Mass Spectrometry in Plant-omics

Potential mechanism of Laportea bulbifera on treating inflammation and tumor via metabolomics, network pharmacology and molecular docking

This study aimed to utilize metabolomics, network pharmacology, and molecular docking techniques to identify the major active components of Laportea bulbifera and investigate their anti-inflammatory and potential anti-tumor mechanisms. The metabolic constituents of L. bulbifera were examined utilizing UPLC-ESI-MS/MS. PPI networks and compound-target-pathway networks were established using resources such as TCMSP, Swiss Target Prediction, DAVID, STRING database, and Cytoscape software. Molecular docking analysis of the most important compounds and targets was conducted using Autodock4, followed by validation of the molecular docking results' stability using GROMACS. The UPLC-ESI-MS/MS analysis identified a total of 798 compounds. A network pharmacology-based analysis was conducted, revealing that eight compounds and four molecular targets-namely, TNF, IL6, PIK3CA, and HDAC1-were enriched in the network. Pathway analysis of the identified targets demonstrated enrichment in 217 KEGG pathways. Molecular docking analysis and molecular dynamics simulations demonstrated strong therapeutic potential of N-feruloyltyramine, N-feruloylagmatine, and Ellagic acid against various inflammatory and tumor diseases. This study, for the first time, employed an integrated strategy of metabolomics, network pharmacology, molecular docking, and molecular dynamics, elucidating the mechanisms underlying the anti-inflammatory and potential anti-tumor effects of L. bulbifera, laying the foundation for subsequent drug development endeavors.

Visualization of metabolite distribution based on matrix-assisted laser desorption/ionization-mass spectrometry imaging of tea seedlings (Camellia sinensis)

Tea seedlings (Camellia sinensis) have a well-developed root system with a strong taproot and lateral roots. Compared with ordinary cuttings, tea has stronger vitality and environmental adaptability, thus facilitating the promotion of good varieties. However, there is less of detailed research on the rooting and germination process of tea seeds. In this study, matrix-assisted laser desorption ionization time-of-flight-mass spectrometry was used to conduct non-targeted spatial mass spectrometry imaging of the main organs during growth of tea seedlings. A total of 1234 compounds were identified, which could be divided into 24 classes. Among them, theanine, as the most prominent nitrogen compound, was synthesized rapidly at the early stage of embryo germination, accounting for >90% of the total free amino acids in the radicle, and it was then transferred to each meristem region through the mesocolumnar sheath, indicating that theanine-based nitrogen flow plays a decisive role in organ formation during the development of tea seedlings. Nutrients stored in the cotyledon were rapidly hydrolyzed to dextrin and 3-phosphoglyceraldehyde at the early stages of germination, and subsequently converted to other forms that provided carbon and energy for development, such as raffinose and d-galactose (glucose), which were mainly distributed in the growing zones of the root apex and the apical meristems of the stem. This study provides a new perspective on the synthesis and metabolism of substances during the development of tea seedlings and contributes to a better understanding of the biological characteristics of tea varieties.

Advances in mass spectrometry imaging for plant metabolomics-Expanding the analytical toolbox

Mass spectrometry imaging (MSI) has become increasingly popular in plant science due to its ability to characterize complex chemical, spatial, and temporal aspects of plant metabolism. Over the past decade, as the emerging and unique features of various MSI techniques have continued to support new discoveries in studies of plant metabolism closely associated with various aspects of plant function and physiology, spatial metabolomics based on MSI techniques has positioned it at the forefront of plant metabolic studies, providing the opportunity for far higher resolution than was previously available. Despite these efforts, profound challenges at the levels of spatial resolution, sensitivity, quantitative ability, chemical confidence, isomer discrimination, and spatial multi-omics integration, undoubtedly remain. In this Perspective, we provide a contemporary overview of the emergent MSI techniques widely used in the plant sciences, with particular emphasis on recent advances in methodological breakthroughs. Having established the detailed context of MSI, we outline both the golden opportunities and key challenges currently facing plant metabolomics, presenting our vision as to how the enormous potential of MSI technologies will contribute to progress in plant science in the coming years.

A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends

Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020-2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE.

Unveiling targeted spatial metabolome of rice seed at the dough stage using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry imaging

Rice (Oryza sativa) seeds contain a variety of metabolites, which not only provide energy for their own growth and development, but also are an important source of nutrition for humans. It is crucial to study the distribution of metabolites in rice seeds, but the spatial metabolome of rice seeds is rarely investigated. In this study, Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) imaging was used to reveal the spatial distribution of free soluble sugars (glucose, fructose, sucrose, and maltose), amino acids (9 essential amino acids and 2 amino acids affecting rice eating quality: L-aspartic acid and L-glutamic acid), and 4 metabolites in the flavonoids synthesis pathway (cinnamic acid, naringenin chalcone, naringenin, and dihydrokaempferol) in rice seed at the dough stage. It was found that the 4 free soluble sugars present similar spatial distribution, mainly distributed in the seed cortex and embryo with high abundance. The majority of amino acids are also concentrated in the rice cortex and embryo, while the others are abundant in the whole seed. Besides cinnamic acid distributed in the seed cortex and embryo, the naringenin chalcone, naringenin, and dihydrokaempferol were also found in the endosperm and had lower content. Furthermore, a colocalization phylogenetic tree according to the spatial distribution imaging of each metabolite was constructed. This study revealed the distribution diversity of metabolites in different segmentations of rice seed at the dough stage, providing clues for the nutritional differences between brown rice and white rice, and serving as a reference for people to target a healthy diet.

