bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of non‐covalent ligand binding to the intact streptavidin tetramer by electrospray ionization mass spectrometry
Authors: Schwartz Brenda L. , Gale David C. , Smith Richard D. , Chilkoti Ashutosh , Stayton Patrick S. 
Published: May 2005

AbstractThe relative non‐covalent binding behavior of two small molecule ligands to the tetrameric protein streptavidin was investigated by electrospray ionization mass spectrometry (ESI‐MS). An extended m/z range quadrupole mass spectrometer was employed to observe the intact multimeric form of the protein and to probe the relative stabilities of the tetrameric protein‐ ligand complexes in the gas phase. Various protein:ligand molar ratio concentrations and incubation times were studied for the ligands biotin (Kd ≈ 10−15 M) and iminobiotin (Kd ≈ 10−7 M), in combination with the adjustment of variables in the ESI atmosphere‐vacuum interface region. Positive‐ion ESI‐MS of a 1:7 molar ratio streptvidin–biotin sample produced peaks corresponding to the intact tetrameric complex (16+ to 14+ charge states) with four ligands binding to the active from of the protein. Only the expected specific non‐covalent complexes of four ligand molecules binding to the protein tetramer were detected, consistent with known solution behavior and without the appearance of any random aggregation. However, under identical interface conditions, complete iminobiotin binding to the protein was not observed, even when higher ligand concentrations, longer complexation times and gentler interface conditions were employed. The thermally induced dissociation (TID) of the non‐covalent complexes was studied by applying more severe conditions in the ESI interface region. In addition, observation of an intact streptavidin–biotinylated oligonucleotide non‐covalent complex (17– to 14– tetrameric charge states) by negative‐ion ESI‐MS at m/z 4500–5000 is presented. The results show that the complexes observed in the mass spectrometer are representative of those that exist in solution, under the ESI conditions employed, and that the ability to observe such complexes is at least qualitatively related to stability in solution.
HD exchange kinetics of alcohols and protonated peptides: Effects of structure and proton affinity
Authors: Green M. Kirk , Gard Eric , Bregar Jennifer , Lebrilla Carlito B. 
Published: May 2005

AbstractThe kinetics of gas‐phase HD exchange reactions of a series of protonated amino acids and peptides with deuterium‐substituted alcohols (D2O, CH3OD, C2H5OD and 1‐C4H9OD) were studied in an external source Fourier transform mass spectrometer. The number of exchanges observed on the time‐scale of these experiments ranged from one to the total number of ‘labile’ substrate hydrogens, depending on the amino acid and the deuterating reagent. Exchange efficiencies, k/kADO, varied from <0.001 to 0.3. Within the series ROD, the reactivity increased with increasing size of the R group. For the amino acids with alkyl side‐chains, a roughly linear correlation of log(k/kADO) with proton affinity difference (ΔPA = PA of unprotonated substrate ‐ PA of reagent) was observed. The amino acids lysine and histidine and the dipeptides alanylglycine and diglycine showed higher reactivity and greater tendency for multiple exchange, with a weaker dependence on ΔPA. The ability of a peptide and an alcohol to exchange efficiently even when ΔPA is larger is attributed to the occurrence of exchange within a cyclic hydrogen‐bonded complex, in which the deuterating agent forms a bridge between the site of protonation and a basic site on the substrate.
Fragmentation mechanisms of protonated actinomycins and their use in structural determination of unknown analogues
Authors: Thomas Darren , Morris Michael , Curtis Jonathan M. , Boyd Robert K. 
Published: May 2005

AbstractA combination of mass shifts arising from known structural variations of neutral precursors, and accurate mass measurements of key fragment tions, has led to a proposed systematization of the low‐energy fragmentation mechanisms for MH+ ions of actinomycins. These rationalizations are used in a predictive manner to interpret fragment ion spectra, of unknown impurities in actinomycin standards, in terms of structure. Both the strengths and limitations of this approach are emphasized. This work has uncovered actinomycin variants in which one of the threonine residues is substituted by serine, a structural variation which does not appear to have been reported previously.
Structural determination of 1,4‐naphthoquinones by mass spectrometry/mass spectrometry
Authors: Stensen Wenche G. , Jensen Einar 
Published: May 2005

AbstractThe fragmentation pathways of several substituted 1,4‐naphthoquinones have been studied by multi stage mass spectrometry. Methods for the recognition and identification of 1,4‐naphthoquinones and of substitution patterns on the naphthoquinone nucleus are outlined.
Trace determination of alkyl methylphosphonic acids in environmental and biological samples using gas chromatography/negative‐ion chemical ionization mass spectrometry and tandem mass spectrometry
Authors: Fredriksson Sten‐Åke , Hammarström Lars‐Gunnar , Henriksson Liselott , Lakso Hans‐Åke 
Published: May 2005

