Probability-based protein identification by searching sequence databases using mass spectrometry data

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.     

Detection of chlorinated methanes by tin oxide gas sensors

Tin oxide thin films prepared by thermal oxidation of Sn films were used for the detection of chlorinated methanes (CH2Cl2, CHCl3 and CCl4). This resulted in better chemical selectivity, sensitivity, response speed and detection limit than seen with previous detectors. The temperature dependence of the sensing of 1% CCl4 gas was studied and the best sensing behavior was observed at 300 degrees C. The films showed different chemical selectivity in both speed and direction of sensing response to each gas and were stable for more than 3 weeks under operating conditions. The films showed rapid gas sensing (<40 s to reach 90% of full response) and low detection limits (< 4 ppm CCl4). The role of oxygen in the detection of chlorinated methanes and in resistance changes without chlorinated methanes was also studied. The changes at the surface of the film after gas sensing were examined using scanning electron microscopy with energy-dispersive X-ray spectrometry.     

Modified entropic elasticity of rubberlike materials

In the first part of the paper, consisting of Sections 2 and 3, physical grounds are adduced for weakening the concept of strictly entropic elasticity as applied to elastomeric materials. The resulting notion of modified entropic elasticity is shown to provide an alternative formulation of a model of rubberlike thermoelasticity proposed by Chadwick (1974). In the second part (Sections 4 and 5) Chadwick's model is generalized by allowing the deformation-dependent part of the internal energy to be a symmetric function of the principal stretches rather than depending only on their product, as in the original development. Consistently with the molecular theory of polymer networks, and with experimental findings, the extended model predicts that the deviatoric stress is not entirely entropic in origin, but arises in part from changes of internal energy. The energetic fraction of the retractive force in an extended cylinder is calculated and discussed in some detail and the paper concludes with a correlation of theoretical results with measurements on specimens of a lightly cross-linked natural rubber.     

Postcolumn derivatization liquid chromatography/mass spectrometry for detection of chemical-weapons-related compounds

Postcolumn derivatization for liquid chromatography/mass spectrometry (LC/MS) analysis was characterized for detection of some compounds related to chemical-weapons (CW) agents using an Atmospheric Pressure Chemical Ionization (APCI) source. The derivatizing reagents were added directly to the LC eluent flow, and the derivatization reactions occurred in the APCI source under typical operating conditions. The compound S-[2-(diisopropylamino)ethyl] methylphosphonothioic acid was methylated using the derivatizing reagent trimethylphenyl ammonium hydroxide (TMPAH). Methylphosphonic acid was doubly derivatized to form dimethyl methylphosphonate, although the signal for the derivatization product was very sensitive to the amount of TMPAH. Arsenic compounds related to the CW agent lewisite, including chlorovinyl arsonous acid and arsenic (III) oxide, were derivatized using 2-mercaptopyridine. The thiol group reacted readily with the arsenic (III) center and provided a significant improvement in sensitivity relative to the underivatized signal using APCI or electrospray ionization. Triethanolamine and ethyl diethanolamine were derivatized with benzoyl chloride, a commonly used LC derivatizing reagent for alcohols, to modify their mass spectra. Postcolumn derivatization using an APCI source gives an alternative for detecting some difficult-to-ionize compounds. It has the limitations that sensitivity was not always improved even though the major mass spectral peaks can be shifted; it is necessary to carefully select the reagent; and some reagents introduced strong interference peaks at specific masses in the spectrum and may suppress the ionization of some derivatized analyte ions. The reagent also produced contamination in the source, which had to be cleaned daily.     

On a class of exact solutions in nonlinear elasticity

A class of exact solutions to the equations of nonlinear elasticity that occur at constant pressure on the boundary of the body and null Cauchy deviatoric stress is presented. Stability analysis shows that the solutions in this class are at best neutrally stable.     

