Exact mass GC-MS analysis: Protocol, database, advantages and application to plant metabolic profiling

Advances in mycotoxin detection techniques and the crucial role of reference material in ensuring food safety. A review

Mycotoxins, toxic secondary metabolites produced by fungi, pose a significant threat to food safety and human health. The occurrence of mycotoxins in food commodities necessitates accurate and reliable detection methods. Advanced detection techniques, such as chromatographic techniques and immunochemical assays, have improved sensitivity and specificity. However, the lack of standardized reference material, particularly in less privileged countries, hinders method validation and proficiency testing, ultimately affecting mycotoxin testing and regulation. Moreover, these techniques are complex as they require specialized equipment, and well-trained personnel, thus limiting their practical applications. This comprehensive review provides an up-to-date overview of the occurrence of mycotoxins and recent advancements in detection methods. It examines the crucial role of mycotoxin standards as reference materials for ensuring reliable results in mycotoxins analysis in agriculture commodities. The review addresses emerging challenges, knowledge gaps, and future research directions in mycotoxin detection and reference material development. By synthesizing existing literature, this review aims to provide valuable resources for researchers, policymakers, and other stakeholders in food safety, highlighting the importance of integrated approaches to mitigate mycotoxin contamination and ensuring food safety.

Response mechanism of extracellular polymers in the remediation of chromium pollution by carbonate mineralizing bacteria

This study examines the adaptability of carbonate mineralizing bacteria in Cr(iii)-contaminated environments with varying Cr(iii) concentrations and their response mechanism via EPS. Cr(iii) removal efficiency declined with concentrations exceeding 1000 mg L-1, while the removal amount continued to rise, indicating strong Cr(iii) tolerance in the bacterium. Analysis of dynamic changes in EPS revealed a significant increase in production, with polysaccharides and proteins playing key roles in Cr(iii) binding. A notable increase in mannose in the monosaccharide composition of EPS suggests its involvement in Cr(iii) binding. Moreover, alterations in the protein secondary structure, such as a reduction in α-helix content and an increase in β-sheet and random coil structures, may enhance EPS interaction with Cr(iii). These findings demonstrate that EPS contributes to heavy metal remediation not only through its polysaccharide components but also through changes in protein structure, offering a new theoretical foundation for Cr(iii) bioremediation.

Research note: Compound-specific isotopic analysis in 34S-labelled chicken tissues using high resolution gas chromatography/mass spectrometry

Many food supplements include sulphur (S)-containing additives such as methionine or synthetic compounds like 2‑hydroxy-S-methyl-thiobutyric acid (HMTBA). However, monitoring the metabolic use efficiency of S-containing additive is challenging, and requires specific methods, based on isotopic labelling. The most direct route is the utilisation of 34S-enriched material and subsequent measurement of 34S-abundance in tissues. While this can be carried out routinely using elemental analysis coupled with isotope ratio mass spectrometry (IRMS) for bulk S from raw tissue material, there is currently no IRMS-based method adapted to compound-specific isotopic analysis for sulphur. Here, we present a method based on gas chromatography coupled to high resolution mass spectrometry (GC-MS) to measure 34S-abundance in both free and protein-bound S containing amino acids. This method elaborates on metabolomics based on GC-MS analysis of trimethylsilylated extracts. Specific ion fragments comprising a sulphur atom could be identified and their isotopic pattern was used to compute % 34S. The high resolution was useful to avoid the confounding effect of natural carbon (13C2) or (18O) isotopologues but required a correction for silicium (Si) isotope because the mass excess of 30Si (+ 1.9968 a.m.u.) was close to that of 34S (+ 1.9957 a.m.u.) and therefore the 30Si and 34S isotopologues could not be separated. This technique was applied to broilers fed with 34S-labelled methionine and showed that 34S could be easily traced in different organs. 34S-methionine redistributed mostly to homocysteine with little 34S-enrichment in cysteine and taurine, due to the isotopic dilution by food cysteine supply. The results show that our method can be implemented to follow the metabolic incorporation of S-containing additives such as methionine in broilers.

