Identification of Silylated Derivatives of Alkylphosphonic, Alkylthiophosphonic, and Dialkylamidophosphoric Acids by Mass Spectrometry

Mass spectra were studied for silylated destruction products of toxic chemicals that belong to classes of alkylphosphonic, alkylthiophosphonic, and dialkylamidophosphoric acid derivatives. The analysis of mass spectra and the study of regularities in the fragmentation of some compounds of these classes revealed some characteristic features of the formation of fragment ions by electron impact. These features are related to the formation of ions that include the phosphoryldimethylcyclosiloxane or phosphorylthiodimethylcyclosiloxane fragment, and their formation is responsible for the majority of the most intense characteristic peaks in the mass spectrum.     

Unknown identification using reference mass spectra. Quality evaluation of databases

The high success of the “uncertified” mass spectrometry spectral collection started in 1956 demonstrated qualitatively that a partial reference mass spectrum, even one measured routinely, can be of real value. Correct matchings were still possible despite reference errors, which almost never led to close matches that were incorrect. This study shows quantitatively that the number of different compounds, not the number of peaks in a spectrum, is by far the most important determinant of database efficiency for identifying a “global” unknown. A statistical evaluation of matching performance shows that only 6, 12, and 18 peaks in a reference spectrum are 13%, 67%, and 96%, respectively, as valuable as hundreds of peaks. Also, a separately measured second spectrum of the same compound is 50% as valuable as the first. Database expansion that tripled the number of possible wrong answers only reduced the proportion of correct identifications by 5%. Corrections of a mass or abundance error in each of six reference spectra increase the database matching performance by as much as the addition of one spectrum of a new compound. A new “matching quality index” based statistically on these values indicates that the largest database is also by far the most effective for matching unknowns.     

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.     

Kombination von Feldionen- und Elektronestoß-Massenspektren zur Struckturbestimmung,Demonstriert am Beispiel von Monoterpenen

The field ionization and electron impact mass spectra of some monoterpenes are compared. Some general rules applicable also to other substances are derived, summarizing the new structural information that can be obtained by combination of field ionization and electron impact data. The general conclusions are: (1) By comparison of FI and EI mass spectra one can recognize which of the most intense peaks in the EI mass spectra are originating from rearrangement or multistip dissociation processes on the one hand, or from simple direct bond rupture on the other hand. (2) The molecular weight of each substance containing C, H, O, N atoms (or some of them) can be determined unambiguously by field ionization, even if there is no parent peak detectable by electron impact. (3) Extremely strong metastable peaks in the FI mass spectrum are indicative of the splitting off of a polar group from a highly branched carbon atom, under rearrangement of the molecular ion. (4) Ions of about double the molecular weight are often found in the FI mass spectra if the molecule contains carbonyl or hydroxyl groups, or conjugated multiple bonds in aliphatic compounds.     

Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification

Tandem mass spectra contain noisy peaks which make peak picking for peptide identification difficult. Moreover, all spectral peaks can be shifted due to systematic measurement errors. In this paper, a novel use of an isotope pattern vector (IPV) is proposed for denoising and systematic measurement error prediction. By matching the experimental IPVs with the theoretical IPVs of candidate fragment ions, true ionic peaks can be identified. Furthermore, these identified experimental IPVs and their corresponding theoretical IPVs are used in an optimization process to predict the systematic measurement error associated with the target spectrum. In return, the subsequent spectral data calibration based on the predicted systematic measurement error enhances the data quality. We show that such an integrated denoising and calibration process leads to significantly improved peptide and protein identification. Different from the commonly employed chemical calibration methods, our IPV‐based method is a purely computational method for individual spectra analysis and globally optimizes the use of spectral data. Copyright © 2009 John Wiley & Sons, Ltd.     

Spectroscopic Properties of Lumiflavin: A Quantum Chemical Study

In this work, the electronic structure and spectroscopic properties of lumiflavin are calculated using various quantum chemical methods. The excitation energies for ten singlet and triplet states as well as the analysis of the electron density difference are assessed using various wave function‐based methods and density functionals. The relative order of singlet and triplet excited states is established on the basis of the coupled cluster method CC2. We find that at least seven singlet excited states are required to assign all peaks in the UV/Vis spectrum. In addition, we have studied the solvatochromic effect on the excitation energies and found differential effects except for the first bright excited state. Vibrational frequencies as well as IR, Raman and resonance Raman intensities are simulated and compared to their experimental counterparts. We have assigned peaks, assessed the effect of anharmonicity, and confirmed the previous assignments in case of the most intense transitions. Finally, we have studied the NMR shieldings and established the effect of the solvent polarity. The present study provides data for lumiflavin in the gas phase and in implicit solvent model that can be used as a reference for the protein‐embedded flavin simulations and assignment of experimental spectra.     

