bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tandem mass spectrometry of peptides: Sequence information based on neutral losses. I—isomeric dipeptides
Authors: Cordero Marcela M. , Wesdemiotis Chrys 
Published: May 2005

AbstractThe neutral losses arising on the collisionally activated dissociation (CAD) of protonated dipeptides (MH+) are reionized by collision and detected in neutral fragment‐reionization (NfR) mass spectra. For the dipeptides investigated, which encompass Ala–Gly/Gly–Ala, Asp–Gly/Gly–Asp, Phe–Gly/Gly–Phe and Trp–Ala/Ala–Trp, the NfR spectra of each pair of isomers are distinct and permit the identification of the correct C‐terminal amino acid. The precise structure of this amino acid is elucidated by comparison of the NfR spectra with reference collision‐induced dissociative ionization (CIDI) mass spectra of authentic Gly, Ala, Asp, Phe and Trp, acquired from beams of these amino acids formed by dissociation of their proton‐bound dimers.
Fragmentation reactions of singly and doubly charged alkali metal ion–peptide complexes: A reaction specific to C‐terminal arginine residues
Authors: Tang Xue‐Jun , Thibault Pierre , Boyd Robert K. 
Published: May 2005

AbstractIonspray ionization of solutions containing peptides (M) plus alkali metal ions X+ produces [M + X]+, [M + H + X]2+ and [M + 2X]2+ ions. Low‐energy collision‐induced dissociation of these species demonstrated a marked trend towards decreased strength of the M–X+ interaction with increasing size of X+. For example, the [M +2X]2+ species yield predominantly [M + X]+ plus X+ for X+ = K+, Rb+, Cs+, but rich spectra of fragment ions incorporating X+ when X+ = Li+ or Na+. In general, these fragmentation reactions correspond to those established previously for the corresponding [M + X]+ precursor, including formation of [bi + X + OH]+ and [bi + X – H]+ fragments. As a special case, complexes of Li+ or Na+ with peptides having Arg (but not Lys or other basic residues) at the C‐terminus undergo a facile loss of 60 u. The resulting [M + X – 60]+ ions also fragment further to yield [yi′ + X – 60]+ fragments. Characterization of the 60 u neutral loss was undertaken by using tandem mass spectrometry plus hydrogen–deuterium exchange, and a mechanism is proposed to account for the characteristics of the process.
Intermediate ion–neutral complexes formed during the gas‐phase protonolysis of p‐(tert‐butyl)‐substituted α,ω‐diphenylalkanes
Authors: Matthias Carsten , Kuck Dietmar 
Published: May 2005

AbstractLoss of isobutane is the exclusive fragmentation channel of long‐lived protonated tert‐butyl‐substituted α,ω‐diphenylalkanes with chain lengths n = 2–12. Methane chemical ionization/mass‐analysed ion kinetic energy spectrometry of the [M + H]+ ions and several deuterium‐labelled tert‐butyl‐substituted 1,2‐, 1,3‐ and 1,10‐diphenylalkanes revealed that the reaction involves with equal probability and maximum regioselectivity a hydride ion from both the adjacent and the remote benzylic methylene groups, irrespective of the length of the aliphatic chain. The isotope effect of the hydride abstraction step was found to be same in all cases, k[C4H10]/k[C4H9D] = 1.6 ± 0.1. A sterically restricted system, protonated 1‐benzyl‐4‐(tert‐butylbenzyl)benzene, shows the same behaviour. This implies, as a general phenomenon, the formation of intermediate ion–neutral complexes [C4H9+ Ar(CH2)n Ar] along with (or instead of) the corresponding π complexes [C4H9+ …︁ Ar(CH2)nAr] prior to isobutane elimination (Ar represents a phenyl or substituted‐phenyl group).
Structures of product ions C6H7+ and C6H9+ of ion–molecule reactions with allyl bromide
Authors: Zhu Zhiqing , Gäumann Tino 
Published: May 2005

AbstractThe ion–molecule reactions of allyl bromide with the molecular ion of allyl bromide and with its major fragment, the allyl ion, yield the C6H7+ and C6H9+ ions. The structure of these product ions was explored by means of photofragmentation with laser light in the 10 μm region and by proton transfer reaction to selected reagents. These product ions were also formed by other reactions and their reactivities compared. In both cases the presence of at least two populations is demonstrated. For C6H9+ these two populations are initially present, whereas for C6H7+ an isomer is formed by the infrared light before the loss of H2. When this ion is produced by photofragmentation of C6H7+, at least one third, stable isomer is formed. Two isomers of C6H5+ are formed in the photofragmentation of C6H7+, but only one form photofragments further by loss of C2H2. The use of non‐linear least‐squares fitting does not allow definite conclusions to be drawn concerning the kinetics of the consecutive photofragmentations.
Collision‐induced dissociation in a tandem time‐of‐flight mass spectrometer with two single‐stage reflectrons
Authors: Cornish Timothy J. , Cotter Robert J. 
Published: May 2005

