Enhanced Ion Yields Using High Energy Water Cluster Beams for Secondary Ion Mass Spectrometry Analysis and Imaging

Reactive Gas Cluster Ion Beams for Enhanced Drug Analysis by Secondary Ion Mass Spectrometry

In this study, we investigate the formation and composition of Gas Cluster Ion Beams (GCIBs) and their application in Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) analysis. We focus on altering the carrier gas composition, leading to the formation of (Ar/CO2)n or (H2O)n GCIBs. Our results demonstrate that the addition of a reactive species (CO2) to water GCIBs significantly enhances the secondary ion yield of small pharmaceutical compounds in the positive ion mode. In negative ion mode, the addition of CO2 resulted in either a positive enhancement or no effect, depending on the sample. However, an excess of CO2 in the carrier gas leads to the formation of carbon dioxide clusters, resulting in reduced yields compared to that of water cluster beams. Cluster size also plays a crucial role in overall yields. In a simple two-drug system, CO2-doped water clusters prove effective in mitigating matrix effects in positive ion mode compared to pure water cluster, while in negative ion mode, this effect is limited. These clusters are also applied to the analysis of drugs in a biological matrix, leading to more quantitative measurements as shown by a better fitting calibration curve. Overall, the doping of water clusters with small amounts of a reactive gas demonstrates promising benefits for higher sensitivity, higher resolution molecular analysis, and imaging using ToF-SIMS. The effectiveness of these reactive cluster beams varies depending on the experimental parameters and sample type.

Visualisation of drug distribution in skin using correlative optical spectroscopy and mass spectrometry imaging

A correlative methodology for label-free chemical imaging of soft tissue has been developed, combining non-linear optical spectroscopies and mass spectrometry to achieve sub-micron spatial resolution and critically improved drug detection sensitivity. The approach was applied to visualise the kinetics of drug reservoir formation within human skin following in vitro topical treatment with a commercial diclofenac gel. Non-destructive optical spectroscopic techniques, namely stimulated Raman scattering, second harmonic generation and two photon fluorescence microscopies, were used to provide chemical and structural contrast. The same tissue sections were subsequently analysed by secondary ion mass spectrometry, which offered higher sensitivity for diclofenac detection throughout the epidermis and dermis. A method was developed to combine the optical and mass spectrometric datasets using image registration techniques. The label-free, high-resolution visualisation of tissue structure coupled with sensitive chemical detection offers a powerful method for drug biodistribution studies in the skin that impact directly on topical pharmaceutical product development.

Advancements in ToF-SIMS imaging for life sciences

In the last 2 decades, Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) has gained significant prominence as a powerful imaging technique in the field of life sciences. This comprehensive review provides an in-depth overview of recent advancements in ToF-SIMS instrument technology and its applications in metabolomics, lipidomics, and single-cell analysis. We highlight the use of ToF-SIMS imaging for studying lipid distribution, composition, and interactions in cells and tissues, and discuss its application in metabolomics, including the analysis of metabolic pathways. Furthermore, we review recent progress in single-cell analysis using ToF-SIMS, focusing on sample preparation techniques, in situ investigation for subcellular distribution of drugs, and interactions between drug molecules and biological targets. The high spatial resolution and potential for multimodal analysis of ToF-SIMS make it a promising tool for unraveling the complex molecular landscape of biological systems. We also discuss future prospects and potential advancements of ToF-SIMS in the research of life sciences, with the expectation of a significant impact in the field.

Recent advances in mass spectrometry imaging of single cells

Mass spectrometry imaging (MSI) is a sensitive, specific, label-free imaging analysis technique that can simultaneously obtain the spatial distribution, relative content, and structural information of hundreds of biomolecules in cells and tissues, such as lipids, small drug molecules, peptides, proteins, and other compounds. The study of molecular mapping of single cells can reveal major scientific issues such as the activity pattern of living organisms, disease pathogenesis, drug-targeted therapy, and cellular heterogeneity. Applying MSI technology to the molecular mapping of single cells can provide new insights and ideas for the study of single-cell metabolomics. This review aims to provide an informative resource for those in the MSI community who are interested in single-cell imaging. Particularly, we discuss advances in imaging schemes and sample preparation, instrumentation improvements, data processing and analysis, and 3D MSI over the past few years that have allowed MSI to emerge as a powerful technique in the molecular imaging of single cells. Also, we highlight some of the most cutting-edge studies in single-cell MSI, demonstrating the future potential of single-cell MSI. Visualizing molecular distribution at the single-cell or even sub-cellular level can provide us with richer cell information, which strongly contributes to advancing research fields such as biomedicine, life sciences, pharmacodynamic testing, and metabolomics. At the end of the review, we summarize the current development of single-cell MSI technology and look into the future of this technology.

