Ambient mass spectrometry in metabolomics

Tidy-Direct-to-MS: An Open-Source Data-Processing Pipeline for Direct Mass Spectrometry-Based Metabolomics Experiments

Direct-to-Mass Spectrometry and ambient ionization techniques can be used for biochemical fingerprinting in a fast way. Data processing is typically accomplished with vendor-provided software tools. Here, a novel, open-source functionality, entitled Tidy-Direct-to-MS, was developed for data processing of direct-to-MS data sets. It allows for fast and user-friendly processing using different modules for optional sample position detection and separation, mass-to-charge ratio drift detection and correction, consensus spectra calculation, and bracketing across sample positions as well as feature abundance calculation. The tool also provides functionality for the automated comparison of different sets of parameters, thereby assisting the user in the complex task of finding an optimal combination to maximize the total number of detected features while also checking for the detection of user-provided reference features. In addition, Tidy-Direct-to-MS has the capability for data quality review and subsequent data analysis, thereby simplifying the workflow of untargeted ambient MS-based metabolomics studies. Tidy-Direct-to-MS is implemented in the Python programming language as part of the TidyMS library and can thus be easily extended. Capabilities of Tidy-Direct-to-MS are showcased in a data set acquired in a marine metabolomics study reported in MetaboLights (MTBLS1198) using a transmission mode Direct Analysis in Real Time-Mass Spectrometry (TM-DART-MS)-based method.

Modern machine-learning applications in ambient ionization mass spectrometry

This article provides a comprehensive overview of the applications of methods of machine learning (ML) and artificial intelligence (AI) in ambient ionization mass spectrometry (AIMS). AIMS has emerged as a powerful analytical tool in recent years, allowing for rapid and sensitive analysis of various samples without the need for extensive sample preparation. The integration of ML/AI algorithms with AIMS has further expanded its capabilities, enabling enhanced data analysis. This review discusses ML/AI algorithms applicable to the AIMS data and highlights the key advancements and potential benefits of utilizing ML/AI in the field of mass spectrometry, with a focus on the AIMS community.

Putative Identification of New Phragmaline-Type Limonoids from the Leaves of Swietenia macrophylla King: A Case Study Using Mass Spectrometry-Based Molecular Networking

Swietenia macrophylla King is a plant commonly known as Brazilian mahogany. The wood from its stem is highly prized for its exceptional quality, while its leaves are valued for their high content of phragmalin-type limonoids, a subclass of compounds known for their significant biological activities, including antimalarial, antitumor, antiviral, and anti-inflammatory properties. In this context, twelve isolated limonoids from S. macrophylla leaves were employed as standards in mass spectrometry-based molecular networking to unveil new potential mass spectrometry signatures for phragmalin-type limonoids. Consequently, ultra-performance liquid chromatography coupled with high-resolution mass spectrometry was utilized for data acquisition. Subsequently, the obtained data were analyzed using the Global Natural Products Social Molecular Networking platform based on spectral similarity. In summary, this study identified 24 new putative phragmalin-type limonoids for the first time in S. macrophylla. These compounds may prove valuable in guiding future drug development efforts, leveraging the already established biological activities associated with limonoids.

Promise of spatially resolved omics for tumor research

Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures. By interacting with the microenvironment, tumor cells undergo dynamic changes in gene expression and metabolism, resulting in spatiotemporal variations in their capacity for proliferation and metastasis. In recent years, the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis. By preserving location information while obtaining a large number of gene and molecular data, spatially resolved metabolomics (SRM) and spatially resolved transcriptomics (SRT) approaches can offer new ideas and reliable tools for the in-depth study of tumors. This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques, as well as a review of their applications in cancer-related fields.

The Study of Alanine Transaminase Activity in Tissues of Silkworm (Bombyx mori) via Direct Analysis in Real-Time (DART) Mass Spectrometry

Alanine transaminase (ALT) is an important amino acid-metabolizing enzyme in silkworm Bombyx mori L., and is mainly involved in transferring glutamate to alanine (serving as an essential precursor in silk protein synthesis) through transamination. Therefore, it is generally believed that silk protein synthesis in the silk gland and the cocoon quantity increase with the increase in ALT activity to a certain extent. Here, a novel analytical method was developed to determine the ALT activity in several key tissues of Bombyx mori L. including the posterior silk gland, midgut, fat body, middle silk gland, trachea and hemolymph, by combining the direct-analysis-in-real-time (DART) ion source with a triple-quadrupole mass spectrometer. In addition, a traditional ALT activity assay, the Reitman-Frankel method, was also used to measure ALT activity for comparison. The ALT activity results obtained via the DART-MS method are in good agreement with those obtained via the Reitman-Frankel method. However, the present DART-MS method provides a more convenient, rapid and environmentally friendly quantitative method for ALT measurement. Especially, this method can also monitor ALT activity in different tissues of Bombyx mori L. in real time.

