bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the conformation of folding initiation sites in proteins by computer simulation
Authors: Avbelj Franc , Moult John
Published: May 2005

Experimental evidence and theoretical models both suggest that protein folding begins by specific short regions of the polypeptide chain intermittently assuming conformations close to their final ones. The independent folding properties and small size of these folding initiation sites make them suitable subjects for computational methods aimed at deriving structure from sequence. We have used a torsion space Monte Carlo procedure together with an all‐atom free energy function to investigate the folding of a set of such sites. The free energy function is derived by a potential of mean force analysis of experimental protein structures. The most important contributions to the total free energy are the local main chain electrostatics, main chain hydrogen bonds, and the burial of nonpolar area. Six proposed independent folding units and four control peptides 11–14 residues long have been investigated. Thirty Monte Carlo simulations were performed on each peptide, starting from different random conformations. Five of the six folding units adopted conformations close to the experimental ones in some of the runs. None of the controls did so, as expected. The generated conformations which are close to the experimental ones have among the lowest free energies encountered, although some less native like low free energy conformations were also found. The effectiveness of the method on these peptides, which have a wide variety of experimental conformations, is encouraging in two ways: First, it provides independent evidence that these regions of the sequences are able to adopt native like conformations early in folding, and therefore are most probably key components of the folding pathways. Second, it demonstrates that available simulation methods and free energy functions are able to produce reasonably accurate structures. Extensions of the methods to the folding of larger portions of proteins are suggested. © 1995 Wiley‐Liss, Inc.
Progress of 1D protein structure prediction at last
Authors: Rost Burkhard , Sander Chris
Published: May 2005

Accuracy of predicting protein secondary structure and solvent accessibility from sequence information has been improved significantly by using information contained in multiple sequence alignments as input to a neural 'network system. For the Asilomar meeting, predictions for 13 proteins were generated automatically using the publicly available prediction method PHD. The results confirm the estimate of 72% three‐state prediction accuracy. The fairly accurate predictions of secondary structure segments made the tool useful as a starting point for modeling of higher dimensional aspects of protein structure. © 1995 Wiley‐Liss, Inc.
Confronting the problem of interconnected structural changes in the comparative modeling of proteins
Authors: Samudrala Ram , Pedersen Jan T. , Zhou Huai‐bei , Luo Rui , Fidelis Krzysztof , Moult John
Published: May 2005

Comparative models of three proteins have been built using a variety of computational methods, heavily supplemented by visual inspection. We consider the accuracy obtained to be worse than expected. A careful analysis of the models shows that a major reason for the poor results is the interconnectedness of the structural differences between the target proteins and the template structures they were modeled from. Side chain conformations are often determined by details of the structure remote in the sequence, and can be influenced by relatively small main chain changes. Almost all of the regions of substantial main chain conformational change interact with at least one other such region, so that they often cannot be modeled independently. Visual inspection is sometimes effective in correcting errors in sequence alignment and in spotting when an alternative template structure is more appropriate. We expect some improvements in the near future through the development of structure‐based sequence alignment tools, side chain interconnectedness rotamer choice algorithms, and a better understanding of the context sensitivity of conformational features. © 1995 Wiley‐Liss, Inc.
Protein structure prediction by threading methods: Evaluation of current techniques
Authors: Lemer Christian M.‐R. , Rooman Marianne J. , Wodak Shoshana J.
Published: May 2005

This paper evaluates the results of a protein structure prediction contest. The predictions were made using threading procedures, which employ techniques for aligning sequences with 3D structures to select the correct fold of a given sequence from a set of alternatives. Nine different teams submitted 86 predictions, on a total of 21 target proteins with little or no sequence homology to proteins of known structure. The 3D structures of these proteins were newly determined by experimental methods, but not yet published or otherwise available to the predictors. The predictions, made from the amino acid sequence alone, thus represent a genuine test of the current performance of threading methods. Only a subset of all the predictions is evaluated here. It corresponds to the 44 predictions submitted for the 11 target proteins seen to adopt known folds. The predictions for the remaining 10 proteins were not analyzed, although weak similarities with known folds may also exist in these proteins. We find that threading methods are capable of identifying the correct fold in many cases, but not reliably enough as yet. Every team predicts correctly a different set of targets, with virtually all targets predicted correctly by at least one team. Also, common folds such as TIM barrels are recognized more readily than folds with only a few known examples. However, quite surprisingly, the quality of the sequence‐structure alignments, corresponding to correctly recognized folds, is generally very poor, as judged by comparison with the corresponding 3D structure alignments. Thus, threading can presently not be relied upon to derive a detailed 3D model from the amino acid sequence. This raises a very intriguing question: how is fold recognition achieved? Our analysis suggests that it may be achieved because threading procedures maximize hydrophobic interactions in the protein core, and are reasonably good at recognizing local secondary structure. © 1995 Wiley‐Liss, Inc.
Homology modeling of histidine‐containing phosphocarrier protein and eosinophil‐derived neurotoxin: Construction of models and comparison with experiment
Authors: Church W. Bret , Palmer Anneliese , Wathey John C. , Kitson David H.
Published: May 2005

