Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography–mass spectrometry

Metabolomic profiling involves relative quantification of metabolites in comparative samples and identification of the significant metabolites that differentiate different groups (e.g., diseased vs. controls). Chemical isotope labeling (CIL) liquid chromatography–mass spectrometry (LC–MS) is an enabling technique that can provide improved metabolome coverage and metabolite quantification. However, chemical identification of labeled metabolites can still be a challenge. In this work, a new set of isotopic labeling reagents offering versatile properties to enhance both detection and identification are described. They were prepared by a glycine molecule (or its isotopic counterpart) and an aromatic acid with varying structures through a simple three-step synthesis route. In addition to relatively low costs of synthesizing the reagents, this reaction route allows adjusting reagent property in accordance with the desired application objective. To date, two isotopic reagents, 4-dimethylaminobenzoylamido acetic acid N-hydroxylsuccinimide ester (DBAA-NHS) and 4-methoxybenzoylamido acetic acid N-hydroxylsuccinimide ester (MBAA-NHS), for labeling the amine-containing metabolites (i.e., amine submetabolome) have been synthesized. The labeling conditions and the related LC–MS method have been optimized. We demonstrate that DBAA labeling can increase the metabolite detectability because of the presence of an electrospray ionization (ESI)-active dimethylaminobenzoyl group. On the other hand, MBAA labeled metabolites can be fragmented in MS/MS and pseudo MS³ experiments to provide structural information on metabolites of interest. Thus, these reagents can be tailored to quantitative profiling of the amine submetabolome as well as metabolite identification in metabolomics applications.     

Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci

The simultaneous amplification of multiple regions of a DNA template is routinely performed using the polymerase chain reaction (PCR) in a process termed multiplex PCR. A useful strategy involving the design, testing, and optimization of multiplex PCR primer mixtures will be presented. Other multiplex design protocols have focused on the testing and optimization of primers, or the use of chimeric primers. The design of primers, through the close examination of predicted DNA oligomer melting temperatures ( T(m)) and primer-dimer interactions, can reduce the amount of testing and optimization required to obtain a well-balanced set of amplicons. The testing and optimization of the multiplex PCR primer mixture constructed here revolves around varying the primer concentrations rather than testing multiple primer combinations. By solely adjusting primer concentrations, a well-balanced set of amplicons should result if the primers were designed properly. As a model system to illustrate this multiplex design protocol, a 10-loci multiplex (10plex) Y chromosome short tandem repeat (STR) assay is used.     

Development and characterisation of a new interface for coupling capillary LC with collision-cell ICP–MS and its application for phosphorylation profiling of tryptic protein digests

A comparison of different nebulisers for direct hyphenation of capillary and nano liquid chromatography (Cap-LC, Nano-LC) and quadrupole-based collision cell inductively coupled plasma mass spectrometry (CC-ICP–MS) for phosphorylation profiling of tryptic protein digests is described. Helium was used as cell gas and specially tuned instrumental conditions were used to achieve background minimisation at the mass of phosphorus, because of kinetic energy discrimination of the interfering polyatomic ions. The proposed set-up is based on a modified capillary electrophoresis interface and a home-made 4 mL spray chamber. It enables the use of gradient conditions with a highly concentrated organic mobile phase as often used in protein phosphorylation analysis, without the need to apply membrane desolvation for removal of the organic phase or further background minimisation. No significant signal suppression or other negative effects caused by the organic mobile phase occur, because of the low flow rates used in Cap-LC and the robust plasma conditions of the CC-ICP–MS instrument. A tryptic digest of beta-casein was investigated as model compound to demonstrate the applicability of the proposed set-up for phosphorylation profiling in protein analysis using quadrupole based collision-cell ICP–MS as phosphorus-specific detector. Detection limits for phosphorylated peptides down to the sub picomole level were obtained. As a complementary technique, electrospray ionisation tandem mass spectrometry (ESI–MS–MS) with data base searching was used for further characterisation of the phosphorylated peptides detected.     

Development of technique for synthesis of methyl(β-oxyethyl) sulfide by the reaction of ethylene oxide with methyl mercaptan

Reaction of ethylene oxide with methyl mercaptan in the presence of a catalyst, a solution of potassium hydroxide in methyl(β-oxyethyl) sulfide, was studied. Various technological procedures for synthesis of methyl(β-oxyethyl) sulfide were analyzed. The process conditions providing a 98–99% conversion of the starting reagents at a selectivity of 97–98% were suggested.     

