bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of coulomb energy in promoting collisionally activated dissociation of multiply charged peptides formed by electrospray ionization
Authors: Ishikawa Keiichiro , Nishimura Toshihide , Koga Yoshinori , Niwa Yoshio
Published: May 2005

Electrospray ionization tandem quadrupole mass spectrometry has been applied to a series of lysine‐substituted octaalanines and some naturally occurring peptides containing more than two basic amino acid residues. Unusually high fragmentation efficiency along with site‐specific cleavages at the outer side of and remote from basic residues were observed for collisionally activated dissociation spectra of multiply charged peptides (MCP) with basic residues in close proximity. It was suggested that Coulomb energy (CE) rather than Coulomb repulsion (CR) was responsible for promoting fragmentation of the MCP studied. A possible fragmentation mechanism of MCP is proposed, in which the conversion of CE into internal vibrational energy was brought about by intramolecular proton migration in the presence of CR between charged sites.
Plasma desorption mass spectrometry of two synthetic sarafotoxins: Side reactions and characterization of the intermediates
Authors: Lamthanh Hung , Deprun Claude , Beyec Yvon Le
Published: May 2005

Sarafotoxins (SRTXs) form a family of toxic and potent vasoconstrictor peptides of 21 amino acids and two disulfide bonds. They are present in the venom of the burrowing asp Atractaspis engaddensis. We have made two derivatives of the amino acid sequence of SRTX‐b, one of the most potent isotoxins, in the solid phase. First, we replaced Ser2 by Thr, to investigate whether, as previously postulated, this change is responsible for the weak activities of SRTXs c and d. Secondly, we replaced Ser2, Asp18 and Val19 respectively by Thr, Gly and He, with a view to generating SRTX‐e whose amino acid sequence was deduced from cDNA.

Solid‐phase peptide synthesis (SPPS) was performed according to the tert‐butyloxycarbonyl strategy and the disulfides were paired sequentially using a selective chemistry. The disulfide 1–15 was formed by oxidation of cysteines1,15 with ferricyanide, whereas disulfide 3–11 was made by iodine oxidation of Acm‐blocked cysteines3,11. By plasma desorption mass spectrometry (PDMS), we monitored all possible side reactions that occurred during the synthesis. We thus observed a benzyl shift in mass spectra when aspartic and glutamic acid side chains were protected by a benzyl group during the SPPS. This could be circumvented by using instead, a cyclohexyl protecting group. We also noted the oxidation of the methionine and the tryptophan side chain (formation of methionine sulfoxide and oxindole ring of tryptophan) to a small extent during the cleavage peptide/solid phase oxidation of the methionine side chain during the formation of the disulfide 1–15 by ferricyanide. These known side reactions could be avoided by using a mixture of scavengers (ethanedithiol, dimethylsulfide, thioanisole, m‐cresol and skatole) and by shortening the ferricyanide oxidation time to one hour. The sequential disulfied bond formation starting from the linear peptide (mono‐disulfied and bi‐disulfide) was also monitored by PDMS. PDMS therefore proved to be a sensitive analytical method for the measurement of the molecular weights of synthetic or natural peptides (SRTX peptides in this application) in the field of peptide and protein chemistry.
Matrix‐free desorption of biomolecules using massive cluster impact
Authors: Shannon Cornett D. , Lee Terry D. , Mahoney John F. , Todd P. J.
Published: May 2005

Massive‐cluster impact (MCI) ionization was found to be capable of producing high secondary‐ion yields from biological samples without the use of a liquid matrix. Dry samples of molecules as large as cytochrome c were observed to be efficiently desorbed without significant fragmentation by the MCI beam of glycerol clusters. In addition, signals from protonated molecules retained a significant proportion of their initial intensity even after several minutes exposure to the primary beam. It was determined that these remarkable phenomena are not the result of the build‐up of a layer of glycerol caused by the cluster bombardment.
Peptide fingerprints after partial acid hydrolysis: Analysis by matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Knierman Michael D. , Coligan John E. , Parker Kenneth C. , Chait B. T.
Published: May 2005

A method is described by which a sequence‐dependent peptide fingerprint can be rapidly obtained upon partial hydrolysis of peptides with hydrochloric acid and subsequent analysis by matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). When synthetic peptides are treated with 3M HCI for 5 min at 110°C, amino acids are released in turn from the C‐terminus or, depending on the peptide, from the N‐terminus. Sequence information can be deduced by identifying the amino acid whose mass corresponds to the difference in MW between the major hydrolysis products, beginning from the MW of the starting peptide. A similar pattern exclusively from the C‐terminus has been obtained using pentafluoropropionic acid as a hydrolyzing agent (Tsugita et al. Eur. J. Biochem. 206, 691 (1992)), but required longer hydrolysis time and more handling prior to analysis. The technique we have developed could be used to obtain a sequence‐dependent ‘fingerprint’ for a peptide cheaply and rapidly, starting with picomole amounts of peptide, because the hydrolysate can be directly analyzed by MALDI. This methodology might be especially useful for confirming the identity of peptides during peptide mapping.
The unimolecular dissociation of the molecular ion of acetophenone induced by thermal radiation
Authors: Sena Marcelo , Riveros José M. , Nibbering N. M. M.
Published: May 2005

