass quasimolecular ions from proteins by matrix‐assisted ultraviolet laser desorption is described. A simple time‐of‐fight system using a Q‐switched frequency‐quadrupled Nd‐YAG laser to desorb protein molecules is shown to have a mass range of up to 116 000 u by the observation of intact, singly charged quasimolecular ions from 700 fmol of β‐galactosidase subunit (mol.wt = 116 336 Da). Both positive‐ and negative‐ion spectra of proteins are shown. Four new matrix materials, with properties as good as or better than nicotinic acid, are described. A mass resolution of approximately 500 (full width at half maximum definition) is demonstrated for proteins with mol.wt < 20 000 Da. Product species, formed by fast photochemical reactions in the matrix, are observed to form adduct ions with protein molecules. These adduct ions are a significant cause of the observed broadness of protein quasimolecular ion peaks. The practical physical considerations in detection of large‐mass quasimolecular ions from laser desorption, such as detector overloading, are discussed.
A novel fragmentation process in the fast‐atom bombardment/tandem mass spectra of peptides cationized with Na+, determining the identity of the C‐terminal amino acid
Authors: Kulik Willem , Heerma Wigger , Terlouw Johan K.
Published: May 2005

The metastable ion spectra of the [M + Na]+ ions generated by fast‐atom bombardment of sodium chloride containing oligopeptide samples are shown to produce an intense sequence ion from which the identity of the C‐terminal amino acid can be readily established.
Determination of linkage position in disaccharides by negative‐ion fast‐atom bombardment mass spectrometry
Authors: Ballistreri Alberto , Montaudo Giorgio , Garozzo Domenico , Giuffrida Mario , Impallomeni Giuseppe , Daolio S.
Published: May 2005

Negative‐ion fast‐atom bombardment linked‐scan spectra at constant B/E have been shown to allow differentiation of the linkage position in hexose‐hexose‐disaccharides. Sequence information can also be obtained when there is a molecular weight difference between the monosaccharide units in the carbohydrate molecule.
Performance of a liquid‐junction interface for capillary electrophoresis mass spectrometry using continuous‐flow fast‐atom bombardment
Authors: Reinhoud N. J. , Niessen W. M. A. , Tjaden U. R. , Gramberg L. G. , Verheij E. R. , van der Greef J.
Published: May 2005

The on‐line coupling of capillary electrophoresis and mass spectrometry using a continuous‐flow fast‐atom bombardment system in combination with a liquid‐junction interface is described. The influence of the liquid‐junction coupling on the efficiency and the resolution is investigated. Qualitative analysis of small peptides and quantitative analysis of dextromethorphan is demonstrated with detection limits in the low ng/mL range, indicating the feasibility of the method in bioanalysis.
Effect of trifluoroacetic acid on the reduction of disulfide bridges in peptides analyzed by fast‐atom bombardment mass spectrometry
Authors: Visentini J. , Gauthier J. , Bertrand M. J.
Published: May 2005

Some of the factors that influence the reduction of disulfide‐containing peptides under fast‐atom bombardment have been investigated using two neurohormonal peptides that include disulfide bridges in their structures. Deaminoarginine‐vasopressin (DAVP) and arginine‐vasopressin (AVP) have been analyzed as their acetate and trifluoroacetate salts. Results obtained in a thioglycerol matrix indicate that the peptides analyzed as their acetate salts are completely reduced under bombardment, whereas the trifluoroacetate salts show little evidence of reduction. Addition of trifluoroacetic acid to the acetate sample prior to bombardment inhibits reduction whereas addition after bombardment shows no effect on the reduction, thereby indicating the irreversibility of the process. Time‐monitoring experiments conducted with the acetate salts of DAVP and AVP in common matrices such as thioglycerol, dithiothreitol + diethioerythritol, glycerol, hydroxyethyldisulfide and nitrobenzyl‐alcohol demonstrate an important effect of the chemical nature of the matrix on reduction. In matrices containing thiol groups, the reduction is extensive, whereas it is almost suppressed in matrices such as hydroxyethyldisulfide and nitrobenzylalcohol. However, the addition of trifluoroacetic acid to all of these matrices essentially eliminates reduction and provides measured isotopic peak ratios that are in agreement with theoretically calculated values for these peptides.
Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins
Authors: Beavis Ronald C. , Chait Brain T. , Fales H. M.
Published: May 2005