AbstractAlkyl methylphosphonic acids (AMPA) are metabolites and primary hydrolysis products of the organophosphorus nerve agents listed in the Chemical Weapons Convention (CWC). Gas chromatography/negative‐ion chemical ionization mass spectrometry and tandem mass spectrometry (GC/NICI‐MS and GC/NICI‐MS/MS) were used for the determination of AMPA as their pentafluorobenzyl esters. Extremely high sensitivity was obtained and low attogram amounts could be detected by GC/NICI‐MS. Ion‐exchange chromatography was employed for selective isolation and enrichment of AMPA in serum, urine, water and soil samples. Collision‐induced dissociation (CID) of the single methylphosphonate anion peak from NICI of the pentafluorobenzyl ester produced fragment ions specific for the methylphosphonate structure, allowing positive identification of AMPA. CID conditions optimized for structure information and for sensitivity were investigated. The improved selectivity of GC/MS/MS allows the detection of femtogram amounts of AMPA in samples where chemical background inhibits detection by GC/MS.
Structures and stabilities of XCCY2+ dications (X, Y = O, S and NH), doubly charged isoelectronic analogues of cyanogen
Authors: Wong Ming Wah 
Published: May 2005

AbstractConsistent with experimental observations, high‐level ab initio calculations, at the G2(MP2) level of theory, predict that the XCCY2+ (X, Y = O, S and NH) dications are remarkably stable species in the gas phase. OCCS2+, SCCS2+, HNCCO2+, HNCCS2+ and HNCCNH2+ are calculated to be thermodynamically stable species, whereas OCCO2+ is predicted to lie in a deep potential well, separated from exothermic CC cleavage by a large barrier. All the doubly charged species are calculated to have a linear skeleton. Despite the inherent strong Coulombic repulsion, these species are characterized by short CX or CY triple bonds. Vertical and adiabatic ionization energies of the XCCY+· monocations and the heats of formation of the resulting dications are reported. There are remarkable changes in the structures and stability ordering of isomers on going from the XCCY neutrals to the XCCY+· monocations and to the XCCY2+ dications. The rationalization of these results is discussed.
Quantification of the anti‐HIV drug saquinavir by high‐speed on‐line high‐performance liquid chromatography/tandem mass spectrometry
Authors: Knebel N. G. , Sharp S. R. , Madigan M. J. 
Published: May 2005

AbstractA method is described for the fast routine determination of the anti‐HIV drug saquinavir and its pentadeuterated analogue [2H5] saquinavir in the plasma of healthy volunteers. The method is based on high‐performance liquid chromatography (HPLC)/atmospheric pressure positive‐ion chemical ionization (APCI) mass spectrometry, with a stable labelled form of saquinavir (13C6–2H3–15N) as internal standard. Automated solid‐phase extraction in combination with short‐column HPLC and multiple reaction monitoring is employed for high selectivity and sensitivity, and this also permits rapid quantification (the run time per sample is 1.5 min) over the range of 0.4–200 ng ml−1 with excellent accuracy and precision. Up to 200 samples per analyst per day can be analysed. This assay methodology illustrates the versatility of APCI tandem mass spectrometry, in conjunction with high‐speed HPLC, for the fast routine quantification of drugs in the nanograms per millilitre range, which is essential for clinical pharmacokinetic studies.
Characterization of endogenous DNA adducts by liquid chromatography/electrospray ionization tandem mass spectrometry
Authors: Chaudhary Ajai K. , Nokubo Munetaka , Oglesby Thomas D. , Marnett Lawrence J. , Blair Ian A. 
Published: May 2005

AbstractEndogenous carcinogens arising from normal metabolism are known to cause modifications to DNA by reacting with bases to form adducts. Malondialdehyde is a well characterized endogenous carcinogen that forms an adduct with 2′‐deoxyguanosine. This adduct has been detected in rat and human liver DNA by gas chromatography/electron capture negative‐ion chemical ionization mass spectrometry. A method has been developed based on liquid chromatography/electrospray ionization tandem mass spectrometry for the characterization of endogenous DNA adducts. Using this method, it was unequivocally established that the malondialdehyde adduct of 2′‐deoxyguanosine was a constituent of human liver DNA. The methodology that has been developed should be applicable to the characterization of other endogenous DNA adducts. There are few structural or biological data available to assess the importance of endogenous DNA adducts as premutagenic lesions responsible for the development of cancer. The availability of methodology based on liquid chromatography/electrospray ionization tandem mass spectrometry for the characterization of DNA adducts should greatly facilitate future studies in this area.
Electron affinities of polycyclic aromatic hydrocarbons determined by the kinetic method
Authors: Chen Guodong , Cooks R. Graham 
Published: May 2005