Homology modeling methods have been used to construct models of two proteins—the histidine‐containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil‐derived neurotoxin (EDN). Comparison of the models with the subsequently determined X‐ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X‐ray structures in these regions—possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X‐ray structure. The loop regions of EDN were incorrectly modeled—reasons for this and possible enhancements are discussed. © 1995 Wiley‐Liss, Inc.
Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms
Authors: Pedersen Jan T. , Moult John
Published: May 2005

Ab initio folding simulations have been performed on three peptides, using a genetic algorithm‐based search method which operates on a full atom representation. Conformations are evaluated with an empirical force field parameterized by a potential of mean force analysis of experimental structures. The dominant terms in the force field are local and nonlocal main chain electrostatics and the hydrophobic effect. Two of the simulated structures were for fragments of complete proteins (eosinophil‐derived neurotoxin (EDN) and the subtilisin propeptide) that were identified as being likely initiation sites for folding. The experimental structure of one of these (EDN) was subsequently found to be consistent with that prediction (using local hydrophobic burial as the determinant for independent folding). The simulations of the structures of these two peptides were only partly successful. The most successful folding simulation was that of a 22‐residue peptide corresponding to the membrane binding domain of blood coagulation factor VIII (Membind). Three simulations were performed on this peptide and the lowest energy conformation was found to be the most similar to the experimental structure. The conformation of this peptide was determined with a Cα rms deviation of 4.4 Å. Although these simulations were partly successful there are still many unresolved problems, which we expect to be able to address in the next structure prediction experiment. © 1995 Wiley‐Liss, Inc.
Atomic and residue hydrophilicity in the context of folded protein structures
Authors: Kuhn Leslie A. , Swanson Craig A. , Pique Michael E. , Tainer John A. , Getzoff Elizabeth D.
Published: May 2005

Water‐protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen‐bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively‐charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side‐chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U‐75875 inhibitor complexes. © 1995 Wiley‐Liss, Inc.
Control of crystal forms of apoferritin by site‐directed mutagenesis
Authors: Takeda Shigeki , Yoshimura Hideyuki , Endo Sigeru , Takahashi Takuya , Nagayama Kuniaki
Published: May 2005

Surface charges of protein molecules are not only important to biological functions but also crucial to the molecular assembly responsible for crystallization. Appropriate alteration in the surface charge distribution of a protein molecule induces new molecular alignment in the proper direction in the crystal and, hence, controls the crystal form. Apoferritin molecules are known to crystallize in two‐ and three‐dimensional forms in the presence of cadmium ions, which bridge neighboring protein molecules. Here we report a controlled transformation of the apoferritin 2‐D crystal by site‐directed mutagenesis. In mutant apoferritin, two amino acid residues binding a cadmium‐ion through their negative charge, were replaced by one type of nonionic amino acid residues. The amino acid residues, Asp‐84 and Gln‐86 in the sequence of recombinant (i.e., wild‐type) horse L‐apoferritin, were replaced by Ser. The wild‐type apoferritin yielded a hexagonal lattice 2‐D crystal in the presence of cadmium ions. In contrast, the mutant apoferritin yielded two types of oblique crystals independent of the presence of cadmium ions. Image reconstruction of electron micrographs of the mutant crystals made clear that the mutant apoferritin molecules oriented themselves with the 2‐fold symmetry axis perpendicular to the crystal plane in both crystals, while the wild‐type apoferritin molecules oriented themselves with the 3‐fold symmetry axis perpendicular to the crystal plane. The changes of crystal forms and molecular orientation in the 2‐D crystals were well explained by a change of the electrostatic interactions induced by the mutagenesis. © 1995 Wiley‐Liss, Inc.
Knowledge‐based protein secondary structure assignment
Authors: Frishman Dmitrij , Argos Patrick
Published: May 2005

We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard‐of‐truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 22:2577‐2637, 1983) shows that STRIDE and DSSP assign secondary structural states in 58 and 31% of 226 protein chains in our data sample, respectively, in greater agreement with the specific residue‐by‐residue definitions provided by the discoverers of the structures while in 11% of the chains, the assignments are the same. STRIDE delineates every 11th helix and every 32nd strand more in accord with published assignments. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic study of human lithostathine
Authors: Pignol David , Bertrand Jay A. , Bernard Jean‐Paul , Verdier Jean‐Michel , Dagorn Jean‐Charles , Fontecilla‐Camps Juan Carlos
Published: May 2005

Crystals of human lithostathine, a pancreatic glycoprotein which inhibits the growth and nucleation of calcium carbonate crystals, were grown using PEG 4000 as the precipitating agent. The crystals belong to the hexagonal space group P61 (or its enantiomorph P65) and diffract to 1.55 Å resolution. There is one molecule in the asymmetric unit and the crystals have 39% solvent. © 1995 Wiley‐Liss, Inc.
A method for determining the elemental compositions of daughter ions in simple tandem mass spectrometry spectra
Authors: Bozorgzadeh Mohammed Hossein
Published: May 2005