Effect of clove flower extract ( ) administration timing on skeletal muscle damage induced by eccentric exercise: An in vivo study

Eccentric exercise often leads to oxidative stress, inflammation, and muscle damage that impair athletic performance. To counter these adverse effects, clove flower extract (Syzygium aromaticum) offers promising potential as a natural remedy to promote muscle repair with its potent antioxidant and anti-inflammatory properties. The aim of this study was to assess the effects of clove flower extract administration timing on oxidative stress and inflammatory responses in skeletal muscle damage induced by acute eccentric exercise in mice. This study used a post-test-only control group design, involving 35 male mice (Mus musculus, Balb/c) randomly divided into five groups: a healthy control group (HG) with no exercise and no treatment, a negative control group (NG) with exercise but no treatment, T1 group (receiving clove flower extract 24 hours before exercise), T2 group (receiving clove flower extract immediately after exercise), and T3 group (receiving clove flower extract 24 hours after exercise). The treatment groups received a single dose of clove flower extract (500 mg/kg body weight (BW)). The skeletal muscle damage in mice was collected by measuring NADPH oxidase (NOX) and superoxide dismutase (SOD) activities using spectrophotometry, as well as toll-like receptor 4 (TLR4) and interleukin-8 (IL-8) levels using an enzyme-linked immunosorbent assay (ELISA). Moreover, the skeletal muscle damage was analyzed through the histopathological method. Data were analyzed using one-way analysis of variance (ANOVA) followed by Fisher's least significant difference (LSD) tests as a post hoc test. The result showed that clove flower extract significantly reduced NOX (p=0.049) and IL-8 (p=0.032) levels, increased SOD activity (p=0.001), and did not significantly affect TLR4 levels (p=0.532). Moreover, the results showed a significant reduction in muscle damage (p=0.001). The study highlights that the administration of clove flower extract (500 mg/kg BW) 24 hours before exercise, immediately after exercise, or 24 hours after exercise can help prevent muscle damage.

Metabolomic Characterization and Bioinformatic Studies of Bioactive Compounds in Two Varieties of Psidium guajava L. Leaf by GC-MS Analysis

The guava tree (Psidium guajava L.) is a tropical plant from the Myrtaceae family. Leaf extracts from this plant have been used in traditional medicine to treat gastrointestinal disorders and exhibit several functional activities that benefit human health. Different varieties of guava trees produce fruits in colors ranging from white to red and present a characteristic metabolic profile in both their leaves and fruits. This study presents a metabolomic characterization of the leaves from two guava varieties: the Caxcana cultivar with yellow fruits and the S-56 accession with pink fruits. Metabolite profiling was conducted using Gas Chromatography-Mass Spectrometry (GC-MS) on methanol extracts, followed by multivariate statistical analysis, including Principal Component Analysis (PCA), and a heat map visualization of compound concentrations in the two varieties. The results identified β-caryophyllene as the major secondary metabolite present in both varieties, with a relative abundance of 16.46% in the Caxcana variety and 23.06% in the S-56 cultivar. Furthermore, in silico analyses, such as network pharmacology and molecular docking, revealed key interactions with proteins such as CB2, PPARα, BAX, BCL2, and AKT1, suggesting potential therapeutic relevance. These findings highlight the pharmacological potential of guava leaf metabolites in natural product chemistry and drug discovery.

Qualitative and quantitative analyses of the changes in the chemical composition of frankincense before and after stir-frying using GC-MS and LC-MS

Frankincense is a resin drug used widely in the medical field. Comprehensive qualitative and quantitative analyses of the differences in the chemical composition of frankincense, stir-fried frankincense and vinegar frankincense were done by combining GC-MS and LC-MS. GC-MS revealed six chemical compositions with high content in frankincense: β-ocimene, 1-octanol, acetic acid, octyl ester, nerolidol, lauric acid and incensole acetate. LC-MS revealed eight more widely studied chemical compositions: 11-keto-β-boswellic acid, β-elemolic acid, acetyl-11-keto-β-boswellic acid, β-elemonic acid, α-boswellic acid, β-boswellic acid, 3-O-acetyl-α-boswellic acid and 3-O-acetyl-β-boswellic acid. In addition, the chemical composition of frankincense was identified by the fragmentation information afforded by LC-MS.

Comprehensive Analysis of Metabolic Changes in Mice Exposed to Corilagin Based on GC-MS Analysis

Background

Corilagin is widely distributed in various medicinal plants. In recent years, numerous pharmacological activities of Corilagin have been reported, including anti-inflammatory, antiviral, hepatoprotective, anti-tumor, and anti-fibrosis effects. However, there is still a need for systematic metabolomics analysis to further elucidate its mechanisms of action. The aim of this study was to explore the pharmacological mechanism of Corilagin.

