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.

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.

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.

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

Previous studies have shown that the use of a 20 keV water cluster beam as a primary beam for the analysis of organic and bio-organic systems resulted in a 10-100 times increase in positive molecular ion yield for a range of typical analytes compared to C60 and argon cluster beams. This resulted in increased sensitivity to important lipid molecules in the bioimaging of rat brain. Building on these studies, the present work compares 40 and 70 keV water cluster beams with cluster beams composed of pure argon, argon and 10%CO2, and pure CO2. First, as previously, we show that for E/nucleon about 0.3 eV/nucleon water and nonwater containing cluster beams generate very similar ion yields, but below this value, the water beams yields of BOTH negative and positive "molecular" ions increase, in many cases reaching a maximum in the <0.2 region, with yield increases of ∼10-100. Ion fragment yields in general decrease quite dramatically in this region. Second, for water cluster beams at a constant E/nucleon, "molecular" ion yield increases with beam energy and hence cluster size due to increased sputter yield (ionization probability is constant). Third, as a consequence of the increased ion yield and the improved focusability using high-energy cluster beams, imaging in the 1 µm spatial resolution region is demonstrated on HeLa cells and rat brain tissue, monitoring molecules that were previously difficult to detect with other primary beams. Finally, the suggestion that the secondary ion emission zone has quasi-aqueous character seems to be sustained.

Secondary-Ion Mass Spectrometry Images Cardiolipins and Phosphatidylethanolamines at the Subcellular Level.

Millions of diverse molecules constituting the lipidome act as important signals within cells. Of these, cardiolipin (CL) and phosphatidylethanolamine (PE) participate in apoptosis and ferroptosis, respectively. Their subcellular distribution is largely unknown. Imaging mass spectrometry is capable of deciphering the spatial distribution of multiple lipids at subcellular levels. Here we report the development of a unique 70 keV gas-cluster ion beam that consists of (CO2 )n+ (n>10 000) projectiles. Coupled with direct current beam buncher-time-of-flight secondary-ion mass spectrometry, it is optimized for sensitivity towards high-mass species (up to m/z 3000) at high spatial resolution (1 µm). In combination with immunohistochemistry, phospholipids, including PE and CL, have been assessed in subcellular compartments of mouse hippocampal neuronal cells and rat brain tissue.

Subcellular Chemical Imaging of Antibiotics in Single Bacteria Using C60-Secondary Ion Mass Spectrometry.

The inherent difficulty of discovering new and effective antibacterials and the rapid development of resistance particularly in Gram-negative bacteria, illustrates the urgent need for new methods that enable rational drug design. Here we report the development of 3D imaging cluster Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) as a label-free approach to chemically map small molecules in aggregated and single Escherichia coli cells, with ∼300 nm spatial resolution and high chemical sensitivity. The feasibility of quantitative analysis was explored, and a nonlinear relationship between treatment dose and signal for tetracycline and ampicillin, two clinically used antibacterials, was observed. The methodology was further validated by the observation of reduction in tetracycline accumulation in an E. coli strain expressing the tetracycline-specific efflux pump (TetA) compared to the isogenic control. This study serves as a proof-of-concept for a new strategy for chemical imaging at the nanoscale and has the potential to aid discovery of new antibacterials.

Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry High-Resolution Imaging of Cardiolipin Speciation in the Brain: Identification of Molecular Losses after Traumatic Injury.

