Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments

Diverse mass spectrometric instruments have been used to provide data for accurate mass and retention time (AMT) tag proteomics analyses, including ion trap, quadrupole time-of-flight, and Fourier transform mass spectrometry (FTMS). An important attribute of these instruments, beside mass accuracy, is their spectral resolution. In fact, the ability to separate peaks with close m/z values is likely to play a major role in enabling species identification and matching in analyses of very complex proteomics samples. In FTMS, resolution is directly proportional to the detection period and can therefore be easily tuned. We took advantage of this feature to investigate the effect of resolution on species identification and matching in an AMT tag experiment. Using an Arabidopsis thaliana chloroplast protein extract as prototypical 'real-life' sample, we have compared the number of detected features, the optimal mass tolerance for species matching, the number of matched species and the false discovery rate obtained at various resolution settings. It appears that while the total number of matches is not significantly affected by a reduction of resolution in the range investigated, the confidence level of identifications significantly drops as evidenced by the estimated false discovery rate.     

Uncertainties in the oxygen isotopic composition of barium sulfate induced by coprecipitation of nitrate

Coprecipitation of nitrate and sulfate by barium has probably resulted in significant error in numerous studies dealing with the oxygen isotopic composition of natural sulfates using chemical/thermal conversion of BaSO(4) and analysis by isotope ratio mass spectrometry. In solutions where NO(3) (-)/SO(4) (2-) molar ratios are above 2 the amount of nitrate coprecipitated with BaSO(4) reaches a maximum of approximately 7% and decreases roughly linearly as the molar ratio decreases. The fraction of coprecipitated nitrate appears to increase with decreasing pH and is also affected by the nature of the cations in the precipitating solution. The size of the oxygen isotope artifact in sulfate depends both on the amount of coprecipitated nitrate and the delta(18)O and Delta(17)O values of the nitrate, both of which can be highly variable. The oxygen isotopic composition of sulfate extracted from atmospheric aerosols or rain waters are probably severely biased because photochemical nitrate is usually also present and it is highly enriched in (18)O (delta(18)O approximately 50-90 per thousand) and has a large mass-independent isotopic composition (Delta(17)O approximately 20-32 per thousand). The sulfate delta(18)O error can be 2-5 per thousand with Delta(17)O artifacts reaching as high as 4.0 per thousand. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Imaging of uranium on rat brain sections using laser ablation inductively coupled plasma mass spectrometry: a new tool for the study of critical substructures affined to heavy metals in tissues

The specific toxicity of trace metals and compounds largely depends on their bioavailability in different organs or compartments of the organism considered. Imaging mass spectrometry (IMS) using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) with a spatial resolution in the 100 microm range was developed and employed to study heavy metal distribution in brain tissues for toxicological screening. Rat brain post-mortem tissues were stained in an aqueous solution of either uranium or neodymium (metal concentration 100 microg g(-1)) for 3 h. The incubation of heavy metal in thin slices of brain tissue is followed by an imaging mass spectrometric LA-ICP-MS technique. Stained rat brain tissue (thickness 30 microm) were scanned with a focused laser beam (wavelength 266 nm, diameter of laser crater 100 microm and laser power density 3 x 10(9) W cm(-2)). The ion intensities of (235)U(+), (238)U(+), (145)Nd(+) and (146)Nd(+) were measured by LA-ICP-MS within the ablated area. For quantification purposes, matrix-matched laboratory standards were prepared by dosing each analyte to the pieces of homogenized brain tissue. Imaging LA-ICP-MS allows structures of interest to be identified and the relevant dose range to be estimated. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Detection of carbohydrate-binding proteins by oligosaccharide-modified polypyrrole interfaces using electrochemical surface plasmon resonance

This paper reports on the use of electrochemical surface plasmon resonance (E-SPR) for the detection of carbohydrate-binding proteins. The generation of an SPR sensor specific to lectins Arachis hypogaea (PNA) and Maackia amurensis (MAA) is based on the electrochemical polymerization of oligosaccharide derivatives functionalized by pyrrole groups. The resulting thin conducting polymer films were characterized using E-SPR and atomic force microscopy (AFM). The specific binding of PNA to polypyrrole-lactosyl and of MAA to polypyrrole-3'-sialyllactosyl films was investigated using SPR. The detection limit was 41 nM for PNA and 83 nM for MAA. Through Scatchard analysis and linear transformation of the SPR sensorgram data, association (k(ass)) and dissociation rate constants (k(diss)) could be determined.     