The molecular ion of acetophenone is shown to undergo unimolecular dissociation to the benzoyl cation in an ICR cell at low pressures and in the vicinity of 333 K with rate constants in the range of 2 to 4 s−1. Pressure and temperature dependence of this process reveal that the process is primarily induced by absorption of thermal radiation driving ions to energies above the dissociation limit. Collisional effects also enhance this dissociation by a mechanism that attempts to restore a full Boltzmann distribution of the molecular ions.
Electrospray mass spectrometry for the characterization of the purity of natural and modified oligodeoxynucleotides
Authors: Deroussent Alain , Le Caer Jean‐Pierre , Rossier Jean , Gouyette Alain
Published: May 2005

Electrospray ionization mass spectrometry is an accurate and sensitive analytical method to characterize the purity of oligodeoxynucleotides being tested for pharmacological studies. We report the preparation procedure (‘desalting’) of natural and modified oligodeoxynucleotides (ODNs) and their analysis by negative‐ion electrospray mass spectrometry. We evaluate the sensitivity and the accuracy of the method for two antisense ODN sequences. Mass analysis of the 25‐mer phosphorothioate can be performed to within 0.001% accuracy (standard error of 0.05 Da) for a sample concentration of 12 pmol/μL. In addition, the adduct ion and the failure sequence can be identified to characterize the antisense ODN.
Formation of protonated phosphonates in the ion‐trap mass spectrometer under electron impact conditions
Authors: Méchin N. , Plomley J. , March R. E. , Blasco T. , Tabet J.‐C.
Published: May 2005

The gas‐phase behaviour of organophosphorus compounds such as diethylmethylphosphonate towards electron impact (EI) ionization occurring in a quadrupole ion‐trap instrument is investigated. If all ions observed in conventional EI mass spectra are detected, ion/molecule reactions are seen to occur leading to formation of protonated molecules and adduct ions such as 2M+· and [2M + H]+. The keto‐to‐enol‐like isomerization of the molecular M+· ion seems to favour proton transfer to neutral M species and a “self chemical ionization” ion is observed with corresponding fragment ions.
Stereospecific decompositions induced by low‐energy collision‐induced dissociation of MH+ ions of epimeric alkaloids
Authors: Grégoire S. , Dugat D. , Fournier F. , Gramain J.‐C. , Tabet J.‐C.
Published: May 2005

Several studies have investigated stereochemical effects observed in the electron ionization and low‐energy collision‐induced dissociation (CID) mass spectra of molecular ions from synthetic and natural alkaloids. More recently, it has been shown that low‐collision‐energy CID spectra of protonated epimeric alkaloids can yield additional information. For instance, three epimeric tetracyclic alkaloids studied in the present work are characterized by different cis/trans ring junction geometries and by different configurations of the ethyl group linked to the C‐ring. Low‐energy collisional spectra of the epimeric MH+ ions show large differences depending both on the ring junction geometry and the stereochemistry of the side chain. Interpretation of certain specific processes invokes ion‐dipole formation, allowing internal electron transfer. Consecutive decompositions have also been scrutinized.
Sequencing of hydrophobic peptides as lithiated adducts using liquid secondary‐ion mass spectrometry without tandem mass spectrometry
Authors: Becchi M. , Rebuffat S. , Dugast J‐Y. , Hlimi S. , Bodo B. , Molle G.
Published: May 2005

Lithium cationized hydrophobic peptides in the molecular weight range 1900–2650 Da have been studied by liquid secondary‐ion mass spectrometry. The mass spectra exhibit characteristic lithiated sequence ions. N‐terminal [an+LiH]+ and [dn+LiH]+ ions together with limited C‐terminal [ypro+Li+H]+ ions lead to an easy sequencing of the peptides studied, without the need for tandem mass spectrometry.
Particle size distribution is not the major factor explaining variable analyte transmission efficiency in liquid chromatography/particle beam/mass spectrometry
Authors: Wilkes Jon G. , Zarrin Fahimeh , Lay Jackson O. , Vestal Marvin L.
Published: May 2005

We characterized the particle size distribution and the analyte transmission efficiency of a liquid chromatography/particle beam/mass spectrometry (LC/PB/MS) system as a function of experimental variations normally used to optimize the LC/PB/MS system. The particle size distribution was evaluated using an electrical differential mobility particle sizer (DMPS) and both the DMPS and the mass spectrometer were used to evaluate transmission. The latter results were correlated to provide evidence related to mechanisms which contribute to poor sample transmission. Addition of ammonium acetate buffer did not increase the aerosol particle riean diameter. However, it did lead to significant increases in caffeine transmission efficiency observed in both the DMPS and the mass spectrometer. Our results were interpreted to suggest a possible electrostatic cause for quantitative anomalies in LC/PB/MS rather than simple mass discrimination in the particle beam momentum separator.
Fast‐atom bombardment mass spectrometry of some pharmacologically relevant anthraquinone derivatives
Authors: Maccioni Elias , Delogu Giovanna , Podda Gianni , Palumbo Manlio , Zagotto Giuseppe , Seraglia Roberta , Traldi Pietro
Published: May 2005

The mass spectrometric behaviour of some anthraquinone derivatives has been studied by fast‐atom bombardment ionization. For all the compounds under study, a retrosynthetic process, consisting in the cleavage of the NHCO bond with hydrogen rearrangement, has been detected. This decomposition pathway leads to the formation of the protonated molecule of 1,4‐diaminoanthraquinone or to the 1‐amino‐4,5,8‐trihydroxy‐anthraquinone, representing the basic synthetic elements of the compounds under investigation.
Matrix‐assisted laser desorption and fast‐atom bombardment mass spectrometry of water‐soluble phthalocyanines and their carboxyl derivatives
Authors: Shankai Zhao , Feng Zhong , Weide He , Zhongping Yao , Hanhui Wen
Published: May 2005