AbstractThe kinetic method has been applied in the determination of electron affinities (EA) of polycyclic aromatic hydrocarbons (PAHs) using electron attachment desorption chemical ionization mass spectrometry (DCI‐MS) and triple quadrupole tandem mass spectrometry. Electron‐bound dimers of PAHs (viz. solvated radical anions) are generated in the ion source and they fragment competitively upon collisional activation to yield the intact monomeric molecular radical anions. The ratio of the abundances of these two ions reflects the difference in electron affinities of the PAHs. Relative electron affinities are ordered as phenanthrene < perylene < 1,2‐benzanthracene < benzo [ghi] perylene < anthracene < pyrene < fluoranthene < biphenylene on the basis of multiple pairwise measurements. On the assumption that the effective temperature of the electron‐bound dimers is constant, under fixed desorption conditions, and using phenanthrene (EA = 0.307 eV), anthracene (EA = 0.556 eV), pyrene (EA = 0.591 eV) and fluoranthene (EA = 0.63 eV) as reference compounds, the electron affinities of several PAHs are estimated as perylene (0.35 eV), 1,2‐benzanthracene (0.39 eV), benzo [ghi] perylene (0.42 eV) and biphenylene (0.89 eV). The calculated effective temperature using the known EAs of the reference compounds, phenanthrene, anthracene, pyrene and fluoranthene, is 1251 K. The high effective temperature in the electron‐bound dimer is ascribed to both the weak binding in the electron‐bound dimer and to the choice of ionization conditions. The same methodology was applied to estimate the electron affinities of substituted PAHs. For alkyl‐substituted PAHs, e.g. 1‐methylanthracene, the estimated electron affinity (0.55 ± 0.10 eV) is consistent with electron transfer equilibrium studies. However, for halogenated PAHs, the ratio of fragment ion abundances does not correlate with the known electron affinity difference when a PAH and a halogenated PAH comprise the electron‐bound dimer. This is suggested to be due to differences in the structures of the cluster ions generated upon halogen substitution. The expected affinity results are obtained when the electron‐bound dimer is comprised of two halogenated PAHs. Estimated electron affinity values for 1‐bromopyrene (0.72 ± 0.10 eV) and 9‐bromoanthracene (0.61 ± 0.10 eV) are slightly higher than the electron affinities of pyrene and anthracene, respectively.
Effect on conformation on proton affinities of stereoisomeric ethers
Authors: Denekamp C. , Etinger A. , Fokkens R. H. , Khaselev N. , Mandelbaum A. , Nibbering N. M. M. 
Published: May 2005

AbstractThe proton affinity (PA) of cis‐4‐tert‐butylcyclohexyl methyl either with an axial methoxy group is higher by ∼0.1 kcal mol−1 (1 kcal = 4.184 kJ) than the trans isomer with the equatorial ether group. The gas‐phase basicity shows a similar small difference of 0.1 kcal mol−1 between the two stereoisomeric ethers. A greater difference in PA has been observed between the stereoisomeric 4‐phenylcyclohexyl methyl and ethyl ethers (1.0 and 1.2 kcal mol−1, respectively), in favour of the cis isomers with the equatorial ether groups. The latter result is explained by the internal hydrogen bond with the π‐system of the phenyl ring.
Reactions of protonated acetic acid clusters (CH3COOH)nH+ (n = 1–3)
Authors: Feng Wan Yong , Lifshitz Chava 
Published: May 2005

