Development of high throughput 96-blade solid phase microextraction-liquid chromatrography-mass spectrometry protocol for metabolomics

A new chemical derivatization reagent sulfonyl piperazinyl for the quantification of fatty acids using LC-MS/MS

In our previous study, a chemical derivatization reagent named 5-(dimethylamino) naphthalene-1-sulfonyl piperazine (Dns-PP) was developed to enhance the chromatographic retention and the mass spectrometric response of free fatty acids (FFAs) in reversed-phase liquid chromatography coupled with electrospray ionization-mass spectrometry (RPLC-ESI-MS). However, Dns-PP exhibited strong preferences for long-chain FFAs, with limited improvement for short- or medium-chain FFAs. In this study, a new series of labeling reagents targeting FFAs were designed, synthesized, and evaluated. Among these reagents, Tmt-PP (N2, N2, N4, N4-tetramethyl-6-(4-(piperazin-1-ylsulfonyl) phenyl)-1,3,5-triazine-2,4-diamine) exhibited the best MS response and was selected for further evaluations. We compared Tmt-PP with Dns-PP and four commonly used carboxyl labeling reagents from existing studies, demonstrating the advantages of Tmt-PP. Further comparisons between Tmt-PP and Dns-PP in measuring FFAs from biological samples revealed that Tmt-PP labeling enhanced the MS response for about 80 % (30/38) of the measured FFAs, particularly for short- and medium-chain FFAs. Moreover, Tmt-PP labeling significantly improved the chromatographic retention of short-chain FFAs. To ensure accurate quantification, we developed a stable isotope-labeled Tmt-PP (i.e., d12-Tmt-PP) to react with chemical standards and serve as one-to-one internal standards (IS). The method was validated for accuracy, precision, sensitivity, linearity, stability, extraction efficiency, as well as matrix effect. Overall, this study introduced a new chemical derivatization reagent Tmt-PP (d12-Tmt-PP), providing a sensitive and accurate option for quantifying FFAs in biological samples.

PANAMA-enabled high-sensitivity dual nanoflow LC-MS metabolomics and proteomics analysis

High-sensitivity nanoflow liquid chromatography (nLC) is seldom employed in untargeted metabolomics because current sample preparation techniques are inefficient at preventing nanocapillary column performance degradation. Here, we describe an nLC-based tandem mass spectrometry workflow that enables seamless joint analysis and integration of metabolomics (including lipidomics) and proteomics from the same samples without instrument duplication. This workflow is based on a robust solid-phase micro-extraction step for routine sample cleanup and bioactive molecule enrichment. Our method, termed proteomic and nanoflow metabolomic analysis (PANAMA), improves compound resolution and detection sensitivity without compromising the depth of coverage as compared with existing widely used analytical procedures. Notably, PANAMA can be applied to a broad array of specimens, including biofluids, cell lines, and tissue samples. It generates high-quality, information-rich metabolite-protein datasets while bypassing the need for specialized instrumentation.

Exploring sample treatment strategies for untargeted metabolomics: A comparative study of solid phase microextraction (SPME) and homogenization with solid-liquid extraction (SLE) in renal tissue

BACKGROUND

The selection of the sample treatment strategy is a crucial step in the metabolomics workflow. Solid phase microextraction (SPME) is a sample processing methodology with great potential for use in untargeted metabolomics of tissue samples. However, its utilization is not as widespread as other standard protocols involving steps of tissue collection, metabolism quenching, homogenization, and extraction of metabolites by solvents. Since SPME allows us to perform all these steps in one action in tissue samples, in addition to other advantages, it is necessary to know whether this methodology produces similar or comparable metabolome and lipidome coverage and performance to classical methods.

RESULTS

SPME and homogenization with solid-liquid extraction (Homo-SLE) sample treatment methods were applied to healthy murine kidney tissue, followed by comprehensive metabolomics and lipidomics analyses. In addition, it has been tested whether freezing and storage of the tissue causes alterations in the renal metabolome and lipidome, so the analyses were performed on fresh and frozen tissue samples Lipidomics analysis revealed the exclusive presence of different structural membrane and intracellular lipids in the Homo-SLE group. Conversely, all annotated metabolites were detected in both groups. Notably, the freezing of the sample mainly causes a decrease in the levels of most lipid species and an increase in metabolites such as amino acids, purines, and pyrimidines. These alterations are principally detected in a statistically significant way by SPME methodology. Finally, the samples of both methodologies show a positive correlation in all the analyses.

SIGNIFICANCE

These results demonstrate that in SPME processing, as long as the fundamentals of non-exhaustive extraction in a pre-equilibrium kinetic regime, extraction in a tissue localized area, the chemistry of the fiber coating and non-homogenization of the tissue are taken into account, is an excellent method to use in kidney tissue metabolomics; since this methodology presents an easy-to-use, efficient, and less invasive approach that simplifies the different sample processing steps.