GC-MS, quantum mechanics calculation and the antifungal activity of river red gum essential oil when applied to four natural textiles

The most important uses of old fabrics include clothing, mummification, and bookbinding. However, because they are predominantly constructed of natural materials, they are particularly susceptible to physical and chemical deterioration brought on by fungi. The treatments that are typically used to preserve old textiles focus on the use of synthetic fungicides, which have the potential to be dangerous for both human health and the environment. Essential oils (EOs), which are safe for the environment and have no negative effects on human health, have been widely advocated as an alternative to conventional antifungals. Four natural fabrics-linen, cotton, wool, and silk-were utilized in the current work. The extracted EO from leaves of river red gum (Eucalyptus camaldulensis Dehnh.) were prepared at 125, 250, and 500 µL/L. Aspergillus flavus, Fusarium culmorum and Aspergillus niger were inoculated separately into the treated four fabrics with the EO at concentrations of 125, 250, and 500 µL/L or the main compounds (spathulenol and eucalyptol) at the concentrations of 6, 12, 25, and 50 µL/L and were then compared to the un-treated samples. GC-MS was used to analyze the EO chemical composition, while visual observations and scanning electron microscopic (SEM) were used to study the fungal growth inhibition. Spathulenol (26.56%), eucalyptol (14.91%), and p-cymene (12.40%) were the principal chemical components found in E. camaldulensis EO by GC-MS. Spathulenol molecule displayed the highest electrostatic potential (ESP) compared with the other primary compound, as calculated by quantum mechanics. In the untreated textile samples, SEM analysis revealed substantial proliferation of hyphae from A. flavus, F. culmorum, and A. niger. The fungal growth was completely inhibited at a concentration of 500 µL/L from the EO. Both eucalyptol and spathulenol completely inhibited the formation of the fungal spores at a concentration of 50 µL/L, although eucalyptol was more effective than spathulenol across the board for all four textiles. The results support E. camaldulensis EO functionalized textiles as an effective active antifungal agent.

Profiling and Localization of Stilbene Phytoalexins Revealed by MALDI-MSI during the Grapevine-Botrytis cinerea Interaction

Stilbene phytoalexins are among the most accumulated compounds during grapevine-pathogen interactions. However, their steady-state accumulation level and spatial distribution within the tissues to counteract Botrytis cinerea infection remain to be explored. In this work, matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was used to determine the spatial distribution of different phytoalexins in grapevine leaves upon infection with B. cinerea. Ultraperformance liquid chromatography-fluorescence (UPLC-FL) was also employed to monitor the accumulation pattern of these phytoalexins. This study showed that stilbene compounds accumulate in areas close to the pathogen infection sites. It was also revealed that the accumulation patterns of the stilbene phytoalexins can vary from one time point postinfection to another with specific accumulation patterns within each time point. To the best of our knowledge, this is the first time that the separate localization of grapevine stilbene phytoalexins has been revealed following B. cinerea infection.

Lipid and Amino Acid Pathway Metabolites Contribute to Cold Tolerance in Quercus wutaishanica

Cold is an important environmental stress affecting the growth, productivity, and geographic distribution of tree species. Oaks are important for environmental conservation and wood supplies. Oak metabolites respond to low temperatures (LTs). In this study, the physiological and metabolic responses of two oak species to cold stress were investigated and compared. The field observations and physiological responses showed that Quercus wutaishanica was more cold-tolerant than Q. acutissima. After frost, the one-year-old twigs of Q. wutaishanica had higher survival rates, accumulated more soluble sugar and protein, and exhibited higher superoxide dismutase (SOD) activity than those of Q. acutissima. Untargeted metabolomics identified 102 and 78 differentially accumulated metabolites in Q. acutissima and Q. wutaishanica, respectively, when the leaves were subjected to LTs (4 °C for 24 h). The carbohydrate and flavonoid metabolites contributed to the cold tolerance of both oak species. Succinate, an intermediate in the citric acid cycle, was significantly inhibited by LTs, a potential energy conservation strategy. Unlike Q. acutissima, Q. wutaishanica underwent metabolic reprogramming that significantly increased the contents of phosphatidylcholine, gallic acid, oxidized glutathione, shikimate, and phenylpyruvate under LTs. Our data provide a reference for characterizing the mechanisms involved in the response of oak species to cold temperatures and enhancing the cold tolerance of forest trees.

