Methods for Cryosectioning and Mass Spectrometry Imaging of Whole-Body Zebrafish

Oversampling for Enhanced Spatial Resolution of Zebrafish by Top-Hat IR-MALDESI-MSI

Mass spectrometry imaging (MSI) has become a significant tool for measuring chemical species in biological tissues, where much of the impact of these platforms lies in their capability to report the spatial distribution of analytes for correlation to sample morphology. As a result, enhancement of spatial resolution has become a frontier of innovation in the field, and necessary developments are dependent on the ionization source. More particularly, laser-based imaging sources may require modifications to the optical train or alternative sampling techniques. These challenges are heightened for systems with infrared (IR) lasers, as their operating wavelength generates spot sizes that are inherently larger than their ultraviolet counterparts. Recently, the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source has shown the utility of a diffractive optical element (DOE) to produce square ablation patterns, termed top-hat IR-MALDESI. If the DOE optic is combined with oversampling methods, smaller ablation volumes can be sampled to render higher spatial resolution imaging experiments. Further, this approach enables reproducible spot sizes and ablation volumes for better comparison between scans. Herein, we investigate the utility of oversampling with top-hat IR-MALDESI to enhance the spatial resolution of measured lipids localized within the head of sectioned zebrafish tissue. Four different spatial resolutions were evaluated for data quality (e.g., mass measurement accuracy, spectral accuracy) and quantity of annotations. Other experimental parameters to consider for high spatial resolution imaging are also discussed. Ultimately, 20 μm spatial resolution was achieved in this work and supports feasibility for use in future IR-MALDESI studies.

Optimizing neurotransmitter pathway detection by IR-MALDESI-MSI in mouse brain

Mass spectrometry imaging (MSI) platforms such as infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) are advantageous for a variety of applications, including elucidating the localization of neurotransmitters (NTs) and related molecules with respect to ion abundance across a sample without the need for derivatization or organic matrix application. While IR-MALDESI-MSI conventionally uses a thin exogenous ice matrix to improve signal abundance, it has been previously determined that sucrose embedding without the ice matrix improves detection of lipid species in striatal, coronal mouse brain sections. This work considers components of this workflow to determine the optimal sample preparation and matrix to enhance the detection of NTs and their related metabolites in coronal sections from the striatal region of the mouse brain. The discoveries herein will enable more comprehensive follow-on studies for the investigation of NTs to enrich biological pathways and interpretation related to neurodegenerative diseases and ischemic stroke.

Mapping the Metabolic Characteristics and Perturbation of Adult Casper Zebrafish by Ambient Mass Spectrometry Imaging

Casper, a type of transparent mutant-line zebrafish, was generated to overcome the opaque trunk of an adult zebrafish for tumor modeling to realize real-time visualization of transplanted cells in vivo. However, the molecular information at the metabolic level has not received much attention. Herein, a spatially resolved metabolomics method based on an airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) system for whole-body zebrafish was used to investigate small molecules and the distribution of adult casper (Mitfaw2/w2, roya9/a9) and the differences from wild-type zebrafish. Finally, the spatial distribution information of more than 1500 endogenous ions was obtained in positive and negative detection modes, and 186 metabolites belonging to a variety of structural categories were identified or annotated. Compared with wild-type samples, 85 variables, including 37 known metabolites, were screened out. In addition, the disordered metabolic pathways caused by the genetic mutation were excavated, involving downregulation of purine metabolism and arachidonic acid metabolism, upregulation of glycerophospholipid metabolism, and biosynthesis of unsaturated fatty acids. All these results were observed in the most intuitive way through MSI. This study revealed important metabolic characteristics of and perturbation in adult casper zebrafish, and provides indispensable fundamental knowledge for tumor research based on it.

