New algorithm for the identification of mass spectra by the computer library search

A library search algorithm for the identification of mass spectra is described. The algorithm creates the mass vector of an unknown compound spectrum and sequentially compares it with the library files vector. A measure indicating similarity of compares vectors - similarity index is calculated on the basis of weighted factors of identical elements of both vectors. A diagnosticity of vectors element defined as a function of mass distribution of library file is taken as an important parameter in similarity index calculation.     

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.     

Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures

The performance of the algorithm COMPLX for detecting protein-ligand or other macromolecular complexes has been tested for highly complex data sets. These data contain m/z values for ions of proteins of the SWISS-PROT database within simulated biological mixtures where each component shares a similar molecular weight and/or isoelectric point (pI). As many as 1600 ion signals were entered to challenge the algorithm to identify ion signals associated with a single protein complex that has been ionised and detected within a mass spectrometer. Despite the complexity of such data sets, the algorithm is shown to be able to identify the presence of individual bimolecular complexes. The output data can be re-evaluated by the user as necessary in light of any additional information that is known concerning the nature of predicted associations, as well as the quality of the data-set in terms of errors in m/z values as a direct consequence of the mass calibration or resolution achieved. The data presented illustrates that the best results are obtained when output results are ranked according to the largest continuous series of ion pairs detected for a protein or macromolecule and its complex for which the ligand mass is assigned the lowest mass error.     

A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification

Since cellular functionality is typically envisioned as having a hierarchical structure, we propose a framework to identify modules (or clusters) within protein-protein interaction (PPI) networks in this paper. Based on the within-module and between-module edges of subgraphs and degree distribution, we present a formal module definition in PPI networks. Using the new module definition, an effective quantitative measure is introduced for the evaluation of the partition of PPI networks. Because of the hierarchical nature of functional modules, a hierarchical agglomerative clustering algorithm is developed based on the new measure in order to solve the problem of complexes detection within PPI networks. We use gold standard sets of protein complexes to validate the biological significance of predicted complexes. A comprehensive comparison is performed between our method and other four representative methods. The results show that our algorithm finds more protein complexes with high biological significance and a significant improvement. Furthermore, the predicted complexes by our method, whether dense or sparse, match well with known biological characteristics.     

A novel approach for protein identification from complex cell proteome using modified peptide mass fingerprinting algorithm

A unique peptide based search algorithm for identification of protein mixture using PMF is proposed. The proposed search algorithm utilizes binary search and heapsort programs to generate frequency chart depicting the unique peptides corresponding to all proteins in a proteome. The use of binary search program significantly reduces the time for frequency chart preparation to ～2 s for a proteome comprising ～23 000 proteins. The algorithm was applied to a three‐protein mixture identification, host cell protein (HCP) analysis, and a simulation‐generated data set. It was found that the algorithm could identify at least one unique peptide of a protein even in the presence of fourfold higher concentration of another protein. In addition, two HCPs that are known to be difficult to remove were missed by MS/MS approach and were exclusively identified using the presented algorithm. Thus, the proposed algorithm when used along with standard proteomic approaches present avenues for enhanced protein identification efficiency, particularly for applications such as HCP analysis in biopharmaceutical research, where identification of low‐abundance proteins are generally not achieved due to dynamic range limitations between the target product and HCPs.     

A computer system for measuring fast-scan lowresolution mass spectra

A microprocessor-based satellite computer system (MASDAT) controls a low-resolution, fast-scan mass spectrometer for the measurement of series of spectra. Special digitization hardware (logarithmic A/D converter) and software algorithms are necessary to achieve a dynamic range (ratio of highest to lowest intensity) of about 10⁵ in peak heights. Up to three MASDAT satellites can be connected to a host computer. Synchronized parallel programs in the host system communicate with the operator, calibrate the mass scale, print an interscan report, and store final spectra and, optionally, unreduced data on mass storage devices. Host software is described for a RSX11M and for a VAX/VMS operating system.     

A simple computer program for high resolution gamma-ray spectra

A computer program is presented, which locates peaks in high-resolution γ-ray spectra and determines their content. The program has been written in Basic; ‘translations’ have been made into Fortran and Algol. For detailed information the reader is referred to the original TNO Report CL 69/137.     

