CIFTER: automated charge-state determination for peptide tandem mass spectra

Tandem mass spectrometry (MS/MS) has become a common and useful tool for analyzing complex protein mixtures. Database search programs are the most popular means for peptide identification from MS/MS spectra. However, estimations of charge states of peptide MS/MS spectra obtained from low-resolution mass spectrometers have not been reliable. They require repetitive database searches and additional analyses of the search results. We propose here an algorithm designed to reliably differentiate doubly charged spectra from triply charged ones. We conducted a rigorous analysis of various spectral features and their effects. We employed the distinguishing features found in our analysis and developed a classifier for multiply charged spectra using a machine learning approach. The test on various data sets showed that our method could be successfully applied independent of experimental setup and mass instrument. This algorithm can be used to prefilter spectra so that only reasonably good spectra are submitted to database search programs, thereby saving considerable time. The software for MS/MS charge-state determination, which we named "CIFTER", is available at a website http://prix.uos.ac.kr/sifter/cifter.     

Development of an XML-based structural product retrieval system for virtual enterprises

A single company cannot survive in today's global business environment without collaborating with others. A virtual enterprise is good practice for sharing core resources, experiences and information between companies with the same business goal. Through sharing product information, a company can prevent unnecessary spending in developing similar products that already exist. Although some attempts have been made to facilitate product searches, these methods are typically not suitable for structural product searches under virtual enterprise environments. In this work, an XML (eXtensible Markup Language) based structural product retrieval system for virtual enterprises is proposed to conquer this deficiency. A structural product is first transformed into component strings using a structure parsing algorithm. The structural similarity measurement between a product query and target product is designated and evaluated using a component matching algorithm and fuzzy mode composition. XML technology is used as the data exchange standard so that variant product information can be exchanged smoothly among heterogeneous database platforms. A comparison with a general Boolean search approach shows that the proposed structural search method can help users find desired product information more quickly and correctly. It is believed that virtual enterprise partners can benefit from using this system to increase their competitive advantage.     

Effects of binary encoding on pattern recognition and library matching of spectral data

Scott, D.R., 1988. Effects of binary encoding on pattern recognition and library matching of spectral data. Chemometrics and Intelligent Laboratory Systems, 4: 47–63.Binary encoding is frequently employed in pattern recognition studies and matching of unknown against library spectral data. In this study the effect of binary encoding on pattern recognition and library searches is determined using the Hamming and Euclidean distance metrics. The effect on a full intensity spectrum is to compress the total information into a qualitative spectral data vector, the most basic information in the full spectrum. Geometrically, binary encoding of unit normalized spectral data can be visualized as shifting spectral points on the faces of the measurement space hypercube to the corners of a Hamming hypercube. A new classification scheme for comparison of analytical spectra based on their binary encoded spectra is introduced. Quantitative expressions for the effect of binary encoding on general Euclidean distances between spectral points are derived and shown to depend upon their spectral classification. Generally binary encoding increases the interclass distances in pattern recognition and may decrease the intraclass distances. This effect is illustrated with a mass spectral pattern recognition example. The effect of binary encoding on library searches is to produce possible false compound identification in identity searches and to flag spectrally similar compounds in structure searches. A scheme which uses both the Hamming and the Euclidean metrics is proposed for improved library searches. This scheme is illustrated with searches of a small mass spectral library for benzene and p-dioxane spectra.     

