Desorption Electrospray Ionization Mass Spectrometry: 20 Years

Profiling and visualization of organic acids in grape plants by desorption electrospray ionization imaging

Organic acids play a crucial role in determining the quality of grapes and their derived products, such as wine and juice. Despite their critical role in grapevine physiology and fruit quality, limited research has investigated the distribution of these acids within grape plants. This study employed desorption electrospray ionization (DESI) imaging to rapidly profile and image key organic acids across various grape tissues. By analyzing the ratios of tartaric and malic acids in different tissues, we leveraged DESI's semi-quantitative capabilities. The results not only align with previous quantitative findings but also reveal distinct spatial distributions of these acids. Malic acid was predominantly localized in the cortex and epidermis, while tartaric acid was concentrated in the pith region of stems, stem junctions, and near veins in leaf blades. These patterns suggest tissue-specific biosynthetic activities and provide spatial evidence for multiple active pathways in tartaric acid synthesis within grape plants. Overall, this study advances our understanding of organic acid metabolism in grapes and highlights DESI as a powerful and high throughput tool for obtaining semi-quantitative chemical data with high spatial resolution in plant science.

Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering

Super-resolution imaging of cell metabolism is hindered by the incompatibility of small metabolites with fluorescent dyes and the limited resolution of imaging mass spectrometry. We present ultrasensitive reweighted visible stimulated Raman scattering (URV-SRS), a label-free vibrational imaging technique for multiplexed nanoscopy of intracellular metabolites. We developed a visible SRS microscope with extensive pulse chirping to improve the detection limit to ~4,000 molecules and introduced a self-supervised multi-agent denoiser to suppress non-independent noise in SRS by over 7.2 dB, resulting in a 50-fold sensitivity enhancement over near-infrared SRS. Leveraging the enhanced sensitivity, we employed Fourier reweighting to amplify sub-100-nm spatial frequencies that were previously overwhelmed by noise. Validated by Fourier ring correlation, we achieved a lateral resolution of 86 nm in cell imaging. We visualized the reprogramming of metabolic nanostructures associated with virus replication in host cells and subcellular fatty acid synthesis in engineered bacteria, demonstrating its capability towards nanoscopic spatial metabolomics.

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section

An increasing number of spatial multiomic workflows have recently been developed. Some of these approaches have leveraged initial mass spectrometry imaging (MSI)-based spatial metabolomics to inform the region of interest (ROI) selection for downstream spatial proteomics. However, these workflows have been limited by varied substrate requirements between modalities or have required analyzing serial sections (i.e., one section per modality). To mitigate these issues, we present a new multiomic workflow that uses desorption electrospray ionization (DESI)-MSI to identify representative spatial metabolite patterns on-tissue prior to spatial proteomic analyses on the same tissue section. This workflow is demonstrated here with a model mammalian tissue (coronal rat brain section) mounted on a poly(ethylene naphthalate)-membrane slide. Initial DESI-MSI resulted in 160 annotations (SwissLipids) within the METASPACE platform (≤20% false discovery rate). A segmentation map from the annotated ion images informed the downstream ROI selection for spatial proteomics characterization from the same sample. The unspecific substrate requirements and minimal sample disruption inherent to DESI-MSI allowed for an optimized, downstream spatial proteomics assay, resulting in 3888 ± 240 to 4717 ± 48 proteins being confidently directed per ROI (200 μm × 200 μm). Finally, we demonstrate the integration of multiomic information, where we found ceramide localization to be correlated with SMPD3 abundance (ceramide synthesis protein), and we also utilized protein abundance to resolve metabolite isomeric ambiguity. Overall, the integration of DESI-MSI into the multiomic workflow allows for complementary spatial- and molecular-level information to be achieved from optimized implementations of each MS assay inherent to the workflow itself.

[Progress in applications of ambient ionization mass spectrometry for lipids identification]

