Comparative metabolite profiling of carboxylic acids in rat urine by CE-ESI MS/MS through positively pre-charged and (2)H-coded derivatization

An innovative detection technique for capillary electrophoresis: Localized terahertz emission-time domain spectroscopy

Terahertz (THz) time-domain spectroscopy (TDS) is a recently emerging analysis method which can provide unique information on molecular vibration and rotation induced by inter/intra-molecular interactions. Although the application of THz-TDS to high-performance microscale separation methods like capillary electrophoresis (CE) has been anticipated, it has been hindered due to the diffraction limit of THz wave (typically, hundreds µm). In order to realize CE-THz-TDS, in this study, we placed a narrow open-tubular capillary on the surface of a GaAs semiconductor substrate as a "localized" THz-emitter. By focusing femtosecond pulsed laser beams at the surface of a gallium arsenide (GaAs) substrate closest to the capillary, THz waves were locally generated to pass through the capillary, so that THz absorbance spectra were obtained from the capillary which has narrower inner diameter than the diffraction limit. As a typical result from acetic acid analysis in the CE-THz-TDS platform, information on the refractive index and extinction coefficient was obtained, which showed non-linear and linear concentration dependence, respectively, similar to conventional THz-TDS using large liquid cells. Finally, CE-THz-TDS analysis of several carboxylic acids was demonstrated. Two acids were successfully separated and detected with THz-TDS, where their electrophoretic mobility values were estimated as close to those obtained with conventional contactless conductivity detection. Our proposed CE-THz-TDS showed the potential for the systematic analysis of inter/intra-molecular weak interactions like hydrogen bonds, which are unable to obtain with conventional detectors.

Chemical Derivatization to Enhance Capillary Electrophoresis Mass Spectrometric Analysis of Acidic Metabolites in Mammalian Cells

The simultaneous analysis of cationic and anionic metabolites using capillary electrophoresis-mass spectrometry (CE-MS) has been considered challenging, as often two different analytical methods are required. Although CE-MS methods for cationic metabolite profiling have already shown good performance metrics, the profiling of anionic metabolites often results in relatively low sensitivity and poor repeatability caused by problems related to unstable electrospray and corona discharge when using reversed CE polarity and detection by MS in negative ionization mode. In this protocol, we describe a chemical derivatization procedure that provides a permanent positive charge to acidic metabolites, thereby allowing us to profile anionic metabolites by CE-MS using exactly the same separation conditions as employed for the analysis of basic metabolites. The utility of the overall approach is demonstrated for the analysis of energy metabolism-related metabolites in low numbers of HepG2 cells.

Determination of up to twenty carboxylic acid containing compounds in clinically relevant matrices by o-benzylhydroxylamine derivatization and liquid chromatography-tandem mass spectrometry

Carboxylic acid containing compounds (R-COOH) are involved in a large number of biological processes and they are relevant for several pathological processes such as neurodegeneration or cancer. Comprehensive methodologies for the quantitative determination of R-COOH in biological samples are required. In this study we have developed a LC-MS/MS method for the quantification of 20 endogenous R-COOH belonging to different pathways such as kynurenine metabolism, serotoninergic pathway, glycolysis, tricarboxylic acid cycle, dopaminergic pathway, short chain fatty acids and glycine metabolism. The approach included derivatization with o-benzylhydroxylamine (reaction time 1 h), liquid-liquid extraction with ethyl acetate and LC-MS/MS detection (run time 10 min). The method was optimized and validated in 5 different matrices (urine, plasma, saliva, brain and liver) following two different approaches: (i) using surrogate matrices and (ii) using actual human samples by standard additions. A suitable linearity was obtained in the endogenous range of the analytes. Adequate intra and inter-assay accuracies (80-120%) and intra- and inter-assay precisions (<20%) were achieved for almost all analytes in all studied matrices. The method was applied in several scenarios to confirm (i) human urinary changes produced in glycolysis after exercise, (ii) metabolic changes produced in rat brain and plasma by methamphetamine administration and (iii) metabolic alterations in human plasma caused by vitamin B6 deficiency. Additionally, the application of the method allowed for establishing previously unreported alterations in R-COOH metabolites under these conditions. Due to the comprehensive analyte and matrix coverage and the wide applicability of the developed methodology, it can be considered as a suitable tool for the study of R-COOH status in health and disease by targeted metabolomics.

Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry

The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.

Chemical Isotope Labeling LC-MS for Metabolomics

Due to the great diversity of chemical and physical properties of metabolites as well as a wide range of concentrations of metabolites present in metabolomic samples, performing comprehensive and quantitative metabolome analysis is a major analytical challenge. Conventional approach of combining various techniques and methods with each detecting a fraction of the metabolome can lead to the increase in overall metabolomic coverage. However, this approach requires extensive investment in equipment and analytical expertise with still relatively low coverage and low sample throughput. Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) offers an alternative means of increasing metabolomic coverage while maintaining high quantification precision and accuracy. This chapter describes the CIL LC-MS method and its key features for metabolomic analysis.

