Multidimensional computer evaluation of mass spectra

The increasing importance of spectroscopic methods as an analytical tool in industry, combined with the trend to automatize spectrometers, demands new standards in the quantity and quality of spectrum interpretation. Suitable computer programs should be able to predict structural features from mass spectral properties. The knowledge base is a structure-oriented mass spectral data collection consisting of some 42000 spectra and topologies. The comparison of selected mass spectral properties such as similarity, neutral losses and ion series of the unknown with the equivalent properties of the library spectra results in a set of corresponding structures. Subsequent substructure analysis yields a histogram of substructure frequencies containing information about their statistical relevance. The relevant substructure set may be recombined to produce a structure proposal, as is demonstrated for 1-acetyl-2-methoxy-4-trimethylsilyioxybenzene. In a second example, the relevant substructures derived by the interpretation system are used as input for the ¹³C-NMR substructure generator. This procedure reduces the solution space of the structure prediction algorithm considerably. Besides the spectrum interpretation, additional possibilities are available. The substructure search enables us, for example, to look for mass spectrometric reaction centres. Beyond that, substructure analysis is applicable to the determination of structural features typical of certain combinations of neutral losses and/or characteristic fragments.     

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.     

MS-Pep: a computer program for the interpretation of mass spectra of peptide libraries

Electrospray mass spectrometry (ESI-MS) is an established method for the qualitative analysis of synthetic peptide libraries and combinatorial mixtures or collections of small organic compounds. However, the calculation of the mass distribution of even small peptide mixtures is a time-consuming and error-proned task. Therefore, the computer program MS-Pep has been developed, which calculates the masses of expected peptides, byproducts and the mass distributions of peptide libraries. Received: 2 December 1996 / Revised: 17 April 1997 / Accepted: 21 April 1997     

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.     

MS-Pep: a computer program for the interpretation of mass spectra of peptide libraries

Electrospray mass spectrometry (ESI-MS) is an established method for the qualitative analysis of synthetic peptide libraries and combinatorial mixtures or collections of small organic compounds. However, the calculation of the mass distribution of even small peptide mixtures is a time-consuming and error-proned task. Therefore, the computer program MS-Pep has been developed, which calculates the masses of expected peptides, byproducts and the mass distributions of peptide libraries.     

Computer aided processing of laser microprobe mass spectra

This article describes the development and subsequent application of a computer aided method, based on the library search strategy, for the interpretation of laser microprobe mass analysis (LAMMA) spectra. Such a routine is essential whenever huge amounts of spectra are needed to obtain relevant results, as e.g. in environmental research. The main handicap for a straightforward automation is the poor reproducibility of the analytical technique.     

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.     

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.     

Computer calculations on ESR spectra

Conclusions These computations on ESR spectra provide useful general suggestions for approximate analyses of unresolved ESR spectra; means of more rigorous analysis are also indicated. It is probable that the theoretical spectra and nomograms will provide a means of facilitating the various methods of analysis as applied to ESR spectra; this should make ESR methods all the more valuable for a variety of purposes.Translated from Zhurnal Strukturnoi Khimii, Vol. 2, No. 6. pp. 690–695, November–December, 1961     

Determination of the elemental composition of a substance from low-resolution mass spectra with the aid of a computer

The possibility of using low- and medium-resolution mass spectra for determining the composition of -diketonates, coronands, and other types of substances was studied. Several versions of a microcomputer program were developed that helped to determine the empirical formula of an unknown compound from generated values of ionic mass and distribution moments of the isotopic peaks of a molecular and protonated quasimolecular ion.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 2, pp. 394–396, February, 1991.     