Back to the basics of time-of-flight secondary ion mass spectrometry of bio-related samples. I. Instrumentation and data collection

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is used widely throughout industrial and academic research due to the high information content of the chemically specific data it produces. Modern ToF-SIMS instruments can generate high mass resolution data that can be displayed as spectra and images (2D and 3D). This enables determining the distribution of molecules across and into a surface and provides access to information not obtainable from other methods. With this detailed chemical information comes a steep learning curve in how to properly acquire and interpret the data. This Tutorial is aimed at helping ToF-SIMS users to plan for and collect ToF-SIMS data. The second Tutorial in this series will cover how to process, display, and interpret ToF-SIMS data.

Using mass spectrometry imaging to visualize age-related subcellular disruption

Metabolic homeostasis balances the production and consumption of energetic molecules to maintain active, healthy cells. Cellular stress, which disrupts metabolism and leads to the loss of cellular homeostasis, is important in age-related diseases. We focus here on the role of organelle dysfunction in age-related diseases, including the roles of energy deficiencies, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, changes in metabolic flux in aging (e.g., Ca2+ and nicotinamide adenine dinucleotide), and alterations in the endoplasmic reticulum-mitochondria contact sites that regulate the trafficking of metabolites. Tools for single-cell resolution of metabolite pools and metabolic flux in animal models of aging and age-related diseases are urgently needed. High-resolution mass spectrometry imaging (MSI) provides a revolutionary approach for capturing the metabolic states of individual cells and cellular interactions without the dissociation of tissues. mass spectrometry imaging can be a powerful tool to elucidate the role of stress-induced cellular dysfunction in aging.

Gold-Conjugated Nanobodies for Targeted Imaging Using High-Resolution Secondary Ion Mass Spectrometry

Nanoscale imaging with the ability to identify cellular organelles and protein complexes has been a highly challenging subject in the secondary ion mass spectrometry (SIMS) of biological samples. This is because only a few isotopic tags can be used successfully to target specific proteins or organelles. To address this, we generated gold nanoprobes, in which gold nanoparticles are conjugated to nanobodies. The nanoprobes were well suited for specific molecular imaging using NanoSIMS at subcellular resolution. They were demonstrated to be highly selective to different proteins of interest and sufficiently sensitive for SIMS detection. The nanoprobes offer the possibility of correlating the investigation of cellular isotopic turnover to the positions of specific proteins and organelles, thereby enabling an understanding of functional and structural relations that are currently obscure.

Imaging mass spectrometry: a new way to distinguish dermal contact from administration of cocaine, using a single fingerprint

Here we show a new and significant application area for mass spectrometry imaging. The potential for fingerprints to reveal drug use has been widely reported, with potential applications in forensics and workplace drug testing. However, one unsolved issue is the inability to distinguish between drug administration and contamination by contact. Previous work using bulk mass spectrometry analysis has shown that this distinction can only be definitively made if the hands are washed prior to sample collection. Here, we illustrate how three mass spectrometry imaging approaches, desorption electrospray ionisation (DESI), matrix assisted laser desorption ionisation (MALDI) and time of flight secondary ion mass spectrometry (ToF-SIMS) can be used to visualise fingerprints at different pixel sizes, ranging from the whole fingerprint down to the pore structure. We show how each of these magnification scales can be used to distinguish between cocaine use and contact. We also demonstrate the first application of water cluster SIMS to a fingerprint sample, which was the sole method tested here that was capable of detecting excreted drug metabolites in fingerprints, while providing spatial resolution sufficient to resolve individual pore structure. We show that after administration of cocaine, lipids and salts in the fingerprint ridges spatially correlate with the cocaine metabolite, benzoylecgonine. In contrast after contact, we have observed that cocaine and its metabolite show a poor spatial correlation with the flow of the ridges.

Successive High-Resolution (H2O)n-GCIB and C60-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue

The temporo-spatial organization of different cells in the tumor microenvironment (TME) is the key to understanding their complex communication networks and the immune landscape that exists within compromised tissues. Multi-omics profiling of single-interacting cells in the native TME is critical for providing further information regarding the reprograming mechanisms leading to immunosuppression and tumor progression. This requires new technologies for biomolecular profiling of phenotypically heterogeneous cells on the same tissue sample. Here, we developed a new methodology for comprehensive lipidomic and metabolomic profiling of individual cells on frozen-hydrated tissue sections using water gas cluster ion beam secondary ion mass spectrometry ((H2O)n-GCIB-SIMS) (at 1.6 μm beam spot size), followed by profiling cell-type specific lanthanide antibodies on the same tissue section using C60-SIMS (at 1.1 μm beam spot size). We revealed distinct variations of distribution and intensities of >150 key ions (e.g., lipids and important metabolites) in different types of the TME individual cells, such as actively proliferating tumor cells as well as infiltrating immune cells. The demonstrated feasibility of SIMS imaging to integrate the multi-omics profiling in the same tissue section at the single-cell level will lead to new insights into the role of lipid reprogramming and metabolic response in normal regulation or pathogenic discoordination of cell-cell interactions in a variety of tissue microenvironments.

Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H2O)n-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue

Integration of multiomics at the single-cell level allows the unambiguous dissecting of phenotypic heterogeneity at different states such as health, disease, and biomedical response. Imaging mass spectrometry holds the promise of being able to measure multiple types of biomolecules in parallel in the same cell. We have explored the possibility of using water gas cluster ion beam secondary ion mass spectrometry [(H2O)n-GCIB-SIMS] as an analytical tool for multiomics assay. (H2O)n-GCIB has been hailed as an ideal ionization source for biological sampling owing to the enhanced chemical sensitivity and reduced matrix effect. Taking advantage of 1 μm spatial resolution by using a high-energy beam system, we have clearly shown the enhancement of multiple intact biomolecules up to a few hundredfold in single cells. Coupled with the cryogenic sample preparation/measurement, the lipids and metabolites were imaged simultaneously within the cellular region, uncovering the pristine chemistry for integrated omics in the same sample. We have demonstrated that double-charged myelin protein fragments and single-charged multiple lipids and metabolites can be localized in the same cells/tissue with a single acquisition. Our exploration has also been extended to the capability of (H2O)n-GCIB in the generation of multiple charged peptides on protein standards. Frozen hydration combined with (H2O)n-GCIB provides the possibility of universal enhancement for the ionization of multiple bio-molecules, including peptides/proteins which has allowed "omics" to become feasible in the same sample using SIMS.

Direct Mapping of Phospholipid Ferroptotic Death Signals in Cells and Tissues by Gas Cluster Ion Beam Secondary Ion Mass Spectrometry (GCIB-SIMS)

Peroxidized phosphatidylethanolamine (PEox) species have been identified by liquid chromatography mass spectrometry (LC-MS) as predictive biomarkers of ferroptosis, a new program of regulated cell death. However, the presence and subcellular distribution of PEox in specific cell types and tissues have not been directly detected by imaging protocols. By applying gas cluster ion beam secondary ion mass spectrometry (GCIB-SIMS) imaging with a 70 keV (H2 O)n+ (n>28 000) cluster ion beam, we were able to map PEox with 1.2 μm spatial resolution at the single cell/subcellular level in ferroptotic H9c2 cardiomyocytes and cortical/hippocampal neurons after traumatic brain injury. Application of this protocol affords visualization of physiologically relevant levels of very low abundance (20 pmol μmol-1 lipid) peroxidized lipids in subcellular compartments and their accumulation in disease conditions.

(CO2)n+, (H2O)n+, and (H2O)n+ (CO2) gas cluster ion beam secondary ion mass spectrometry: analysis of lipid extracts, cells, and Alzheimer's model mouse brain tissue

This work assesses the potential of new water cluster-based ion beams for improving the capabilities of secondary ion mass spectrometry (SIMS) for in situ lipidomics. The effect of water clusters was compared to carbon dioxide clusters, along with the effect of using pure water clusters compared to mixed water and carbon dioxide clusters. A signal increase was found when using pure water clusters. However, when analyzing cells, a more substantial signal increase was found in positive ion mode when the water clusters also contained carbon dioxide, suggesting that additional reactions are in play. The effects of using a water primary ion beam on a more complex sample were investigated by analyzing brain tissue from an Alzheimer’s disease transgenic mouse model. The results indicate that the ToF-SIMS results are approaching those from MALDI as ToF-SIMS was able to image lyso-phosphocholine (LPC) lipids, a lipid class that for a long time has eluded detection during SIMS analyses. Gangliosides, sulfatides, and cholesterol were also imaged.

Large Molecular Cluster Formation from Liquid Materials and Its Application to ToF-SIMS

Since molecular cluster ion beams are expected to have various chemical effects, they are promising candidates for improving the secondary ion yield of Tof-SIMS. However, in order to clarify the effect and its mechanism, it is necessary to generate molecular cluster ion beams with various chemical properties and systematically examine it. In this study, we have established a method to stably form various molecular cluster ion beams from relatively small amounts of liquid materials for a long time by the bubbling method. Furthermore, we applied the cluster ion beams of water, methanol, methane, and benzene to the primary beam of SIMS and compared the molecular ion yields of aspartic acid. The effect of enhancing the yields of [M+H]+ ion of aspartic acid was found to be the largest for the water cluster and small for the methane and benzene clusters. These results indicate that the chemical effect contributes to the desorption/ionization process of organic molecules by the molecular cluster ion beam.