[Application advances of mass spectrometry imaging technology in environmental pollutants analysis and their toxicity research]

Environmental exposures have significant impacts on human health and can contribute to the occurrence and development of diseases. Pollutants can enter the body through ingestion, inhalation, dermal absorption, or mother-to-child transmission, and can metabolize and/or accumulate in different tissues and organs. These pollutants can recognize and interact with various biomolecules, including DNA, RNA, proteins, and metabolites, disrupting biological processes and leading to adverse effects in living organisms. Thus, it is crucial to analysis the exogenous pollutants in the body, identify potential biomarkers and investigate their toxic effects. Numerous studies have shown that the metabolism rate of environmental pollutants greatly differs in various tissues and organs, their accumulation is also heterogeneous and dynamically changing. Moreover, the synthesis and accumulation of endogenous metabolites exhibit precise spatial distributions in tissues and cells. Mapping the spatial distributions of both pollutants and endogenous metabolites can discover relevant exposure biomarkers and provide a better understanding of their toxic effects and molecular mechanisms. Mass spectrometry is currently the preferred method for the qualitative and quantitative analysis of various compounds, and has been extensively utilized in pollutant and metabolomics analyses. Mass spectrometry imaging (MSI) is an emerging technology for molecular imaging that combines the information obtained by mass spectrometry with the visualization of the two- and three-dimensional spatial distributions of various molecular species in thin sample sections. Unlike other molecular imaging techniques, MSI can perform the label-free and untargeted analysis of thousands of molecules, such as elements, metabolites, lipids, peptides, proteins, pollutants, and drugs, in a single experiment with high sensitivity and throughput. Different MSI technologies, such as matrix-assisted laser desorption ionization mass spectrometry imaging, secondary ion mass spectrometry imaging, desorption electrospray ionization mass spectrometry imaging, and laser ablation inductively coupled plasma mass spectrometry imaging, have been introduced for the mapping of compounds and elements in biological, medical, and clinical research. MSI technologies have recently been utilized to characterize the spatial distribution of pollutants in the whole body and specific tissues of organisms, assess the toxic effects of pollutants at the molecular level, and identify exposure biomarkers. Such developments have brought new perspectives to investigate the toxicity of environmental pollutants. In this review, we provide an overview of the principles, characteristics, mass analyzers, and workflows of different MSI techniques and introduce their latest application advances in the analysis of environmental pollutants and their toxic effects.

Achieving Cross-Ring Fragmentation of N-Linked Glycans by IR-MALDESI

Glycans are complex structures that require MS/MS for detailed structural elucidation. Incorporating metals can provide more structural information by inhibiting glycosidic cleavage and enhancing cross-ring fragmentation. A direct analysis was performed using lithium doping and IR-MALDESI to induce cross-ring fragmentation of glycans. The protonated and lithiated versions of the two glycans were isolated and subjected to HCD. For protonated glycans, only glycosidic cleavages were observed. Using lithium doping, MS/MS consisted of abundant cross-ring fragments. Seventeen cross-ring fragments were detected across both glycans using lithium-doped ESI. This is the first incorporation of metal doping in IR-MALDESI to achieve cross-ring fragments in MS/MS analysis.

Comparative analysis of sucrose-embedding for whole-body zebrafish MSI by IR-MALDESI

Infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI) conventionally utilizes fresh-frozen biological tissues with an ice matrix to improve the detection of analytes. Sucrose-embedding with paraformaldehyde fixation has demonstrated feasibility as an alternative matrix for analysis by IR-MALDESI by preserving tissue features and enhancing ionization of lipids. However, investigating multi-organ systems provides broader context for a biological study and can elucidate more information about a disease state as opposed to a single organ. Danio rerio, or zebrafish, are model organisms for various disease states and can be imaged as a multi-organ sample to analyze morphological and metabolomic preservation as a result of sample preparation. Herein, whole-body zebrafish were imaged to compare sucrose-embedding with paraformaldehyde fixation against conventional fresh-frozen sample preparation. Serial sections were analyzed with and without an ice matrix to evaluate if sucrose functions as an alternative energy-absorbing matrix for IR-MALDESI applications across whole-body tissues. The resulting four conditions were compared in terms of total putative lipid annotations and category diversity, coverage across the entire m/z range, and ion abundance. Ultimately, sucrose-embedded zebrafish had an increase in putative lipid annotations for the combination of putative annotations with and without the application of an ice matrix relative to fresh-frozen tissues which require the application of an ice matrix. Upon the use of an ice matrix, a greater number of high mass putative lipid annotations (e.g., glycerophospholipids, glycerolipids, and sphingolipids) were identified. Conversely, without an ice matrix, sucrose-embedded sections elucidated more putative annotations in lower molecular weight lipids, including fatty acyls and sterol lipids. Similar to the mouse brain model, sucrose-embedding increased putative lipid annotation and abundance for whole-body zebrafish.

