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.     

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.     

Comprehensive two-dimensional gas chromatography, retention indices and time-of-flight mass spectra of flavonoids and chalcones

The applicability of comprehensive two-dimensional gas chromatography (GC×GC) for flavonoids analysis was investigated by separation and identification of flavonoids in standards, and a complex matrix natural sample. The modulation temperature was optimized to achieve the best separation and signal enhancement. The separation pattern of trimethylsilyl (TMS) derivatives of flavonoids was compared on two complementary column sets. Whilst the BPX5/BPX50 (NP/P) column set offers better overall separation, BPX50/BPX5 (P/NP) provides better peak shape and sensitivity. Comparison of the identification power of GC×GC-TOFMS against both the NIST05 MS library and a laboratory (created in-house) TOFMS library was carried out on a flavonoid mixture. The basic retention index information on high-performance capillary columns with a non-polar stationary phase was established and database of mass spectra of trimethylsilyl derivatives of flavonoids was compiled. TOFMS coupled to GC×GC enabled satisfactory identification of flavonoids in complex matrix samples at their LOD over a range of 0.5-10 μg/mL. Detection of all compounds was based on full-scan mass spectra and for each compound a characteristic ion was chosen for further quantification. This study shows that GC×GC-TOFMS yields high specificity for flavonoids derived from real natural samples, dark chocolate, propolis, and chrysanthemum.     

Fragmentation and rearrangement processes in the high resolution mass spectra of diphenylsilyl compounds

High resolution mass spectra of a series of diphenylsilyl compounds, Ph₂SiX₂(X=H, F, Cl) and Ph₂Si(oy)₂ (Y=Et, Me, H), were recorded. Results from selected metastable defocusing experiments showed that if X or OY can be readily lost stepwise, the relative abundance of the biphenyl radical rearrangement ion (d) is small; if neutral silicon species such as :SiX₂, SiX or :Si(OY)₂ are readily eliminated, the relative abundance of the ion d will be large. The ion d originates from both odd- and even-electron ions, thus making the radical site mechanism, which requires a phenyl radical to polarize the other phenyl group, rather unlikely to be an important general driving force. The condensation of phenyl groups could be more appropriately viewed in terms of bond liability and product stability. In the special case of diphenylsilyl catecholate, in addition to geminal cleavage of phenyl groups, complex fragmentation and rearrangement processes were also observed.     

Program for elemental analysis using low or medium resolution mass spectra

A program, called ELANAL, has been written in basic which computes all possible empirical formulae for a molecular ion or a fragment ion containing up to eleven common elements. The program then calculates the expected intensities of the peaks following the molecular or fragment ion due to heavier isotopes in the formulae. These calculated intensities are compared with the intensities in an experimentally determined mass spectrum.     

Prediction of molecular structures of aza-arenes by retention indices and fluorescence spectra

Two methods are described for predicting the molecular structures of aza-arenes eluted from a capillary column. The first is based on a combination of retention indexes (RI) and a post-column reaction. The RI of an aza-arene is calculated by using the incremental contributions of some atomic groups to RI. Once the molecular weight is determined by the mass spectrum, the possible compounds are picked up, based on comparison of the observed RI with the calculated RI values and information about the intramolecular environment around the nitrogen atom obtained from the degree of peak shift resulting from interaction with Ni(II). The second is due to combination of information from fluorescence spectrometry and TLC fractionation. The fluorescence spectrum allows the identification of the fused ring system.     

Comparative chemical ionization mass spectra of tricyclic antidepressant amines and related compounds

Positive-ion methane chemical ionization (CI) mass spectra were obtained for seven underivatized tricyclic amines: amitriptyline, nortriptyline, protriptyline, imipramine, desipramine, cyclobenzaprine and cyproheptadine. Some discrepancies in previously reported spectra were noted. Spectra of protriptyline, cyclobenzaprine and cyproheptadine are reported for the first time. Comparisons are made among the CI spectra and with electron ionization spectra, and relative abundances of major CI ions among the seven compounds are rationalized in terms of substituent and geometric effects. In most cases low-mass iminium ions from anion abstraction were more abundant than [MH]⁺. Hydride abstraction and adduct formation with reagent-gas ions were important. The three heterocyclic amines gave abundant [M]⁺˙ by electron transfer. Protonation at the nitrogen atom on the side chain followed by amine elimination gave tricyclic aromatic fragment ions.     

Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments

Diverse mass spectrometric instruments have been used to provide data for accurate mass and retention time (AMT) tag proteomics analyses, including ion trap, quadrupole time-of-flight, and Fourier transform mass spectrometry (FTMS). An important attribute of these instruments, beside mass accuracy, is their spectral resolution. In fact, the ability to separate peaks with close m/z values is likely to play a major role in enabling species identification and matching in analyses of very complex proteomics samples. In FTMS, resolution is directly proportional to the detection period and can therefore be easily tuned. We took advantage of this feature to investigate the effect of resolution on species identification and matching in an AMT tag experiment. Using an Arabidopsis thaliana chloroplast protein extract as prototypical 'real-life' sample, we have compared the number of detected features, the optimal mass tolerance for species matching, the number of matched species and the false discovery rate obtained at various resolution settings. It appears that while the total number of matches is not significantly affected by a reduction of resolution in the range investigated, the confidence level of identifications significantly drops as evidenced by the estimated false discovery rate.     