Discrimination for geographical origin of Panax quinquefolius L. using UPLC Q-Orbitrap MS-based metabolomics approach

American ginseng, Panax quinquefolius L., is an important medicinal plant with multiple pharmacological effects and high nutritional value. American ginseng from different geographical origins varies in quality and price. However, there was no approach for discriminating American ginseng from different geographical origins to date. In this study, a metabolomic method based on the UPLC-Orbitrap fusion platform was established to comprehensively determine and analyze metabolites of American ginseng from America and Canada, Heilongjiang, Jilin, Liaoning, and Shandong provinces in China. A total of 382 metabolites were detected, including 230 saponins, 30 amino acids and derivatives, 27 organic acids and derivatives, 25 lipids, 17 carbohydrates and derivatives, 10 phenols, 8 nucleotides, and derivatives, as well as 35 other metabolites. Metabolite differences between North America and Asia producing areas were more obvious than within Asia. Twenty metabolites, contributed most to the differentiation of producing areas, were identified as potential markers with prediction accuracy higher than 91%. The results provide new insights into the metabolite composition of American ginseng from different origins, which will help discriminate origins and promote quality control of American ginseng.

A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India

The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.

Peptidomics Methods Applied to the Study of Flower Development

Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6-7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.

Recent advances in proteomics and metabolomics in plants

Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.

Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn

The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.

Metabolomics Analysis of Morchella sp. From Different Geographical Origins of China Using UPLC-Q-TOF-MS

The morel mushroom (Morchella sp.) is reputed as one of the most highly-prized edible fungi with mounting cultivated area as well as commercial popularity in China. To date, optimized methods specific for quality evaluation and constituent analysis of Morchella sp. are still non-available, impeding the healthy and sustainable development of this industry. Herein, an untargeted UPLC-Q-TOF-MS-based metabolomics approach was performed to characterize the metabolite profiles of morel samples from four distinct geographical origins of China, viz. Gansu, Guizhou, Liaoning, and Henan province. A total of 32 significantly different metabolites assigned to lipids (19), organic acids (9), amino acids (3), and ketones (1) were identified to distinguish the geographic-segregation samples amenable to multivariate analysis. These metabolites may serve as molecular markers indicative of specific regions. More importantly, the lipid, protein and amino acid metabolism were responsible for geographic differences as revealed by KEGG pathway enrichment analysis. Collectively, this study not only pioneered high-throughput methodology to evaluate quality of Morchella sp. and distinguish geographical origins in a sensitive, rapid and efficient manner, but also shed light on the potential link between physiochemical variation and geological origins from a metabolic perspective, which may be conducive to the advancement of edible fungi industry and establishment of food traceability system.

Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family

Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS/MS untargeted metabolomics, spectral searches, and recently described in silico classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the in silico classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups.

Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures

Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.

Mass Spectrometry as a Crucial Analytical Basis for Omics Sciences

This review is devoted to the consideration of mass spectrometric platforms as applied to omics sciences. The most significant attention is paid to omics related to life sciences (genomics, proteomics, meta-bolomics, lipidomics, glycomics, plantomics, etc.). Mass spectrometric approaches to solving the problems of petroleomics, polymeromics, foodomics, humeomics, and exosomics, related to inorganic sciences, are also discussed. The review comparatively presents the advantages of various principles of separation and mass spectral techniques, complementary derivatization, used to obtain large arrays of various structural and quantitative information in the mentioned omics sciences.

Multimodal Spectroscopic Imaging of Pea Root Nodules to Assess the Nitrogen Fixation in the Presence of Biofertilizer Based on Nod-Factors

Multimodal spectroscopic imaging methods such as Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI), Fourier Transform Infrared spectroscopy (FT-IR) and Raman spectroscopy were used to monitor the changes in distribution and to determine semi quantitatively selected metabolites involved in nitrogen fixation in pea root nodules. These approaches were used to evaluate the effectiveness of nitrogen fixation by pea plants treated with biofertilizer preparations containing Nod factors. To assess the effectiveness of biofertilizer, the fresh and dry masses of plants were determined. The biofertilizer was shown to be effective in enhancing the growth of the pea plants. In case of metabolic changes, the biofertilizer caused a change in the apparent distribution of the leghaemoglobin from the edges of the nodule to its centre (the active zone of nodule). Moreover, the enhanced nitrogen fixation and presumably the accelerated maturation form of the nodules were observed with the use of a biofertilizer.

