Computerized Interpretation of the Electron Ionization Mass Spectra of Nucleoside TMS Derivatives

Abstract

A computer program has been developed for the automated interpretation of mass spectra of TMS derivatives of nucleosides found in human urine. The m/z values in the unknown spectrum are compared to m/z values of 3 different ion series commonly observed in the mass spectra of nucleoside TMS derivatives.¹ If a correlation exists, the unknown spectra are marked with color according to the scheme: 1) blue—molecular ion series, 2) red—base ion series and 3) yellow—sugar ion series. The program suggests a structural assignment for each of the marked ions and calculates a series related ion current. The calculated ion current is used to assign the of sugar contained in the unknown nucleoside.     

Chemical Modification and Structure-Activity Correlation of Salinomycin

A number of the chemically modified compounds of salinomycin have been prepared and the structure-activity correlation between complexation affinity for cations, ion transport ability and antimicrobial activity have been investigated.

The results indicate that the terminal carboxylic acid, β-hydroxyketone and allylic alcohol functions in the molecule played an important role in the exhibition of biological activity of the antibiotic.

On the basis of these data, it was concluded that there is a closer parallelism between the antimicrobial and ion-transport activities of salinomycin and its derivatives.     

Synthesis of the Deuterated Sex Pheromone Components of the Grape Borer,Xylotrechus pyrrhoderus

Adult males of the grape borer, Xylotrechus pyrrhoderus, secrete (S)-2-hydroxy-3-octanone [(S)-1] and (2S,3S)-2,3-octanediol [(2S,3S)-2] from their nota of prothoraces as sex pheromone components. Their structural similarity suggests that one of them is the biosynthetic precursor of the other component. In order to confirm the biochemical conversion, deuterated derivatives of both components were synthesized by starting from a Wittig reaction between hexanal and an ylide derived from D₅-iodoethane and ending with enantiomeric resolution by chiral HPLC. The molecular ions of 1 and 2 could scarcely be detected by using a GC-MS analysis, and the labeled compounds showed similar mass spectra to the unlabeled pheromone components. However, several fragment ions, including four deuterium atoms, were observed in the mass spectra of their acetate derivatives, indicating that the conversion could be confirmed by examining a compound with the diagnostic ions after acetylation of the volatiles collected from insects treated with the labeled precursors.     

The Mass Spectra of the Lankacidin Antibiotics

Bundlins A and B, antibiotics elaborated by Streptomyces sp. 6642 GC₁, have the unique structures which possess a seventeen-membered carbon skeleton fused with an unusual β-keto-δ-Mactonic system and a pyruvamide side chain. In the course of the structural studies of the antibiotics, we found that these compounds showed the interesting fragmentations in their mass spectra and in consequence, the investigation about the interpretation of the principal peaks together with their formation mechanism was undertaken by the aid of high resolution mass spectrometry and the measurement of meta stable ions. In addition to the two antibiotics, the mass spectra of related compounds designated T–2636 D and T-2636 F were also investigated.     

Mass spectra of prostaglandins. IV. Trimethylsilyl derivatives of prostaglandins of the F series

The mass spectra of the trimethylsilyl ester trimethylsilyl ether derivatives of prostaglandins F_1α, F_2α and F_2β are reported and discussed. Accurate masses from the high resolution spectra of these compounds are also presented. These spectra are interpreted with the aid of those of the corresponding d₉-trimethylsilyl derivatives and selectively labeled trimethylsilyl ester-d₉-trimethylsilyl ether derivatives. It was found that metastabledefocusing was helpful in elucidation of the mechanisms of formation of some ions.     

