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Mass Analysis (mass + analysis)
Selected AbstractsHPLC purification and re-evaluation of chemical identity of two circular bacteriocins, gassericin A and reutericin 6LETTERS IN APPLIED MICROBIOLOGY, Issue 4 2010K. Arakawa Abstract Aim:, The study aimed for the complete purification and recharacterization of the highly hydrophobic circular bacteriocins, gassericin A and reutericin 6. Methods and Results:, Gassericin A and reutericin 6 were purified to homogeneity using previously described method and reverse-phase HPLC with an octyl column and eluents of aqueous acetonitrile and 2-propanol. Mass analysis, N-terminal sequencing and bacteriocin assay of the HPLC-purified bacteriocins showed the two bacteriocins had identical seamless circular structures with the same m/z value (5651) of [M + H]+ and both had the same specific activity. d/l- amino acid composition analysis using two distinct methods with the chiral fluorescent derivatization reagents (+)-1-(9-fluorenyl)ethyl chloroformate and o -phthalaldehyde/N -acetyl- l -cystein revealed neither gassericin A nor reutericin 6 contained d -alanine residues contrary to our previous results. Conclusion:, Purified gassericin A and reutericin 6 are chemically identical circular molecules containing no d -alanine residues. Significance and Impact of the Study:, The HPLC conditions developed in this study will facilitate advanced purification and correct characterization of other highly hydrophobic bacteriocins. [source] Neuropeptide and neurohormone precursors in the pea aphid, Acyrthosiphon pisumINSECT MOLECULAR BIOLOGY, Issue 2010J. Huybrechts Abstract Aphids respond to environmental changes by developing alternative phenotypes with differing reproductive modes. Parthenogenetic reproduction occurs in spring and summer, whereas decreasing day lengths in autumn provoke the production of sexual forms. Changing environmental signals are relayed by brain neuroendocrine signals to the ovarioles. We combined bioinformatic analyses with brain peptidomics and cDNA analyses to establish a catalogue of pea aphid neuropeptides and neurohormones. 42 genes encoding neuropeptides and neurohormones were identified, of which several were supported by expressed sequence tags and/or peptide mass analyses. Interesting features of the pea aphid peptidome are the absence of genes coding for corazonin, vasopressin and sulfakinin and the presence of 10 different genes coding insulin related peptides, one of which appears to be very abundantly expressed. [source] Why ,2 -antiplasmin must be converted to a derivative form for optimal functionJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 10 2007K. N. LEE Summary.,Background:,Human ,2 -antiplasmin (,2AP), the primary inhibitor of fibrinolysis, is secreted from the liver into plasma as a 464-residue protein with Met as the N-terminus. An R6W polymorphism has been suggested to affect fibrinolytic rate. Within circulating blood, antiplasmin-cleaving enzyme (APCE) cleaves Met-,2AP(R6) faster than Met-,2AP(W6) at the Pro12,Asn13 bond to yield Asn-,2AP. Objectives:,To compare Met-,2AP(R6), Met-,2AP(W6) and Asn-,2AP for crosslinking with fibrin and the ability to protect fibrin from digestion by plasmin. Methods and results:,Asn-,2AP utilizes Gln2 (Gln14 in Met-,2AP) to become crosslinked to fibrin approximately twelvefold faster than Met-,2AP(R6) or Met-,2AP(W6), and this enhances the resistance of fibrin to plasmin. All three forms of ,2AP inhibit plasmin at identical rates. The N-terminal 12-residue peptide of Met-,2AP slows crosslinking of Met-,2AP(R6) or Met-,2AP(W6) by limiting access of factor XIIIa to Gln14 rather than shifting crosslinking to other Gln residues. Edman sequencing and mass analyses of tryptic peptides from each ,2AP crosslinked with 5-(biotinamido)pentylamine showed Gln14 as the only major crosslinking site. Residues 5,8, GRQL in Met-,2AP(R6), and residues 1,8, MEPLGWQL in Met-,2AP(W6), slow fibrin crosslinking. Conclusion:,Gln14 in both Met-,2AP(R6) and Met-,2AP(W6) is sheltered by the N-terminal 12-residue peptide, which, when cleaved, yields Asn-,2AP, which is rapidly crosslinked to fibrin and maximally protects it from plasmin. The R6 W polymorphism in Met-,2AP does not affect its crosslinking to fibrin, but it does slow cleavage by APCE and reduces the amount of Asn-,2AP available for rapid crosslinking to fibrin. [source] A highly efficient synthesis of (Z)-1-aryl-2-silyl-1- stannylethenes and their conversion to (E)-2- arylethenyl-, (Z)-2-(2-pyridyl)ethenyl- and allenyl-silanesAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 3 2007Takanori Endo Abstract A Pd(dba)2,P(OEt)3 combination allowed the silastannation of arylacetylenes, 1-hexyne or propargyl alcohols with tributyl(trimethylsilyl)stannane to take place at room temperature, producing (Z)-2-silyl-1-stannyl-1-substituted ethenes in high yields. Novel silyl(stannyl)ethenes were fully characterized by 1H-, 13C-, 29Si- and 119Sn-NMR as well as infrared and mass analyses. Treatment of a series of (Z)-1-aryl-2-silyl-1-stannylethenes