Identification of unknown compounds using data bases and computer simulation of mass spectra

The possibility of identification based on the comparison of experimental electron-ionization mass spectrum of an unknown (in our case, model) compound with the mass spectra of the candidate compounds generated by the Mass Frontier software has been demonstrated by the example of three model compounds. The structural isomers of the identified substances found in the ChemExper database have been used as the candidate compounds. The candidate substances have been ranged by the degree of similarity between their simulated mass spectra and the experimental mass spectrum of the unknown compound. The mass spectra have been compared on the basis of the algorithm used in the NIST MS Search standard search system. In all three cases, the sought-after structure has been indicated as the most probable one of all the candidate structures.     

Computer aided mathematical analysis of interferences in spark source mass spectrometry spectra

Summary When analysing sulphide ores by spark source mass spectrometry different interferences on some mass-to-charge ratios, such as 60–62 (Ni) and 193–197 (Ir,Pt,Au), have been observed. These lines should be used in the estimation of element concentrations. Our program (SM13) gives hints to possible molecular ions derived from the matrix of the sample by using the theory of combination.The validity of this theory was checked by analysing the ASK III standard [3] and mixtures of sulphides and oxides. The formation of interfering molecular ions such as SiS⁺ and AgFeS⁺ was checked.

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Computergestützte mathematische Auswertung von Interferenzen in Funken-Massenspektren

Zusammenfassung Bei der Analyse sulfidischer Erze wurden in der Funken-Massenspektrometrie für die Masse-zu-Ladungs-Verhältnisse 60–62 (Ni) sowie 193–197 (Ir,Pt,Au), die für die Elementbestimmungen verwendet werden sollten, Interferenzen beobachtet. Hierzu wurden mit Hilfe eines Auswertungsprogramms (SM13) durch mathematische Kombinatorik Hinweise auf Interferenzen durch mögliche Molekülionen aus der Matrixzusammensetzung abgeleitet.Die Anwendbarkeit des mathematischen Modells wurde am ASK III Standard [3] sowie an Mischungen von Sulfiden und Oxiden erprobt. Die Bildung der interferierenden Molekülionen des Typs SiS⁺ und AgFeS⁺ konnte nachgewiesen werden.

     

Computer generated optoacoustic spectra for a two-layer solid sample system

Summary A computer program has been devised to generate from two optoacoustic spectra of a two-layer solid sample, spectra at any phase angle from 0°–360°.

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Computer-erzeugte optoakustische Spektren für ein Zweischichtsystem einer festen Probe

Zusammenfassung Ein Computer-Programm wurde ausgearbeitet, mit dessen Hilfe aus einem experimentell aufgenommenen optoakustischen Spektrum einer festen Zweischichtenprobe Spektren für jeden beliebigen Phasenwinkel von 0°–360° erstellt werden können.

     

Symmetric distance measures for mass spectra

Several symmetric distance measures are tested on complete mass spectra by four different test methods, based on linear and hierarchical library search. The euclidean distance measure is tested with several normalization procedures by the same methods. The results show that no single distance measure is optimal in all situations. In particular, different types of noise in the spectrum may require different distance measures for optimal identification. Normalization of the spectrum to unit vector length or standard measure can improve the results.     

Siscom — a new library search system for mass spectra

SISCOM is a library search system for mass spectrometry which is based on a new method of coding spectra by selecting the most important peaks within homologous ion series, and on a multiple factor assessment of the result. Examples demonstrate the ability of the system to identify various compounds, even from mixtures or by reference spectra which differ from those measured. SISCOM is especially suitable for detecting structural similarities like common substructures, even in cases where no similarity can be recognized by visual comparison of patterns or by human interpretation of the spectrum.     

Computer processing and interpretation of mass spectral information. Part IX—generalized characteristics of mass spectra

The formation of numerical generalized characteristics (indices) of mass spectra by using one or two experimental parameters (mass numbers and/or ion peak amplitudes) is suggested. The influence of the measuring error of peak amplitudes on the statistical characteristics of indices was studied. It was ascertained by four classes of organometallic compounds that within an isolated class the value of each index is distributed by a normal law. The possibility of using mass spectral indices for the identification of unknown compounds is demonstrated.