Single-Cell On-Probe Derivatization-Noncontact Nanocarbon Fiber Ionization: Unraveling Cellular Heterogeneity of Fatty Alcohol and Sterol Metabolites

Graphene Oxide/TiO2 Nanocomposite-Assisted Two-Step Ambient Liquid Extraction Mass Spectrometry Imaging for Comprehensively Enhancing Lipid Coverage in Spatial Lipidomics

It is challenging to have comprehensive spatial lipidomic analysis by mass spectrometry imaging (MSI) due to the strong ion suppression and peak interference from high-abundance polar lipids to low-abundance poorly ionizable lipids. In this work, we proposed a new MSI approach via ambient liquid extraction techniques assisted by a new mixed-mode adsorptive material, graphene oxide (GO)/TiO2 nanocomposite. The material combines chelation affinity from TiO2 and hydrophobic interaction from GO. By finely tuning the adsorption solvent as 9% H2O-6% ammonia-85% methanol/acetonitrile (1:1, v/v), simultaneous enrichment of poorly ionizable glycolipids and glycerides with separation from high-abundance phospholipids was achieved on the material. In 10 mg/mL glucose-6% ammonia-94% methanol, all of the adsorbed glycolipids and glycerides could be desorbed from the material efficiently. Then, GO/TiO2 nanocomposite was coated onto the sample plate for thaw-mounting the tissue section, and ambient liquid extraction probe was used to have pixel-to-pixel desorption of the lipids on the section in two steps with the above two solvents. The results show that most of the phospholipids were imaged in the first step MSI, and glycolipids and glycerides were selectively imaged in the second step MSI, largely reducing ion suppression and peak interference. Compared with direct ambient liquid extraction MSI, much more glycolipid species (22 vs 9), glyceride species (10 vs 5), phosphatidylethanolamines (11 vs 3), and lysophospholipids (12 vs 2) were detected via GO/TiO2 nanocomposite-assisted two-step MSI. The ion images of most lipids show much higher signals and imaging quality with the new method than with the traditional method. Thus, comprehensive enhancement of lipid coverage in MSI by on-tissue separation was achieved here for the first time, providing more information about spatial lipidomics studies.

Photoinduced Online Enrichment-Deglycosylation of Glycolipids for Enhancing Lipid Coverage and Identification in Single-Cell Mass Spectrometry

Single-cell lipidomics provides important information for molecular mechanisms of living processes and diseases at the individual cell level. However, single-cell lipidomic mass spectrometry (MS) techniques suffer from low lipid coverage and incomplete structural elucidation, especially for poorly ionizable glycosphingolipids (GSLs). Herein, a photoinduced enrichment-deglycosylation method of GSLs was developed and introduced into an ambient liquid extraction MS system for enhancing detection coverage and identification accuracy of GSLs in single-cell MS. GSL standards were selectively adsorbed on TiO2 in ammonia-added protic solvents. Under UV irradiation, the adsorbed GSLs would lose one hexosyl group (deglycosylation), and the products (>70% conversion efficiency) were desorbed from TiO2. By coating porous TiO2 into the capillary of the ambient liquid extraction MS system, online adsorption of GSLs and their separation from high-abundance phospholipids were achieved, largely reducing ion suppression. By UV irradiation, captured GSLs were rapidly deglycosylated and photodesorbed from TiO2 coating without solvent switching, resulting in 6-fold enrichment. With the new method, the detection coverage of GSLs was enhanced 9-fold without losing other lipidomes, compared with the conventional method. Moreover, deglycosylated GSLs from photodesorption had more MS/MS fragments than intact GSLs, facilitating detailed fatty acyl and sphingosine chain elucidation. Seven deglycosylated GSL peaks were identified with the confirmed hydroxyl group location in the fatty acyl chain, while only 1 was identified for intact GSL. The new method was applied to the single-cell lipidomics study of two types of nerve cells. Totally, 31 lipids including 11 GSLs were identified in a single cell, and 5 hexosylceramides were found significantly altered after neuron injury.

Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective

Recent advancements in single-cell (sc) resolution analyses, particularly in sc transcriptomics and sc proteomics, have revolutionized our ability to probe and understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level of information otherwise unattainable by transcriptomics or proteomics by shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical in health and disease, impacts developmental outcomes, disease progression, and treatment responses. However, dedicated approaches probing the sc metabolome have not reached the maturity of other sc omics technologies. Over the past decade, innovations in sc metabolomics have addressed some of the practical limitations, including cell isolation, signal sensitivity, and throughput. To fully exploit their potential in biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating sc metabolomics with orthogonal sc techniques will be required to validate relevant results and gain systems-level understanding. This perspective offers a broad-stroke overview of recent mass spectrometry (MS)-based sc metabolomics advancements, focusing on ongoing challenges from a biologist's viewpoint, aimed at addressing pertinent and innovative biological questions. Additionally, we emphasize the use of orthogonal approaches and showcase biological systems that these sophisticated methodologies are apt to explore.

Polarization of Macrophages in Tumor Microenvironment Using High-Throughput Single-Cell Metabolomics

Macrophages consist of a heterogeneous population of functionally distinct cells that participate in many physiological and pathological processes. They exhibit prominent plasticity by changing their different functional phenotypes represented by proinflammatory (M1) and anti-inflammatory (M2) in response to different environmental stimuli. Emerging evidence illustrates the importance of intracellular metabolic pathways in macrophage polarizations and functions. In the tumor microenvironment (TME), macrophages tend to M2 polarization, which promotes tumor growth and leads to adverse physiological effects. Due to the lack of highly specific antigens in M1 and M2 macrophages, significant challenges present in isolating these subtypes from clinical samples or in vitro coculture models of tumor-immune cells. In reverse, the single-cell technique provides the possibility to investigate the factors influencing macrophage polarization in the TME. In this research, we employed inertial microfluidic chip-mass spectrometry (IMC-MS) to conduct single-cell metabolomics analysis of macrophages polarized into the two major phenotypes, respectively, and 213 metabolites were identified in total. Subsequently, differential metabolites between macrophage phenotypes were analyzed using volcano plots and binary logistic regression models. Glutamine was pinpointed as a key metabolite for the M1 and M2 phenotypes. Experimental results from both monoculture and coculture cell models demonstrated that M1 polarization is more reliant on the presence of glutamine in the culture environment than M2 polarization. Glutamine deficiency resulted in failed M1 polarization, while its absence had a less pronounced effect on M2 polarization. Replenishing an appropriate amount of glutamine during the intermediate stages of coculture models significantly enhanced the proportion of M1 polarization and suppressed the growth of tumor cells. This research elucidated glutamine as a key factor influencing macrophage polarization in the TME via single-cell metabolomics based on IMC-MS, offering promising insights and targets for tumor therapies.

Carbon fiber-sampling combined flame ionization mass spectrometry for direct analysis of drugs in oral fluid

Drug-impaired driving poses a significant risk of collisions and other hazardous accidents, emphasizing the urgent need for simple and rapid roadside detection methods. Oral fluid, as an easily collectible and non-invasive test material, has gained widespread use in detecting drug-impaired driving. In this study, we have devised a method for direct sampling using a carbon fiber bundle combined with flame ionization mass spectrometry. The essence of this method lies in the synergy between the adsorption properties of carbon fiber and the plasma characteristics of the flame. Leveraging the strong adsorption capabilities of the carbon fiber bundle allows for the use of a minimal sample size (<100 μL) during sampling, presenting a distinct advantage in the roadside inspection and sampling process. Throughout the flame ionization process, proteins and salts within the oral fluid matrix adhere well to the carbon fiber bundle, while small molecule targets can be efficiently desorbed and react with charged species in the flame, leading to ionization. The results demonstrate the successful development of carbon fiber-sampling combined flame ionization mass spectrometry, capable of qualitative and quantitative analysis of drugs in oral fluid without the need for sample pre-treatment. Its quantitative capabilities are sufficient for real sample detection, providing an effective analytical method for the roadside detection of drugs in oral fluids.