The paper reports the discovery of three new matrices for the matrix‐assisted laser desorption of proteins. These new matrices (sinapic, ferulic and caffeic acids) are cinnamic acid derivatives that have several pratical advantages over the nicotinic acid matrices previously used. These materials form much less intense photochemically generated adduct peaks in the protein quasimolecular ion signal and the adduct peaks that are present are easier to resolve. These new matrices are produce intense protonated‐molecule ions from all of the proteins (over 50) so far examined. These new matrices are also very stable in a vacuum, allowing for their convenient use in very high vacuum applications (e.g., Fourier transform ion cyclotron resonance mass spectrometry).
Cluster‐ion abundances and geometrical structures of magnesium oxide clusters generated by bombardment with xenon and oxygen ions
Authors: Katakuse I. , Ichihara T. , Ito H. , Hirai M.
Published: May 2005

Two types of magnesium oxide clusters, (MgO) and (MgO)nMg+ have been obtained by the bombardment of magnesium with a mixture of xenon and oxygen ions. Enhanced ion intensity in the cluster mass spectra was observed at certain n values. The correlation between the geometrical structures of the clusters and their abundances is discussed.
Methodological approach to the characterization of diacylphosphatidyl cholines in rabbit lung lavage fluid by fast‐atom bombardment mass spectrometry
Authors: Allmaier G. , Schmid E. R. , Gasser H. , Strohmaier W. , Schlag G.
Published: May 2005

Strong evidence exists that the distribution of phospholipids in the lung is a function of the degree of adult respiratory distress syndrome. The capabilities of positive‐ion fast‐atom bombardment (FAB) mass spectrometry for the determination of the relative distribution of intact diacylphosphatidylcholine species in lung lavage fluid were investigated. Two different FAB matrices and two different isolation/purification procedures—extraction/thin layer chromatography—high performance liquid chromatography (TLC‐HPLC)—have been evaluated. In addition the relative fatty acid composition of the diacylphosphatidylcholines was determined by negative‐ion FAB mass spectrometry using the [RCOO]− fragment ion. These results were compared with those obtained by gas chromatographic determination of the fatty acid methylesters.
Collisionally activated dissociation of peptides using a quadrupole ion‐trap mass spectrometer
Authors: Kaiser Raymond E. , Cooks R. Graham , Syka John E. P. , Stafford George C.
Published: May 2005

The ion‐trap mass spectrometer can be used to record mass and multi‐stage tandem mass spectra (MSn) on small peptides. The compounds are ionized by Cs+ surface ionization, injected into the trap, mass selected, activated by collision, resulting in dissociation and mass‐selectively ejected. Tandem mass spectrometric data on sub‐fmol amounts of Gramicidin S are shown, along with tandem mass spectrometric and MSn data on two other peptides. The experiment is distinguished by its very high sensitivity and the high quality of sequence information obtained.
A method based on catalytic hydrogenation for the identification of monohydroxy metabolites of isomeric tetrahydrocannabinols
Authors: Harvey D. J. , Brown N. K.
Published: May 2005