AbstractReactions of (CH3COOH)nH+ (n = 1–3) with a series of base molecules B were studied using a selected ion flow tube. All the reactions observed proceed at near gas kinetic collision rates for bases having higher proton affinities than acetic acid. Different reaction channels are observed with increasing proton affinity of the neutral: association and proton transfer for the proton‐bound monomer; association, ligand switching and proton transfer for the dimer; association, ligand switching, switching with solvent evaporation and proton transfer for the trimer. A thermochemical comparison of the appearance enthalpy and free energy for proton transfer from (CH3COOH)3H+ and (C2H5OH)3H+ established that both sets of reactions take place by forming BH+ with evaporation of three monomeric units (of acetic acid or ethanol, respectively) rather than evaporation of neutral dimers. Proton transfer from (CH3COOH)2H+ is fast provided that the reaction is exothermic; proton transfer from (CH3COOH)3H+ is fast even if the reaction is endothermic (but exergonic).
Identification of quaternary ammonium and tertiary sulfonium compounds by plasma desorption mass spectrometry
Authors: Bonham Connie C. , Wood Karl V. , Yang Wen‐Ju , Nadolska‐Orczyk Anna , Samaras Yiannis , Gage Douglas A. , Poupart Julie , Burnet Michael , Hanson Andrew D. , Rhodes David 
Published: May 2005

AbstractA rapid and sensitive method for the identification of quaternary ammonium and tertiary sulfonium compounds is described. The method utilizes plasma desorption mass spectrometry (PDMS) in which a 252Cf ionizing source produces fission fragments which interact with the sample to yield ions which are then analyzed by a time‐of‐flight mass spectrometer. The method was applied to analyses of authentic standards and to the identification of quaternary ammonium and tertiary sulfonium compounds in higher plant leaf extracts purifed by ion‐exchange chromatography. Plant species from 14 different families were tested, including species which are known glycinebetaine, β‐alaninebetaine, prolinebetaine or β‐dimethylsulfoniopropionate accumulators. PDMS results confirmed and extended the known taxonomic distributions of these compounds. Glycinebetaine was found in one species Krameria parvifolia from a family (Krameriaceae) not previously known to accumulate this compound. Pipecolatebetaine was identified in Achillea filipendulina (Asteraceae). The occurrence of prolinebetaine and hydroxyprolinebetaine(s) was confirmed in three species (Lamium maculatum, Stachys byzantina and Phlomis fruticosa) of the tribe Lamieae of the subfamily Lamioideae in the family Lamiaceae, but not in a fourth member of this tribe (Physostegia virginiana). The last species accumulated only trigonelline. The PDMS method was also used to identify trigonelline‐deficient Zea mays lines.
Cycloreversal reaction and ortho interactions in 2‐aryl‐4H‐3, 1‐benzoxazin‐4‐ones on electron impact
Authors: Ramana D. V. , Kantharaj E. 
Published: May 2005

AbstractA cycloreversal reaction, leading to aroyl cations, is the major process in 2‐aryl‐4H‐3,1‐benzoxazin‐4‐ones under electron impact conditions. The ortho interaction of the methoxy and the nitro groups in the 2‐phenyl moieties in these compounds present the most abundant ions at m/z 119 and 134, respectively, in their mass spectra as a result of the transfer of a hydrogen atom from the former and an oxygen atom from the latter to the imine nitrogen of the heterocycle. The ion structures and the mechanisms for the proposed fragmentations are based on high‐resolution data, B/E and B2/E linked‐scan spectra, collision‐activated decomposition–B‐/E linked‐scan spectra and deuterium labelling.
Special feature: Historical. Collision‐induced dissociation: Readings and commentary
Authors: Cooks R. Graham 
Published: May 2005

AbstractCollision‐induced dissociation (CID), also known as collision‐activated dissociation (CAD), is now central to the practice of mass spectrometry. The story of its discovery, fundamental basis, and its development as a technique applicable to different types of instruments has evolved over many decades. In this paper, these topics are explored by reference to and commentary on particular texts, chosen to represent milestones in the development of CID over the period 1910–1970.
Magnitude‐mode multiple‐derivative spectra for resolution enhancement without loss in signal‐to‐noise ratio in Fourier transform spectroscopy
Authors: Kim Hyun Sik , Marshall Alan G. 
Published: May 2005

AbstractAn nth‐derivative Fourier transform complex spectrum, dnF(ω)/dωn, may be generated by multiplying at time‐domain signal by (−it)n before Fourier transformation. The resolving power of the magnitude‐mode nth‐derivative spectrum, |dnF(ω)/dωn|, increases monotonically with increasing derivative order, but with concomitant decrease in signal‐to‐noise ratio. However, application of time‐domain exponential windowing can restore the signal‐to‐noise ratio. The combined derivatization–windowing process yields a magnitude‐mode nth‐derivative Fourier transform spectrum with significantly enhanced resolution near the peak base without loss in signal‐to‐noise ratio. A theoretical analysis of the trade‐off between resolving power and signal‐to‐noise ratio for magnitude‐mode nth‐derivative Fourier transform spectra as a function of time‐domain signal truncation, time‐domain windowing (exponential) and derivative order is presented. The method is demonstrated experimentally for Fourier transform ion cyclotron resonance mass spectra.
Mass discrimination in matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry: A study using cross‐linked oligomeric complexes
Authors: Farmer Terry B. , Caprioli Richard M. 
Published: May 2005