Molecular imaging of plant-microbe interactions on the Brachypodium seed surface

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and within plant tissues, however the mechanisms by which plants associate with PGPR to elicit such beneficial effects need further study. Here, we present time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.). Delayed image extraction was used to image PGPR-treated seed sections to reveal morphological changes. ToF-SIMS spectral comparison, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and indole-3-acetic acid (IAA), were identified on the PGPR-treated seed surfaces. These compounds have different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicit distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interactions and to provide insightful information with submicrometer lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

Metabolome profiling and molecular docking analysis revealed the metabolic differences and potential pharmacological mechanisms of the inflorescence and succulent stem of Cistanche deserticola

Cistanche deserticola is an endangered plant used for medicine and food. Our purpose is to explore the differences in metabolism between inflorescences in non-medicinal parts and succulent stems in medicinal parts in order to strengthen the application and development of the non-medicinal parts of C. deserticola. We performed metabolomics analysis through LC-ESI-MS/MS on the inflorescences and succulent stems of three ecotypes (saline-alkali land, grassland and sandy land) of C. deserticola. A total of 391 common metabolites in six groups were identified, of which isorhamnetin O-hexoside (inflorescence) and rosinidin O-hexoside (succulent stems) can be used as chemical markers to distinguish succulent stems and inflorescences. Comparing the metabolic differences of three ecotypes, we found that most of the different metabolites related to salt-alkali stress were flavonoids. In particular, we mapped the biosynthetic pathway of phenylethanoid glycosides (PhGs) and showed the metabolic differences in the six groups. To better understand the pharmacodynamic mechanisms and targets of C. deserticola, we screened 88 chemical components and 15 potential disease targets through molecular docking. The active ingredients of C. deserticola have a remarkable docking effect on the targets of aging diseases such as osteoporosis, vascular disease and atherosclerosis. To explore the use value of inflorescence, we analyzed the molecular docking of the unique flavonoid metabolites in inflorescence with inflammation targets. The results showed that chrysoeriol and cynaroside had higher scores for inflammation targets. This study provides a scientific basis for the discovery and industrialization of the resource value of the non-medicinal parts of C. deserticola, and the realization of the sustainable development of C. deserticola. It also provides a novel strategy for exploring indications of Chinese herb.

Flow chart for exploring the metabolic and pharmacological characteristics of different parts of Cistanche deserticola.

Unveiling spatial metabolome of Paeonia suffruticosa and Paeonia lactiflora roots using MALDI MS imaging

Paeonia suffruticosa (PS) and Paeonia lactiflora (PL) belong to the only genus in the family Paeoniaceae. Comparative analysis of the spatial metabolomes of PS and PL has rarely been performed. In this work, combined with multiple matrixes and dual-polarity detection, high mass resolution matrix-assisted laser desorption/ionization MS imaging (MALDI MSI) and MALDI tandem MSI were performed on the root sections of the two Paeonia species. The spatial distributions of many metabolites including monoterpene and paeonol glycosides, tannins, flavonoids, saccharides and lipids were systematically characterized. The ambiguous tissue distribution of the two isomers paeoniflorin and albiflorin were distinguished by tandem MSI using lithium salt doped 2,5-dihydroxybenzoate matrix. In addition, the major intermediates involved in the biosynthetic pathway of gallotannins were successfully localized and visualized in the root sections. High-mass resolution MALDI full-scan MSI provides comprehensive and accurate spatial distribution of metabolites. The analytical power of the technique was further tested in the tandem MSI of two isomers. The ion images of individual metabolites provide chemical and microscopic characteristics beyond morphological identification, and the detailed spatiochemical information could not only improve our understanding of the biosynthetic pathway of hydrolyzable tannins, but also ensure the safety and effectiveness of their medicinal use.

Spatiotemporal Visualization of Insecticides and Fungicides within Fruits and Vegetables Using Gold Nanoparticle-Immersed Paper Imprinting Mass Spectrometry Imaging

Food safety issues caused by pesticide residue have exerted far-reaching impacts on human daily life, yet the available detection methods normally focus on surface residue rather than pesticide penetration to the internal area of foods. Herein, we demonstrated gold nanoparticle (AuNP)-immersed paper imprinting mass spectrometry imaging (MSI) for monitoring pesticide migration behaviors in various fruits and vegetables (i.e., apple, cucumber, pepper, plum, carrot, and strawberry). By manually stamping food tissues onto AuNP-immersed paper, this method affords the spatiotemporal visualization of insecticides and fungicides within fruits and vegetables, avoiding tedious and time-consuming sample preparation. Using the established MSI platform, we can track the migration of insecticides and fungicides into the inner region of foods. The results revealed that both the octanol-water partition coefficient of pesticides and water content of garden stuffs could influence the discrepancy in the migration speed of pesticides into food kernels. Taken together, this nanopaper imprinting MSI is poised to be a powerful tool because of its simplicity, rapidity, and easy operation, offering the potential to facilitate further applications in food analysis. Moreover, new perspectives are given to provide guidelines for the rational design of novel pesticide candidates, reducing the risk of food safety issues caused by pesticide residue.

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.

Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana

Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.