Identification of isomeric monohydroxy metabolites of 6a,10a‐trans‐tetrahydrocannabinols (THCs) by gas chromatography/mass spectrometry as their trimethylsilyl derivatives is aided by catalytic hydrogenation to hydroxyhexahydrocannabinols (hydroxy‐HHCs) in cases where the metabolites themselves give similar spectra. This method gives common products from a range of hydroxy metabolites of isomeric‐THCs which can be compared with reference compounds synthesized from available hydroxy‐THCs from the Δ8 and Δ9‐series. Sufficient of these compounds are available to enable hydroxy‐HHCs to be prepared with hydroxy groups in most positions accessible to metabolic enzymes. This technique provides a simple alternative to a laborious synthesis of each new metabolite for confirmatory purposes and enables all metabolites in a metabolic experiment to be identified in a single sample. Catalytic hydrogenation was achieved using rhodium on alumina in methanol; this gave rapid, quantitative hydrogenation of underivatized metabolites without the elimination of the hydroxy groups inherent with hydrogenation with other common catalysts. The method was validated by an examination of the metabolites of Δ11 THC in rats and comparison of the results with published work.
Use of charge‐separation reactions for sequencing peptides
Authors: Vékey Kàroly , Candido Manuela , Traldi Piero
Published: May 2005

Charge‐separation reactions of the doubly charged molecular ion of bradykinin, generated by fast‐atom bombardment, were studied. The same types of reactions occurred as in singly charged ions, but fragmentations around the middle of the peptide chain were much more abundant. This suggests that charge separation of doubly charged ions may provide more sequence information than fragmentation of singly charged species.
An electrospray‐ionization mass spectrometer with new features
Authors: Chowdhury Swapan K. , Katta Viswanatham , Chait Brian T.
Published: May 2005

The construction and performance of an electrospray‐ionization mass spectrometer with new features are described. The mass spectrometer consists of a newly designed electrospray ion‐source that is plugged directly into a modified commercial quadrupole mass spectrometer with the ions entering the mass analyzer through a long metal capillary tube and three stages of differential pumping. The present ion source differs from previous designs in the combination of techniques employed in the transportation and desolvation of solvated biomolecule ions, prior to mass analysis. Transport of ionized entities between atmospheric pressure and vacuum is carried out through a 203 mm long stainless steel capillary tube with a 0.5 mm bore. Desolvation is effected by the use of controlled heat transfer through the long capillary tube and collisional activation in a region of reduced pressure between the capillary tube exit and the skimmer. Desolvation with this system is convenient and effective and does not involve the strong countercurrent flows of gases that have been used by all previous workers. The effects on the spectra of peptides of capillary tube temperature and desolvation collision energy are investigated. Electrospray‐ionization mass spectrometric results are described for thirteen proteins with molecular masses ranging from 5000 to 77 000 Da. The performance of the present instrument, with respect to mass accuracy and sensitivity, is comparable with previously reported systems. The effect of protein concentration in solution on the electrospray mass spectrometric response and charge‐state distribution is discussed.
Molecular weight determination of underivatized oligodeoxyribonucleotides by positive‐ion matrix‐assisted ultraviolet laser‐desorption mass spectrometry
Authors: Spengler Bernhard , Pan Ying , Cotter Robert J. , Kan Lou‐Sing
Published: May 2005

A Wiley‐McLaren type time‐of‐flight mass spectrometer has been used for molecular weight measurements of several unprotected oligodeoxyribonucleotides using matrix‐assisted UV laser desorption. Approximately 10 to 100 pmol of sample was required for recording their positive‐ion mass spectra with a mass resolution in the range of 150 to 300 (Full width at half maximum) (FWHM). Little fragmentation was observed.
The use of dynamically programmed scans to generate parent‐ion tandem mass spectra with the ion‐trap mass spectrometer
Authors: Todd J. F. J. , Penman A. D. , Thorner D. A. , Smith R. D.
Published: May 2005

A method is described whereby, under software control, the scan function employed to collisionally excite ions in an ion‐trap mass spectrometer is regulated so as to obtain parent ion (fixed product) tandem mass spectral data. At the same time, constant neutral‐loss information is also provided. Key features are the automatic ‘intelligent’ selection of parent ions from observation of the initial mass spectrum and the scanning of the applied ‘tickle’ frequency in order to locate the precise resonance points for excitation of these ions. Results for the model compounds perfluorotributylamine (‘FC43’) and n‐butylbenzene are reported and complicating effects such as the unimolecular decay of the precursor ion species and charge exchange between product ions and the original sample material are discussed.
The formation of HOS− from deprotonated dimethyl sulphoxide and related species
Authors: Bowie John H. , Stringer Michael B. , Hayes Roger N.
Published: May 2005