Methods

This study utilized gas chromatography-mass spectrometry (GC-MS) to analyze central target tissues, comprehensively exploring the pharmacological mechanism of Corilagin in mouse models. We identified the differential metabolites by multivariate analyses, which include principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). Using MetaboAnalyst 5.0 and the KEGG database was used to depict the 12 key metabolic pathways.

Results

Compared with the control group, the Corilagin induced 20, 9, 11, 7, 16, 19, 14, 15, and 16 differential metabolites in the intestine, lung, kidney, stomach, heart, liver, hippocampus, cerebral cortex, and serum, respectively. And 12 key pathways involving glucose metabolism, lipid metabolism, and amino acid metabolism were identified following Corilagin treatment.

Conclusion

This research provides insight into the action mechanism of Corilagin's anti-oxidative, anti-inflammatory, anti-atherosclerotic, hepatoprotective, anti-tumor, and neuroprotective properties.

Unlocking the pharmacological potential of Brennnesselwurzel (Urtica dioica L.): an in-depth study on multifaceted biological activities

Brennnesselwurzel (Urtica dioica L.) is recognized for its diverse pharmacological properties. With a range of chemical constituents, such as vitamins, minerals, phenolic compounds, fibers, and amino acids, Brennnesselwurzel (BWE) has a long history of traditional medicinal use in Europe and Asia. The correlation between a plant's metabolite composition and its activity can vary depending on considerations such as geographic location, environmental conditions, and genetic variations. In the present study, we explore the phytochemical profile and biological activity of the 70% acetone extract of the BWE plant. The chemical profile of the BWE extract was explored using several techniques, including amino acid analyzer, HPLC, GC-MS, and other colorimetric analysis. The antioxidant activity of the BWE extract was assessed by evaluating the total antioxidant, free radical scavenging activity (DPPH, ABTS, H2O2), and metal chelating scavenging activity (FRAP, CUPRAC, metal chelating). Furthermore, we assessed the antimicrobial and antiproliferation activities of the BWE extract against 29 microbial strains and 15 cell lines, respectively. Our phytochemical analyzes revealed that the BWE extract has a unique profile of metabolites including amino acids, flavonoids, phenolics, volatile oils, lipids, and vitamins. The BWE extract showed a total antioxidant capacity of 30.94 ± 1.58 mg GAE/g, together with potential free radical scavenging activity towards ABTS (IC50 = 153.51 ± 3.97 µg/ml), DPPH (IC50 = 195.75 ± 5.91 µg/ml), and H2O2 (IC50 = 230.67 ± 5.98 µg/ml). Although the BWE extract showed no significant antifungal activity, our findings revealed that the BWE extract possesses substantial antibacterial activity against Staphylococcus epidermidi, Streptococcus mutants, Enterococcus faecalis, Micrococcus sp., Klebsiella pneumonia and Porphyromonas gingivalis. Furthermore, the BWE extract demonstrated potential antiproliferative activity toward a panel of cancer cell lines with a high selectivity index. Among the cells examined, the BWE extract exhibited significant cytotoxic activity toward HCT-116, A-549, MDA-MB-231 cells with IC50 of 15.11, 15.32, 15.79 µg/mL, respectively, while it possessed no significant cytotoxic activity towards WI-38 cells (IC50 119.62 µg/mL). Taken together, our findings reveal that BWE extract possesses a wide spectrum of biological activities, including antioxidant, antibacterial, and antitumor activities, and could be considered for further research to explore its potential as a natural plant-based supplement for human diseases.

Metabolomics-Assisted Breeding in Oil Palm: Potential and Current Perspectives

Oil palm is presently the most important oil-producing crop worldwide in terms of oil production and consumption. However, oil palm cultivation faces important challenges such as adverse climatic conditions, expensive fertilization requirements, and fungal pathogens, including Ganoderma. Intense efforts in oil palm breeding are devoted to improving both oil production yield and resistance to environmental cues. Metabolomics can be of interest because it provides many quantitative traits and metabolic signatures that can be selected for to optimize oil palm performance. Here, we briefly review how metabolomics can help oil palm breeding, and to do so, we give examples of recent metabolomics analyses and provide a roadmap to use metabolomics-assisted breeding.

