Win X-ray: a new Monte Carlo program that computes X-ray spectra obtained with a scanning electron microscope.

A new Monte Carlo program, Win X-ray, is presented that predicts X-ray spectra measured with an energy dispersive spectrometer (EDS) attached to a scanning electron microscope (SEM) operating between 10 and 40 keV. All the underlying equations of the Monte Carlo simulation model are included. By simulating X-ray spectra, it is possible to establish the optimum conditions to perform a specific analysis as well as establish detection limits or explore possible peak overlaps. Examples of simulations are also presented to demonstrate the utility of this new program. Although this article concentrates on the simulation of spectra obtained from what are considered conventional thick samples routinely explored by conventional microanalysis techniques, its real power will be in future refinements to address the analysis of sample classifications that include rough surfaces, fine structures, thin films, and inclined surfaces because many of these can be best characterized by Monte Carlo methods. The first step, however, is to develop, refine, and validate a viable Monte Carlo program for simulating spectra from conventional samples.     

Contribution to the use of data processing to establish instrumental multi-element activation analysis as a routine method

A computer program has been worked out for the following requirements: (1) The program is to render a listing of the elements detected, together with their respective concentrations, not just an evaluation of the gamma-spectrum (peak energies and areas). (2) There should be no necessity to intermediate decisions, i.e. execution of the program should be possible by auxiliary personnel. (3) Gamma-ray spectra recorded under widely different conditions should be amenable to evaluation. This implies a large range of variation of the number of channels per peak. (4) In order to have the most extensive capability of executing multi-element analyses instrumentally, it must be possible to evaluate complex spectra with many superpositions. The program involves the fitting of Gaussians. It is shown that this evaluation method gives more precise peak area determinations than the summation method and also yields reasonable results in the case of strong superposition.     

Web-based spectrum analysis software for photon activation analysis

Photon activation analysis (PAA) includes extensive data evaluation that is sensitive to error. In order to save time and minimize human error, a new computer program—photon activation analysis system (PAAS)—was designed, built and implemented using the SQL language and Asp.net technology to analyze PAA data. Given peak information from PAA spectra and aided by a photonuclear data library, the program identifies the product isotopes, recognizes the possible nuclear reactions, and evaluates the concentration of target elements. Uncertainties of concentrations are estimated using standard error propagation techniques. The program can be accessed conveniently anywhere the internet is available and gives a fast and reliable determination of the trace elemental content of samples. Furthermore, this program also allow one to search its database for the information of general photonuclear reactions (e.g. energy lines, line intensities, target and product nuclides, photonuclear reactions, cross sections, natural abundance, etc.) and estimating the activity even before the activation begins. By switching the nuclide libraries, the program could also be expanded to neutron activation analysis and charged particle activation analysis (CPAA) without any difficulty. This program can be a versatile tool for the daily use of the nuclear and radiochemistry laboratories that conduct activation analysis.     

Programmierte gemeinsame Auswertung charakteristischer Banden in den Raman- und Infrarotspektren organischer Substanzen

The presence or absence of skeletal elements and substituents of an “unknown” sample may be determined by a sequence of yes/no decisions, concerning frequency and relative intensity of the characteristic bands in its infrared and Raman spectrum. The decision criteria given as a table may also be used in a graphical form or as a computer program for automatical interpretation. This simultaneous evaluation of both spectra is more reliable than the usual procedure of treating the spectra separately.     

Non-destructive analysis of inorganic impurities in Brazilian coals by epithermal neutron activation

Twenty-two elements were identified and determined in different Brazilian coal samples by an epithermal neutron activation technique developed by the authors. The detection limits and the uncertainties of the results show that the technique can be used for routine analysis. The analysis of the complex gamma-ray spectra and the evaluation of the interfering activities are discussed in detail.     

CreateTarget and Analyze This!: new software assisting imaging mass spectrometry on Bruker Reflex IV and Ultraflex II instruments

Two new software programs are presented which enable matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI-IMS) on Bruker Reflex and Ultraflex instruments. The first program, CreateTarget, creates a high density raster with the dimensions of the tissue section, and converts these parameters into a virtual target plate file that can be imported in the normal mass spectrometer control software. Following automated spectrum acquisition, the second program, Analyze This!, converts the array of spectra into an Analyze 7.5 image format that can be read by image analysis software. These two tools are sufficient to allow IMS, and offer a valid alternative to commercially available software. CreateTarget and Analyze This! are available free of charge.     