AbstractThe determination of the mass discrimination effect of matrix‐assisted laser desorption ionization mass spectrometry (MALDI MS) over a wide m/z range was made by determining the relative amounts of prepurified protein monomer and dimer species present in reconstituted mixtures. Protein complexes were covalently cross‐linked with glutaraldehyde and monomeric and dimeric species were separated by gel filtration chromatography. Individual protein species were recombined in specific ratios and analyzed by both MALDI MS and sodium dodecyl sulfate polyacrylamide gel electrophoresis. The contributions of the peak areas of the doubly charged ions and singlycharged dimeric ions generated during the MALDI MS analyses relative to that of the singly‐charged [M + H]+ species were measured. The calculation of mass discrimination for two different MALDI time‐of‐flight instruments showed the loss of a factor of ∼2.6 in relative peak area as the m/z value doubled over the m/z range 30 000–145 000. An overall correction factor for mass discrimination is given which includes effects associated with sample preparation, sample desorption/ion formation, ion transmission and ion detection.
Two‐dimensional mass spectra of 2‐phenylethylamines
Authors: Cardoso Ana M. , Correia A. J. Ferrer 
Published: May 2005

AbstractThe two‐dimensional mass spectra (metastable mapping) of ten biogenic amines derived from the amino acid 2‐phenylalanine are described. This technique permitted the identification of almost all the fragmentations of singly and doubly charged positive ions formed by electron impact and decomposing in the different parts of a reverse‐geometry mass spectrometer. The results obtained are discussed in order to establish the main fragmentation pathways common to all the amines belonging to the general class of 2‐phenylethylamines and to identify the fragmentations characteristic of each amine.
Simultaneous determination of concentrations and stable isotope enrichments of α‐ketoisocaproic acid, leucine, phenylalanine and tyrosine in blood plasma by gas chromatography/negative ion mass spectrometry
Authors: Kulik W. , van Toledo‐Eppinga L. , Kok R. M. , Guérand W. S. , Lafeber H. N. 
Published: May 2005

AbstractA simple procedure for the extraction and derivatization of α‐amino acids and α‐keto acids from human plasma is described. This stable isotope dilution method permits the quantification of isotopic enrichment and concentrations of several α‐keto and α‐amino acids simultaneously. The derivatization process results in methylformated, pentafluorobenzylated α‐amino acids and pentafluorobenzylated α‐keto acids. The derivatives proved to be very stable when stored at 5°C. Under electron capture chemical ionization (ECCI) conditions the derivatized amino acid produces abundant [M – PFB]− or [M – PFB – CH3OH]− anions; the α‐keto acid gives abundant [M – PFB]− anions. The method was applied to the analyses of 100 μl plasma samples in studies on protein metabolism. For the determination of concentrations [α‐ketoisocaproic acid (α‐KIC), Leu, Phe and Tyr] and enrichments ([1‐13C]‐α‐KIC, [1‐13C]‐Leu, D5‐Phe, D2‐Tyr, D4‐Tyr), resulting from administered tracers, the corresponding [M – PFB]− or [M – PFB – CH3OH]− anions were monitored. Higher labelled analogues were used as internal standards. The overall sensitivity was sufficient to study isotopic enrichments in the range 0.2–10 at.% excess.
Site of gas‐phase methylation of alkyl phenyl ketones
Authors: Cheung Mary , Harrison Alex G. 
Published: May 2005

AbstractThe CH adducts of benzaldehyde, acetophenone, propiophenone and butyrophenone were prepared using CH3FCH4 and CH3ClCH4 mixtures under chemical ionization conditions and the unimolecular and collision‐induced fragmentation reactions of their adduct ions were studied. For comparison, the fragmentation reactions of the protonated p‐methylphenyl alkyl ketones were studied as models of the ring‐methylated species and the fragmentation reactions of [C6H5C(R)OCH3]+, produced by electron impact ionization of the appropriate methyl ether, were studied as models of the O‐methylated species. From these comparisons it is concluded that methyl cation addition occurs predominantly at the carbonyl oxygen under our experimental conditions. However, for methyl‐cationated acetophenone there is extensive migration of the methyl group from the oxygen to the ring prior to fragmentation of the adduct.