Chemical ionization mass spectrometry of trimethylsilylated carbohydrates and organic acids retained in uremic serum

After appropriate sample pretreatment and derivatization, uremic serum was investigated by combined high resolution gas chromatography and mass spectrometry, using both electron impact and chemical ionization methods. Electron impact and chemical ionization spectra of a number of identified (trimethylsilylated) carbohydrates and organic acids are compared. The utilization of chemical ionization mass spectrometry, with isobutane as the reagent gas, is discussed in detail. The influence of the reagent gas pressure on the total ion current and on the spectral appearance was studied. The identification of compounds, based on electron impact mass spectral data, was confirmed and often aided appreciably by using this technique. The chemical ionization spectra of trimethylsilyated alditols and aldonic acids, as well as of other organic acids showed protonated molecular ions, whereas aldoses did not. Differences with electron impact spectra are found mainly in the high mass region. The loss of one or more trimethylsilanol groups becomes the predominating fragmentation route at higher reagent gas pressures.     

Mass spectrometry of Alternaria mali toxins and related cyclodepsipeptides

The structures of AM-toxins I, II and III, host specific phytotoxic metabolites of Alternaria mali, can be readily deduced from low and high resolution mass spectral data, since the amino acids and their sequences are demonstrated by this technique. Additionally, the general fragmentation of these compounds by electron impact is discussed by comparing the spectra of analogous synthetic compounds.     

Systematic toxicological analysis: computer-assisted identification of poisons in biological materials

A new software was developed to improve the chances for identification of a "general unknown" in complex biological materials. To achieve this goal, the total ion current chromatogram was simplified by filtering the acquired mass spectra via an automated subtraction procedure, which removed mass spectra originating from the sample matrix, as well as interfering substances from the extraction procedure. It could be shown that this tool emphasizes mass spectra of exceptional compounds, and therefore provides the forensic toxicologist with further evidence-even in cases where mass spectral data of the unknown compound are not available in "standard" spectral libraries.     

The synthesis and characterization of nucleotide complexes involving an asymmetric metal

The synthesis of cobalt and chromium complexes of H₄ATP and H₄GTP in which the metal is asymmetric are reported. These compounds were characterized by visible spectroscopy, fast atom bombardment mass spectroscopy (FAB MS), and ³¹P NMR. The mass spectral data allow identification of the complexes to be made from ions in the molecular weight region. The effect of an asymmetric metal greatly alters the appearance of the ³¹P NMR spectra in comparison to complexes which do not have this feature. Complexes of uridine diphosphoglucose, UDPG, are also reported. The effect of an asymmetric metal ion on the chromatographic and spectral properties of the complexes are discussed.     

Identification of methotrexate and folic acid analogs by mass spectrometry

Methotrexate and folic acid analogs are polar molecules and attempts to obtain electron impact and chemical ionization mass spectra of these compounds by several laboratories have failed. We have found that methylation of this important class of compounds with diazomethane produces derivatives which are sufficiently volatile to allow their mass spectra to be recorded. The mass spectra of the methyl derivatives of five compounds, 4-amino-4-deoxy-N10-methylpteroylglutamic acid, 4-amimo-4-deoxypteroylglutamic acid, pteroylglutamic acid, 4-amino-4-deoxypteroic acid and N10-methylpteroylglutamic acid are presented, and the fragmentation pathways of these compounds discussed.     

An Interpretation of the Mass Spectra of Salinomycin and Its Derivatives

Salinomycin is a new polyether antibiotic elaborated by Streptomyces albus. An interpretation of the mass spectra of salinomycin and its derivatives has been achieved with the aid of high resolution mass spectrometry along with measurement of the metastable ions. Interesting aspects of the mass spectral data of these compounds are that the characteristic cleavage occurred at the ring C of the tricyclic spiroketal system, and that the sodium salts of salinomycin itself and some derivatives thereof are volatile enough to give distinct spectra which showed fragmentations comparable with those of the free acid and the methyl ester.

An interpretation of the principal fragment ions and their formation mechanism for salinomycin and its derivatives is discussed.     

In vivo labeling with stable isotopes as a tool for the identification of unidentified peaks in the metabolome analysis of Corynebacterium glutamicum by GC/MS

Of the hyphenated techniques used for metabolic profiling of cell and tissue extracts, GC/MS is in some ways advantageous as it allows the simultaneous fingerprinting of chemically very different metabolites, and the electron impact mass spectra recorded in many cases lead to unambiguous identification of the compounds. However, prior to chromatography, the hydrophilic substances of the cell extracts have to be converted to vaporizable derivatives, the mass spectra of which often are not known or not listed in the available spectral libraries, even if they are derived from simple biochemicals. Thus, numerous chromatographic peaks remain as yet unidentified. Attempts to identify these peaks afford the acquisition of more data on these compounds. The value of in vivo labeling of metabolites with (13)C and (15)N for this purpose is described.     

Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS

An overview is presented of gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS), the two major hyphenated techniques employed in metabolic profiling that complement direct 'fingerprinting' methods such as atmospheric pressure ionization (API) quadrupole time-of-flight MS, API Fourier transform MS, and NMR. In GC/MS, the analytes are normally derivatized prior to analysis in order to reduce their polarity and facilitate chromatographic separation. The electron ionization mass spectra obtained are reproducible and suitable for library matching, mass spectral collections being readily available. In LC/MS, derivatization and library matching are at an early stage of development and mini-reviews are provided. Chemical derivatization can dramatically increase the sensitivity and specificity of LC/MS methods for less polar compounds and provides additional structural information. The potential of derivatization for metabolic profiling in LC/MS is demonstrated by the enhanced analysis of plant extracts, including the potential to measure volatile acids such as formic acid, difficult to achieve by GC/MS. The important role of mass spectral library creation and usage in these techniques is discussed and illustrated by examples.     

Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.     

In silico fragmentation for computer assisted identification of metabolite mass spectra

Background  

Mass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to the precursor mass, tandem MS spectra carry informative fragment peaks, but the coverage of spectral libraries of measured reference compounds are far from covering the complete chemical space. Compound libraries such as PubChem or KEGG describe a larger number of compounds, which can be used to compare their in silico fragmentation with spectra of unknown metabolites.     

Electrospray ionization mass spectrometry of platinum anticancer agents.

Quantification and identification of platinum drugs and their metabolites in biological samples has always been difficult because these compounds are thermally unstable, non-volatile and insoluble. We have demonstrated that electrospray ionization mass spectrometry can be a valuable technique for direct mass spectral analysis of platinum anticancer agents and for obtaining structural information as a result of fragmentation. Full-scan spectra were obtained with approximately 10 pmol samples. These results show the potential of applying this technique in pharmacokinetic studies of platinum anticancer drugs.     

Optimization of mass spectral features in MALDI-TOF MS profiling of Acinetobacter species

The influence of the matrix solution, sample form and deposition technique on the quality MALDI-TOF mass spectra was examined and assessed with the aim to improve MALDI-TOF MS performance for the identification of microorganisms and to enable automatic spectra acquisition. It was observed that the use of matrix compounds ferulic and sinapinic acid may result in improved mass spectral features, in terms of signal resolution and S/N ratio, as compared to alpha-cyano-4-hydroxycinnamic acid, which was, on the other hand, found to be the only matrix compound that enabled fully automatic mass spectra acquisition. The robustness of the whole sample preparation procedure was then assessed on a set of 25 strains of four Acinetobacter species. Results showed reproducible detection of subtle mass spectral differences between strains belonging to the same species, although they do not confirm the possibility of reliable strain typing.     

HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models.

Peptide identification by tandem mass spectrometry is the dominant proteomics workflow for protein characterization in complex samples. The peptide fragmentation spectra generated by these workflows exhibit characteristic fragmentation patterns that can be used to identify the peptide. In other fields, where the compounds of interest do not have the convenient linear structure of peptides, fragmentation spectra are identified by comparing new spectra with libraries of identified spectra, an approach called spectral matching. In contrast to sequence-based tandem mass spectrometry search engines used for peptides, spectral matching can make use of the intensities of fragment peaks in library spectra to assess the quality of a match. We evaluate a hidden Markov model approach (HMMatch) to spectral matching, in which many examples of a peptide's fragmentation spectrum are summarized in a generative probabilistic model that captures the consensus and variation of each peak's intensity. We demonstrate that HMMatch has good specificity and superior sensitivity, compared to sequence database search engines such as X!Tandem. HMMatch achieves good results from relatively few training spectra, is fast to train, and can evaluate many spectra per second. A statistical significance model permits HMMatch scores to be compared with each other, and with other peptide identification tools, on a unified scale. HMMatch shows a similar degree of concordance with X!Tandem, Mascot, and NIST's MS Search, as they do with each other, suggesting that each tool can assign peptides to spectra that the others miss. Finally, we show that it is possible to extrapolate HMMatch models beyond a single peptide's training spectra to the spectra of related peptides, expanding the application of spectral matching techniques beyond the set of peptides previously observed.     