Aluminium phthalocyanine and copper, nickel and zinc 4,4′,4″,4‴‐tetra carboxyl phthalocyanines have been studied by matrix‐assisted laser desorption ionization(MALDI) and fast‐atom bombardment(FAB) mass spectrometry. Aluminium phthalocyanines can be analysed by both FAB and MALDI with promising results but FAB provides more fragment information. The carboxyl derivatives are less volatile than the unsubstituted compounds and their mass spectra cannot be obtained by FAB, but can be obtained by MALDI with good results.
Peptide mapping of recombinant human parathyroid hormone by enzymatic digestion and subsequent fast‐atom bombardment mass spectrometry
Authors: Nabuchi Yoshiaki , Kuboniwa Hitoshi , Takasu Hisashi , Asoh Yoshinori , Ushio Hidetoshi
Published: May 2005

Peptide maps of recombinant human parathyroid hormone (rhPTH) were determined by both trypsin and V‐8 protease digestion with subsequent fast‐atom bombardment mass spectrometry (FAB‐MS). Coverage of the sequence was 85% when using trypsin and 90% when using V‐8 protease. Five rhPTH variants that were recombinantly produced as models of Asn deamidated type degradation products were measured, and molecular weight differences between their respective deamidated peptide fragments were completely detected. In the V‐8 protease digests of some variants, characteristic peptide ions caused by the deamidation were observed and this greatly facilitated the assignment and recognition of the deamidated position. Our data suggest that FAB‐mapping of rhPTH via the protease digestion methods used, appears to have great potential for structural investigations of the peptide.
Reduction phenomenon in frit fast‐atom bombardment mass spectrometry
Authors: Aubagnac Jean‐Louis , Gilles Isabelle , Lazaro René , Claramunt Rosa‐Maria , Gosselin Gilles , Martinez Jean
Published: May 2005

The reduction phenomenon of polar compounds that has already been described in fast‐atom bombardment (FAB) mass spectrometry also occurs in frit‐FAB mass spectrometry.
Compact Wien filter/magnetic sector double‐focusing mass spectrometer
Authors: Ioanoviciu Damaschin , Cuna Cornel
Published: May 2005

A compact Wien filter/magnetic deflector, double‐focusing mass spectrometer was constructed and tested. The Wien filter is sited inside the gap common with the magnetic deflector. The instrument first‐order ion‐optical parameters and the second‐order aberration coefficients are given. A brief description of the instrument is followed by the experimental results obtained on a methane sample. Jon currents of 1.6 × 10−8 A were collected at a resolution of 170 for a main path radius of 56 mm.
Influence of the laser beam direction on the molecular ion ejection angle in matrix‐assisted laser desorption/ionization
Authors: Aksouh Farouk , Chaurand Pierre , Deprun Claude , Della‐Negra Serge , Beyec Yvon Le , Hoyes John , Pinho Roberto Rosas
Published: May 2005

Angular intensity distribution of molecular ions ejected in matrix‐assisted laser desorption/ionization (MALDI) have been measured for two symmetrical positions of the laser beam with respect to the sample surface normal (+60° and −60°). It is shown that the molecular ions are ejected in the direction opposite to the incident laser beam with an average angle of ∼30° which does not depend on the molecular weight in the mass range m/z = 1000 to 25 000. Experiments were performed with the matrix α‐cyano4‐hydroxy‐cinnamic acid.
7‐Deaza purine bases offer a higher ion stability in the analysis of dna by matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Kirpekar F. , Nordhoff E. , Kristiansen K. , Roepstorff P. , Hahner S. , Hillenkamp F.
Published: May 2005

Oligodeoxynucleotides which contain 7‐deaza analogues of the normal purine nucleotides have been synthesized both enzymatically and chemically. When subjected to matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) analysis, the modified samples offer both higher stability and increased sensitivity compared to otherwise identical unmodified Oligodeoxynucleotides. In view of these observations, models for the fragmentation of oligodeoxynucleotides in MALDI‐MS with positive ion detection mode are presented. Additionally, the potential use of 7‐deaza purine nucleotides in the MALDI‐MS analysis of DNA sequencing reactions is discussed.
Examination of recombinant truncated mature human fibroblast collagenase by mass spectrometry: Identification of differences with the published sequence and determination of stable isotope incorporation
Authors: Chowdhury Swapan K. , Eshraghi Jamshid , Gonyea George , Brake Patricia G. , Vavra Karen J. , Banks Tracey , Falvo Joseph , Wahl Robert , Chait Brian T. , Vestal Christina H.
Published: May 2005

Human fibroblast collagenase belongs to a family of matrix metalloproteinases which have been implicated in a number of connective tissue disorders ranging from rheumatoid arthritis to tumor invasion. To examine the active site of this enzyme by biophysical studies, a 19 kDa recombinant truncated mature collagenase (mCL‐t) was prepared. Electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry have been utilized for the characterization of mCL‐t. The molecular weights measured by these techniques identified the presence of two closely related protein components separated by approximately 100 Da. Edman sequence analysis demonstrated that the two protein components differ from each other by an amino terminal valine, consistent with the mass spectrometric data. In addition, the molecular weight of mCL‐t determined by mass spectrometry did not agree with that calculated from the reported sequence. To identify the origin of this discrepancy, the DNA sequence of the mCL‐t clone was examined. Several differences were noted between the DNA sequence of mCL‐t and the published collagenase gene sequence. When these differences were taken into account, the measured molecular weights were found to be in good agreement with that calculated for the modified sequence. In separate experiments, both ESI and MALDI mass spectrometry have been used to determine molecular weights of mCL‐t samples enriched with stable isotopes 15N and (15N+13C). The measured molecular weights demonstrated a 97% (15N) and 99% (15N+13C) incorporation of labeled isotopes in the two samples.
Mass spectrometry of phosphorus‐containing acids chemisorbed on a disperse silica surface
Authors: Bogatyr'ov Viktor M. , Pokrovskiy Valeriy A.
Published: May 2005