Metabolomic analysis of mammalian cells and human tissue through one-pot two stage derivatizations using sheathless capillary electrophoresis-electrospray ionization-mass spectrometry

Analysis of metabolites is often performed using separations coupled to mass spectrometry which is challenging due to their vast structural heterogeneity and variable charge states. Metabolites are often separated based on their class/functional group which in large part determine their acidity or basicity. This charge state dictates the ionization mode and efficiency of the molecule. To improve the sensitivity and expand the coverage of the mammalian metabolome, multifunctional derivatization with sheathless CE-ESI-MS was undertaken. In this work, amines, hydroxyls and carboxylates were labeled with tertiary amines tags. This derivatization was performed in under 100 min and resulted in high positive charge states for all analytes investigated. Amino acids and organic acids showed average limits of detection of 76 nM with good linearity of 0.96 and 10% RSD for peak area. Applying this metabolomic profiling system to bovine aortic endothelial cells showed changes in 15 metabolites after treatment with high glucose. The sample injection volume on-capillary was <300 cells for quantitative analyses. Targeted metabolites were found in human tissue, which indicates possible application of the system complex metabolome quantitation.

Mass spectrometric based approaches in urine metabolomics and biomarker discovery

Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.

Hyphenated MS-based targeted approaches in metabolomics

Review of targeted metabolomics, with a focus on the description of analytical methods.

Capillary Electrophoresis in Metabolomics

Metabolomics is an analytical toolbox to describe (all) low-molecular-weight compounds in a biological system, as cells, tissues, urine, and feces, as well as in serum and plasma. To analyze such complex biological samples, high requirements on the analytical technique are needed due to the high variation in compound physico-chemistry (cholesterol derivatives, amino acids, fatty acids as SCFA, MCFA, or LCFA, or pathway-related metabolites belonging to each individual organism) and concentration dynamic range. All main separation techniques (LC-MS, GC-MS) are applied in routine to metabolomics hyphenated or not to mass spectrometry, and capillary electrophoresis is a powerful high-resolving technique but still underused in this field of complex samples. Metabolomics can be performed in the non-targeted way to gain an overview on metabolite profiles in biological samples. Targeted metabolomics is applied to analyze quantitatively pre-selected metabolites. This chapter reviews the use of capillary electrophoresis in the field of metabolomics and exemplifies solutions in metabolite profiling and analysis in urine and plasma.

DnsID in MyCompoundID for rapid identification of dansylated amine- and phenol-containing metabolites in LC-MS-based metabolomics

High-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is an enabling technology based on rational design of labeling reagents to target a class of metabolites sharing the same functional group (e.g., all the amine-containing metabolites or the amine submetabolome) to provide concomitant improvements in metabolite separation, detection, and quantification. However, identification of labeled metabolites remains to be an analytical challenge. In this work, we describe a library of labeled standards and a search method for metabolite identification in CIL LC-MS. The current library consists of 273 unique metabolites, mainly amines and phenols that are individually labeled by dansylation (Dns). Some of them produced more than one Dns-derivative (isomers or multiple labeled products), resulting in a total of 315 dansyl compounds in the library. These metabolites cover 42 metabolic pathways, allowing the possibility of probing their changes in metabolomics studies. Each labeled metabolite contains three searchable parameters: molecular ion mass, MS/MS spectrum, and retention time (RT). To overcome RT variations caused by experimental conditions used, we have developed a calibration method to normalize RTs of labeled metabolites using a mixture of RT calibrants. A search program, DnsID, has been developed in www.MyCompoundID.org for automated identification of dansyl labeled metabolites in a sample based on matching one or more of the three parameters with those of the library standards. Using human urine as an example, we illustrate the workflow and analytical performance of this method for metabolite identification. This freely accessible resource is expandable by adding more amine and phenol standards in the future. In addition, the same strategy should be applicable for developing other labeled standards libraries to cover different classes of metabolites for comprehensive metabolomics using CIL LC-MS.

Derivatization of the tricarboxylic acid intermediates with O-benzylhydroxylamine for liquid chromatography-tandem mass spectrometry detection

The tricarboxylic acid (TCA) cycle is an interface among glycolysis, lipid metabolism, and amino acid metabolism. Increasing interest in cancer metabolism has created a demand for rapid and sensitive methods for quantifying the TCA cycle intermediates and related organic acids. We have developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify the TCA cycle intermediates in a 96-well format after O-benzylhydroxylamine (O-BHA) derivatization under aqueous conditions. This method was validated for quantitation of all common TCA cycle intermediates with good sensitivity, including α-ketoglutarate, malate, fumarate, succinate, 2-hydroxyglutarate, citrate, oxaloacetate, pyruvate, isocitrate, and lactate using a 8-min run time in cancer cells and tissues. The method was used to detect and quantify changes in metabolite levels in cancer cells and tumor tissues treated with a pharmacological inhibitor of nicotinamide phosphoribosyl transferase (NAMPT). This method is rapid, sensitive, and reproducible, and it can be used to assess metabolic changes in cancer cells and tumor samples.

