Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection

We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point and molecular weight, as well as chemical modifications or number of missed cleavages of a protein, the program performs a fully automated identification of the protein. The first step is a peak detection algorithm, which allows precise and fast determination of peptide masses, even if the peaks are of low intensity or they overlap. In the second step the masses and environmental data are used by the identification algorithm to search in protein sequence databases (SWISS-PROT and/or TrEMBL) for protein entries that match the input data. Consequently, a list of candidate proteins is selected from the database, and a score calculation provides a ranking according to the quality of the match. To define the most discriminating scoring calculation we analyzed the respective role of each parameter in two directions. The first one is based on filtering and exploratory effects, while the second direction focuses on the levels where the parameters intervene in the identification process. Thus, according to our analysis, all input parameters contribute to the score, however with different weights. Since it is difficult to estimate the weights in advance, they have been computed with a generic algorithm, using a training set of 91 protein spectra with their environmental data. We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs.     

Product of hyperfunctions on the circle

Let φ and ψ be two hyperfunctions on the circle which have disjoint support. We interpret in terms of Fourier coefficients the fact that their product, defined in the sense of sheaf theory, vanishes.     

Preparation and characterization of a suite of ephedra-containing standard reference materials

The National Institute of Standards and Technology, the U.S. Food and Drug Administration, Center for Drug Evaluation and Research and Center for Food Safety and Applied Nutrition, and the National Institutes of Health, Office of Dietary Supplements, are collaborating to produce a series of Standard Reference Materials (SRMs) for dietary supplements. A suite of ephedra materials is the first in the series, and this paper describes the acquisition, preparation, and value assignment of these materials: SRMs 3240 Ephedra sinica Stapf Aerial Parts, 3241 E. sinica Stapf Native Extract, 3242 E. sinica Stapf Commercial Extract, 3243 Ephedra-Containing Solid Oral Dosage Form, and 3244 Ephedra-Containing Protein Powder. Values are assigned for ephedrine alkaloids and toxic elements in all 5 materials. Values are assigned for other analytes (e.g., caffeine, nutrient elements, proximates, etc.) in some of the materials, as appropriate. Materials in this suite of SRMs are intended for use as primary control materials when values are assigned to in-house (secondary) control materials and for validation of analytical methods for the measurement of alkaloids, toxic elements, and, in the case of SRM 3244, nutrients in similar materials.     

EFFECTS OF UV IRRADIATION ON A LIVING SKIN EQUIVALENT

Abstract— The Living Skin Equivalent (LSE™) is an organotypic coculture composed of human dermal fibroblasts interspersed in a collagen-containing matrix and overlaid with human keratinocytes forming a stratified epidermis. The LSE has a dry, air-exposed epidermal surface suitable for the application of oils, creams and emulsions. These features suggested its feasibility as an in vitro skin model for studying the protective effects of sunscreens. Using the thiazolyl blue (MTT) conversion assay as a measure of mitochondrial function, the extent of cytotoxicity induced by various doses of UV-R (280–400 nm) or UV-A (320–400 nm) was evaluated in the LSE. The doses of UV radiation that caused 50% reductions in MTT conversion (UV-R₅₀ or UV-A₅₀) in different lots of LSE were 0.053 ± 0.021 J/cm² (n = 29) and 11.6 ± 4.9 J/cm² (n = 17) for UV-R and UV-A, respectively. The protective effects of an 8% homosylate standard and of five UV-A sunscreens, topically applied to the LSE, were determined and compared with their reported protection factors in human skin. Morphological changes and the release of proinflammatory mediators (interleukin-1-α, tumor necrosis factor-α and prostaglandin E2) implicated in UV-induced erythema were also demonstrated in the LSE exposed to UV-A or UV-B. The data suggest that the LSE can be used for studying the effects of U V radiation on skin and may have utility for assessing the efficacy of certain sunscreens against UV-B and UV-A.     

The nature of alkanethiol self-assembled monolayer adsorption on sputtered gold substrates

A detailed study of the self-assembly and coverage by 1-nonanethiol of sputtered Au surfaces using molecular resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) is presented. The monolayer self-assembles on a smooth Au surface composed predominantly of [111] oriented grains. The domains of the alkanethiol monolayer are observed with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. STM imaging shows that the (4 x 2) superlattice structure is observed as a (3 x 2) structure when imaged under noncontact AFM conditions. The 1-nonanethiol molecules reside in the threefold hollow sites of the Au[111] lattice and aligned along its [112] lattice vectors. The self-assembled monolayer (SAM) contains many nonuniformities such as pinholes, domain boundaries, and monatomic depressions which are present in the Au surface prior to SAM adsorption. The detailed observations demonstrate limitations to the application of 1-nonanethiol as a resist in atomic nanolithography experiments to feature sizes of approximately 20 nm.     

Determination of 8[(3S)-3-amino-1-pyrrolidinyl]-1-cyclopropyl-7-fluoro-9-methyl-4-oxo-4H-quinolizine-3-carboxylic acid hydrochloride and related substances by high performance liquid chromatography

Summary The purity of the investigational antibacterial Abbott-086719.1 (I) which is 8[(3S)-3-amino-1-pyrrolidinyl]-1-cyclopropyl-7-fluoro-9-methyl-4-oxo-4H-quinolizine-3-carboxylic acid hydrochloride is determined using gradient elution HPLC. The chromatographic separation was optimized and the chromatographic parameters critical to separation are discussed in detail. Most acceptable separations were achieved using an Alltima C18 column (5 μm) measuring 4.6 mm I.D. × 15 cm with 0.01M–0.03M citrate eluents which were modified with acetonitrile or with mixtures of acetonitrile and methanol. Related substances in I were determinable to 0.05 %. Repeatability (RSD values) for determining related substances at levels of 0.50 to 0.06 % ranged from ±1.9 to ±10 %. Determinations of I in 5 % dextrose in water and in hydroxypropyl methylcellulose were made using the same column and a simple isocratic system. The determination of I was stability indicating with precision (RSD values) of ±0.5 % to ±2.0 % and good agreement with theory for formulations containing I at 1.0 to 95 mg/mL concentrations. Recoveries of I from the vehicles were quantitative and linearity of the detector response of I was demonstrated to at least 0.10 mg/mL.     

Additional J/\Psi suppression from high density effects

At high energies the saturation effects associated to the high parton density should modify the behavior of the observables in proton-nucleus and nucleus-nucleus scattering. In this paper we investigate the saturation effects in the nuclear production and estimate the modifications in the energy dependence of the cross section as well as in the length of the nuclear medium. In particular, we calculate the ratio of to Drell-Yan cross sections and show that it is strongly modified if the high density effects are included. Moreover, our results are compared with the data from the NA50 Collaboration and predictions for the RHIC and LHC kinematic regions are presented. We predict an additional suppression associated to the high density effects.Received: 10 October 2003, Revised: 23 December 2003, Published online: 25 February 2004