Elucidating the spatial distribution of organic contaminants and their biotransformation products in amphipod tissue by MALDI- and DESI-MS-imaging

The application of mass spectrometry imaging (MSI) is a promising tool to analyze the spatial distribution of organic contaminants in organisms and thereby improve the understanding of toxicokinetic and toxicodynamic processes. MSI is a common method in medical research but has been rarely applied in environmental science. In the present study, the suitability of MSI to assess the spatial distribution of organic contaminants and their biotransformation products (BTPs) in the aquatic invertebrate key species Gammarus pulex was studied. Gammarids were exposed to a mixture of common organic contaminants (carbamazepine, citalopram, cyprodinil, efavirenz, fluopyram and terbutryn). The distribution of the parent compounds and their BTPs in the organisms was analyzed by two MSI methods (MALDI- and DESI-HRMSI) after cryo-sectioning, and by LC-HRMS/MS after dissection into different organ compartments. The spatial distribution of contaminats in gammarid tissue could be successfully analyzed by the different analytical methods. The intestinal system was identified as the main site of biotransformation, possibly due to the presence of biotransforming enzymes. LC-HRMS/MS was more sensitive and provided higher confidence in BTP identification due to chromatographic separation and MS/MS. DESI was found to be the more sensitive MSI method for the analyzed contaminants, whereas additional biomarkers were found using MALDI. The results demonstrate the suitability of MSI for investigations on the spatial distribution of accumulated organic contaminants. However, both MSI methods required high exposure concentrations. Further improvements of ionization methods would be needed to address environmentally relevant concentrations.

Maximized Spatial Information and Minimized Acquisition Time of Top-Hat IR-MALDESI-MSI of Zebrafish Using Nested Regions of Interest (nROIs)

Increasing the spatial resolution of a mass spectrometry imaging (MSI) method results in a more defined heatmap of the spatial distribution of molecules across a sample, but it is also associated with the disadvantage of increased acquisition time. Decreasing the area of the region of interest to achieve shorter durations results in the loss of potentially valuable information in larger specimens. This work presents a novel MSI method to reduce the time of MSI data acquisition with variable step size imaging: nested regions of interest (nROIs). Using nROIs, a small ROI may be imaged at a higher spatial resolution while nested inside a lower-spatial-resolution peripheral ROI. This conserves the maximal spatial and chemical information generated from target regions while also decreasing the necessary acquisition time. In this work, the nROI method was characterized on mouse liver and applied to top-hat MSI of zebrafish using a novel optical train, which resulted in a significant improvement in both acquisition time and spatial detail of the zebrafish. The nROI method can be employed with any step size pairing and adapted to any method in which the acquisition time of larger high-resolution ROIs poses a practical challenge.

Predicting Sialic Acid Content of N-Linked Glycans Using the Isotopic Pattern of Chlorine

Sialic acids play several roles in both physiological and pathological processes; however, due to their labile nature, they are difficult to analyze using mass spectrometry. Previous work has shown that infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is able to detect intact sialylated N-linked glycans without the use of chemical derivatization. In this work, we describe a new rule that can predict the number of sialic acids on a glycan. Formalin-fixed paraffin-embedded human kidney tissue was prepared using previously established methods and analyzed using IR-MALDESI in negative-ion mode mass spectrometry. Using the experimental isotopic distribution of a detected glycan, we can predict the number of sialic acids on the glycan; #sialic acids is equal to the charge state minus the number of chlorine adducts, or z - #Cl^-. This new rule grants confident glycan annotations and compositions beyond accurate mass measurements, thereby further improving the capability of IR-MALDESI to study sialylated N-linked glycans within biological tissues.

The development and application of matrix assisted laser desorption electrospray ionization: The teenage years

In the past 15 years, ambient ionization techniques have witnessed a significant incursion into the field of mass spectrometry imaging, demonstrating their ability to provide complementary information to matrix-assisted laser desorption ionization. Matrix-assisted laser desorption electrospray ionization is one such technique that has evolved since its first demonstrations with ultraviolet lasers coupled to Fourier transform-ion cyclotron resonance mass spectrometers to extensive use with infrared lasers coupled to orbitrap-based mass spectrometers. Concurrently, there have been transformative developments of this imaging platform due to the high level of control the principal group has retained over the laser technology, data acquisition software (RastirX), instrument communication, and image processing software (MSiReader). This review will discuss the developments of MALDESI since its first laboratory demonstration in 2005 to the most recent advances in 2021.

