Simple In Vitro 18O Labeling for Improved Mass Spectrometry-Based Drug Metabolites Identification: Deep Drug Metabolism Study.

The identification of drug metabolites formed with different in vitro systems by HPLC-MS is a standard step in preclinical research. In vitro systems allow modeling of real metabolic pathways of a drug candidate. Despite the emergence of various software and databases, identification of compounds is still a complex task. Measurement of the accurate mass, correlation of chromatographic retention times and fragmentation spectra are often insufficient for identification of compounds especially in the absence of reference materials. Metabolites can "slip under the nose", since it is often not possible to reliably confirm that a signal belongs to a metabolite and not to other compounds in complex systems. Isotope labeling has proved to be a tool that aids in small molecule identification. The introduction of heavy isotopes is done with isotope exchange reactions or with complicated synthetic schemes. Here, we present an approach based on the biocatalytic insertion of oxygen-18 isotope under the action of liver microsomes enzymes in the presence of 18O2. Using the local anesthetic bupivacaine as an example, more than 20 previously unknown metabolites were reliably discovered and annotated in the absence of the reference materials. In combination with high-resolution mass spectrometry and modern methods of mass spectrometric metabolism data processing, we demonstrated the ability of the proposed approach to increase the degree of confidence in interpretating metabolism data.

Untargeted Lipidomics after D2O Administration Reveals the Turnover Rate of Individual Lipids in Various Organs of Living Organisms.

The administration of low doses of D2O to living organisms was used for decades for the investigation of metabolic pathways and for the measurement of the turnover rate for specific compounds. Usually, the investigation of the deuterium uptake in lipids is performed by measuring the deuteration level of the palmitic acid residue using GC-MS instruments, and to our knowledge, the application of the modern untargeted LC-MS/MS lipidomics approaches was only reported a few times. Here, we investigated the deuterium uptake for >500 lipids for 13 organs and body liquids of mice (brain, lung, heart, liver, kidney, spleen, plasma, urine, etc.) after 4 days of 100% D2O administration. The maximum deuteration level was observed in the liver, plasma, and lung, while in the brain and heart, the deuteration level was lower. Using MS/MS, we demonstrated the incorporation of deuterium in palmitic and stearic fragments in lipids (PC, PE, TAG, PG, etc.) but not in the corresponding free forms. Our results were analyzed based on the metabolic pathways of lipids.

Investigating the Metabolism of Plants Germinated in Heavy Water, D2O, and H218O-Enriched Media Using High-Resolution Mass Spectrometry.

Mass spectrometry has been an essential technique for the investigation of the metabolic pathways of living organisms since its appearance at the beginning of the 20th century. Due to its capability to resolve isotopically labeled species, it can be applied together with stable isotope tracers to reveal the transformation of particular biologically relevant molecules. However, low-resolution techniques, which were used for decades, had limited capabilities for untargeted metabolomics, especially when a large number of compounds are labelled simultaneously. Such untargeted studies may provide new information about metabolism and can be performed with high-resolution mass spectrometry. Here, we demonstrate the capabilities of high-resolution mass spectrometry to obtain insights on the metabolism of a model plant, Lepidium sativum, germinated in D2O and H218O-enriched media. In particular, we demonstrated that in vivo labeling with heavy water helps to identify if a compound is being synthesized at a particular stage of germination or if it originates from seed content, and tandem mass spectrometry allows us to highlight the substructures with incorporated isotope labels. Additionally, we found in vivo labeling useful to distinguish between isomeric compounds with identical fragmentation patterns due to the differences in their formation rates that can be compared by the extent of heavy atom incorporation.

Amine additives for improved in-ESI H/D exchange.

In-ESI H/D exchange is a convenient technique for analyzing small-molecular complex mixtures. However, such experiments do not yield sufficient levels of exchange or require an elevated temperature of the ion transfer capillary. Increased temperature may result in unexpected additional exchanges of -CH groups that may complicate the interpretation of the H/D exchange data used for identification. Gas-phase H/D exchange depends on the gas-phase basicity of the deuterating agent. In-ESI exchange involves both droplet-phase and gas-phase mechanisms, depending on a particular ion source setup and the deuterating agent used. Therefore, the addition of strong bases to the reaction mixture should facilitate in-ESI exchange. This work aimed to investigate the capabilities of different amines to improve in-ESI H/D exchange compared with pure D2O and to choose an amine modifier to increase the extent of H/D exchange. It was shown that such additives substantially enhanced the extent of H/D exchange in small molecules, peptides, and proteins even without heating the capillary. It was found that the extent of exchange increases in the following order: tertiary amines < secondary amines < primary amines. Therefore, we suggest that amines act as deuterating agents after being exchanged with D2O. These findings may improve H/D exchange applications, especially in small molecule analysis. The observation of improved H/D exchange with amine additives in peptides and proteins may become a subject of future research.

