Solid-phase microextraction in metabolomics

The use of solid phase microextraction for metabolomic analysis of non-small cell lung carcinoma cell line (A549) after administration of combretastatin A4

Use of solid phase microextraction (SPME) for cell culture metabolomic analysis allows for the attainment of more sophisticated data from in vitro cell cultures. Moreover, considering that SPME allows the implementation of multiple extractions from the same sample due to its non/low-depletive nature, time course studies using the same set of samples are thus facilitated via this method. Such an approach results in a reduction in the number of samples needed for analysis thus eliminates inter-batch variability related to biological variation occurring during cell culturing. The current work aims to demonstrate the capability of SPME for measurements of combretastatin A4 (CA4) effectiveness on non-small cell cancer cell line. A cultivation protocol was established in the 96-well plate, and a fiber format of SPME was selected for metabolite extraction. The extracellular metabolic pattern of cells was changed after administration of the tested drug. This suggests pharmacological activity of the administered compound towards the studied cell line model. Results support that the use of direct immersion SPME for analysis of cell cultures does not affect cells growth or contaminate sample. Consequently, SPME allows the attainment of accurate information regarding drug uptake, metabolism, and metabolomic changes in the studied cells induced by exposure to the drug simultaneously in a single experiment.

Volatile Compounds of Selected Raw and Cooked Brassica Vegetables

Brassica vegetables are a significant component of the human diet and their popularity is systematically increasing. The interest in plants from this group is growing because of numerous reports focused on their pro-health properties. However, some consumers are not enthusiastic about these vegetables because of their specific bitter taste and sharp, sulfurous aroma. In this study, the volatile composition of 15 Brassica cultivars (five Brussels sprouts, four kohlrabi, three cauliflower and three broccoli), both raw and cooked, was analyzed by solid phase microextraction and comprehensive two-dimensional gas chromatography with time of flight mass spectrometry (SPME-GC×GC-ToFMS). Differences were found between the analyzed vegetables, as well as different cultivars of the same vegetable. Moreover, the influence of cooking on the composition of volatile compounds was evaluated. All the vegetables were frozen before analyses, which is why the impact of this process on the volatile organic compounds (VOCs) was included. The most abundant groups of compounds were sulfur components (including bioactive isothiocyanates), nitriles, aldehydes and alcohols. Cooking in general caused a decrease in the abundance of main volatiles. However, the amount of bioactive isothiocyanates increased in most cultivars after cooking. The effect of freezing on the volatile fraction was presented based on the Brussels sprout cultivars. Most of the changes were closely related to the activity of the lipoxygenase (LOX) pathway enzymes. These are characterized by a marked reduction in alcohol contents and an increment in aldehyde contents. Moreover, important changes were noted in the concentrations of bioactive components, e.g., isothiocyanates. This research included a large set of samples consisting of many cultivars of each analyzed vegetable, which is why it provides a considerable body of general information concerning volatiles in Brassica vegetables.

High-Throughput Solid-Phase Microextraction-Liquid Chromatography-Mass Spectrometry for Microbial Untargeted Metabolomics

Nowadays, metabolomics data, when combined with other "omics" data, can provide important information regarding systems biology. Acquiring a comprehensive untargeted metabolome snapshot of complex sample matrices requires proper sample preparation, and access to sophisticated analytical instrumentation such as mass spectrometry. In metabolomics, sample preparation has substantial influence on the quality of the obtained metabolome profile. To achieve a real snapshot of the metabolome, the analysis method must be capable of inhibiting metabolite interconversion by immediately quenching all metabolome activity. Application of solid-phase microextraction (SPME), particularly in its in vivo set up, when undertaken in conjunction with a conscious selection of coating type based on the chosen sample matrix and the physicochemical properties of the analytes under study, is capable of providing extraction of representative metabolomes for many biological matrices. Metabolomes identified by SPME include low-abundance species and short-lived or unstable metabolites hardly captured by traditional extraction techniques. SPME coupled to liquid chromatography-high-resolution mass spectrometry has recently been introduced as an innovative alternative technique that integrates sampling, sample preparation, and extraction for metabolic profiling and isolation of candidate biomarkers. This chapter presents a detailed protocol for microbial metabolome analysis of Escherichia coli as a model organism, applying the high-throughput SPME-LC-MS workflow.

