Modeling of isotopomeric cluster of the molecular ion

The occurrence of poly-isotopic elements in a molecule or ion can result in complex isotopomeric cluster of an ion. The “isotopomer” better and correctly indicates different isotopic compositions of a molecule (compound) or ion and not a single atom. The ions of organic compounds show in accurate mass spectra single, isolated peaks or narrow sub-clusters regardless of their molecular masses. The occurrence of a PIE makes the molecular ion cluster more complex and significantly influences the location of the most abundant peak and the form of the cluster. The present study is an attempt at answering the following question: what is the mechanism of the molecular ion’s isotopomeric cluster formation and is it step-by-step predictable? The accurate mass-resolved isotopomer cluster can be predicted from accurate masses and abundances of the stable isotopes. The cluster consists of several sub-patterns, each of which is composed of near signals (at the same nominal m/z). The range of the sub-cluster usually does not exceed 0.005 u. The low-resolution cluster can be predicted from the high-resolution pattern by addition of all peaks occurring over a given narrow mass range (m/z - 0.5; m/z+0.49). Surprisingly, predicting the accurate mass cluster is simpler than predicting the low-resolution one. A compliance of the model results with the experimental ones suggests a correct prediction. Figure: Isotopomeric genesis of the mass spectral cluster.

A rapid boiling method for the preparation of bacterial plasmids

Compounds separated on polyamide thin-layers and located in an appropriate manner can be introduced directly into the ion source of the mass spectrometer together with the chromatographic polyamide adsorbent. In spite of the large excess of polyamide, excellent mass spectra are obtained exhibiting low backgrounds. In this way, organic compounds can be rationally identified on a nanogram scale not requiring reference substances. The application of the procedure is described for selected compounds of different classes of substances, e.g., phenols, steroids, nucleosides, biogenic amines, and amino acids.     

Characterization of the macrocyclic carbon suboxide factors as potent Na,K-ATPase and SR Ca-ATPase inhibitors

Recently discovered macrocyclic carbon suboxide (MCS) factors with the general formula (C(3)O(2))(n) were found to strongly inhibit rabbit and rat Na,K-ATPase as well as SR Ca-ATPase. Highly active MCS factors were obtained by a base/acid treatment of their lipophilic precursor isolated from plants. In the ESI-MS spectra, the dominant molar mass ion of 431 Da corresponds to a 1:1 complex of the carbon suboxide hexamer (n=6; M(r)=408 Da) with a Na(+) ion. Additional mass ions identified in positive and negative ion mode were assigned as complexes of the MCS hexamer (n=6) and octamer (n=8) with Na(+) or with TFA(-) in various ratios. The dominant mass ion values of these active MCS factors from plants are also found in mass spectra of previously described endogenous digitalis-like factors (EDLF) from animals. This would suggest that ubiquitously distributed MCS factors may function as putative endogenous regulatory substances of Na,K-ATPase and possibly of other ATPases. With the symmetric display of several equivalent carbonyl or hydroxy groups, the structure of MCS factors is particularly suited for interactions with proteins and other bio-molecules. This could explain the high biological activity and the unusual properties of the MCS factors.     

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.     

Liquid chromatography/mass spectrometry analysis of mixtures of rhamnolipids produced by Pseudomonas aeruginosa strain 57RP grown on mannitol or naphthalene.

Liquid chromatography/mass spectrometry using electrospray ionisation was used to analyse rhamnolipids produced by a Pseudomonas aeruginosa strain with mannitol or naphthalene as carbon source. Identification and quantification of 28 different rhamnolipid congeners was accomplished using a reverse-phase C(18) column and a 30 min chromatographic run. Isomeric rhamnolipids that were not chromatographically resolved could be identified by interpretation of their mass spectra and their relative proportions estimated. The most abundant rhamnolipid produced on mannitol contained two rhamnoses and two 3-hydroxydecanoic acid groups. The most abundant rhamnolipid produced from naphthalene contained two rhamnoses and one 3-hydroxydecanoic acid group.     

