Spatial lipidomics of eight edible nuts by desorption electrospray ionization with ion mobility mass spectrometry imaging

Overview and limitations of database in global traditional medicines: A narrative review

The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.

Mass spectrometry imaging as a promising analytical technique for herbal medicines: an updated review

Herbal medicines (HMs) have long played a pivotal role in preventing and treating various human diseases and have been studied widely. However, the complexities present in HM metabolites and their unclear mechanisms of action have posed significant challenges in the modernization of traditional Chinese medicine (TCM). Over the past two decades, mass spectrometry imaging (MSI) has garnered increasing attention as a robust analytical technique that enables the simultaneous execution of qualitative, quantitative, and localization analyses without complex sample pretreatment. With advances in technical solutions, MSI has been extensively applied in the field of HMs. MSI, a label-free ion imaging technique can comprehensively map the spatial distribution of HM metabolites in plant native tissues, thereby facilitating the effective quality control of HMs. Furthermore, the spatial dimension information of small molecule endogenous metabolites within animal tissues provided by MSI can also serve as a supplement to uncover pharmacological and toxicological mechanisms of HMs. In the review, we provide an overview of the three most common MSI techniques. In addition, representative applications in HM are highlighted. Finally, we discuss the current challenges and propose several potential solutions. We hope that the summary of recent findings will contribute to the application of MSI in exploring metabolites and mechanisms of action of HMs.

Revolutionizing food science with mass spectrometry imaging: A comprehensive review of applications and challenges

Food science encounters increasing complexity and challenges, necessitating more efficient, accurate, and sensitive analytical techniques. Mass spectrometry imaging (MSI) emerges as a revolutionary tool, offering more molecular-level insights. This review delves into MSI's applications and challenges in food science. It introduces MSI principles and instruments such as matrix-assisted laser desorption/ionization, desorption electrospray ionization, secondary ion mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry, highlighting their application in chemical composition analysis, variety identification, authenticity assessment, endogenous substance, exogenous contaminant and residue analysis, quality control, and process monitoring in food processing and food storage. Despite its potential, MSI faces hurdles such as the complexity and cost of instrumentation, complexity in sample preparation, limited analytical capabilities, and lack of standardization of MSI for food samples. While MSI has a wide range of applications in food analysis and can provide more comprehensive and accurate analytical results, challenges persist, demanding further research and solutions. The future development directions include miniaturization of imaging devices, high-resolution and high-speed MSI, multiomics and multimodal data fusion, as well as the application of data analysis and artificial intelligence. These findings and conclusions provide valuable references and insights for the field of food science and offer theoretical and methodological support for further research and practice in food science.

Evaluation of Lipid Quality in Fruit: Utilizing Lipidomic Approaches for Assessing the Impact of Biotic Stress on Pecans (Carya illinoinensis)

There is a scarcity of data on how the lipid composition of oily seeds changes in response to biotic stress. Yellow peach moth (Conogethes punctiferalis) has caused massive economic losses on the pecan (Carya illinoinensis) industry. Lipidomics is used in this study to determine the lipid composition of pecan and how it changes in response to insect attack. Pecan had 167 lipids, including 34 glycerolipids (GL), 62 glycerophospholipids (GP), 17 fatty acyls (FA), 41 sphingolipids (SP), and 13 saccharolipids (SL). The effects of biotic stress on lipids, particularly GL and GP, were significant. Biotic stress significantly reduced the lipid content of chains longer than 48. Forty-four significantly different lipids were discovered as potential biomarkers for distinguishing non-infected pecans from infested pecans. In addition, we used bioinformatics to identify the five most important metabolic pathways in order to investigate the processes underlying the changes. Our discoveries may offer valuable insights for enhancing pecan production in the future and contribute novel perspectives towards enhancing the nutritional value of pecans.

Unveiling the distribution of chemical constituents at different body parts and maturity stages of Ganoderma lingzhi by combining metabolomics with desorption electrospray ionization mass spectrometry imaging (DESI)

