Increased identification of peptides by enhanced data processing of high-resolution MALDI TOF/TOF mass spectra prior to database searching

This paper presents application of sequential enhanced data processing procedures to high-resolution tandem mass spectra for identification of peptides using the Mascot database search algorithm. A strategy for (1) selection of fragment ion peaks from MS/MS spectra, (2) utilization of improved mass accuracy of the precursor ions, and (3) wavelet denoising of the mass spectra prior to fragment ion selection have been developed. The number of peptide identifications obtained using the enhanced processing was then compared with that obtained using software provided by the instrument manufacturer. Approximately 9000 MS/MS spectra acquired by the Applied Biosystems 4700 TOF/TOF MS instrument were used as a model data set. After application of the new processing, an increase of 33% unique peptides and 22% protein identifications with at least two unique peptides were found. The influence of the processing on the percentage of false positives, estimated by searching against a randomized database, was estimated to increase false positive identifications from 2.7 to 3.9%, which was still below the 5% error rate specified in the Mascot search. These data processing approaches increase the amount of information that can be extracted from LC-MS analysis without the necessity of additional experiments.     

Etude cristallographique du systeme FeSSc2S3 preparations et structures de FeSc2S4 et Fe0.85Sc2.10S4

The crystal structures of FeSc₂S₄ and Fe_0.85Sc_2.10S₄ have been determined by three dimensional X-ray diffraction. The cubic cells, space group Fd3m, have lattice constants $\text{a}\text{= 10,501}\text{A}\text{?}$ for FeSc₂S₄ and $\text{a}\text{= 10,444}\text{A}\text{?}$ for Fe_0.85Sc_2.10S₄. Iron is divalent and scandium trivalent. FeSc₂S₄ is a direct spinel structure, Fe_0.85Sc_2.10S₄ is near a spinel structure. Only 0,5 iron atom is on every 8a position; 0,175 Fe and 1,05 Sc lie on octahedral 16d and 16c site.     

Accurate wavelength measurements of a putative standard for near-infrared diffuse reflection spectrometry

The diffuse reflection (DR) spectrum of a sample consisting of a mixture of rare earth oxides and talc was measured at 2 cm-1 resolution, using five different accessories installed on five different Fourier transform near-infrared (FT-NIR) spectrometers from four manufacturers. Peak positions for 37 peaks were determined using two peak-picking algorithms: center-of-mass and polynomial fitting. The wavenumber of the band center reported by either of these techniques was sensitive to the slope of the baseline, and so the baseline of the spectra was corrected using either a polynomial fit or conversion to the second derivative. Significantly different results were obtained with one combination of spectrometer and accessory than the others. Apparently, the beam path through the interferometer and DR accessory was different for this accessory than for any of the other measurements, causing a severe degradation of the resolution. Spectra measured on this instrument were removed as outliers. For measurements made on FT-NIR spectrometers, it is shown that it is important to check the resolution at which the spectrum has been measured using lines in the vibration-rotation spectrum of atmospheric water vapor and to specify the peak-picking and baseline-correction algorithms that are used to process the measured spectra. The variance between the results given by the four different methods of peak-picking and baseline correction was substantially larger than the variance between the remaining five measurements. Certain bands were found to be more suitable than others for use as wavelength standards. A band at 5943.13 cm-1 (1682.62 nm) was found to be the most stable band between the four methods and the six measurements. A band at 5177.04 cm-1 (1931.61 nm) has the highest precision between different measurements when polynomial baseline correction and polynomial peak-picking algorithms are used.     

A microfluidic electrocapture device in sample preparation for protein analysis by MALDI mass spectrometry

The design and operation of a microfluidic device for sample preparation in MALDI mass spectrometry of peptides and proteins is described. It is particularly useful for proteomics applications and for mass determination of proteins in salt- and detergent-containing solutions. The system consists of a flow channel with two conductive areas or electrical junctions where proteins and peptides are retained by means of an electric field. The microfluidic device is made of PEEK tubing, and the junctions are covered with a conductive polymeric membrane. A syringe pump connected to the device produces a flow stream, and injection of sample is carried out manually via hydrodynamic pressure. Proteolytic peptides and intact proteins in salt- and detergent-containing acidic media were captured at the cathode junction followed by exchange of the original solution to a solvent suitable for subsequent mass spectrometry. Using this principle, a significant desalting effect was obtained for tryptic peptides in mass-mapping experiments. Protein sequence coverages were high (up to 40%) at subpicomole levels with results better than those obtained using reversed-phase solid-phase extraction. In contrast to the latter technique, the microfluidic device has the capacity to efficiently remove detergents such as CHAPS before peptide mapping and protein analysis.     