Hevea brasiliensis latex proteomics: a review of analytical methods and the way forward

Natural rubber or latex from the Hevea brasiliensis is an important commodity in various economic sectors in today's modern society. Proteins have been detected in latex since the early twentieth century, and they are known to regulate various biological pathways within the H. brasiliensis trees such as the natural rubber biosynthesis, defence against pathogens, wound healing, and stress tolerance. However, the exact mechanisms of the pathways are still not clear. Proteomic analyses on latex have found various proteins and revealed how they fit into the mechanisms of the biological pathways. In the past three decades, there has been rapid latex protein identification due to the improvement of latex protein extraction methods, as well as the emergence of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). In this manuscript, we reviewed the methods of latex protein extraction that keeps on improving over the past three decades as well as the results of numerous latex protein identification and quantitation.

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Uncovering the antioxidant characteristics of black tea by coupling in vitro free radical scavenging assay with UHPLC-HRMS analysis

Black tea (BT) is rich in dietary antioxidants, but its antioxidant composition has not been fully understood. To identify the true antioxidants occurring in BT, we established an approach based on 2,2-diphenyl-1-picrylhydrazyl radical scavenging assay coupled with ultra-high performance liquid chromatography-high resolution mass spectrometry (DPPH-UHPLC-HRMS). The employment of HRMS enable us to detect trace antioxidants, resolve co-eluted antioxidants, and characterize chemical structures of unknown antioxidants. In total, 56 phenolic compounds were screened as potential antioxidants from 106 compounds identified in BT. Catechol and pyrogallol were revealed as the key substructures in enhancing the antioxidant abilities of phenolic compounds. During BT brewing, high temperature with extended time promote antioxidant leaching but may induce the degradation of esterified and glycosylated compounds such as theaflavin-3-gallate and rutin. In conclusion, this work identified the true antioxidant constituents of BT, their structural characteristics, and their dynamic changes under various brewing conditions.

Phosphoproteomic and Metabolomic Analyses Reveal Sexually Differential Regulatory Mechanisms in Poplar to Nitrogen Deficiency

Nitrogen (N) is a key factor impacting physiological processes in plants. Many proteins have been investigated in male and female poplars under N limitation. However, little is known about sex differences in the protein modifications and metabolites that occur in poplar leaves in response to N deficiency. In this study, as compared to N-deficient males, N-deficient females suffered greater damage from N deficiency, including chloroplast disorganization and lipid peroxidation of cellular membranes. Male poplars had greater osmotic adjustment ability than did females, allowing greater accumulation of soluble metabolites. In addition, as compared to that in N-deficient males, glycolysis was less suppressed in N-deficient females for increased enzyme activities to consume excess energy. Moreover, we found that pronounced protein phosphorylation occurred during carbon metabolism and substance transport processes in both sexes of poplar under N-limiting conditions. Sex-specific metabolites mainly included intermediates in glycolysis, amino acids, and phenylpropanoid-derived metabolites. This study provides new molecular evidence that female poplars suffer greater negative effects from N deficiency than do male poplars.

The role of peptides cleaved from protein precursors in eliciting plant stress reactions

As sessile organisms, plants are exposed to diverse abiotic and biotic stresses, and thus have developed complex signaling mechanisms that orchestrate multiple stress responses. Plant peptides have recently emerged as key signaling molecules of stress responses, not only to mechanical wounding and pathogen infection but also to nutrient imbalance, drought and high salinity. The currently identified stress-related signaling peptides in plants are derived from proteolytic processing of protein precursors. Here, we review these protein-derived peptides and the evidence for their functions in stress signaling. We recommend potential research directions that could clarify their roles in stress biology, and propose possible crosstalk with regard to the physiological outcome. The stress-centric perspective allows us to highlight the crucial roles of peptides in regulating the dynamics of stress physiology. Inspired by historic and recent findings, we review how peptides initiate complex molecular interactions to coordinate biotic and abiotic stress responses in plants.

Mass Spectroscopic Analysis, MNDO Quantum Chemical Studies and Antifungal Activity of Essential and Recovered Oil Constituents of Lemon-Scented Gum against Three Common Molds