Ganoderma lingzhi is an important medicinal fungus, which is widely used as dietary supplement and for pharmaceutical industries. However, the spatial distribution and dynamic accumulation pattern of active components such as ganoderic acids (GAs) among different parts of G. lingzhi fruiting body are still unclear. In this study, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) with untargeted metabolomics analysis was applied to investigate the metabolites distribution within G. lingzhi fruiting body at four different maturity stages (squaring, opening, maturation and harvesting stage). A total of 132 metabolites were characterized from G. lingzhi, including 115 triterpenoids, 11 fatty acids and other component. Most of the GAs content in the cap was significantly higher than that in the stipe, with six components such as ganoderic acid B being extremely significant. GAs in the cap was mainly present in the bottom edge of the mediostratum layer, such as ganoderic A-I and ganoderic GS-1, while in the stipe, they were mainly distributed in the shell layer and the context layer, such as ganoderic A-F. Most ganoderic acids content in both the stipe and the cap of G. lingzhi was gradually decreased with the development of G. lingzhi. The GAs in the stipe was gradually transferred from the shell layer to the content layer, while the distribution of GAs among different tissues of the cap was not significantly changed. In addition, linoleic acid, 9-HODE, 9-KODE and other fatty acids were mainly accumulated in the opening and maturing stage of the caps. This study further clarifies the spatial dynamic distribution of GAs in G. lingzhi fruiting body at four different maturity stages (squaring, opening, maturation and harvesting stage), which provides a basis for the rational utilization of the medicinal parts of G. lingzhi. Furthermore, mass spectrometry imaging combined with non-target metabolome analysis provides a powerful tool for the spatial distribution of active substances in the different regions of the medicinal edible fungi.

Energy preservation for skeletal muscles: Shenqi Fuzheng injection prevents tissue wasting and restores bioenergetic profiles in a mouse model of chemotherapy-induced cachexia

BACKGROUND

Energy deficiency is the characteristic of chemotherapy-induced cachexia (CIC) which is manifested by muscle wasting. glycolysis, tricarboxylic acid (TCA) cycle, and lipid metabolism are central to muscle bioenergy production, which is vulnerable to chemotherapy during cancer treatment. Recent investigations have spotlighted the potential of Shenqi Fuzheng injection (SQ), a Chinese proprietary medicine comprising Radix Codonopsis and Radix Astragali, in alleviating CIC. However, the specific effects of SQ on muscle energy metabolism remains less explored.

PURPOSE AND METHODS

Here, we integrated transcriptomics, spatial metabolomics, gas chromatography-mass spectrometry targeted quantitative analysis, and transmission electron microscopy techniques, combined with Seahorse live-cell metabolic analysis to reveal the changes in genes and pathways related to energy metabolism in the CIC model and SQ's protective effects at molecular and functional levels.

RESULTS

Our data showed that chemotherapeutic agents caused glycolysis imbalance, which further leads to metabolic derangements of TCA cycle intermediates. SQ maintained glycolysis balance by facilitating pyruvate fluxing to mitochondria for more efficient bioenergy production, which involved a dual effect on promoting functions of mitochondrial pyruvate dehydrogenase complexes and inhibiting lactate dehydrogenase for lactate production. As a result of the sustained pyruvate level achieved by SQ administration, glycolysis balance was maintained, which further led to the preservation of mitochondrial integrity and function of electron transport chain, thereby, ensuring the normal operation of the TCA cycle and the proper synthesis of adenosine triphosphate (ATP). The above results were further validated using the Seahorse live-cell assay.

CONCLUSION

In conclusion, our study highlights SQ as a promising strategy for CIC management, emphasizing its ability to harmonize the homeostasis of the muscle bioenergetic profile. Beyond its therapeutic implications, this study also offers a novel perspective for the development of innovative treatments in the realm of herbal medicine.

Combined Widely Targeted Metabolomic, Transcriptomic, and Spatial Metabolomic Analysis Reveals the Potential Mechanism of Coloration and Fruit Quality Formation in Actinidia chinensis cv. Hongyang

Postharvest kiwifruit (Actinidia chinensis cv. Hongyang) pulp is mainly composed of outer yellow-flesh (LR) and inner red-flesh (HR). However, information about the differences in coloration and fruit quality between these two parts are limited. In this study, widely targeted metabolomic, transcriptomic, and spatial metabolomic analyses were used to reveal the potential mechanism of coloration and fruit quality formation. The results show that a total of 1001 metabolites were identified in Hongyang kiwifruit, and the accumulation of 211 metabolites were significantly higher in the HR than LR, including 69 flavonoids, 53 phenolic acids, and 38 terpenoids. There were no significant differences in the content of citric acid, quinic acid, glucose, fructose, or sucrose between the LR and HR. These results were consistent with the results from the RNA-seq profile and spatial metabolomic analysis. In addition, a total of 23 key candidate genes related to flesh color and fruit quality formation were identified and validated by qRT-PCR analysis. This study provides a theoretical basis for elucidating the underlying mechanism of the formation of kiwifruit flesh color and fruit quality.

