Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

We describe the application of capillary liquid chromatography (LC) time-of-flight (TOF) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. Previously (Lipton et al., Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049) the peptides from a series of growth conditions of Deinococcus radiodurans have been characterized using capillary LC MS/MS and accurate mass measurements which are captured as an accurate mass and time (AMT) tag database. Using this AMT tag database, detected peptides can be assigned using measurements obtained on a TOF due to the additional use of elution time data as a constraint. When peptide matches are obtained using AMT tags (i.e., using both constraints) unique matches of a mass spectral peak occurs 88% of the time. Not only are AMT tag matches unique in most cases, the coverage of the proteome is high; approximately 3500 unique peptide AMT tags are found on average per capillary LC run. From the results of the AMT tag database search, approximately 900 ORFs detected using LC-TOFMS, with approximately 500 ORFs covered by at least two AMT tags. These results indicate that AMT database searches with modest mass and elution time criteria can provide proteomic information for approximately one thousand proteins in a single run of <3 h. The advantage of this method over using MS/MS based techniques is the large number of identifications that occur in a single experiment as well as the basis for improved quantitation. For MS/MS experiments, the number of peptide identifications is severely restricted because of the time required to dissociate the peptides individually. These results demonstrate the utility of the AMT tag approach using capillary LC-TOF MS instruments, and also show that AMT tags developed using other instrumentation can be effectively utilized.     

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.     

Thermal decomposition of HO2NO2 (peroxynitric acid, PNA): rate coefficient and determination of the enthalpy of formation

Rate coefficients for the gas-phase thermal decomposition of HO(2)NO(2) (peroxynitric acid, PNA) are reported at temperatures between 331 and 350 K at total pressures of 25 and 50 Torr of N(2). Rate coefficients were determined by measuring the steady-state OH concentration in a mixture of known concentrations of HO(2)NO(2) and NO. The measured thermal decomposition rate coefficients k(-)(1)(T,P) are used in combination with previously published rate coefficient data for the HO(2)NO(2) formation reaction to yield a standard enthalpy for reaction 1 of Delta(r)H degrees (298K) = -24.0 +/- 0.5 kcal mol(-1) (uncertainties are 2sigma values and include estimated systematic errors). A HO(2)NO(2) standard heat of formation, Delta(f)H degrees (298K)(HO(2)NO(2)), of -12.6 +/- 1.0 kcal mol(-1) was calculated from this value. Some of the previously reported data on the thermal decomposition of HO(2)NO(2) have been reanalyzed and shown to be in good agreement with our reported value.     

Nitrosyl derivatives of tricobaltcarbon clusters

The nitrosyl clusters PPN[YCCo₃(CO)₇(NO)] (Y = Me, Ph, COOH, (C₅H₅)Fe(C₅H₄)) have been prepared in high yield from the reaction of YCCo₃(CO)₉ with PPN(NO₂) in THF, acetone or acetonitrile. Spectroscopic evidence indicates the structure of the nitrosyl anions is derived from that of YCCo₃(CO)₉ by the replacement of two CO ligands on one cobalt atom by a linear, terminal nitrosyl group. The nitrosyl metallates are extremely sensitive to oxidation and attempts to protonate the anions resulted in the reformation of the parent YCCo₃(CO)₉, molecules. The oxidative electrochemistry of the ferrocene complex, PPN[(C₅H₅)Fe(C₅H₄CCo₃(CO)₇(NO)] is also discussed.     

Parameterization and evaluation of a flexible water model

The thermodynamic, dielectric, and dynamic properties of a newly parameterized flexible water model are studied using molecular dynamics simulations. The potential function developed is based on the popular simple point charge (SPC) rigid model with the addition of appropriate harmonic and anharmonic energy terms for stretching and bending. Care was taken to account for the self-polarization and gas-phase monomer energy corrections during the parameterization, which have typically been ignored in past studies. The results indicate that an increased Lennard-Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ? O radial distribution function of water at 298 K and 1 atm. Analysis of the power spectrum derived from the H-velocity autocorrelation function allowed the water potential to be evaluated further and refined by adjusting the valence forces to fit the vibrational frequencies of the gas and liquid. Once a consistent set of parameters was determined, the static dielectric properties of the water model were calculated at two temperatures using the reaction field method to treat long-range forces and correlations. The dielectric constant of 75 ± 7 calculated at 300 K is in good agreement with the experimental value of 78.5. The Kirkwood g factor was also examined for temperature dependence and showed the correct increasing behavior with decreasing T. As a final check of the water potential, the free energies of solvation of a flexible water molecule and neon were predicted using thermodynamic perturbation methods. The calculated solvation energies of ?7.0 ± 0.8 for water and 2.7 ± 0.7 for neon are both consistent with the experimental values of ?6.3 and 2.7 kcal/mol. Comparisons are made throughout the study with the results of previous rigid and flexible model simulations. © 1995 by John Wiley & Sons, Inc.     