15N-cholamine--a smart isotope tag for combining NMR- and MS-based metabolite profiling

Recently, the enhanced resolution and sensitivity offered by chemoselective isotope tags have enabled new and enhanced methods for detecting hundreds of quantifiable metabolites in biofluids using nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry. However, the inability to effectively detect the same metabolites using both complementary analytical techniques has hindered the correlation of data derived from the two powerful platforms and thereby the maximization of their combined strengths for applications such as biomarker discovery and the identification of unknown metabolites. With the goal of alleviating this bottleneck, we describe a smart isotope tag, (15)N-cholamine, which possesses two important properties: an NMR sensitive isotope and a permanent charge for MS sensitivity. Using this tag, we demonstrate the detection of carboxyl group containing metabolites in both human serum and urine. By combining the individual strengths of the (15)N label and permanent charge, the smart isotope tag facilitates effective detection of the carboxyl-containing metabolome by both analytical methods. This study demonstrates a unique approach to exploit the combined strength of MS and NMR in the field of metabolomics.

Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysis

Sheath-flow capillary electrophoresis-mass spectrometry (CE-MS) has emerged as a new tool for comprehensive analysis of charged metabolites. However, it needs to be more sensitive. Here, we report a sheathless capillary electrophoresis-electrospray ionization-mass spectrometry method for cationic metabolome analysis. This system used a high-sensitivity porous sprayer interface and 10% (v/v) acetic acid as the background electrolyte (BGE). Under optimized conditions, 53 cationic metabolites, including amino acids and their derivatives, amines, nucleic acids and small peptides, were successfully separated and selectively detected with a time-of-flight mass spectrometer. At a signal-to-noise ratio of three, the concentration detection limits for these compounds were between 0.004 and 0.8 μmol L(-1) (amount detection limit, 0.01 to 2 fmol) with pressure injection at 20.7 kPa for 5 s (2.6 nL). Compared with conventional sheath-flow CE-MS, the detection limit of the present method was increased more than 5-fold for 21 (40%) of the compounds detected. When the method was applied to the analysis of cationic metabolites obtained from human urine, there was a 10-fold increase in the number of detected peaks compared with conventional methods. More than 180 successive runs could be conducted without any problems, and only the BGE needed to be changed.

Nutritional biomarkers and foodomic methodologies for qualitative and quantitative analysis of bioactive ingredients in dietary intervention studies

Traditional dietary assessment methods, such as 24-h recalls, weighted food diaries and food frequency questionnaires (FFQs) are highly subjective and impair the assessment of successfully accomplished dietary interventions. Foodomic technologies offer promising methodologies for gathering scientific evidence from clinical trials with sensitive methods (e.g., GC-MS, LC-MS, CE, NMR) to detect and quantify markers of nutrient exposure or subtle changes in dietary patterns. This review provides a summary of recently developed foodomic methodologies for the detection of suggested biomarkers, including the food specificity for each suggested biomarker and a brief description of the key aspects of 24-h recalls that may affect marker detection and stability, such as mixed nutrients and cooking processes. The primary aim of this review is to contribute to the assessment of the metabolic effects of active ingredients and foods using cutting-edge methods to improve approaches to future nutritional programs tailored for health maintenance and disease prevention.

Capillary electrophoresis as a metabolomics tool for non-targeted fingerprinting of biological samples

Metabolomics, understood as a data driven strategy trying to find markers of a situation under study without a priori hypothesis, has rapidly caught the attention and evolved from the simple pattern recognition strategy, which was a great innovation at its origins, to the interest for the final identification of markers responsible for class separation, i.e., from data to knowledge. Due to differences in physico-chemical properties and concentrations of the metabolites, but also due to differences in matrix properties, cross-platform approaches are proving to increase the capability of information. Once more techniques do not compete. This is the scene where capillary electrophoresis (CE) has its niche to provide information mainly on polar or ionic compounds in biological fluids. General advantages and disadvantages of CE for sample fingerprinting will be discussed and methods will be classified depending on the detection system (UV or MS) as this strongly affects all the conditions. Recent developments will be presented in different biological fluids, although urine is without a doubt the preferred sample for CE analysis.

Capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS)-based metabolomics

Metabolomics is a rapidly emerging field of functional genomics research whose aim is the comprehensive analysis of low molecular weight metabolites in a biological sample. Capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) represents a promising hyphenated microseparation platform in metabolomics, since a majority of primary metabolites are intrinsically polar. CE-ESI-MS offers a convenient format for the separation of complex mixtures of cationic, anionic, and/or zwitterionic metabolites, as well as their isobaric/isomeric ions without complicated sample handling. Moreover, online sample preconcentration with desalting is readily integrated during separation prior to ionization, where the migration behavior and ionization response of metabolites can be predicted based on their fundamental physicochemical properties. Herein, we describe recent developments in CE-ESI-MS with emphasis on practical protocols necessary for realizing reliable analyses as applied to targeted metabolite profiling and untargeted metabolomic studies in various biological samples.

Quantification of pentose phosphate pathway (PPP) metabolites by liquid chromatography-mass spectrometry (LC-MS)

The pentose phosphate pathway plays an important role in several cellular processes including biosynthesis and catabolism of five-carbon sugars and generation of reducing power through NADPH synthesis. Although the pentose phosphate metabolic reaction network has been mapped in substantial detail, the comprehensive quantitative analysis of the rates and regulation of individual reactions remains a major interest for various biofields. Here we describe a simple method for comprehensive quantitative analysis of pentose phosphate pathway intermediates. The method is based on Group Specific Internal Standard Technology (GSIST) labeling in which an experimental sample and corresponding internal standards are derivatized in vitro with isotope-coded reagents in separate reactions, then mixed and analyzed in a single LC-MS run. The use of co-eluting isotope-coded internal standards and experimental molecules eliminates potential issues with ion suppression and allows for precise quantification of individual metabolites. Derivatization also increases hydrophobicity of the metabolites enabling their effective separation using reversed-phase chromatography.

Comparative high-speed profiling of carboxylic acid metabolite levels by differential isotope-coded MALDI mass spectrometry

This present work describes the development of a novel high throughput comparative matrix-assisted laser desorption ionization (MALDI) mass spectrometry profiling technique for endogenous compounds using a new isotope-coded label for relative quantitation of carboxylic acids. The key new aspect of this technique was a differential label, 3-hydroxymethyl-1-ethylpyrididinium iodide (HMEP), designed specifically for simultaneous quantitative MALDI analysis of two physiological states. The HMEP-d(0) and HMEP-d(5) variants of the label were applied to profiling endogenous fatty acid levels during a fish oil intervention study, using the metabolite profile of every individual person in the study as their own personal analytical reference standard. Initially, analytical figures of merit such as sensitivity, linear dynamic range, limit of quantitation, and precision were determined from the comparative quantitation experiments. Importantly, the permanently charged HMEP mass tag not only increased the ionization efficiency of the studied fatty acids but also ensured that the solution phase properties of the analytes became more similar, allowing the use of CHCA as a single MALDI matrix compound for the entire range of analytes. The label exhibited a further very unique feature; it provided complete suppression of MALDI matrix-related ions. The MALDI assay was able to generate the data much faster than conventional gas chromatography (GC) methods for fatty acids. It is shown in this study that analyzing a single sample took less than 10 s with analytical results of comparable quality to those obtained by GC.

In vitro stable isotope labeling for discovery of novel metabolites by liquid chromatography-mass spectrometry: Confirmation of gamma-tocopherol metabolism in human A549 cell

A general approach for discovering novel catabolic metabolites from a parent biocompound was developed and validated on the metabolism of gamma-tocopherol in human A549 cell. The method is based on LC-MS analysis of in vitro stable isotope-labeled metabolites and assumes that a parent compound and its metabolites share a common functional group that can be derivatized by well-documented reagents. In this method, two equal aliquots of extracted metabolites are separately derivatized with isotope-coded (heavy) and non-isotope-coded (light) form of derivatizing reagent, mixed at 1:1 ratio and analyzed using LC-MS. The metabolites with common functional group are then easily recognized by determination of a chromatographically co-eluted pair of isotopomers (MS doublet peaks) with similar peak intensities and mass difference corresponding to the mass difference between heavy and light form of derivatization reagent. The feasibility of this approach was demonstrated and validated by the identification of products of gamma-tocopherol catabolism in human A549 cell culture media using N-methyl-nicotinic acid N-hydroxysuccinimide ester (C1-NANHS) and N-methyl-d3-nicotinic acid N-hydroxysuccinimide ester (C1-d3-NANHS) derivatizing reagent. Overall four gamma-tocopherol metabolites were identified including 9'-COOH, 11'-COOH, 13'-COOH and 13'-OH. In addition, the developed LC-MS method can also be used for the fast and sensitive quantitative analysis of gamma-tocopherol and other forms of vitamin E related compounds.