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees

Multistage mass spectrometry (MS(n)) generating so-called spectral trees is a powerful tool in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics to identify unknown, but biologically relevant, compounds. As a consequence, there is a growing need for computational tools specifically designed for the processing and interpretation of MS(n) data. Here, we present a novel approach to represent and calculate the similarity between high-resolution mass spectral fragmentation trees. This approach can be used to query multiple-stage mass spectra in MS spectral libraries. Additionally the method can be used to calculate structure-spectrum correlations and potentially deduce substructures from spectra of unknown compounds. The approach was tested using two different spectral libraries composed of either human or plant metabolites which currently contain 872 MS(n) spectra acquired from 549 metabolites using Orbitrap FTMS(n). For validation purposes, for 282 of these 549 metabolites, 765 additional replicate MS(n) spectra acquired with the same instrument were used. Both the dereplication and de novo identification functionalities of the comparison approach are discussed. This novel MS(n) spectral processing and comparison approach increases the probability to assign the correct identity to an experimentally obtained fragmentation tree. Ultimately, this tool may pave the way for constructing and populating large MS(n) spectral libraries that can be used for searching and matching experimental MS(n) spectra for annotation and structural elucidation of unknown metabolites detected in untargeted metabolomics studies.     

Designing a practical system for spectral imaging of skylight

In earlier work [J. Opt. Soc. Am. A 21, 13-23 (2004)], we showed that a combination of linear models and optimum Gaussian sensors obtained by an exhaustive search can recover daylight spectra reliably from broadband sensor data. Thus our algorithm and sensors could be used to design an accurate, relatively inexpensive system for spectral imaging of daylight. Here we improve our simulation of the multispectral system by (1) considering the different kinds of noise inherent in electronic devices such as change-coupled devices (CCDs) or complementary metal-oxide semiconductors (CMOS) and (2) extending our research to a different kind of natural illumination, skylight. Because exhaustive searches are expensive computationally, here we switch to a simulated annealing algorithm to define the optimum sensors for recovering skylight spectra. The annealing algorithm requires us to minimize a single cost function, and so we develop one that calculates both the spectral and colorimetric similarity of any pair of skylight spectra. We show that the simulated annealing algorithm yields results similar to the exhaustive search but with much less computational effort. Our technique lets us study the properties of optimum sensors in the presence of noise, one side effect of which is that adding more sensors may not improve the spectral recovery.     

船体结构钢及焊接材料数据库应用系统设计开发

为了解决结构钢及焊接材料数据的有效存储及高效利用问题,使用SQL Server作为后台数据仓库,VB作系统开发,ODBC数据源作为连接技术,设计开发了船体结构钢及焊接材料数据库应用系统.系统具有结构钢及焊接材料信息查询、标准及报告查询等四大功能模块,并以结构钢配套焊条为例,通过性能预测智慧框架和神经网络模型构建、神经网...     

基于二维码技术的弹药包装信息管理系统设计

目的 为解决弹药序号化管理技术难题,提升产品质量管理水平,实现弹药信息的数字化管理。方法 基于SQL Server 2019建立数据库,并使用Python编写数据库管理软件来实现弹药产品信息的输入、生成、识别,以及信息综合查询功能。结果 该系统能够实现以二维码的方式生成弹药产品信息,并且能够对二维码上产品信息进行识别,对相关信息进行展示。结论 基于二维码技术的弹药包装信息管理系统,可提高弹药产品信息管理数字化水平,也是为满足工业自动化生产需求的一次实践,具有较大的实用价值和参考价值。     

Web的财务查询系统的性能优化与实现

在数据库和应用程序设计等方面探讨了信息查询的性能问题,研究了基于Web方式数据查询的优化方法.在高校财务信息查询系统的设计中,通过物理数据库的优化设计、使用优化的SQL语句、使用存储过程和基于存储过程的分页显示技术等优化信息查询性能,并给出了具体的代码实现,从而在软件方面解决了信息查询系统的性能问题.     