Octadecyl-fibrous mesoporous silica nanospheres coated 96-blade thin-film microextraction for high-throughput analysis of phthalic acid esters in food and migration from food packages

A high-throughput sample pre-treatment method combined with high-performance liquid chromatography (HPLC) was developed to analyze phthalates (PAEs) in food and food contact package samples. Thin film microextraction (TFME) in 96-blade format was used to pre-treat 96 samples simultaneously. Octadecyl groups functionalized fibrous mesoporous silica nanospheres, namely C18-FMSNs, were synthesized and used as TFME coating material. The coating was fabricated by spraying a slurry of C18-FMSNs and polyacrylontrile (PAN) mixture with a commercial portable spraypen. The prepared C18-FMSNs/PAN coatings exhibited good reproducibility, repeatability and reusability. The optimized TFME conditions for PAEs consisted of extraction at pH 4.0 for 50 min, and desorption by methanol/acetonitrile (25/75, V/V) for 40 min. The pretreatment time for each sample was approximately 1.3 min. This TFME-HPLC method showed good linearity for eight PAEs within the concentration range of 0.5-1000 ng mL-1, with the coefficients higher than 0.9972. The limits of detection and quantification were 0.096-0.26 ng mL-1 and 0.32-0.86 ng mL-1, respectively. The intra-day and inter-day RSD % were below 6.6 % and 8.4 %, respectively, indicating good precision. The PAEs analysis in real samples showed that dibutyl phthalate (DBP) of 2.3 ± 0.3 ng mL-1 and di-(2-ethylhexyl) phthalate (DEHP) of 5.5 ± 0.8 ng mL-1 in boxed milk, dimethyl phthalate (DMP) of 12.6 ± 0.8 ng mL-1, DBP of 3.2 ± 0.4 ng mL-1and DEHP of 14.3 ± 0.7 ng mL-1 in the simulated water migration of plastic box, as well as DMP of 19.0 ± 0.6 ng mL-1, DBP of 25.6 ± 0.9 ng mL-1 and DEHP of 49.5 ± 2.8 ng mL-1 in the simulated ethanol migration of plastic box were determined, respectively. In addition, the detection of PAEs in all the real samples showed good recovery ranging from 85.6 to 110 % and lower RSDs % (<7.2 %).

Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite-Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.

Benefits of Innovative and Fully Water-Compatible Stationary Phases of Thin-Film Microextraction (TFME) Blades

Octadecyl (C₁₈) groups are arguably the most popular ligands used for preparation of solid phase microextraction (SPME) devices. However, conventional C₁₈-bonded silica particles are not fully compatible with the nearly 100% aqueous composition of typical biological samples (e.g., plasma, saliva, or urine). This study presents the first evaluation of thin-film SPME devices coated with special water-compatible C₁₈-bonded particles. Device performance was assessed by extracting a mixture of 30 model compounds that exhibited various chemical structures and properties, such as hydrophobicity. Additionally, nine unique compositions of desorption solvents were tested. Thin-film SPME devices coated with C₁₈-bonded silica particles with polar end-capping groups (10 µm) were compared with conventional trimethylsilane end-capped C₁₈-bonded silica particles of various sizes (5, 10, and 45 µm) and characteristics. Polar end-capped particles provided the best extraction efficacy and were characterized by the strongest correlations between the efficacy of the extraction process and the hydrophobicity of the analytes. The results suggest that the original features of octadecyl ligands are best preserved in aqueous conditions by polar end-capped particles, unlike with conventional trimethylsilane end-capped particles that are currently used to prepare SPME devices. The benefits associated with this improved type of coating encourage further implementation of microextractraction as greener alternative to the traditional sample preparation methods.

High throughput determination of free biogenic monoamines and their metabolites in urine using thin-film solid phase microextraction