A method has been developed and generalized to determine the elemental compositions of daughter ions in simple MS/MS spectra. To employ the method, it is necessary to take the daughter ion spectra of the m and [m1+1]+ ions, where m is the parent ion and [m1+1]+ is the same ion with a replaced naturally‐occurring heavier isotope of mass 1 greater than that of the main isotope. For each daughter ion produced from m, two may be produced from [m1+1]+; one of these will contain the heavy isotope and the other one will not. The ratio of the abundances of these two daughter ions in the spectrum of [m1+1]+ is equal to the ratio of the probabilities of finding the heavy isotope in the ion fragment or in the corresponding neutral fragment(s), and these probabilities are termed the “relative isotope abundances” of the two fragments. An equation is derived for calculating these relative isotope abundances of the daughter ion versus that of the parent. The effectiveness of the method has been tested by applying it to a compound whose spectrum has daughter ions of known formulae. Errors have been measured, and the limitations of the method assessed. Also, several compounds that could produce daughter ions of more than one possible formula were used as tests of the method.
Sputter yields of ammonium chloride and solid glycerol
Authors: Gillen Greg , Christiansen J. W. , Tsong I. S. T. , Kimball B. , Williams Peter , Cooks R. Graham
Published: May 2005

We have measured the sputtering yields of ammonium chloride and of frozen glycerol films under 8 keV Ar+˙ bombardment using a thin film depth profiling technique. The sputtering yield of ammonium chloride was 34±3 molecules (NH4Cl)/ion; for frozen glycerol the sputter yield was 54±9 molecules/ion. The results constrain possible mechanisms of damage suppression in organic secondary ion mass spectrometry.
Product excitation in collision‐induced dissociative ionization of acetone: Internal energy distribution
Authors: Vékey K. , Brenton A. G.
Published: May 2005

Charge stripping of a neutral acetone beam, C3H6O, produced by the unimolecular fragmentation of a proton‐bound dimer by the reaction [(C3H6O)2H]+ → C3H6O +[C3H7O]+, was studied for various target gases. The singly‐charged acetone ions, formed after charge stripping of the neutral acetone beam, contained a significant amount of internal energy (dependent on the collision gas), and its distribution was measured. Collision cross‐sections, total and partial, were measured for charge stripping of acetone neutrals. Comparison of the present results with electron‐transfer processes was also made.
The calibration of the energy‐loss scale for charge‐stripping reactions of singly‐charged positive ions
Authors: Langford M. L. , Mathur D. , Harris F. M.
Published: May 2005

Two methods of calibrating the energy‐loss scale in charge‐stripping experiments are compared. It is shown that the linear‐offset method rather than the multiplicative method should be used.
A pulsed time‐of‐flight mass spectrometer for liquid secondary ion mass spectrometry
Authors: Olthoff J. K. , Lys I. A. , Cotter R. J.
Published: May 2005

The design and performance of a new time‐of‐flight mass spectrometer is reported. The instrument combines the advantages of a pulsed drawout TOF analyzer with a liquid secondary ion source. Differences from commercially available pulsed TOF analyzers (Wiley/McLaren type) are discussed with regard to operation with ion desorption from a liquid matrix.
A continuous‐flow probe high performance liquid chromatography interface to a liquid secondary‐ion time‐of‐flight mass spectrometer
Authors: Chen Kai‐Hsien , Cotter Robert J. , Caprioli R. M.
Published: May 2005

The possibilities for using the time‐of‐flight analyzer as a liquid chromatography detector are evaluated using a continuous flow probe and keV ion bombardment on a specially designed time‐of‐flight instrument.
Gas‐phase acidity of nitrobenzene from flowing afterglow bracketing studies
Authors: Cheng Xueheng , Grabowski Joseph J.
Published: May 2005

Room temperature ion/molecule reactions in 0.30 Torr of helium, carried out in a flowing afterglow, show that the gas‐phase acidity of nitrobenzene is intermediate between those of ethanol and isopropanol, in contrast to published high‐pressure mass spectrometer data. The revised gas‐phase acidity of nitrobenzene, ΔHºacid(C6H5NO2) = 377 ± 3 kcal mol−1, is shown to be consistent with known acidifying effects when a hydrogen atom is replaced by a nitro group in a Brönsted acid. Additional reactions involving nitrobenzene or its conjugate base are noted.
Capillary‐zone electrophoresis/fast‐atom bombardment mass spectrometry: Design of an on‐line coaxial continuous‐flow interface
Authors: Moseley M. Arthur , Deterding Leesa J. , Tomer Kenneth B. , Jorgenson James W.
Published: May 2005

An on‐line coaxial continuous‐flow capillary‐zone electrophoresis/fast‐atom bombardment mass spectrometry (CZE/FAB‐MS) interface is described. This interface is shown to be capable of acquiring mass spectra in an online fashion from low femtomole amounts of peptides while maintaining high (hundreds of thousands of plates) electrophoretic separation efficiencies. Active electrophoretic transport of the analytes directly to the FAB probe tip obviates the need for a transfer line from the end of the CZE capillary to this point, and thereby precludes the zone broadening that would otherwise occur both within such a transfer line and in the connections between the CZE column and the transfer line. The capability of acquiring an on‐line tandem mass spectrometry (MS/MS) spectrum of an electrophoretically separated analyte using this interface is also demonstrated.
Comparison of amino acid‐sequence analysis by electron ionization and negative‐ion chemical ionization mass spectrometry
Authors: Reinhard H. , Lauber R. , Schlunegger U. P.
Published: May 2005