The present study described the possibility of using wood-treated oil-fungicide of lemon-scented gum (Corymbia citriodora) from newly emerged leaves and unripened fruits against the infestation of Fusarium culmorum, Rhizoctonia solani and Penicillium chrysogenum. Air-dried wood samples of Melia azedarach were treated with the extracted oils from leaves and unripened fruits from C. citriodora. The main chemical constituents identified in the essential oil (EO) from leaves were citronellal (55.31%), citronellol (21.03%) and isopulegol (10.79%), while in unripened fruits were α-pinene (17.86%), eudesmol (13.9%), limonene (9.19%), γ-terpinen (8.21%), and guaiol (7.88%). For recovered oils (ROs), the major components from leaves were D-limonene (70.23%), γ-terpinene (13.58%), β-pinene (2.40%) and isopregol (2.23%), while, 4-terpineol (21.35%), cis-β-terpineol, (19.33%), D-limonene (14.75%), and γ-terpinene (7.42%) represented the main components in fruits. EOs from leaves and fruits at the amounts of 100, 50 and 25 µL showed the highest inhibition percentage (IP) of 100% against F. culmorum and P. chrysogenum compared to control treatment, while at the amounts of 100, and 50 µL showed 100% IP of R. solani. Wood treated with ROs from leaves and fruits showed IPs of 96.66% and 93.33%, respectively, against the growth of R. solani. The mass spectra of the main components of C. citriodora leaves and fruits’ EOs have been recorded in electron ionization mode at 70 eV and fragmentation has been reported and discussed. On the other hand, different quantum parameters such as the heat of formation, ionization energy total energy, binding energy, electronic energy and dipole moment using the modified neglect of diatomic overlap (MNDO) semi-empirical method have been calculated.

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix⁺) or a fix^- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix^- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix^- strain, perhaps reflecting a plant defense response.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

Epoxiconazole exposure affects terpenoid profiles of oilseed rape plantlets based on a targeted metabolomic approach

Epoxiconazole is a broad-spectrum fungicide described as highly persistent in soil and as such can be considered as an abiotic agent like other problematic agrochemicals. Furthermore, the plant phenotyping tool involving non-invasive monitoring of plant-emitted volatile organic compounds (VOCs) may be useful in the identification of metabolic markers for abiotic stress. We therefore decided to profile the VOCs from secondary metabolism of oilseed rape through a dose-response experiment under several epoxiconazole concentrations (0, 0.01, 0.1 and 1 mg L^-1). VOC collections of 35-day-old whole plantlets were performed through a dynamic headspace sampling technique under defined and controlled conditions. The plantlets grew freely within a home-made, laboratory and high-throughput glass chamber without any disturbance. Putative metabolic markers were analysed using a targeted metabolomic approach based on TD-GC-MS method coupled with data acquisition in SIM mode in order to focus on terpenes and sulphur-containing volatiles. Chromatograms of emitted terpenes were achieved accurately for the 35-day-old oilseed rape plantlets. We also analysed the presence of sulphur-containing volatiles in samples of shoot and root tissues using an innovative DHS-TD-GC-MS method, but no difference was found between qualitative profiles. Nevertheless, we demonstrated through this experiment that sesquiterpenes such as β-elemene and (E,E)-α-farnesene are involved in epoxiconazole dose-response. In particular, (E,E)-α-farnesene could serve as a metabolic marker of fungicide exposure for oilseed rape plantlets.

An improved scoring method for the identification of endogenous peptides based on the Mascot MS/MS ion search

To identify endogenous peptides using MS/MS analysis and searching against a polypeptide sequence database, a non-enzyme specific (NES) search considering all of the possible proteolytic cleavages is required. However, the use of a NES search generates more false positive hits than an enzyme specific search, and therefore shows lower identification performance. In this study, the use of the sub-ranked matches for improving the identification performance of the Mascot NES search was investigated and a new scoring method was developed that considered the contribution of all sub-ranked random match probabilities, named the contribution score (CS). The CS showed the highest identification sensitivity using the Mascot NES search with a full protein database when compared to the use of the Mascot first ranked score and the delta score (DS). The confident peptides identified by DS and CS were shown to be complementary. When applied to plant endogenous peptide identification, the identification numbers of tomato endogenous peptides using DS and CS were 176.3% and 184.2%, respectively, higher than the use of the first ranked score of Mascot. The combination of DS and CS identified 200.0% and 8.6% more tomato endogenous peptides compared to the use of Mascot and DS, respectively. This method by combining the CS and DS can significantly improve the identification performance of endogenous peptides without complex computational steps and is also able to improve the identification performance of the enzyme specific search. In addition to the application in the plant peptidomics analysis, this method may be applied to the improvement of peptidomics studies in different species. A web interface for calculating the DS and CS based on Mascot search results was developed herein.

Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry

Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.

Spatial distribution mapping of molecules in the grains of different rice landraces, using desorption electrospray ionization mass spectrometry

RATIONALE

Documentation of the metabolite profiles of rice landraces is essential as most of them have been lost due to the conventional practices of cultivation. Therefore, application of mass spectrometry imaging (MSI) will be an appropriate analytical platform for molecular profiling, as it can provide a detailed understanding of the site-specific localization patterns of biomolecules, and the cues concerning metabolic pathways in organisms.

METHODS

Desorption electrospray ionization mass spectrometry (DESI-MS) is a relatively non-destructive analytical technique for surface sampling in natural conditions. Here, we report the spatial distribution of diverse molecules in the grains of different rice landraces of India using DESI-MSI. Molecules were identified by ESI-MS and tandem MS analysis of rice extracts. Scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) were used for the elemental mapping on the rice grains.

