Improvement of the Correlative AFM and ToF-SIMS Approach Using an Empirical Sputter Model for 3D Chemical Characterization

Toward Understanding the Subcellular Distributions of Cholesterol and Sphingolipids Using High-Resolution NanoSIMS Imaging

ConspectusCharacterizing the subcellular distributions of biomolecules of interest is a basic inquiry that helps inform on the potential roles of these molecules in biological functions. Presently, the functions of specific lipid species and cholesterol are not well understood, partially because cholesterol and lipid species of interest are difficult to image with high spatial resolution but without perturbing them. Because cholesterol and lipids are relatively small and their distributions are influenced by noncovalent interactions with other biomolecules, functionalizing them with relatively large labels that permit their detection may alter their distributions in membranes and between organelles. This challenge has been surmounted by exploiting rare stable isotopes as labels that may be metabolically incorporated into cholesterol and lipids without altering their chemical compositions, and the Cameca NanoSIMS 50 instrument's ability to image rare stable isotope labels with high spatial resolution. This Account covers the use of secondary ion mass spectrometry (SIMS) performed with a Cameca NanoSIMS 50 instrument for imaging cholesterol and sphingolipids in the membranes of mammalian cells. The NanoSIMS 50 detects monatomic and diatomic secondary ions ejected from the sample to map the elemental and isotopic composition at the surface of the sample with better than 50 nm lateral resolution and 5 nm depth resolution. Much effort has focused on using NanoSIMS imaging of rare isotope-labeled cholesterol and sphingolipids for testing the long-standing hypothesis that cholesterol and sphingolipids colocalize within distinct domains in the plasma membrane. By using a NanoSIMS 50 to image rare isotope-labeled cholesterol and sphingolipids in parallel with affinity-labeled proteins of interest, a hypothesis regarding the colocalization of specific membrane proteins with cholesterol and sphingolipids in distinct plasma membrane domains has been tested. NanoSIMS performed in a depth profiling mode has enabled imaging the intracellular distributions of cholesterol and sphingolipids. Important progress has also been made in developing a computational depth correction strategy for constructing more accurate three-dimensional (3D) NanoSIMS depth profiling images of intracellular component distribution without requiring additional measurements with complementary techniques or signal collection. This Account provides an overview of this exciting progress, focusing on the studies from our laboratory that shifted understanding of plasma membrane organization, and the development of enabling tools for visualizing intracellular lipids.

Review of Recent Advances in Gas-Assisted Focused Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS)

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a powerful chemical characterization technique allowing for the distribution of all material components (including light and heavy elements and molecules) to be analyzed in 3D with nanoscale resolution. Furthermore, the sample's surface can be probed over a wide analytical area range (usually between 1 µm² and 10⁴ µm²) providing insights into local variations in sample composition, as well as giving a general overview of the sample's structure. Finally, as long as the sample's surface is flat and conductive, no additional sample preparation is needed prior to TOF-SIMS measurements. Despite many advantages, TOF-SIMS analysis can be challenging, especially in the case of weakly ionizing elements. Furthermore, mass interference, different component polarity of complex samples, and matrix effect are the main drawbacks of this technique. This implies a strong need for developing new methods, which could help improve TOF-SIMS signal quality and facilitate data interpretation. In this review, we primarily focus on gas-assisted TOF-SIMS, which has proven to have potential for overcoming most of the aforementioned difficulties. In particular, the recently proposed use of XeF₂ during sample bombardment with a Ga⁺ primary ion beam exhibits outstanding properties, which can lead to significant positive secondary ion yield enhancement, separation of mass interference, and inversion of secondary ion charge polarity from negative to positive. The implementation of the presented experimental protocols can be easily achieved by upgrading commonly used focused ion beam/scanning electron microscopes (FIB/SEM) with a high vacuum (HV)-compatible TOF-SIMS detector and a commercial gas injection system (GIS), making it an attractive solution for both academic centers and the industrial sectors.