Electrochemical and associated techniques for the study of the inclusion complexes of thymol and β-cyclodextrin and its interaction with DNA

Journal of Solid State Electrochemistry - Thymol, a potent agent for microbial, fungal, and bacterial disease, has low aqueous solubility and it is genotoxic, i.e., is capable of damaging...     

Novel concept for the mass spectrometric determination of absolute isotopic abundances with improved measurement uncertainty: Part 2 – Development of an experimental procedure for the determination of the molar mass of silicon using MC-ICP-MS

The isotopic abundances and thus molar mass M(Si) of a silicon crystal material with natural isotopic abundances have been measured for the first time using multicollector-ICP-mass spectrometry (MC-ICP-MS) in combination with a novel concept of a modified isotope dilution mass spectrometry (IDMS)-method. This experimental work is the further development of part 1 of this series of papers. While part 1 describes the theoretical background and the mathematical derivation of the novel concept in detail, the measurements presented here serve to validate the novel concept and give experimental proof of its capability. Moreover, the also new method for the analytical calculation of calibration factors needed in the determination of absolute isotope amount ratios has been tested successfully. Silicon isotopic abundances have been measured directly from an aqueous alkaline matrix following a new sample preparation protocol developed within the framework of this study. A molar mass of M(Si) = 28.08548(13) g/mol with an associated relative uncertainty of u_rel = 4.6 × 10^?6 (k = 1) has been measured. This is in excellent agreement with the current IUPAC value for the molar mass of natural silicon M(Si_nat) = 28.08550(15) g/mol with u_rel = 5.3 × 10^?6 (k = 1). An uncertainty budget according to the Guide to the Expression of Uncertainty in Measurement (GUM) was calculated to assess the presented results and to validate the novel concept with the help of experimental data. The development of a new experimental procedure is presented in detail and the contributions to the uncertainty are discussed in comparison to part 1 of this work.     

Use of SEC–ICP–MS with a collision cell for determining the interaction of chromium with DNA extracted from metal-contaminated soils

The potential of chromium to bind to DNA isolated directly from soil microbial communities was investigated in this study. An analytical scheme was developed to distinguish between chromium bound to DNA and its fragments or chromium contained elsewhere in an environmental DNA extract. DNA was extracted from chromium-contaminated soils and purified using DNA clean-up resins. Size-exclusion chromatography was employed due to its advantages in the separation and molecular weight approximation of large biomolecules. It was coupled with two on-line detection systems (spectrophotometric and inductively coupled plasma mass spectrometric) to study the binding of chromium to DNA or other components in a DNA extract. A collision cell was pressurized with helium to remove diatomic and polyatomic interferents resulting from the chosen mobile phase. Chromium peaks were observed in both the large and small molecular weight regions of the chromatogram; to further confirm that the environmentally extracted DNA contained Cr, the subsequently purified DNA was examined for total Cr using flow injection ICP–MS to accommodate small sample volumes. DNA samples isolated from the two soils examined contained 0.5–0.7 ppb Cr, indicating that DNA isolated directly from a chromium-contaminated soil has chromium bound to the nucleic acids.     

Development of chemiluminescent assays for the quantitative detection and imaging of 5-bromo-2′deoxyuridine-labeled DNA in parvovirus B19-infected cells

Incorporation of exogenous analogues is a widely used method to evaluate DNA synthesis in cultured cells exposed to exogenous factors such as infectious agents. Herein, two new quantitative methodologies exploiting ultrasensitive chemiluminescence (CL) detection of 5-bromo-2′-deoxyuridine (BrdU) have been developed: a CL microscope imaging assay to evaluate BrdU labelling at single-cell level and a CL dot-blot assay to measure the amounts of DNA produced in the course of an in vitro infection of proliferating cells. The assays have been optimized on UT7/EpoS1 cells cultured in presence of different concentrations of BrdU (from 3 to 100 μM) and used to monitor parvovirus B19 (B19) life cycle in infected cells. The CL microscope imaging assay provided a detailed localization of BrdU-labelled nuclei allowing to count positive cells and measure their related CL intensity signals. The CL dot-blot assay, coupled with a B19 capture procedure performed with a specific peptide nucleic acid probe, has been designed to discriminate and selectively quantify cellular and viral BrdU-labelled genomes. Quantitative evaluation of BrdU-labelled B19 DNA has been achieved by means of a CL calibration curve. The high detectability, down to 2?×?10⁶ B19 genome copies, and the linear range extending up to 5?×?10⁸ copies make the method suitable to evaluate the amounts of B19 DNA produced throughout a replicative viral cycle.