The positive electron ionization and negative chemical ionization mass spectra of 15 different derivatives of the tripeptide Phe‐Ala‐Leu have been compared. Total ion currents and ion currents of sequence‐characterizing ions have been measured and compared. The negative‐ion spectra, using 10% carbon dioxide in argon as moderator gas, proved to be simpler and contained more abundant sequence ions than the positive electron ionization spectra.
Separation and identification of intact glucosinolates using direct coupling of high‐performance liquid chromatography with frit to fast‐atom bombardment mass spectrometry
Authors: Kokkonen P. , van der Greef J. , Niessen W. M. A. , Tjaden U. R. , ten Hove G. J. , van de Werken G.
Published: May 2005

Intact glucosinolates are separated and identified in standard mixtures and in plant extract of Brussels sprouts by using the liquid chromatography frit to fast‐atom bombardment mass spectrometry technique. The separation of the individual glucosinolates is achieved by using a conventional‐bore high‐performance liquid chromatography column with an aqueous ammonium acetate – acetonitrile gradient. The mandatory flow‐rate reduction is achieved by using a pneumatic splitter. The determination limits are estimated to be below 20 μg/g in plant material for various glucosinolates using the sample pretreatment described.
Linked scans of peptides and protein digests: Amino acid sequence determination of components of complex mixtures
Authors: Morris Howard R. , Chatterjee Ashraf , Panico Maria , Green Brian N. , da Silva Maria A. A. Almeida , Hartley Brian S.
Published: May 2005

Two‐sector linked‐scan analysis of an unpurified proteolytic digest of a pyruvate decarboxylase enzyme (60 000 Da) has allowed the discovery and assignment of an amino‐terminal post‐translational modification and processing event. A difference in amino acid sequence from that predicted by a recently published nucleotide sequence has also been found. These results illustrate both the use and considerable potential of linked‐scan methods for the analysis of complex biopolymer mixtures.
Sequence determination of multiply charged peptide molecular ions by electrospray–ionization tandem mass spectrometry
Authors: Barinaga Charles J. , Edmonds Charles G. , Udseth Harold R. , Smith Richard D.
Published: May 2005

Electrospray ionization generates multiply charged peptide molecular ions which are efficiently dissociated by collision with a neutral gas to provide sequence‐specific daughter ions. The scope for application of this phenomenon is illustrated by the nearly complete sequencing of melittin (relative molecular mass (Mr) 2846.5) employing a tandem quadrupole mass spectrometer having a mass limit of m/z 1400.
The application of a membrane interface to on‐line mass spectrometric measurements of volatile compounds in aqueous solutions
Authors: Dheandhanoo Seksan , Dulak John
Published: May 2005

A simply designed silicon rubber membrane interface was used as a gas/liquid separator. This technique is based on the selectivity of the membrane. The combination of the membrane interface and a quadrupole mass spectrometer results in a simple and inexpensive instrument which can be used for both quantitative and qualitative determination of volatile compounds in aqueous solution. The response of the membrane‐interface/mass spectrometer to several volatile organic compounds in water was investigated. The detection limit of this instrument can be as low as the sub ppm range with a response time of a few minutes.
The use of two different buffers for unequivocal molecular weight determination in liquid chromatography/thermospray mass spectrometry
Authors: Maeder H.
Published: May 2005

High‐performance liquid chromatography (HPLC) in combination with thermospray mass spectrometry (LC/TSP‐MS) is an important method for molecular weight determination of unknown compounds. In addition to the well‐known ammonium acetate buffer (NH4OAc) the use of methylammonium acetate (CH3NH3OAc) in the positive‐ and ammonium formate (NH4OFo) in the negative‐ion mode is recommended. Performing a second run with these buffers, even from spectra with only one single quasimolecular ion, an unequivocal molecular weight can be obtained. For correct assignment, the shift in mass of the corresponding quasimolecular ions in each mode is used. Finally, the use of a second buffer greatly facilitates the recognition of superimposed HPLC peaks.
Fragmentation of 2‐Acylcyclohexane‐1,3‐dione Ions and Their 4‐hydroxy derivatives. Elimination of water via an enol
Authors: Mudd A.
Published: May 2005

2‐Acylcyclohexane‐1,3‐diones and their 4‐hydroxy analogues were analysed by gas chromatography/mass spectrometry. Fragmentation pathways for the formation of diagnostic ions are suggested.
Elucidation of some fragmentations of small peptides using sequential mass spectrometry on a hybrid instrument
Authors: Thorne Gareth C. , Gaskell Simon J. , Gross M. L.
Published: May 2005

Sequential daughter‐ion‐scanning analyses of small peptides have been performed using a hybrid tandem instrument of BEqQ configuration. Precursor ions are selected by B and allowed or induced (by high‐energy collisional activation) to decompose in the region preceding E. Decoupling of E from the accelerating voltage permits the selection of the first‐generation daughter ion whilst retaining appropriate float voltages for the quadrupole assemblies. The daughter ion selected by E is further subjected to low‐energy collisional‐activation dissociation (CAD) in q and the fragment‐ion spectrum is obtained by scanning Q. The sequential daughter‐ion‐scanning technique has been used to establish that ‘internal’ fragments of the types, (AY′) and (BY′), are formed via initial Y‐type cleavage. Fragmentation of a protonated peptide (angiotensin III) by loss of the C‐terminal amino acid residue, yielding a (B + OH) ion, is reported for the first time. This process is analogous to that previously described for metal‐cationized peptides.
Extending the mass range of the quadrupole ion trap using axial modulation
Authors: Kaiser Raymond E. , Louris John N. , Amy Jonathan W. , Cooks R. Graham , Hunt D. F.
Published: May 2005