and (Z)-1-(3-pyridyl)-2-silyl-1-stannylethene with hydrochloric acid or hydroiodic acid in the presence of tetraethylammonium chloride (TEACl) or tetrabutylammonium iodide (TBAI) led to the exclusive formation of (E)-trimethyl(2-arylethenyl)silanes with high stereoselectivity. A similar reaction of (Z)-1-(2-anisyl)-2-silyl-1-stannylethene also produced E -type trimethyl[2-(2-anisyl)ethenyl]silane, while (Z)-trimethyl [2-(2-pyridyl)ethenyl]silane was produced exclusively from (Z)-1-(2-pyridyl)-2-silyl-1-stannylethene. Protodestannylation of (Z)-1-[hydroxy(phenyl)methyl]-2-silyl-1-stannylethene with trifluoroacetic acid took place via the ,-elimination of hydroxystannane, providing trimethyl(3-phenylpropa-1,2-dienyl)silane quite easily. The destannylation products were also fully characterized. Copyright © 2007 John Wiley & Sons, Ltd. [source] Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ionsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2008Jeremiah J. Bowers Abstract A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion. Copyright © 2007 John Wiley & Sons, Ltd. [source] The Orbitrap: a new mass spectrometerJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2005Qizhi Hu Abstract Research areas such as proteomics and metabolomics are driving the demand for mass spectrometers that have high performance but modest power requirements, size, and cost. This paper describes such an instrument, the Orbitrap, based on a new type of mass analyzer invented by Makarov. The Orbitrap operates by radially trapping ions about a central spindle electrode. An outer barrel-like electrode is coaxial with the inner spindlelike electrode and mass/charge values are measured from the frequency of harmonic ion oscillations, along the axis of the electric field, undergone by the orbitally trapped ions. This axial frequency is independent of the energy and spatial spread of the ions. Ion frequencies are measured non-destructively by acquisition of time-domain image current transients, with subsequent fast Fourier transforms (FFTs) being used to obtain the mass spectra. In addition to describing the Orbitrap mass analyzer, this paper also describes a complete Orbitrap-based mass spectrometer, equipped with an electrospray ionization source (ESI). Ions are transferred from the ESI source through three stages of differential pumping using RF guide quadrupoles. The third quadrupole, pressurized to less than 10,3 Torr with collision gas, acts as an ion accumulator; ion/neutral collisions slow the ions and cause them to pool in an axial potential well at the end of the quadrupole. Ion bunches are injected from this pool into the Orbitrap analyzer for mass analysis. The ion injection process is described in a simplified way, including a description of electrodynamic squeezing, field compensation for the effects of the ion injection slit, and criteria for orbital stability. Features of the Orbitrap at its present stage of development include high mass resolution (up to 150 000), large space charge capacity, high mass accuracy (2,5 ppm), a mass/charge range of at least 6000, and dynamic range greater than 10.3 Applications based on electrospray ionization are described, including characterization of transition-metal complexes, oligosaccharides, peptides, and proteins. Use is also made of the high-resolution capabilities of the Orbitrap to confirm the presence of metaclusters of serine octamers in ESI mass spectra and to perform H/D exchange experiments on these ions in the storage quadrupole. Copyright © 2005 John Wiley & Sons, Ltd. [source] Plate-out in PVC extrusion.JOURNAL OF VINYL & ADDITIVE TECHNOLOGY, Issue 1 2008Samples of extruder plate-out from industrial rigid PVC production lines were investigated by using a number of analytical techniques. The combined use of SEM-EDX (scanning electron microscopy , energy dispersive X-ray analysis), thermal analysis, FTIR (Fourier transform infrared spectrophotometry), and LIMA (laser-induced mass analysis) enabled most plate-out components to be identified and linked to likely formulation ingredients. The FTIR and thermal analyses were used to identify organic components. The FTIR analysis was also useful for identifying some inorganic compounds present in sufficient quantities, while EDX detected the elements present. The LIMA was the most sensitive technique, detecting trace quantities of both cations and anions. Calcium carbonate, titanium dioxide, and lead stabilizers were found in all die plate-out samples studied, together with small amounts of lubricants. J. VINYL ADDIT. TECHNOL., 2008. © 2008 Society of Plastics Engineers. [source] IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteinsMOLECULAR MICROBIOLOGY, Issue 1 2006Won-Sik Yeo Summary In Escherichia coli, Fe-S clusters are assembled by gene products encoded from the isc and suf operons. Both the iscRSUA and sufABCDSE operons are induced highly by oxidants, reflecting an increased need for providing and maintaining Fe-S clusters under oxidative stress conditions. Three cis -acting oxidant-responsive elements (ORE-I, II, III) in