Variation in leaf dark respiration among C3 and C4 grasses is associated with use of different substrates

Measurements of respiratory properties have often been made at a single time point either during daytime using dark-adapted leaves or during nighttime. The influence of the day-night cycle on respiratory metabolism has received less attention but is crucial to understand photosynthesis and photorespiration. Here, we examined how CO2- and O2-based rates of leaf dark respiration (Rdark) differed between midday (after 30-min dark adaptation) and midnight in 8 C3 and C4 grasses. We used these data to calculate the respiratory quotient (RQ; ratio of CO2 release to O2 uptake), and assessed relationships between Rdark and leaf metabolome. Rdark was higher at midday than midnight, especially in C4 species. The day-night difference in Rdark was more evident when expressed on a CO2 than O2 basis, with the RQ being higher at midday than midnight in all species, except in rice (Oryza sativa). Metabolomic analyses showed little correlation of Rdark or RQ with leaf carbohydrates (sucrose, glucose, fructose, or starch) but strong multivariate relationships with other metabolites. The results suggest that rates of Rdark and differences in RQ were determined by several concurrent CO2-producing and O2-consuming metabolic pathways, not only the tricarboxylic acid cycle (organic acids utilization) but also the pentose phosphate pathway, galactose metabolism, and secondary metabolism. As such, Rdark was time-, type- (C3/C4) and species-dependent, due to the use of different substrates.

Chemical analysis of wetland plants to evaluate the bioaccumulation and metabolism of hexachlorocyclohexane (HCH)

Hexachlorocyclohexanes (HCH) belong to the banned pesticides with short-time production and use during the last century. However, the consequences of this short period are still present as persistent environmental contamination. This study represents the large lab-scale experiment focused on the HCH accumulation and metabolism in selected wetland plants (Juncus effuses, Typha latifolia, Phragmites australis) and trees (Alnus glutinosa) after the exposure to the technical mix of HCH isomers (t-HCH) or δ-HCH at three different concentration. During the three-month exposure, morphological (biomass, height, relative chlorophyll content) and physiological (photosynthetic measurements - photosynthetic rate, stomatal conductance, transpiration and dark transpiration) parameters were measured to assess the HCH effect on plant's growth. The results showed that all selected plant species supported HCH removal from the soil. The total removal efficiency was lower for the t-HCH than for δ-HCH exposure, and the best results were provided by Alnus glutinosa tree. Also, no isomer preference was observed in plants exposed to t-HCH. Most HCH remained accumulated in the root biomass, and mainly α-HCH and δ-HCH were transported to the above-ground parts due to their physicochemical properties. Simultaneously, HCH uptake and metabolization to chlorobenzenes (CB) and chlorophenols (CP) occur. Non-targeted analysis showed that CP could be conjugated to glucose and malonyl in plant tissue, and secondary plant metabolism is affected positively and negatively after exposure to t-HCH depending on plant species and chemical concentration. Luteolin, quercetin and quercetin-3-O-glucoside found common to all species showed quantitative changes due to HCH. Nevertheless, most morphological and physiological parameters were adversely affected without statistical significance. This large-scale study provides information on the fate of HCH in the soil-plant system, the suitability of selected plants and their adaptation to chemical stress for use in the phytoremediation process.

The role of metabolomics in informing strategies for improving photosynthesis

Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.

Untargeted metabolomic in basil cell cultures - a case study of Ocimum basilicum L. var. minimum Alef

AIMS

Due to the lack of experimental databases, together with the chemical complexity and the dynamic nature of plants' metabolome, most of the metabolites in complex biological materials (like plant in vitro tissue cultures) are not-annotated, unidentified metabolites. In this study, a method for further metabolite characterization and classification based on the UPLC-HESI-HRMS/MS approach for small-leaved basil (Ocimum basilicum L. var. minimum Alef.) callus and cell suspension culture is presented.

KEY RESULTS

A total of 2168 metabolic features were detected, out of which the database for exact mass metabolic profiling for 1949 metabolites is presented here since there is no available database dedicated to O. basilicum. We further focused on secondary metabolites (particularly phenolic compounds). The presence of 60 different phenolic compounds belonging mainly to the groups of flavonoids, glycosides, terpenoids, and phenolic acids is confirmed. By comparing relative abundances of phenolic compounds from callus culture and cell suspension culture, both grown on two types of media, via svd-PCА, univariate analysis, post-hoc tests, and heatmapping of metabolites, we provided a practical example of how resources presented here can be further applied in tissue culture-based basil metabolomics studies.

UTILITY

This study represents the first approach toward routine targeted investigation of secondary metabolites in basil in vitro cultures and provides various opportunities for new-generation analyses.