Recent advances in entirely hand-held ionization sources for mass spectrometry

Ambient ionization mass spectrometry (AIMS) has been developing explosively since its first debut. The ionization process was hence able to be achieved under atmospheric pressure, facilitating on-site field analysis in a variety of areas, such as clinical diagnosis, metabolic phenotyping, and surface analysis. As part of the ambitious goal of making MS a general device that can be used in everyday life, lots of efforts have been paid to miniaturize the ionization source. This review discusses avant-garde sources that could be entirely hand-held without any accessories. The structure and applications of the devices are described in detail as well. They could be expediently used in real-time and on-site analysis, presenting a great future potential for the routinizing of MS.

Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis

Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.

Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles

Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.

Recent developments in ionization techniques for single-cell mass spectrometry

The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.

Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics

Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.

Chemical tagging mass spectrometry: an approach for single-cell omics

Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.

Single-Cell Lipidomics Using Analytical Flow LC-MS Characterizes the Response to Chemotherapy in Cultured Pancreatic Cancer Cells

In this work, we demonstrate the development and first application of nanocapillary sampling followed by analytical flow liquid chromatography-mass spectrometry for single-cell lipidomics. Around 260 lipids were tentatively identified in a single cell, demonstrating remarkable sensitivity. Human pancreatic ductal adenocarcinoma cells (PANC-1) treated with the chemotherapeutic drug gemcitabine can be distinguished from controls solely on the basis of their single-cell lipid profiles. Notably, the relative abundance of LPC(0:0/16:0) was significantly affected in gemcitabine-treated cells, in agreement with previous work in bulk. This work serves as a proof of concept that live cells can be sampled selectively and then characterized using automated and widely available analytical workflows, providing biologically relevant outputs.

Spatial single cell metabolomics: Current challenges and future developments

Single cell metabolomics is a rapidly advancing field of bio-analytical chemistry which aims to observe cellular biology with the greatest detail possible. Mass spectrometry imaging and selective cell sampling (e.g. using nanocapillaries) are two common approaches within the field. Recent achievements such as observation of cell-cell interactions, lipids determining cell states and rapid phenotypic identification demonstrate the efficacy of these approaches and the momentum of the field. However, single cell metabolomics can only continue with the same impetus if the universal challenges to the field are met, such as the lack of strategies for standardisation and quantification, and lack of specificity/sensitivity. Mass spectrometry imaging and selective cell sampling come with unique advantages and challenges which, in many cases are complementary to each other. We propose here that the challenges specific to each approach could be ameliorated with collaboration between the two communities driving these approaches.

Chloramine-T-Enabled Mass Spectrometric Analysis of C═C Isomers of Unsaturated Fatty Acids and Phosphatidylcholines in Human Thyroids

Specific locations of carbon-carbon double bonds (C═C) in lipids often play an essential role in biological processes, and there has been a booming development in C═C composition analysis by mass spectrometry. However, a universal derivatization and fragmentation pattern for the annotation of C═C positions in lipids is still challenging and attractive. To expand this field in lipidomics, a flexible and convenient N-tosylaziridination method was developed, with high derivatization efficiency, sensitivity, and specificity. The derivatization was very fast (15 s), and C═C numbers as well as locations could be pinpointed specifically in tandem mass spectra. By qualitative and quantitative studies of paratumor and tumor thyroid tissues of human beings, the total content of unsaturated fatty acids was suggested to be increased in tumor tissues, and good correlations in and between lysophosphatidylcholines and phosphatidylcholines were revealed by Spearman analysis. Further studies of C═C isomers showed that n-6/n-3 ratios were closely associated with human thyroid tumorigenesis, and high ratios of n-6/n-3 isomers seemed to suffer a high risk of carcinogenesis. Other isomers were not very representative; however, C═C in n-9/n-7 could also be significant for oncology research. Generally, it is supposed that both total amounts and C═C isomer ratios were related to cancer, and N-tosylaziridine derivatization could provide an alternative strategy for the C═C isomer study of disease models.