Sample Preparation Focusing on Plant Omics

Because of strong impact of omics in many fields, and the complexity of the samples when focusing on areas such as genomics, (metallo)proteomics, metabolomics, among others, it is easy to rationalize the great importance that sample preparation has for achieving reliable results, mainly considering plant science. Then, this chapter points out applications of the sample preparation focusing on such areas, and a diversity of strategies, techniques, and procedures is highlighted and commented.

Application of Direct Immersion Solid-Phase Microextraction (DI-SPME) for Understanding Biological Changes of Mediterranean Fruit Fly (Ceratitis capitata) During Mating Procedures

Samples from three different mating stages (before, during and after mating) of the Mediterranean fruit fly Ceratitis capitata were used in this experiment. Samples obtained from whole insects were subjected to extraction with the two mixtures of solvents (acetonitrile/water (A) and methanol/acetonitrile/water (B)) and a comparative study of the extractions using the different solvents was performed. Direct immersion-solid phase microextraction (DI-SPME) was employed, followed by gas chromatographic-mass spectrometry analyses (GC/MS) for the collection, separation and identification of compounds. The method was validated by testing its sensitivity, linearity and reproducibility. The main compounds identified in the three different mating stages were ethyl glycolate, α-farnesene, decanoic acid octyl ester, 2,6,10,15-tetramethylheptadecane, 11-tricosene, 9,12-(Z,Z)-octadecadienoic acid, methyl stearate, 9-(Z)-tricosene, 9,11-didehydro-lumisterol acetate; 1,54-dibromotetrapentacontane, 9-(Z)-hexadecenoic acid hexadecyl ester, 9-(E)-octadecenoic acid and 9-(Z)-hexadecenoic acid octadecyl ester. The novel findings indicated that compound compositions were not significantly different before and during mating. However, new chemical compounds were generated after mating, such as 1-iodododecane, 9-(Z)-tricosene and 11,13-dimethyl-12-tetradecen-1-acetate which were extracted with both (A) and (B) and dodecanoic acid, (Z)-oleic acid, octadecanoic acid and hentriacontane which were extracted with (A) and ethyl glycolate, 9-hexadecenoic acid hexadecyl ester, palmitoleic acid and 9-(E)-octadecenoic acid, which were extracted with solvent (B). This study has demonstrated that DI-SPME is useful in quantitative insect metabolomics by determining changes in the metabolic compounds in response to mating periods. DI-SPME chemical extraction technology might offer analysis of metabolites that could potentially enhance our understanding on the evolution of the medfly.

Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry

Advances in liquid chromatography-mass spectrometry (LC-MS) instruments and analytical strategies have brought about great progress in targeted metabolomics analysis. This methodology is now capable of performing precise targeted measurement of dozens or hundreds of metabolites in complex biological samples. Classic targeted quantification assay using the multiple reaction monitoring (MRM) mode has been the foundation of high-quality metabolite quantitation. However, utilization of this strategy in biological studies has been limited by its relatively low metabolite coverage and throughput capacity. A number of methods for large-scale targeted metabolomics assay which have been developed overcome these limitations. These strategies have enabled extended metabolite coverage which is defined as targeting of large numbers of metabolites, while maintaining reliable quantification performance. These recently developed techniques thus bridge the gap between traditional targeted metabolite quantification and untargeted metabolomics profiling, and have proven to be powerful tools for metabolomics study. Although the LC-MRM-MS strategy has been used widely in large-scale metabolomics quantification analysis due to its fast scan speed and ideal analytic stability, there are still drawbacks which are due to the low resolution of the triple quadrupole instruments used for MRM assays. New approaches have been developed to expand the options for large-scale targeted metabolomics study, using high-resolution instruments such as parallel reaction monitoring (PRM). MRM and PRM-based techniques are now attractive strategies for quantitative metabolomics analysis and high-throughput biomarker discovery. Here we provide an overview of the major developments in LC-MS-based strategies for large-scale targeted metabolomics quantification in biological samples. The advantages of LC-MRM/PRM-MS based analytical strategies which may be used in multiplexed and high throughput quantitation for a wide range of metabolites are highlighted. In particular, PRM and MRM strategies are compared, and we summarize the work flow commonly used for large-scale targeted metabolomics analysis including sample preparation, LC separation and data analysis, as well as recent applications in biological studies.

Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery

This Feature Article highlights some of the key challenges within the field of metabolomics and examines what role separation and analytical sciences can play to improve the use of metabolomics in biomarker discovery and personalized medicine. Recent progress in four key areas is highlighted: (i) improving metabolite coverage, (ii) developing accurate methods for unstable metabolites including in vivo global metabolomics methods, (iii) advancing inter-laboratory studies and reference materials and (iv) improving data quality, standardization and quality control of metabolomics studies.

