Considerations on the Interpretation of Mass Spectra via Learning Machines

The application of learning machine techniques to the interpretation of mass spectra is investigated. An attempt to improve the characteristic ratio of the number of training points to the number of adjustable parameters is made by the use of reduced spectra. The ensuing results are corrected for the unequal representation of the different substances in the data bank. Reasonable performance is obtained for spectra of simple (monofunctional) substances, but predictive abilities are poor for more complicated substances.     

Basic rules for the interpretation of atmospheric pressure ionization mass spectra of small molecules

This review summarizes the basic rules for the interpretation of atmospheric pressure ionization (API) mass spectra of small molecules written with the style primarily intended for beginners and low-experienced researchers with the mass spectra interpretation. The first and basic step in any interpretation of mass spectra is always the determination of molecular weight, which is relatively easy in case of soft ionization techniques due to the limited extend of fragmentation and the prevailing presence of (de)protonated molecules in the full scan mass spectra. These [M+H]⁺ and [M−H]⁻ ions are often accompanied by low abundant molecular adducts, which can be used as the supplementary information for the unambiguous determination of molecular weights. In certain cases, adduct ions may dominate the spectra. The subsequent interpretation of full scan and tandem mass spectra is more complicated due to a high number of possible functional groups, structural subunits and their combinations resulting in numerous competitive fragmentation pathways. Typical neutral losses and the effect of individual functional groups on the fragmentation are discussed in detail and illustrated with selected examples. Modern mass analyzers have powerful features for the structural elucidation, for example high resolving power, high mass accuracy, multistage tandem mass spectrometry, dedicated softwares for the interpretation of mass spectra and prediction of their fragmentation. Background information on differences among individual ionization techniques suitable for the HPLC–MS coupling and basic types of mass analyzers with consequences for the data interpretation is briefly discussed as well. Selected examples illustrate that the right optimization of chromatographic separation and the use of other than mass spectrometric detectors can bring valuable complementary information.     

Spectroscopy of perylene van der waals complexes: the effect of blocking one site with benzene

The fluorescence excitation spectra obtained on further complexation of perylene-benzene by other species in quaternary supersonic expansions have been used to confirm a number of important structural assignments in molecular complexes. The interpretation of spectra of species such as perylene-Ar_n is complicated by the fact that there are two equivalent adsorption sites above and below the aromatic ring plane. It is shown here that benzene effectively blocks perylene to close approach by species such as Ar, N₂ cyclopropane. Thus, red-shifted sequences of resonances may be generated from which two-sided complexation has effectively been eliminated. The resulting simplified spectra have been used to confirm previous structural assignments.     

Etude de la fragmentation de semi-carbazones terpeniques

Terpene semicarbazones have been investigated using high resolution mass spectrometry. We have studied correlations between rings and functional semicarbazone degradations. The mass spectra are more complicated than the mass spectra of oximes, methyloximes and hydrazones. Cleavages are explained by known mechanisms. An interpretation of almost all the peaks is offered. The fragmentation of the semicarbazone skeleton is less marked than in the oximes. Fragmentation processes induced by the functional group are numerous. Ions obtained are concerned in secondary cleavages. Thus it is not surprising that the predominant feature is localisation of charge upon the imino nitrogen atom. Other centres may, however, be responsible for the appearance of several peaks.     

Pepto: An expert system for automatic peak assignment of two-dimensional nuclear magnetic resonance spectra of proteins

Two-dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two-dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.     

Plasmon profiles and deformations of sodium clusters in the 1g-shell

Absolute photoabsorption cross sections have been measured for free, singly ionized sodium clusters in the size range of 48 to 60 atoms. The measurements cover the wavelength interval from 390 to 590 nm (3.2-2.1 eV) in 14 steps. As in a previous series of measurements on smaller clusters, the spectra are dominated by a surface plasma oscillation of the valence electrons, that exhausts 70–80% of the dipole sum rule. The previously observed double structure of the resonance peak is not found, and therefore the interpretation of the profiles in terms of spheroidal deformations becomes more complicated. In this situation we compare the spectra with new calculations of the optical response of deformed clusters by Hirschmann. The calculations, which are made in a local representation of the Random Phase Approximation, agree well with the measured photoabsorption spectra.     

Determination of Long Range Proton Carbon Coupling Constants by Modified Semi-Selective Two-Dimensional Inept: An Application in Stereochemical Analysis of Saccharides

Abstract

Long-range proton-carbon coupling constants are useful in the assignment of ¹³C NMR spectra and in stereochemical analysis. The measurement of vicinal coupling constants, ³J_C-H, and their interpretation based on appropriate Karplus-type relationships (e.g. for ³J_H-C-C-C or ³J_H-C-O-C)^1–3 provide valuable information in conformational studies of carbohydrates. Nevertheless, the use of ³J_C-H in carbohydrate studies is rather rare because their measurement is time consuming and analysis of ¹H-coupled ¹³C NMR spectra is complicated. However, 2D NMR methods ^4–6 that allow precise measurement of long-range couplings in a reasonable time have become available recently.     