Non-invasive Sampling of Human Body Fluids Using In Vivo SPME

Noninvasive body fluids offer attractive sources to gain insights into human health. The in vivo solid-phase microextraction (SPME) technique is a fast and versatile sample preparation technique for the noninvasive sampling of human body fluids in various fields. This chapter summarizes the applications of SPME coupled with mass spectrometry (MS)-based approaches for noninvasive investigations of human body fluids, including urine, sweat, and saliva. New features of noninvasive SPME sampling and MS-based analysis are highlighted, and the prospects on their further development are also discussed.

Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry

Direct observation of metabolites in living cells by mass spectrometry offers a bright future for biological studies but also suffers a severe challenge to untargeted peak assignment to tentative metabolite candidates. In this study, we developed a method combining stable isotope tracing and induced electrospray mass spectrometry for living-cells metabolite measurement and identification. By using ¹³C₆-glucose and ammonium chloride-¹⁵N as the sole carbon and nitrogen sources for cell culture, Escherichia coli synthesized metabolites with ¹⁵N and ¹³C elements. Tracing the number of carbon and nitrogen atoms could offer a complementary dimension for candidate peak searching. As a result, the identification confidence of metabolites achieved a universal improvement based on carbon/nitrogen labelling and filtration.

Cutting-edge strategies and critical advancements in characterization and quantification of metabolites concerning translational metabolomics

Despite remarkable progress in drug discovery strategies, significant challenges are still remaining in translating new insights into clinical applications. Scientists are devising creative approaches to bridge the gap between scientific and translational research. Metabolomics is a unique field among other omics techniques for identifying novel metabolites and biomarkers. Fortunately, characterization and quantification of metabolites are becoming faster due to the progress in the field of orthogonal analytical techniques. This review detailed the advancement in the progress of sample preparation, and data processing techniques including data mining tools, database, and their quality control (QC). Advances in data processing tools make it easier to acquire unbiased data that includes a diverse set of metabolites. In addition, novel breakthroughs including, miniaturization as well as their integration with other devices, metabolite array technology, and crystalline sponge-based method have led to faster, more efficient, cost-effective, and holistic metabolomic analysis. The use of cutting-edge techniques to identify the human metabolite, including biomarkers has proven to be advantageous in terms of early disease identification, tracking the progression of illness, and possibility of personalized treatments. This review addressed the constraints of current metabolomics research, which are impeding the facilitation of translation of research from bench to bedside. Nevertheless, the possible way out from such constraints and future direction of translational metabolomics has been conferred.

A Direct Infusion Probe for Rapid Metabolomics of Low-Volume Samples

Targeted and nontargeted metabolomics has the potential to evaluate and detect global metabolite changes in biological systems. Direct infusion mass spectrometric analysis enables detection of all ionizable small molecules, thus simultaneously providing information on both metabolites and lipids in chemically complex samples. However, to unravel the heterogeneity of the metabolic status of cells in culture and tissue a low number of cells per sample should be analyzed with high sensitivity, which requires low sample volumes. Here, we present the design and characterization of the direct infusion probe, DIP. The DIP is simple to build and position directly in front of a mass spectrometer for rapid metabolomics of chemically complex biological samples using pneumatically assisted electrospray ionization at 1 μL/min flow rate. The resulting data is acquired in a square wave profile with minimal carryover between samples that enhances throughput and enables several minutes of uniform MS signal from 5 μL sample volumes. The DIP was applied to study the intracellular metabolism of insulin secreting INS-1 cells and the results show that exposure to 20 mM glucose for 15 min significantly alters the abundance of several small metabolites, amino acids, and lipids.

Mass Spectrometry-Based Nontargeted and Targeted Analytical Approaches in Fingerprinting and Metabolomics of Food and Agricultural Research

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatography-tandem MS metabolomics, direct analysis using ambient mass spectrometry, as well as development in MS data deconvolution software packages and databases for metabolomic studies. Various nontargeted and targeted approaches are employed in marker compounds identification, material adulteration detection, and the analysis of specific classes of secondary metabolites. In the newly emerged applications, the recent advances in computer tools for the fast deconvolution of MS data in targeted secondary metabolite analysis are highlighted.

Mass Spectrometry Imaging technology in metabolomics: a systematic review

Mass spectrometry imaging (MSI) is a powerful label-free analysis technique that can provide simultaneous spatial distribution of multiple compounds in a single experiment. By combining the sensitive and rapid screening of high-throughput mass spectrometry with spatial chemical information, metabolite analysis and morphological characteristics are presented in a single image. MSI can be used for qualitative and quantitative analysis of metabolic profiles and it can provide visual analysis of spatial distribution information of complex biological and microbial systems. Matrix assisted laser desorption ionization, laser ablation electrospray ionization and desorption electrospray ionization are commonly used in MSI. Here, we summarize and compare these three technologies, as well as the applications and prospects of MSI in metabolomics.