Secondary‐ion mass spectrometry, using Cs+ ion bombardment of solid and liquid matrices, has been implemented on a quadrupole ion trap. Tetraalkylammonium cations and protonated peptides, generated in an external source using a pulsed primary‐ion beam, are injected into the ion trap where they are decelerated and trapped in the course of collisions with the helium bath gas. The contents of the trap are then examined by recording a mass spectrum using the mass‐selective instability scan. To improve performance in the examination of these trapped ions, the technique of axial modulation is used to cause resonance ejection of ions from the trap during the mass‐analysis step. The supplementary AC voltage applied to the end‐caps causes resonant ejection of ions at qz values below those which correspond to the normal stability limit. This is demonstrated to increase the mass limit of a commercial ion trap from 650 Da to approximately 1300 Da with no loss in resolution or sensitivity, and to more than 20 000 Da at reduced sensitivity.
Use of gas chromatography/mass spectrometry selected‐ion recording for sterol content pattern recognition in fungal classification
Authors: Howell S. A. , Noble W. C. , Mallet A. I. , Minnikin D. E.
Published: May 2005

Chemotaxonomic studies are frequently limited by the volume of data obtained and the difficulty of reducing this to statistically interpretable results. This paper describes the use of a straightforward procedure for relating the pattern of occurrence of sterols in fungi, analysed by mass spectrometry, to their classification.
Loss of oligomer information in pyrolysis‐desorption/chemical‐ionization mass spectrometry of amylose, due to the influence of potassium hydroxide
Authors: Scheijen Martin A. , Boon Jaap J. , van der Greef J.
Published: May 2005

Pyrolysis‐desorption/chemical‐ionisation mass spectrometry (PyD/CIMS), using ammonia as ionization gas, was employed to investigate the influence of potassium hydroxide on the pyrolytic behaviour of glucans. The mass spectrum of native amylose, a 1 → 4 linked α‐D‐glucan, revealed an ion series pointing to desorption of intact 1,6‐anhydro‐oligosaccharides. Ions indicating oligomers up to the nonamer were observed. Addition of trace amounts of potassium hydroxide to amylose resulted in reduction in the size of the 1,6‐anhydro‐oligosaccharide ions and a simultaneous increase of ions resulting from ring rearrangements. Larger amounts of potassium hydroxide led to a complete loss of mass spectral information at the oligomer level.

Similar mass spectrometric distributions in the PyD/CIMS data of a potassium hydroxide extracted tobacco fraction clearly reveal that alkali remnants must be present in this sample, which severly reduce the mass spectrometric information from polysaccharide oligomers. It is important to evaluate the role of inorganics on the thermal activation and subsequent fragmentation of biopolymers in PyD/CIMS experiments.
Laser‐induced desorption of proteins
Authors: Salehpour M. , Perera I. , Kjellberg J. , Hedin A. , Islamian M. A. , Håkansson P. , Sundqvist B. U. R.
Published: May 2005

Laser‐induced desorption mass spectrometry has been applied to a number of proteins in the mass range 5000–150 000 u. The beam from an excimer‐laser‐pumped dye‐laser at 266 nm has been focused to a spot of about 50 μm in diameter with irradiances in the 107W/cm2 region. A linear time‐of‐flight mass spectrometer has been used for mass spectrometric measurements, where positive and negative secondary ions of large proteins have been studied. The effect of different experimental parameters on the protein ion‐signal intensities are discussed.
Characterization of phosphorylated amino acids by fast‐atom bombardment mass spectrometry
Authors: Dass Chhabil
Published: May 2005

Positive‐ and negative‐ion fast‐atom bombardment (FAB) mass spectrometry and linked‐field scan techniques at constant B/E are used to characterize phosphorylated serine, threonine, and tyrosine amino acids. Abundant molecular ions are formed for all three amino acids in both modes of ionization. The dominant fragmentation is cleavage of the phosphate ester bond with charge retention in positive‐ion FAB by the amino acid backbone and in the negative‐ion mode by the phosphate group. The unique feature of positive‐ion FAB mass spectra of phosphoserine and ‐threonine is the loss, from the ion [M+H]+, of a molecule of phosphoric acid (98 Da), whereas the corresponding tyrosine expels a HPO4 (96 Da) moiety to yield a stable phenylalanine ion.
Collision‐induced dissociation of Cs4I. An Example of Superelastic Collisions?
Authors: Alexander A. J. , Thibault P. , Boyd R. K.
Published: May 2005