On the use of ESI‐QqTOF‐MS/MS for the comparative sequencing of nucleic acids

The usability of a quadrupole—quadrupole—time‐of‐flight (QqTOF) instrument for the tandem mass spectrometric sequencing of oligodeoxynuleotides was investigated. The sample set consisted of 21 synthetic oligodeoxynucleotides ranging in length from 5 to 42 nucleotides. The sequences were randomly selected. For the majority of tested oligonucleotides, two or three different charge states were selected as precursor ions. Each precursor ion was fragmented applying several different collision voltages. Overall 282 fragment ion mass spectra were acquired. Computer‐aided interpretation of fragment ion mass spectra was accomplished with a recently introduced comparative sequencing algorithm (COMPAS). The applied version of COMPAS was specifically optimized for the interpretation of information‐rich spectra obtained on the QqTOF. Sequences of oligodeoxynucleotides as large as 26‐mers were correctly verified in >94% of cases (182 of 192 spectra acquired). Fragment ion mass spectra of larger oligonucleotides were not specific enough for sequencing. Because of the occurrence of extensive internal fragmentation causing low sequence coverage paired with a high probability of assigning fragment ions to wrong sequences, tandem mass spectra obtained from oligonucleotides consisting of 30 and more nucleotides could not be used for sequence verification neither manually nor with COMPAS. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 401–409, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Selectivity of cation transport across lipid membranes by the antibiotic salinomycin

The ionophoric antibiotic salinomycin is in the phase of preclinical tests against several types of malignant tumors including breast cancer. Notwithstanding, the data on its ion selectivity, although being critical for its therapeutic activity, are rather scarce. In the present work, we studied the ability of salinomycin to exert cation/H⁺-exchange across artificial bilayer lipid membranes (BLM) by measuring electrical potential on planar BLM in the presence of a protonophore and fluorescence responses of the pH-sensitive dye pyranine entrapped in liposomes. The following order of ion selectivity was obtained by these two methods: K⁺ > Na⁺ > Rb⁺ > Cs⁺ > Li⁺. Measurements of the monovalent cation-induced quenching of fluorescence of thallium ions in methanol showed that salinomycin effectively binds potassium and calcium but poorly binds sodium and lithium ions. At high concentrations, salinomycin transports Ca²⁺ through membranes of liposomes and mitochondria, as measured by using the calcium-sensitive dye Fluo-5 N. The data obtained can be used in the mechanistic studies of the anti-tumor activity of salinomycin and its selective cytotoxicity towards cancer stem cells.     

Amino acid sequencing by gas chromatography-mass spectrometry using perfluoro-dideuteroalkylated peptide derivatives: B. Interpretation of the mass spectra

The mass spectra of the O-trimethylsilylated trifluoro-dideuteroethyl polyamino alcohols, produced by LiAlD₄-reduction and O-trimethylsilylation of N-trifluororacetyl oligopeptide methyl esters, are evaluated. Characteristic mass spectra of derivatives are shown which are derived from peptides containing all protein amino acids including Arg, His, Trp, Gln, Asn and carboxyl terminal amides as well as modified Cys-residues. The mass spectra of these derivatives can be easily interpreted in terms of the amino acid sequence of the original peptides since they contain abundant and intensity-balanced sequence-determining ions.     

Distinction between α- and γ-Glutamyl Dipeptides by Means of NMR Spectrometer and Amino Acid Analyzer

Conjugated metabolites of abscisic acid (ABA) have been characterized by their chemical ionization (CI) mass spectra using isobutane and ammonia as reagent gases. The CI mass spectra usually consist of quasimolecular ions ([QM]⁺), and constituent aglycone- and.sugar-derived ions. Hence, the spectra are simply interpreted and afford useful information for structutal characterization. CI examinations of ABA and its unconjugated metabolites and collisionally activated dissociation (CAD) measurements of selected ions were helpful in characterizing the constituent aglycones. The distinction between the two glycosidal forms, glycoside and glycosyl ester, has been also discussed in the corresponding conjugates. Confirmation of the fragmentation pathways via recognition of the diagnostic ions can be made by the extensive use of ammonia- d₃ as an additional reagent gas.     