RESULTS

DESI-MSI showed a uniform distribution of choline (m/z 104.1), sucrose in the form of its sodium (m/z 365.1) and potassium (m/z 381.0) adducts, linoleic acid (m/z 279.2), 13-HODE-9-HODE (m/z 295.2), unidentified molecules with m/z 535.3, 559.5, and 561.5 and isoschaftoside (m/z 563.1) in the endosperm of rice grains. Gluconic acid (m/z 195.0) and signalling phospholipid intermediate molecules were localized in the embryo whereas oryzanol A (m/z 601.5) and oryzanol C (m/z 615.5) had a restricted localization in the bran region of the grain. SEM-EDS mapping showed the localization of potassium and phosphorus along the bran and embryo.

CONCLUSIONS

DESI-MSI revealed the distribution of lipids and sugar molecules in the specific regions of the rice grains. Thus, molecules unique to some rice varieties were identified with this analytical platform. Mass spectrometry imaging of rice along with the elemental mapping by SEM-EDS will be of use in understanding the localization pattern of certain molecules in the context of metals present in the grain.

Identification and screening of cardiac glycosides in Streptocaulon griffithii using an integrated data mining strategy based on high resolution mass spectrometry

The present study was designed to develop a practical strategy to tackle the problem of lacking standard compounds and limited references for identifying structure-related compounds in Streptocaulon griffithii Hook. f., especially those in trace concentrations, with a focus on antitumor activity. The cardiac glycosides (CGs)-enriched part was determined using in vitro bioactive assays in three cancer cell lines and then isolated using macroporous resins. The MS and MS/MS data were acquired using a high performance liquid chromatography coupled with hybrid quadrupole-time of flight (HPLC-Q-TOF-MS) system. To acquire data of trace compound in the extract, a multiple segment program was applied to modify the HPLC-Q-TOF-MS method. A mass defect filter (MDF) approach was employed to make a primary MS data filtration. Utilizing a MATLAB program, the redundant peaks obtained by imprecise MDF template calculated with limited references were excluded by fragment ion classification, which was based on the ion occurrence number in the MDF-filtered total ion chromatograms (TIC). Additionally, the complete cleavage pathways of CG aglycones were proposed to assist the structural identification of 29 common fragment ions (CFIs, ion occurrence number ≥ 5) and diagnostic fragment ions (DFIs, ion occurrence number < 5). As a result, 30 CGs were filtered out from the MDF results, among which 23 were identified. This newly developed strategy may provide a rapid and effective tool for identifying structure-related compounds in herbal medicines.

Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants

INTRODUCTION

Mass spectrometry imaging (MSI) as a label-free and powerful imaging technique enables in situ evaluation of a tissue metabolome and/or proteome, becoming increasingly popular in the detection of plant endogenous molecules.

OBJECTIVE

The characterisation of structure and spatial information of endogenous molecules in plants are both very important aspects to better understand the physiological mechanism of plant organism.

METHODS

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a commonly-used tissue imaging technique, which requires matrix to assist in situ detection of a variety of molecules on the surface of a tissue section. In previous studies, MALDI-MSI was mostly used for the detection of molecules from animal tissue sections, compared to plant samples due to cell structural limitations, such as plant cuticles, epicuticular waxes, and cell walls. Despite the enormous progress that has been made in tissue imaging, there is still a challenge for MALDI-MSI suitable for the imaging of endogenous compounds in plants.

RESULTS

This review summarises the recent advances in MALDI-MSI, focusing on the application of in situ detection of endogenous molecules in different plant organs, i.e. root, stem, leaf, flower, fruit, and seed.

CONCLUSION

Further improvements on instrumentation sensitivity, matrix selection, image processing and sample preparation will expand the application of MALDI-MSI in plant research.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Untargeted profiling of Glycyrrhiza glabra extract with comprehensive two-dimensional liquid chromatography-mass spectrometry using multi-segmented shift gradients in the second dimension: Expanding the metabolic coverage

Metabolic profiling of Glycyrrhiza glabra using comprehensive two-dimensional liquid chromatography (LC × LC) coupled with photodiode array (PDA) and mass spectrometry (MS) detection is described. The separation was conducted under reversed-phase conditions, using a combination of first dimension (1 D) 150 mm microbore cyano column utilising 2.7 μm diameter (dp ) particles, and second dimension (2 D) 50 mm superficially porous octadecylsilica column with 2.7 μm dp particles. A multi-segmented shift gradient (MSG) for the 2 D separation was developed, and the orthogonality achieved was compared with other modes of gradients, such as full in-fraction, and shift gradient systems. Results demonstrated a significant expansion of metabolic coverage using MSG in 2 D, providing the highest measure of orthogonality compared to other gradient modes. Compound identifications were performed by employing complementary data from PDA and MS detection, with reference to structural group-type distribution in 2D space. A total of ca. 120 compounds were detected, and among them 37 were tentatively identified, distributed over the chemical families of glycosylated flavanones, triterpene saponins, and others. In comparison with one-dimensional LC, the total number of compounds detected was ca. 2-fold greater when LC × LC was employed. To the best of our knowledge, this is the first demonstration of the MSG mode in LC × LC, representing a powerful strategy to expand the metabolic coverage for analysis of plant-derived extracts, containing a multitude of different phytochemical classes.