气相色谱-单光子电离飞行时间质谱的联用及在柴油组分表征中的应用

建立了一种气相色谱(GC)与单光子电离-飞行时间质谱(SPI-TOF MS)联用(GC/SPI-TOF MS)的分析方法。首先,设计了一种双层套管的传输管用于连接GC与SPI-TOF MS,实现了GC与单光子电离离子源的无缝连接。在此基础上,以n-十五烷标准品和苯/甲苯/二甲苯的标准气为对象,对电离源的重要电压参数进行了优化,得到了纯净的分子离子峰,实现了对各类有机物的快速和准确定性。最后,将该方法用于分析柴油中的挥发性与半挥发性有机物,获得了柴油组分的二维GC×SPI-TOF MS谱图。不需要复杂的谱图解析和数据处理,根据谱图中离子的质荷比(m/z)归纳了柴油的主要成分,包括脂肪烃、芳香烃和含量很低的苯并吡咯等含氮化合物;根据色谱的保留时间将柴油中的同分异构体区分开来。结果表明GC/SPI-TOF MS法是一种简单、有效的分析方法,非常适于柴油及复杂环境样品等的分析表征。     

Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra

Glycoprotein function is controlled by several biological factors, one of them being the structure of carbohydrate chains (glycans) attached to specific amino acids of the protein backbone. Changes in glycan structures have been shown to modify the secondary and tertiary conformation of glycoproteins, thus their function. Powerful analytical tools are available for the characterization of sugar structures, and recently mass spectrometry (MS) has been increasingly useful for this purpose. Manual interpretation of tandem mass spectrum is possible but tedious. Automated interpretation should speed the analysis and enhance the results obtained. A new computer program for automated interpretation of tandem MS spectra of complex N-linked glycans oligosaccharides from mammals will be described. N-Linked oligosaccharides standards were derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP) and analyzed by matrix-assisted laser desorption/ionization (MALDI)-tandem MS. Simulated tandem mass spectra of other common glycans were also generated to test the algorithm. The MALDI-MS/MS spectra featured resolved isotopic distributions for the [M + H](+) and fragment ions of oligosaccharides. These isotopic distributions complicated the automated analysis of the spectra and were removed to leave only monoisotopic peaks. An algorithm was written for this purpose, yielding simplified tandem mass spectra. Another algorithm is then used to determine the structure of the oligosaccharide. A score is then given to each structure, depending on agreement with experimental results. The program successfully assigned the true structure in 24 out of the 28 cases (86%) and the true structure was among the three top scoring structures in all cases.     

Quantifying the exclusion rule

A simple method is proposed for the determination of relative intensities of “forbidden” vibrational transitions in molecular spectra. When a symmetry-forbidden band may appear in spectra owing to perturbation of the ideal molecular geometry, the intensity of the forbidden band may be computed from other experimental observables. The use of such calculations in the interpretation of spectra is described, and applications to molecular ions in solid solution are presented.     

Automated mass analysis of low-molecular-mass bacterial proteome by liquid chromatography-electrospray ionization mass spectrometry

Due to the presence of a large number of proteins in cell extracts, ion chromatograms of cell extracts obtained by electrospray ionization mass spectrometry (ESI-MS) can be quite complicated. It is found that the elevated baseline in an ion chromatogram contains many protein signals. One deficiency of current commercially available LC-ESI-MS data interpretation software is found to be the lack of functional operation that allows automated mass spectral integration and interpretation over signals hidden in the baseline. This current limitation can be overcome by a technique that involves the introduction of artificial pulses to an ion chromatogram by removing the solvent mixer in the HPLC pump. These artificial pulses are treated as chromatographic peaks by the software, thereby allowing automated spectral integration over the duration of a pulse. The reliability of mass analysis from the integrated spectra is shown to be dependent on spectral interpretation parameters such as mass spectral baseline threshold. The application of this method is demonstrated for rapid detection and mass analysis of low-molecular-mass proteins from cell extracts of Escherichia coli or Bacillus globigii.     

Protein Structure Determination with Three- and Four-Dimensional NMR Spectroscopy

Structural biology has made important contributions to the understanding of biological processes. In recent years an increasing amount of structural information has also been derived from NMR spectroscopic studies, often with special emphasis on dynamic aspects. The introduction of three- and four-dimensional techniques has greatly simplified protein structure determination by NMR Spectroscopy, which has in fact become routine. In the past it was more of an art to interpret the complicated NOESY spectra of proteins, but the application of three-dimensional techniques now makes the interpretation of protein spectra straightforward. In this review we discuss the most important multidimensional NMR techniques along with suitable applications. The emphasis is put less on the discussion of individual pulse sequences than on their application to the structure determination of proteins.     