Gas cluster ion beam-secondary ion mass spectrometry (GCIB-SIMS) has shown the full potential of mapping intact lipids in biological systems with better than 10 µm lateral resolution. This study investigated further the capability of GCIB-SIMS in imaging high-mass signals from intact cardiolipin (CL) and gangliosides in normal brain and the effect of a controlled cortical impact model (CCI) of traumatic brain injury (TBI) on their distribution. A combination of enzymatic and chemical treatments was employed to suppress the signals from the most abundant phospholipids (phosphatidylcholine (PC) and phosphatidylethanolamine (PE)) and enhance the signals from the low-abundance CLs and gangliosides to allow their GCIB-SIMS detection at 8 and 16 µm spatial resolution. Brain CLs have not been observed previously using other contemporary imaging mass spectrometry techniques at better than 50 µm spatial resolution. High-resolution images of naive and injured brain tissue facilitated the comparison of CL species across three multicell layers in the CA1, CA3, and DG regions of the hippocampus. GCIB-SIMS also reliably mapped losses of oxidizable polyunsaturated CL species (but not the oxidation-resistant saturated and monounsaturated gangliosides) to regions including the CA1 and CA3 of the hippocampus after CCI. This work extends the detection range for SIMS measurements of intact lipids to above m/z 2000, bridging the mass range gap compared with MALDI. Further advances in high-resolution SIMS of CLs, with the potential for single cell or supra-cellular imaging, will be essential for the understanding of CL's functional and structural organization in normal and injured brain.

Label-free visualization of nilotinib-functionalized gold nanoparticles within single mammalian cells by C60- SIMS imaging.

Obtaining a comprehensive grasp of the behavior and interaction of pharmaceutical compounds within single cells provides some of the fundamental details necessary for more effective drug development. In particular, the changes ensuing in the carrier, drug, and host environment in targeted drug therapy applications must be explored in greater detail, as these are still not well understood. Here, nilotinib-functionalized gold nanoparticles are examined within single mammalian cells with use of imaging cluster secondary ion mass spectrometry in a model study designed to enhance our understanding of what occurs to these particles once that have been internalized. Nilotinib, several types of gold nanoparticles, and the functionalized combination of the two were surveyed and successfully imaged within single cells to determine uptake and performance. Both nilotinib and the gold particle are able to be distinguished and visualized in the functionalized nanoparticle assembly within the cell. These compounds, while both internalized, do not appear to be present in the same pixels of the chemical image, indicating possible cleavage of nilotinib from the particle after cell uptake. The method provided in this work is a direct measurement of uptake and subcellular distribution of an active drug and its carrier within a framework. The results obtained from this study have the potential to be applied to future studies to provide more effective and specific cellular delivery of a relevant pharmaceutical compound.

Cluster secondary ion mass spectrometry imaging of interfacial reactions of TiO2 microspheres embedded in ionic liquids.

RATIONALE: Our goal is to develop protocols for the elucidation of the identity and structure of reaction products embedded in a reaction medium. Results should find significance in a variety of disciplines ranging from the study of biological cells and tissues, to the steps associated with the functionalization of nanoparticles. METHODS: We utilize cluster secondary ion mass spectrometry (cluster-SIMS) to acquire three-dimensional (3D) information about 5-30 µm TiO2 microspheres imbedded into an ionic liquid. The method allows molecular depth profiling with submicron spatial resolution and depth profiling with a resolution of several tens of nanometers. The ionic liquid matrix enshrouds the spheres, allowing them to be introduced into the vacuum environment of the mass spectrometer. RESULTS: The results provide 3D chemical information about these microspheres as they are synthesized by interfacial sol-gel reactions. We show that with 40 keV C60 (+) , it is possible to erode through the reaction medium and map the distribution of those embedded TiO2 microspheres. Moreover, we demonstrate that it is possible to monitor surface modification of the particles and, via ion beam drilling, elucidate their internal structure. CONCLUSIONS: Using cluster-SIMS imaging, we are able to elucidate the identity and structure of reaction products embedded in a reaction medium, a problem of long-standing interest for materials characterization. With this strategy, we have provided a new approach that may be especially useful for the characterization of biological tissue and cells within the vacuum confines of the mass spectrometer. Copyright © 2015 John Wiley & Sons, Ltd.

Imaging mass spectrometry on the nanoscale with cluster ion beams.