Online Quaternized Derivatization Mapping and Glycerides Profiling of Cancer Tissues by Laser Ablation Carbon Fiber Ionization Mass Spectrometry

Mass spectrometry imaging has become a hot research field owing to its ability to reflect the distribution of multiple metabolites in tissue. However, not all kinds of metabolites have great ionization efficiency in mass spectrometry imaging. The mass signals of low polar metabolites like monoglycerides and diglycerides may be seriously suppressed. Many strategies have been proposed to fix the problem, such as on-tissue derivatization and online derivatization. Also, some challenges were encountered when implementing these approaches. Herein, a platform coupled online quaternized derivatization and laser ablation carbon fiber ionization mass spectrometry imaging has been developed. The mass signals of monoglycerides and diglycerides were drastically increased in the platform, and high-quality mass images of these metabolites could be acquired readily. In the platform, metabolites were first desorbed by a laser and then reacted online with a derivatization reagent transmitted by carbon fiber ionization, which also undertook the postionization of derivatization products. Pyridine acted as the main derivatization reagent to target metabolites with hydroxyl groups. Remarkably, the derivatization reaction proceeded rapidly without any catalyst owing to the high energy provided by the laser. The mass images of eight monoglycerides and 21 diglycerides were achieved after applying the platform into human ovarian cancer tissues. Notably, a higher mass intensity of these glycerides was captured in cancerous tissues than in para-cancerous tissues, which might infer aberrations in glyceride metabolisms of cancerous tissues.

Chiral Analysis of Lactate during Direct Contact Coculture by Single-Cell On-Probe Enzymatic Dehydrogenation Derivatization: Unraveling Metabolic Changes Caused by d-Lactate

In vitro noncontact cell-based coculture models are frequently employed to study cell-to-cell communication. However, these models cannot accurately represent the complexity of in vivo signaling. d-Lactate is an unusual metabolite produced and released by cancer cells. The characterization of d-lactate is challenging as it shares the same mass but has much lower amounts compared with l-lactate. Herein, d-α-hydroxy acids were specifically recognized and dehydrogenated by d-α-hydroxy acid dehydrogenase. The dehydrogenation products were rapidly quaternized for enhancement of mass signals. An on-probe enzymatic dehydrogenation-derivatization method was proposed for chiral analysis of α-hydroxy acids at the single-cell level. It is a promising amplification methodology and affords over 3 orders of magnitude signal enhancement. Furthermore, direct contact coculture models were used to precisely mimic the tumor microenvironment and explore the communication between cancer and normal cells. Single-cell mass spectrometry (SCMS) was further applied to easily sample cell extracts and study the differences of the aspects of small molecule metabolism in cocultured cells. On the basis of direct contact coculture SCMS, several differential small molecule metabolites and differences of oxidative stress between cocultured and monocultured normal cells were successfully detected. Additionally, d-lactate was discovered as a valuable differential metabolite with application of the two developed methods. It may account for the cancer-associated metabolic behavior of normal cells. These changes could be relieved after d-lactate metabolism-related drug treatment. This discovery may promote the investigation of d-lactate metabolism, which may provide a novel direction for cancer therapy.

Single cell metabolomics using mass spectrometry: Techniques and data analysis

Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.

Collection and Characterization by Mass Spectrometry of the Neutral Serine Octamer Generated upon Sublimation

Serine forms neutral octameric clusters during sublimation, as demonstrated by electrostatically deflecting thermally ionized serine species from the sublimate, then gently ionizing the remaining neutrals for examination by mass spectrometry (MS). The MS results demonstrate a strong homochiral preference in the neutral octamer (measured after its gentle ionization), while the smaller serine clusters are achiral. In the initial stages of its sublimation, nonracemic solid serine generates a neutral serine monomer as the principal species in the vapor phase, with a significant enantiomeric enrichment relative to the solid. The serine monomer, when the flux is sufficient, assembles into the octamer, which displays a much higher chiral purity than the monomer. The serine octamer is separated from other neutral clusters in the sublimate by a new method based on the different distances that the clusters travel in an inert gas stream before they condense in a cooled collector. The deposited octamer is subsequently dissolved, and the solution is investigated by MS. The spectrum confirms that the collected serine octamer has undergone chiral enrichment relative to the starting solid used in the sublimation. The chiral enrichment observed in going from the serine monomer to octamer can be accommodated using a chemical model, grounded on the homochiral preference of the neutral serine octamer. Using the enantiomeric excess (ee %) of the vapor-phase monomer as the input, the model output matches the experimental octamer ee % when subliming solid serine with various initial ee % values.