Development of cVSSI-APCI for the Improvement of Ion Suppression and Matrix Effects in Complex Mixtures

The new ionization technique termed vibrating sharp-edge spray ionization (cVSSI) has been coupled with corona discharge to investigate atmospheric pressure chemical ionization (APCI) capabilities. The optimized source was evaluated for its ability to enhance ion signal intensity, overcome matrix effects, and limit ion suppression. The results have been compared with state-of-the-art ESI source performance as well as a new APCI-like source. In methanol, the ion signal intensity increased 10-fold and >10-fold for cocaine and the suppressed analytes, respectively. The ability to overcome ion suppression was improved from 2-fold to 16-fold for theophylline and vitamin D2, respectively. For aqueous samples, ion signal levels increased by two orders of magnitude for all analytes. In both solvent systems, the signal-to-noise ratios also increased for all suppressed analytes. One example of the characterization of low-ionizing (by ESI or cVSSI alone) species in the presence of high-ionizing species by direct analysis from a cotton swab is presented. The work is discussed with respect to the advantages of cVSSI-APCI for direct, in situ, and field analyses.

Ambient mass spectrometry for rapid authentication of milk from Alpine or lowland forage

Metabolomics approaches, such as direct analysis in real time-high resolution mass spectrometry (DART-HRMS), allow characterising many polar and non-polar compounds useful as authentication biomarkers of dairy chains. By using both a partial least squares discriminant analysis (PLS-DA) and a linear discriminant analysis (LDA), this study aimed to assess the capability of DART-HRMS, coupled with a low-level data fusion, discriminate among milk samples from lowland (silages vs. hay) and Alpine (grazing; APS) systems and identify the most informative biomarkers associated with the main dietary forage. As confirmed also by the LDA performed against the test set, DART-HRMS analysis provided an accurate discrimination of Alpine samples; meanwhile, there was a limited capacity to correctly recognise silage- vs. hay-milks. Supervised multivariate statistics followed by metabolomics hierarchical cluster analysis allowed extrapolating the most significant metabolites. Lowland milk was characterised by a pool of energetic compounds, ketoacid derivates, amines and organic acids. Seven informative DART-HRMS molecular features, mainly monoacylglycerols, could strongly explain the metabolomic variation of Alpine grazing milk and contributed to its classification. The misclassification between the two lowland groups confirmed that the intensive dairy systems would be characterised by a small variation in milk composition.

Build, Share and Remix: 3D Printing for Speeding Up the Innovation Cycles in Ambient Ionisation Mass Spectrometry (AIMS)

Ambient ionisation mass spectrometry (AIMS) enables studying biological systems in their native state and direct high-throughput analyses. The ionisation occurs in the physical conditions of the surrounding environment. Simple spray or plasma-based AIMS devices allow the desorption and ionisation of molecules from solid, liquid and gaseous samples. 3D printing helps to implement new ideas and concepts in AIMS quickly. Here, we present examples of 3D printed AIMS sources and devices for ion transfer and manipulation. Further, we show the use of 3D printer parts for building custom AIMS sampling robots and imaging systems. Using 3D printing technology allows upgrading existing mass spectrometers with relatively low cost and effort.

Internal extractive electrospray ionization mass spectrometry for investigating the phospholipid dysregulation induced by perfluorooctanoic acid in Nile tilapia

Direct profiling of endogenous biomolecules in tissue samples is considered to be a promising approach to investigate metabolic-related toxicity in organisms induced by emerging pollutants.

The effect of sample age on the metabolic information extracted from formalin-fixed and paraffin embedded tissue samples using desorption electrospray ionization mass spectrometry imaging

Background: Metabolites, especially lipids, have been shown to be promising therapeutic targets. In conjugation with genes and proteins they can be used to identify phenotypes of disease and support the development of targeted treatments. The majority of clinically collected tissue samples are stored in formalin-fixed and paraffin embedded (FFPE) blocks due to their tissue conservation ability and indefinite storage capacity. For metabolic analysis, however, fresh frozen (FF) samples are currently preferred over FFPE samples due to concerns of metabolic information being lost when preparing the samples. With little or no sample preparation, desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) allows for the study of spatial as well as spectral information. Methods: DESI-MSI analysis was performed on FFPE breast cancer tissue microarray samples from 213 patients collected between the years 1935-2013. Logistic regression (LR) models were built to classify samples based on age and FF samples were used for feature validation. Results: LR models developed on the FFPE samples achieved an average classification accuracy of 96% when predicting their age with a 10-year grouping. Closer examination of the metabolic change over time revealed that the mean signal intensities for the lower mass range (100 - 500 m/z) linearly decrease over time, while the mean intensities for the higher mass range (500 - 900 m/z), remained relatively constant. Conclusions: In our samples, which span over 70 years, sample age has a weak yet quantifiable impact on metabolite content in FFPE samples, while the higher mass range is seemingly unaffected. FFPE samples thus provide an alternative avenue for metabolic analysis of lipids.