基于中国规范的近断层区竖向抗震设计谱研究

针对近断层区结构抗震设计缺乏专门竖向抗震设计谱的现状,以近断层竖向地震动为研究对象,基于《建筑抗震设计规范》,开展近断层区竖向抗震设计谱的研究。选取198条近断层脉冲型地震动的竖向分量,分析得到实际近断层地震动竖向反应谱,将计算得到的反应谱与中国抗震规范中的近断层竖向设计谱进行了对比。研究结果表明,中国抗震规范未充分考虑近断层竖向地震动的特点,表现为部分周期段上规范设计谱的谱值小于实际近断层竖向地震动反应谱,难以保证近断层区结构具有足够的抗震安全性。根据近断层竖向地震动的分析结果,基于中国抗震规范设计谱的基本形式,提出了谱值放大系数取1.5、特征周期下限取0.40 s(多遇地震)和0.45 s(罕遇地震)及减小曲线下降段衰减系数的修正方法。该竖向抗震设计谱工程应用简便,可为近断层区的结构竖向抗震设计提供参考。     

Compound identification using partial and semipartial correlations for gas chromatography-mass spectrometry data

Compound identification is a key component of data analysis in the applications of gas chromatography-mass spectrometry (GC-MS). Currently, the most widely used compound identification is mass spectrum matching, in which the dot product and its composite version are employed as spectral similarity measures. Several forms of transformations for fragment ion intensities have also been proposed to increase the accuracy of compound identification. In this study, we introduced partial and semipartial correlations as mass spectral similarity measures and applied them to identify compounds along with different transformations of peak intensity. The mixture versions of the proposed method were also developed to further improve the accuracy of compound identification. To demonstrate the performance of the proposed spectral similarity measures, the National Institute of Standards and Technology (NIST) mass spectral library and replicate spectral library were used as the reference library and the query spectra, respectively. Identification results showed that the mixture partial and semipartial correlations always outperform both the dot product and its composite measure. The mixture similarity with semipartial correlation has the highest accuracy of 84.6% in compound identification with a transformation of (0.53,1.3) for fragment ion intensity and m/z value, respectively.     

圆高强钢管UHPC梁抗弯性能研究

以含钢率和套箍系数为参数,开展5根圆高强钢管超高性能混凝土(UHPC)梁和2根圆普通钢管UHPC对比梁的纯弯试验;而后,采用已验证的有限元模型,对套箍系数进行了参数分析。试验研究表明,高强钢管UHPC梁发生延性破坏,组合截面满足平截面假定,受压区高强钢管对核心UHPC的套箍作用应被考虑。较普通强度的钢管,高强钢管能更及时地约束UHPC的横向膨胀。随着套箍系数的增加,钢管混凝土梁达抗弯承载力时,中性轴趋近截面中线,受拉区钢管应力减小,受压区钢管和混凝土的应力则增大。承载力计算分析发现,对于高强钢管UHPC梁而言,现有中国规范GB50936?2014的实用计算方法存在不准确且离散性较大等问题,为此该文提出了新实用计算方法。     

The multi-reconstruction entropy minimization method: unsupervised spectral reconstruction of pure components from mixture spectra, without the use of a priori information

The band-target entropy minimization method (BTEM) and its variant methods excel at reconstructing known/unknown pure spectra from mixtures without prior information. These mixtures may represent either non-reactive or even reactive systems. In this work, an unsupervised form of the entropy minimization curve resolution, namely, the multi-reconstruction entropy minimization method (MREM), is presented. MREM differs from BTEM by removing the need for band-targets and by introducing a multiple search routine to find multiple local entropy minima. This multiple search routine, which provides a rapid survey of spectral estimates, utilizes a localized form of Corona's simulated annealing method in the optimization. The objective functions and penalty functions of the BTEM type methods are essentially retained. Compared to BTEM type methods, MREM (1) searches for multiple local minima instead of a single global minimum and hence reconstructs many pure component spectra at once instead of one pure spectrum; and (2) utilizes a user-defined broad spectral range [v1, v2] for all searches instead of multiple user-defined narrow "targets" as in BTEM. The new MREM has been tested on four sets of real spectra using Fourier transform infrared spectroscopy (FT-IR), mass spectroscopy (MS), and ultraviolet-visible (UV-Vis) spectroscopy. The results show that MREM is computationally much faster than BTEM for finding the major components present. Also, because MREM does not rely on band targeting, it is very useful for spectra that have no localized features and are highly overlapping, such as UV-Vis.     