AbstractA tandem time‐of‐flight mass spectrometer was developed to be used for the study of collision‐induced dissociation (CID) products of peptides and small proteins. The instrument incorporates two single‐stage reflectrons, the first to energy focus the precursor ions to be fragmented and the second to both energy focus and disperse the product ions formed in the collision cell. Single‐stage rather than two‐stage reflectrons were used because the overall transmission is higher, interferences with grid wire fields are minimized and the mass calibration of product ion spectra is exactly linear with time. The CID product ion spectra of rhodamine and several peptides were acquired and found to exhibit very similar fragmentation patterns to those acquired in the B/E linked scan mode of a magnetic sector mass spectrometer.
The Precursor scan. A new type of experiment in neutralization–reionization mass spectrometry
Authors: Gu Ming , Tureček František 
Published: May 2005

AbstractA new scan technique utilizing the tandem quadrupole acceleration–deceleration mass spectrometer is described. The technique is based on combined monitoring of neutral and ion precursors that fragment following collisional electron transfer to give rise to a selected low‐mass neutral species and its ion, respectively. PO˙ is found to be a stable neutral species formed by dissociations of a variety of oxidized phosphorus compounds, such as di‐ and trialkyl phosphites, phosphates and phosphonic esters. These compounds can be selectively monitored through PO˙. precursor scans in multi‐component mixtures. Interferences from isobaric neutral species, 35CIC˙, CH3S˙, CH330SiH2˙, and their precursors are discussed. Neutralization–reionization spectra of phosphorus‐containing radicals, PO˙, CH3OPH˙, CH3OPOH˙, ˙P(OCH3)2 and (CH3O)2PO˙, are also reported.
Skeletal rearrangements preceding CO loss from metastable phenoxymethylene ions derived from phenoxyacetic acid and anisole
Authors: Molenaar‐Langeveld Tineke A. , Ingemann Steen , Nibeering Nico M. M. 
Published: May 2005

AbstractThe loss of CH2˙ from the molecular ion of phenoxyacetic acid and the expulsion of an H˙ atom from ionized anisole lead to phenoxymethylen ions, which fragment predominantly by CO loss on the microsecond time‐scale. Carbon‐13 labelling reveals that ∼90% of the CO molecules expelled from the metastable ions derived from phenoxyacetic acid incorporate the carbon atom from the 1‐position of the phenyl group of the parent compound, whereas the residual CO molecules contain one of the other carbon atoms of the aromatic ring. The 2‐fluoro‐ and 2‐methylphenoxymethylene ions derived from the appropriate aryloxyacetic acids behave similarly, i.e. the carbon atom of the methylene group of the parent compound is not incorporated in the expelled CO molecules. In contrast, ∼45% of the CO molecules eliminated from the metastable phenoxymethylene ions formed from ionized anisole contain the carbon atom of the methyl group, while the remaining part contains the carbon atom from the 1‐position of the phenyl ring of the parent compound. This result is taken as evidence for the occurrence of a skeletal rearrangement of the anisole molecular ion leading to an interchange between the carbon atom of the methyl group and the carbon atom at the 1‐position of the ring. The elimination of CO from the metastable ions generated from either phenoxyacetic acid or anisole gives rise to a composite metastable peak. Conclusive evidence as to the formation of [C7H7O]+ isomers other than the phenoxymethylene ion is not obtained, indicating that the composite metastable peak is a result of two competing reactions both leading to CO loss. Possible mechanisms of these reactions are discussed together with the mechanism of the skeletal rearrangement of the molecular ion of anisole prior to H˙ loss.
Novel Ortho effects detected in the fast atom bombardment mass spectra of substituted bisaryl phosphate antagonists of platelet‐activating factor
Authors: Siegel Marshall M. , Tsao Rushung , Wissner Allan 
Published: May 2005