The liquid micro junction-surface sampling probe (LMJ-SSP); a versatile ambient mass spectrometry interface

Ambient ionization methods have become important tools in mass spectrometry. The LMJ-SSP can significantly simplify/reduce lengthy sample preparation requirements associated with mass spectrometry analysis. Samples may be introduced through direct contact, insertion and droplet injection, enabling applications from drug discovery and surface analysis to tissue profiling and metabolic mapping. This review examines the underlying principles associated with the LMJ-SSP interface and highlights modifications of the original design that have extended its capability. We summarize different application areas that have exploited the method and describe potential future directions for the adaptable ambient ionization source.

Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology

High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.

New Advances in Tissue Metabolomics: A Review

Metabolomics offers a hypothesis-generating approach for biomarker discovery in clinical medicine while also providing better understanding of the underlying mechanisms of chronic diseases. Clinical metabolomic studies largely rely on human biofluids (e.g., plasma, urine) as a more convenient specimen type for investigation. However, biofluids are non-organ specific reflecting complex biochemical processes throughout the body, which may complicate biochemical interpretations. For these reasons, tissue metabolomic studies enable deeper insights into aberrant metabolism occurring at the direct site of disease pathogenesis. This review highlights new advances in metabolomics for ex vivo analysis, as well as in situ imaging of tissue specimens, including diverse tissue types from animal models and human participants. Moreover, we discuss key pre-analytical and post-analytical challenges in tissue metabolomics for robust biomarker discovery with a focus on new methodological advances introduced over the past six years, including innovative clinical applications for improved screening, diagnostic testing, and therapeutic interventions for cancer.

Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry

Of the many metabolites involved in any clinical condition, only a narrow range of biomarkers is currently being used in the clinical setting. A key to personalized medicine would be to extend this range. Metabolic fingerprinting provides a more comprehensive insight, but many methods used for metabolomics analysis are too complex and time-consuming to be diagnostically useful. Here, a rapid evaporative ionization mass spectrometry (REIMS) system for direct ex vivo real-time analysis of biofluids with minor sample pretreatment is detailed. The REIMS can be linked to various laser wavelength systems (such as optical parametric oscillator or CO₂ laser) and with automation for high-throughput analysis. Laser-induced sample evaporation occurs within seconds through radiative heating with the plume guided to the MS instrument. The presented procedure includes (i) laser setup with automation, (ii) analysis of biofluids (blood/urine/stool/saliva/sputum/breast milk) and (iii) data analysis. We provide the optimal settings for biofluid analysis and quality control, enabling sensitive, precise and robust analysis. Using the automated setup, 96 samples can be analyzed in ~35-40 min per ionization mode, with no intervention required. Metabolic fingerprints are made up of 2,000-4,000 features, for which relative quantification can be achieved at high repeatability when total ion current normalization is applied. With saliva and feces as example matrices, >70% of features had a coefficient of variance ≤30%. However, to achieve acceptable long-term reproducibility, additional normalizations by, e.g., LOESS are recommended, especially for positive ionization.

Metabolomics meets lipidomics: Assessing the small molecule component of metabolism

Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward-looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective.

Metabolomics-based predictive biomarkers of radiation injury and countermeasure efficacy: current status and future perspectives

INTRODUCTION

There is an urgent need for specific and sensitive bioassays to augment biodosimetric assessments of unwanted and excessive radiation exposures that originate from unexpected nuclear/radiological events, including nuclear accidents, acts of terrorism, or the use of a radiological dispersal device. If sufficiently intense, such ionizing radiation exposures are likely to impact normal metabolic processes within the cells and organs of the body, thus inducing multifaceted biological responses.

AREAS COVERED

This review covers the application of metabolomics, an emerging and promising technology based on quantitative and qualitative determinations of small molecules in biological samples for the rapid assessment of an individual's exposure to ionizing radiation. Recent advancements in the analytics of high-resolution chromatography, mass spectrometry, and bioinformatics have led to untargeted (global) and targeted (quantitative phase) approaches to identify biomarkers of radiation injury and countermeasure efficacy. Biomarkers are deemed essential for both assessing the radiation exposure levels and for extrapolative processes involved in determining scaling factors of a given radiation countering medicinal between experimental animals and humans.

EXPERT OPINION

The discipline of metabolomics appears to be highly informative in assessing radiation exposure levels and for identifying biomarkers of radiation injury and countermeasure efficacy.

Neutral Desorption Extractive Electrospray Ionization Mass Spectrometry Analysis Sputum for Non-Invasive Lung Adenocarcinoma Detection

Purpose

Increased use of low-dose spiral computed tomography (LDCT: low-dose computed tomography) screening has contributed to more frequent incidental detection of peripheral lung nodules, part of them were adenocarcinoma, which need to be further evaluated to establish a definitive diagnosis. Here, our primary objective was to evaluate the ambient mass spectrometry (AMS) sputum analysis as a non-invasive lung adenocarcinoma (LAC) diagnosis solution.