The collision‐induced dissociation (CID) of Cs4I to form Cs3I has been investigated by mass‐analysed ion kinetic energy spectroscopy, When helium was used as collision gas the CID process was accompanied by sizable loss of translational energy in the collisional‐activation step. However, use of krypton or xenon as collision gas yielded product ions with translational energies higher than that observed for unimolecular reaction in the absence of collision gas. Neon and argon provided intermediate behaviour. Extensive experiments designed to investigate possible explanations for these observations left superelastic collisions of an excited state as the only possibility. Since nothing is known about the structures and electronic states of species like Cs4I, the necessarily speculative discussion is based upon general considerations of coupling of translational and electronic energies via crossings between states of the transitory collision complex. These observations emphasise the complexity of the possible processes which can occur as a result of collisions in the keV range.
A simple and effective way to enhanee fast‐atom bombardment mass spectra of sulfonic acids
Authors: Shimanskas Charles , Ng Kenneth , Karliner Jerrold
Published: May 2005

A technique for the simplification of fast‐atom bombardment (FAB) spectra of polysulfonic acids, especially azo dyes complicated by sodium, is discussed. The sodium may be present as the sulfonate salt or the salt may be formed during FAB analysis from impurities present in the sample. The incorporated sodium as well as other impurities which may be present in commercial samples are removed by means of a simple cationic‐exchange‐resin procedure, yielding simplified and unambiguous FAB spectra of the sodium‐free material.
Observation of sequence‐specific peptide fragmentation using extended tandem mass spectrometry experiments
Authors: Schey Kevin L. , Schwartz Jae C. , Cooks R. Graham , Caprioli R. M.
Published: May 2005

Reaction‐intermediate spectra are reported for peptide mixtures using a hybrid BEQQ and a pentaquadrupole mass spectrometer. In this extended tandem mass spectrometry scan, the protonated molecule and a terminal fragment ion are selected with the first and third mass analyzers, respectively. A subsequent linked scan at constant B/E (hybrid instrument) or a scan of the middle quadrupole (pentaquadrupole instrument) produces the reaction‐intermediate spectrum. The resulting spectra are simpler than conventional tandem mass spectrometry daughter‐ion spectra and display only sequence ions of one group, viz. A, B and C or X, Y and Z. This information facilitates structural elucidation and is obtainable on nanomole amounts of peptide.
Direct synthesis and electron‐ionization positive‐ion mass spectrum of tetrakis(acetylacetonato)cerium(IV), Ce(C5H7O2)4
Authors: Chaudhuri Mihir K. , Islam Nashreen S. , Khathing Darlando T. , Shylla Vicky G. , Mathur D.
Published: May 2005

Crystalline Ce(C5H7O2)4 has been synthesized directly from the reaction of hydrated cerium(IV) oxide with acetylacetone, (C5H8O2), and its electron‐ionization (EI) mass spectrom is reported. The compound exists as a monomer (mass 536) in the gaseous state. The mass spectrum, like those of M(C5H7O2)4 (M = Zr or Th) and CeL4 (L = fluorinated β‐diketonate), shows the dominant ion signal to be due to the [Ce(C5H7O2)3]+ ion that arises from the loss of one C5H7O2 from the molecular ion. An internal electron‐transfer affords [Ce(C5H7O2)3]+˙. Fragmentation of [Ce(C5H7O2)3]+˙ to [Ce(C5H7O2)2]+ is similar to that observed for the tris‐chelates of trivalent transition metals and La(C5H7O2)3. The ion [Ce(C5H7O2)2]+ ultimately breaks down to [CeO]+ through the sequential loss of three even‐electron neutral species, CH3COCHCCH2, H2O and CH3COCHCCH2 without invoking any further reduction of the Ce centre. Mechanisms are given for the loss of the three even‐electron species from the bis(acetylacetonato)cerium(III) ion fragment. Theoretical simulations of patterns of the fragment ions [Ce(C5H7O2)3]+˙, [Ce(C5H7O2)2]+˙, and [Ce(C5H7O2)OH]+ have been made and compared with those of the corresponding experimental results in support of the suggested mode of fragmentation.
Transmission characteristics of a radio‐frequency‐only quadrupole gas‐collision cell at high axial energies in a hybrid tandem mass spectrometer
Authors: Alexander A. J. , Dyer E. W. , Boyd R. K.
Published: May 2005

Collision induced dissociation (CID) experiments using RF‐only quadrupole collision cells normally employ laboratory‐frame collision energies Elab of a few tens of eV. Difficulties in inducing CID reactions for larger precursors (> 600–800 Da) can be attributed in part to collision energies, in the appropriate centre‐of‐mass reference frame, which are too low. Attempts to overcome this problem by using values of Elab in the range of a few hundreds of eV have been largely unsuccessful. The present work shows that a major reason for this lack of success has been an inability of the instruments used to fulfil the focusing requirements of an RF‐only quadrupole cell for such precursors, and their higher mass fragments, in this range of values for Elab. A simple modification permitting use of much higher values of the RF amplitude has been shown to permit the collision cell to be operated so that the ion‐beam profile at the entrance aperture is imaged at the exit; improvements in precursor transmission efficiency by up to two orders of magnitude are thus obtainable. Examples of corresponding improvements in fragment‐ion spectra of a test octapeptide are also demonstrated. The principal drawback of this approach concerns the poor transmission for low‐mass fragments near the stability cut‐off (Mathieu parameter qu > 0.91); reasons for the non‐zero transmission efficiency for fragments with qu > 0.91 are discussed, together with methods for alleviating the low‐mass transmission problem.
Instrument‐independent database for collisionally activated dissociation in RF‐only quadrupoles. The case of C2H3O+ and C3H
Authors: Martinez Richard I. , Ganguli B.
Published: May 2005

