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Mass Spectrometry Experiments (mass + spectrometry_experiment)
Selected AbstractsStructural analysis of the lipopolysaccharide from Chlamydophila psittaci strain 6BCFEBS JOURNAL, Issue 18 2000Sabine Rund The lipopolysaccaride of Chlamydophila psittaci 6BC was isolated from tissue culture-grown elementary bodies using a modified phenol/water procedure followed by extraction with phenol/chloroform/light petroleum. Compositional analyses indicated the presence of 3-deoxy- dmanno -oct-2-ulosonic acid, GlcN, organic bound phosphate and fatty acids in a molar ratio of ,,3.3 : 2 : 1.8 : 4.6. Deacylated lipopolysaccharide was obtained after successive microscale treatment with hydrazine and potassium hydroxide, and was then separated by high performance anion-exchange chromatography into two major fractions, the structures of which were determined by 600 MHz NMR spectroscopy as ,-Kdo-(2,8)-,-Kdo-(2,4)-,-Kdo-(2,6)-,- d -GlcpN-(1,6)-,- d -GlcpN 1,4,-bisphosphate and ,-Kdo-(2,4)-[,-Kdo-(2,8)]-,-Kdo-(2,4)-,-Kdo-(2,6)-,- d -GlcpN-(1,6)-,- d -GlcpN 1,4,-bisphosphate. The distribution of fatty acids in lipid A was determined by compositional analyses and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry experiments on lipid A and de-O-acylated lipid A. It was shown that the carbohydrate backbone of lipid A is replaced by a complex mixture of fatty acids, including long-chain and branched (R)-configured 3-hydroxy fatty acids, the latter being exclusively present in an amide linkage. [source] Role of 2-oxo and 2-thioxo modifications on the proton affinity of histidine and fragmentation reactions of protonated histidine,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2010Adrian K. Y. Lam A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments was used to compare the gas-phase chemistry of the amino acids histidine (1), 2-oxo-histidine (2), and 2-thioxo-histidine (3). Collision-induced dissociation (CID) of all three different proton-bound heterodimers of these amino acids led to the relative gas-phase proton affinity order of: histidine >2-thioxo-histidine >2-oxo-histidine. Density functional theory (DFT) calculations confirm this order, with the lower proton affinities of the oxidised histidine derivatives arising from their ability to adopt the more stable keto/thioketo tautomeric forms. All protonated amino acids predominately fragment via the combined loss of H2O and CO to yield a1 ions. Protonated 2 and 3 also undergo other small molecule losses including NH3 and the imine HN=CHCO2H. The observed differences in the fragmentation pathways are rationalised through DFT calculations, which reveal that while modification of histidine via the introduction of the oxygen atom in 2 or the sulfur atom in 3 does not affect the barriers against the loss of H2O+CO, barriers against the losses of NH3 and HN=CHCO2H are lowered relative to protonated histidine. Copyright © 2010 John Wiley & Sons, Ltd. [source] Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 10 2009King Wai Lau Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument-specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole-time-of-flight and quadrupole ion trap instruments. Specifically, quadrupole-time-of-flight tandem mass spectra show a significant under-representation of N-terminal b-type fragments in comparison to quadrupole ion trap product ion spectra. Energy-resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b-type ions are significantly less stable than their y-type N-terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole-time-of-flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. Copyright © 2009 John Wiley & Sons, Ltd. [source] Towards a universal product ion mass spectral library , reproducibility of product ion spectra across eleven different mass spectrometersRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2008Chris Hopley Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments , a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns. The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS. The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC/MS/MS identification using instruments of the same type from different manufacturers. Copyright © 2008 John Wiley & Sons, Ltd. [source] Electrospray ionization from a gap with adjustable widthRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 21 2006Patrik Ek In this paper, we present a new concept for electrospray ionization mass spectrometry, where the sample is applied in a gap which is formed between the edges of two triangular-shaped tips. The size of the spray orifice can be changed by varying the gap width. The tips were fabricated from polyethylene terephthalate film with a thickness of 36,µm. To improve the wetting of the gap and sample