Lipids are indispensable components of living organisms and play pivotal roles in cell-membrane fluidity, energy provision, and neurotransmitter transmission and transport. Lipids can act as potential biomarkers of diseases given their abilities to indicate cell-growth status. For example, the lipid-metabolism processes of cancer cells are distinct from those of normal cells owing to their rapid proliferation and adaptation to ever-changing biological environments. As a result, the ability to rapidly detect, identify, and monitor lipid components is critical for tracking life-related processes and may enhance cancer diagnosis and treatment efficacy. Mass spectrometry (MS) is regarded to be among the most efficient methods for directly obtaining molecular-structural information, and is distinctly advantageous for identifying lipids. Recent years have witnessed the emergence of ambient mass spectrometry (AMS), which enables direct analyte sampling and ionization without the need for sample preprocessing. These characteristics endow AMS with special advantages for identifying and monitoring lipids. Furthermore, the ongoing development of soft ionization technologies has led to the widespread use of AMS for the detection of complex and diverse lipid molecules. Electrospray ionization (ESI) is a gentle ionization method that can be used to detect medium-to-high-polarity compounds and provide detailed chemical information for lipids by producing a fine mist of charged droplets from a liquid sample. Consequently, a series of ESI-based ionization methods have been developed for fabricating different AMS systems capable of rapidly detecting lipids in a simple manner. For example, desorption electrospray ionization (DESI) is among the most extensively employed ambient ionization techniques, and has been used to detect a wide range of samples, including solids, liquids, and gases. DESI involves spraying a charged solvent onto the surface of a sample, after which the solvent is desorbed, the analyte is ionized, and the generated ions are transferred to the detector of the mass spectrometer via a gas plume. DESI can easily and precisely regulate the sampling space, thereby offering a highly effective approach for the in-situ detection of lipids from tissue samples. Additionally, single-cell lipid analysis is limited by small cell volumes, complex cellular matrices, and minimal absolute amounts of analyte. Common detection methods for single cells include flow cytometry and fluorescence microscopy, both of which require fluorescent labeling to detect specific target molecules, which limits detection selectivity and reproducibility to some extent. ESI-based single-cell mass spectrometry has emerged as a more-effective method for detecting cellular lipids owing to advantages that include high sensitivity, low sample consumption, high throughput, and multiple-detection capabilities. Moreover, lipid chemical diversity poses a significant challenge for determining structural details. Therefore, AMS-based lipid detection has been augmented with a series of chemical-treatment methods that provide more-comprehensive structural information for lipids. For example, diverse gas-phase dissociation techniques have been used to discriminate between lipid C=C-bond isomers and their sn-positions. Strategies that involve chemically modifying specific target C=C bonds prior to MS detection have also been employed. For example, the Paternò-Büchi (P-B) photochemical reaction oxidizes C=C bonds in unsaturated lipids to form oxetane structures, C=C bonds can be epoxidized to form the corresponding oxaziridines, the N-H aziridination reaction converts C=C bonds into aziridines, and the 1ΔO2 ene reaction adds an OOH group to a C=C bond. In this review, we discuss various environmental ionization techniques for lipid AMS developed over the past five years, with an emphasis on typical chemical strategies used to analyze lipid fine structures. Obtaining a high-coverage, high-sensitivity lipid-detection platform based on AMS remains challenging and requires further in-depth studies despite significant improvements in lipid MS-based detection techniques.

Are Hydroxyl Radicals Spontaneously Generated in Unactivated Water Droplets?

Spontaneous ionization/breakup of water at the surface of aqueous droplets has been reported with evidence ranging from formation of hydrogen peroxide and hydroxyl radicals, indicated by ions at m/z 36 attributed to OH⋅-H3O+ or (H2O-OH2)+⋅ as well as oxidation products of radical scavengers in mass spectra of water droplets formed by pneumatic nebulization. Here, aqueous droplets are formed both by nanoelectrospray, which produces highly charged nanodrops with initial diameters ~100 nm, and a vibrating mesh nebulizer, which produces 2-20 μm droplets that are initially less highly charged. The lifetimes of these droplets range from 10s of μs to 560 ms and the surface-to-volume ratios span ~100-fold range. No ions at m/z 36 are detected with pure water, nor are significant oxidation products for the two radical scavengers that were previously reported to be formed in high abundance. These and other results indicate that prior conclusions about spontaneous hydroxyl radical formation in unactivated water droplets are not supported by the evidence and that water appears to be stable at droplet surfaces over a wide range of droplet size, charge and lifetime.

Tumor-Promoted Changes in Pediatric Brain Histology Can Be Distinguished from Normal Parenchyma by Desorption Electrospray Ionization Mass Spectrometry Imaging