Studies related to the metabolism of anabolic steroids in the horse: the metabolism of 1-dehydrotestosterone and the use of fast atom bombardment mass spectrometry in the identification of steroid conjugates

The metabolism and urinary excretion of 1,2(n)-3H-1-dehydrotestosterone were studied in cross-bred gelded horses. Approximately 40% of the dose was excreted in 24 h. The steroid metabolites were extracted by Amberlite XAD-2 resin and fractionated into glucuronides and sulphoconjugates. Unchanged 1-dehydrotestosterone was the only component identified by gas chromatography mass spectrometry after solvolysis of the sulphoconjugates. Positive and negative ion fast atom bombardment mass spectra were obtained on the purified 1-dehydrotestosterone sulphoconjugate isolated from horse urine and on the alkali metal salts of three standard steroid conjugates. Spectra obtained in the different modes were of comparable intensity. Positive ion spectra were generally more complex due to the formation of alkali metal adduct ions containing several sodium cations. The most abundant ion in the negative ion spectra corresponded to the loss of the alkali metal cation to give [M]-. Thus, the structure of a conjugate can be defined from the combination of mass spectrometric techniques.     

Reaction mechanism and fragment ion structure determination of deprotonated small oligosaccharides, studied by negative ion fast atom bombardment (tandem) mass spectrometry

The negative ion mass spectrometric characteristics of a series of di- and trisaccharides and the tetrasaccharide stachyose have been studied using fast atom bombardment mass spectrometry. The molecular weight of the compounds can easily be derived from their mass spectra, which all show an abundant [M - H]- ion peak. The application of metastable ion and collisional activation techniques to selected pseudomolecular and fragment ions appears to be appropriate for the determination of the position and anomeric type of linkage in the molecules, and provides information concerning the monosaccharide units involved. Important fragmentation reactions have been traced and reaction mechanisms, supported by deuterium labelling experiments, are proposed. An experiment describing the application of the findings of this study to a glycosphingolipid molecule demonstrates its potential value for biological systems.     

Defining parameters for homology-tolerant database searching.

De novo interpretation of tandem mass spectrometry (MS/MS) spectra provides sequences for searching protein databases when limited sequence information is present in the database. Our objective was to define a strategy for this type of homology-tolerant database search. Homology searches, using MS-Homology software, were conducted with 20, 10, or 5 of the most abundant peptides from 9 proteins, based either on precursor trigger intensity or on total ion current, and allowing for 50%, 30%, or 10% mismatch in the search. Protein scores were corrected by subtracting a threshold score that was calculated from random peptides. The highest (p < .01) corrected protein scores (i.e., above the threshold) were obtained by submitting 20 peptides and allowing 30% mismatch. Using these criteria, protein identification based on ion mass searching using MS/MS data (i.e., Mascot) was compared with that obtained using homology search. The highest-ranking protein was the same using Mascot, homology search using the 20 most intense peptides, or homology search using all peptides, for 63.4% of 112 spots from two-dimensional polyacrylamide gel electrophoresis gels. For these proteins, the percent coverage was greatest using Mascot compared with the use of all or just the 20 most intense peptides in a homology search (25.1%, 18.3%, and 10.6%, respectively). Finally, 35% of de novo sequences completely matched the corresponding known amino acid sequence of the matching peptide. This percentage increased when the search was limited to the 20 most intense peptides (44.0%). After identifying the protein using MS-Homology, a peptide mass search may increase the percent coverage of the protein identified.     

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.     

Structuring of bacterioplankton communities by specific dissolved organic carbon compounds

The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis 'fingerprints' and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.     

干旱区典型盐生植物群落土壤团聚体组成及有机碳分布

以干旱区玛纳斯河流域扇缘带为研究区,分析了花花柴(Karelinia caspia)、雾冰藜(Bassia dasyphylla)、梭梭(Haloxylon ammodendron)和柽柳(Tamarix ramosissima)4个典型盐生植物群落土壤团聚体的组成及有机碳分布。研究表明:不同植物群落土壤团聚体均以0.25—0.053 mm粒径为主,占了46.7%—74.6%,且与其他粒径差异显著(P0.05),0.25 mm和0.053mm粒径土壤团聚体含量较少,仅占7.8%—43%。梭梭群落0.25 mm团聚体平均含量较高,达32%。不同植被群落土壤总有机碳介于2.01—8.73 g/kg之间,不同粒径团聚体有机碳介于1.70—13.68 g/kg之间。不同群落之间,梭梭和柽柳群落总有机碳和团聚体有机碳含量均相对较高,且随着土层深度下降而下降。不同粒径之间,有机碳含量在0.25—0.053 mm粒径最低,在0.25 mm和0.053 mm粒径中最高,呈现"V"型分布且差异显著(P0.05)。0.25—0.053 mm团聚体中有机碳含量的贡献率最高,达43.43%,而0.053 mm粒级贡献率较低,但有机碳含量较高,说明了小粒径团聚体对有机碳保护能力较强。土壤有机碳含量与0.25—0.053 mm团聚体含量呈显著负相关(P0.05)。而从整体来看,梭梭群落0.25 mm团聚体比例较高,且土壤有机碳和团聚体有机碳含量也较高,说明了在该研究区,梭梭群落聚集土壤养分能力较强,相对其他群落更有利于土壤有机碳的积累。     