Unraveling the mystery of efficacy in Chinese medicine formula: New approaches and technologies for research on pharmacodynamic substances

Traditional Chinese medicine (TCM) is the key to unlock treasures of Chinese civilization. TCM and its compound play a beneficial role in medical activities to cure diseases, especially in major public health events such as novel coronavirus epidemics across the globe. The chemical composition in Chinese medicine formula is complex and diverse, but their effective substances resemble "mystery boxes". Revealing their active ingredients and their mechanisms of action has become focal point and difficulty of research for herbalists. Although the existing research methods are numerous and constantly updated iteratively, there is remain a lack of prospective reviews. Hence, this paper provides a comprehensive account of existing new approaches and technologies based on previous studies with an in vitro to in vivo perspective. In addition, the bottlenecks of studies on Chinese medicine formula effective substances are also revealed. Especially, we look ahead to new perspectives, technologies and applications for its future development. This work reviews based on new perspectives to open horizons for the future research. Consequently, herbal compounding pharmaceutical substances study should carry on the essence of TCM while pursuing innovations in the field.

Rapid and Automatic Annotation of Multiple On-Tissue Chemical Modifications in Mass Spectrometry Imaging with Metaspace

On-tissue chemical derivatization is a valuable tool for expanding compound coverage in untargeted metabolomic studies with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Applying multiple derivatization agents in parallel increases metabolite coverage even further but results in large and more complex datasets that can be challenging to analyze. In this work, we present a pipeline to provide rigorous annotations for on-tissue derivatized MSI data using Metaspace. To test and validate the pipeline, maize roots were used as a model system to obtain MSI datasets after chemical derivatization with four different reagents, Girard's T and P for carbonyl groups, coniferyl aldehyde for primary amines, and 2-picolylamine for carboxylic acids. Using this pipeline helped us annotate 631 unique metabolites from the CornCyc/BraChem database compared to 256 in the underivatized dataset, yet, at the same time, shortening the processing time compared to manual processing and providing robust and systematic scoring and annotation. We have also developed a method to remove false derivatized annotations, which can clean 5-25% of false derivatized annotations from the derivatized data, depending on the reagent. Taken together, our pipeline facilitates the use of broadly targeted spatial metabolomics using multiple derivatization reagents.

MALDI mass spectrometry imaging workflow for the aquatic model organisms Danio rerio and Daphnia magna

Lipids play various essential roles in the physiology of animals. They are also highly dependent on cellular metabolism or status. It is therefore crucial to understand to which extent animals can stabilize their lipid composition in the presence of external stressors, such as chemicals that are released into the environment. We developed a MALDI MS imaging workflow for two important aquatic model organisms, the zebrafish (Danio rerio) and water flea (Daphnia magna). Owing to the heterogeneous structure of these organisms, developing a suitable sample preparation workflow is a highly non-trivial but crucial part of this work and needs to be established first. Relevant parameters and practical considerations in order to preserve tissue structure and composition in tissue sections are discussed for each application. All measurements were based on high mass accuracy enabling reliable identification of imaged compounds. In zebrafish we demonstrate that a detailed mapping between histology and simultaneously determined lipid composition is possible at various scales, from extended structures such as the brain or gills down to subcellular structures such as a single axon in the central nervous system. For D. magna we present for the first time a MALDI MSI workflow, that demonstrably maintains tissue integrity during cryosectioning of non-preserved samples, and allows the mapping of lipids in the entire body and the brood chamber inside the carapace. In conclusion, the lipid signatures that we were able to detect with our method provide an ideal basis to analyze changes caused by pollutants in two key aquatic model organisms.

Mass Spectrometry Imaging of N-Linked Glycans in a Formalin-Fixed Paraffin-Embedded Human Prostate by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization

N-Linked glycans are structurally diverse polysaccharides that represent significant biological relevance due to their involvement in disease progression and cancer. Due to their complex nature, N-linked glycans pose many analytical challenges requiring the continued development of analytical technologies. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a hybrid ionization technique commonly used for mass spectrometry imaging (MSI) applications. Previous work demonstrated IR-MALDESI to significantly preserve sialic acid containing N-linked glycans that otherwise require chemical derivatization prior to detection. Here, we demonstrate the first analysis of N-linked glycans in situ by IR-MALDESI MSI. A formalin-fixed paraffin-embedded human prostate tissue was analyzed in negative ionization mode after tissue washing, antigen retrieval, and pneumatic application of PNGase F for enzymatic digestion of N-linked glycans. Fifty-three N-linked glycans were confidently identified in the prostate sample where more than 60% contained sialic acid residues. This work demonstrates the first steps in N-linked glycan imaging of biological tissues by IR-MALDESI MSI. Raw data files are available in MassIVE (identifier: MSV000088414).