Collisional activation of MeSOCH and PhCH2SOC̄HPh (but not PhSOCH) yields an ion of m/z 49, identified as HOS−. It is proposed that this ion is formed following proton transfer to oxygen followed by cyclization and elimination.
A fast array detector system
Authors: Brunnée Curt , Pesch Reinhold , Schröder Ernst
Published: May 2005

The performance of a novel array detector system which can be operated during scanning of the magnetic field of a sector mass spectrometer is investigated. The increase in sensitivity as compared to a standard secondary‐electron multiplier slit detector is about 100 times. It is shown that the product of the mass window of the array detector and the resolution is constant. The maximum resolution which can be achieved with the array detector is 7500 full width at half maximum. The solid secondary‐ion mass spectrum of 12 attomol of gramicidin S demonstrates the extreme sensitivity of the system.
Mass spectrometric characterization of different norandrosterone derivatives by low‐cost mass spectrometric detectors using electron ionization and chemical ionization
Authors: de Boer D. , de Jong E. G. , Maes R. A. A.
Published: May 2005

The abuse of nortestosterone in sport is an important problem in doping‐control analysis. In order to detect the main urinary metabolite of nortestosterone, norandrosterone (NA), sensitive and specific methodology is necessary. In this context the use of a low‐cost mass spectrometric detector such as the Finnigan MAT ion‐trap detector (ITD) was studied. The electron ionization (EI) and positive‐ion chemical ionization (PICI) mass spectra of the methoxime‐trimethylsilyi, trimethylsilyl‐enol trimethylsilyl ether and pentafluoropropionic ester derivatives of NA are described. The limits of detection of these derivatives are compared with those obtained by the Hewlett‐Packard mass selective detector (MSD), another low‐cost mass spectrometric detector and operating only in the EI mode. For the derivatives of the reference standard of NA the ITD has in the EI mode the same limit of detection, in the range of 0.5 to 1 ng injected on the column, as the MSD. However, under these conditions the ITD provides more spectrometric information, because it gives full scan data. Moreover, with the same or even improved limits of detection the ITD can operate in the PICI mode. On the other hand, for the analysis of NA isolated from urine samples, the performance of the MSD was better than that of the ITD. The ion trapping technique is probably limited when the chemical background is high.
Computer modelling of fragmentation processes in radio frequency multipole collision cells
Authors: Davis Stephen C. , Wright Barry
Published: May 2005

To date, methods for calculating the trajectories of ions in radio frequency (RF) multipole fields have involved solving, analytically or numerically, the appropriate equations of motion. Another method is presented here whereby a non‐ideal distribution of field may be modelled and the position of an ion can be tracked, as it traverses the multipole. The validity of the calculations is discussed and some of the properties of collision cells are explained. Fragmentation processes within the cell are modelled showing that the focusing properties within the cell have a striking effect on parent‐ and daughter‐ion transmission.
Particle beam liquid chromatography/mass spectrometry on a double‐focusing high resolution mass spectrometer
Authors: Baczynskyj Lubomir
Published: May 2005

The particle beam liquid chromatography/mass spectrometry (LC/MS) interface has been adapted to a double‐focusing sector instrument of reversed geometry. Electron ionizaition (EI) mass spectra of single components injected through a loop or of mixtures separated via a reversed‐phase LC column have been recorded. These are superimposable with EI mass spectra obtained via a direct‐insertion probe. Sensitivity tests show that high picogram and low nanogram amounts of samples can be detected. Complete high‐resolution mass spectra on standards (single components and mixtures) were recorded. Good accuracy (better than 5 mmu) was obtained in most cases on 5 μg samples. To illustrate the versatility of the system, mass‐analysed ion kinetic energy scans and linked scans at constant B/E were obtained on the molecular ion of cholesterol (2.5 μg and 500 pg). Parameters relating to various parts of a commercial interface are briefly reported.
Homogeneous bottleneck model of matrix‐assisted ultraviolet laser desorption of large molecules
Authors: Vertes Akos , Gijbels R. , Levine R. D.
Published: May 2005