Future of biological aerosol detection

Biological aerosol detection in real time is an urgent civilian and military requirement. Such detection capability will be useful in environmental monitoring, for example, in gathering information in perceived hazardous areas such as housing developments downwind of sewage treatment plants. To be truly functional, the instrument has to operate continuously, 24 h a day and 7 days a week with minimal maintenance and few false alarms. A novel concept is proposed. The system employs a rapid front-end warning/alarming mechanism based on optical technologies that provides useful information for protection decision makers. This is connected to a sample collector that feeds a slower back-end liquid chemistry system that provides analytical results to the medical personnel to assist in prophylaxis and therapy decisions. Experience gained from measuring fluorescence signals of single bacterial spores under flow cytometry (FCM) using UV excitation at 340-360 nm, was applied to concept testing of a prototype instrument, built to do the same for aerosols. This machine was capable of resolving particle size as well as fluorescence intensity of each particle under laboratory and field conditions; it was called the fluorescent aerodynamic particle sizer (FLAPS). This paper describes practical aspects of measuring biological aerosols when the results must be compared to reference samplers that provide culturable or “live” data. Treatment of particle size and fluorescence information is discussed with respect to FLAPS and reference data fidelity. Along with an objective method to evaluate FLAPS data correlation to reference data, an approach for determining limit of detection in the field is discussed. In addressing the back-end detector chemistry, we have prioritized a number of important biological characteristics that must be given to a clinician to help in prophylaxis and therapy decisions. A series of biochemical measurements are proposed to define the threat of a sample and different solutions are given to implement these tests. We predict that the future for biological detection looks promising for fluorescence in situ hybridization (FISH) techniques in identifying microorganisms. A conceptual instrument based on merging FCM and microchip-based analysis is described.     

Comparative assessment of solid-phase extraction clean-up procedures, GC columns and perfluoroacylation reagents for determination of type B trichothecenes in wheat by GC-ECD

Various solid-phase extraction (SPE) procedures for clean-up, two perfluoroacylation reagents (pentafluoropropionic anhydride (PFPA) and heptafluorobutyric anhydride (HFBA)) and two chromatographic columns (HP-1701 and HP-5) have been assessed comparatively to achieve the determination of type B trichothecenes (deoxynivalenol (DON), nivalenol (NIV), 3- and 15-acetyldeoxynivalenol (3- and 15-ADON)) in wheat grain by gas chromatography (GC)-electron-capture detection (ECD). Spiked wheat samples were extracted with acetonitrile-water (84:16, v/v). Tested SPE procedures were MycoSep 225 column, Florisil and different cartridges prepared in the laboratory with mixtures of various sorbents like alumina, Celite 545, C18, silica and charcoal. We propose MycoSep 225 column, and cartridges made with alumina-charcoal-silica and alumina-charcoal-C18 silica mixtures as clean-up procedures on the basis of recovery values (89.6, 87.3 and 86.1% for deoxynivalenol, respectively, at 1.0 mg/kg spiking level). The two last procedures are less expensive. Pentafluoropropionic anhydride was more stable against moisture and less expensive, while recoveries were similar to those obtained with heptafluorobutyric anhydride. HP-1701 column can separate 3- and 15-acetyldeoxynivalenol derivatives while HP-5 cannot, although this last column provided lower bleed and better sensitivity.     

Determination of azolic fungicides in wine by solid-phase extraction and high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry

A method for simultaneous analysis of eight azolic fungicides: cyproconazole, diniconazole, tetraconazole, thiabendazole, flusilazole, triadimenol, triadimefon, carbendazim and the degradation product 2-aminobenzimidazole in wine samples is described. The compounds are isolated from the samples and concentrated by solid-phase extraction on polymeric cartridges. The determination is carried out by liquid chromatography with mass spectrometric detection in positive ionization and selected ion monitoring modes. The influence of parameters such as the mobile phase composition, column temperature, corona current and fragmentor voltage is studied and the proposed method is validated. Recoveries of the nine compounds added to wine samples range from 83 to 109%, with relative standard deviations below 10%. The quantitation limits are between 9 and 31 microg/L. Real wine samples are analyzed by the proposed method, also.