SPME-GC×GC-TOF MS fingerprint of virally-infected cell culture: Sample preparation optimization and data processing evaluation

Untargeted metabolomics study of volatile organic compounds produced by different cell cultures is a field that has gained increasing attention over the years. Solid-phase microextraction has been the sampling technique of choice for most of the applications mainly due to its simplicity to implement. However, a careful optimization of the analytical conditions is necessary to obtain the best performances, which are highly matrix-dependent. In this work, five different solid-phase microextraction fibers were compared for the analysis of the volatiles produced by cell culture infected with the human respiratory syncytial virus. A central composite design was applied to determine the best time-temperature combination to maximize the extraction efficiency and the salting-out effect was evaluated as well. The linearity of the optimized method, along with limits of detection and quantification and repeatability was assessed. Finally, the effect of i) different normalization techniques (i.e. z-score and probabilistic quotient normalization), ii) data transformation (i.e. in logarithmic scale), and iii) different feature selection algorithms (i.e. Fisher ratio and random forest) on the capability of discriminating between infected and not-infected cell culture was evaluated.

A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage

Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.

Coated blade spray: shifting the paradigm of direct sample introduction to MS

Coated blade spray (CBS) is a solid-phase microextraction-based technology that can be directly coupled to MS to enable the rapid qualitative and quantitative analysis of complex matrices. The goal of this mini review is to concisely introduce CBS's operational fundamentals and to consider how it correlates/contrasts with existing direct-to-MS technologies suitable for bioanalytical applications. In addition, we provide a fair comparison of CBS to other existing solid-phase microextraction-to-MS approaches, as well as an overview of recent CBS applications/strategies that have been developed to analyze diverse compounds present in biofluids.

Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review

Metabolomics and lipidomics generally targets a huge number of intermediate and end products of cellular metabolism in body fluids, tissues, and cells etc. At present, mass spectrometry (MS) based metabolic or lipid profiling of routine biological specimens including the whole cells, tissues, plasma, serum and urine etc., can cover hundreds of metabolites or lipid species in one analysis, which has qualified deep elucidation of global metabolic and lipid networks. Mitochondria are important intracellular organelles and many critical biochemical reactions occur here, they provide building block for new cells, control redox balance, participate in apoptosis and behave as a signalling platform. Evidence suggests high prevalence of mitochondrial dysfunction occurs in a variety of cancers and other diseases, thus there is an urgent demand for investigating and clarifying mitochondrial metabolic and lipid alterations induced by diseases. Nevertheless, mitochondria contribute a small fraction to cellular contents, profiling of whole cell is probably unsuitable for monitoring alterations in mitochondria. Therefore, metabolomics and lipidomics analyses specially for mitochondria are necessary to understand disturbed metabolic and lipid pathways induced by environment and diseases. However, methods for comprehensively profiling metabolites and lipids in mitochondria have been limited at present. This review summarizes the current states and progress of MS-based mitochondrial metabolomics and lipidomics study. Details of mitochondrial isolation procedure, analytical methods and their applications are described. The challenges and opportunities are also given.

The Saliva Exposome for Monitoring of Individuals' Health Trajectories

BACKGROUND

There is increasing evidence that environmental, rather than genetic, factors are the major causes of most chronic diseases. By measuring entire classes of chemicals in archived biospecimens, exposome-wide association studies (EWAS) are being conducted to investigate associations between a myriad of exposures received during life and chronic diseases.

OBJECTIVES

Because the intraindividual variability in biomarker levels, arising from changes in environmental exposures from conception onwards, leads to attenuation of exposure-disease associations, we posit that saliva can be collected repeatedly in longitudinal studies to reduce exposure-measurement errors in EWAS.

METHODS

From the literature and an open-source saliva-metabolome database, we obtained concentrations of 1,233 chemicals that had been detected in saliva. We connected salivary metabolites with human metabolic pathways and PubMed Medical Subject Heading (MeSH) terms, and performed pathway enrichment and pathway topology analyses.

RESULTS

One hundred ninety-six salivary metabolites were mapped into 49 metabolic pathways and connected with human metabolic diseases, central nervous system diseases, and neoplasms. We found that the saliva exposome represents at least 14 metabolic pathways, including amino acid metabolism, TCA cycle, gluconeogenesis, glutathione metabolism, pantothenate and CoA biosynthesis, and butanoate metabolism.