Patients and Methods

Neutral desorption extractive electrospray ionization mass spectrometry (ND-EESI-MS) and collision induced dissociation (CID) were used to detect sputum metabolites from 143 spontaneous sputum samples. Partial least squares-discriminant analysis (PLS-DA) was used to refine the biomarker panel, whereas orthogonal PLS-DA (OPLS-DA) was used to operationalize the enhanced biomarker panel for diagnosis.

Results

In this approach, 19 altered metabolites were detected by ND-EESI-MS from 76 cases of LAC and 67 cases of control. Significance testing and receiver operating characteristic (ROC) analysis identified 5 metabolites [hydroxyphenyllactic acid, phytosphingosine, N-nonanoylglycine, sphinganine, S-carboxymethyl-L-cysteine] with p <0.05 and AUC >0.75, respectively. Evaluation of model performance for prediction of LAC resulted in a cross-validation classification accuracy of 87.9%. Metabolic pathway analysis showed that sphingolipid metabolism, fatty acid metabolism, carnitine synthesis and Warburg effect were most impacted in response to disease.

Conclusion

This study indicates that the application of ND-EESI-MS to sputum analysis can be used as a non-invasive detection of peripheral lung nodules. The use of sputum metabolite biomarkers may aid in the development of a further evaluation program for lung adenocarcinoma.

Vibrating Sharp-edge Spray Ionization (VSSI) for voltage-free direct analysis of samples using mass spectrometry

RATIONALE

The development of miniaturized and field portable mass spectrometers could not succeed without a simple, compact, and robust ionization source. Here we present a voltage-free ionization method, Vibrating Sharp-edge Spray Ionization (VSSI), which can generate a spray of liquid samples using only one standard microscope glass slide to which a piezoelectric transducer is attached. Compared with existing ambient ionization methods, VSSI eliminates the need for a high electric field (~5000 V·cm-1 ) for spray generation, while sharing a similar level of simplicity and flexibility with the simplest direct ionization techniques currently available such as paper spray ionization (PSI) and other solid substrate-based electrospray ionization methods.

METHODS

The VSSI device was fabricated by attaching a piezoelectric transducer onto a standard glass microscope slide using epoxy glue. Liquid sample was aerosolized by either placing a droplet onto the vibrating edge of the glass slide or touching a wet surface with the glass edge. Mass spectrometric detection was achieved by placing the VSSI device 0.5-1 cm from the inlet of the mass spectrometer (Q-Exactive, ThermoScientific).

RESULTS

VSSI is demonstrated to ionize a diverse array of chemical species, including small organic molecules, carbohydrates, peptides, proteins, and nucleic acids. Preliminary sensitivity experiments show that high-quality mass spectra of acetaminophen can be obtained by consuming 100 femtomoles of the target. The dual spray of VSSI was also demonstrated by performing in-droplet denaturation of ubiquitin. Finally, due to the voltage-free nature and the direct-contact working mode of VSSI, it has been successfully applied for the detection of chemicals directly from human fingertips.

CONCLUSIONS

Overall, we report a compact ionization method based on vibrating sharp-edges. The simplicity and voltage-free nature of VSSI make it an attractive option for field portable applications or analyzing biological samples that are sensitive to high voltage or difficult to access by conventional ionization methods.

Potential impact of tissue molecular heterogeneity on ambient mass spectrometry profiles: a note of caution in choosing the right disease model

This review provides a summary of known molecular alterations in commonly used cancer models and strives to stipulate how they may affect ambient mass spectrometry profiles. Immortalized cell lines are known to accumulate mutations, and xenografts derived from cell lines are known to contain tumour microenvironment elements from the host animal. While the use of human specimens for mass spectrometry profiling studies is highly encouraged, patient-derived xenografts with low passage numbers could provide an alternative means of amplifying material for ambient MS research when needed. Similarly, genetic preservation of patient tissue seen in some organoid models, further verified by qualitative proteomic and transcriptomic analyses, may argue in favor of organoid suitability for certain ambient profiling studies. However, to choose the appropriate model, pre-evaluation of the model's molecular characteristics in the context of the research question(s) being asked will likely provide the most appropriate strategy to move research forward. This can be achieved by performing comparative ambient MS analysis of the disease model of choice against a small amount of patient tissue to verify concordance. Disease models, however, will continue to be useful tools to orthogonally validate metabolic states of patient tissues through controlled genetic alterations that are not possible with patient specimens.