AbstractA series of substituted bisaryl phosphate compounds, (R1CH2)+ ArOP = O(O−)(OArR2R3), was analyzed and characterized by fast atom bombardment mass spectrometry. Abundant fragment ions were observed and correlated with the proposed structures. From fragmentation pattersn, ‘ortho effect’ reactions were demonstrated to have occurred when the phosphoryl oxygen reacted with the (CH2R1)+ and CO(OCH3) substituents in the ortho position, relative to the phosphate group, and displaced the R1 and OCH3 groups, respectively, to produce phosphorus containing six‐membered rings fused to the aryl moiety. When the (CH2R1)+ substituents were in the meta position relative to the phosphate group, the ‘ortho effect’ reactions were not observed. However, when the CO(OCH3) substituent was in the meta position relative to the phosphate group, an abundant fragment ion containing a five‐membered phosphate ring fused to the aryl ring was detected with the original phosphoryl oxygen ortho to both the phosphate oxygen and a formyl group, formed from the original CO(OCH3) substituent. All other fragmentations not involving the ‘ortho effect’ reactions were nearly identical for the different structural isomers of the substituted bisaryl phosphate compounds.
Electrophilic bromination of gaseous aromatic compounds: Mechanism and linear free energy effects on reaction rates
Authors: Bortolini Olga , Yang Sheng Sheng , Cooks R. G. 
Published: May 2005

AbstractElectrophilic bromination of monosubstituted aromatic compounds is effected in a pentaquadrupole mass spectrometer using BrCO+ and CH3NH2Br+ as mass‐selected reagent ions. Reaction normally occurs at the ring and the brominated product can be mass selected in turn and caused to dissociate by Br˙ loss upon collision‐induced dissociation. Linear free energy correlations with Brown substituent σ+ constants describe the extent of gas‐phase bromine cation addition under the non‐equilibrium, low‐pressure and solvent‐free conditions which pertain in quadruple collision cells. The electrophilic addition reaction proceeds via a σ‐complex to the ring as suggested by MS3 spectra, except in the case of nitrobenzene, where substituent bromination is suggested by the occurrence of a competitive process in which the nitrosubstituent is displaced by bromine. The reactivity parameters ρ are −0.23 and −0.56 for the gaseous reagents, BrCO+ and CH3NH2Br+, respectively. Both values are much less negative than corresponding values for bromination in solution. The greater reactivity of BrCO+ is evident by the fact that it reacts even with the strongly deactivated substrates and this is consistent with a weak BrCO bond. Competitive protonation occurs in the case of CH3NH2Br+ and, unlike bromination, the rate of this reaction does not correlate with σ+ values. This is suggested to be a consequence of protonation at the ring in some cases and at the substituent in others, including acetophenone and benzonitrile. Evidence for this is that, in contrast to its lack of correlation with substituent constants, the rate of protonation correlates linearly with proton affinity.
Rearrangements accompanying the fragmentation of ionized 1‐phenylalkan‐1‐ols
Authors: Budzikiewicz H. , Drabner G. , Hammes Ch. 
Published: May 2005

AbstractSome aspects of the fragmentation sequence of 1‐phenylalkan‐1‐ols (C6H5CH(OH)R), which consists of the loss of R˙ followed by the elimination of CO and subsequently of H2, are discussed. Labelling studies and collision activation data of reference compounds allow a mechanism to be proposed for this rearrangement.
Intra‐ and intermolecular reactions of aromatic radical cations: An account of mechanistic concepts and methods in mass spectrometry
Authors: Grützmacher Hans‐Friedrich 
Published: May 2005

AbstractInvestigations in the authors's laboratory in Bielefeld and elsewhere on the mechanism of the intramolecular and intermolecular aromatic substitution via radical cations are reviewed with the aim of presenting an example for the development of mass spectrometric methods and concepts for the study of the mechanisms of gaseous ionic reactions. An intramolecular aromatic substitution resulting in the loss of a hydrogen or a substituent from an aromatic ring of the molecule ions by the attack of a nucleophilic heteroatom in the side‐chain was first observed in the normal electron impact (EI) mass spectra and was studied by substituent effects on ion abundance, ionization energy and appearance energy. This led to the construction of a two‐step mechanism of the intramolecular aromatic substitution with a rate‐determining first addition step. Subsequently, this fragmentation reaction was studied for a series of systems by tandem mass spectrometry, confirming the two‐step mechanism and yielding an excellent insight into the dynamics of the substitution process. The bimolecular variety of the nucleophilic aromatic substitution via radical cations was investigated recently by Fourier transform ion cyclotron resonance spectrometry. The results for a series of halogenated benzenes and NH3, CH3NH2 and (CH3)2NH as the nucleophile corroborate the conclusions drawn from the study of unimolecular reaction mechanisms. It is shown that in all cases the formation and further reaction of the addition intermediate play a crucial role. This can be perceived by the application of the configuration mixing reactivity model to the addition reaction, and by the concept of classical and distonic radical cations. This review on a specific reaction mechanism shows clearly the excellent techniques and methods which the developments in mass spectrometry have provided for a detailed study of the mechanisms of ionic reactions in the gas phase.
Sequencing membrane proteins by tandem mass spectrometry
Authors: Orlando Ron , Kenny Peter T. M. , Moquin‐Pattey Carole , Lerro Keith A. , Nakanishi Koji 
Published: May 2005