In situ separation and visualization of isomeric auxin derivatives in Arabidopsis by ion mobility mass spectrometry imaging

In situ separation and visualization of synthetic and naturally occurring isomers from heterogeneous plant tissues, especially when they share similar molecular structures, are a challenging task. In this study, we combined the ion mobility separation with desorption electrospray ionization mass spectrometry imaging (DESI-IM-MSI) to achieve a direct separation and visualization of two synthetic auxin derivatives, auxinole and its structural isomer 4pTb-MeIAA, as well as endogenous auxins from Arabidopsis samples. Distinct distribution of these synthetic isomers and endogenous auxins in Arabidopsis primary roots and hypocotyls was achieved in the same imaging analysis from both individually treated and cotreated samples. We also observed putative metabolites of synthetic auxin derivatives, i.e. auxinole amino acid conjugates and hydrolysed 4pTb-MeIAA product - 4pTb-IAA, based on their unique drifting ion intensity patterns. Furthermore, DESI-IM-MSI-revealed abundance of endogenous auxins and synthetic isomers was validated by liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that DESI-IM-MSI could be used as a robust technique for detecting endogenous and exogenous isomers and provide a spatiotemporal evaluation of hormonomics profiles in plants.

Spatial Distribution and Characterization of the Small-Molecule Metabolites and In Situ Hydrolyzed Oligosaccharides in the Rhizome of Glycyrrhiza uralensis by Desorption Electrospray Ionization-Mass Spectrometry Imaging and High-Resolution Liquid Chromatography-Mass Spectrometry

Characterization and spatial distribution studies of the metabolome in plants are crucial for revealing the physiology of plants and developing functional foods. Using the rhizome of Glycyrrhiza uralensis as a case, we integrated desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) and high-resolution liquid chromatography/mass spectrometry approaches aimed at characterizing and locating both the small molecules and the macromolecular polysaccharides. Under the optimal conditions, 21 flavonoids and 12 triterpenoids were detected and characterized in different tissues of the rhizome and another 19 components were characterized exclusively by DESI-MSI. Combined with hydrophilic interaction chromatography/ion mobility-quadrupole time-of-flight mass spectrometry, eight different degrees of polymerization of oligosaccharides (after in situ acid hydrolysis) were characterized from the rhizome of G. uralensis. Majority of these metabolites are located in the cortex, phloem, and medulla, which lays the foundation for understanding the physiology of G. uralensis. The useful information can benefit the sustainable utilization and further development of Glycyrrhiza resource.

MALDI MS Imaging of Chickpea Seeds (Cicer arietinum) and Crab's Eye Vine (Abrus precatorius) after Tryptic Digestion Allows Spatially Resolved Identification of Plant Proteins

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) imaging following in situ enzymatic digestion is a versatile analytical method for the untargeted investigation of protein distributions, which has rarely been used for plants so far. The present study describes a workflow for in situ tryptic digestion of plant seed tissue for MALDI MS imaging. Substantial modifications to the sample preparation procedure for mammalian tissues were necessary to cater to the specific properties of plant materials. For the first time, distributions of tryptic peptides were successfully visualized in plant tissue using MS imaging with accurate mass detection. Sixteen proteins were visualized and identified in chickpea seeds showing different distribution patterns, e.g., in the cotyledons, radicle, or testa. All tryptic peptides were detected with a mass resolution higher than 60,000 as well as a mass accuracy better than 1.5 ppm root-mean-square error and were matched to results from complementary liquid chromatography-MS/MS (LC-MS/MS) data. The developed method was also applied to crab's eye vine seeds for targeted MS imaging of the toxic protein abrin, showing the presence of abrin-a in all compartments. Abrin (59 kDa), as well as the majority of proteins visualized in chickpeas, was larger than 50 kDa and would thus not be readily accessible by top-down MS imaging. Since antibodies for plant proteins are often not readily available, in situ digestion MS imaging provides unique information, as it makes the distribution and identification of larger proteins in plant tissues accessible in an untargeted manner. This opens up new possibilities in the field of plant science as well as to assess the nutritional quality and/or safety of crops.

Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution

Untargeted separation of isomeric and isobaric species in mass spectrometry imaging (MSI) is challenging. The combination of ion mobility spectrometry (IMS) with MSI has emerged as an effective strategy for differentiating isomeric and isobaric species, which substantially enhances the molecular coverage and specificity of MSI experiments. In this study, we have implemented nanospray desorption electrospray ionization (nano-DESI) MSI on a trapped ion mobility spectrometry (TIMS) mass spectrometer. A new nano-DESI source was constructed, and a specially designed inlet extension was fabricated to accommodate the new source. The nano-DESI-TIMS-MSI platform was evaluated by imaging mouse brain tissue sections. We achieved high ion mobility resolution by utilizing three narrow mobility scan windows that covered the majority of the lipid molecules. Notably, the mobility resolution reaching up to 300 in this study is much higher than the resolution obtained in our previous study using drift tube IMS. High-resolution TIMS successfully separated lipid isomers and isobars, revealing their distinct localizations in tissue samples. Our results further demonstrate the power of high-mobility-resolution IMS for unraveling the complexity of biomolecular mixtures analyzed in MSI experiments.