Development and validation of volumetric absorptive microsampling coupled with UHPLC–MS/MS for the analysis of gamma-hydroxybutyric acid in human blood

A volumetric microsampling (VAMS) device (20 μl) was evaluated and validated for the analysis of γ-hydroxybutyric acid (GHB) in venous blood using a simple ultra-high-pressure liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) method. GHB was extracted from VAMS device by acetonitrile, after a re-hydration step in a temperature-controlled ultrasonic bath at 60°C for 10 min. Chromatographic analysis was carried out on a Kinetex C₁₈ column using 0.1% formic acid in water and acetonitrile as binary gradient mobile phase (from 5 to 95% of acetonitrile from 1 to 2.5 min) at a flow rate of 0.3 ml/min. The VAMS method was fully validated according to current guidelines with satisfactory results in terms of linearity, selectivity, precision, absolute recovery, matrix effect and stability. The linearity was determined from 0.5 to 200 μg/ml and the lower limit of quantitation was 0.5 μg/ml. The novel VAMS–UHPLC–MS/MS method was successfully compared with plasma-based method in a GHB-treated patient as a proof of concept.     

Disposable DNA biosensor with the carbon nanotubes–polyethyleneimine interface at a screen-printed carbon electrode for tests of DNA layer damage by quinazolines

A screen-printed carbon working electrode within a commercially available screen-printed three-electrode assembly was modified by using a composite of multiwalled carbon nanotubes (MWCNT) dispersed in polyethylenimine (PEI) followed by covering with the calf thymus dsDNA layer. Several electrochemical methods were used to characterize the biosensor and to evaluate damage to the surface-attached DNA: square wave voltammetry of the [Ru(bpy)₃]²⁺ redox indicator and mediator of the guanine moiety oxidation, cyclic voltammetry and electrochemical impedance spectroscopy in the presence of the [Fe(CN)₆]^3−/4− indicator in solution. Due to high electroconductivity and large surface area of MWCNT and positive charge of PEI, the MWCNT–PEI composite is an advantageous platform for the DNA immobilization by the polyelectrolyte complexation and its voltammetric and impedimetric detection. In this respect, the MWCNT–PEI interface exhibited better properties than the MWCNT–chitosan one reported from our laboratory previously. A deep DNA layer damage at incubation of the biosensor in quinazoline solution was found, which depends on the quinazoline concentration and incubation time. Figure Impedance spectra for the modified electrodes. Conditions: 1 mM [Fe(CN)₆]^3–/4– in 0.1 M PBS (pH = 7.0), potential amplitude 10 m V, frequency range 12–1×10₄ Hz. Dedicated to Professor Jan Garaj on the occasion of his 75th birthday     

Development of a fast and selective method for the sensitive determination of anatoxin-a in lake waters using liquid chromatography–tandem mass spectrometry and phenylalanine-d 5 as internal standard

Anatoxin-a is a potent alkaloid neurotoxin produced by a number of cyanobacterial species and released in freshwaters during cyanobacterial blooms. Its high toxicity is responsible for several incidents of lethal intoxications of birds and mammals around the world; therefore anatoxin-a has to be regarded as a health risk and its concentration in lakes and water reservoirs should be monitored. Phenylalanine is a natural amino acid, also present in freshwaters, isobaric to anatoxin-a, with a very similar fragmentation pattern and LC retention. Since misidentification of phenylalanine as anatoxin-a has been reported in forensic investigations, special care must be taken in order to selectively determine traces of anatoxin-a in the presence of naturally occurring phenylalanine. A fast LC tandem MS method was developed by using a 1.8 μm 50 × 2.1 mm C18 column for the separation of anatoxin-a and phenylalanine, achieving a 3-min analysis time. Isotopically labelled phenylalanine-d ₅ was employed as internal standard to compensate for electrospray ion suppression and sample preconcentration losses. Both compounds were preconcentrated 1,000-fold on a porous graphitic carbon solid-phase extraction (SPE) cartridge after adjustment of sample pH to 10.5. The method was validated by using lake water spiked at four different levels from 0.01 to 1 μg L⁻¹. Anatoxin-a recovery ranged from 73 to 97%, intra-day precision (RSD%) ranged from 4.2 to 5.9, while inter-day precision (RSD%) ranged from 4.2 to 9.1%. Limits of detection and quantification were 0.65 and 1.96 ng L⁻¹ respectively. The method was successfully applied for the detection of anatoxin-a in Greek lakes at concentrations ranging from less than 0.6 to 9.1 ng L⁻¹.     

