Monte Carlo simulation of ion transport in non-linear ion mobility spectrometry

A program for Monte Carlo simulation of ion transport in non-linear ion mobility spectrometry, also known as field asymmetric ion mobility spectrometry (FAIMS) or differential mobility spectrometry (DMS), has been developed. Simulations are based on elastic collisions between the ions and the gas particles, and take into account the effects of flow dynamics and asymmetric electric fields. Using this program, the separation and diffusion of the ions moving in a planar DMS filtration gap are demonstrated. Ion focusing in a cylindrical filtration gap is also confirmed. A characteristic compensation voltage is found to provide insight for understanding separation in non-linear ion mobility spectrometry. The simulation program is used to study the characteristics of non-linear ion mobility spectrometry, the effect of the carrier gas flow, and the dependence of the compensation voltage and nonlinear mobility coefficient (α) on the applied asymmetric electric field.     

Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry

Peptide sequencing by mass spectrometry is gaining increasing importance for peptide chemistry and proteomics. However, available tools for interpreting matrix-assisted laser desorption/ionization post-source decay (MALDI-PSD) mass spectra depend on databases, and identify peptides by matching experimental data with spectra calculated from database sequences. This severely obstructs the identification of proteins and peptides not listed in databases or of variations, e.g. mutated proteins. The development of a new computer program for database-independent peptide sequencing by MALDI-PSD mass spectrometry is reported here. This computer program was validated by the determination of the correct sequences for various peptides including sequences listed in the sequence databases, but also for peptides that deviate from database sequences or are completely artificial. This strategy should substantially facilitate the identification of novel or variant peptides and proteins, and increase the power of MALDI-PSD analyses in proteomics.     

MS Interview: An elemental mass spectrometry spectral interference data base

A graphically-oriented data base of spectral interferences dut occur in inductively coupled plasma-mais spectrometry and glow discharge-mass spectrometry has been developed. The program is called “MS Interview” and runs on a Macintosh computer. The program allows one to specify which technique (ICP or GD) the various interferences will be presented for, and for the case of the ICP, the acid matrix background. Bated on these parameters the program provides a listing of interferences broken down into the following categories: Isobarics, Oxides, Doubly Charged Species, Background Dependent, and Matrix Dependent. For the glow discharge case there are two additional categories: Argides and Dimers. Interference information is provided for all masses of all elements and is easily accessed via mouse operations from a periodic table window and element mass spectral windows. The program is expandable to include other ion sources and interferences can be added or deleted as required by the user. Finally, the program also includes a small library of typical background spectra that can be displayed and manipulated. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta B (SAB). The hardcopy text is accompanied by a disk containing the program MS Interview, a manual, a reference list, and a bar graph format mass spectral library of the elements.     

Assessment of various mathematical correction methods of matrix effects in X-ray fluorescence analysis

Several methods for mathematical corrections of matrix effects in X-ray fluorescence spectrometry were studied. A computer program to elaborate spectral data by means of different and selected mathematical algorithms was set up. The results obtained using the proposed methods for the elemental analysis of some series of samples are reported.     

Probability-based protein identification by searching sequence databases using mass spectrometry data

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.     

MoWeD, a computer program to rapidly deconvolute low resolution electrospray liquid chromatography/mass spectrometry runs to determine component molecular weights

A computer program is described that can rapidly process low-resolution electrospray liquid chromatography/mass spectrometry (LC/MS) for peptides and proteins and assign molecular weights for observed components. The program first analyzes individual scans using a deconvolution algorithm similar to that previously described by Zhang and Marshall. Results for the entire run are then sorted by mass and those values found in adjacent scans are grouped together. The list of found components can also be compared to a user defined list of target molecular weight values making it easy to compare the results from different analyses. The program also has the capability to process a rolling average of scans that improves the performance when analyzing high molecular weight components. Other program features facilitate closer examination of selected spectra or regions of the chromatogram to check the MoWeD mass assignments. The utility of the program was demonstrated by the analysis of LC/MS data derived from a complex mixture of proteins derived from a bacterial whole cell lysate that had previously been analyzed manually. The MoWeD analysis was 30 times faster and provided a more comprehensive list of the components present.     

A selenium-selective chromatoraphic detector based on isotope cluster

A selenium-selective chromatograhic detector based on mass spectrometry is described. Full mass spectra are collected continously from the gas chromatographic effuent. A computer program then searches the spectra for the naturall-occurring selenium isotope cluster, indicating which spectra in the data set are most likely to contain those clusters. The device involves a selective data-reduction technqiue, as opposed to a selective data-collection process; it therefore possesses some useful advantages. The method was tested on the EPA/NIH Mass Spectral Data Base and on the analysis of trimethylsilylated amino-acid mixtures including selenomethionine.     