Novel beta-lactam antibiotics synthesized by amination of catechols using fungal laccase

Novel cephalosporins, penicillins, and carbacephems were synthesized by amination of catechols with amino-beta-lactams like cefadroxil, amoxicillin, ampicillin and the structurally related carbacephem loracarbef using laccase from Trametes sp. All isolated monoaminated products inhibited the growth of several Gram positive bacterial strains in the agar diffusion assay, among them methicillin-resistant Staphylococcus aureus strains and vancomycin-resistant Enterococci. Observed differences in the cytotoxicity and in vivo activity in a "Staphylococcus-infected, immune suppressed mouse" model are discussed.     

Structural Polymorphism and Thin Film Transistor Behavior in the Fullerene Framework Molecule 5,6;11,12‐di‐o‐Phenylenetetracene

The molecular structure of the hydrocarbon 5,6;11,12‐di‐o‐phenylenetetracene (DOPT), its material characterization and evaluation of electronic properties is reported for the first time. A single‐crystal X‐ray study reveals two different motifs of intramolecular overlap with herringbone‐type arrangement displaying either face‐to‐edge or co‐facial face‐to‐face packing depicting intensive π–π interactions. Density functional theory (DFT) calculations underpin that a favorable electronic transport mechanism occurs by a charge hopping process due to a π‐bond overlap in the DOPT polymorph with co‐facial arene orientation. The performance of polycrystalline DOPT films as active organic semiconducting layer in a state‐of‐the‐art organic field effect transistor (OFET) device was evaluated and proves to be film thickness dependent. For 40 nm layer thickness it displays a saturation hole mobility (μ_hole) of up to 0.01 cm² V^?1 s^?1 and an on/off‐ratio (I_on/I_off) of 1.5×10³.     

δ‐Methyl Branching in the Side Chain Makes the Difference: Access to Room‐Temperature Discotics

Although discotic liquid crystals are attractive functional materials, their use in electronic devices is often restricted by high melting and clearing points. Among the promising candidates for applications are [15]crown‐5 ether‐based liquid crystals with peripheral n‐alkoxy side chains, which, however, still have melting points above room temperature. To overcome this problem, a series of o‐terphenyl and triphenylene [15]crown‐5 ether derivatives was prepared in which δ‐methyl‐branched alkoxy side chains of varying lengths substitute the peripheral linear alkoxy chains. The mesomorphic properties of the novel crown ethers were studied by differential scanning calorimetry, polarizing optical microscopy, and X‐ray diffraction. δ‐Methyl branching indeed lowers melting points resulting in room‐temperature hexagonal columnar mesophases. The mesophase widths, which ranged from 87 to 30 K for o‐terphenyls, significantly increased to 106–147 K for the triphenylenes depending on the chain lengths, revealing the beneficial effect of a flat mesogen, due to improved π–π interactions.     

Enzyme Shielding in an Enzyme‐thin and Soft Organosilica Layer

The fragile nature of most enzymes is a major hindrance to their use in industrial processes. Herein, we describe a synthetic chemical strategy to produce hybrid organic/inorganic nanobiocatalysts; it exploits the self‐assembly of silane building blocks at the surface of enzymes to grow an organosilica layer, of controlled thickness, that fully shields the enzyme. Remarkably, the enzyme triggers a rearrangement of this organosilica layer into a significantly soft structure. We demonstrate that this change in stiffness correlates with the biocatalytic turnover rate, and that the organosilica layer shields the enzyme in a soft environment with a markedly enhanced resistance to denaturing stresses.     

Ca2+‐complex stability of GAPAGPLIVPY peptide in gas and aqueous phase,investigated by affinity capillary electrophoresis and molecular dynamics simulations and compared to mass spectrometric results

Strong, sequence‐specific gas‐phase bindings between proline‐rich peptides and alkaline earth metal ions in nanoESI‐MS experiments were reported by Lehmann et al. (Rapid Commun. Mass Spectrom. 2006, 20, 2404–2410), however its relevance for physiological‐like aqueous phase is uncertain. Therefore, the complexes should also be studied in aqueous solution and the relevance of the MS method for binding studies be evaluated. A mobility shift ACE method was used for determining the binding between the small peptide GAPAGPLIVPY and various metal ions in aqueous solution. The findings were compared to the MS results and further explained using computational methods. While the MS data showed a strong alkaline earth ion binding, the ACE results showed nonsignificant binding. The proposed vacuum state complex also decomposed during a molecular dynamic simulation in aqueous solution. This study shows that the formed stable peptide–metal ion adducts in the gas phase by ESI‐MS does not imply the existence of analogous adducts in the aqueous phase. Comparing peptide–metal ion interaction under the gaseous MS and aqueous ACE conditions showed huge difference in binding behavior.