Depth Correction of 3D NanoSIMS Images Shows Intracellular Lipid and Cholesterol Distributions while Capturing the Effects of Differential Sputter Rate

Knowledge of the distributions of drugs, metabolites, and drug carriers within cells is a prerequisite for the development of effective disease treatments. Intracellular component distribution may be imaged with high sensitivity and spatial resolution by using a NanoSIMS in the depth profiling mode. Depth correction strategies that capture the effects of differential sputtering without requiring additional measurements could enable producing accurate 3D NanoSIMS depth profiling images of intracellular component distributions. Here we describe an approach for depth correcting 3D NanoSIMS depth profiling images of cells that accounts for differential sputter rates. Our approach uses the secondary ion and secondary electron depth profiling images to reconstruct the cell's morphology at every raster plane. These cell morphology reconstructions are used to adjust the z-positions and heights of the voxels in the component-specific 3D NanoSIMS images. We validated this strategy using AFM topography data and reconstructions created from depth profiling images acquired with focused ion beam-secondary electron microscopy. Good agreement was found for the shapes and relative heights of the reconstructed morphologies. Application of this depth correction strategy to 3D NanoSIMS depth profiling images of a metabolically labeled cell better resolved the transport vesicles, organelles, and organellar membranes containing ¹⁸O-cholesterol and ¹⁵N-sphingolipids. Accurate 3D NanoSIMS images of intracellular component distributions may now be produced without requiring correlated analyses with separate instruments or the assumption of a constant sputter rate. This will allow visualization of the subcellular distributions of lipids, metabolites, drugs, and nanoparticles in 3D, information pivotal to understanding and treating disease.

Depth correction of 3D NanoSIMS images using secondary electron pixel intensities

Strategies that do not require additional characterization to be performed on the sample or the collection of additional secondary ion signals are needed to depth correct 3D SIMS images of cells. Here, we develop a depth correction strategy that uses the pixel intensities in the secondary electron images acquired during negative-ion NanoSIMS depth profiling to reconstruct the sample morphology. This morphology reconstruction was then used to depth correct the 3D SIMS images that show the components of interest in the sample. As a proof of concept, we applied this approach to NanoSIMS depth profiling data that show the 15N-enrichment and 18O-enrichment from 15N-sphingolipids and 18O-cholesterol, respectively, within a metabolically labeled Madin-Darby canine kidney cell. Comparison of the cell morphology reconstruction to the secondary electron images collected with the NanoSIMS revealed that the assumption of a constant sputter rate produced small inaccuracies in sample morphology after approximately 0.66 μm of material was sputtered from the cell. Nonetheless, the resulting 3D renderings of the lipid-specific isotope enrichments better matched the shapes and positions of the subcellular compartments that contained 15N-sphingolipids and 18O-cholesterol than the uncorrected 3D SIMS images. This depth correction of the 3D SIMS images also facilitated the detection of spherical cholesterol-rich compartments that were surrounded by membranes containing cholesterol and sphingolipids. Thus, we expect this approach will facilitate identifying the subcellular structures that are enriched with biomolecules of interest in 3D SIMS images while eliminating the need for correlated analyses or additional secondary ion signals for the depth correction of 3D NanoSIMS images.

4D Surface Reconstructions to Study Microscale Structures and Functions in Soil Biogeochemistry

The development of high-resolution microscopy and spectroscopy techniques has allowed the analysis of microscopic 3D objects in fields like nanotechnology and life and soil sciences. Soils have the ability to incorporate and store large amounts of organic carbon. To study this organic matter (OM) sequestration, it is essential to analyze its association with soil minerals at the relevant microaggregate scale. This has been previously studied in 2D. However, 3D surface representations would allow a variable angle and magnification analysis, providing detailed insight on their architecture. Here we illustrate a 4D surface reconstruction workflow able to locate preferential sites for OM deposition with respect to microaggregate topography. We used Helium Ion Microscopy to acquire overlapping Secondary Electron (SE) images to reconstruct the soil topography in 3D. Then we used nanoscale Secondary Ion Mass Spectrometry imaging to chemically differentiate between the OM and mineral constituents forming the microaggregates. This image was projected onto the 3D SE model to create a 4D surface reconstruction. Our results show that organo-mineral associations mainly form at medium curvatures while flat and highly curved surfaces are avoided. This method presents an important step forward to survey the 3D physical structure and chemical composition of microscale biogeochemical systems correlatively.