Development and application of lipidomics for food research

Lipidomics is an emerging and promising omics derived from metabolomics to comprehensively analyze all of lipid molecules in biological matrices. The purpose of this chapter is to introduce the development and application of lipidomics for food research. First, three aspects of sample preparation are introduced: food sampling, lipid extraction, and transportation and storage. Second, five types of instruments for data acquisition are summarized: direct infusion-mass spectrometry (MS), chromatographic separation-MS, ion mobility-MS, MS imaging, and nuclear magnetic resonance spectroscopy. Third, data acquisition and analysis software are described for the lipidomics software development. Fourth, the application of lipidomics for food research is discussed such as food origin and adulteration analysis, food processing research, food preservation research, and food nutrition and health research. All the contents suggest that lipidomics is a powerful tool for food research based on its ability of lipid component profile analysis.

Autofocusing MALDI MS imaging of processed food exemplified by the contaminant acrylamide in German gingerbread

Acrylamide is a toxic reaction product occurring in dry-heated food such as bakery products. To meet the requirements laid down in recent international legal norms calling for reduction strategies in food prone to acrylamide formation, efficient chromatography-based quantification methods are available. However, for an efficient mitigation of acrylamide levels, not only the quantity, but also the contaminant's distributions are of interest especially in inhomogeneous food consisting of multiple ingredients. A promising tool to investigate the spatial distribution of analytes in food matrices is mass spectrometry imaging (MS imaging). In this study, an autofocusing MALDI MS imaging method was developed for German gingerbread as an example for highly processed and instable food with uneven surfaces. Next to endogenous food constituents, the process contaminant acrylamide was identified and visualized keeping a constant laser focus throughout the measurement. Statistical analyses based on relative acrylamide intensities suggest a higher contamination of nut fragments compared to the dough. In a proof-of-concept experiment, a newly developed in-situ chemical derivatization protocol is described using thiosalicylic acid for highly selective detection of acrylamide. This study presents autofocusing MS imaging as a suitable complementary method for the investigation of analytes' distributions in complex and highly processed food.

Mass spectrometry imaging: new eyes on natural products for drug research and development

Natural products (NPs) and their structural analogs represent a major source of novel drug development for disease prevention and treatment. The development of new drugs from NPs includes two crucial aspects. One is the discovery of NPs from medicinal plants/microorganisms, and the other is the evaluation of the NPs in vivo at various physiological and pathological states. The heterogeneous spatial distribution of NPs in medicinal plants/microorganisms or in vivo can provide valuable information for drug development. However, few molecular imaging technologies can detect thousands of compounds simultaneously on a label-free basis. Over the last two decades, mass spectrometry imaging (MSI) methods have progressively improved and diversified, thereby allowing for the development of various applications of NPs in plants/microorganisms and in vivo NP research. Because MSI allows for the spatial mapping of the production and distribution of numerous molecules in situ without labeling, it provides a visualization tool for NP research. Therefore, we have focused this mini-review on summarizing the applications of MSI technology in discovering NPs from medicinal plants and evaluating NPs in preclinical studies from the perspective of new drug research and development (R&D). Additionally, we briefly reviewed the factors that should be carefully considered to obtain the desired MSI results. Finally, the future development of MSI in new drug R&D is proposed.

Visualizing the Distribution of Lipids in Peanut Seeds by MALDI Mass Spectrometric Imaging

Peanut (also called groundnut, Arachis hypogaea L.) seeds are used for producing edible oils and functional foods, and offer a rich source of lipids, proteins and carbohydrates. However, the location of these metabolites has not yet been firmly established. In the present study, the matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) technique was applied to investigate spatial distribution of lipids and other key components in seeds of three peanut cultivars (ZH9, KQBH, HP). A total of 103 metabolites, including 34 lipid compounds, were putatively identified by MALDI-MSI. The abundance and spatial distribution of glycerolipids (GLs) and glycerophospholipids (GPs) were compared among the three peanut cultivars. All the identified lysophosphatidylcholine (LPC), phosphatidylethanolamine (PE) and phosphatidylcholines (PCs) were distributed mainly in the inner part of seeds. The visualization of phosphatidic acids (PAs) and triacylglycerols (TGs) revealed a dramatic metabolic heterogeneity between the different tissues making up the seed. The non-homogeneous spatial distribution of metabolites appeared to be related to the different functions of particular tissue regions. These results indicated that MALDI-MSI could be useful for investigating the lipids of foodstuffs from a spatial perspective. The present study may contribute to the development of oil crops with higher oil yields, and to improvement of food processing.