The factors affecting the yield of high‐mass molecules by matrix‐assisted ultraviolet laser volatilization are examined in a simple model. The key material factors appear to be a low heat of sublimation, subcritical concentration of the guest molecules and a high irradiance input in a short time compared to the sublimation induction period. The model is homogeneous in that the energy density is taken to be uniform within the ‘hot region’ of the matrix. The two competing effects are the rates of energy transfer from the matrix to the guest molecules and the desorption by sublimation. It is the bottleneck for energy transfer to the embedded guest molecules that makes their energy content lag behind that of the matrix. This is particularly the case for an initially cold sample. When a sufficiently high rate of sublimation can be achieved (e.g., using a high‐power laser), the guest molecules (or adduct ions) will desorb internally cold and will thus not fragment. Numerical simulations of the sublimation kinetics using realistic laser and material parameters support the conclusions and delineate the ranges of the critical factors.
Vibrational excitation of N2 by C+ ions
Authors: Lee A. R. , Enos C. S. , Brenton A. G.
Published: May 2005

High‐resolution translational energy spectroscopy (0.1 eV full width at half maximum) has been performed on 3 keV C+ ions scattered off N2 molecules. The intriguing energy loss spectrum with well‐resolved vibrational structure is explained on the basis of simultaneous transitions involving changes of states in the C+ ion and the N2 molecule.
Endothermic ion/molecule reactions III. High energy collisional activation at low kinetic energies
Authors: Orlando Ron , Fenselau Catherine , Cotter Robert J.
Published: May 2005

Endothermic reactions between leucine enkephalin and ammonia have been carried out at very low beam energies, and compared with activation obtained by conventional collision‐induced dissociation at both low and high energies. The similarity between the high‐energy and the reactive‐collisions spectra suggest that comparable energies are imparted by these two methods. The upper limit of the collision energy deposited by reactive collisions is only 0.30 eV. In addition, a substantial increase in the collection efficiency is observed with endothermic reactions, with the sum of the fragment ions exceeding the intensity of the surviving parent ions.
A study of relevant parameters in collisional‐activation of ions in the ion‐trap mass spectrometer
Authors: Gronowska Janina , Paradisi Christina , Traldi Pietro , Vettori Umberto
Published: May 2005

Variously substituted aryl ketones served as models to gain insight into the collisional‐activation process in an ion‐trap mass spectrometer. The effects of different targets (helium, argon) at different pressures were examined. The investigation also involved the comparison of the results of tandem mass spectrometry experiments in the ion trap with those obtained in high‐energy collision and mass‐analysed ion kinetic energy experiments in a sector instrument. Use of argon and low helium pressures in the ion trap results in both an increase of the average internal energy of the activated ion and, presumably, a less broad energy deposition profile. The results indicate that the maximum value of internal energy achieved by an ion through multiple collisions in the ion‐trap mass spectrometer is limited by the presence of low‐energy reaction channels.
Ion/molecule reactions of protonated bases of atmospheric importance
Authors: Iraqi M. , Peres M. , Petrank A. , Lifshitz C.
Published: May 2005

Reaction rates for proton transfer and association reactions of protonated bases of atmospheric importance were determined on a selected‐ion flow tube (SIFT) at 300 K.
High‐temperature gas chromatography/mass spectrometry of triacylglycerols with ammonia negative‐ion chemical ionization
Authors: Evershed R. P. , Prescott M. C. , Goad L. J.
Published: May 2005