Increasing the reliability of compound identification in biological samples using 16O/18O-exchange mass spectrometry.

The task of multipurpose analysis of biological samples and identification of individual compounds in them is actual for many organizations in various fields; the results of such analyses can affect lives. The most frequently used, most accurate, and highly sensitive method used for this kind of analysis is the combination of gas/liquid chromatography and high-resolution mass spectrometry. However, in some areas, it is necessary to increase the reliability of compound identification. In this paper, we present a method that combines the reaction of oxygen isotope exchange with mass spectrometry; the method allows to increase the reliability of identification of individual compounds. Oxygen isotope exchange reaction is a "selective" one, which means that not all oxygen present in the molecule can exchange, but only in certain functional groups. Thus, by the number of isotope exchanges that have occurred in this molecule, the right structural formula might be more accurately chosen. The method was tested both on pure pharmaceutical substances and on real human urine samples. In both cases, the effectiveness of the method was shown: the number of expected exchanges in known substances coincided with the experimental one, and from several possible structures of unknown substances, the correct one was chosen based on the number of isotope exchanges.

Analysis of 16O/18O and H/D Exchange Reactions between Carbohydrates and Heavy Water Using High-Resolution Mass Spectrometry.

Mono- and polysaccharides are an essential part of every biological system. Identifying underivatized carbohydrates using mass spectrometry is still a challenge because carbohydrates have a low capacity for ionization. Normally, the intensities of protonated carbohydrates are relatively low, and in order to increase the corresponding peak height, researchers add Na+, K+, or NH4+to the solution. However, the fragmentation spectra of the corresponding ions are very poor. Based on this, reliably identifying carbohydrates in complex natural and biological objects can benefit frommeasuring additional molecular descriptors, especially those directly connected to the molecular structure. Previously, we reported that the application of the isotope exchange approach (H/D and 16O/18O) to high-resolution mass spectrometry can increase the reliability of identifying drug-like compounds. Carbohydrates possess many -OH and -COOH groups, making it reasonable to expect that the isotope exchange approach would have considerable potential for detecting carbohydrates. Here, we used a collection of standard carbohydrates to investigate the isotope exchange reaction (H/D and 16O/18O) in carbohydrates and estimate its analytical applications.

Structure-Preserving and Perceptually Consistent Approach for Visualization of Mass Spectrometry Imaging Datasets.

Mass spectrometry imaging (MSI) has become an important tool for 2D profiling of biological tissues, allowing for the visualization of individual compound distributions in the sample. Based on this information, it is possible to investigate the molecular organization within any particular tissue and detect abnormal regions (such as tumor regions) and many other biologically relevant phenomena. However, the large number of compounds present in the spectra hinders the productive analysis of large MSI datasets when utilizing standard tools. The heterogeneity of samples makes exploratory visualization (a presentation of the general idea of the molecular and structural organization of the inspected tissues) challenging. Here, we explore the application of various dimensionality reduction techniques that have been used extensively in the visualization of hyperspectral images and the MSI data specifically, such as principal component analysis, independent component analysis, non-negative matrix factorization, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. Further, we propose a new approach based on a combination of structure preserving visualization with nonlinear manifold embedding of normalized spectral data. This way, we aim to preserve as much spatially overlapping signals as possible while augmenting them with information on compositional (spectral) variation. The proposed approach can be used for exploratory visualization of MSI datasets without prior deep chemical or histological knowledge of the sample. Thus, different datasets can be visually compared employing the proposed method. The proposed approach allowed for the clear visualization of the molecular layer, granular layer, and white matter in chimpanzee and macaque cerebellum slices.

Hydrogen/Deuterium and 16O/18O-Exchange Mass Spectrometry Boosting the Reliability of Compound Identification.