AbstractTandem mass spectrometry (MS/MS) is an attractive technique for sequencing membrane proteins because it can be applied to peptides in mixtures that are difficult to separate chromatographically. To evaluate the suitability of MS/MS sequencing for membrane proteins and to develop protocols for the preparation of the cleaved peptides, we employed the well characterized apoproteins of bacteriorhodopsin and bovine rhodopsin, i.e. bacterioopsin and opsin, respectively. Without separation, nine out of ten peptides resulting from cyanogen bromide cleavage of bacterioopsin were detected by fast atom bombardment MS, the single undetected fragment being a tetrapeptide that was presumably hidden in the low‐m/z matrix background. Furthermore, MS/MS was used to confirm the sequence of all the peptides detected with m/z values below 3.5 kDa (40% of the protein). Bovine opsin was analyzed in a similar fashion. Tandem MS/MS has thus allowed the sequencing of substantial portions of two integral membrane proteins by the analysis of unseparated peptide mixtures, demonstrating for the first time that this technique can obviate some of the most serious difficulties associated with sequencing membrane proteins, namely the difficult‐to‐achieve separation of the ‘sticky’ peptide fragments.
Some pitfalls in using the reaction intermediate scan (RIS)
Authors: Eller Karsten , Drewello Thomas 
Published: May 2005

AbstractThe reaction intermediate scan (RIS) represents a most instructive triple mass spectrometric (MS/MS/MS) experiment allowing the elucidation of sequential dissociation cascades. Preferably the RIS is performed by utilizing triple‐stage mass spectrometers. Considering experimental findings obtained with BEB‐ and BEqQ‐configurated instruments, some aspects regarding the collision processes and the applicability of linked scanning are discussed with special emphasis on the reliability of RIS.
Determination of glycosylation sites in O‐linked glycopeptides: A sensitive mass spectrometric protocol
Authors: Rademaker Geert Jan , Haverkamp Johan , Thomas‐Oates Jane 
Published: May 2005

AbstractA sensitive mass spectrometric method for the specific identification of O‐glycosylation sites in glycopeptides is presented. Reductive β‐elimination liberates a peptide containing a specifically modified amino acid at the former site of carbohydrate attachment. Mass spectrometry is used to determine the sequence of the modified peptide, in which the position of the modified amino acid marks the site of O‐glycosylation. The method also provides information on the carbohydrate chain and is applicable at the low nanomolar level.
Intrinsic specificity of Ca2+–protein binding sites
Authors: Reiter Alex , Zhao Hong , Adams Jeanette 
Published: May 2005

AbstractThe gas‐phase chemistry of anionic [M + Cat2+ – 3H]− complexes between Ca2+‐specific peptides and the alkaline earth metal ions Mg2+, Ca2+ and Ba2+ is reported. The metal ion complexes were studied using fast atom bombardment, collision‐induced decomposition (CID) and molecular mechanical calculations. The CID reactions and molecular mechanical calculations revealed that the Ca2+–peptide complexes are bound differently to the Mg2+– and Ba2+–peptide complexes and that the intrinsic (gas‐phase) chemistry is reflected by known aqueousphase chemistry.
Systematic study of the effects of experimental parameters on the beam‐induced dehalogenation of chlorpromazine in liquid secondary ion mass spectrometry
Authors: Théberge R. , Paul G. J. C. , Bertrand M. J. 
Published: May 2005