confinement, the edges of the tips forming the gap were hydrophilized by means of silicon dioxide deposition. Electrospray was performed with gap widths between 1 and 36,µm and flow rates down to 75,nL/min. The gap width could be adjusted in situ during the mass spectrometry experiments and nozzle clogging could be managed by simply widening the gap. Using angiotensin I as analyte, the signal-to-noise ratio increased as the gap width was decreased, and a shift towards higher charge states was observed. The detection limit for angiotensin I was in the low nM range. Copyright © 2006 John Wiley & Sons, Ltd. [source] A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristicsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 2 2006Peter B. O'Connor A new hybrid electrospray quadrupole Fourier transform mass spectrometry (FTMS) instrument design is shown and characterized. This instrument involves coupling an electrospray source and mass-resolving quadrupole, ion accumulation, and collision cell linear ion trap system developed by MDS Sciex with a home-built ion guide and ion cyclotron resonance (ICR) cell. The iterative progression of this design is shown. The final design involves a set of hexapole ion guides to transfer the ions from the accumulation/collision trap through the magnetic field gradient and into the cell. These hexapole ion guides are separated by a thin gate valve and two conduction limits to maintain the required <10,9,mbar vacuum for FTICR. Low-attomole detection limits for a pure peptide are shown, 220,000 resolving power in broadband mode and 820,000 resolving power in narrow-band mode are demonstrated, and mass accuracy in the <2,ppm range is routinely available provided the signal is abundant, cleanly resolved, and internally calibrated. This instrument design provides high experimental flexibility, allowing Q2 CAD, SORI-CAD, IRMPD, and ECD experiments with selected ion accumulation as well as experiments such as nozzle skimmer dissociation. Initial top-down mass spectrometry experiments on a protein is shown using ECD. Copyright © 2005 John Wiley & Sons, Ltd. [source] Identification of substituted sites on MUC5AC mucin motif peptides after enzymatic O-glycosylation combining ,-elimination and fixed-charge derivatizationRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 1 2002X. Czeszak A strategy for determination of O-glycosylation site(s) in glycopeptides has been developed using model compounds obtained by enzymatic glycosylation (by human GaNTase-T2 isoform) on peptides derived from the human MUC5AC mucin tandem repeat motif. The ,-elimination-addition reaction (using dimethylamine and concomitantly ethanethiol) on the formerly glycosylated sites through a Michael-type condensation produced efficient deglycosylation with appropriate chemical modification. After N-terminal derivatization by a phosphonium group, peptide sequencing was then carried out by nanospray tandem mass spectrometry experiments. The highly predictable fragmentation pathways of these fixed-charge phosphonium derivatives enable straightforward recognition of glycosylation site(s) based on the mass increment of +44,Da for originally glycosylated threonine compared to the mass of fragments containing nonglycosylated residues. Copyright ©,2001 John Wiley & Sons, Ltd. [source] Cooperative 2:1 Binding of a Bisphenothiazine to Duplex DNACHEMBIOCHEM, Issue 6 2008Frédéric Rosu Dr. DNA,drug dimers: Drugs based on the phenothiazine scaffold have a wide variety of therapeutic applications and are also used as DNA photosensitizers. Highly cooperative formation of a 2:1 complex was revealed by electrospray mass spectrometry experiments, and a structural model is proposed. This bisphenothiazine scaffold can therefore be exploited for future design of new minor groove binding agents having photosensitizing properties. [source] Organometallic Ruthenium Inhibitors of Glutathione- S -Transferase P1-1 as Anticancer DrugsCHEMMEDCHEM, Issue 12 2007Han Ang Dr. Abstract Ruthenium,arene complexes conjugated to ethacrynic acid were prepared as part of a strategy to develop novel glutathione- S -transferase (GST) inhibitors with alternate modes of activity through the organometallic fragment, ultimately to provide targeted ruthenium-based anticancer drugs. Enzyme kinetics and electrospray mass spectrometry experiments using GST P1-1 and its cysteine-modified mutant forms revealed that the complexes are effective enzyme inhibitors, but they also rapidly inactivate the enzyme by covalent binding at Cys,47 and, to a lesser extent, Cys,101. They are highly effective against the GST Pi-positive A2780 and A2780cisR ovarian carcinoma cell lines, are among the most effective ruthenium complexes reported so far, and target ubiquitous GST Pi overexpressed in many cancers. [source] | ||||||||||