Visualization of dietary docosahexaenoic acid in whole-body zebrafish using matrix-assisted laser desorption/ionization mass spectrometry imaging

Zebrafish models have been developed for several studies involving lipid metabolism and lipid-related diseases. In the present study, the migration of dietary docosahexaenoic acid (DHA) in whole-body zebrafish was estimated by stable-isotope tracer and matrix-assisted laser desorption/ionization mass spectrometry imaging. Administration of 1-¹³C-2,2-D₂-labeled DHA ((+3)DHA) ethyl ester to male zebrafish was conducted to evaluate its accumulation, migration, and distribution in the body. The (+3)DHA content in the body of zebrafish after administering (+3)DHA for 10 and 15 d was significantly higher than that in the control group. (+3)DHA was observed as a constituent of phosphatidylcholine (PC) in the intestine of zebrafish that were administered (+3)DHA for 5 and 10 d. (+3)DHA-containing PC tended to accumulate in the intestines of zebrafish administered (+3)DHA for 1 d, indicating that recombination of (+3)DHA from ethyl ester to PC occurs quickly at intestine. After administration for 15 d, (+3)DHA-containing PC accumulated in the intestine, liver, and muscle of whole-body zebrafish. In contrast, (+3)DHA-containing PC was not detected in the brain. These results showed that dietary DHA is initially constructed into PC as a structural component of intestinal cell membranes and gradually migrates into peripheral tissues such as muscle.

Vitamin D deficiency promotes accumulation of bioactive lipids and increased endocannabinoid tone in zebrafish

Vitamin D is well known for its traditional role in bone mineral homeostasis; however, recent evidence suggests that vitamin D also plays a significant role in metabolic control. This study served to investigate putative linkages between vitamin D deficiency (VDD) and metabolic disruption of bioactive lipids by MS imaging. Our approach employed infrared-matrix-assisted laser desorption electrospray ionization MS imaging for lipid metabolite profiling in 6-month-old zebrafish fed either a VDD or a vitamin D-sufficient (VDS) diet. Using a lipidomics pipeline, we found that VDD zebrafish had a greater abundance of bioactive lipids (N-acyls, endocannabinoids [ECs], diacylglycerols/triacylglycerols, bile acids/bile alcohols, and vitamin D derivatives) suggestive of increased EC tone compared with VDS zebrafish. Tandem MS was performed on several differentially expressed metabolites with sufficient ion abundances to aid in structural elucidation and provide additional support for MS annotations. To confirm activation of the EC pathways, we subsequently examined expression of genes involved in EC biosynthesis, metabolism, and receptor signaling in adipose tissue and liver from VDD and VDS zebrafish. Gene expression changes were congruent with increased EC tone, with VDD zebrafish demonstrating increased synthesis and metabolism of anandamide compared with VDS zebrafish. Taken together, our data suggest that VDD may promote accumulation of bioactive lipids and increased EC tone in zebrafish.

Three-Dimensional Imaging of Whole-Body Zebrafish Revealed Lipid Disorders Associated with Niemann-Pick Disease Type C1

Imaging of lipids of whole-body specimens in two-dimensional (2D) analysis provides a global picture of the lipid changes in lipid-disturbed diseases, enabling a better understanding of lipid functions and lipid-modulation processes in different organs. However, 2D imaging of a single cross section can hardly characterize the whole-body lipid alterations. In this work, a three-dimensional matrix-assisted laser desorption/ionization mass spectrometry imaging (3D MALDI-MSI) approach was developed for analysis of whole-body zebrafish, for the first time, and applied to identify altered lipids and map their spatial distributions by using a zebrafish model of Niemann-Pick disease type C1 (NPC1), a neurovisceral lipid storage disorder causing both neurodegenerative disorder and visceral organ damage. The constructed 3D fish model provided comprehensive information on the 3D distribution of lipids of interest and allowed direct correlations between these lipids and organs of the fish. Obtained results revealed that several sphingolipids and phospholipids showed significant alterations and exhibited different localization patterns in various organs such as the brain, spinal cord, intestines, and liver-spleen region in the npc1 gene mutant fish compared to those of the wild type. The whole-body 3D MALDI-MSI approach revealed unique lipid signatures for different NPC1-affected organs, which might offer insights into the link between the impaired lipid storage and subsequent clinical symptoms, such as neurodegeneration and hepatosplenomegaly.

