A Check Total for Validating Standardless and Normalised EDX Analysis at Low kV

Overlay of fitted peaks on spectra or goodness of fit indices do not always reveal element misidentifications and cannot confirm accuracy of composition, particularly at low kV where there are often strong peak interferences. The conventional Analysis Total requires beam current stability and measurement of at least one standard and is not available if results have to be normalised. If an accurate method is available to predict theoretical spectra, consistency of the peak and background content in spectra can be used to validate analyses even when results are normalised. A new Check Total is proposed that has properties similar to the conventional Analysis Total and can be used to validate a normalised set of concentrations. Check Total is calculated from the ratio of (total area of peaks/total background area) in observed and theoretically simulated spectra. If peak to total background can be predicted with an accuracy of 10% standard deviation, Check Total is useful for alerting the analyst to missing peaks, deconvolution errors at low kV and specimen charging. More accurate spectrum synthesis would make Check Total also sensitive to small errors in microscope kV calibration.     

Quantitative Auger electron spectroscopic analysis of carbides,nitrides and carbonitrides

A novel method for the quantitative evaluation of Auger electron spectra based on peak areas is presented. Sample and reference spectra in integral mode are filtered by an area conserving digital filter. This transforms the peak shapes influenced by chemical effects into standard peak shapes. After filtering a linear combination of reference spectra, differentiated spectra accounting for peak shifts and some low order polynomials to account for variations in the background is fitted to the sample spectrum by a least squares method. The need to approximate the spectrum of the secondary electron background explicitly for direct calculation of peak areas is thus eliminated. Filters of different widths are applied to reduce errors by chemical effects. The composition of the sample is computed from the composition of the reference samples and the coefficients obtained from the fit.To demonstrate the validity of this technique it has been applied to both, Gaussian model peaks and spectra of titanium carbonitrides. A further test on an alloy series is under investigation. The results show that the method works as predicted and gives accurate quantification.     

Probability for Type I errors in gamma-ray spectrometric measurements of drinking water samples

In gamma-ray spectra, acquired in the absence of the sample, peaks occur which belong to the spectrometer background. When samples are measured, which contain radionuclides that appear in the background also and have activities near the detection level, the background contributes substantially to the peak areas. In the extreme case, when the contribution of the sample is much smaller than the contribution of the background, the peak area attributed to the radionuclide within a sample has the same probability of being positive or negative. Therefore, to interpret the results obtained from measurements of low-activity samples, the performance of the spectrum analysis procedure near the detection level must be known. To test the performance of the spectrum analysis procedure at low activities, the spectrometer background spectra were analyzed as if they had been water samples, prepared as dry residue obtained by evaporation of 50 L of water. The probabilities for false positives together with their decision thresholds are given for radionuclides appearing in the background spectra. For some of the radionuclides that do not appear in the background spectra, probabilities for false detection are given as well.     

Teabags: Computer programs for instrumental neutron activation analysis

Described is a series of INAA data reduction programs collectively known as TEABAGS (Trace Element Analysis By Automated Gamma-ray Spectrometry). The programs are written in FORTRAN and run on a Nuclear Data ND-6620 computer system, but should be adaptable to any medium-sized minicomputer. They are designed to monitor the status of all spectra obtained from samples and comparison standards irradiated together and to do all pending calculations without operator intervention. Major emphasis is placed on finding all peaks in the spectrum, properly identifying all nuclides present and all contributors to each peak, determining accurate estimates of the background continua under peaks, and producing realistic uncertainties on peak areas and final abundances.     

Determination in gas chromatography—mass spectrometry data of mass spectra free of background and neighboring substance contributions

The determination in a g.c.—m.s. data matrix by singular value analysis and least squares of the mass spectra of the substances present and of their corresponding resolved g.c. peak profiles has been supplemented by the determination of a background for each mass, assumed to be constant over 10–12 contiguous scans. The norm for the g.c. peaks has been changed to a maximum of one so that the mass spectral intensities are proportional to the true ion currents at the respective g.c. peak maxima. Complete resolved spectra are computed by using all measured masses. Examples are given of close resolutions (less than one scan separation) and multiple overlap resolution (8 overlapping substances). The method is compared with other published clean-up methods.     