Mass spectrometry-based metabolomics for an in-depth questioning of human health

Today, metabolomics is becoming an indispensable tool to get a more comprehensive analysis of complex living systems, providing insights on multiple aspects of physiology. Although its application in large scale population-based studies is very challenging due to the processing of large sample sets as well as the complexity of data information, its potential to characterize human health is well recognized. Technological advances in metabolomics pave the way for the efficient biomarker discovery of disease etiology, diagnosis and prognosis. Here, different steps of the metabolomics workflow, particularly mass spectrometry-based approaches, are discussed to demonstrate the potential of metabolomics to address biological questioning in human health. First an overview of metabolomics is provided with its interest in human health studies. Analytical development and advances in mass spectrometry instrumentation and computational tools are discussed regarding their application limits. Advancing metabolomics for applicability in human health and large-scale studies is presented and discussed in conclusion.

Rapid detection of asperphenamate in a hay batch associated with constipation and deaths in dairy cattle. The application of DART-HRMS to veterinary forensic toxicology

Direct analysis in real time (DART) coupled to high-resolution mass spectrometry (HRMS) was applied for the first time to veterinary forensic toxicology to investigate the presence of toxic compounds in hay after an episode of acute intoxication in a dairy cattle farm. In addition to gross field necropsy and histological examination, microbial cultures, and heavy metals analysis, the molecular fingerprinting of the suspected hay batch was investigated by DART-HRMS. DART-HRMS revealed a distinct signal of m/z 507.2289 in the hay batch thought to be associated with the digestive complications. A search on chemical structure databases matched the ion with asperphenamate, a toxin produced by Penicillium spp. and Aspergillus spp. Liquid Chromatography-HMRS analysis and electrospray-HRMS-MS/MS of the hay extracts further characterized the structure and confirmed the identification of the compound as asperphenamate. Asperphenamate is fungal metabolite which can have cytotoxic and antitumor activity in humans, and it is classified as acute toxicant and harmful if swallowed.

Metabolomics in Radiation Biodosimetry: Current Approaches and Advances

Triage and medical intervention strategies for unanticipated exposure during a radiation incident benefit from the early, rapid and accurate assessment of dose level. Radiation exposure results in complex and persistent molecular and cellular responses that ultimately alter the levels of many biological markers, including the metabolomic phenotype. Metabolomics is an emerging field that promises the determination of radiation exposure by the qualitative and quantitative measurements of small molecules in a biological sample. This review highlights the current role of metabolomics in assessing radiation injury, as well as considerations for the diverse range of bioanalytical and sampling technologies that are being used to detect these changes. The authors also address the influence of the physiological status of an individual, the animal models studied, the technology and analysis employed in interrogating response to the radiation insult, and variables that factor into discovery and development of robust biomarker signatures. Furthermore, available databases for these studies have been reviewed, and existing regulatory guidance for metabolomics are discussed, with the ultimate goal of providing both context for this area of radiation research and the consideration of pathways for continued development.

Determination of citalopram in fish brain tissue: benefits of coupling laser diode thermal desorption with low- and high-resolution mass spectrometry

Recent state-of-the-art methods developed for the analysis of polar xenobiotics from different types of biological matrices usually employ liquid chromatography with mass spectrometry. However, there are limitations when a small amount of sample mass is available. For example, individual benthic invertebrates or fish tissue samples often weigh less than 100 mg (e.g., brain, liver) but are necessary to understand environmental fate and bioaccumulation dynamics. We developed ultra-fast methods based on a direct sample introduction technique. This included coupling laser diode thermal desorption with atmospheric pressure chemical ionization mass spectrometry (LDTD-APCI-MS). We then quantitated a common selective serotonin reuptake inhibitor (citalopram) in brain tissues of individual juvenile fish after in vivo exposure to environmentally relevant concentration. Two mass spectrometric methods based on low (LDTD-APCI-triple quadrupole (QqQ)-MS/MS) and high (LDTD-APCI-high-resolution product scan (HRPS)) resolutions were developed and evaluated. Individual instrument conditions were optimized to achieve an accurate and robust analytical method with minimum sample preparation requirements. We achieved very good recovery (97-108%) across the range of 1-100 ng g^-1 for LDTD-APCI-HRPS. LDTD-APCI-QqQ-MS/MS showed poorer performance due to interferences from the matrix at the lowest concentration level. LDTD-APCI ionization was successfully validated for analysis of non-filtered sample extracts. Evaluation of final methods was performed for a set of real fish brain samples, including comparison of LDTD-APCI-HRPS with a previously validated LC-heated electrospray ionization-HRPS method. This new LDTD-APCI-HRPS method avoids the chromatographic step and provides important benefits such as analysis of limited sample masses, lower total sample volume (typically μL), and reduction in analysis time per sample run to a few seconds. Graphical abstract.

Metabolomic profiling in children with inflammatory bowel disease

Ulcerative colitis (UC) and Crohn's disease (CD) represent inflammatory bowel diseases (IBD) with multifactorial pathogenesis, involving genetic, environmental and microbial factors. Interactions between gut microbiota and immune system result in changes in metabolic pathways. Metabolomics is a comprehensive and quantitative (or semi-quantitative) analysis of metabolites synthetized in human's biological system. It has been shown that metabolic profiling might be used to identify disease biomarkers. Recent findings confirmed alterations in the number of metabolites in patients with IBD. However, most of the studies included adult individuals with ongoing treatment which might have affected the metabolite profiling. Therefore, the aim of our study was to collect the knowledge about metabolomics in paediatric patients with CD or UC based on the currently published literature.