A computer program in ALGOL-60 for the location and evaluation of peaks in Ge(Li) gamma ray spectra

A program is presented for the analysis of γ-ray spectra from Ge(Li) multichannel spectrometer systems. The program is written in ALGOL-60 for off-line working with a large Philips Electrologica X8 computer. It has been extensively used in thermal neutron activation analysis practice.     

COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra

A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts.     

A BSSE-free SCF algorithm for intermolecular interactions

A very simple modification of the usual (～N⁴) SCF procedure is proposed, permitting the exclusion of basis set superposition errors (BSSE ) in problems of intermolecular interactions. No a posteriori corrections are required. The results of this “CHA /F method” are numerically close to those of the Boys–Bernardi correction scheme but are free from the “overcompensation” characteristic of the latter at smaller distances.     

A computer system for structural identification of organic compounds from 13C NMR data

A computerised library search system for ¹³C NMR data is described. Given the spectral data of an unknown compound, the system will retrieve from the library those reference compounds exhibiting similar spectra. For comparison the spectral data are converted into a binary code, designed to reflect the underlying structure rather than exact values for chemical shifts. Thus, the ability of the system to retrieve compounds similar to the unknown (as opposed to identical) is greatly enhanced. A sophisticated search strategy adapting itself automatically to the problem at hand makes the system highly efficient.     

A fast computer algorithm for finding the permanent of adjacency matrices

A fast computer algorithm is described which brings computation of the permanents of sparse matrices, specifically, chemical adjacency matrices, within the reach of a desktop computer. Examples and results are presented, along with a discussion of the relationship of the permanent to the Kekulé structure count. Also presented is a C-language implementation which was deliberately written for ease of translation into other high-level languages.     

A computer program for the collection,reduction and analysis of echelle spectra

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text, comprising the main article and an appendix, is accompanied by a disk containing the compiled program, a manual, the source code and tutorial in ASCII format, and data files. The work presented is a result of the need to facilitate collection, calibration, and extraction of data from an echelle spectrometer employing charge coupled array detection (CCD). A computer program, written using Microsoft's BASIC Professional Development System version 7.1 under MS DOS, is explained and demonstrated. Wavelength calibration requires critical spectrometer dimensions, grating counter settings, and the identification of a single spectral line. Calibration accuracies are better than ± 1 pixel across a 576 × 384 pixel array. Extraction of intensity-normalized spectra for all detected orders requires less than 3 min on a 33 MHz 80386 personal computer with an 80387 math coprocessor.     

Stereoselective cycloaddition of 1,3-cyclohexadiene on Si(100): a simple algorithm for product identification based on secondary orbital interactions

We consider the reaction of 1,3-cyclohexadiene (1,3-CHD) on Si(100) and show that the observed reactivity and stereoselectivity cannot be explained on the basis of thermodynamics. We postulate the existence of secondary orbital interactions (SOIs) and introduce a simple algorithm that examines all possible secondary interactions between the frontier orbitals of the molecule and the surface. We demonstrate using an orbital symmetry-based algorithm supported by DFT calculations that SOIs favor a particular molecular configuration, consistent with the experimental observations. The potential role of SOIs in controlling surface chemical reactions is discussed.     

完全未知混合体系的纯物种光谱辨析

基于因子分析的迭代目标转换算法,本文提出一种从完全未知混合物体系中获取纯物种光谱的解析方法。该法简单明了,不增加任何困难即可拓广至含n组份的混合体系,对光谱峰形状亦无任何附加限制要求。先采用计算机模拟技术对该法进行了校验,继用于紫外可见与荧光光谱的实际混合体系的解析,均获满意结果。     

A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein

A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.     

Application of simulated standard spectra for the analysis of complex sample spectra from NaI(Tl) detectors

The most accurate method for the analysis of complex gamma ray spectra from scintillation detectors is least squares method. The major requirement of this method is individual standard spectra of all nuclides expected in the complex spectrum which is not possible and feasible for some nuclides. In the present work, an approach of using simulated standard spectrum of the radionuclides for the least squares analysis is studied. The paper describes the methodology used for the generation of simulated spectrum which is the main objective, and validation of results using standard sources in the Sodium Iodide (NaI(Tl)) based gamma ray spectrometer.