Imaging with cluster secondary ion mass spectrometry (SIMS) is reaching a mature level of development. Using a variety of molecular ion projectiles to stimulate desorption, 3-dimensional imaging with the selectivity of mass spectrometry can now be achieved with submicrometer spatial resolution and <10 nm depth resolution. In this Perspective, stock is taken regarding what it will require to routinely achieve these remarkable properties. Issues include the chemical nature of the projectile, topography formation, differential erosion rates, and perhaps most importantly, ionization efficiency. Shortcomings of existing instrumentation are also noted. Speculation about how to successfully resolve these issues is a key part of the discussion.

Near infrared (NIR) strong field ionization and imaging of C60 sputtered molecules: overcoming matrix effects and improving sensitivity.

Strong field ionization (SFI) was applied for the secondary neutral mass spectrometry (SNMS) of patterned rubrene films, mouse brain sections, and Botryococcus braunii algal cell colonies. Molecular ions of rubrene, cholesterol, C31 diene/triene, and three wax monoesters were detected, representing some of the largest organic molecules ever ionized intact by a laser post-ionization experiment. In rubrene, the SFI SNMS molecular ion signal was ~4 times higher than in the corresponding secondary-ion mass spectroscopy (SIMS) analysis. In the biological samples, the achieved signal improvements varied among molecules and sampling locations, with SFI SNMS, in some cases, revealing analytes made completely undetectable by the influence of matrix effects in SIMS.

A mixed cluster ion beam to enhance the ionization efficiency in molecular secondary ion mass spectrometry.

RATIONALE: Chemical modification of a rare gas cluster ion beam (GCIB) to increase the intensity of desorbed molecular ions in secondary ion mass spectrometry experiments relative to the pure Ar cluster. METHODS: Doping of the GCIB by mixing small concentration levels (1-3% relative partial pressure) of CH4 into the Ar gas driving the cluster ion source. RESULTS: Mass spectra measured on a trehalose film using the doped GCIB exhibit enhanced molecular ion signals. From depth profiling experiments, the results are shown to arise from an increase in the ionization efficiency of the sputtered molecules rather than a change in the sputtering yield of neutral species. CONCLUSIONS: Tuning of the chemistry of mixed clusters is suggested as a general approach to enhancing the ionization probability of sputtered molecules.

Formation of neutral In(m)C(n) clusters under C60 ion bombardment of indium.

The formation of neutral gas phase indium carbide clusters under C60(+) ion bombardment of solid indium was investigated using laser based postionization prior to mass spectrometric detection. Two different postionization methods were used and shown to provide saturated photoionization efficiency, thereby delivering nearly the same information about the composition of the sputtered material. The resulting size distributions of neutral In(m)C(n) clusters are compared with those of the corresponding cationic secondary cluster ions and discussed in terms of calculated cluster properties. Investigating the dependence on C60(+) ion fluence, we demonstrate that clusters containing only one carbon atom are formed in single impact events, whereas the formation of more carbon-rich clusters results from carbon accumulation at the bombarded surface.

Multimodal mass spectrometry imaging identifies cell-type-specific metabolic and lipidomic variation in the mammalian liver.

Spatial single-cell omics provides a readout of biochemical processes. It is challenging to capture the transient lipidome/metabolome from cells in a native tissue environment. We employed water gas cluster ion beam secondary ion mass spectrometry imaging ([H2O]n>28K-GCIB-SIMS) at ≤3 µm resolution using a cryogenic imaging workflow. This allowed multiple biomolecular imaging modes on the near-native-state liver at single-cell resolution. Our workflow utilizes desorption electrospray ionization (DESI) to build a reference map of metabolic heterogeneity and zonation across liver functional units at tissue level. Cryogenic dual-SIMS integrated metabolomics, lipidomics, and proteomics in the same liver lobules at single-cell level, characterizing the cellular landscape and metabolic states in different cell types. Lipids and metabolites classified liver metabolic zones, cell types and subtypes, highlighting the power of spatial multi-omics at high spatial resolution for understanding celluar and biomolecular organizations in the mammalian liver.