Thermal transformations of phosphorus and phosphoric acid were studied on a pyrogenic silica surface. Complete binding of phosphoric acid with the surface was observed as a result of thermal vacuum treatment. Oxidation‐reduction disproportion reactions in the samples containing phosphorus acid resulted in removal of molecular phosphorus in two stages which were attributed to disproportion of phosphorus atoms in the surface monolayer (high‐temperature stage) and in the bulk layers (low‐temperature stage).
Biosynthesis of melanin from dopamine. An investigation of early oligomerization products
Authors: Bertazzo Antonella , Costa Carlo , Allegri Graziella , Seraglia Roberta , Traldi Pietro
Published: May 2005

Matrix‐assisted laser desorption/ionization (MALDI) and fast‐atom bombardment (FAB) mass spectrometry experiments were applied to the study of the early stages of the oligomerization reaction of dopamine with mushroom tyrosinase. Ultrafiltration was employed to remove the enzyme at various reaction times, to prevent possible attachment of the protein to the highly reactive intermediates. Two sets of five samples each, obtained at different reaction times, in one case immediately lyophilized and in the other left to react under an oxygen stream for 24 h before lyophilization, were compared. FAB showed the presence of various species and of these, that at m/z 305 increased in abundance with reaction time in the immediately lyophilized set of samples only. Accurate mass measurements and tandem mass spectrometric experiments indicated the structure of a dopamine protonated dimer for this ion. MALDI measurements showed that all samples were composed of clusters of oligomers differing in degree of oligomerization. Oligomerization increases with reaction time, resulting in the formation of species at 2643–2911 Da. These clusters in turn were formed of species with a different degree of oxidation, detected in both sets of samples.
Bio‐affinity characterization mass spectrometry
Authors: Bruce James E. , Anderson Gordon A. , Chen Ruidan , Cheng Xueheng , Gale David C. , Hofstadler Steven A. , Schwartz Brenda L. , Smith Richard D.
Published: May 2005

A new approach, bio‐affinity characterization mass spectrometry (BACMS), aimed at providing a more rapid, sensitive and potentially more flexible alternative to techniques presently employed for the characterization of noncovalent interactions in mixtures, such as would be encountered in combinatorial chemistry, is presented. BACMS avoids some of the difficulties and potential artifacts associated with affinity chromatography since the noncovalent associations occur in solution; thus, BACMS avoids the requirement of solid support media and the development of non‐interfering linker species. This paper describes the conceptual basis for the methodology and its potential use in applications which include the screening of high affinity ligands in support of new drug development. BACMS exploits new Fourier‐transform ion cyclotron resonance (FTICR) mass spectrometry technologies which, when coupled to electrospray ionization (ESI), allow the investigation of specific noncovalent complexes formed in solution. BACMS utilizes the well‐known attributes of FTICR, such as the high resolution mass analysis and (MS)n (n ⩾ 2) capabilities; however, it is even more directly a result of recently developed techniques involving quadrupolar excitation, such as selected‐ion accumulation. These tools are demonstrated and the results illustrate the extraordinary sensitivity achievable (solution concentrations of 1 × 10−9 M without the use of separations prior to ESI). Thus, the new capabilities demonstrated here, in conjunction with ESI, will be useful for the investigation of very low relative concentration noncovalent association directly from solution, and promote a faster alternative for combinatorial mixture screening and analysis.
An electrostatic ion guide interface for combining electrospray with Fourier transform ion cyclotron resonance mass spectrometry
Authors: Tang Liang , Hettich Robert L. , Hurst Gregory B. , Buchanan Michelle V.
Published: May 2005

A new interface for coupling electrospray (ES) ionization and Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has been developed based on an electrostatic ion guide (EIG). In these initial studies, the EIG interface has been demonstrated to be a simple but effective means of transmitting ES ions generated outside the magnetic field to the FTICR cell. In the current system, the pressures in the EIG region and front FTICR cell are 10−5 and 10−6 Torr, respectively. Under these conditions, ions may be accumulated with low trapping voltages (0.5–0.75 V) and without a high pressure pulse of buffer gas. ES‐FTICR spectra of picomole to femtomole quantities of several peptides, proteins, nucleotides and dinucleotides have been obtained. Modifications currently in progress should enhance performance with respect both to limits of detection and to mass resolution.
Mass spectra of dicarboxylic acid dianilides III. Furan‐based compounds
Authors: Karminski‐Zamola Grace , Fiš;er‐Jakić Lelja , Bajić Miroslav , Boykin David W.
Published: May 2005

The main fragmentation pathways in the mass spectra of five 3,4‐furan‐dicarboxylic acid dianilides are presented and discussed.
Gas‐phase basicities of some amino acid dimers
Authors: Vékey Károly , Czira Gábor
Published: May 2005