Chemical ionization-mass spectra of aldobiouronic acids and dialdose dianhydrides

Chemical ionization (c.i.) mass spectra with isobutane as the reagent gas are reported for the peracetates of aldobiouronic acids and related compounds, and for peracetates and permethylated derivatives of dialdose dianhydrides. Ions (M⁺ + 43) having relatively high intensities were detected in the spectra of disaccharides lacking the dianhydride structure. Peracetylated dialdose dianhydrides showed very weak (M⁺ + 43) ions, and permethylated dianhydrides did not show them. The (M⁺ + 43) ion consisted of molecular ion and acetoxyl radical (but not of the reagent gas). In the c.i. mass spectra of the usual disaccharide peracetates, (M⁺ ? 31) and (M⁺ ? 60) ions had large intensities. In contrast, c.i. mass spectra extremely similar to the corresponding e.i. mass spectra were obtained for dialdose dianhydrides.     

基于数据非依赖采集的蛋白质组质谱数据解析方法研究进展

数据非依赖采集（DIA）是蛋白质组学领域近年来快速发展的质谱采集技术，其通过无偏碎裂隔离窗口内的所有母离子采集二级谱图，理论上可实现蛋白质样品的深度覆盖，同时具有高通量、高重现性和高灵敏度的优点。现有的DIA数据采集方法可以分为全窗口碎裂方法、隔离窗口序列碎裂方法和四维DIA数据采集方法（4D-DIA）3大类。针对DIA数据的不同特点，主要数据解析方法包括谱库搜索方法、蛋白质序列库直接搜索方法、伪二级谱图鉴定方法和从头测序方法4大类。解析得到的肽段鉴定结果需要进行可信度评估，包括使用机器学习方法的重排序和对报告结果集合的假发现率估计两个步骤，实现对数据解析结果的质控。本文对DIA数据的采集方法、数据解析方法及软件和鉴定结果可信度评估方法进行了整理和综述，并展望了未来的发展方向。     

Epoxy ceriporic acid produced by selective lignin-degrading fungus Ceriporiopsis subvermispora

Ceriporiopsis subvermispora is a selective white rot basidiomycete which degrades lignin in wood at a distance far from enzymes. Low molecular mass metabolites play a central role in the oxidative degradation of lignin. To understand the unique wood-decaying mechanism, we surveyed the oxidized derivatives of ceriporic acids (alk(en)ylitaconic acids) produced by C. subvermispora using high-resolution liquid chromatography multiple-stage mass spectrometry (HR-LC/MSⁿ). The analysis of the precursor and product ions from the extract suggested that an epoxidized derivative of ceriporic acid is produced by the fungus. To identify the new metabolite, an authentic compound of ceriporic acid epoxide was synthesized in vitro by reacting (R)-3-[(Z)-hexadec-7-enyl]-itaconic acid (ceriporic acid C) with m-chloroperbenzoic acid. The precursor and product ions from the natural metabolite and authentic epoxide were identical and distinguishable from those of hydroxy and hydroperoxy derivatives after reduction with NaBD₄. Feeding experiments with [U-¹³C]-glucose, 99% and the subsequent analyses of the first and second generation product ions demonstrated that the oxidized ceriporic acid was (R)-3-(7,8-epoxy-hexadecyl)-itaconic acid. To our knowledge, this study is the first to report that natural alkylitaconic acid bears an epoxy group on its side chain.     

Distribution of l-Leucine-pyruvate Transaminase in Bacteria

Dodecadien-1-ols, tetradecadien-1-ols and hexadecadien-1-ols with a conjugated (E,E)- or (E)-diene system between the ωl,ω3- and ω5, ω7-positions, their acetates, and aldeh?de derivatives (lepidopterous sex pheromones and candidates) were analyzed by electron impact mass spectrometry, which was operated at 70 eV ionization voltage. Three functional derivatives with a same diene system presented a similar spectral pattern, except for the molecular ions (M⁺), [M ? H₂O]⁺ of the alcohols and [M ? CH₃CO₂H]⁺ of the acetates. Each isomer showed a characteristic fragment ion series of C_nH_2n?2⁺ ~C_nH_2n?5⁺ (C₄~C₉), which reflected the double-bond position in the molecule, indicating a method for determining the position of a natural diene pheromone by comparing its mass spectrum with those of the synthetic dienes. By this method, the natural pheromone of Hellula undalis was confirmed to be a ω3, ω5-diene. Furthermore, the fitness indexes proposed by Kuwahara et al. were calculated for some pheromone components, using the mass spectra of synthetic dienes, in order to examine the possibility and limitation for applications of those mass spectra to natural pheromone studies.     

