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.     

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 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.     

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 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.     

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 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.     

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.     

A new matching algorithm for high resolution mass spectra

We present a new matching algorithm designed to compare high-resolution spectra. Whereas existing methods are bound to compare fixed intervals of ion masses, the accurate mass spectrum (AMS) distance method presented here is independent of any alignment. Based on the Jeffreys-Matusitas (JM) distance, a difference between observed peaks across pairs of spectra can be calculated, and used to find a unique correspondence between the peaks. The method takes into account that there may be differences in resolution of the spectra. The algorithm is used for indexing in a database containing 80 accurate mass spectra from an analysis of extracts of 80 isolates representing the nine closely related species in the Penicillium series Viridicata. Using this algorithm we can obtain a retrieval performance of approximately 97-98% that is comparable with the best of the existing methods (e.g., the dot-product distance). Furthermore, the presented method is independent of any variable alignment procedures or binning.     

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.     

PIAD — A computer code for peak identification and activity determination

A Peak Identification and Activity Determination (PIAD) computer program has been developed. A new concept of peak significance is introduced and a great change has been made to the currently used associated gamma lines technique in calculating the confidence index; confidence factor is also given to the gamma line of a nuclide that is not seen in the spectrum. The program is written in Fortran IV under the operating system of RSX-11M.     

A computer program (COMPOST) for predicting mass spectrometric information from known amino acid sequences

A computer program (COMPOST) is described that carries out predictive computations on known amino acid sequences. The program is designed to be of use to mass spectrometrists with an interest in protein and peptide sequencing. Mass values (monoisotopic and average) for protonated peptide and protein molecules and elemental compositions are calculated. COMPOST also calculates mass to charge ratio values for protonated peptides expected from specified digests, locates specified amino acid subsequences or peptides of a specifIed molecular weight within a longer sequence, and predicts mass to charge ratio values for fragment ions from high-energy collision-induced dissociation of protonated peptides.     

The effects of solute-solvent interactions on the electronic visible spectra of bis(β-diketonato)oxovanadium(IV) complexes

Summary The solvatochromic behaviour of bis(-diketonato)oxovanadium(IV) complexes is quantitatively correlated by an approach that models specific and non-specific solute-solvent interactions. The applicability of the Selbin-Gutmann relation is discussed. The solvent-induced spectral shifts in VO(acac)₂ are dominated by specific interactions of the donor-acceptor type, whereas for VO(tfa)₂, the nonspecific solute-solvent interactions make the dominant contribution.

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Der Einfluß von Wechselwirkungen zwischen Lösungsmittel und gelöstem Stoff auf die VIS-Spektren von Bis(-diketonato)oxovanadium(IV)-Komplexen

Zusammenfassung Das solvatochrome Verhalten von Bis(-diketonato)oxovanadium(IV)-Komplexen wird mit einem Modell, das spezifische und nichtspezifische Wechselwirkungen in Lösung berücksichtigt, quantitativ beschrieben. Es wird die Anwendbarkeit der Selbin-Gutmann-Relation diskutiert. Die Solvens-induzierten Verschiebungen in den VIS-Spektren von VO(acac)₂ werden von den spezifischen Wechselwirkungen vom Donor-Acceptor-Typ bestimmt, währenddessen für VO(tfa)₂ die nichtspezifischen Wechselwirkungen zwischen Substrat und Lösungsmittel den dominierenden Beitrag liefern.

     

A computer search system for chemical structure elucidation based on low-resolution mass spectra

A computerized search system which employs the data on the masses and relative abundances of spectral peaks and primary neutral losses is designed for computer elucidation of chemical structures. Recognition of structural fragments is based on analysis of the structures of reference compounds selected as best matches to the mass spectrum of the compound under investigation. Tests of the system on 67 “unknowns” show that the probability of recognizing a large structural fragment lies in the interval 60–80%, depending on the fragment size (100–50% of molecular weight), and that the reliability of the corresponding structural conclusion is 98%. An approach to automatic selection of the substructure common to all or several of the selected compounds is discussed.     

A modular cross-linking approach for exploring protein interactions

A method is described for the elucidation of protein-protein interactions using novel cross-linking reagents and mass spectrometry. The method incorporates (1) a modular solid-phase synthetic strategy for generating the cross-linking reagents, (2) enrichment and digestion of cross-linked proteins using microconcentrators, (3) mass spectrometric analysis of cross-linked peptides, and (4) comprehensive computational analysis of the cross-linking data. This integrated approach has been applied to the study of cross-linking between the components of the heterodimeric protein complex negative cofactor 2.