This paper gives the first demonstration that the kinetic method can be used to determine molecular pair thermochemical values. Fragmentation of proton‐bound trimers is used to determine the gas‐phase basicities (GB) of molecular dimers (the so‐called molecular‐pair gas‐phase basicities). The set of equations necessary for data evaluation, i.e. extension of the so‐called kinetic method, is discussed. Proton‐bound amino acid trimers have been studied as examples. The GB of glycine dimers (G2) is 190.1 kcal/mol at 970 K, 4.0kcal/mol higher than that of glycine (G). The GB of alanine (A) and valine (V) dimers have also been determined; these are 192.4 (A2) and 194.4 (V2) kcal/mol. The GB of mixed dimers is very close to the average of the respective homo dimers, 191.4 (GA); 192.0 (GV) and 193.2 (AV) kcal/mol. Experimental errors in the relative GB values of various dimers are estimated to be less than 0.3 kcal/mol.
Mass spectrometric study of some zirconocene and hafnocene diadamantanolates
Authors: Grafov Andrei V. , Koval Ludmila I. , Traldi Pietro , Catinella Silvia , Battiston Giovanni A. , Zanella Pierino
Published: May 2005

The electron ionization mass spectrometric behaviour of a new series of hafnocene and zirconocene diadamantanolates is discussed. They are also compared on the basis of mass‐analyzed ion kinetic energy spectrometry. Fragmentation patterns of the complexes in question give relevant information on their gas‐phase behaviour as MO2/MC (M = Zr, Hf) precursors for metal‐organic chemical vapour deposition.
A new hybrid mass spectrometer for the investigation of ion/molecule reactions
Authors: Flammang Robert , Van Haverbeke Yves , Braybrook Carl , Brown Jeff
Published: May 2005

An RF‐only quadrupole collision cell, fitted with retardation and acceleration lenses, has been installed in a field‐free region of a large‐scale tandem mass spectrometer. This new arrangement has allowed decelerated, mass‐selected ions (ca. 5 eV kinetic energy) to react with reagent gases and reaccelerated, mass‐selected products (ca. 8 keV) to be subsequently identified by collisional activation mass spectrometry. The system was tested by looking at ion/molecule reactions of cyclobutanone molecular ions, previously studied by FTICR mass spectrormetry.
The diagnostic value of the m/z 102 peak in the positive‐ion fast‐atom bombardment mass spectra of peptides
Authors: van Dongen W. D. , Heerma W. , Haverkamp J. , de Koster C. G.
Published: May 2005

The mass spectrometric characteristics of a number of different m/z 102 ions, which might occur in the fast‐atom bombardment mass spectra of peptides, appeared to be sufficiently different for an unequivocal structural assignment and they have successfully been applied in the structural analysis of an unknown. Special attention has been paid to the structure of m/z 102 ions from threonine‐containing compounds. Attempts to generate m/z 102 product ions from peptides containing threonine at the N‐terminus were not successful. From experiments with 18O‐labelled threonine it was concluded that the side‐chain hydroxyl group is exclusively involved in the water loss from protonated threonine. Based on ab initio calculations of feasible m/z 102 production structures, N‐protonated dehydroamino‐2‐butyric acid from protonated threonine and peptides containing threonine at the C‐terminus seems to be the most likely product‐ion structure. Although relative stability calculations revealed that the threonine B1‐type ion has the lowest heat of formation, it could also be concluded that a B1‐type ion from threonine should be considered as an electrostatically bound ion/molecule complex, which will immediately dissociate into a threonine immonium ion (A1) and a carbon monoxide molecule. The energy requirement for this fragmentation reaction (B1→A1 + CO) is less than 7 kJ/mol without an energy barrier, which makes B1‐type ions of threonine unlikely to exist in the gas phase.
The unimolecular chemistry of the enol of ionized methyl glycolate: Formation of the hydrogen‐bridged radical cation [CH3O(H)…︁H…︁OCH].+
Authors: Suh Dennis , Terlouw Johan K. , Burgers Peter C.
Published: May 2005

Dissociative ionization of methyl 2‐hydroxy‐isovalerate and dimethyl tartrate cleanly generate, via McLafferty rearrangements, the 1‐methoxy‐ethene‐1,2‐diol ion HOCHC(OH)OCH, 2. The unimolecular chemistry of 2, the enol form of ionized methyl glycolate, HOCH2C(O)OCH, 1, was investigated by a variety of tandem‐mass spectrometry‐based techniques using D‐ and 18O‐labelled precursor molecules. The enol ion undergoes four major dissociations viz. loss of CH, CO, CH3OH and C2HO. Loss of CH involves isomerization of 2, via a 1,4 H shift, into the distonic ion HC(O.)C(OH)O+(H)CH3, 4, followed by direct bond cleavage yielding the product ion HC(O)C(OH). A second 1,4 H shift yields the hydroxyketene/methanol ion–dipole complex which serves as the precursor for the losses of CH3OH and C2HO, yielding HO(H)CCO+· and CH3OH respectively. A further isomerization step leads to the loss of CO, yielding the O…︁H ⃛O bridged ion [CH3O(H) ⃛H…︁ OCH]+·, one of the most stable isomers on the C2H6O potential energy surface. Ionized methyl acetate, CH3C(O)OCH and related aliphatic esters, readily interconvert with their enol isomers prior to dissociation, but no such tautomerization occurs in 1. This is because the HOCH functionality opens up facile rearrangement/dissociation pathways in 1 and 2 whose energy requirements lie below the tautomerization barrier 1→2.
Procedures for detection of DNA by matrix‐assisted laser desorption/ionization mass spectrometry using a modified nafion film substrate
Authors: Bai Jian , Liu Yan‐Hui , Liang Xiaoli , Zhu Yongdong , Lubman David M.
Published: May 2005