CONCLUSIONS

Saliva contains molecular information worthy of interrogation via EWAS. The simplicity of specimen collection suggests that saliva offers a practical alternative to blood for measurements that can be used to characterize individual exposomes. https://doi.org/10.1289/EHP1011.

Review of geometries and coating materials in solid phase microextraction: Opportunities, limitations, and future perspectives

The development of new support and geometries of solid phase microextraction (SPME), including metal fiber assemblies, coated-tip, and thin film microextraction (TFME) (i.e. self-supported, fabric and blade supported), as well as their effects on diffusion and extraction rate of analytes were discussed in the current review. Application of main techniques widely used for preparation of a variety of coating materials of SPME, including sol-gel technique, electrochemical and electrospinning methods as well as the available commercial coatings, were presented. Advantages and limitations of each technique from several aspects, such as range of application, biocompatibility, availability in different geometrical configurations, method of preparation, incorporation of various materials to tune the coating properties, and thermal and physical stability, were also investigated. Future perspectives of each technique to improve the efficiency and stability of the coatings were also summarized. Some interesting materials including ionic liquids (ILs), metal organic frameworks (MOFs) and particle loaded coatings were briefly presented.

In vivo microsampling to capture the elusive exposome

Loss and/or degradation of small molecules during sampling, sample transportation and storage can adversely impact biological interpretation of metabolomics data. In this study, we performed in vivo sampling using solid-phase microextraction (SPME) in combination with non-targeted liquid chromatography and high-resolution tandem mass spectrometry (LC-MS/MS) to capture the fish tissue exposome using molecular networking analysis, and the results were contrasted with molecular differences obtained with ex vivo SPME sampling. Based on 494 MS/MS spectra comparisons, we demonstrated that in vivo SPME sampling provided better extraction and stabilization of highly reactive molecules, such as 1-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoleoyl-glycero-3-phosphocholine, from fish tissue samples. This sampling approach, that minimizes sample handling and preparation, offers the opportunity to perform longitudinal monitoring of the exposome in biological systems and improve the reliability of exposure-measurement in exposome-wide association studies.

The Recent Developments in Sample Preparation for Mass Spectrometry-Based Metabolomics

Metabolomics is a critical member in systems biology. Although great progress has been achieved in metabolomics, there are still some problems in sample preparation, data processing and data interpretation. In this review, we intend to explore the roles, challenges and trends in sample preparation for mass spectrometry- (MS-) based metabolomics. The newly emerged sample preparation methods were also critically examined, including laser microdissection, in vivo sampling, dried blood spot, microwave, ultrasound and enzyme-assisted extraction, as well as microextraction techniques. Finally, we provide some conclusions and perspectives for sample preparation in MS-based metabolomics.

Sample Preparation for Bioanalytical and Pharmaceutical Analysis

Biological and pharmaceutical samples represent formidable challenges in sample preparation that hold important consequences for bioanalysis and genotoxic impurity quantification. This Feature will emphasize significant advances toward the development of rapid, sensitive, and selective sample preparation methods.

In vivo tissue sampling using solid-phase microextraction for non-lethal exposome-wide association study of CYP1A1 induction in Catostomus commersonii

Fish are widely used for monitoring aquatic ecosystem health and water contamination by organic toxicants from natural and anthropogenic sources. However, most of these studies only focused on the measurement of specific toxicants and did not examine the impact of chemical mixtures. In this study, we examined whether the tissue exposome captured in vivo with solid-phase microextraction (SPME) without lethal sampling and analyzed by liquid chromatography-high resolution mass spectrometry can detect differences between Catostomus commersonii exhibiting a significant induction of CYP1A1, through case/control comparisons, controlling for false discovery rates. We observed the presence of environmental toxicants in induced case fish known as potential inducers of CYP1A1. We also found significant changes in the levels of anti-oxidants, short-lived oxysterols and other lipids associated with CYP1A1 induction, possibly due to oxidative stress, lipid peroxidation and free fatty acids mobilization to maintain homeostatic state. In vivo SPME opens the way to perform repeated sampling on the same animal over the time and explore the individual internal exposome trajectory for better characterization of the links between toxicant load and health effects, at the individual scale.