The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip

Nitrogen is the most limiting nutrient for plants, and it is preferentially absorbed in the form of nitrate by roots, which adapt to nitrate fluctuations by remodelling their architecture. Although core mechanisms of the response to nitrate availability are relatively well-known, signalling events controlling root growth and architecture have not all been identified, in particular in Legumes. However, the developmental effect of nitrate in Legumes is critical since external nitrate not only regulates root architecture but also N2-fixing nodule development. We have previously shown that in barrel medic (Medicago truncatula), the nitrate transporter MtNPF6.8 is required for nitrate sensitivity in root tip. However, uncertainty remains as to whether nitrogen metabolism itself is involved in the MtNPF6.8-mediated response. Here, we examine the metabolic effects of MtNPF6.8-dependent nitrate signalling using metabolomics and proteomics in WT and mtnpf6.8 root tips in presence or absence of nitrate. We found a reorchestration of metabolism due to the mutation, in favour of the branched chain amino acids/pantothenate metabolic pathway, and lipid catabolism via glyoxylate. That is, the mtnpf6.8 mutation was likely associated with a specific rerouting of acetyl-CoA production (glyoxylic cycle) and utilisation (pantothenate and branched chain amino acid synthesis). In agreement with our previous findings, class III peroxidases were confirmed as the main protein class responsive to nitrate, although in an MtNPF6.8-independent fashion. Our data rather suggest the involvement of other pathways within mtnpf6.8 root tips, such as Ca2+ signalling or cell wall methylation.

Combining Gas Exchange and Rapid Quenching of Leaf Tissue for Mass Spectrometry and NMR Analysis Using an External Chamber

We describe here a method to study and manipulate photorespiration in intact illuminated leaves. When the CO2/O2 mole fraction ratio changes, instant sampling is critical, to quench leaf metabolism and thus trace rapid metabolic modification due to gaseous conditions. To do so, we combine 13CO2 labeling and gas exchange, using a large custom leaf chamber to facilitate fast sampling by direct liquid nitrogen spraying. Moreover, the use of a high chamber surface area (about 130 cm2) allows one to sample a large amount of leaf material to carry out 13C-nuclear magnetic resonance (NMR) analysis and complementary analyses, such as isotopic analyses by high-resolution mass spectrometry (by both GC and LC-MS). 13C-NMR gives access to absolute 13C amounts at the specific carbon atom position in the labeled molecules and thereby provides an estimate of 13C-flux of photorespiratory intermediates. Since NMR analysis is not very sensitive and can miss minor metabolites, GC or LC-MS analyses are useful to monitor metabolites at low concentrations. Furthermore, 13C-NMR and high-resolution LC-MS allow to estimate isotopologue distribution in response to 13CO2 labeling while modifying photorespiration activity.

Evaluation of GC/MS-Based 13C-Positional Approaches for TMS Derivatives of Organic and Amino Acids and Application to Plant 13C-Labeled Experiments

Analysis of plant metabolite ¹³C-enrichments with gas-chromatography mass spectrometry (GC/MS) has gained interest recently. By combining multiple fragments of a trimethylsilyl (TMS) derivative, ¹³C-positional enrichments can be calculated. However, this new approach may suffer from analytical biases depending on the fragments selected for calculation leading to significant errors in the final results. The goal of this study was to provide a framework for the validation of ¹³C-positional approaches and their application to plants based on some key metabolites (glycine, serine, glutamate, proline, α-alanine and malate). For this purpose, we used tailor-made ¹³C-PT standards, harboring known carbon isotopologue distributions and ¹³C-positional enrichments, to evaluate the reliability of GC-MS measurements and positional calculations. Overall, we showed that some mass fragments of proline_2TMS, glutamate_3TMS, malate_3TMS and α-alanine_2TMS had important biases for ¹³C measurements resulting in significant errors in the computational estimation of ¹³C-positional enrichments. Nevertheless, we validated a GC/MS-based ¹³C-positional approach for the following atomic positions: (i) C1 and C2 of glycine_3TMS, (ii) C1, C2 and C3 of serine_3TMS, and (iii) C1 of malate_3TMS and glutamate_3TMS. We successfully applied this approach to plant ¹³C-labeled experiments for investigating key metabolic fluxes of plant primary metabolism (photorespiration, tricarboxylic acid cycle and phosphoenolpyruvate carboxylase activity).