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6‐311 + G* level of theory. This prediction is performed ‘ab initio’, i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^? when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.     

Comparison of algorithms and databases for matching unknown mass spectra

The most used algorithms for the identification of electron-ionization mass spectra are INCOS and probability based matching (PBM). For unknown spectra of high purity, ～75% of rank 1 answers are correct for both algorithms, matched against the National Institute of Standards and Technology 62,235 spectrum database. With matching criteria that retrieve 50% of the possible correct answers from the Wiley 228,998 spectrum database, 54% of the PBM and 42% of the INCOS answers are correct; for 85% purity unknowns, 48% and 27% are correct. For an unknown spectrum of two compounds, neither was reported in the first three INCOS answers; eight of the first ten PBM answers identify both components.     

An Enlarged Data Base of Electron-Ionization Mass Spectra

The computer-searchable data base of reference mass spectra described earlier has been increased in size by 76%, so that it now contains 139,859 different spectra of 118,144 different compounds. The average number of peaks per spectrum is 53. All spectra were examined for errors by the Probability Based Matching (PBM) and the Quality Index (QI) algorithms and by human inspection. An improvement to the QI algorithm is based on the Terwilliger suggestion concerning saturated spectra. The number of different elemental compositions of compounds has increased by 64%. By using unknowns from the original data base with PBM, the probability that these incorrectly match a new spectrum is only 33% of that of incorrectly matching a spectrum in the original data base, further demonstrating that the variety of data in the library has been substantially expanded. Including additional reference spectra (measured under different conditions) of the same compound in the data base reduced the proportion of incorrect best-matching spectra by 42%.     

Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self‐consistent peak‐picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto‐assignment routine used is based on branch‐and‐bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web‐based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.     

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

We present the first global computer-aided sequencing algorithm for the de novo determination of short nucleic acid sequences. The method compares the fragment ion spectra generated by collision-induced dissociation of multiply charged oligodeoxynucleotide-ions to the m/z values predicted employing established fragmentation pathways from a known reference sequence. The closeness of matching between the measured spectrum and the predicted set of fragment ions is characterized by the fitness, which takes into account the difference between measured and predicted m/z values, the intensity of the fragment ions, the number of fragments assigned, and the number of nucleotide positions not covered by fragment ions in the experimental spectrum. Smaller values for the fitness indicate a closer match between the measured spectrum and predicted m/z values. In order to find the sequence most closely matching the experimental spectrum, starting from a given nucleotide composition all possible oligonucleotide sequences are assembled followed by identification of the correct sequence by the lowest fitness value. Using this concept, sequences of 5- to 12-mer oligodeoxynucleotides were successfully de novo determined. High sequence coverage with fragment ions was essential for obtaining unequivocal sequencing results. Moreover, the collision energy was shown to have an impact on the interpretability of tandem mass spectra by the de novo sequencing algorithm. Experiments revealed that the optimal collision energy should be set to a value just sufficient for complete fragmentation of the precursor ion.     

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.     

MassBank: a public repository for sharing mass spectral data for life sciences

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron‐ionization mass spectrometry(EI‐MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)‐MSⁿ data of 2337 authentic compounds of metabolites, 11 545 EI‐MS and 834 other‐MS data of 10 286 volatile natural and synthetic compounds, and 3045 ESI‐MS² data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI‐MS² data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS² data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI‐MS² data on an identical compound under different collision‐induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21–23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. Copyright © 2010 John Wiley & Sons, Ltd.     

An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data

A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.     

Analysis of the volatile compounds in Senecio scandens Buch-Ham by gas chromatography-tandem mass spectrometry based on diversified scan technologies

Static headspace gas chromatography-tandem mass spectrometry was used to identify volatile compounds from Senecio scandens Buch-Ham. The elemental composition of compounds was confirmed by exploiting the tandem mass spectra of isotopic peaks from the precursor ion. Some isomers were well distinguished by the diversified scan technologies of tandem mass spectrometry (MS/MS). The MS/MS included a product ion scan, a precursor ion scan and a neutral loss scan. The results showed that 46 volatile compounds were completely identified, and the great of majority compounds were α-pinene (11.93%), n-caproaldehyde (9.02%) and dehydrosabinene (6.22%). This qualitative method is convenient and accurate and can be considered as a complementary identification method for the qualitative analysis of volatile compounds in complex samples.     