Effect of different polypropylenes and compatibilizers on the rheological,mechanical and morphological properties of nylon 6/PP blends

In this work, the rheological, mechanical and morphological properties of nylon 6/polypropylene compatibilized blends were investigated. Two types of polypropylene were used. One with MFI of 40 g/10 min (PP H103) and the other with MFI of 3.5 g/10 min (PP H503). The compatibilizers used were polypropylene grafted with 6% of acrylic acid (PPgAA) and polypropylene grafted with 1% of maleic anhydride (PPgMA). The blends composition was 80/20 (wt%) for the PA6/PP binary blends and 80/10/10(wt%) for the nylon 6/PPgAA/polypropylene and nylon 6/PPgMA/polypropylene ternary blends. Torque rheometry analysis showed that when PPgAA and PPgMA were added to nylon 6/polypropylene blends, there was an increase in the torque, indicating that reactive compatibilization has occurred. There is no influence of the polypropylene MFI on the mechanical properties of the uncompatibilized and compatibilized blends. The impact strength of the blends containing PPgMA were greater than those of the blends containing PPgAA. The blends containing PPgAA are unstable. SEM analysis showed that PPgMA improves considerably the adhesion between PA6/PP phases, leading to good mechanical properties.     

Impact of a satellite-derived leaf area index monthly climatology in a global numerical weather prediction model

The leaf area index (LAI), defined as the one-sided green leaf area per unit ground area, is used in many numerical weather prediction (NWP) models as an indicator of the vegetation development state, which is of paramount importance to characterize land evaporation, photosynthesis, and carbon-uptake processes. LAI is often simply represented by lookup tables, dependent on the vegetation type and seasons. However, global LAI datasets derived from remote sensing observations have more recently become available. These products are based on sensors such as the Advanced Very High Resolution Radiometer (AVHRR) or the Moderate Resolution Imaging Spectroradiometer (MODIS), onboard polar orbiting satellites that can cover the entire globe within typically 3 days and with a spatial resolution of the order of 1 km.

We examine the meteorological impact of satellite-derived LAI products on near-surface air temperature and humidity, which comes both from the stomatal transpiration of leaves and from the intercepted water on the surface of leaves, re-evaporating into the atmosphere.

Two distinct monthly LAI climatology datasets derived respectively from AVHRR and MODIS sensors are tested. A set of forecasts and data assimilation experiments with the integrated forecasting system of the European Centre for Medium-range Weather Forecasts is performed with the monthly LAI climatology datasets as opposed to a vegetation-dependent constant LAI. The monthly LAI is shown to improve the forecasts of near-surface (screen-level) air temperature and relative humidity through its effect on evapotranspiration, with the largest impact obtained over needleleaf forests, crops, and grassland. At longer time-scales, the introduction of the monthly LAI is shown to have a positive impact on the model climate particularly during the boreal spring, where the LAI climatology has a large seasonal cycle.     

Multiple Compression of Moist Spherical Elastic‐Plastic Zeolite 4A Granules

The compression, deformation and material behavior of moist spherical elastic‐plastic zeolite 4A granules under multiple stressing conditions at unique and random contacts were experimentally studied with the help of uniaxial diametrical compression tests. The force‐displacement curves were approximated and the coefficient of restitution was determined using appropriate mechanical models from literature. The phenomenon of cyclic hardening was studied and the critical number of cycles required to reach fracture was determined. Furthermore, the influence of particle size and moisture content on the material behavior at cyclic loading, the coefficient of restitution, and the critical number of cycles required to reach fracture were investigated.     

Influence of solvent and temperature on extraction of phenolic compounds from grape seed,antioxidant activity and colour of extract

This study was aimed to investigate the influence of solvent (water and ethanol in concentration: 50%, 70% and 96%) and extraction temperature (25–80) °C on polyphenols extraction of grape seed (Vitis vinifera L. cv. “Frankovka”) cultivated in Eastern Croatia. The best results were reached using 50% ethanol at 80 °C. The most abundant individual polyphenolic compound was catechin which makes the average of 45.11% of the total phenolic content followed by epicatechin (34.45%), procyanidin B₂ (12.90%), gallic acid (5.34%), gallocatechin (1.58%), epicatechin gallate (1.01%). The antioxidant activity of extracts was determined by DPPH‐method and it was highly dependent on extraction solvent and temperature. The total extractable proanthocyanidins content of extract had the highest positive correlation (r = 0.994) with antioxidant activity, which indicated that these compounds might be the most important antioxidant in examined grape seed extracts. Relationship between phenolic content and colour of extracts was observed.     

Fast radix-2 division with quotient-digit prediction

An implementation of a radix-2 division unit is presented that uses prediction of the quotient digit. This prediction allows the concurrent computation of the quotient digit and the partial remainder. To achieve a simple quotient-digit selection, resulting in a step time roughly half of that of SRT division (without prediction), a simple estimate of the partial remainder is used, which requires that the divisor be scaled close to unity. This prescaling is simple to implement and increases the execution time by two cycles. We estimate a speed-up of 1.5 with respect to SRT division with redundant remainders.