Information Entropy-Based Strategy for the Quantitative Evaluation of Extensive Hyperspectral Images to Better Unveil Spatial Heterogeneity in Mass Spectrometry Imaging

Hyperspectral images can be generated from mass spectrometry imaging (MSI) data for the intuitive data visualization purpose. However, hundreds of HSIs can be generated by different dimensionality reduction methods, which poses great challenges in selecting the high-quality images with the best intuitive visualization results of the MSI data. Here, we presented a novel approach that objectively evaluates the image quality of the hyperspectral images. The applicability of this method was demonstrated by analyzing the MSI data acquired from human prostate cancer biopsy samples and mouse brain tissue section, which harbored an intrinsic tissue heterogeneity. Our method was based on the information entropy and contrast measured from image information content and image definition, respectively. The heterogeneity of the MSI data from high-dimensional space was reduced to three-dimensional embeddings and thoroughly evaluated to achieve satisfactory visualization results. The application of information entropy and contrast can be used to choose the optimized visualization results rapidly and objectively from an extensive number of hyperspectral images and be adopted to evaluate and optimize different dimensionality reduction algorithms and their hyperparameter combinations. In conclusion, the information entropy-based strategy could be a bridge between chemometrician and biologists.

In situ Chemical Profiling and Imaging of Cultured and Natural Cordyceps sinensis by TOF-SIMS

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a sensitive surface analytical technology, which can simultaneously acquire diverse chemical components and their precise locations on the surfaces of samples without any requirements for chemical damage pretreatments or additional matrices. Commonly, the quality control of TCMs (traditional Chinese medicines) is limited by the qualitative and quantitative evaluations of the specifically extractive constituents. In this study, a practical sample preparation strategy named two-layered media embedding sample preparation was developed to obtain ideal freezing sections of dried materials of Cordyceps sinensis. Meanwhile, the well-established sample preparation method was applied for in situ chemical profiling and imaging of natural (NCS) and cultured Cordyceps sinensis (CCS) by using TOF-SIMS. More than 200 components were tentatively identified and imaged in NCS and CCS at the same time. Mass spectrometry imaging revealed that most components have even distributions in caterpillars of Cordyceps sinensis, while TAGs, DAGs, MAGs, and FAs only have distributions outside caterpillars’ digestive chambers. This is the first time that components were in situ imaged for Cordyceps sinensis to exhibit the chemical distributions which have never been achieved by other analytical techniques so far. In addition, chemometrics was used to simplify and explain the massive TOF-SIMS mass data sets, which revealed the high chemical similarity between CCS and NCS. Furthermore, the relative quantification of TOF-SIMS data showed that CCS has comparable proportions of amino acids, nucleosides, monosaccharides, sphingolipids, sterols and other principles to NCS except for fatty acids, glycerides and glycerophospholipids. The higher amounts of TAGs and DAGs in CCS were confirmed by quantitative ¹H-NMR, indicating reliable relative quantification of TOF-SIMS. In general, our research developed a novel approach of TOF-SIMS for in situ chemical analysis of TCMs, and its successful application in comparative study of CCS and NCS suggested that TOF-SIMS is an advanced and promising analytical technology for the research of TCMs.

Time-Series Lipidomics Insights into the Progressive Characteristics of Lipid Constituents of Fresh Walnut during Postharvest Storage

A high-throughput lipid profiling platform adopting an accurate quantification strategy was built based on Q-Orbitrap mass spectrometry. Lipid components of fresh walnut during postharvest storage were determined, and the fatty acid distributions in triacylglycerol and polar lipids were also characterized. A total of 554 individual lipids in fresh walnut were mainly glycerolipids (56.7%), glycerophospholipids (32.4%), and sphingolipids (11%). With the progress of postharvest storage, 16 lipid subclasses in the stored walnut sample were significantly degraded, in which 34 lipids changed significantly between the fresh and stored groups. The sphingolipid metabolism, glycerolipid metabolism, and linoleic acid metabolism pathways were significantly enriched. The oxidation and degradation mechanism of linoleic acid in walnut kernel during postharvest storage was proposed. The established lipidomics platform can supply reliable and traceable lipid profiling data, help to improve the understanding of lipid degradation in fresh walnut, and offer a framework for analyzing lipid metabolisms in other tree nuts.