Robustness of biological activity spectra predicting by computer program PASS for noncongeneric sets of chemical compounds

The computer system PASS provides simultaneous prediction of several hundreds of biological activity types for any drug-like compound. The prediction is based on the analysis of structure-activity relationships of the training set including more than 30000 known biologically active compounds. In this paper we investigate the influence on the accuracy of predicting the types of activity with PASS by (a) reduction of the number of structures in the training set and (b) reduction of the number of known activities in the training set. The compounds from the MDDR database are used to create heterogeneous training and evaluation sets. We demonstrate that predictions are robust despite the exclusion of up to 60% of information.     

Kovats and lee retention indices determined by gas chromatography/mass spectrometry for organic compounds of environmental interest

Retention indices of standard organic compounds of environmental interest were determined by gas chromatography/mass spectrometry, using a DB-5 fused-silica capillary column. Retention indices are useful references for tentative compound identification by gas chromatography, or confirmation by gas chromatography/mass spectrometry. They provide elution order for isomers that might be indistinguishable based on mass spectra. Modified Kovats and Lee retention indices are given for polycyclic aromatic hydrocarbons; sulfur heterocycles; nitrogen heterocycles; aromatic amines; oxygen heterocycles; phenols; alcohols; ketones; alkanes; nitriles; and methylesters of fatty, dicarboxylic, and aromatic acids for comparison and reference. Retention index values for heterocycles by gas chromatography/mass spectrometry are comparable with gas chromatography values previously reported.     

Probability based matching of mass spectra. Rapid identification of specific compounds in mixtures

An automated system is described for computer examination of the mass spectrum of an unknown mixture for the presence of a specific compound. The probability that the compound is present is indicated as a ‘confidence index’ K; 2^K should signify the average number of compounds, selected at random, whose mass spectra would have to be examined to find data which match the target spectrum to the same degree as does the unknown. The value of K is determined by the uniqueness U of the m/e value, the abundance A, and the criterion of abundance agreement W of the matching peaks, and of the compound concentration D in the sample. Application to spectra from a variety of compounds, including illicit drugs, indicates that the system has high sensitivity and selectivity, and that the value of K is a useful index of the reliability of the identification. Initial testing of this system has utilized an automated quadrupole mass spectrometer under control of a dedicated microcomputer with sample introduction through a flash evaporator and membrane separator.     

A small computer data system for low resolution magnetic deflection mass spectrometers

A small on-line computer system for complete processing of low resolution magnetic deflection mass spectrometric data has been demonstrated. An interpolated mass scale accuracy of 200ppm was achieved for both repetitive (five or ten second cycle times) and single scan modes. Identification of m/e values above 1000 is possible with an accuracy of 500 ppm to m/e 3600. Mass scale assignments are time based and externally calibrated (pfa).     

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 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.     

Anomalous ions in the chemical ionization mass spectra of aromatic nitro and nitroso compounds

The appearance of [MH-30]⁺ ions in the chemical ionization mass spectra of aromatic nitro compounds may be due to their initial reduction to the corresponding amines within the ion source. Aromatic nitroso compounds may be similarly reduced to yield [MH-14]⁺ ions. The hydroxy derivatives of the nitroso compounds yield further anomalous ions at [MH-16]⁺ probably due to the reduction of the hydroxy groups.     

Computer-aided identification of compounds by comparison of mass spectra

A new identity-orientated search procedure for mass spectral libraries (IDS) was developed by extending the similarity search system SISCOM. The aim of IDS is an exact identification of pure compounds and mixtures on the basis of their mass spectra. The concepts and methods applied, e.g., filtering, feature selection and optimization with pattern recognition, are described. Chracteristics of IDS are summarized and demonstrated for several examples.     

Gas chromatographic retention indices of sulfur vesicants and related compounds

Temperature-programmed retention indices, relative to a n-alkane homologous series, were determined for 37 sulfur vesicant or vesicant-related compounds using DB-1, DB-5 and DB-1701 fused-silica capillary columns. Many of the compounds, including long chain dichloro, vinylchloro, vinylalcohol and macrocyclic compounds have either not been previously identified or have not been associated with sulfur vesicant analysis. Reproducibility of the retention indices, based on Van den Dool's equation, was excellent over the course of the study. In addition, changes in retention index (delta RI), which may enable the prediction of uncharacterized homologue chromatographic behaviour, were calculated for several homologous series.     

The mass spectra of reissert compounds

A series of Reissert compounds containing the quinoline, isoquinoline and phthalazine nuclei show the common feature in their mass spectra of the initial loss of the N-substituent and either of the substituents attached to the adjacent carbon atom.     

Negative chemical ionization mass spectra of multifunctional polar,and underivatized compounds of biological interest

Intense pseudomolecular ions were observed for underivatized, multifunctional compounds of low volatilty (e.g., bile acid conjugates, alkaloids, antibiotics) by employing the direct probe technique of NCI MS; especially effective was the use of CF₂CL₂ as the reagent gas for producing chloride ion adduct negative ions.