Numeric Databases for Chemical Analysis

Databases for use with analytical chemistry instrumental techniques are surveyed, with attention to existing databases and collection efforts now underway, as well as needs for new data-bases. Collections of spectra for use in NMR, infrared spectroscopy, and mass spectroscopy are described. Using mass spectral databases as an example, a critique is presented of automated quality control procedures used to evaluate individual spectra in large collections; the kinds of problems which have been en-countered in using these procedures are discussed. Finally, a brief critical review is presented covering the application of computers to the identification of unknown compounds using spectral data-bases; again, algorithms used with mass spectrometry are taken as the example. Ongoing work at NIST with the NIST/EPA/MSDC Mass Spectral Database is concerned with many of these problems; recent developments are described.     

Optimization of Temperature Controller for Electric Furnace

Genetic algorithms are based on the principle of natural selection and the optimization of natural generation. We can select the number of the bit strings and mutation rate reasonably, the global optimal solution can be obtained. GAs adopt the binary code as optimizing parameter and this binary code can be used in computer controller easily. This paper studies the application of the GAs to the electric furnace temperature control. When the electric furnace mathematics model varies with the working condition, the parameter of controller can be optimized on line. So the system performance can be improved effectively.     

The measurement of neutron and neutron induced photon spectra in fusion reactor related assemblies

The spectral neutron and photon fluence (or flux) measured outside and inside of assemblies related to fusion reactor constructions are basic quantities of fusion neutronics. The comparison of measured spectra with the results of MCNP neutron and photon transport calculations allows a crucial test of evaluated nuclear data as generally used in fusion applications to be carried out.The experiments concern mixed neutron/photon fields with about the same intensity of the two components. An NE-213 scintillation spectrometer, well described by response matrices for both neutrons and photons, is used as proton-recoil and Compton spectrometer. The experiments described here in more detail address the background problematic of two applications, an iron benchmark experiment with an ns-pulsed neutron source and a deep penetration mock-up experiment for the investigation of the ITER in-board shield system. The measured spectral neutron and photon fluences are compared with spectra calculated with the MCNP code on the basis of FENDL-1 data. The agreement is better than 10% except for the photon fluence from the iron benchmark experiment, which is underestimated in the calculations by 25%.     

Building knowledge into an expert system

The organization of a knowledge base within a laboratory expert system for solving C-13 NMR spectroscopy oriented problems is discussed. Four different forms for storing knowledge (formulas, tables, libraries, and hierarchical trees) used in the expert system CARBON are described. The emphasis is put on describing the flow of information and organization of knowledge in the system, which is designed to run on personal computers. In particular, we describe the implementation of the knowledge in such a way that it not only yields relevant (requested) information but also informs the user about missing information and possibly locates wrong data or wrong conclusions inferred. The two-way information flow enables the user to check retrieved information: if the query is a structure and the retrieved result is a spectrum, the check is made by spectral simulation; or, on the other hand, if the query is a spectrum and the yielded result a structure, the structural features can be checked by a decision tree or by assignation of spectra. Due to the built-in two-way handling of information the user can obtain the answer to his problem in an iterative way, testing a number of hypotheses.     

Web server based complex mixture analysis by NMR

Comprehensive metabolite identification and quantification of complex biological mixtures are central aspects of metabolomics. NMR shows excellent promise for these tasks. An automated fingerprinting strategy is presented, termed COLMAR query, which screens NMR chemical shift lists or raw 1D NMR cross sections taken from covariance total correlation spectroscopy (TOCSY) spectra or other multidimensional NMR spectra against an NMR spectral database. Cross peaks are selected using local clustering to avoid ambiguities between chemical shifts and scalar J-coupling effects. With the use of three different algorithms, the corresponding chemical shift list is then screened against chemical shift lists extracted from 1D spectra of a NMR database. The resulting query scores produced by forward assignment, reverse assignment, and bipartite weighted-matching algorithms are combined into a consensus score, which provides a robust means for identifying the correct compound. The approach is demonstrated for a metabolite model mixture that is screened against the metabolomics BioMagResDatabank (BMRB). This NMR-based compound identification approach has been implemented in a public Web server that allows the efficient analysis of a wide range of metabolite mixtures.     