The implications and limitations of the findings of the Viking organic analysis experiment

Summary The gas chromatograph mass spectrometer instrument of the Viking mission has demonstrated the absence of organic compounds in the immediate surface layer of the two landing sites. The demonstration of the successful operation of the instrument (comparison of ground-based test data with those obtained during interplanetary flight and the data from the surface of the planet) and its limitations (e.g., the detection of highly cross-linked polymers or polymeric carbon suboxide) are reviewed. The measurements for bound water are based on indirect data, the detectability of evolved carbon dioxide and ammonia is poor, and oxygen, liberated from the soil samples, can not be detected.     

Evidence for the contribution of humic substances to conditioning films from natural waters

The presence of humic substances in conditioning films deposited on solid surfaces from natural waters was investigated using electron impact (EI), chemical ionization (CI) and secondary ion time-of-flight mass spectrometry (TOFSIMS). EI and CI spectra of a freshwater sample from a pond in Centennial Park, Sydney, Australia, showed a high degree of similarity with spectra of humic acids purchased from Fluka and Sigma as well as with reference humic acid and fulvic acid from the International Humic Substances Society, suggesting that most of the organic matter in the pond water was of humic origin. All the complex electron impact mass spectra feature series of high-intensity ions separated by 14 Da or 18 Da, which can be attributed to CH(2) and OH(2) respectively. Thermal desorption profiles of all samples generated by EI and CI were qualitatively similar. The secondary desorption peaks were less well-defined in CI compared to EI. Positive ion thermal desorption profiles displayed a two-step ionisation, with a sharp and well-defined initial desorption peak at t～50s, followed by a broader desorption peak with a maximum intensity at t ～ 100 s post-heating. The Centennial Park natural organic matter (NOM) differed from the other humic fractions in having two additional broad desorption peaks between the two described previously, and a less-defined initial peak. Infrared spectroscopy showed that proteinaceous matter in the lake water was insignificant in comparison with functional groups indicative of humic substances. TOFSIMS characterization showed almost identical spectra for Aldrich humic acid and Centennial Park NOM in the high mass region of 2000 Da to 3000 Da. Each spectrum contains approximately 25 groups of ion peaks, separated by 74 Da from group to group. Each group is composed of 6 or 7 individual peaks. The spectral features are consistent with a macromolecular structure of humic acid where aromatic rings are joined to the macrostructure via aliphatic spacer molecules.     

Organic Carbon in a Eutrophic Fishpond

Accumulation of dissolved organic carbon (DOC) was studied in a eutrophic pond and in cultures of Scenedesmus abundans. Samples of pond water and media were treated with a cation exchanger in Na cycle and chromatographed on Sephadex G 25 and G 10. — UV spectra of the peak fractions were recorded. In the pond about half of the organic carbon is in fractions with an apparent molecular weight (AMW) of 500–1000, while in the algal medium (after cultivation) most of organic carbon has an AMW of about 120. These and spectral data did not suggest that aromatics and compounds with conjugated double bonds were major organic constituents of DOC.     

Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein.     

Structural and quantitative analysis of N-linked glycans by matrix-assisted laser desorption ionization and negative ion nanospray mass spectrometry

Negative ion electrospray (ESI) fragmentation spectra derived from anion-adducted glycans were evaluated for structural determination of N-linked glycans and found to be among the most useful mass spectrometric techniques yet developed for this purpose. In contrast to the more commonly used positive ion spectra that contain isobaric ions formed by losses from different regions of the molecules and often lead to ambiguous deductions, the negative ion spectra contain ions that directly reflect structural features such as the branching pattern, location of fucose, and the presence of bisecting GlcNAc. These structural features are sometimes difficult to determine by traditional methods. Furthermore, the spectra give structural information from mixtures of isomers and from single compounds. The method was evaluated with well-characterized glycans from IgG and used to explore structures of N-linked glycans released from serum glycoproteins with the aim of identifying biomarkers for cancer. Quantities of glycans were measured by ESI and by matrix-assisted laser desorption ionization mass spectrometry; each technique produced virtually identical results for the neutral desialylated glycans.     