The program “MULTINAA” for various standardization methods in neutron activation analysis

A compute program MULTINAA was developed to facilitate the evaluation of NAA data. It is written for the VAX/VMS syste and opeates in the Canberra/ND Genie spectroscopy software environment. MULTIINAA can be appliede to relative,k ₀-, monostandard (modified) and absolute methods, including the fast neutron threshold reaction. For each calculation, the available standardizations can be used individually or mixed. In all the standardization modes MULTINAA fetches the data directly from the -ray spectra and libraries, thus reducing the manual work to a minimum. MULTINAA is flexibkle to meet various situations in NAA practical work. The required neutron flux parameters all the non-relative methods are supplied by an accompanying program MULTIFLUX.     

A computer program for automatic gamma-ray spectra analysis with isotope identification for the purpose of activation analysis

A FORTRAN IV program for a PDP-9 computer, with 16 K storage capacity, is developed performing automatic analysis of complex γ-spectra, taken with Ge(Li) detectors. It searches for full energy peaks and evaluates the peak areas. The program features an automatically performed isotope identification. It is written in such a flexible manner that after reactor irradiation, spectra from samples of any composition can be evaluated for activation analysis.     

New possibilities for least-squares fitting of mössbauer spectra

A non-linear least-squares program for the analysis of Mössbauer spectra is presented. The program is capable of resolving very complex spectra and can be used on a minicomputer system, with regard to both calculation time and memory requirements. The commonly used x²-minimization algorithm was slightly adapted, so as to broaden its working range. All possibilities for fixing or changing parameters are provided. Two new parameter limitation techniques, which greatly reduce the need for manual intervention during the fitting process, are discussed extensively.     

Infia—program for rotational analysis of linear molecule spectra

A software package for spectral rotation analysis is described. The Infia a program features multiple simultaneous views of the analysis data, including a spectrum view with assignment markers; a Loomis–Wood-type view; and lists of assignments, bands, and vibrational states. Automatic combination difference prediction and parameter calculation are included for linear molecules, but the program can also be used to assign spectra for symmetric top molecules. The interactive nature of the program combined with the high level of automation makes possible rapid and reliable analyses even for difficult spectra with many overlapping bands and high peak densities. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 610–622, 1999     

GlycoMiner: a new software tool to elucidate glycopeptide composition

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.     

Dechaos — A program for automatic or interactive analysis of gamma-ray spectra

DECHAOS is a gamma-ray spectral analysis program for personal computers. The program offers two modes of operation, automatic or interactive. The spectra to be analyzed can be acquired using any pulse height analyzer. The program includes routines for energy calibration, peak shape and efficiency calibration. Complex multiplets can be resolved automatically with the peak areas being determined using least-squares fitting techniques. Output tables include all data used in the calculation and peak information. The program is public domain software.     

Mass spectrometric and factor discriminant analysis of complex organic matter from the bacterial culture environment of Bacteroides gingivalis

Curie point evaporation and pyrolysis mass spectrometry were applied to the analysis of samples from cultures of Bacteroides gingivalis, an anaerobic microorganism isolated from the dental sulcus of human patients. Gaseous metabolites were sampled on ferromagnetic wires with an absorbent coating of activated carbon. Smears of bacteria and media after growth were analysed on normal ferromagnetic wires. The mass spectra from analyses at the Curie-point temperatures of 358°C and 510°C were examined with a specially adapted factor discriminant analysis program based on ARTHUR. The bacteria were characterized mainly by their volatile fractious. Mass spectra of the media after growth reflected physiological differences between the strains. The absorbent wire technique proved useful for evaluation of gaseous metabolites. Curie-point evaporation and pyrolysis mass spectrometry was found to be especially useful for preliminary screening of samples of organic matter from the various compartments of the bacterial environment.     