Improving diagnosis of genitourinary cancers: Biomarker discovery strategies through mass spectrometry-based metabolomics

The genitourinary oncology field needs integration of results from basic science, epidemiological studies, clinical and translational research to improve the current methods for diagnosis. MS-based metabolomics can be transformative for disease diagnosis and contribute to global health parity. Metabolite panels are promising to translate metabolomic findings into the clinics, changing the current diagnosis paradigm based on single biomarker analysis. This review article describes capabilities of the MS-based oncometabolomics field for improving kidney, prostate, and bladder cancer detection, early diagnosis, risk stratification, and outcome. Published works are critically discussed based on the study design; type and number of samples analyzed; data quality assessment through quality assurance and quality control practices; data analysis workflows; confidence levels reported for identified metabolites; validation attempts; the overlap of discriminant metabolites for the different genitourinary cancers; and the translation capability of findings into clinical settings. Ongoing challenges are discussed, and future directions are delineated.

Combined use of tandem mass spectrometry and computational chemistry to study 2H-chromenes from Piper aduncum

Natural 2H-chromenes were isolated from the crude extract of Piper aduncum (Piperaceae) and analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS) applying collision-induced dissociation. Density functional theory (DFT) calculations were used to explain the preferred protonation sites of the 2H-chromenes based on thermochemical parameters, including atomic charges, proton affinity, and gas-phase basicity. After identifying the nucleophilic sites, the pathways were proposed to justify the formation of the diagnostic ions under ESI-MS/MS conditions. The calculated relative energy for each pathway was in good agreement with the energy-resolved plot obtained from ESI-MS/MS data. Moreover, the 2H-chromene underwent proton attachment on the prenyl moiety via a six-membered transition state. This behavior resulted in the formation of a diagnostic ion due to 2-methylpropene loss. These studies provide novel insights into gas-phase dissociation for natural benzopyran compounds, indicating how reactivity is correlated to the intrinsic acid-base equilibrium and structural aspects, including the substitution pattern on the aromatic moiety. Therefore, these results can be applied in the identification of benzopyran derivatives in a variety of biological samples.

Temporal Effects on Radiation Responses in Nonhuman Primates: Identification of Biofluid Small Molecule Signatures by Gas Chromatography⁻Mass Spectrometry Metabolomics

Whole body exposure to ionizing radiation damages tissues leading to physical symptoms which contribute to acute radiation syndrome. Radiation biodosimetry aims to determine characteristic early biomarkers indicative of radiation exposure and is necessary for effective triage after an unanticipated radiological incident. Radiation metabolomics can address this aim by assessing metabolic perturbations following exposure. Gas chromatography-mass spectrometry (GC-MS) is a standardized platform ideal for compound identification. We performed GC time-of-flight MS for the global profiling of nonhuman primate urine and serum samples up to 60 d after a single 4 Gy γ-ray total body exposure. Multivariate statistical analysis showed higher group separation in urine vs. serum. We identified biofluid markers involved in amino acid, lipid, purine, and serotonin metabolism, some of which may indicate host microbiome dysbiosis. Sex differences were observed for amino acid fold changes in serum samples. Additionally, we explored mitochondrial dysfunction by tricarboxylic acid intermediate analysis in the first week with a GC tandem quadrupole MS platform. By adding this temporal component to our previous work exploring dose effects at 7 d, we observed the highest fold changes occurring at 3 d, returning closer to basal levels by 7 d. These results emphasize the utility of both MS-based metabolomics for biodosimetry and complementary analytical platforms for increased metabolome coverage.

The Ion Source of Nitrogen Direct Analysis in Real-Time Mass Spectrometry as a Highly Efficient Reactor: Generation of Reactive Oxygen Species

An innovative strategy for sustainably active oxygen capture using nitrogen (N₂) instead of helium (He) as direct analysis in real-time (DART) gas is demonstrated in this work. DART MS was carried out to analyze different polarity compounds including organophosphorus pesticides, amino acids, hormones, and poly brominated diphenyl ethers by using He and N₂ as DART gas, respectively. The unexpectedly characteristic ionization reactions, including replacement reaction where the sulfur atom of P=S group, were replaced by oxygen atom, oxidation ([M + nO + H]⁺ or [M + nO-H]^- (n = 1, 2, 3, 4, 5)), and hydrogen loss (loss of two hydrogens) rapidly occurred in situ in the presence of N₂ under ambient conditions without any additives. The reaction mechanisms were proposed and further confirmed by high-resolution tandem mass spectrometry. Our study under high temperature and high voltage provides a powerful tool for generating unique ionic species that may be difficult to form by other means, which also creates favorable conditions for the future study of the mechanism of DART MS. Graphical Abstract.