Targeted analysis of glycomics liquid chromatography/mass spectrometry data

Hydrophilic interaction chromatography (HILIC) liquid chromatography/mass spectrometry (LC/MS) is appropriate for all native and reductively aminated glycan classes. HILIC carries the advantage that retention times vary predictably according to oligosaccharide composition. Chromatographic conditions are compatible with sensitive and reproducible glycomics analysis of large numbers of samples. The data are extremely useful for quantitative profiling of glycans expressed in biological tissues. With these analytical developments, the rate-limiting factor for widespread use of HILIC LC/MS in glycomics is the analysis of the data. In order to eliminate this problem, a Java-based open source software tool, Manatee, was developed for targeted analysis of HILIC LC/MS glycan datasets. This tool uses user-defined lists of compositions that specify the glycan chemical space in a given biological context. The program accepts high-resolution LC/MS data using the public mzXML format and is capable of processing a large data file in a few minutes on a standard desktop computer. The program allows mining of HILIC LC/MS data with an output compatible with multivariate statistical analysis. It is envisaged that the Manatee tool will complement more computationally intensive LC/MS processing tools based on deconvolution and deisotoping of LC/MS data. The capabilities of the tool were demonstrated using a set of HILIC LC/MS data on organ-specific heparan sulfates.     

Development of algorithms for automated elucidation of spectral feature/substructure relationships in tandem mass spectrometry

A pattern-recognition/artificial-intelligence program, referred to as MAPS (method for analyzing patterns in spectra), is described for the identification of relationships that exist between the presence of substructures in molecules and the characteristic features they produce in mass spectrometry (MS) and MS/MS data. The MAPS algorithm discovers these relationships by intelligent analysis of a data base of MS and MS/MS spectra. The relationships found are expressed as rules, which may then be used to identify characterized substructures in “unknowns”. No prior knowledge of fragmentation pathways or rearrangements is assumed in the rule-generation process. While MAPS currently uses MS and MS/MS data, the approach (and much of the software) is equally suited to multiple-stage mass spectrometric data.     

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu .     

Methods of calibration in the direct analysis of solid samples by electrothermal atomic absorption spectrometry

One of the major problems involved in the direct analysis of solid samples by electrothermal atomic absorption spectrometry (ETAAS) lies in the calibration step because non-spectral interference effects are often pronounced. Three standardization techniques have been described and used in solid sampling-ETAAS: (i) standard additions method; (ii) calibration relative to a certified reference material; and (iii) calibration curve technique. However, an adequate statistical evaluation of the uncertainty in the analyte concentration in the solid sample is most frequently neglected, and reported errors may be seriously underestimated. This can be attributed directly to the complexity of the statistical expressions required to accurately account for errors in each of the calibration techniques mentioned above, and the general lack of relevant reference literature. The object of this work has been to develop a computer package which will perform the necessary statistical analyses of solid sampling-ETAAS data; the result is the program “SOLIDS” described here in the form of an electronic publication in Spectrochimica Acta Electronica, the electronic section of Spectrochimica Acta Part B. The program could also be useful in other analytical fields where similar calibration methods are used. The hard copy text, outlining the calibration models and their associated errors, is accompanied by a diskette containing the program, some data files, and a manual. Use of the program is exemplified in the text, with some of the data files discussed included on the diskette which, together with the manual, should enable the reader to become familiarized with the operation of the program, and the results generated.     

Mass spectrometry fingerprinting coupled to National Institute of Standards and Technology Mass Spectral search algorithm for pattern recognition

A new analytical strategy based on mass spectrometry fingerprinting combined with the NIST-MS search program for pattern recognition is evaluated and validated. A case study dealing with the tracing of the geographical origin of virgin olive oils (VOOs) proves the capabilities of mass spectrometry fingerprinting coupled with NIST-MS search program for classification. The volatile profiles of 220 VOOs from Liguria and other Mediterranean regions were analysed by secondary electrospray ionization-mass spectrometry (SESI-MS). MS spectra of VOOs were classified according to their origin by the freeware NIST-MS search v 2.0. The NIST classification results were compared to well-known pattern recognition techniques, such as linear discriminant analysis (LDA), partial least-squares discriminant analysis (PLS-DA), k-nearest neighbours (kNN), and counter-propagation artificial neural networks (CP-ANN). The NIST-MS search program predicted correctly 96% of the Ligurian VOOs and 92% of the non-Ligurian ones of an external independent data set; outperforming the traditional chemometric techniques (prediction abilities in the external validation achieved by kNN were 88% and 84% for the Ligurian and non-Ligurian categories respectively). This proves that the NIST-MS search software is a useful classification tool.     