Detailed peak fitting analysis of the Zn 2p photoemission spectrum for metallic films and its initial oxidation stages

The metallic Zn 2p photoemission spectra hold a complex background that requires individual assignment of Shirley background for each peak comprising the spectra. For this reason, a close fit requires the use of the Shirley‐Vegh‐Salvi‐Castle background‐type under the active background approach. We found that the intensity of the plasmon peaks and their associated background cannot be described through existing energy loss (intrinsic and extrinsic) formalisms. We also analyzed the Zn 2p and O 1s spectra for the initial stages of oxide formation at various oxygen exposures. We found that the composition of the oxide layer is ZnO_1.00±0.10 for all exposures, suggesting that our assessment of the primary function of metallic Zn is accurate and can be employed for quantitative studies. We also present a set of parameters to accurately fit and resolve the metallic and oxide Zn 2p peaks.     

Experimental derivation of Auger transition probabilities from X-ray excited Auger electron spectra in XPS

Auger transition probabilities were experimentally derived from dominant XAES and related XPS peaks observed in XPS spectra. Some values of derived probabilities were higher than 1, because of addition or subtraction of background signal from the XAES or/and XPS peak intensity. However, the probabilities obtained are recognized to be useful for practical quantification by XAES and AES.     

Raman spectroscopy of aminated and ultrafine 1,3,5-triamino-2,4,6-trinitrobenzene and PBX 9502 as a function of pressing pressure

The Raman spectra of emulsion aminated, wet aminated, dry aminated, and ultrafine 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and PBX 9502 explosive powders are measured in a pellet die at pressures from ambient to 180 MPa with a 632.8 nm helium-neon laser. Raman peak frequencies and line widths are calculated from accurately calibrated spectra. The spectral region below 400 cm(-1), where the pressure shifts of the Raman peaks are larger, is emphasized. The most salient effect of pressing is an approximate permanent doubling of the line width of the ambient 56.9 cm(-1) peak for all TATB types. This peak is also much wider in the ultrafine TATB powder than in the other TATB powders, which indicates that the process of creating the ultrafine powder also creates changes in the TATB crystals. The peaks in the spectra of the aminated TATBs and PBX 9502 are very similar, but differences in the fluorescence backgrounds correlate with the expected crystalline purity differences from the different amination processes. The peak frequencies versus pressure for several of the more intense low-frequency peaks can be fit well to linear functions between 40 and 180 MPa. The pressure slopes of the emulsion aminated peaks are consistently larger than the slopes of the other powders. Grüneisen parameters calculated from peaks below 100 cm(-1) are scattered, which is probably caused by the anisotropy of TATB crystals and different types of intermolecular bonds.     

Efficiency of visual peak detection in X‐ray photoelectron spectra

We report initial results of a VAMAS/TWA2 project to evaluate procedures for automated peak detection in X‐ray photoelectron spectra. As a reference for investigations of the efficiency of automated peak‐detection software, we report the efficiency of visual peak detection in three test spectra. It was found that (i) characteristics of analysts are grouped into four categories using principal component analysis (PCA); the first participant group to detect large numbers of peaks for the three test spectra, the second one to detect small numbers of peaks for them, the third one to detect similar numbers of peaks, and the fourth one to detect a relatively large number of peaks for one of them and small numbers for two of them, (ii) scattering of detected peak numbers seems to depend on detection of medium‐intensity peaks because of participants' subjectivity or ambivalence for judgment of intensity, and (iii) the peaks that are detected by the analysts with a detectability more than 75% almost correspond to the peak signal‐to‐noise(S/N) ratio of more than 10 in logarithmic expression. Copyright © 2008 John Wiley & Sons, Ltd.     

Computerized separation of chromatographically unresolved peaks

A computerized peak deconvolution software and mass spectra were successfully applied for the deconvolution of overlapped peak cluster in the chromatogram obtained separating the complex mixture of pesticides by retention time locking gas chromatography-mass spectroscopy. The method based on the unique fragment ions in the spectra can be used for deconvolution of peak clusters if mass spectra of overlapped peaks differ. This method allows determining actual retention times of overlapped peaks. Peak areas found by this method however, cannot be used naturally for the quantitative purposes as the abundance of fragment ions used for this deconvolution procedure can dramatically differ. Computer assisted deconvolution of peaks in the peak clusters gives more realistic peak area ratios as at this method it is supposed equal response for all peaks overlapped in a cluster.     