UPLC-MS/MS methods are the gold standard for routine, high-throughput measurements of biogenic monoamines for the diagnosis of catecholamine-producing tumors. However, this cannot be achieved without employing efficient sample pretreatment methods. Therefore, two pretreatment methods, thin-film solid phase microextraction (TF-SPME) and packed fibers solid phase extraction (PFSPE), were developed and evaluated for the analysis of biogenic monoamines and their metabolites in urine. A hydrophilic-lipophilic balance (HLB) coating was chosen for the thin-film blade format SPME method and compared with a Polycrown ether (PCE) composite nanofiber used as an adsorbent for the PFSPE method. Under optimal conditions, the absolute extraction recovery and relative matrix effect of the newly developed TF-SPME method were determined to be 35.7-74.8% and 0.47-3.63%, respectively. The linearity was 0.25-500 ng mL^-1 for norepinephrine, epinephrine, dopamine, normetanephrine 3-methoxytyramine, serotonin, histamine, and 0.1-500 ng mL^-1 for metanephrine. The intra-and inter-assay coefficients of variation were 0.7-8.7%, and the respective accuracies were calculated to be 90.8-104.7% and 89.5-104.5% for TF-SPME. Compared with the PFSPE method, the TF-SPME method had a higher extraction efficiency, lower matrix effects and a wider linear range for eight target substances, which ensured higher accuracy of simultaneous detection of all compounds of interest. Therefore, the proposed TF-SPME method can be employed for the high throughput screening for neuroendocrine tumors in a routine clinical setting and other relative research by simultaneous quantitation of urine eight biological monoamines in a single run.

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.

Assessment of solid phase microextraction as a sample preparation tool for untargeted analysis of brain tissue using liquid chromatography-mass spectrometry

This work presents an evaluation of solid-phase microextraction (SPME) SPME in combination with liquid chromatography-high resolution mass spectrometry (LC-HRMS) as an analytical approach for untargeted brain analysis. The study included a characterization of the metabolite coverage provided by C18, mixed-mode (MM, with benzene sulfonic acid and C18 functionalities), and hydrophilic lipophilic balanced (HLB) particles as sorbents in SPME coatings after extraction from cow brain homogenate at static conditions. The effects of desorption solvent, extraction time, and chromatographic modes on the metabolite features detected were investigated. Method precision and absolute matrix effects were also assessed. Among the main findings of this work, it was observed that all three tested coating chemistries were able to provide comparable brain tissue information. HLB provided higher responses for polar metabolites; however, as these fibers were prepared in-house, higher inter-fiber relative standard deviations were also observed. C18 and HLB coatings offered similar responses with respect to lipid-related features, whereas MM and C18 provided the best results in terms of method precision. Our results also showed that the use of methanol is essential for effective desorption of non-polar metabolites. Using a reversed-phase chromatographic method, an average of 800 and 1200 brain metabolite features detected in positive and negative modes, respectively, met inter-fibre RSD values below 30% (n=4) after removal of fibre and solvent artefacts from the associated datasets. For features detected using a lipidomics method, a total of 900 and 1800 features detected using C18 fibers in positive and negative mode, respectively, met the same criteria. In terms of absolute matrix effects, the majority of the model metabolites tested showed values between 80 and 120%, which are within the acceptable range. Overall, the findings of this work lay the foundation for further optimization of parameters for SPME-LC-HRMS methods suitable for in vivo and ex vivo brain (and other tissue) untargeted studies, and support the applicability of this approach for non-destructive tissue metabolomics.

Systematic Evaluation of Different Coating Chemistries Used in Thin-Film Microextraction

A systematic evaluation of eight different coatings made of solid phase extraction (SPE) and carbon-based sorbents immobilized with polyacrylonitrile in the thin-film microextraction (TFME) format using LC-MS/MS was described. The investigated coatings included graphene, graphene oxide, multi-walled carbon nanotubes (MWCNTs), carboxylated MWCNTs, as carbon-based coatings, and polystyrene-divinylbenzene (PS-DVB), octadecyl-silica particles (C18), hydrophilic-hydrophobic balance particles (HLB) and phenyl-boronic acid modified particles (PBA), as SPE-based coatings. A total of 24 compounds of diverse moieties and of a wide range of polarities (log P from -2.99 to 6.98) were selected as probes. The investigated coatings were characterized based on their extraction performance toward the selected probes at different pH values and at optimized desorption conditions. In the case of SPE-based coatings, PS-DVB and HLB exhibited a balanced extraction for compounds within a wide range of polarities, and C18 showed superior extraction recoveries for non-polar analytes. Carbon-based coatings showed high affinity for non-polar compounds given that their main driving force for extraction is hydrophobic interactions. Interestingly, among the studied carbon-based coatings, graphene oxide showed the best extraction capabilities toward polar compounds owing to its oxygen-containing groups. Overall, this work provided important insights about the extraction mechanisms and properties of the investigated coatings, facilitating the coating selection when developing new TFME applications.