Background: Central nervous system (CNS) tumors are the second most frequent type of neoplasm in childhood and adolescence, after leukemia. Despite the incorporation of molecular classification and improvement of protocols combining chemotherapy, surgery, and radiotherapy, CNS tumors are still the most lethal neoplasm in this age group. Mass spectrometry imaging (MSI) is a powerful tool to map the distribution of molecular species in tissue sections. Among MSI techniques, desorption electrospray ionization (DESI-MSI) has been demonstrated to enable reliable agreement with the pathological evaluation of different adult cancer types, along with an acceptable time scale for intraoperative use. Methods: In the present work, we aimed to investigate the chemical profile obtained by DESI-MSI as an intraoperative surgical management tool by profiling 162 pediatric brain biopsies and reporting the results according to the histopathology and molecular profile of the tumors. Results: The 2D chemical images obtained by DESI-MSI allowed us to distinguish tumor-transformed tissue from non-tumor tissue with an accuracy of 96.8% in the training set and 94.3% in the validation set after statistical modeling of our data using Lasso. In addition, high-grade and low-grade tumors also displayed a distinct chemical profile when analyzed by DESI-MSI. We also provided evidence that the chemical profile of brain tumors obtained by DESI-MSI correlates with methylation-based molecular classes and specific immunophenotypes found in brain biopsies. Conclusions: The results presented herein support the incorporation of DESI-MSI analysis as an intraoperative assistive tool in prospective clinical trials for pediatric brain tumors management in the near future.

Detection of IDH mutation in glioma by desorption electrospray ionization (DESI) tandem mass spectrometry

Desorption electrospray ionization (DESI) tandem mass spectrometry (MS) is used to assess mutation status of isocitrate dehydrogenase (IDH) in human gliomas. Due to the diffuse nature of gliomas, total gross resection is not normally achieved during surgery, leading to tumor recurrence. The mutation status of IDH has clinical significance due to better prognosis in IDH-mutant patients. The mutant IDH converts alpha-ketoglutaric acid (α-KG) into 2-hydroxyglutarate (2HG), which accumulates abnormally in cells. Immunohistochemical staining (IHC) and genetic testing, the gold standards, are incompatible with intraoperative applications but DESI tandem mass spectrometry (MS/MS) can be used to assess the mutation status of IDH enzyme from tissue intraoperatively. Here, on off-line evaluation is made of the performance of two different types of mass spectrometers in characterization of IDH mutation status. The intensity of 2HG is measured against glutamate (Glu), an intrinsic reference molecule, in both tandem MS measurements. In both cases using DESI clear separation between IDH-mutant (mut) and IDH-wildtype (wt) samples (p < 0.0001) is observed, despite the short analysis time. Due to the higher detection sensitivity, multiple reaction monitoring experiments using a triple quadrupole show slightly better performance compared to product ion MS/MS performed on a simple linear ion trap. Both DESI-MS platforms are capable of providing information on IDH mutation status, which might in future be used at the time of surgery to support decision-making on resection regions, especially at tumor margins.

Hydrogen Is the Superior Nebulization Gas for Desorption and Electrospray Ionization

A previous comparative study between helium and nitrogen as nebulizing and desolvation gases in electrospray ionization (ESI) and desorption electrospray ionization (DESI) found that the signal responses of compounds of varying sizes and polarities were improved. Here, an expanded selection of nebulizing gases was evaluated to investigate mechanisms of improvement. The set of nebulizing gases included hydrogen, helium, nitrogen, argon, and carbon dioxide. Results indicate that the signal enhancements are achieved by gases lighter than nitrogen and that the previously described helium effects can be improved by using the more economical and sustainable hydrogen as a nebulizing gas. Additionally, H2 and He reduce the desorption footprint, which could be potentially useful in increasing the resolution of chemical imaging microscopy, especially since, despite the smaller footprint obtained using helium and hydrogen, higher signals are obtained compared to nitrogen.

The burgeoning spatial multi-omics in human gastrointestinal cancers

The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body's three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.

High-Throughput Assessment of Bile Salt Export Pump Inhibition Using RapidFire-MS and DESI-MS

The bile salt export pump (BSEP) assay is widely used to evaluate the potential for drug-induced liver injury (DILI) early in the drug discovery process. While traditional liquid chromatography-mass spectrometry (LC-MS)-based approaches have been utilized for BSEP activity testing, they have intrinsic limitations in either throughput or the requirement for sample preparation and are difficult to scale up in order to screen drug candidates. Here we demonstrate the use of two different high-throughput MS methods based on solid-phase extraction (SPE) and desorption electrospray ionization (DESI) for high-throughput BSEP activity assessment in a label-free manner, with minimal needs for sample workup, at sampling rates of ∼11 and ∼5.5 s/sample, respectively. Both approaches were validated, compared, and successfully applied to the evaluation of 96 drug candidates for the inhibition of taurocholic acid (TCA) transport using BSEP vesicles.

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.

High-throughput label-free opioid receptor binding assays using an automated desorption electrospray ionization mass spectrometry platform

The current opioid epidemic has incentivized the discovery of new non-addictive analgesics, a process that requires the screening of opioid receptor binding, traditionally performed using radiometric assays. Here we describe a label-free alternative based on high-throughput (1 Hz) ambient mass spectrometry for screening the receptor binding of new opioid analogues.