果菠萝蛋白酶在有机溶剂微扰时的分子折叠与活力变化的研究

本文用荧光、紫外差示及CD光谱研究果菠萝蛋白酶经甲醇、乙醇、乙二醇微扰后的构象与活力变化情况.酶的荧光强度随有机溶剂浓度增大而增强,表明Tyr、Trp微环境发生明显变化。232nm和285nm处出现紫外差吸收正峰。前峰与酶分于折叠的变化有关,而后峰与Tyr、Trp微环境的变化相关.甲醇、乙醇微扰后,天然酶的208nm和225nmCD双负峰逐渐加强,而乙二醇微扰后,225nm负峰加强。208nm负峰减弱并红移直至完全消失,说明酶分子完全伸展.     

Automatic poisson peak harvesting for high throughput protein identification

High throughput identification of proteins by peptide mass fingerprinting requires an efficient means of picking peaks from mass spectra. Here, we report the development of a peak harvester to automatically pick monoisotopic peaks from spectra generated on matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometers. The peak harvester uses advanced mathematical morphology and watershed algorithms to first process spectra to stick representations. Subsequently, Poisson modelling is applied to determine which peak in an isotopically resolved group represents the monoisotopic mass of a peptide. We illustrate the features of the peak harvester with mass spectra of standard peptides, digests of gel-separated bovine serum albumin, and with Escherictia coli proteins prepared by two-dimensional polyacrylamide gel electrophoresis. In all cases, the peak harvester proved effective in its ability to pick similar monoisotopic peaks as an experienced human operator, and also proved effective in the identification of monoisotopic masses in cases where isotopic distributions of peptides were overlapping. The peak harvester can be operated in an interactive mode, or can be completely automated and linked through to peptide mass fingerprinting protein identification tools to achieve high throughput automated protein identification.     

A NEW GLOW PEAK, IN RHODOPSEUDOMONAS SPHAEROIDES

Abstract— A new glow peak at 120 K has been observed in Rhodopseudomanas sphaeroides and in its carotenoidless green mutant. This peak (labelled Z_n ), which is composed of two peaks at 120 and 150 K, appears when the bacteria are illuminated with white light while being cooled to 77 K and then warmed in darkness at a heating rate of 10 K per min. Delayed light emission and prompt fluorescence spectra show peaks around 530, 610 and 660 nm. The action spectra of light emission show a major peak at 410 nm and a smaller peak around 545 nm. The pigment responsible for the light emission is also leached out in the suspension medium. The chromophore responsible for the light emission appears to be magnesium protoporphyrin IX, not bacteriochlorophyll.     

Experimental derivation of Auger transition probabilities from X-ray excited Auger electron spectra in XPS

Auger transition probabilities were experimentally derived from dominant XAES and related XPS peaks observed in XPS spectra. Some values of derived probabilities were higher than 1, because of addition or subtraction of background signal from the XAES or/and XPS peak intensity. However, the probabilities obtained are recognized to be useful for practical quantification by XAES and AES. Received: 6 April 1999 / Revised: 25 June 1999 / Accepted: 6 July 1999     

Excitation energy dependence for the Li 1s X-ray photoelectron spectra of LiMn2O4.

The Li 1s XPS (X-ray Photoelectron Spectroscopy) spectra of LiMn2O4, which is one of the major positive-electrode materials in lithium-ion rechargeable batteries, and MnO2 as a reference material, were measured by a laboratory-type XPS spectrometer. The Li 1s peak was not observed in the spectra excited by the Mg Kalpha line (1253.6 eV), because the Li 1s peak overlapped the background of the Mn 3p peak of LiMn2O4. The photoionization cross section of Mn 3p was larger than that of Li 1s for Mg Kalpha excitation. Therefore, the XPS measurement of LiMn2O4 by soft X-ray synchrotron excitation was carried out at beamline BL-7B on NewSUBARU synchrotron facility. Excitation energies of 110, 120, 130, 140, 150 and 151.4 eV were selected. The Li 1s peak was clearly observed in these XPS spectra. In order to investigate the excitation energy dependence, the area ratio of the Li 1s and Mn 3p peaks in the XPS spectra was plotted against the excitation energy. As a result, when the excitation energy was 110 eV, the area ratio had the maximum value.     