On the calculation of circular dichroism spectra using quantum wave-packet dynamics with an application to molecular dimers

Circular dichroism (CD) spectra are calculated from the Fourier transform of a time-correlation function. The latter can efficiently be evaluated by wave-packet propagation methods. This approach is similar to the time-dependent evaluation of absorption or Raman spectra. As an application, correlation functions and CD spectra for a molecular dimer are determined and compared to the case of absorption.     

Simplification of gamma-ray spectral data by using Fourier transform

A method is proposed to represent gamma-ray response spectra by Fourier series for the purpose of compressing spectral data. The usefulness of the method was confirmed by applying it to a spectral library of a NaI detector. In the method, a response spectrum as a wave is described by superposition of sine (cosine) waves with low frequencies, whose coefficient parameters can be obtained by a Fast Fourier Transform program. The relation between the number of parameters and the fitting error is discussed, and as the result, it is shown that the number of parameters can be reduced to about a half. The merits and features are presented in practical application of the method to the analysis of gamma-ray spectra.     

EDXTOOLS — Computer Programmes for the Determination of Critical EDX Spectrometer Parameters

 Quality assurance according to ISO or EN norms entails a periodical check of critical instrumental parameters. Not yet all commercial software purchased with instruments supports the related measurements and their fast evaluation. EDXTOOLS consist of a programme library which complements the existing software for electron excited energy dispersive X-ray spectrometry (EDS) in this respect. EDXTOOLS can be used to check the detection efficiency by the evaluation of the L/K intensity ratio in a copper or nickel spectrum or by the calculation of the thickness of absorbing detector layers from experiments, which can be performed on any scanning electron microscope. Moreover, measured spectra can be modified by the transmission curve of absorbing media to estimate their influence on the result of quantitative analysis. EDXTOOLS allow the determination of the signal to background ratio from an Fe-55 spectrum and the fitting of measured FWHM’s of K-lines to find the resolution curve . They are completed by the possibility of calculating EDX spectra for the K-lines of light elements and to compare the resulting spectra for different formulae, physical data tables, and detector parameters chosen for the calculation. EDXTOOLS are written in MATLAB?, a wide spread interpreter language. This has the advantage that the programmes are readable text files. A user can check each computational step and modify it. The installation of MATLAB? and its optimization toolbox is necessary to work with EDXTOOLS.     

Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument

The automated use of a matrix-assisted laser desorption ionization (MALDI) mass spectrometer (MS) is described for image analysis of samples through implementation of new software for instrument control, data acquisition, and data analysis. The software permits automated acquisition of MS MALDI spectra to form an ordered data array and contains display features to provide images at one or more mass-to-charge ratio values. The technique can be used to scan tissue samples, blotted samples, gels, or other sample surfaces where the image analysis of that sample is required. The program achieves a time of typically 1 s per image point, permitting an analysis made up of large numbers of points with high spatial resolution up to 850 dpi. The features of the software are demonstrated in this paper with samples of printed images, where visible images can be compared to those obtained by mass spectrometry. Quantitative aspects are introduced by analyzing a series of sample spots containing different amounts of several proteins.     

Computerunterstützte Identifizierung von Isotopenmustern in niederaufgelösten Massenspektren

The identification of isotopic patterns in low resolution mass spectra with the aid of a computer program is described. Those masses in the mass spectra which coincide with the isotopic patterns are printed out. As additional information, a criterion is given indicating the quality of correlation between the measured and calculated isotopic pattern. The program is written as a subroutine in FORTRAN IV and can be executed by small computers too.     

NICOLET定量分析程序及ATR技术的应用研究——研究柞丝绸在紫外光辐照下结构的变化

采用ATR技术测定柞丝绸随紫外光辐照时间的增加,某些结构特征吸收强度的变化规律,研究了柞丝绸经辐照后结构的改变及泛黄的机理。采用特征峰高比值与参比峰高比值的办法观测强度的改变。峰高值则是应用改进的NICOLET定量分析程序(宏指令方式)计算的,改进后的程序操作简便,运算快、能连续地调出已存入定量程序盘中的光谱图,自动算出吸收强度并打印结果。