A Nafion film substrate modified with concentrated ammonia was shown to improve the detection of DNA using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS), especially for DNA strands greater than 200 base pairs. Experimental procedures relating to the detection of DNA by MALDI‐MS using this modified Nafion substrate are described.
Charge separation reaction dynamics from pepipico using a position‐sensitive detector
Authors: Hsieh S. , Eland J. H. D.
Published: May 2005

The combination of a position‐sensitive detector with the photoelectron–photoion–photoion coincidence (PEPIPICO) technique allows complete determination of the laboratory momenta and angles of ions in coincidence. The technique yields angular distributions of fragment ions, high resolution kinetic energy distributions for two‐body reactions and Newton diagrams for three‐body dication dissociation. The reactions SF→F++SF+F2 and cyclo‐C4F→CF+C2F+CF are shown to follow sequential mechanisms as determined previously. The technique's potential for elucidating more complex reactions is illustrated for SO→O++S++O and CF3I2+→CF+I++F, which show variations in mechanism as a function of total kinetic energy release.
A Faraday cup detector for high‐mass ions in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Imrie D. C. , Pentney J. M. , Cottrell J. S.
Published: May 2005

A detector has been developed, which collects and amplifies the electric charge of an incoming bunch of ions, for use in matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight (TOF) mass spectrometry. The detector has a time‐of‐flight resolution of about 50 ns and a noise level of 750 electrons rms. It has been tested in a Finnigan LaserMAT spectrometer with a number of samples which Were expected to give reliable results in MALDI time‐of‐flight mass spectrometry. Clear mass peaks have been observed from samples with masses above 300 kDa.
Electron impact mass spectra of some 1‐(2‐furyl)‐ and 1‐(2‐thienyl)‐2‐(2‐benzothiazolyl)ethenes
Authors: Karminski‐Zamola Grace , Tralić‐Kulenović Vesna , Fišer‐Jakić Lelja , Bajić Miroslav , Boykin David W.
Published: May 2005

The electron impact mass spectra of some 1‐(2‐furyl)‐ and 1‐(2‐thienyl)‐2‐(2‐benzothiazolyl) ethenes have been recorded and the identity of various ions in the mass spectra established. The compounds examined (1–10) exhibit two main fragmentation routes. On one hand, fragmentation of the furan and thiophene nuclei and the formation of cyclopropenylethyne cations with very significant abundance and on the other hand, fragmentation of the benzothiazole nuclei on characteristic pathways. Compounds 6–10 also show two additional fragmentation routes.
Investigation of crudes of synthesis of [Leu31, Pro34]‐neuropeptide Y by capillary zone electrophoresis/mass spectrometry
Authors: Zaramella Alessio , Curcuruto Ornella , Hamdan Mahmoud , Cabrele Chiara , Peggion Evaristo
Published: May 2005

[Leu31, Pro34]‐Neuropeptide Y is a thirty‐six amino‐acid peptide which has a measured relative molecular mass of 4222. Solid‐phase synthesis of this peptide resulted in complex crudes of synthesis which were examined by capillary zone electrophoresis (CZE)/electrospray ionization mass spectrometry (ES‐MS). The separation efficiency of CZE combined with the mass specificity of mass spectrometry yielded rapid and reliable information on the target peptide and a number of associated side products, which were mainly acetylated peptide sequences having relative molecular masses in the range 2240–4101. Such incomplete or, as they are commonly called, difficult sequences are provoked by problems of swelling and aggregation of the growing peptide chains in the course of synthesis. The use of mass spectrometry is indispensable for obtaining reliable information on the inevitable side products. Initial tuning of the ion source and optimization of the coupling between the CZE system and the mass spectrometer were achieved by performing a number of measurements pertaining to artificially made mixtures of commercial neuropeptides.
Synthetic pyrethroid insecticides analysis by gas chromatography/mass spectrometry operated in negative‐ion chemical ionization mode in soil, moss and fish tissue
Authors: Yasin M. , Baugh P. J. , Hancock P. , Bonwick G. A. , Davies D. H. , Armitage R.
Published: May 2005

A gas chromatographic/mass spectrometric method was developed for the simultaneous determination of five synthetic pyrethroid insecticides in soil, moss and fish tissue. These pyrethroids were extracted with hexane‐dichloromethane by ultrasonication and cleaned up on Florisil (soil and moss) and mixed acid/base alumina (fish) columns prior to determination by gas chromatography/negative‐ion chemical ionization mass spectrometry in selected ion monitoring mode. All the pyrethroids were analyzed simultaneously in a single run on a DB5‐MS 15 m capillary column. Recoveries of the pyrethroids from the three matrices at fortification levels of 10, 50 and 100 μg/kg ranged from 80 to 117%. Four determinations were made at each concentration level for each matrix. The practical determination limit of the method was in the range 0.5 to 5 μg/kg depending on the compound. This method was also applied to samples obtained from a contaminated ecosystem.
Combinatorial chemistry: Direct analysis of bead surface associated materials
Authors: Haskins Neville J. , Hunter David J. , Rahman Shahzad S. , Organ Andrew J. , Thom Catriona
Published: May 2005