Neue Methode zur quantitativen Analyse von AES-Spektren

Summary The quantitative analysis of Auger electron spectra may lead to problems using Auger peak-to-peak heights (APPH), especially in connection with chemical peak deformation and peak overlap. To eliminate these problems a method has been developed and was applied to metalnonmetal compounds. An integral spectrum is fitted with reference spectra and correction spectra, background differences are compensated. To deal with chemical effects a digital filter process is used. In order to test this method a copper-palladium alloy series has been measured and evaluated according to this method. The results show that a more accurate quantification could be obtained than by using APPHs and sensitivity factors. As a further advantage, relative sensitivity factors are no longer necessary due to peak/background standardization.     

Fast-atom bombardment mass spectrometry of conjugated benzo(a)pyrene metabolites

Fast-atom bombardment mass spectrometry has been used to obtain spectra of conjugated benzo(a)pyrene (bap) metabolites using a 1:1, glycerol + thioglycerol matrix, bap Glucuronides give positive- and negative-ion spectra with peaks due to [M + H]+ and [M - H]- ions and a major fragment peak (base peak) at [bap-OH]+ and [bap-O]-. bap Sulfates (sodium salts) give similar negative-ion spectra with [M - Na]- and [bap-O]- peaks, but the positive-ion spectra are dominated by sodium and glycerol adducts of the bap sulfates.     

Proof of principle of a generalized fuzzy Hough transform approach to peak alignment of one-dimensional <Superscript>1</Superscript>H NMR data

In metabolic profiling, multivariate data analysis techniques are used to interpret one-dimensional (1D) ¹H NMR data. Multivariate data analysis techniques require that peaks are characterised by the same variables in every spectrum. This location constraint is essential for correct comparison of the intensities of several NMR spectra. However, variations in physicochemical factors can cause the locations of the peaks to shift. The location prerequisite may thus not be met, and so, to solve this problem, alignment methods have been developed. However, current state-of-the-art algorithms for data alignment cannot resolve the inherent problems encountered when analysing NMR data of biological origin, because they are unable to align peaks when the spatial order of the peaks changes—a commonly occurring phenomenon. In this paper a new algorithm is proposed, based on the Hough transform operating on an image representation of the NMR dataset that is capable of correctly aligning peaks when existing methods fail. The proposed algorithm was compared with current state-of-the-art algorithms operating on a selected plasma dataset to demonstrate its potential. A urine dataset was also processed using the algorithm as a further demonstration. The method is capable of successfully aligning the plasma data but further development is needed to address more challenging applications, for example urine data. Figure Traces of NMR peaks visualizing the Generalized Fuzzy Hough Transform (GFHT) method for elucidating peak correspondence between samples. The spectra are sorted according to one shift sensitive peak and reveals that other peaks exhibit a similar shift pattern. This pattern(s) can now be searched for using the GFHT. The red and black spectra in the figure are the most shifting spectra (top and bottom), by following the GFHT traces peak correspondence is easily established although peaks change spatial location Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm

We report a novel peak sorting method for the two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/TOF-MS) system. The objective of peak sorting is to recognize peaks from the same metabolite occurring in different samples from thousands of peaks detected in the analytical procedure. The developed algorithm is based on the fact that the chromatographic peaks for a given analyte have similar retention times in all of the chromatograms. Raw instrument data are first processed by ChromaTOF (Leco) software to provide the peak tables. Our algorithm achieves peak sorting by utilizing the first- and second-dimension retention times in the peak tables and the mass spectra generated during the process of electron impact ionization. The algorithm searches the peak tables for the peaks generated by the same type of metabolite using several search criteria. Our software also includes options to eliminate non-target peaks from the sorting results, e.g., peaks of contaminants. The developed software package has been tested using a mixture of standard metabolites and another mixture of standard metabolites spiked into human serum. Manual validation demonstrates high accuracy of peak sorting with this algorithm.