Accurate and reliable identification of chemical compounds is the ultimate goal of mass spectrometry analyses. Currently, identification of compounds is usually based on the measurement of the accurate mass and fragmentation spectrum, chromatographic elution time, and collisional cross section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud and Metlin) and developing software for predicting MS/MS fragments in silico from SMILES patterns (such as MetFrag, CFM-ID, and Ms-Finder), the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of big help for LC-MS/MS-based omics. Our approach is based on the characterization of compounds by the number of labile hydrogen and oxygen atoms in the molecule, which can be measured using hydrogen/deuterium and 16O/18O-exchange approaches. The number of labile atoms (those from -OH, -NH, ═O, and -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing a database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here, we present an approach utilizing the selection of structural candidates from a database on the basis of the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reduction of the search space by a factor of 10 and considerably increases the reliability of the compound identification.

Refinement of Compound Aromaticity in Complex Organic Mixtures by Stable Isotope Label Assisted Ultrahigh-Resolution Mass Spectrometry.

Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a unique opportunity for molecular analysis of natural complex mixtures. In many geochemical and environmental studies structure-propertry relations are based solely on the elemental compositional information. Several calculated parameters were proposed to increase reliability of structural attribution, among which aromaticity indices (AI and AImod) are widely used. Herein, we applied a combination of selective labeling reactions in order to obtain direct structural information on the individual components of lignin-derived polyphenolic material. Carboxylic (COOH), carbonyl (C═O), and hydroxyl (OH) groups were enumerated by esterification, reducing, and acetylation reactions, respectively, followed by FTICR MS analyses. Obtained information was enabled to constrain aromaticity accounting for the carbon skeleton only. We found that actual aromaticity of components may be both higher or lower than approximated values depending on the abundance of COOH, C═O, and OH groups. The results are of importance for the geochemical community studying terrestrial NOM with structural gradients.

Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines.

BACKGROUND: Flax (Linum usitatissimum L.) is grown for fiber and seed in many countries. Flax cultivars differ in the oil composition and, depending on the ratio of fatty acids, are used in pharmaceutical, food, or paint industries. It is known that genes of SAD (stearoyl-ACP desaturase) and FAD (fatty acid desaturase) families play a key role in the synthesis of fatty acids, and some alleles of these genes are associated with a certain composition of flax oil. However, data on genetic polymorphism of these genes are still insufficient. RESULTS: On the basis of the collection of the Institute for Flax (Torzhok, Russia), we formed a representative set of 84 cultivars and lines reflecting the diversity of fatty acid composition of flax oil. An approach for the determination of full-length sequences of SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes using the Illumina platform was developed and deep sequencing of the 6 genes in 84 flax samples was performed on MiSeq. The obtained high coverage (about 400x on average) enabled accurate assessment of polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes and evaluation of cultivar/line heterogeneity. The highest level of genetic diversity was observed for FAD3A and FAD3B genes - 91 and 62 polymorphisms respectively. Correlation analysis revealed associations between particular variants in SAD and FAD genes and predominantly those fatty acids whose conversion they catalyze: SAD - stearic and oleic acids, FAD2 - oleic and linoleic acids, FAD3 - linoleic and linolenic acids. All except one low-linolenic flax cultivars/lines contained both the substitution of tryptophan to stop codon in the FAD3A gene and histidine to tyrosine substitution in the FAD3B gene, while samples with only one of these polymorphisms had medium content of linolenic acid and cultivars/lines without them were high-linolenic. CONCLUSIONS: Genetic polymorphism of SAD and FAD genes was evaluated in the collection of flax cultivars and lines with diverse oil composition, and associations between particular polymorphisms and the ratio of fatty acids were revealed. The achieved results are the basis for the development of marker-assisted selection and DNA-based certification of flax cultivars.

Machine learning to predict retention time of small molecules in nano-HPLC.

Retention time is an important parameter for identification in untargeted LC-MS screening. Precise retention time prediction facilitates the annotation process and is well known for proteomics. However, the lack of available experimental information for a long time has limited the prediction accuracy for small molecules. Recently introduced large databases for small-molecule retention times make possible reliable machine learning-based predictions for the whole diversity of compounds. Applying simple projections may expand these predictions on various LC systems and conditions. In our work, we describe a complex approach to predict retention times for nano-HPLC that includes the consequent deployment of binary and regression gradient boosting models trained on the METLIN small-molecule dataset and simple projection of the results with a small number of easily available compounds onto nano-HPLC separations. The proposed model outperforms previous attempts to use machine learning for predictions with a 46-s mean absolute error. The overall performance after transfer to nano-LC conditions is less than 155 s (10.8%) in terms of the median absolute (relative) error. To illustrate the applicability of the described approach, we successfully managed to eliminate averagely 25 to 42% of false-positives with a filter threshold derived from ROC curves. Thus, the proposed approach should be used in addition to other well-established in silico methods and their integration may broaden the range of correctly identified molecules.

i-Clamp phenoxazine for the fine tuning of DNA i-motif stability.

Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2'-deoxynucleotide (i-clamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing. We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10-11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.

Hydrogen/Deuterium Exchange Aiding Compound Identification for LC-MS and MALDI Imaging Lipidomics.

We present a novel approach for the increasing reliability of compound identification for LC-MS and MALDI imaging lipidomics. Our approach is based on the characterization of compounds not only by the elution time, accurate mass, and fragmentation spectra but also by the number of labile hydrogens that can be measured using the hydrogen/deuterium (H/D) exchange approach. The number of labile hydrogens (those from -OH and -NH groups) serves as an additional structural descriptor used when performing a database search. For LC-MS experiment, the H/D exchange was performed in the heating capillary of the modified electrospray ionization (ESI) source, while for MALDI imaging, the exchange was performed in the ion funnel at 10 Torr pressure. It was observed that such an approach allowed one to achieve a considerable degree of deuteration, enough to unambiguously distinguish between different classes of lipids. The proposed analytical approach may be successfully used for the identification not only of lipids but also of peptides and metabolites. A special software for the automatic filtration of molecules based on the number of functional groups was also developed.

Hydrogen/deuterium exchange in mass spectrometry.

The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

Methylene Group Transfer in Carbonyl Compounds Discovered in†silico and Detected Experimentally.

A previously unknown transformation of aldehydes, ketones, and carboxylic acid derivatives leads to the formation of substituted oxiranes, aziridines, and azirines as shown by DFT and MP2 computations. Formations of 2,2-dimethyloxirane-d8 from acetone-d6 , phenylazirine-d2 from benzonitrile and 2-methyl-2-(4-hydroxyphenyl)-oxirane from 4-hydroxyacetophenone were detected experimentally by electrospray ionization mass-spectrometry with a heated desolvating capillary. This reaction is a truly concerted process characterized by high activation barriers (activation enthalpies 320-480 kJ mol-1 ).

Structural investigation of coal humic substances by selective isotopic exchange and high-resolution mass spectrometry.

Here, we report the application of a selective liquid-phase hydrogen/deuterium exchange (HDX) coupled to ultra-high resolution FTICR MS for structural investigations of individual constituents of humic substances (HS) isolated from three coal samples of different geographical origin. Selectivity was achieved by conducting reactions in DCl or NaOD solutions for catalyzing HDX in aromatic ring and side-chain positions with enhanced C-H acidity, respectively. FTICR MS analysis showed a significant overlap of molecular compositions in the HS samples under study, with 2000 common formulae. Using HDX, we demonstrated that the determined common formulae are presented by different structural isomers. We found that aromatic compounds varied both in the substitution pattern and the number of aromatic protons. Depending on the sample, lignin components with the same molecular formulae were composed of coumaryl, coniferyl or sinapyl moieties. Enumeration of HDX series for the 800 most abundant compounds showed that the results of HDX agreed well with the model structures suggested for humic components occupying a van Krevelen plot. In addition, we explored chemical transformations, which could connect individual constituents of coal HS. These transformations included hydrolysis of a guaiacyl moiety and reduction of a catechol unit, which corresponds to the conversion of a coniferyl fragment into a coumaryl unit. The obtained results were supportive of the hypothesis of the reducing humification pathway suggested for lignin transformation in the environment. The conclusion was made that the molecular ensemble of coal HS is composed of individual constituents produced at different humification stages.

Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry.