Mathematical modelling of the anaerobic digestion process: Application of dynamic mass-energy balance

The method of mass and energy balance was used in the design of a dynamic model of anaerobic digestion of complex organic substrates with production of methane. Distribution of mass flow, represented by the most abundant elements (C, H, N, O), and energy flow, represented by redoxons (available electrons), into gas and liquid output streams is influenced by environmental conditions in a continuous flow digester. Two pathways of methane generation,via cleavage of acetate andvia carbon dioxide reduction by hydrogen, are described in the model. The model was compared with experimental data from laboratory and pilot-plant experiments     

Molecular Regulation of β-Lactam Biosynthesis in Filamentous Fungi

The most commonly used β-lactam antibiotics for the therapy of infectious diseases are penicillin and cephalosporin. Penicillin is produced as an end product by some fungi, most notably by Aspergillus (Emericella) nidulans and Penicillium chrysogenum. Cephalosporins are synthesized by both bacteria and fungi, e.g., by the fungus Acremonium chrysogenum (Cephalosporium acremonium). The biosynthetic pathways leading to both secondary metabolites start from the same three amino acid precursors and have the first two enzymatic reactions in common. Penicillin biosynthesis is catalyzed by three enzymes encoded by acvA (pcbAB), ipnA (pcbC), and aatA (penDE). The genes are organized into a cluster. In A. chrysogenum, in addition to acvA and ipnA, a second cluster contains the genes encoding enzymes that catalyze the reactions of the later steps of the cephalosporin pathway (cefEF and cefG). Within the last few years, several studies have indicated that the fungal β-lactam biosynthesis genes are controlled by a complex regulatory network, e.g., by the ambient pH, carbon source, and amino acids. A comparison with the regulatory mechanisms (regulatory proteins and DNA elements) involved in the regulation of genes of primary metabolism in lower eukaryotes is thus of great interest. This has already led to the elucidation of new regulatory mechanisms. Furthermore, such investigations have contributed to the elucidation of signals leading to the production of β-lactams and their physiological meaning for the producing fungi, and they can be expected to have a major impact on rational strain improvement programs. The knowledge of biosynthesis genes has already been used to produce new compounds.     

Silver(I) carboxylates. I. Mass spectra and low frequency infrared spectra

The mass spectra six silver(I) carboxylates, AgO₂CR, (R = Me, Et, Prⁿ, Ph, CF₃ and (CF₂)₂CF₃) show these compounds to be dimeric in the vapour phase, the base peak being the ion Ag₂(O₂CR)⁺ in each case. Two fragmentation pathways are observed. The alkyl carboxylates initially lose mainly RCO₂· from the radical ion Ag₂O₂CR)₂⁺, whereas the benzoate and the perfluorocarboxylates also easily lose carbon dioxide from the radical ion leading to the formation of abundant organosilver ions. The low frequency (500−40 cm⁻¹) infrared spectra of these silver(I) carboxylates are compared with the spectra of the copper(I) analogues and bands selected which may be assigned to predominantly skeletal modes.     

The electron impact, chemical ionization and fast atom bombardment positive ion mass spectra of 1,2-bis(sulfonyl)methylhydrazines.

A series of bis(sulfonyl)-1-methylhydrazines were analyzed by positive ion electron impact (EI), chemical ionization (CI) and fast atom bombardment (FAB) mass spectrometry. Since these compounds showed activity against the L1210 leukemia, an understanding of their mass spectral behavior is important should the structural characterization of metabolites be required. FAB proved to be the most useful technique, generally providing abundant protonated molecule ion peaks, in contrast to the weak peaks observed with CI (ammonia or isobutane) and the total absence of molecular ion peaks in the EI mass spectra. In addition, utilizing FAB eliminated the problem of thermal decomposition, which was very difficult to control under EI and CI experimental conditions. Fragments observed in FAB and CI mass spectra were consistent with protonation at the methyl-bearing nitrogen. One can locate the R1 and R2 moieties relative to the methyl-bearing nitrogen in FAB and CI by assigning that nitrogen as the site of protonation, with subsequent elimination of R2SO2H.