Dynamically correct (i.e., instrument‐independent) branching ratios can be measured under single‐collision conditions in tandem mass spectrometers incorporating RF‐only quadrupole collision cells. The absolute branching ratios were measured as a function of the center‐of‐mass interaction energy ECM for the collisionally activated dissociation (CAD) of CH3CO+ (m/z43) from several source compounds (ethanol, oxirane), and CH3CO‐X (where X = H, CH3, CH3CH2, CH3CO, CH3COCH2, and C6H5)). The energy dependences of the branching ratios for C2H3O+ from CH3CO‐X source compounds are quite distinct from those observed for C2H3O+ from ethanol or ethylene oxide, or for the C3H+7 ions (also m/z 43) from n‐pentane. Hence, one can use the CAD of m/z 43 to distinguish CH3CO‐X compounds from other source compounds, including sources of C3H7+ ions. Therefore, the characteristic branching ratios of ionic substructures may provide for tandem mass spectrometry a „fingerprinting”︁ capability analogous to the use of group frequencies in infrared spectroscopy.
Electron ionization mass spectrometry for sequence analysis of glycosphingolipid mixtures by fractional evaporation in the ion source. Mass spectrometric evidence for an eleven‐sugar glycolipid
Authors: Holgersson J. , Pimlott W. , Samuelsson B. E. , Breimer M. E.
Published: May 2005

This paper describes the use of electron ionization mass spectrometry for structural characterization of a mixture of glycosphingolipids from a single human kidney and presents mass spectrometric evidence for the presence of an eleven‐sugar glycolipid. A large amount of structural information is obtained from minor glycolipid constituents having long sugar chains by a fractional evaporation in the ion source, achieved by steadily increasing the ion‐source temperature.
Structural characterization of two isomeric dimethoxyindoles of biological interest, using high‐ and low‐energy collisional spectroscopy
Authors: Emary W. Bart , Allegri G. , Costa C. , Frison G. , Traldi P.
Published: May 2005

It is not possible to distinguish isomers of biologically important dimethoxyindoles using electron‐ionization mass spectra, but they may be distinguished by collisionally activated dissociation. In particular, energy‐resolved mass spectrometry yields the best data for distinguishing between these isomers.
Ion optical considerations of a quadrupole–octapole lens system for varying mass range on a simultaneous detector
Authors: Ishihara Morio , Kammei Yoshihiro , Matsuo Takekiyo
Published: May 2005

The sensitivity and mass resolution of a conventional double‐focusing mass spectrometer equipped with an array detector are limited by the fixed range of masses that can be detected simultaneously. This paper describes ion‐optical properties of a new lens system for varying the relative mass range on the simultaneous detector.
Matrix‐assisted laser‐desorption mass spectrometry using 355 nm radiation
Authors: Beavis Ronald C. , Chait Brian T. , Standing K. G.
Published: May 2005

Matrix‐assisted laser desorption of proteins with the 355 nm frequency‐tripled output of a neodymium:yttrium‐aluminium‐garnet laser has been demonstrated. In order to produce desorption at this wavelength, the cinnamic acid derivatives ferulic, caffeic and sinapinic acids have been employed as matrices. Excellent sensitivity (routinely one pmol of protein) and good mass resolution (m/Δm 400, Full width at half maximum) have been obtained by this new method. Ultraviolet photo‐spectrometry of the cinnamic acid derivative matrices suggests strongly that they can be used as protein laser‐desorption matrices at any wavelength between 260 nm and 360 nm, allowing the development of laser‐desorption mass spectrometers based on nitrogen or excimer lasers.
The dissociative ionization of H2 by electrons
Authors: Krishnakumar E. , Mathur D.
Published: May 2005

Dissociative ionization of H2 by low‐energy monoenergetic electrons has been studied in a crossed electron‐beam/molecular‐beam apparatus incorporating a quadrupole mass spectrometer with a view to examining the influence, if any, of the quadrupole RF fields on neutral Rydberg species, the associated physical mechanisms and their effect on H+ kinetic‐energy distribution functions.
Discrimination effects in inorganic ion‐cluster detection by secondary‐electron multiplier in mass spectrometry experiments
Authors: Alexandrov M. L. , Gall L. N. , Krasnov N. V. , Lokshin L. R. , Chuprikov A. V.
Published: May 2005

Discrimination effects in secondary electron multipliers due to the differences in kinetic energy with which ions of different masses strike the dynode surface are investigated. The threshold energy at which ions of a particular mass can be detected is discussed. The efficiencies of such multipliers when used with cluster ions such as H+(H2O)N (where Cat+ represents an alkali‐metal cation) are investigated and discussed, in terms of both the ‘kinetic’ and ‘potential’ emission coefficients.
Abnormal effects in the detection of ions from bioorganic substances by mass spectrometry
Authors: Alexandrov M. L. , Gall L. N. , Krasnov N. V. , Lokshin L. R. , Chuprikov A. V.
Published: May 2005