A comparative UPLC-Q/TOF-MS-based metabolomics approach for distinguishing Zingiber officinale Roscoe of two geographical origins

Ginger, the rhizome of Zingiber officinale Roscoe, is a popular spice used in the food, beverage and confectionary industries. In this study, we report an untargeted UPLC-Q/TOF-MS-based metabolomics approach for comprehensively discriminating between ginger from two geographical locations, Ghana in West Africa and China. Forty batches of fresh ginger from both countries were discriminated using principal component analysis and orthogonal partial least squares discrimination analysis. Sixteen differential metabolites were identified between the gingers from the two geographical locations, six of which were identified as the marker compounds responsible for the discrimination. Our study highlights the essence and predictive power of metabolomics in detecting minute differences in same varieties of plants/plant samples based on the levels and composition of their metabolites.

Direct detection of surface localized specialized metabolites from Glycyrrhiza lepidota (American licorice) by leaf spray mass spectrometry

Leaf spray-MS minimizes tissue manipulation by effectively and quickly assessing in vivo specialized metabolites from intact plant tissue surfaces, including trichome metabolites. Intact leaves of Glycyrrhiza lepidota Pursh. (American licorice) were analyzed by direct electrospray leaf spray-MS, an ambient ionization technique. Comparison of metabolites detected by leaf spray-MS to those from LC-MS of bulk tissue and trichome enriched extracts showed dramatic differences. Leaf spray-MS results suggest that in specific situations this approach could complement traditional LC-MS analysis of bulk extracts. Leaf spray-MS as a metabolomics technique eliminates sample pretreatment and preparation allowing for rapid sampling in real time of living intact tissues. Specialized metabolites on the surface of tissues such as glandular trichomes metabolites are detected by leaf spray-MS.

Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana

With the applications of engineered nanomaterials (ENMs) continually expanding and production quickly growing, residues of ENMs will end up in the environment at levels that may be harmful to non-target organisms. Many of the tunable properties that have made them desirable, such as type, size, charge, or coating, also contribute to the current difficulties in understanding the fate of ENMs in the environment. This review article focuses on studies that investigate plant-ENM interactions, including techniques used to study these interactions and documented plant responses due to the phytotoxic effects of ENMs. The many variables which can be altered for an experiment, such as type, size, and concentration of ENMs, make it difficult to formulate generalizations about the uptake mechanism involved, or to make an inference on the subcellular localization and distribution of the internalized ENMs in plant tissue. In order to avoid these challenges, studies can utilize a model organism such as Arabidopsis thaliana, and a combination of analytical techniques that can reveal complementary information in order to assess how the different experimental conditions influence the uptake and phytotoxicity of ENMs. This review presents recent studies regarding plant-ENM interactions employing Arabidopsis to demonstrate how the use of this model plant can advance our understanding of plant-ENM interactions and guide additional studies using other plant species. Overarching results suggest that more sensitive tests and consistency in experimental designs are needed to fully assess and understand the phytotoxic effects of ENMs in the environment.

Laser Desorption/Ionisation Mass Spectrometry Imaging of European Yew (Taxus baccata) on Gold Nanoparticle-enhanced Target

INTRODUCTION

European yew (Taxus baccata) is a plant known to man for centuries as it produces many interesting and important metabolites. These chemical compounds were repeatedly analysed by various analytical techniques, but none of the methods used so far allowed the localisation of the chemical compounds within the tissue and also correlation between plant morphology and its biochemistry.

OBJECTIVE

Visualisation of the spatial distribution of yew metabolites with nanoparticle-based mass spectrometry imaging.

METHODOLOGY

Compounds occurring on cross-section of a one-year yew sprig has been transferred to gold nanoparticle-enhanced target (AuNPET) by imprinting. The imprint was then subjected to mass spectrometry imaging analysis.

RESULTS

Nanoparticle-enhanced mass spectrometry imaging made it possible to study the distribution of selected compounds in the European yew tissue, including taxanes - terpene alkaloids characteristic for the Taxus genus. Results prove that aspartate, taxinine M, baccatin IV and taxine B are located mainly in the cortex. Taxuspine W was located in the vascular tissue. Maleate was found to be located mainly in the phloem tissue. In contrast, the proton adduct of chlorophyll b was found in the external layer of twigs.

CONCLUSION

The results presented a high correlation between the location of compounds and the morphology of the plant, thus giving the opportunity to see the selected details of chemical structure of the analysed tissue for the first time. Copyright © 2017 John Wiley & Sons, Ltd.