the upstream of the sufA promoter serve as the binding sites for OxyR, IHF and an uncharacterized factor respectively. Using DNA affinity fractionation, we isolated an ORE-III-binding factor that positively regulates the suf operon in response to various oxidants. MALDI-TOF mass analysis identified it with IscR, known to serve as a repressor of the iscRSUA gene expression under anaerobic condition as a [2Fe-2S]-bound form. The iscR null mutation abolished ORE-III-binding activity in cell extracts, and caused a significant decrease in the oxidant induction of sufA in vivo. OxyR and IscR contributed almost equally to activate the sufA operon in response to oxidants. Purified IscR that lacked Fe-S cluster bound to the ORE-III site and activated transcription from the sufA promoter in vitro. Mutations in Fe-S-binding sites of IscR enabled sufA activation in vivo and in vitro. These results support a model that IscR in its demetallated form directly activates sufA transcription, while it de-represses isc operon, under oxidative stress condition. [source] Fission processes following core level excitation in closo -1,2-orthocarboranePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 7 2009E. Rühl Abstract Time-of-flight mass analysis with multi-stop coincidence detection was used to study the multi-cation ionic fragmentation of the closo carborane cage molecule closo -1,2-orthocarborane (C2B10H12) following inner-shell excitation in or above the B 1s regime. Electron ion coincidence spectra reveal the cationic products which are formed after core level excitation. Distinct changes in fragmentation pattern are observed as a function of excitation energy. Photoelectron,photoion,photoion coincidence (PEPIPICO) spectroscopy was used to study the dominant fission routes in the core level excitation regime. Series of ion pairs are identified, where asymmetric fission dominates, leading to ion pairs of different mass. Suitable fission and fragmentation mechanisms are discussed. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A combination of neutral loss and targeted product ion scanning with two enzymatic digestions facilitates the comprehensive mapping of phosphorylation sitesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2007Juan Casado-Vela Abstract We propose here a new strategy for the exhaustive mapping of phosphorylation sites in the Xenopus laevis Cdc25 phosphatase, which regulates cell cycle progression in eukaryotic cells. Two different MS analyses in a linear IT were used to identify the phosphorylated residues. First, a data-dependent neutral loss (DDNL) analysis triggered the fragmentation of peptides that show enhanced neutral loss of phosphoric acid. Second, a targeted product ion scanning (TPIS) mass analysis was carried out in which MS2 events are triggered for specific m/z values. Full coverage of the protein sequence was obtained by combining the two analyses with two enzymatic digestions, trypsin and chymotrypsin, yielding a comprehensive map of the phosphorylation sites. Previous reports have shown Cdc25C to be phosphorylated by Cdc2,cyclin B at four residues (Thr48, Thr67, Thr138 and Ser205). By using this combination of scan modes, we have identified four additional phosphorylation sites (Thr86, Ser99, Thr112 and Ser163) in a recombinant Cdc25C protein containing 198 residues of the NH2 -terminal noncatalytic domain. The sensitivity of this combined approach makes it extremely useful for the comprehensive characterization of phosphorylation sites, virtually permitting complete coverage of the protein sequence with peptides within the mass detection range of the linear IT. [source] On the high-resolution mass analysis of the product ions in tandem time-of-flight (TOF/TOF) mass spectrometers using a time-dependent re-acceleration techniqueRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 1 2010Sergey Kurnosenko The time-dependent reacceleration of product ions produced as a result of dissociation of a single precursor ion in a tandem time-of-flight mass spectrometer is considered for the first time. Analytical expressions for the shapes of electric pulses bringing all the kinetic energies of the product ions to the same value are derived for two cases: forward acceleration mode and deceleration, followed by re-acceleration in the reversed direction (reversed mode). Secondary time-of-flight focusing resulting from the re-acceleration in the reversed mode is shown to be mass-dependent and, when averaged over a wide mass range, the focusing is tight enough to provide mass resolution exceeding 10,000. After time-dependent re-acceleration, additional compression of the ion packet width leading to better mass resolution can be obtained by decelerating the ions in a constant field. Copyright © 2009 John Wiley & Sons, Ltd. [source] Porous polymer monolith for surface-enhanced laser desorption/ionization time-of-flight mass spectrometry of small moleculesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2004Dominic S. Peterson Porous poly(butyl methacrylate- co -ethylene dimethacrylate), poly(benzyl