Ammonia negative‐ion chemical ionization of intact triacylglycerols at an ion‐source‐block temperature of 300°C produces simple mass spectra from which the nature of the component acyl moieties can be readily deduced. The technique is compatible with combined high‐temperature gas chromatography/mass spectrometry and it has a potentially wide application.
Deconvolution of kinetic‐energy release signals from singly, doubly, and triply charged metastable ions
Authors: Koyanagi Gregory K. , Wang Jianyao , March Raymond E.
Published: May 2005

A new geometric model has been developed and applied to the deconvolution of ion kinetic‐energy release signals observed from fragmentation of metastable ions in the second field‐free region of a reversed geometry mass spectrometer. The model takes account of: (i), fragmentations occurring throughout the entire length of the field‐free region; (ii), the difference in ion beam intensity before and after the intermediate slit; (iii), the slight difference in angular acceptance between backward‐ and forward‐scattered product ions; (iv), fragmentations of singly and multiply charged ions; and (v), ion kinetic‐energy releases of any magnitude. Several examples of metastable peaks are given together with the associated kinetic‐energy release distribution and the theoretical metastable peak generated from the kinetic‐energy release distribution.
A fourier transform‐ion cyclotron resonance study of the reactivity of ionized vinylalcohol with selected unsaturated compounds
Authors: Berruyer Florence , Bouchoux Guy
Published: May 2005

Reactions between CX2CXOX+· (X  H or D) and alkenes, an alkyne, benzene, aldehydes and ketones have been studied by Fourier transform mass spectrometry. Most of the neutral species undergo charge exchange or proton transfer reactions with high rates; l‐alkenes lead to slower cycloaddition reactions. The thermochemistry and considerations on the reaction specificities are discussed.
High‐ and low‐energy tandem mass spectrometry of oxonium ions formed by fast‐atom bombardment ionization of a series of diastereoisomeric 1,2‐trans‐2‐deoxy‐2‐iodoglycosyl azides
Authors: Banoub Joseph , Becchi Michel , Lafont Dominique , Fraisse Daniel , Descotes Gerard
Published: May 2005

Positive‐ion fast‐atom bombardment mass spectrometry has aided the structural characterization of a novel series of diastereomeric 1,2‐trans‐2‐deoxy‐2‐iodoglycosyl azides. Daughter‐ion tandem mass spectrometry (MS/MS) analyses (high‐energy mass‐analysed ion kinetic energy spectrometry and low‐energy MS/MS with collisionally‐activated dissociation), of the precursor oxonium ions for this series of diastereoisomers provided distinct and reproducible fingerprint patterns which permit discrimination amongst the individual configurations.
Mass spectrometric identification of PS, PS and PS˙3
Authors: Srinivas Ragampeta , Sülzle Detlev , Schwarz Helmut
Published: May 2005

Neutralization/reionization mass spectrometry experiments are used to generate and characterize the hitherto unknwon phosphorus trisulfide molecule in the gas phase.
Unimolecular decomposition of M+˙ and [M + H]+ species of some fluorosubstituted acyclic nucleoside analogs
Authors: Favretto Donata , Traldi Pietro , Bravo Pierfrancesco , Viani Fiorenza
Published: May 2005

Electron ionization and fast‐atom bombardment mass spectrometry are shown to provide a valid analytical tool for the structural characterization of the title compounds. In fact, diagnostic fragmentation pathways were observed depending on the presence of different substituents (benzyloxy, p‐tolylthio, p‐tolylsulphinyl) as swell as of different bases. Regioisomeric compounds could be differentiated by kinetic energy release measurements.
Direct determination of the sequence of destruxins (cyclodepsipeptides) using negative‐ion fast‐atom bombardment mass spectrometry
Authors: Lange C. , Mulheim C. , Vey A. , Pais M. , Aubagnac J.‐L.
Published: May 2005

Fast‐atom bombardment negative‐ion mass spectra of various natural destruxins (cyclodepsipeptides) using a glycerol matrix are investigated to clarify their regular pattern of fragmentation. Deprotonated molecules allow characterization of the molecular weight. Also, at lower masses, anion Y of significant intensities permit the determination of their amino acid sequences.