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

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

Molecular insights into symbiosis-mapping sterols in a marine flatworm-algae-system using high spatial resolution MALDI-2-MS imaging with ion mobility separation

Waminoa sp. acoel flatworms hosting Symbiodiniaceae and the related Amphidinium dinoflagellate algae are an interesting model system for symbiosis in marine environments. While the host provides a microhabitat and safety, the algae power the system by photosynthesis and supply the worm with nutrients. Among these nutrients are sterols, including cholesterol and numerous phytosterols. While it is widely accepted that these compounds are produced by the symbiotic dinoflagellates, their transfer to and fate within the sterol-auxotrophic Waminoa worm host as well as their role in its metabolism are unknown. Here we used matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging combined with laser-induced post-ionization and trapped ion mobility spectrometry (MALDI-2-TIMS-MSI) to map the spatial distribution of over 30 different sterol species in sections of the symbiotic system. The use of laser post-ionization crucially increased ion yields and allowed the recording of images with a pixel size of 5 μm. Trapped ion mobility spectrometry (TIMS) helped with the tentative assignment of over 30 sterol species. Correlation with anatomical features of the worm, revealed by host-derived phospholipid signals, and the location of the dinoflagellates, revealed by chlorophyll a signal, disclosed peculiar differences in the distribution of different sterol species (e.g. of cholesterol versus stigmasterol) within the receiving host. These findings point to sterol species-specific roles in the metabolism of Waminoa beyond a mere source of energy. They also underline the value of the MALDI-2-TIMS-MSI method to future research in the spatially resolved analysis of sterols.

Lipid Diversity in Cells and Tissue Using Imaging SIMS

Lipids are an important class of biomolecules with many roles within cells and tissue. As targets for study, they present several challenges. They are difficult to label, as many labels lack the specificity to the many different lipid species or the labels maybe larger than the lipids themselves, thus severely perturbing the natural chemical environment. Mass spectrometry provides exceptional specificity and is often used to examine lipid extracts from different samples. However, spatial information is lost during extraction. Of the different imaging mass spectrometry methods available, secondary ion mass spectrometry (SIMS) is unique in its ability to analyze very small features, with probe sizes <50 nm available. It also offers high surface sensitivity and 3D imaging capability on a subcellular scale. This article reviews the current capabilities and some remaining challenges associated with imaging the diverse lipids present in cell and tissue samples. We show how the technique has moved beyond show-and-tell, proof-of-principle analysis and is now being used to address real biological challenges. These include imaging the microenvironment of cancer tumors, probing the pathophysiology of traumatic brain injury, or tracking the lipid composition through bacterial membranes.

Optimized Alkali-Metal Cationization in Secondary Ion Mass Spectrometry of Polyethylene Glycol Oligomers with up to m/z 10000: Dependence on Cation Species and Concentration

In secondary ion mass spectrometry (SIMS), the detection of large organic molecules is accomplished using cluster ion bombardment. Ion formation often proceeds via cationization, through the attachment of (alkali) metal ions to the molecule. To study this process, the emission of secondary ions sputtered from polyethylene glycol (PEG) samples with molecular weights (MW) of 1000-10000 was examined. They were mixed with alkali-metal trifluoroacetic acid (X-TFA, where X = Li, Na, K, or Cs) in a wide range of concentrations to investigate the efficiency of cationization for 10 keV Ar₂₀₀₀⁺ cluster irradiation. Typically, cationized molecular ions [M + X]⁺ (with repeat units n of up to ∼250, corresponding roughly to m/z 11000) and some characteristic fragment species were observed in the mass spectra. For all alkali cations, the oligomer intensities increase strongly with the molecular composition ratios X-TFA/PEG in the samples, and values of 5-10 seem to be optimal. With increasing molecular weight, the intensity of oligomer ions relative to the total number of ions decreases; as the latter remains rather constant, this implies that more fragment species are formed. The ion yields (detected ions per primary ions) of cationized [M + Na]⁺ oligomers sputtered from a PEG decrease very strongly with their size n: from 5.2 × 10^-6 at n = 21 (MW ∼ 1000) to 4.5 × 10^-10 at n ∼ 245 (MW ∼ 11000). By contrast, the total yields Y_tot⁺ show only a small variation for these different specimens, from 1.3 × 10^-5 to 3.7 × 10^-5.