Introducing a mechanically robust SPME sampler for the on-site sampling and extraction of a wide range of untargeted pollutants in environmental waters

The present study introduces a mechanically robust, sealable SPME sampler for the on-site sampling and extraction of a wide range of untargeted pollutants in environmental waters. Spray-coating and dip coating methodologies were used to coat the surfaces of six stainless steel bolts with a layer of HLB/PAN particles, which served as the extractive substrate in the proposed device. In addition, this sampler was designed to withstand rough handling, long storage times, and various environmental conditions. In order to identify whether the sampler was able to stabilize extracted compounds for long periods of time, the effects of storage time and temperature were evaluated. The results of these tests showed no significant differences in the quantity and quality of the extracted chemicals following 12 days storage at room temperature, thus confirming the device's suitability for use at sampling sites that are far away from the laboratory facilities. The proposed device was also used to perform extraction and untargeted analyses of river waters in five different geographical locations. The constituent chemicals in the samplers were analyzed and determined using high-resolution HPLC-Orbitrap MS. Toxin and Toxin-Target Database was used as a reference database for toxins and environmental contaminants. Ultimately, over 80 tentative chemicals with widely varying hydrophobicities ranging within -2.43 < logP <11.9-including drugs, metabolites, wide ranges of toxins, pesticide, and insecticides-were identified in the samplers used in the different rivers. The log P values for the tentative analytes confirmed that the introduced device is suitable for the extraction and trace analysis of wide ranges of targeted and untargeted pollutants.

Solid-phase microextraction: An appealing alternative for the determination of endogenous substances - A review

The determination of endogenous substances is of great significance for obtaining important biotic information such as biological components, metabolic pathways and disease biomarkers in different living organisms (e.g. plants, insects, animals and humans). However, due to the complex matrix and the trace concentrations of target analytes, the sample preparation procedure is an essential step before the analytes of interest are introduced into a detection instrument. Solid-phase microextraction (SPME), an emerging sample preparation technique that integrates sampling, extraction, concentration, and sample introduction into one step, has gained wide acceptance in various research fields, including in the determination of endogenous compounds. In this review, recent developments and applications of SPME for the determination of endogenous substances over the past five years are summarized. Several aspects, including the design of SPME devices (sampling configuration and coating), applications (in vitro and in vivo sampling), and coupling with emerging instruments (comprehensive two-dimensional gas chromatography (GC × GC), ambient mass spectrometry (AMS) and surface enhanced Raman scattering (SERS)) are involved. Finally, the challenges and opportunities of SPME methods in endogenous substances analysis are also discussed.

Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications

The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted by its ability to influence the genome, transcriptome, and proteome. Consequently, metabolomic information is being used to understand microbial metabolic networks. At the forefront of this work is mass spectrometry, the most popular metabolomics measurement technique. Mass spectrometry-based metabolomic analyses have made significant contributions to microbiological research in the environment and human disease. In this chapter, we break down the technical aspects of mass spectrometry-based metabolomics and discuss its application to microbiological research.

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.

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.

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.

Fused Deposition Modeling Enables the Low-Cost Fabrication of Porous, Customized-Shape Sorbents for Small-Molecule Extraction

Fused deposition modeling, one of the most common techniques in three-dimensional printing and additive manufacturing, has many practical applications in the fields of chemistry and pharmacy. We demonstrate that a thermoplastic elastomer-poly(vinyl alcohol) (PVA) composite material (LAY-FOMM 60), which presents porous properties after PVA removal, is useful for the extraction of small-molecule drug-like compounds from water samples. The usefulness of the proposed approach is demonstrated by the extraction of glimepiride from a water sample, followed by LC-MS analysis. The recovery was 82.24%, with a relative standard deviation of less than 5%. The proposed approach can change the way of thinking about extraction and sample preparation due to a shift to the use of sorbents with customizable size, shape, and chemical properties that do not rely on commercial suppliers.

High throughput solid phase microextraction: A new alternative for analysis of cellular lipidome?

A new SPME method for untargeted lipidomic study of cell line cultures was proposed for the first time. In this study the feasibility to monitor changes in lipid profile after external stimuli was demonstrated and compared to the conventional Bligh & Dyer method. The human hepatocellular carcinoma (HCC) cell line was used as a model. The obtained results provided a list of up-regulated and down-regulated lipids through a comparison between control (non-stimulated) cells versus the group of cells treated with polyunsaturated fatty acid (20:5). Use of the SPME technique yielded a list of 77 lipid species whose concentrations were recognized to be significantly different between control and treated cells, from which 63 lipids were up-regulated in treated cells. In general, the list was comparable to the peer list obtained by the Bligh & Dyer method. However, more diversity of lipid classes and subclasses such as LPC, sphingomyelins, ceramides, and prenol lipids were observed with the application of the SPME method. Method precision for the SPME approach was within the acceptable analytical range (5-18% RSD) for all detected lipids, which was advantageous over solvent extraction applied. The evaluation of ionization efficiency indicated no matrix effect for the SPME technique, while Bligh & Dyer presented significant ionization suppression for low abundant species such as LysoPC, PG, ceramides, and sphingomyelins, and ionization enhancement for high abundant phospholipids such as PE.