The characteristics of the detection of ions of the alkali metals and of cluster ions of the type (H2O)NMH+ (where M is an amino acid) are markedly different from those for the detection of protonated saccharose ions. The latter are shown to produce a signal from a secondary electron multiplier detector at a lower ion energy than the threshold energy for the former ions. An explanation is proposed in terms of the charge localization.
Negative‐ion chemical ionization spectra of oxazolidinone derivatives of amino acids prepared by their reaction with dichlorotetrafluoroacetone
Authors: Macfarlane R. G. , Watson D. G. , Midgley J. M.
Published: May 2005

Oxazolidinone derivatives of glycine, phenylalanine and tyrosine were prepared by their reaction with dichlorotetrafluoroacetone. The derivatives were analyzed by gas chromatography/negative‐ion chemicalionization mass spectrometry with methane as the reagent gas. The mass spectra under these conditions were composed of a few ions resulting largely from the addition of a chlorine radical to the molecular ion and successive losses of up to two HCl moieties from the molecular ion; loss of CO2 was also observed. Comparison of the mass spectrum of glycine and [2H2]glycine indicated that the protons involved in the loss of HCl from the molecular ion were derived in the first instance from the CH2 group in the derivative and secondly from the NH group. The derivatives were applied to the analysis of the amino acid precursors of biogenic amines in nervous tissue from the locust.
Internal energy effects in the collision‐induced dissociation of large biopolymer molecular ions produced by electrospray ionization tandem mass spectrometry of cytochrome c
Authors: Smith Richard D. , Barinaga Charles J.
Published: May 2005

The effects of internal energy upon metastable and collision‐induced dissociation (CID) processes observed in the tandem mass spectrometry of multiply protonated molecules of horse‐heart cytochrome c (Mr 12360) are described. The internal energy of the multiply protonated (15H+) molecules (at m/z 825) formed by electrospray ionization (ESI) was manipulated using electric fields in the atmospheric pressure/vacuum interface region. Highly efficient CID is obtained for molecular ions collisionally activated in the ESI interface. The dissociation efficiency at 3.8 eV to 5.8 eV (center of mass) collision energies for internally “hot” molecular ions under multiple collision conditions in a triple quadrupole mass spectrometer is shown to be much greater than for “cold” ions. The CID spectra show dramatic effects due to internal energy, with charge stripping dominating for cold ions (where CID efficiency is very low) and extensive fragmentation observed for hot ions.
Lowering detection limits in plasma‐desorption mass spectrometry by partial target shielding
Authors: van Veelen P. A. , Tjaden U. R. , van der Greef J.
Published: May 2005

A simple method of improving signal‐to‐noise ratios in plasma‐desorption mass spectrometry of femtomole quantities is described. Background reduction is achieved by effectively shielding of the non‐sample area. It is shown that detection limits can be improved by a factor of 4.
High‐resolution ion partitioning technique for a one‐section ion‐cyclotron‐resonance spectrometer cell
Authors: Nikolaev E. N. , Mordehai A. V. , Talrose V. L.
Published: May 2005

A technique for isolation of mass‐selected ions in a specially designed one‐section ion‐cyclotron‐resonance cell is described. To demonstrate the potentialities of this technique a model experiment has been performed in which all ions (CO+·, H2O+·, Ar+·, H+…︁) were removed from the cell and only ions of N2+ were left. The removal of the ions was carried out simultaneously, in the direction of the magnetic field. The technique is readily adapted to existing instruments.
Recent advances in ion‐trap technology
Authors: Griffiths Iwan W
Published: May 2005

Recent technological improvements in the operation of RF quadrupole ion traps have resulted in spectacular advances in a number of scientific applications. This short review provides a summary of some new results in mass spectrometry and other areas which illustrate the astonishing versatility of this rapidly developing instrument.
Use of m‐nitrobenzyl alcohol as a matrix in fast‐atom bombardment negative‐ion mass spectrometry of polar compounds
Authors: Aubagnac J.‐L.
Published: May 2005

Fast‐atom bombardment negative‐ion mass spectra of various polar compounds (cyclopeptides, nucleosides, organometallic salts) with a m‐nitrobenzyl alcohol (NBA) matrix exhibit identical characteristics. First, several ions at high masses allow characterization of the molecular weight. Second, at low masses, only ions characteristic of the NBA matrix are observed.
Evidence for a reaction window in double‐electron‐capture reactions in collisions involving the molecular target CH3Br
Authors: Langford M. L. , Harris F. M.
Published: May 2005

Double‐electron‐capture reactions in which singly charged projectile ions A+ convert to negative ions A− in collisions with molecules M are endoergic. Non‐zero cross‐sections for the reactions occur when the endoergicities fall within a ‘reaction window’. The existence of a window for reactions with CH3Br molecules is demonstrated in this investigation by altering the population of ground and excited states of the resulting CH3Br2+ ions using three projectile ions, S+˙, OH+ and F+ which markedly alters the endoergicities of the double‐electron‐capture reactions. Analysis of the energy‐loss spectra indicates that the reaction window for CH3Br is between endoergicities of about 8 and 22 eV. Using F+ as the projectile ion, it is shown that the population of the more highly excited states of CH3Br2+ is enhanced.