Single-cell lipidomics: characterizing and imaging lipids on the surface of individual Aplysia californica neurons with cluster secondary ion mass spectrometry.

Neurons isolated from Aplysia californica , an organism with a well-defined neural network, were imaged with secondary ion mass spectrometry, C(60)-SIMS. A major lipid component of the neuronal membrane was identified as 1-hexadecyl-2-octadecenoyl-sn-glycero-3-phosphocholine [PC(16:0e/18:1)] using tandem mass spectrometry (MS/MS). The assignment was made directly off the sample surface using a C(60)-QSTAR instrument, a prototype instrument that combines an ion source with a commercial electrospray ionization/matrix-assisted laser desorption ionization (ESI/MALDI) mass spectrometer. Normal phase liquid chromatography mass spectrometry (NP-LC-MS) was used to confirm the assignment. Cholesterol and vitamin E were also identified with in situ tandem MS analyses that were compared to reference spectra obtained from purified compounds. In order to improve sensitivity on the single-cell level, the tandem MS spectrum of vitamin E reference material was used to extract and compile all the vitamin E related peaks from the cell image. The mass spectrometry images reveal heterogeneous distributions of intact lipid species, PC(16:0e/18:1), vitamin E, and cholesterol on the surface of a single neuron. The ability to detect these molecules and determine their relative distribution on the single-cell level shows that the C(60)-QSTAR is a potential platform for studying important biochemical processes, such as neuron degeneration.

Depth profiling of metal overlayers on organic substrates with cluster SIMS.

Molecular depth profiling of organic thin films by erosion with energetic cluster ion beams is a unique aspect of secondary ion mass spectrometry (SIMS) experiments. Although depth profiles of complex multilayer organic structures can be acquired with little damage accumulation and with depth resolution of <10 nm using either C60(+) or Arx(+) with x = 500-5000, hybrid materials consisting of both organic and inorganic layers often yield poor results. To unravel the factors that lead to this difficulty, we developed a model system composed of a thin gold layer of 1.4 to 3.5 nm deposited either on top of or sandwiched within a cholesterol thin film matrix which is several hundred nanometers thick. For these systems, the results show that by erosion with a 40 keV C60(+) beam, reliable depth profiles can always be acquired as indicated by the presence of a steady state molecular ion signal. During the erosion process, however, gold atoms from the gold overlayer are implanted into the cholesterol matrix beneath it, resulting in a reduced sputter yield, an increase in the amount of cholesterol fragmentation and an increase in the thickness of the cluster ion-induced altered layer. The results also show that the effects of the metal film on the organic substrate are independent of the gold film thickness once the film thickness exceeds 1.4 nm. In general, this model study provides mechanistic insight into the depth profiling of heterogeneous thin film structures and offers a possible path for improving the quality of the depth profiles by employing low energy atomic ion sputtering in the region of the metal layer.

Lipid imaging with time-of-flight secondary ion mass spectrometry (ToF-SIMS).

Fundamental advances in secondary ion mass spectrometry (SIMS) now allow for the examination and characterization of lipids directly from biological materials. The successful application of SIMS-based imaging in the investigation of lipids directly from tissue and cells are demonstrated. Common complications and technical pitfalls are discussed. In this review, we examine the use of cluster ion sources and cryogenically compatible sample handling for improved ion yields and to expand the application potential of SIMS. Methodological improvements, including pre-treating the sample to improve ion yields and protocol development for 3-dimensional analyses (i.e. molecular depth profiling), are also included in this discussion. New high performance SIMS instruments showcasing the most advanced instrumental developments, including tandem MS capabilities and continuous ion beam compatibility, are described and the future direction for SIMS in lipid imaging is evaluated.

Cluster secondary ion mass spectrometry and the temperature dependence of molecular depth profiles.