Development and testing of an algorithm for efficient MP2/CCSD(T) energy estimation of molecular clusters with the 2–body approach

This work reports the development and testing of an automated algorithm for estimating the energies of weakly bound molecular clusters employing correlated theory. Firstly, the monomers and dimers of (homo/hetero) clusters are identified, and the sum of one-body and two-body contributions to correlation energy is calculated. The addition of this contribution to the Hartree-Fock full calculation (FC) energies provides a good estimate of the total energies at Møller–Plesset second-order perturbation theory (MP2)/coupled-cluster method with singles and doubles (CCSD) (T)-level theory using augmented Dunning basis sets. The estimated energies for several test clusters show an excellent agreement with their FC counterparts, with a substantial wall-clock time saving employing off-the-shelf hardware. Furthermore, the complete basis set (CBS) limit for MP2 energy computed using the two-body approach also agrees with its CBS energy with its FC counterpart.     

In vivo and in vitro metabolite profiling of nirmatrelvir using LC–Q-ToF–MS/MS along with the in silico approaches for prediction of metabolites and their toxicity

Nirmatrelvir (NRV), a 3C-like protease or M^pro inhibitor of SARS-CoV-2, is used for the treatment of COVID-19 in adult and paediatric patients. The present study was accomplished to investigate the comprehensive metabolic fate of NRV using in vitro and in vivo models. The in vitro models used for the study were microsomes (human liver microsomes, rat liver microsomes, mouse liver microsomes) and S9 fractions (human liver S9 fractions and rat liver S9 fractions) with the appropriate cofactors, whereas Sprague–Dawley rats were used as the in vivo models. Nirmatrelvir was administered orally to Sprague–Dawley rats, which was followed by the collection of urine, faeces and blood at pre-determined time intervals. Protein precipitation was used as the sample preparation method for all the samples. The samples were then analysed by liquid chromatography–quadrupole time-of-flight tandem mass spectrometry (LC-Q-ToF-MS/MS) using an Acquity BEH C18 column with 0.1% formic acid and acetonitrile as the mobile phase. Four metabolites were found to be novel, which were formed via amide hydrolysis, oxidation and hydroxylation. Furthermore, an in silico analysis was performed using Meteor Nexus software to predict the probable metabolic changes of NRV. The toxicity and mutagenicity of NRV and its metabolites were also determined using DEREK Nexus and SARAH Nexus.     

Development of a Solid‐Phase Extraction‐Enzyme‐Linked Immunosorbent Assay Method with a New Sorbent of Multiwall Carbon Nanotube for the Determination of Estrone in Water

Abstract

A sensitive solid‐phase extraction‐enzyme‐linked immunosorbent assay (SPE‐ELISA) method was developed to analyze the estrone in environmental water. A new SPE sorbent of the multiwall carbon nanotube was tested and proved to have similar adsorbability for estrone comparing to the commercial C₁₈ SPE. A specific polyclonal antibody for estrone (A‐E1) and a broad‐spectrum antibody for estrone, estradiol and estriol (A‐E2) were produced. For A‐E1, the limit detection of estrone was 0.04 µg/l and for A‐E2 were 0.07, 0.04 and 0.2 µg/l of estrone, estradiol and estriol, respectively. Different river water samples were analyzed by ELISA and HPLC method.     

Heterocycles with a bridging nitrogen atom. 19. Development of routes for the synthesis of oxazoloisoquinolinium salts based on phenacylation of α-methyl-1(3)-isoquinolones

Alkylation of 3-methyl-1-isoquinolone and 1-methyl-3-isoquinolone with phenacyl bromides proceeds regioselectively with the formation in the first case of only an N-phenacyl derivative and in the second only the O-derivative. The 5-methyl[1,3]oxazolo[3,2-a]isoquinolinium salt has been synthesized and its reactions with ammonia, morpholine, and sodium methylate have been investigated. For Communication 18 see [1]. Dedicated to Academician B. A. Trofimov on his 70^th jubilee Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 110-123, January, 2009.     