Gas-liquid chromatography-mass spectrometry of methylated and deuteriomethylated per-O-acetyl-aldononitriles from D-mannose

Peracetylated aldononitriles of the tetra-, tri-, and di-methyl ethers of D-mannopyranose were separated by gas-liquid chromatography, and analyzed by mass spectrometry. Through introduction of deuteriomethyl ether groups, various fragmentions constituting the mass spectra were identified and related to the parent methylated sugar structures. Also identified were several characteristic series of fragment ions that are common to two or more methylated D-mannopyranosides. As expected, mass spectra of the D-mannose derivatives were identical to those previously observed for D-glucose methylated in the same positions. Distinctive mass spectra were also recorded for all additional di-O-methyl-D-mannose derivatives. This information permits use of peracetylated aldononitrite derivatives in methylation-fragmentation analysis of aldohexans.     

Characterization of glutathione conjugates of pyrrolylated amino acids and peptides by liquid chromatography-mass spectrometry and tandem mass spectrometry with electrospray ionization

High-performance liquid chromatography (HPLC) coupled with electrospray mass spectrometry (ES-MS) and tandem mass spectrometry (MS-MS) was used to identify the products formed upon reaction of lysine-containing peptides with the neurotoxicant 2,5-hexanedione (2,5-HD). In addition, secondary autoxidative reaction products of the resultant alkylpyrroles with the biological thiol, glutathione, were characterized. ES mass spectra of the HPLC-separated conjugates showed intense [M+H]⁺ ions as well as several ions formed by amide and C-S bond cleavage. The glutathione conjugates of pyrrolylated amino acids and peptides were analyzed by ES ionization and MS-MS, and product-ion spectra showed fragmentation pathways typical of glutathione conjugates. ES-MS-MS analysis of a synthetic nonapeptide modeling a sequence found in neurofilament proteins showed pyrrole formation after incubation with 2,5-HD, and sequence ions were used to assign the position of the pyrrole adduct. Subsequent reaction of the pyrrolylated peptide with reduced glutathione was evidenced by a shift in m/z of the sequence ions of the reaction products with or without prior methylation. The results demonstrate the utility of ES-MS and ES-MS-MS in the characterization of xenobiotic-modified peptides and confirm that stable pyrrole-thiol conjugates are formed by the reaction of biological thils with pyrrolylated peptides.     

Mass spectra of alpha-amino acid oxazolidinones

2-Bis-(chlorodifluoromethyl)-4-substituted-1,3-oxazolidin-5-ones, a new type of alpha-amino acid derivative for gas chromatographic separation, have been studied by low resolution mass spectrometry. These derivatives are obtained by reacting alpha-amino acids with dichlorotetrafluoroacetone. Their structure has been established or confirmed for most protein amino acids and several non-protein alpha-amino acids. The mechanisms responsible for the mass spectral pattern have been rationalized. An interesting feature of this derivatization procedure is that it distinguishes aspartic and glutamic acid from the respective amides. The structure of asparagine and glutamine derivatives has been established. A survey of oxazolidinone mass spectra has provided a list of diagnostically useful ions. Each amino acid can be identified by one or two of its most abundant fragments.     

Mass spectrometry of sterols. Electron ionization induced fragmentation of C-4-alkylated cholesterols

The electron impact ionization of C-4-alkylated cholest-5-en-3β-hydroxysterols has been investigated. The mass spectra of the C-4-alkylated cholesterols contain a number of ions in the high mass region for which analogous ions are not found in the spectrum of cholesterol. Detailed studies of the composition and origin of these ions have been made by high resolution mass spectrometry and analysis of metastable ions. In addition, a large number of isotopically (deuterium and ¹⁸O) substituted C-4-alkylated analogues have been prepared to assist in the interpretation of the spectra. The combined results indicate the occurrence of a number of very complex and unusual electron ionization induced fragmentations. Most notable of the findings reported herein concerns the demonstration of the formation of an ion involving loss of the elements of ring A with an intramolecular shift of the oxygen and hydrogen atoms of the hydroxyl function to the charge-retaining species.     