Protein analysis by desorption electrospray ionization mass spectrometry

This review presents progress made in the ambient analysis of proteins, in particular by desorption electrospray ionization-mass spectrometry (DESI-MS). Related ambient ionization techniques are discussed in comparison to DESI-MS only to illustrate the larger context of protein analysis by ambient ionization mass spectrometry. The review describes early and current approaches for the analysis of undigested proteins, native proteins, tryptic digests, and indirect protein determination through reporter molecules. Applications to mass spectrometry imaging for protein spatial distributions, the identification of posttranslational modifications, determination of binding stoichiometries, and enzymatic transformations are discussed. The analytical capabilities of other ambient ionization techniques such as LESA and nano-DESI currently exceed those of DESI-MS for in situ surface sampling of intact proteins from tissues. This review shows, however, that despite its many limitations, DESI-MS is making valuable contributions to protein analysis. The challenges in sensitivity, spatial resolution, and mass range are surmountable obstacles and further development and improvements to DESI-MS is justified.

Characterisation of Canine and Feline Breast Tumours, Their Metastases, and Corresponding Primary Cell Lines Using LA-REIMS and DESI-MS Imaging

Breast cancer, a complex disease with a significant prevalence to form metastases, necessitates novel therapeutic strategies to improve treatment outcomes. Here, we present the results of a comparative molecular study of primary breast tumours, their metastases, and the corresponding primary cell lines using Desorption Electrospray Ionisation (DESI) and Laser-Assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) imaging. Our results show that ambient ionisation mass spectrometry technology is suitable for rapid characterisation of samples, providing a lipid- and metabolite-rich spectrum within seconds. Our study demonstrates that the lipidomic fingerprint of the primary tumour is not significantly distinguishable from that of its metastasis, in parallel with the similarity observed between their respective primary cell lines. While significant differences were observed between tumours and the corresponding cell lines, distinct lipidomic signatures and several phospholipids such as PA(36:2), PE(36:1), and PE(P-38:4)/PE(O-38:5) for LA-REIMS imaging and PE(P-38:4)/PE(O-38:5), PS(36:1), and PI(38:4) for DESI-MSI were identified in both tumours and cells. We show that the tumours' characteristics can be found in the corresponding primary cell lines, offering a promising avenue for assessing tumour responsiveness to therapeutic interventions. A comparative analysis by DESI-MSI and LA-REIMS imaging revealed complementary information, demonstrating the utility of LA-REIMS in the molecular imaging of cancer.

Challenges of Spatially Resolved Metabolism in Cancer Research

Stable isotope-resolved metabolomics comprises a critical set of technologies that can be applied to a wide variety of systems, from isolated cells to whole organisms, to define metabolic pathway usage and responses to perturbations such as drugs or mutations, as well as providing the basis for flux analysis. As the diversity of stable isotope-enriched compounds is very high, and with newer approaches to multiplexing, the coverage of metabolism is now very extensive. However, as the complexity of the model increases, including more kinds of interacting cell types and interorgan communication, the analytical complexity also increases. Further, as studies move further into spatially resolved biology, new technical problems have to be overcome owing to the small number of analytes present in the confines of a single cell or cell compartment. Here, we review the overall goals and solutions made possible by stable isotope tracing and their applications to models of increasing complexity. Finally, we discuss progress and outstanding difficulties in high-resolution spatially resolved tracer-based metabolic studies.

Skin Surface Sebum Analysis by ESI-MS

The skin surface is an important sample source that the metabolomics community has only just begun to explore. Alterations in sebum, the lipid-rich mixture coating the skin surface, correlate with age, sex, ethnicity, diet, exercise, and disease state, making the skin surface an ideal sample source for future noninvasive biomarker exploration, disease diagnosis, and forensic investigation. The potential of sebum sampling has been realized primarily via electrospray ionization mass spectrometry (ESI-MS), an ideal approach to assess the skin surface lipidome. However, a better understanding of sebum collection and subsequent ESI-MS analysis is required before skin surface sampling can be implemented in routine analyses. Challenges include ambiguity in definitive lipid identification, inherent biological variability in sebum production, and methodological, technical variability in analyses. To overcome these obstacles, avoid common pitfalls, and achieve reproducible, robust outcomes, every portion of the workflow-from sample collection to data analysis-should be carefully considered with the specific application in mind. This review details current practices in sebum sampling, sample preparation, ESI-MS data acquisition, and data analysis, and it provides important considerations in acquiring meaningful lipidomic datasets from the skin surface. Forensic researchers investigating sebum as a means for suspect elimination in lieu of adequate fingerprint ridge detail or database matches, as well as clinical researchers interested in noninvasive biomarker exploration, disease diagnosis, and treatment monitoring, can use this review as a guide for developing methods of best-practice.