Analyzing Raman maps of pharmaceutical products by sample-sample two-dimensional correlation

Sample-sample (SS) two-dimensional (2D) correlation spectroscopy is applied in this study as a spectral selection tool to produce chemical images of real-world pharmaceutical samples consisting of two, three, and four components. The most unique spectra in a Raman mapping spectral matrix are found after analysis of the covariance matrix. (This is obtained by multiplying the original mapping data matrix by itself.) These spectra are identified by analyzing the slices of the covariance matrix at the positions where covariance values are at maxima. Chemical images are subsequently produced in a univariate fashion by visually selecting the wavenumbers in the extracted spectra that are least overlapped. The performance of SS 2D correlation is compared with principal component analysis in terms of highlighting the most prominent spectral differences across the whole data set (which typically comprises several thousand spectra) and determining the total number of species present. In addition, the selection of the unique spectra by SS 2D correlation is compared with the selection obtained by the orthogonal projection approach (OPA). Both comparisons are found to be satisfactory and demonstrate that a quite simple SS 2D correlation routine can be used for producing reliable images of unknown samples. The main benefit of using SS 2D correlation is that it is based on a few data processing commands that can be executed separately and produce results that are closely related to the chemical features of the system.     

Asynchronous orthogonal sample design scheme for two-dimensional correlation spectroscopy (2D-COS) and its application in probing intermolecular interactions from overlapping infrared (IR) bands

This paper introduces a new approach to analysis of spectra called asynchronous orthogonal sample design (AOSD). Specifically designed concentration series are selected according to mathematical analysis of orthogonal vectors. Based on the AOSD approach, the interfering portion of the spectra arising strictly from the concentration effect can be completely removed from the asynchronous spectra. Thus, two-dimensional (2D) asynchronous spectra can be used as an effective tool to characterize intermolecular interactions that lead to apparent deviations from the Beer-Lambert law, even if the characteristic peaks of two compounds are substantially overlapped. A model solution with two solutes is used to investigate the behavior of the 2D asynchronous spectra under different extents of overlap of the characteristic peaks. Simulation results demonstrate that the resulting spectral patterns can reflect subtle spectral variations in bandwidths, peak positions, and absorptivities brought about by intermolecular interaction, which are barely visualized in the conventional one-dimensional (1D) spectra. Intermolecular interactions between butanone and dimethyl formamide (DMF) in CCl(4) solutions were investigated using the proposed AOSD approach to prove the applicability of the AOSD method in real chemical systems.     

Spectral bar coding of polystyrene microbeads using multicolored quantum dots

This paper focuses on encoding polystyrene microbeads, 10-100 microm in diameter, with a luminescent spectral bar code composed of mixtures of quantum dots (QDs) emitting at different wavelengths (colors). The QDs are encapsulated in the bead interior during the bead synthesis using a suspension polymerization, and the bar code is constructed by varying both the number of colors included in the bead and, for each color, the number of QDs of that color. Confocal laser scanning microscopy images of the beads demonstrate that the multicolored QDs are pushed together into inclusions within the bead interior. The encoded bead emission spectrum indicates that the peak position of the included colors does not shift relative to the corresponding peaks of the spectra recorded for the nonaggregated QDs at identical loading concentrations. Due to the spatial proximity of the QDs in the inclusions, electronic energy transfer from the lower wavelength emitting QDs to the higher emitting QDs changes the relative intensities of the colors compared to the values in the nonaggregated spectra. We show that this energy transfer does not obscure the spectral uniqueness of the different codes. Ratiometric encoding, in which the bar code is read as relative color intensity, is shown to remove the dependence of the code on the bead size.