Atmospheric Solid Analysis Probe and Modified Desorption Electrospray Ionization Mass Spectrometry for Rapid Screening and Semi-Quantification of Zilpaterol in Urine and Tissues of Sheep

Ambient ionization mass spectrometric methods including desorption electrospray ionization (DESI) and atmospheric solid analysis probe (ASAP) have great potential for applications requiring real-time screening of target molecules in complex matrixes. Such techniques can also rapidly produce repeatable semiquantitative data, with minimal sample preparation, relative to liquid chromatography-mass spectrometry (LC-MS). In this study, a commercial ASAP probe was used to conduct both ASAP-MS and modified DESI (MDESI) MS analyses. We conducted real-time qualitative and semiquantitative analysis of the leanness-enhancing agent zilpaterol in incurred sheep urine, kidney, muscle, liver, and lung samples using ASAP-MS and MDESI MS. Using ASAP, limits of detection (LOD) and quantitation (LOQ) in urine were 1.1 and 3.7 ng/mL, respectively, while for MDESI MS they were 1.3 and 4.4 ng/mL, respectively. The LODs for tissues were 0.1-0.4 ng/g using ASAP, and 0.2-0.6 ng/g with MDESI MS. The LOQs of the tissues in ASAP were 0.4-1.2 ng/g and 0.5-2.1 ng/g in MDESI MS. Trace levels of zilpaterol were accurately analyzed in urine and tissues of sheep treated with dietary zilpaterol HCl. The correlation coefficient ( R²) between semiquantitative ASAP-MS and MDESI MS results of urine samples was 0.872. The data from ASAP and MDESI MS were validated using LC-MS/MS; urinary zilpaterol concentrations ≥5.0 ng/mL or tissue zilpaterol concentrations ≥1.5 ng/g were detected by ASAP and MDESI MS, respectively, 100% of the time. Forty samples could be analyzed in triplicate, directly from biological matrixes in under an hour.

Recent development in mass spectrometry and its hyphenated techniques for the analysis of medicinal plants

INTRODUCTION

Medicinal plants are gaining increasing attention worldwide due to their empirical therapeutic efficacy and being a huge natural compound pool for new drug discovery and development. The efficacy, safety and quality of medicinal plants are the main concerns, which are highly dependent on the comprehensive analysis of chemical components in the medicinal plants. With the advances in mass spectrometry (MS) techniques, comprehensive analysis and fast identification of complex phytochemical components have become feasible, and may meet the needs, for the analysis of medicinal plants.

OBJECTIVE

Our aim is to provide an overview on the latest developments in MS and its hyphenated technique and their applications for the comprehensive analysis of medicinal plants.

METHODOLOGY

Application of various MS and its hyphenated techniques for the analysis of medicinal plants, including but not limited to one-dimensional chromatography, multiple-dimensional chromatography coupled to MS, ambient ionisation MS, and mass spectral database, have been reviewed and compared in this work.

RESULTS

Recent advancs in MS and its hyphenated techniques have made MS one of the most powerful tools for the analysis of complex extracts from medicinal plants due to its excellent separation and identification ability, high sensitivity and resolution, and wide detection dynamic range.

CONCLUSION

To achieve high-throughput or multi-dimensional analysis of medicinal plants, the state-of-the-art MS and its hyphenated techniques have played, and will continue to play a great role in being the major platform for their further research in order to obtain insight into both their empirical therapeutic efficacy and quality control.

Profiling of small molecule metabolites and neurotransmitters in crustacean hemolymph and neuronal tissues using reversed-phase LC-MS/MS

Crustaceans have been long used as model animals for neuromodulation studies because of their well-defined neural circuitry. The identification of small molecule metabolites and signaling molecules in circulating fluids and neuronal tissues presents unique challenges due to their diverse structures, biological functions, and wide range of concentrations. LC combined with high resolution MS/MS is one of the most powerful tools to uncover endogenous small molecules. Here we explored several sample preparation techniques (solid-phase extraction and denaturing) and MS data acquisition strategies (data-dependent acquisition and targeted MS2-based acquisition) that provided complementary coverage and improved overall identification rate in C18 LC-MS/MS experiment. By MS/MS spectral matching with mzCloud database and those generated from standard compounds, a total of 129 small molecule metabolites and neurotransmitters were identified from crustacean hemolymph and neuronal tissues. These confidently identified small molecules covered predominant biosynthetic pathways for major neurotransmitters, validating the effectiveness of the high-throughput RPLC-MS/MS approach in studying the metabolism of neurotransmitters.

Sample preparation for polar metabolites in bioanalysis

Sample preparation is a primary step of any bioanalytical workflow, especially in metabolomics where maximum information has to be obtained without spoiling the analytical instrument. The sample extraction of polar metabolites is still challenging but strategies exist to enable the phase transfer of hydrophilic metabolites from the biological phase to a clean interference-free phase.