Portable Instrumentation for Ambient Ionization and Miniature Mass Spectrometers

We critically evaluate the current status of portable mass spectrometry (pMS), particularly where this aligns with ambient ionization. Assessing the field of pMS can be quite subjective, especially in relation to the portable aspects of design, deployment, and operation. In this review, we discuss what it means to be portable and introduce a set of criteria by which pMS and ambient ionization sources can be assessed. Moreover, we consider the recent literature in terms of the most popular and significant advances in portable instrumentation for ambient ionization and miniature mass spectrometers. Finally, emerging trends and exciting future prospects are discussed and some recommendations are offered.

Mass spectrometry imaging of N-linked glycans: Fundamentals and recent advances

With implications in several medical conditions, N-linked glycosylation is one of the most important posttranslation modifications present in all living organisms. Due to their nontemplate synthesis, glycan structures are extraordinarily complex and require multiple analytical techniques for complete structural elucidation. Mass spectrometry is the most common way to investigate N-linked glycans; however, with techniques such as liquid-chromatography mass spectrometry, there is complete loss of spatial information. Mass spectrometry imaging is a transformative analytical technique that can visualize the spatial distribution of ions within a biological sample and has been shown to be a powerful tool to investigate N-linked glycosylation. This review covers the fundamentals of mass spectrometry imaging and N-linked glycosylation and highlights important findings of recent key studies aimed at expanding and improving the glycomics imaging field.

Imaging with mass spectrometry: Which ionization technique is best?

The use of mass spectrometry (MS) to acquire molecular images of biological tissues and other substrates has developed into an indispensable analytical tool over the past 25 years. Imaging mass spectrometry technologies are widely used today to study the in situ spatial distributions for a variety of analytes. Early MS images were acquired using secondary ion mass spectrometry and matrix-assisted laser desorption/ionization. Researchers have also designed and developed other ionization techniques in recent years to probe surfaces and generate MS images, including desorption electrospray ionization (DESI), nanoDESI, laser ablation electrospray ionization, and infrared matrix-assisted laser desorption electrospray ionization. Investigators now have a plethora of ionization techniques to select from when performing imaging mass spectrometry experiments. This brief perspective will highlight the utility and relative figures of merit of these techniques within the context of their use in imaging mass spectrometry.

Accurate Clinical Detection of Vitamin D by Mass Spectrometry: A Review

Vitamin D deficiency is thought to be associated with a wide range of diseases, including diabetes, cancer, depression, neurodegenerative diseases, and cardiovascular and cerebrovascular diseases. This vitamin D deficiency is a global epidemic affecting both developing and developed countries and therefore qualitative and quantitative analysis of vitamin D in a clinical context is essential. Mass spectrometry has played an increasingly important role in the clinical analysis of vitamin D because of its accuracy, sensitivity, specificity, and the ability to detect multiple substances at the same time. Despite their many advantages, mass spectrometry-based methods are not without analytical challenges. Front-end and back-end challenges such as protein precipitation, analyte extraction, derivatization, mass spectrometer functionality, must be carefully considered to provide accurate and robust analysis of vitamin D through a well-designed approach with continuous control by internal and external quality control. Therefore, the aim of this review is to provide a comprehensive overview of the development of mass spectrometry methods for vitamin D accurate analysis, including emphasis on status markers, deleterious effects of biological matrices, derivatization reactions, effects of ionization sources, contribution of epimers, standardization of assays between laboratories.

Spatial pharmacology using mass spectrometry imaging

The emerging and powerful field of spatial pharmacology can map the spatial distribution of drugs and their metabolites, as well as their effects on endogenous biomolecules including metabolites, lipids, proteins, peptides, and glycans, without the need for labeling. This is enabled by mass spectrometry imaging (MSI) that provides previously inaccessible information in diverse phases of drug discovery and development. We provide a perspective on how MSI technologies and computational tools can be implemented to reveal quantitative spatial drug pharmacokinetics and toxicology, tissue subtyping, and associated biomarkers. We also highlight the emerging potential of comprehensive spatial pharmacology through integration of multimodal MSI data with other spatial technologies. Finally, we describe how to overcome challenges including improving reproducibility and compound annotation to generate robust conclusions that will improve drug discovery and development processes.