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry has been used to analyse the results of solid‐phase combinatorial chemistry on a single bead. A single component from a five‐membered combinatorial library was positively identified using the method outlined in this paper.
A computer‐based method to increase the signal‐to‐noise ratio of negative‐ion currents in double‐charge‐transfer spectroscopy
Authors: Bayliss Mark A. , Harris Frank M. , Parry David E. , Evans Stephen
Published: May 2005

Double‐charge‐transfer spectroscopy is routinely used to measure double‐ionization energies of molecules to singlet and triplet electronic states of dications, but is experimentally difficult to apply because the yield of negative ions generated in the double‐electron‐capture reactions is low. The use of a data‐acquisition system and repetitive scanning of a spectrum can increase signal‐to‐noise ratios, but the number of scans that can be acquired is limited by drifting in the spectrum position, which results in spectral‐peak broadening. This limitation has been overcome in the present investigation by the application of a computer enhancement program that effectively superimposes successive spectra which are subject to slight drift. Spectra obtained for H+ projectile ions reacting with hexafluorobenzene (C6F6) molecules are presented; use of the program with such spectra reveals features in the computer‐enhanced spectrum which are not clearly evident in the individual spectra.
Surface transient effects in ultralow‐energy O2+ sputtering of silicon
Authors: Chanbasha A. R. , Wee A. T. S.
Published: May 2005

It is known that by lowering the impact energy the sputter rate and surface transient width in SIMS will be reduced. However, few studies have been done at ultralow energies over a wide range of impact angles. This study examines the dependence of sputter rate and transient width as a function of O2+ primary ion energy (Ep = 250 eV, 500 eV and 1 keV) and incidence angles of 0–70°. The instrument used is the Atomika 4500 SIMS depth profiler and the sample was Si with 10 delta‐layers of Si0.7Ge0.3. We observed that the lowest transient width of 0.7 nm is obtainable at normal and near‐normal incidence with Ep ∼ 250 eV and Ep ∼ 500 eV. There is no significant improvement in transient width going down in energy from Ep ∼ 500 to ∼250 eV. The onset of roughening is also not obvious at Ep ∼ 250 eV over the whole angular range studied. Although the sputter rate during the surface transient is normally different from that at steady state, only at Ep ∼ 250 eV was it observed that the sputter rate remained fairly independent of depth. We conclude that the best working ranges to achieve a narrow transient width and accurate depth calibration are at Ep ∼ 250 eV/0° < θ < 20°and 500 eV/0°< θ < 10°. Copyright © 2005 John Wiley & Sons, Ltd.
Characterization of etched glass surfaces by wave scattering
Authors: Jafari G. R. , Mahdavi S. M. , Iraji Zad A. , Kaghazchi P.
Published: May 2005

The roughness of glass surfaces after different stages of etching is investigated by reflection measurements with a spectrophotometer, light scattering, atomic force microscopy (AFM, on a small scale) and profilometry (on a large scale). The results suggest that there are three regimes during etching, according to their optical reflectivity and roughness. The first and the second regimes are studied by the Kirchhoff theory and the third one is studied by the optical geometric theory. Also, the roughness obtained by optical scattering is compared with the AFM results. Copyright © 2005 John Wiley & Sons, Ltd.
Topological properties for characterizing well‐formedness of process components
Authors: Thu Tran Dan , Nhi Tran Hanh , Bich Thuy Dong Thi , Coulette Bernard , Cregut Xavier
Published: May 2005

RHODES is an environment for modelling software processes, in which software processes are described by using a Process Modelling Language called PBOOL+. In this environment, a software process is built from PBOOL+ process components that can be reused to construct other processes. To identify well‐formed process components, we study properties to be able to characterize topological structure of the components. These properties should relate intrinsically to cohesion of a component, and coupling between components. We will consider two classical properties that originated from graph theory, which are connection and transitive closure. These two properties are sometimes too strict to be applied, so we propose several weaker properties that are still useful for characterizing good components. The article aims to present these topological properties and their applications to reusable process components in context of the RHODES environment. Copyright © 2005 John Wiley & Sons, Ltd.
Four mechanisms for adaptable systems: a meta‐level approach to building a software product line
Authors: Fritsch Claudia , Renz Burkhardt
Published: May 2005

Meta‐level architectures combined with domain‐specific languages serve as a powerful tool to build and maintain a software product line: Meta‐level architectures lead to adaptable software systems. Executable descriptions capture expert knowledge.

We have developed a meta‐level architecture for a software product line of legal expert systems. Four meta‐level mechanisms support both variability and evolution of the product line. Domain analysis had shown that separation of expert knowledge from technical code was essential. Descriptions written in domain‐specific languages reside in the meta level, and serve as specification, code, and documentation. Technical code finds its place in interpreting machines in the base level.

We discuss how meta‐level architectures influence the qualities of software product lines and how properties and patterns of the problem space can guide the design of domain‐specific languages. Copyright © 2005 John Wiley & Sons, Ltd.
An evaluation of CMMI process areas for small‐ to medium‐sized software development organisations
Authors: Wilkie F. G. , McFall D. , McCaffery F.
Published: May 2005

In this article, we describe the results of CMMI software process appraisal work with six small‐ to medium‐sized software development companies. Our analysis of six CMMI process areas appraised within each of these organisations is presented. Commonly practiced or not practiced elements of the model are identified, leading to the notion of perceived value associated with each specific CMMI practice. A finer‐grained framework, which encompasses the notion of perceived value within specific practices, is presented. We argue that such a framework provides incentive to small‐ to medium‐sized enterprises starting process improvement programmes. Copyright © 2005 John Wiley & Sons, Ltd.
Staged configuration through specialization and multilevel configuration of feature models
Authors: Czarnecki Krzysztof , Helsen Simon , Eisenecker Ulrich
Published: May 2005