A mass-spectrometric study of arnifolin, a new sesquiterpene lactone from Arnica montana and A. foliosa

Summary The mass spectra of arnifolin and [D]arnifolin have been obtained, and the fragmentation of arnifolin under the action of electron impact has been studied.A scheme of the fragmentation of arnifolin explaining the main peaks in its mass spectrum has been put forward. The mass spectrum agrees well with the structure established for this substance.All-Union Scientific-Research Institute of Medicinal Plants. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 587–590, September–October, 1971.     

Chemical ionization and electron impact mass spectra of thiosulfinates,thiosulfonates and sulfinyl sulfones

The chemical ionization and electron impact mass spectra of some thiosulfinates, thiosulfonates and sulfinyl sulfones have been studied. The electron impact mass spectra of four of the six thiosulfonates show molecular ions of less than 1%. Inconclusive evidence was obtained for sulfenyl sulfinate type intermediates in the electron impact spectra of thiosulfonates. The electron impact spectra of thiosulfonates were similar to those of thiosulfonates. The chemical ionization (isobutane) mass spectra of thiosulfinates and thiosulfonates generally show protonated molecular ions [MH]⁺ as base peaks and [MH+1]⁺ and [MH+2]⁺ peaks.     

Analysis of dammar resin with MALDI‐FT‐ICR‐MS and APCI‐FT‐ICR‐MS

Comprehensive analysis of high‐resolution mass spectra of aged natural dammar resin obtained with Fourier transform ion cyclotron resonance mass spectrometer (FT‐ICR‐MS) using matrix‐assisted laser desorption/ionization (MALDI) and atmospheric pressure chemical ionization (APCI) is presented. Dammar resin is one of the most important components of painting varnishes. Dammar resin is a terpenoid resin (dominated by triterpenoids) with intrinsically very complex composition. This complexity further increases with aging. Ten different solvents and two‐component solvent mixtures were tested for sample preparation. The most suitable solvent mixtures for the MALDI‐FT‐ICR‐MS analysis were dichloromethane‐acetone and dichloromethane‐ethanol. The obtained MALDI‐FTMS mass spectrum contains nine clusters of peaks in the m/z range of 420–2200, and the obtained APCI‐FTMS mass spectrum contains three clusters of peaks in the m/z range of 380–910. The peaks in the clusters correspond to the oxygenated derivatives of terpenoids differing by the number of C₁₅H₂₄ units. The clusters, in turn, are composed of subclusters differing by the number of oxygen atoms in the molecules. Thorough analysis and identification of the components (or groups of components) by their accurate m/z ratios was carried out, and molecular formulas (elemental compositions) of all major peaks in the MALDI‐FTMS and APCI‐FTMS spectra were identified (and groups of possible isomeric compounds were proposed). In the MALDI‐FTMS and APCI‐FTMS mass spectrum, besides the oxidized C₃₀, triterpenoids also peaks corresponding to C₂₉ and C₃₁ derivatives of triterpenoids (demethylated and methylated, correspondingly) were detected. MALDI and APCI are complementary ionization sources for the analysis of natural dammar resin. In the MALDI source, preferably polar (extensively oxidized) components of the resin are ionized (mostly as Na⁺ adducts), whereas in the APCI source, preferably nonpolar (hydrocarbon and slightly oxidized) compounds are ionized (by protonation). Either of the two ionization methods, when used alone, gives an incomplete picture of the dammar resin composition. Copyright © 2012 John Wiley & Sons, Ltd.     

Automatic pre-interpretation of analytical information of GC/MS systems

Summary The procedure of using mass spectrometers as substance specific detectors for gas chromatographs often suffers from the fact that the required analytical information is not readily available from the mass spectrum. The mass spectrum contains the analytical information only in a kind of complex coding. Up to now, mass spectrometry has only been used to identify the unknown GC peaks, or to easily recognize previously known substances within the GC run. Applications in clinical or environmental chemistry, however, often require the recognition of one or more substances out of a whole group of compounds, e.g. drugs, metabolites, or poisons. This task can be performed by applying a technique which rapidly allows to classify the spectra with regard to their membership to such group of compounds. The decision whether a compound belongs to such a group or not is based on a statistical investigation of a large collection of known spectra. The basic principles of this method are discussed. Preliminary results of this method are presented, showing success rates in the range of 90–99%. The method permits to estimate the probability to be correct for a single decision. Possible applications are outlined.     

Distinction between glycosylamines and amadori products by mass spectrometry of their trimethylsilyl derivatives

The TMS-ethers of four glycosylamines and seven Amadori compounds have been investigated by electron impact mass spectrometry. The mass spectra of glycosylamine-TMS derivatives and of their isomeric Amadori rearrangement products are quite characteristic. The two types of compounds can be distinguished by a few characteristic peaks.