Calcium hydride and deuteride studied by neutron diffraction and NMR

The structure of CaD₂ has been redetermined by neutron diffraction and the structure has been confirmed by NMR measurements. However, the interpretation of the NMR measurements is not easy. The unsymmetrical position of the hydrogen (deuterium) atoms and the large range of interatomic distances lead to complicated spectra. Since the spectra for both the hydride and the deuteride seem to be determined mainly by dipolar interactions, one can conclude that the electric field gradient at the D sites must be very small. Line narrowing above 440°K is ascribed to proton diffusion with an activation enthalpy of 17.4 kcal/mol.     

光谱相关色谱及其在中药色谱指纹图谱分析中的应用

基于相同的化学物质具有相同的光谱，在大多数情况下，同一样本的化学成分在同种类型的色谱柱上虽然保留时间不可能完全相同，但是洗脱的顺序应基本一致，提出光谱相关色谱的新概念。利用联用色谱的光谱信息与色谱信息，判断复杂中药色谱指纹图谱中的组分相关性和表征不同实验条件下所得的中药色谱指纹图谱，从而实现仪器的系统误差的化学计量学校准。     

Proton magnetic resonance studies of 8-hydroxyquinoline derivatives

The PMR spectra of 8-hydroxyquinoline and eighteen derivatives have been obtained at 220 MHz. For several of the compounds, PMR spectra have not been reported previously. The use of 220-MHz frequency considerably facilitates the interpretation of spectra from such complex derivatives as 2-(2'-pyridyl) and 2-(2'-thienyl)-8-hydroxyquinoline.     

Characterizing the electrospray ionization mass spectral fragmentation pattern of indole derivatives synthesized from 2-keto glycosides

Four indole derivatives synthesized from 2-keto glycosides were analyzed by electrospray ionization tandem mass spectrometry (ESI-MSn) with low-energy collision-induced dissociation to establish a general structural elucidation of indole derivatives. Their fragmentation pathways are proposed on the basis of the MSn studies and deuterium-labeled experiments. Indole derivatives undergo complicated gas-phase rearrangements in addition to simple bond cleavages. A rearrangement, which involves a contraction of the six-membered ring, was observed and a mechanism was proposed. The observations may have some potential applications in the interpretation of the mass spectra of indole derivatives.     

Application of deuterated THENA for assigning the absolute configuration of chiral secondary alcohols

The structure of a constrained bicyclic chiral derivatizing agent (CDA), 1,2,3,4-tetrahydro-1,4-epoxynaphthalene-1-carboxylic acid, THENA 1, was modified by replacing both exo-methylene protons with deuterium atoms. The modified CDA, THENA-d₂2, could be used to assign the absolute configuration of chiral secondary alcohols with good reliability. Compared with THENA, the multiplicity of the methylene proton signals in the ¹H NMR spectra of THENA-d₂ derivatives is less complicated and the new CDA thus offers simpler NMR spectra for data interpretation.     

Feature extraction from spectral and other data by the principal components and discriminant function techniques

Principal component analysis is applied to the interpretation of ¹³C-n.m.r. spectra and to the resolution of mass spectral data. A procedure is given for determining the relative amounts of pure components, with and without the use of pure mass lines, in mass spectra of mixtures. The use of the Fisher discriminant method in combination with the principal components technique is demonstrated in the treatment of trace element data on hair for environmental purposes. The importance of feature generation and selection is emphasized.     

Collision-induced dissociation pathways of anabolic steroids by electrospray ionization tandem mass spectrometry

Anabolic steroids are structurally similar compounds, and their product-ion spectra obtained by tandem mass spectrometry under electrospray ionization conditions are quite difficult to interpret because of poly-ring structures and lack of a charge-retaining center in their chemical structures. In the present study, the fragmentation of nine anabolic steroids of interest to the racing industry was investigated by using triple quadrupole mass spectrometer, Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and a linear ion trap instrument. With the aid of an expert system software (Mass Frontier version 3.0), accurate mass measurements, and multiple stage tandem mass spectrometric (MS(n)) experiments, fragmentation pathways were elucidated for boldenone, methandrostenolone, tetrahydrogestrinone (THG), trenbolone, normethandrolone and mibolerone. Small differences in the chemical structures of the steroids, such as an additional double-bond or a methyl group, result in significantly different fragmentation pathways. The fragmentation pathways proposed in this paper allow interpretation of major product ions of other anabolic steroids reported by other researchers in a recent publication. The proposed fragmentation pathways are helpful for characterization of new steroids. The approach used in this study for elucidation of the fragmentation pathways is helpful in interpretation of complicated product-ion spectra of other compounds, drugs and their metabolites.     

Simulation of transient infrared spectra of a photoswitchable peptide

In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.