Reaction of nerve agents with phosphate buffer at pH 7

Chemical weapon nerve agents, including isopropyl methylphosphonofluoridate (GB or Sarin), pinacolyl methylphosphonofluoridate (GD or Soman), and S-(2-diisopropylaminoethyl) O-ethyl methylphosphonothioate (VX), are slow to react in aqueous solutions at midrange pH levels. The nerve agent reactivity increases in phosphate buffer at pH 7, relative to distilled water or acetate buffer. Reactions were studied using (31)P NMR. Phosphate causes faster reaction to the corresponding alkyl methylphosphonic acids, and produces a mixed phosphate/phosphonate compound as an intermediate reaction product. GB has the fastest reaction rate, with a bimolecular rate constant of 4.6 × 10(-3) M(-1)s(-1)[PO(4)(3-)]. The molar product branching ratio of GB acid to the pyro product (isopropyl methylphosphonate phosphate anhydride) is 1:1.4, independent of phosphate concentration, and the pyro product continues to react much slower to form GB acid. The pyro product has two doublets in the (31)P NMR spectrum. The rate of reaction for GD is slower than GB, with a rate constant of 1.26 × 10(-3) M(-1)s(-1) [PO(4)(3-)]. The rate for VX is considerably slower, with a rate constant of 1.39 × 10(-5) M(-1)s(-1) [PO(4)(3-)], about 2 orders of magnitude slower than the rate for GD. The rate constant of the reaction of GD with pyrophosphate at pH 8 is 2.04 × 10(-3) min(-1) at a concentration of 0.0145 M. The rate of reaction for diisopropyl fluorophosphate is 2.84 × 10(-3) min(-1) at a concentration of 0.153 M phosphate, a factor of 4 slower than GD and a factor of 15 slower than GB, and there is no detectable pyro product. The half-lives of secondary reaction of the GB pyro product in 0.153 and 0.046 M solution of phosphate are 23.8 and 28.0 h, respectively, which indicates little or no dependence on phosphate.     

Rheology of brown coal-water suspensions

Techniques for measuring the fundamental flow properties of as-mined Victorian brown coal suspensions are developed. Flow properties are presented for Morwell, Yallourn and Loy Yang coals as a function of concentration for fixed particle size distribution. Even at the relatively low solids concentration of 20 to 30 percent by weight, the suspensions exhibit complex non-Newtonian characteristics. Generally at high concentration, the suspensions are thixotropic with a shear rate dependent viscosity and exhibit a yield stress. The inherent thixotropy of the coals can be exploited and it is technically but perhaps not economically feasible to transport the as-mined coals in a pipeline. The power requirement to pump the coals in a pipeline is found to be 10 to 30 times that required to pump black coal in the Black Mesa pipeline in the U.S.A. The differences in the rheological properties of the three coals is related to the surface properties of the coal particle — expressed in terms of carboxylate and inorganic cation content, and to differences in the pore volume of the coals. The flow characteristics of one coal can be converted to that of another simply by varying either the carboxylate or ionic content of the suspension.     

Analysis of vaporous contaminants including low‐volatility analytes permeating textiles at room temperature using headspace solid‐phase microextraction GC–MS

Detection of toxic vapors permeating textiles is an important measure of the efficacy of a protective garment. Here, we demonstrate a method to detect and analyze contaminant vapors as they permeate through cotton textiles. Specifically, we show how this method can be improved upon by the incorporation of solid‐phase microextraction into the sampling process, thereby allowing low‐volatility analytes to be sampled at room temperature without significantly influencing the concentration of the contaminant in the headspace. Furthermore, this technique can be extended to other applications in the development of barrier materials as it lends itself to kinetics as well as direct comparison of materials' total chemical permeation. Copyright © 2015 John Wiley & Sons, Ltd.     

Ring-modified carbon fiber microelectrodes and multi-microelectrode devices

Two new types of modified microelectrodes were used alone and in multi-microelectrode devices. Carbon fibers with diameters of 7.2 μm were modified either by electropolymerization, or by thermal polymerization of a mixture of monomers to give a thick coating of modifier around the cylindrical fiber. The modified fibers were then coated with an insulating layer. The tips of the electrodes were polished perpendicular to the axis of the fiber to give ring-modified disk electrodes. Copolymers of poly(vinylferrocene) and poly(vinylpyridine) with crosslinked polystyrene were used, and demonstrated behavior similar to that for surface modified electrodes, except that the electrodes could be polished to renew the surface. Multi-microelectrode devices were prepared. For example, a ring-modified working electrode, a silver/silver chloride coated practical reference electrode, and a platinum auxiliary electrode were used in a molded epoxy probe in electrolyte solution to give cyclic voltammograms that were similar to those expected for a ring-modified working electrode using traditional reference and auxiliary electrodes.