Structural characterization of wax esters by electron ionization mass spectrometry

The interpretation of the electron ionization mass spectra of straight-chain and methyl-branched saturated and unsaturated wax esters (WEs) is discussed in this study based on the spectra of 154 standards. The most important fragments indicative of the structure of the acid and alcohol chains are identified and summarized for WEs with various number of double bonds in the chains. Briefly, most WEs provide acylium ions allowing structural characterization of the acid part, whereas the alcohol part gives corresponding alkyl radical cations. The elemental composition of selected important fragments is established from a high-resolution accurate mass analysis. The ion abundances are discussed with respect to the length and unsaturation of the aliphatic chains. The interpretation of the spectra of branched or unsaturated WEs requires the recognition of small but important peaks that are difficult to discern among the other fragments. We demonstrate that such fragments are easily detected in differential mass spectra. This approach requires spectra of WE standards (e.g., straight-chain analogs in the case of branched WEs) recorded under the same experimental conditions. The WEs mass spectral database provided in the supplemental data can be used as a reference for the analysis of the GC/EI-MS data.     

Sitting above the maze: recent model discoveries in molecular science

The 2013 Nobel Prize in Chemistry has convinced the world that how important the role that computational sciences play in chemical and materials sciences. In this review, computational methods and rational molecule design, including quantum mechanics and molecular mechanics methods, have been applied to study electronic structures and the interactions in a number of important applications at molecular level. The applications which include bioactive compounds, drug candidates and photoactive molecules at Swinburne University in the past several years are discussed. The research is in close collaboration with world class experimental groups from spectroscopy, organic and medicinal synthesis laboratories and most recently to γ-ray spectroscopy as well as other theory groups in the world. Ionisation spectra of biomolecules and bioactive compounds including amino acids, DNA bases, cyclic dipeptides, drug candidates, complexes and photoactive molecules are discussed. Most recent projects such as infrared spectral studies of ferrocene, rational design of organic dyes in solar cell applications, and recent development in γ-ray spectra of positron annihilation in molecules are highlighted.     

Steroid epimers studied by different mass spectrometric methods

The combined use of different mass spectrometric ionization methods and MS/MS techniques provide the possibility to differentiate between stereoisomers or epimers. In this paper the mass spectral decomposition of 11alpha- and 11beta-substituted estrans was studied. Distinctive stereochemical effects have been observed in their fast atom bombardment product ion spectra. In the electron ionisation (EI) mode, the 5alpha- and 5beta-hydroxylated compounds showed significant differences in the abundance of water elimination. Mass spectrometry has proved to be an effective tool when stereoisomer steroids are compared.     

Gas chromatographic/mass spectrometric analysis of specific isomers of polychlorodibenzofurans

The gas chromatographic/mass spectrometric characteristics of 26 congeners of polychlorinated dibenzofurans, previously characterized by specific synthetic routes and by standard spectroscopic techniques, have been evaluated. The electron impact mass spectra are not particularly isomer-specific, though 2,3,7,8-tetrachlorodibenzofuran is distinguishable on this basis from the three other tetrachloro isomers investigated in this work. Positive ion methane chemical ionization mass spectra do show a greater degree of isomer distinction, and are reasonably reproducible. Electron attachment negative ion spectral characteristics are also presented. Preliminary results on negative ion chemical ionization mass spectra, obtained using methane plus small amounts of oxygen as reagent gas, are reported.     

Synthesis and characterization of some aminoarsonium chlorides

R₃As reacts with NR′R″Cl to give good yields of a new homologous series of aminoarsonium chlorides, [R₃AsNR′R″]Cl, in which R = Me, Et, n-Pr, and Ph; R′ and/or R″ = H, Me. IR, NMR, mass, and X-ray spectral data suggest that the arsenic is tetra- coordinate. Electfical conductivity and temperature and concentration dependent NMR studies suggest that hydrogen-bonding interactions are important in solution. Quaternization of the arsenic produces a downfield ¹H NMR chemical shift for the protons in the alkyl chains and a change from non-equivalence to equivalence of the C-1 protons. The NMR data are compared with those for the analogous phosphorus compounds. The electron impact, chemical ionization, and negative ion mass spectral data and fragment ion identities are given for the compounds. Ions corresponding to a variety of AsCl containing species, in addition to those associated .with fragmentation of the R₃As moieties, are observed in the EI mass spectra. AsN, AsNAs, and AsNAsN containing fragments are observed in the Cl mass spectra and AsCl bonding species in the NI mass spectra. A preliminary X-ray diffraction study of [n-Pr₃AsNH₂]Cl indicates near tetrahedral geometry about the arsenic atom.     

Complete 1H-NMR spectral assignments for globotriaosyl-Z- and isoglobotriaosyl-E-ceramide

Two-dimensional scalar-correlated (COSY) 1H-NMR spectra of the title compounds, and phase-sensitive COSY spectrum of lactosylceramide, have been fully assigned and some spectral reassignments for related structures suggested. Glycosylation-induced shifts, and shielding by Z- and E-ceramide residues are discussed.