methacrylate- co -ethylene dimethacrylate), and poly(styrene- co -divinylbenzene) monoliths have been prepared on the top of standard sample plates used for matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and the modified plates were used for laser desorption/ionization mass spectrometry (LDI-MS). The hydrophobic porous surface of these monoliths enables the transfer of sufficient energy to the analyte to induce desorption and ionization prior to TOFMS analysis. Both UV and thermally initiated polymerization using a mask or circular openings in a thin gasket have been used to define spot locations matching those of the MALDI plates. The desorption/ionization ability of the monolithic materials depends on the applied laser power, the solvent used for sample preparation, and the pore size of the monoliths. The monolithic matrices are very stable and can be used even after long storage times in a typical laboratory environment without observing any deterioration of their properties. The performance of the monolithic material is demonstrated with the mass analysis of several small molecules including drugs, explosives, and acid labile compounds. The macroporous spots also enable the archiving of samples. Copyright © 2004 John Wiley & Sons, Ltd. [source] Electrospray ionization with ambient pressure ion mobility separation and mass analysis by orthogonal time-of-flight mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2001Wes E. Steiner Rapid screening and identification of drug and other mixtures are possible using a novel ambient pressure high-resolution ion mobility (APIMS) orthogonal reflector time-of-flight mass spectrometer (TOFMS). Departing ions from the APIMS drift tube traversed a pressure interface between the APIMS and TOFMS where they were subjected to numerous gas collisions that could produce selective fragmentation. By increasing the accelerating field in the pressure interface region, the ions generated using water-cooled electrospray ionization (ESI) underwent collision-induced dissociation (CID). Mixtures of ESI ions were separated by APIMS based on their respective size-to-charge (s/z) ratios while CID and analysis of mass-to-charge (m/z) ratios occurred in the pressure interface and TOFMS. Product ions that were formed in this pressure interface region could be readily assigned to precursor ions by matching the mobility drift times. This process was demonstrated by the examination of a mixture of amphetamines and the resulting fragmentation patterns of the mobility-separated precursor ion species [M,+,H]+. Copyright © 2001 John Wiley & Sons, Ltd. [source] The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomicsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2001R. Cramer Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed. Copyright © 2001 John Wiley & Sons, Ltd. [source] Copolymerization of Cyclohexene Oxide with CO2 by Using Intramolecular Dinuclear Zinc CatalystsCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2005Youli Xiao Abstract The intramolecular dinuclear zinc complexes generated in situ from the reaction of multidentate semi-azacrown ether ligands with Et2Zn, followed by treatment with an alcohol additive, were found to promote the copolymerization of CO2 and cyclohexene oxide (CHO) with completely alternating polycarbonate selectivity and high efficiency. With this type of novel initiator, the copolymerization could be accomplished under mild conditions at 1 atm pressure of CO2, which represents a significant advantage over most catalytic systems developed for this reaction so far. The copolymerization reaction was demonstrated to be a living process as a result of the narrow polydispersities and the linear increase in the molecular weight with conversion of CHO. In addition, the solid-state structure of the dinuclear zinc complex was characterized by X-ray crystal structural analysis and can be considered as a model of the active catalyst. On the basis of the various efforts made to understand the mechanisms of the catalytic reaction, including MALDI-TOF mass analysis of the copolymers' end-groups, the effect of alcohol additives on the catalysis and CO2 pressure on the conversion of CHO, as well as the kinetic data gained from in situ IR spectroscopy, a plausible catalytic cycle for the present reaction system is outlined. The copolymerization is initiated by the insertion of CO2 into the ZnOEt bond to afford a carbonate,ester-bridged complex. The dinuclear zinc structure of the catalyst remains intact throughout the copolymerization. The bridged zinc centers may have a synergistic effect on the copolymerization reaction; one zinc center could activate the epoxide through its coordination and the second zinc atom may be responsible for carbonate propagation by nucleophilic attack by the carbonate ester on the back side of the cis -epoxide ring to afford the carbonate. The mechanistic implication of this is particularly important for future research into the design of efficient and practical catalysts for the copolymerization of epoxides with CO2. [source] | |||||||||||||