Analysis of warfarin enantiomers: Chromatographic separation of six stereoisomeric esters prepared from (−)-(1S,2R,4R)-endo-1,4,5,6,7,7-hexachlorobicyclo[2.2.1]hept-5-ene-2- carboxylic acid

Reaction of rac-warfarin, (?)-(1S,2R,4R)-endo-1,4,5,6,7,7-hexachlorobicyclo[2.2.1]hept-5-ene-2- carboxylic acid [(?)-HCA] and carbodiimide reagents gave two noncyclic ketonic diastereoisomeric derivatives whereas rac-warfarin and (?)-HCA acid chloride with 4-(dimethylamino)pyridine gave four cyclic hemiketal diastereoisomeric ester derivatives. The structure and stereochemistry of diastereoisomeric esters prepared from warfarin and p-chlorowarfarin were determined from ¹H- and ¹³C-NMR spectra, mass spectra, and hydrolysis to warfarin and p-chlorowarfarin enantiomers. The structure and stereochemistry of one of the cyclic hemiketal diastereoisomeric derivatives of warfarin are supported by an X-ray crystallographic determination. Mechanisms for the formation of all products are proposed. © 1994 Wiley-Liss, Inc.     

Use of chemical ionization for GC–MS metabolite profiling

Metabolite profiling is commonly performed by GC–MS of methoximated trimethylsilyl derivatives. The popularity of this technique owes much to the robust, library searchable spectra produced by electron ionization (EI). However, due to extensive fragmentation, EI spectra of trimethylsilyl derivatives are commonly dominated by trimethylsilyl fragments (e.g. m/z 73 and 147) and higher m/z fragment ions with structural information are at low abundance. Consequently different metabolites can have similar EI spectra, and this presents problems for identification of “unknowns” and the detection and deconvolution of overlapping peaks. The aim of this work is to explore use of positive chemical ionization (CI) as an adjunct to EI for GC–MS metabolite profiling. Two reagent gases differing in proton affinity (CH₄ and NH₃) were used to analyse 111 metabolite standards and extracts from plant samples. NH₃-CI mass spectra were simple and generally dominated by [MH]⁺ and/or the adduct [M+NH₄]⁺. For the 111 metabolite standards, m/z 73 and 147 were less than 3% of basepeak in NH₃-CI and less than 30% of basepeak in CH₄-CI. With CH₄-CI, [MH]⁺ was generally present but at lower relative abundance than for NH₃-CI. CH₄-CI spectra were commonly dominated by losses of CH₄ [M+1-16]⁺, 1–3 TMSOH [M+1-nx90]⁺, and combinations of CH₄ and TMSOH losses [M+1-nx90-16]⁺. CH₄-CI and NH₃-CI mass spectra are presented for 111 common metabolites, and CI is used with real samples to help identify overlapping peaks and aid identification via determination of the pseudomolecular ion with NH₃-CI and structural information with CH₄-CI.

     

Prediction of the doubly charged ion pattern by modelling the high- and low-resolution mass spectra of isotopomeric forms

The presence of doubly charged ions in mass spectra is detected only occasionally because their clusters are observed more rarely than singly charged ones. The patterns connected with doubly charged ions are located in the spectrum below M/2. The narrow shapes of such patterns as well as overlapping with other bands generate significant problems in their interpretation. The method described here is based on modelling of the isotopomeric form of single- and double-charged mass ion clusters. The present work attempts to explain the generation of the double charge disotopomeric patterns of high- as well as low-resolution spectra. Predicting the high-resolution mass cluster is simpler than calculations of the low-resolution cluster. The high-resolution cluster may represent the initial form of low-resolution pattern formation.