The quality of molecular depth profiles created by erosion of organic materials by cluster ion beams exhibits a strong dependence upon temperature. To elucidate the fundamental nature of this dependence, we employ the Irganox 3114/1010 organic delta-layer reference material as a model system. This delta-layer system is interrogated using a 40 keV C(60)(+) primary ion beam. Parameters associated with the depth profile such as depth resolution, uniformity of sputtering yield, and topography are evaluated between 90 and 300 K using a unique wedge-crater beveling strategy that allows these parameters to be determined as a function of erosion depth from atomic force microscope (AFM) measurements. The results show that the erosion rate calibration performed using the known Δ-layer depth in connection with the fluence needed to reach the peak of the corresponding secondary ion mass spectrometry (SIMS) signal response is misleading. Moreover, we show that the degradation of depth resolution is linked to a decrease of the average erosion rate and the buildup of surface topography in a thermally activated manner. This underlying process starts to influence the depth profile above a threshold temperature between 210 and 250 K for the system studied here. Below that threshold, the process is inhibited and steady-state conditions are reached with constant erosion rate, depth resolution, and molecular secondary ion signals from both the matrix and the Δ-layers. In particular, the results indicate that further reduction of the temperature below 90 K does not lead to further improvement of the depth profile. Above the threshold, the process becomes stronger at higher temperature, leading to an immediate decrease of the molecular secondary ion signals. This signal decay is most pronounced for the highest m/z ions but is less for the smaller m/z ions, indicating a shift toward small fragments by accumulation of chemical damage. The erosion rate decay and surface roughness buildup, on the other hand, exhibit a rather sudden delayed onset after erosion of about 150 nm, indicating that a certain damage level must be reached in order to influence the erosion dynamics. Only after that onset does the depth resolution become compromised, indicating that the temperature reduction does not significantly influence parameters like ion-beam mixing or the altered-layer thickness. In general, the wedge-crater beveling protocol is shown to provide a powerful basis for increased understanding of the fundamental factors that affect the important parameters associated with molecular depth profiling.

Argon cluster ion beams for organic depth profiling: results from a VAMAS interlaboratory study.

The depth profiling of organic materials with argon cluster ion sputtering has recently become widely available with several manufacturers of surface analytical instrumentation producing sources suitable for surface analysis. In this work, we assess the performance of argon cluster sources in an interlaboratory study under the auspices of VAMAS (Versailles Project on Advanced Materials and Standards). The results are compared to a previous study that focused on C(60)(q+) cluster sources using similar reference materials. Four laboratories participated using time-of-flight secondary-ion mass spectrometry for analysis, three of them using argon cluster sputtering sources and one using a C(60)(+) cluster source. The samples used for the study were organic multilayer reference materials consisting of a ∼400-nm-thick Irganox 1010 matrix with ∼1 nm marker layers of Irganox 3114 at depths of ∼50, 100, 200, and 300 nm. In accordance with a previous report, argon cluster sputtering is shown to provide effectively constant sputtering yields through these reference materials. The work additionally demonstrates that molecular secondary ions may be used to monitor the depth profile and depth resolutions approaching a full width at half maximum (fwhm) of 5 nm can be achieved. The participants employed energies of 2.5 and 5 keV for the argon clusters, and both the sputtering yields and depth resolutions are similar to those extrapolated from C(60)(+) cluster sputtering data. In contrast to C(60)(+) cluster sputtering, however, a negligible variation in sputtering yield with depth was observed and the repeatability of the sputtering yields obtained by two participants was better than 1%. We observe that, with argon cluster sputtering, the position of the marker layers may change by up to 3 nm, depending on which secondary ion is used to monitor the material in these layers, which is an effect not previously visible with C(60)(+) cluster sputtering. We also note that electron irradiation, used for charge compensation, can induce molecular damage to areas of the reference samples well beyond the analyzed region that significantly affects molecular secondary-ion intensities in the initial stages of a depth profile in these materials.