Chemical Imaging of Retinal Pigment Epithelium in Frozen Sections of Zebrafish Larvae Using ToF-SIMS

Variants of the SLC24A5 gene, which encodes a putative potassium-dependent sodium-calcium exchanger (NCKX5) that most likely resides in the melanosome or its precursor, affect pigmentation in both humans and zebrafish (Danio rerio). This finding suggests that genetic variations influencing human skin pigmentation alter melanosome biogenesis via ionic changes. Gaining an understanding of how changes in the ionic environment of organelles impact melanosome morphogenesis and pigmentation will require a spatially resolved way to characterize the chemical environment of melanosomes in pigmented tissue such as retinal pigment epithelium (RPE). The imaging mass spectrometry technique most suited for this type of cell and tissue analysis is time-of-flight secondary ion mass spectrometry (ToF-SIMS) because it is able to detect many biochemical species with high sensitivity and with submicron spatial resolution. Here, we describe chemical imaging of the RPE in frozen-hydrated sections of larval zebrafish using cryo-ToF-SIMS. To facilitate the data interpretation, positive and negative polarity ToF-SIMS image data were transformed into a single hyperspectral data set and analyzed using principal component analysis. The combination of a novel protocol and the use of multivariate data analysis allowed us to discover new marker ions that are attributable to leucodopachrome, a metabolite specific to the biosynthesis of eumelanin. The described methodology may be adapted for the investigation of other classes of molecules in frozen tissues from zebrafish and other organisms.

Three-dimensional (3D) imaging of lipids in skin tissues with infrared matrix-assisted laser desorption electrospray ionization (MALDESI) mass spectrometry

Three-dimensional (3D) mass spectrometry imaging (MSI) has become a growing frontier as it has the potential to provide a 3D representation of analytes in a label-free, untargeted, and chemically specific manner. The most common 3D MSI is accomplished by the reconstruction of 2D MSI from serial cryosections; however, this presents significant challenges in image alignment and registration. An alternative method would be to sequentially image a sample by consecutive ablation events to create a 3D image. In this study, we describe the use of infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) in ablation-based 3D MSI for analyses of lipids within fresh frozen skin tissue. Depth resolution using different laser energy levels was explored with a confocal laser scanning microscope to establish the imaging parameters for skin. The lowest and highest laser energy level resulted in a depth resolution of 7 μm and 18 μm, respectively. A total of 594 lipids were putatively detected and detailed lipid profiles across different skin layers were revealed in a 56-layer 3D imaging experiment. Correlated with histological information, the skin structure was characterized with differential lipid distributions with a lateral resolution of 50 μm and a z resolution of 7 μm.

Lipidomic profiling of single mammalian cells by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)

To better understand cell-to-cell heterogeneity, advanced analytical tools are in a growing demand for elucidating chemical compositions of each cell within a population. However, the progress of single-cell chemical analysis has been restrained by the limitations of small cell volumes and minute cellular concentrations. Here, we present a rapid and sensitive method for investigating the lipid profiles of isolated single cells using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry (IR-MALDESI-MS). In this work, HeLa cells were dispersed onto a glass slide, and the cellular contents were ionized by IR-MALDESI and measured using a Q-Exactive HF-X mass spectrometer. Importantly, this approach does not require extraction and/or enrichment of analytes prior to MS analysis. Using this approach, 45 distinct lipid species, predominantly phospholipids, were detected and putatively annotated from the single HeLa cells. The proof-of-concept study demonstrates the feasibility and efficacy of IR-MALDESI-MS for rapid lipidomic profiling of single cells, which provides an important basis for future work on differentiation between normal and diseased cells at various developmental states, which can offer new insights into cellular metabolic pathways and pathological processes. Although not yet accomplished, we believe this approach can be readily used as an assessment tool to compare the number of identified species during source evolution and method optimization (intra-laboratory), and also disclose the complementary nature of different direct analytical approaches for the coverage of different types of endogenous analytes (inter-laboratory).Graphical abstract.