Conformation in Ultrathin Polymer Brush Coatings Resolved by Infrared Nanoscopy

Polymer brush coatings are effective in preventing blood coagulation or bacterial attachment, but their chain conformation, while vital for this effect, was never characterized in high spatial resolution. Here, we report mid-infrared spectroscopic nanoscopy studies of few-nanometer-thin poly(ethylene oxide) (PEO) films which reveal marked spectral variations along the surface at a length scale smaller than 100 nm and originating only from the physical conformation of the chains. The conformation and average orientation of the polymer chains in the layer is extracted from the spectra with the aid of theoretic modeling, confirming the spontaneous formation of a crystalline phase. This result suggests spectroscopic nanoscopy as a powerful new tool to characterize polymer brush coatings.

Topography Measurements Using High Mass Resolution Time-of-Flight Secondary Ion Mass Spectrometry: Application to Banknotes

An unconventional approach using the time-of-flight secondary ion mass spectrometry (TOF-SIMS) technique to determine the height topography at the microscale is detailed in this work with an application to cotton paper banknotes. The study was conducted by determining the effect of all related factors and parameters on the height measurement by taking the simplest model made from two Post-it sheets. For each sample, the difference in the TOF of the same secondary ion coming from two different heights was successfully attributed to the step height of the studied areas' topography, which was measured using classic methods. The measurement was independent of the orientation of the topography with regard to the primary ion beam and the electron beam azimuth. Moreover, the adjustment of the extraction gap with different layers has no effect on such measurements. However, a range of the analyzer acceptance energy values could be considered to achieve the expected outcomes only if the different analyzers' component energies are also changing accordingly. Heights between 20 and 180 μm were successfully measured using this new method. An added benefit to this method over other height measurement methods is the ability to discern areas with different chemical compositions, which eventually may help aid understanding of the sample in question.

Correlated Materials Characterization via Multimodal Chemical and Functional Imaging

Multimodal chemical imaging simultaneously offers high-resolution chemical and physical information with nanoscale and, in select cases, atomic resolution. By coupling modalities that collect physical and chemical information, we can address scientific problems in biological systems, battery and fuel cell research, catalysis, pharmaceuticals, photovoltaics, medicine, and many others. The combined systems enable the local correlation of material properties with chemical makeup, making fundamental questions of how chemistry and structure drive functionality approachable. In this Review, we present recent progress and offer a perspective for chemical imaging used to characterize a variety of samples by a number of platforms. Specifically, we present cases of infrared and Raman spectroscopies combined with scanning probe microscopy; optical microscopy and mass spectrometry; nonlinear optical microscopy; and, finally, ion, electron, and probe microscopies with mass spectrometry. We also discuss the challenges associated with the use of data originated by the combinatorial hardware, analysis, and machine learning as well as processing tools necessary for the interpretation of multidimensional data acquired from multimodal studies.

Bimodal atomic force microscopy for the characterization of thiolated self-assembled monolayers

Surface coatings are becoming an integral part of materials. In recent years, molecular coatings have found larger acceptance and uses. Among them, self-assembled monolayers (SAMs) are attractive due to their inherent versatility, manufacturability, and scale up ease. Understanding their structure-properties relationships in realistic conditions remains a major challenge. Here we present a methodology based on simultaneous topographical and nanomechanical characterization of SAMs using a commercially available setup for bimodal atomic force microscopy (AFM). It allows for accurate and quantitative measurement of surface elasticity, which is correlated to molecular ordering through topographical imaging. Our results indicate that effective surface elasticity (E*) scales with monolayer formation-time and ligand-length, parameters known to affect ligand ordering. The method developed, is extended to provide localization of the chemical species present in thiolated binary SAMs. Within the systems tested phase separation down to ∼10 nm domains could be observed both in the topography and in the elasticity channel.