An Effective Method to Detect Volatile Intermediates Generated in the Bioconversion of Coal to Methane by Gas Chromatography-Mass Spectrometry after In-Situ Extraction Using Headspace Solid-Phase Micro-Extraction under Strict Anaerobic Conditions

Bioconversion of coal to methane has gained increased attention in recent decades because of its economic and environmental advantages. However, the mechanism of this process is difficult to study in depth, partly because of difficulties associated with the analysis of intermediates generated in coal bioconversion. In this investigation, we report on an effective method to analyze volatile intermediates generated in the bioconversion of coal under strict anaerobic conditions. We conduct in-situ extraction of intermediates using headspace solid-phase micro-extraction followed by detection by gas chromatography-mass spectrometry. Bioconversion simulation equipment was modified and combined with a solid-phase micro-extraction device. In-situ extraction could be achieved by using the combined units, to avoid a breakdown in anaerobic conditions and to maintain the experiment continuity. More than 30 intermediates were identified qualitatively in the conversion process, and the variation in trends of some typical intermediates has been discussed. Volatile organic acids (C2–C7) were chosen for a quantitative study of the intermediates because of their importance during coal bioconversion to methane. Fiber coating, extraction time, and solution acidity were optimized in the solid-phase micro-extraction procedure. The pressure was enhanced during the bioconversion process to investigate the influence of headspace pressure on analyte extraction. The detection limits of the method ranged from 0.0006 to 0.02 mmol/L for the volatile organic acids and the relative standard deviations were between 4.6% and 11.5%. The volatile organic acids (C2–C7) generated in the bioconversion process were 0.01–1.15 mmol/L with a recovery range from 80% to 105%. The developed method is useful for further in-depth research on the bioconversion of coal to methane.

Recent approaches for on-line analysis of residues and contaminants in food matrices: A review

This review highlights recent developments for on-line determination of residues and contaminants in complex matrices such as food samples. This involves the on-line coupling of a sample preparation technique (as the first "dimension") with a chromatographic system (second "dimension"), usually followed by mass spectrometry. Although frequently treated as quite distinct techniques, the role of all devices utilized as the first dimension in this approach aims to decrease the sample complexity while eliminating as much as possible the matrix contaminants to facilitate the qualitative and quantitative determination of the compounds of interest. This review will focus on the following techniques as the first dimension: (i) on-line solid-phase extraction; (ii) in-tube solid-phase microextraction; (iii) matrix solid-phase dispersion; and (iv) turbulent flow chromatography. The second dimension is usually performed using a chromatographic column to isolate the analyte(s) of interest for further mass spectrometry determination. A description of the basis of this on-line approach and its distinct set up possibilities is presented, which is followed by a critical review of the literature covering this subject in the last ten years (focusing on the last five years) with emphasis on the analysis of residue and contaminants in food samples.

Solid phase microextraction devices prepared on plastic support as potential single-use samplers for bioanalytical applications

This study presents new thin-film solid phase microextraction (SPME) devices prepared on plastic as potential single-use samplers for bioanalysis. Polybutylene terephthalate (PBT) was selected as a support due to its well-known chemical resistance, low cost, and suitability as a material for different medical grade components. The herein proposed samplers were prepared by applying a hydrophilic-lipophilic balanced (HLB)-polyacrylonitrile (PAN) coating on rounded and flat PBT pieces previously sanded with regular sandpaper. SPME devices prepared on PBT were evaluated in terms of robustness, chemical stability, and possible interferences upon exposure to different solvents and matrixes. Rewarding results were found when these samplers were employed for the quantitative analysis of multiple doping substances in common biological matrixes such as urine, plasma, and whole blood. Finally, the proposed thin-film SPME devices made on a PBT were evaluated by conducting multiple extractions from whole blood and plasma using the Concept 96 system. Results showed that more than 20 extractions from plasma and whole blood can be performed without observed decreases in coating performance or peeling of the extraction phase from the plastic surface. These findings demonstrate the robustness of PAN-based coatings applied on such polymeric substrate and open up the possibility of introducing new alternatives and cost-effective materials as support to manufacture SPME biocompatible devices for a wide range of applications, particularly in the clinical field.

Analysis of phenolic and cyclic compounds in plants using derivatization techniques in combination with GC-MS-based metabolite profiling

Metabolite profiling has been established as a modern technology platform for the description of complex chemical matrices and compound identification in biological samples. Gas chromatography coupled with mass spectrometry (GC-MS) in particular is a fast and accurate method widely applied in diagnostics, functional genomics and for screening purposes. Following solvent extraction and derivatization, hundreds of metabolites from different chemical groups can be characterized in one analytical run. Besides sugars, acids, and polyols, diverse phenolic and other cyclic metabolites can be efficiently detected by metabolite profiling. The review describes own results from plant research to exemplify the applicability of GC-MS profiling and concurrent detection and identification of phenolics and other cyclic structures.