Development of a new ultra-high-performance liquid chromatography–tandem mass spectrometry method for the determination of digoxin and digitoxin in plasma: Comparison with a clinical immunoassay

Cardiac glycosides digoxin and digitoxin are used in therapy for the treatment of congestive heart failure. Moreover, these compounds can be responsible for intoxication cases caused by fortuitous ingestion of leaves of Digitalis. Due to the narrow therapeutic range of these drugs, therapeutic drug monitoring is recommended in the clinical practice. In this context, immunoassays-based methods are generally employed but digoxin- and digitoxin-like compounds can interfere with the analysis. The aim of this study was to develop and validate an original UPLC–MS/MS method for the determination of digoxin and digitoxin in plasma. The method shows adequate sensitivity and selectivity with acceptable matrix effects and very good linearity, accuracy, precision, and recovery. A simple liquid–liquid extraction procedure was used for sample clean-up. The method was applied for the analysis of n = 220 plasma samples collected in two different clinical chemistry laboratories and previously tested by the same immunoassay. The statistical comparison showed a relevant negative bias of the UPLC–MS/MS method versus the immunoassay. These results are consistent with an immunoassay overestimation of digoxin plasmatic levels due to cross-reaction events with endogenous digoxin-like substances.     

The immobilization of Cytochrome c on MWNT–PAMAM–Chit nanocomposite incorporated with DNA biocomposite film modified glassy carbon electrode for the determination of nitrite

A novel and sensitive biosensor was developed for the determination of nitrite. Firstly, multi-walled carbon nanotubes–poly(amidoamine)–chitosan (MWNT–PAMAM–Chit) nanocomposite along with the incorporation of DNA was used to modify the glassy carbon electrode. Then the immobilization of Cyt c was accomplished using electrochemical deposition method by consecutive cyclic voltammetry (CV) scanning in a neutral Cyt c solution. CV behaviors of the modified electrodes showed that the MWNT–PAMAM–Chit nanocomposite is a good platform for the immobilization of DNA and Cyt c in order, at the same time, an excellent promoter for the electron transfer between Cyt c and the electrode. At high potential, the immobilized Cyt c could be further oxidized into highly reactive Cyt c π-cation by two-step electrochemical oxidation, which could oxidize NO₂ ⁻ into NO₃ ⁻ in the solution. Therefore, a nitrite biosensor based on the biocatalytic oxidation of the immobilized Cyt c was fabricated, which showed a fast response to nitrite (less than 5 s). The linear range of 0.2–80 μM and a detection limit of 0.03 μM was obtained. Finally, the application in food analysis using sausage as testing samples was also investigated.     

Development of a Modified Bromley's Methodology for the estimation of ionic media effects on solution equilibria: Part 4. The chemical model of Fe(III) with the halide ligands in aqueous solution at 25°C

The Modified Bromley's Methodology (MBM) has been used to construct the basic chemical model between Fe(III) and OH⁻ and the halide ligands Cl⁻, Br⁻ and F⁻ in NaClO₄ medium at 25°C, obtaining the thermodynamic constants and the corresponding interaction parameters for each equilibrium. This basic model has been extended to KNO₃, HCl, and KCl media obtaining the corresponding interaction parameters. The applicability of the model is also discussed.     

Development and application of a comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry method for the analysis of l-β-methylamino-alanine in human tissue

l-β-Methylamino-alanine (BMAA) has been proposed as a worldwide contributor to neurodegenerative diseases, including Parkinson dementia complex (PDC) of Guam and Alzheimer's disease (AD). Recent conflicting reports of the presence of this amino acid in human brain from patients affected by these diseases have made it necessary to develop methods that provide unambiguous detection in complex samples. Comprehensive two-dimensional gas chromatography coupled with time-of-flight-mass-spectrometry analysis (GC × GC–TOFMS) followed by a targeted Parallel Factor Analysis (PARAFAC) deconvolution method has been used recently in metabolomic investigations to separate, identify, and quantify components of complex biological specimens. We have extended and applied this methodology to the toxicological problem of detecting BMAA in extracts of brain tissue. Our results show that BMAA can be isolated from closely eluting compounds and detected in trace amounts in extracts of brain tissue spiked with low levels of this analyte, ranging from 2.5 ppb to 50 ppb, with a limit of detection (LOD) of 0.7 ppb. This new method was sufficiently sensitive to detect BMAA in cerebral extracts of mice fed BMAA. This optimized approach was then applied to analyze tissue from humans; however, no BMAA was detected in the brain extracts from controls or patients with PDC or AD. Our results demonstrate the application of multidimensional chromatography–mass spectrometry methods and computational deconvolution analysis to the problem of detecting trace amounts of a potential toxin in brain extracts from mice and humans.