AbstractThe effect of experimental parameters such as time of irradiation, analyte concentration, primary beam density, matrix selection and matrix additives on the beam‐induced dehalogenation of chlorpromazine in liquid secondary ion mass spectrometry (LSIMS) was investigated. It was found that dehalogenation of chlorpromazine in glycerol increased with increasing time of irradiation, analyte concentration and primary beam density. These results were compared with those obtained using 4‐chlorophenylalanine ethyl ester and the differences observed were rationalized in terms of compound surface activity. Evidence is given that matrix selection is the key experimental parameter affecting the extent of beam‐induced dehalogenation of chlorpromazine in LSIMS. Of the eleven matrices used, the greatest extent of dehalogenation was observed in glycerol. Sulfur‐containing matrices consistently exhibited a lower extent of dehalogenation than oxygen‐containing aliphatic matrices, implying that sulfur is implicated in mitigating the reduction process. Dehalogenation was totally inhibited in 2‐hydroxyethyl disulfide, 4‐hydroxybenzenesulfonic acid and 3‐nitrobenzyl alcohol. Similarly, the use of matrix additives such as 3‐nitrobenzyl alcohol and trifluoroacetic acid was found to be useful in inhibiting the extent of dehalogenation occurring in glycerol.
Photodissociation and collision‐induced dissociation of molecular ions from methylphenol and chloromethylphenol
Authors: Cassady C. J. , Afzaal S. , Freiser B. S. 
Published: May 2005

AbstractThe photodissociation of molecular ions from a series of methylphenols and chloromethylphenols was studied using Fourier transform ion cyclotron resonance mass spectrometry (FTMS). The photodissociation spectra contain both UV and visible absorption maxima. The positions of these bands correlate well with solution electronic absorption spectra and photoelectron spectra, respectively, suggesting that photodissociating populations of the molecular ions have not rearranged. The molecular ion of benzyl alcohol can be readily distinguished from the isomeric 2‐ and 4‐methylphenol ions on the basis of the position and intensity of the photodissociation bands, and the identity of the photoproduct. The p‐chlorophenol isomers, 4‐chloro‐2‐methylphenol and 4‐chloro‐3‐methylphenol, cannot be distinguished by their photodissociation spectra. Minor differences exist between these spectra and that of the o‐chlorophenol isomer 2‐chloro‐5‐methylphenol, suggesting that the relative positions of the chloro and hydroxy groups may have a greater effect on photodissociation than the position of the methyl group. For comparison, low‐energy collision‐induced dissociation using FTMS was also performed on the same ions.
Mass spectrometric fragmentation of isomeric 2‐alkyl‐substituted 1,3‐indandiones and 3‐alkylidenephthalides: a seven‐step consecutive isomerization of regular and distonic molecular radical cations
Authors: Kuck Dietmar 
Published: May 2005

AbstractThe electron impact‐induced fragmentation of 2,2‐dimethyl‐ and 2‐ethyl‐1,3‐indandione, 1 and 2, and their isomers, 3‐isopropylidene‐ and 3‐propylidenephthalide, 3 and 4, respectively, was studied in detail by mass‐analysed ion kinetic energy (MIKE) and collision‐induced dissociation (CID‐MIKE) spectrometry, including 2H and 13C. labelled analogues of 1 and 2. In all regimes of internal energy, the molecular ions 1+. 4+. interconvert by up to seven consecutive, reversible isomerization steps prior to the main fragmentation processes, viz. loss of CH3. and C2H4. 1,3‐Indandione and 3‐methylenephthalide ions with identical alkylidene moieties (i.e. 1+.⇌3+. and 2+.⇌4+.) equilibrate rapidly and completely prior to fragmentation, whereas these pairs of isomers interconvert only slowly via a five‐step rearrangement of the indandione ions 1+.⇌2+.. Distinct from the behaviour of simpler ionized carbonyl species, a 1,2‐C shift of a (formally) neutral carbonyl group is found to occur along with that of a protonated one. Also distinct from simpler cases, methyl loss does not take place from the ionized enol intermediates formed within the interconversion 1+.⇌2+. of the diketone ions but rather from the n‐propylidenephthalide ions 4+.. This follows from CID‐MIKE spectrometry of the [M  CH3]+ ions of 1–4 and two reference C10H7O2+ (m/z 159) ions of authentic structures (protonated 2‐methylene‐1,3‐indandione and protonated 1,4‐naphthoquinone). The characteristic CID fragmentation of the C10H7O2+ ions is rationalized. Finally, the multistep isomerization of ionized 1,3‐indandiones apparently also extends to higher homologues [e.g. 5+. from 2‐ethyl‐2‐methyl‐1,3‐indandione (5) and 6+. from 2,2‐diethyl‐1,3‐indandione (6)]: the ionized phthaloyl group of 1,3‐indandione radical cations 1+., 2+., 5+. and 6+., originally attached with its two acyl functionalities to the same carbon of the aliphatic chain, performs, in fact, a ‘multi‐step migration’.