基本参数法在能量色散X射线荧光分析金属样品中的应用

在X射线荧光分析中,基本参数法是校正元素间吸收增强效应的数学方法之一。我们使用带有不锈钢窗的~(241)Am59.6keVγ射线作为激发源,用Si(Li)半导体探测器和多道脉冲幅度分析器作为实验手段。采用无标样法,即绝对测量法,因而具有更大的广泛性和实用性。实验中,我们除了考虑元素间的二次、三次荧光吸收增强作用外,对样品中元素     

间歇电喷雾的初步研究

设计了一种高灵敏的质谱离子化方法-间歇电喷雾，并介绍了间歇电喷雾的基本原理、稳定性和应用在蛋白质分析上的优势。这种质谱离子化方法能够显著地改善信噪比，降低对样品溶解度的要求，提高样品的离子化效率，减少样品的消耗和仪器的污染，可以预言间歇电喷雾的方法在蛋白质的分析上将会有广泛的应用前景。     

User-oriented software for determination of the precision of signal-integrating analytical methods

A software package for the determination of the uncertainty in signal-integrating analytical techniques is presented. The program can be used to calculate detection limits and to determine baseline drift properties, the influence of drift-correcting procedures and integration time, etc. Complete analytical procedures, e.g., chromatography or atomic emission spectrometry, or parts of a system can be tested. No profound theoretical knowledge is required by the user; confidence intervals are calculated where necessary. The theoretical basis and the structure of the program are evaluated.     

MS-Express: data-extracting and -processing software for high-throughput experimentation with mass spectrometry

High-throughput experiments (HTE) result in large amounts of raw data that have to be evaluated for sample classification. Especially mass spectrometry, a widely used detection method in catalytic HTE applications, produces enormous amounts of data. In the past few years, in catalysts research, several test rigs based on mass spectrometric detection have been independently reported by different groups. In a typical HTE, the catalysts are tested sequentially; the recording of the scans, however, occurs continuously. For this reason, the scans of interest have to be extracted from the raw data, and scans belonging to the same sample have to be averaged in a tedious procedure before further processing. In this publication, we present our custom-designed software MS-Express (mass spectrometry data-extracting and -processing software), an efficient tool for HTE MS data evaluation. MS-Express not only sorts the data, it also establishes statistical significance with the help of reference and blank data and provides concise information about abundance and intensity distributions of expected peaks. A special feature is that the program also reports unexpected MS signals, which potentially lead to unexpected discoveries.     

Plutonium accountability measurements by calorimetry and gamma spectrometry: evaluation of measurement uncertainties and method performance

The calorimetry exchange (CALEX) program is administered by New Brunswick Laboratory (NBL). The main objective of the program is to provide an independent verification of the internal quality control practices in nuclear material safeguards facilities making plutonium accountability measurements by non-destructive calorimetry/gamma spectrometry techniques. Facilities measure the calorimetric power, and plutonium and ²⁴¹Am isotope abundances of CALEX program standards using routine accountability procedures. The measurement results as well as two other quantities (effective specific power and plutonium mass) calculated from these results are evaluated for accuracy (or bias) and precision. In this paper, a limited number of measurement results of a CALEX program standard (identified as Calex I) are evaluated with specific goals to identify a suitable method for uncertainty estimation and to identify the major contributors to the uncertainties. In order to achieve the goals, the Calex I measurement results were evaluated using two different methods: the first method confined to uncertainty estimation from random variations of the measurement results alone, and the second method providing a more comprehensive evaluation of uncertainties from both the measurements and the characterized values of the measured standard according to the Guide to the Expression of Uncertainty in Measurement (GUM). The results of this study, and a subsequent study extended to a larger number of results in the CALEX program database, are expected to provide relevant input for developing the International Target Values for plutonium measurements by the calorimetry/gamma spectrometry method.     

Determination of gold and palladium in rocks and ores by atomic absorption spectrometry using two-stage probe atomization

The efficiency of two-stage probe atomization for the determination of gold and palladium in geological samples by electrothermal atomic absorption spectrometry is studied. The effects of temperature–time program and the position of the probe in an atomizer on the fractionation of sample components and the magnitude of the analytical signal are studied. It is demonstrated that gold and palladium can be quantitatively determined by atomic absorption spectrometry in rocks and ores, using a two-stage probe atomization with the limits of detection for gold and palladium 0.01 and 0.04 g/t, respectively.     

Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures

The structural characterization of proteins and peptides isolated in minute quantities requires the most efficient use of available sample. A mass spectrometer data system was programmed to continuously evaluate incoming liquid chromatography/mass spectrometry data against a user-defined array of information. The resulting conclusions were used to automatically set and modify acquisition parameters in real time to collect collision-induced dissociation spectra for selected ions (tandem mass spectrometry). This approach has provided a mechanism to target specific subsets of masses in a complex mixture and/or to discriminate selectively against masses that are known or not of interest. Masses of contaminants or peptide masses derived from known proteins can be automatically recorded and removed from further consideration for collision-induced dissociation analysis. Once recorded, these “libraries” of masses can be used across multiple analyses. This technique directs the mass spectrometer data system to focus on the analysis of masses significant to the user, even if their signal intensities are well below the intensities of contaminating masses. When combined with a database search program to correlate tandem mass spectra to known protein sequences, the identity of the protein can be established unequivocally by using less than 100 fmol of sample.