Feature modeling is a key technique for capturing commonalities and variabilities in system families and product lines. In this article, we propose a cardinality‐based notation for feature modeling, which integrates a number of existing extensions of previous approaches. We then introduce and motivate the novel concept of staged configuration. Staged configuration can be achieved by the stepwise specialization of feature models or by multilevel configuration, where the configuration choices available in each stage are defined by separate feature models. Staged configuration is important because, in a realistic development process, different groups and different people make product configuration choices in different stages. Finally, we also discuss how multilevel configuration avoids a breakdown between the different abstraction levels of individual features. This problem, sometimes referred to as 'analysis paralysis', easily occurs in feature modeling because features can denote entities at arbitrary levels of abstraction within a system family. Copyright © 2005 John Wiley & Sons, Ltd.
Löslichkeit von Mangandioxyd unter dem Einflusse von metallischem Quecksilber
Authors: Meyer Julius , Kanters Robert
Published: May 2005

Während sich weder Mangandioxyd noch metallisches Quecksilber in kalter verdünnter Schwefel‐oder Salpetersäure auflöst, geben beide zusammen infolge einer gekoppelten Reaktion

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leicht in Lösung. Die Versuchsbedingungen und der quantitative Verlauf dieser Umsetzung wurden untersucht und darauf hingewiesen, daß diese merkwürdige Auflösung sich vielleicht beim Lagern von Trockenelementen zerstörend bemerkbar machen kann.
Dispersal and germination of seeds of Pisonia grandis, an Indo-Pacific tropical tree associated with insular seabird colonies
Authors: Burger Alan E.
Published: May 2005

The distribution of the forest tree Pisonia grandis (Nyctaginaceae) coincides with seabird colonies on small tropical islands. Its seeds are enclosed in a calyx exuding extremely sticky resin which adheres strongly to feathers. Birds are obviously seed-dispersal vectors, but the multi-seeded infructescences frequently entangle birds, often fatally. On Cousin Island, Seychelles, I investigated the production, germination, survival, and tolerance to seawater of Pisonia seeds, and the occurrence of entanglement with birds. Fresh seeds had high germination success (62–87% in experimental trays), but seedling survival in Cousin's forests was low (0.1% of 6020 seeds survived as seedlings after 2–8 mo). Some seeds tolerated 30 min daily immersions in seawater (8–15% germination after 14–28 d treatment), but not continuous immersion in seawater (reduced germination after 5 d and none after 12 d). Inter-island dispersal is likely via living unencumbered seabirds carrying a few seeds, but not on floating carcasses. Seeds attached to carcasses did not have improved germination or survival. Intra-island propagation is almost entirely vegetative, with negligible local seed dispersal. Pisonia plants therefore do not benefit from fatal entanglements. The extreme stickiness of the seeds evidently evolved to resist removal by seabirds and so facilitate long-distance dispersal. The mortality of some potential vectors is an unfortunate consequence, but has little impact on the large populations of tree- and ground-nesting seabirds which nest in or under these trees.
Size-class distribution of Anogeissus leiocarpus (Combretaceae) along forest–savanna ecotones in northern Ivory Coast
Authors: Hennenberg Klaus Josef , Goetze Dethardt , Minden Vanessa , Traoré Dossahoua , Porembski Stefan
Published: May 2005

Along eight forest–savanna transects at seven semi-deciduous forest islands in the southern Comoé National Park data on spatial distribution of tree-size classes and environmental parameters (fuel load, shading by upper tree layers, and soil depth) were collected. For dominant tree species, a sequential series was observed from the forest border into the forest interior. At the forest border, Anogeissus leiocarpus was the most abundant tree with juveniles (<1 cm dbh) reaching highest density values (mean of 502 individuals ha−1) at the outer periphery of the forests. Regression analysis of juveniles of dominant tree species and environmental parameters resulted in a separation of forest and savanna species. Forest tree species regenerated well at forest sites, but also in the shade of A. leiocarpus stands. We conclude that (1) the studied forest islands advance against savanna by sequential succession, and (2) A. leiocarpus has a high potential to regenerate at savanna–forest boundaries under moderate fire impact and on rather shallow soils. The potential of A. leiocarpus to act as an important pioneer in the replacement of savanna by forest due to its effective regeneration at savanna sites and subsequent modification of site conditions, especially fire intensity by shading out savanna grasses, is discussed.
Canopy composition influencing plant patch dynamics in a Brazilian sandy coastal plain
Authors: Corrêa Dias André Tavares , Teixeira Zaluar Henrique Leão , Ganade Gislene , Scarano Fabio Rubio
Published: May 2005

Competition and predation have often been referred to as key forces regulating community structure. However, in the last decade great attention has been paid to the structuring role of positive interactions between plants, which occur when the presence of one species enhances fitness, survival or growth of another (Bruno et al. 2003, Callaway et al. 2002). Positive and negative interactions are unlikely to occur separately in nature (Brooker & Callaghan 1998, Holmgren et al. 1997), and the overall importance of positive interactions on community structure tends to be higher in resource-poor environments (Callaway et al. 2002). Moreover, this balance can be subjected to spatial and temporal shifts (Callaway 1998, Morris & Wood 1989, Tielbörger & Kadmon 1997) linked with plant ontogenetic development and/or changes on resource availability (see Callaway & Walker 1997).