The structures of individual molecules in crude oil remain largely unknown despite the considerable amount of research dedicated to this topic. The extreme complexity of crude oil (recently Marshall reported the observation of more than 400,000 unique compounds in one sample) makes it impossible to separate crude oil into individual compounds and determine their structure by NMR or X-ray spectroscopy. Recently, isotope exchange, performed both in solution and in the gas phase, combined with high-resolution mass spectrometry was used for speciation of certain structural fragments of individual molecules in crude oil and humic substances. 16O/18O exchange allows enumeration of =O groups and speciation of furans, whereas H/D exchange allows enumeration of -OH groups, -NH groups, aromatic hydrogens, alpha hydrogens, etc. Unfortunately, crude oil is insoluble in water (the most available and cleanest source of isotopes), so performance of the exchange in solution requires harsh conditions, such as concentrated acids or bases, which could considerably modify the sample. Here we describe the use of a cheap and simple analytical approach for performing both H/D and 16O/18O exchange in crude oil using only water as the source of the isotopes. Crude oil was incubated in near-critical water and the reaction was monitored by high-resolution Fourier transform mass spectrometry. Although isotope exchange results in complication of the spectrum, the resolving power of modern mass spectrometers is sufficient to determine the number of exchanges for each molecule simultaneously. We determined the number of 16O/18O exchanges in 276 species and the number of H/D exchanges in 150 species. Our results allow deeper investigation of crude oil and other nonpolar samples on the molecular level. Graphical abstract.

Ion Source Multiplexing on a Single Mass Spectrometer.

We present the simple approach for the combination of different ion sources on a single mass spectrometer without any interference between them. Each ion source can be positioned as far as 1 m from the mass spectrometer; ions are transported by the means of flexible copper tubes, which are connected, to the separate inlet capillaries. Special valves enable switching channels on and off. Using this approach, we successfully combined native electrospray ionization (ESI), regular ESI, ß-electrons ionization, and atmospheric pressure photoionization (APPI) of thermally desorbed vapors of petroleum on a single mass spectrometer. In addition, separate channels allow infusing internal calibration mixture or performing ion molecular reactions in one channel and using the other as a reference. Using this idea, we have developed an original sequential window acquisition of all theoretical mass spectra (SWATH MS) approach in which peptide ions are transported in different channels, one of which is heated to high temperature so that ions are thermally fragmented, and the other channel ensures the presence of nonfragmented ions in the spectrum. Also, we demonstrated the possibility to perform gas phase H/D exchange reaction in one channel and using another as reference. Use of valves makes it possible to exclude any interference between them. Thus, we have demonstrated the possibility to create a multichannel system in which ions would be transported through several inlet tubes in which different ion molecular reactions such as Paternò-Büchi, ozonation, or H/D exchange will occur. Comparison of mass spectra recorded when different channels are open will provide structural and chemical information about unknown species.

Analytical Description of the H/D Exchange Kinetic of Macromolecule.

We present the accurate analytical solution obtained for the system of rate equations describing the isotope exchange process for molecules containing an arbitrary number of equivalent labile atoms. The exact solution was obtained using Mathematica 7.0 software, and this solution has the form of the time-dependent Gaussian distribution. For the case when forward exchange considerably overlaps the back exchange, it is possible to estimate the activation energy of the reaction by obtaining a temperature dependence of the reaction degree. Using a previously developed approach for performing H/D exchange directly in the ESI source, we have estimated the activation energies for ions with different functional groups and they were found to be in a range 0.04-0.3 eV. Since the value of the activation energy depends on the type of functional group, the developed approach can have potential analytical applications for determining types of functional groups in complex mixtures, such as petroleum, humic substances, bio-oil, and so on.

Microprobe for the Thermal Analysis of Crude Oil Coupled to Photoionization Fourier Transform Mass Spectrometry.

We present the simple microprobe for the investigation of crude oil by a thermal desorption photoionization coupled to Orbitrap mass spectrometry. The droplet of crude oil was placed on the heating element with controllable temperature. The temperature was linearly increased, and crude oil vapors were ionized by a vacuum ultraviolet (VUV) lamp and detected by Orbitrap mass spectrometer. Use of modified Orbitrap allowed introduction of the heating element and VUV lamp directly into the ion funnel and performing experiment not only at atmosphere pressure but also at 20, 10, and 5 torr. We observed that at high pressure protonated CHN compounds dominate in the spectrum, while at the low pressure CH compounds dominate. Similar to previously reported thermogravimetry coupled to photoionization or chemical ionization mass spectrometry systems we were able to separate compounds with different desorption energy and reliably detect low-abundant compounds. Also, we were able to determine the desorption temperature for each compound of the crude oil. We found that temperature of desorption increases linearly with m/ z for compounds that belong to the same homology series (same Kendrick mass defect). This may serve as indirect evidence that such compounds differ only by the length of aliphatic chains attached to some basic structure.