Compositional mapping of the surface and interior of mammalian cells at submicrometer resolution

Nanocapillary sampling coupled to liquid chromatography mass spectrometry delivers single cell drug measurement and lipid fingerprints

This work describes the development of a new approach to measure drug levels and lipid fingerprints in single living mammalian cells. Nanocapillary sampling is an approach that enables the selection and isolation of single living cells under microscope observation. Here, live single cell nanocapillary sampling is coupled to liquid chromatography for the first time. This allows molecular species to be separated prior to ionisation and improves measurement precision of drug analytes. The efficiency of transferring analytes from the sampling capillary into a vial was optimised in this work. The analysis was carried out using standard flow liquid chromatography coupled to widely available mass spectrometry instrumentation, highlighting opportunities for widespread adoption. The method was applied to 30 living cells, revealing cell-to-cell heterogeneity in the uptake of different drug molecules. Using this system, we detected 14-158 lipid features per single cell, revealing the association between bedaquiline uptake and lipid fingerprints.

FACS-assisted single-cell lipidome analysis of phosphatidylcholines and sphingomyelins in cells of different lineages

Recent advances in single-cell genomics and transcriptomics technologies have transformed our understanding of cellular heterogeneity in growth, development, ageing, and disease; however, methods for single-cell lipidomics have comparatively lagged behind in development. We have developed a method for the detection and quantification of a wide range of phosphatidylcholine and sphingomyelin species from single cells that combines fluorescence-assisted cell sorting with automated chip-based nanoESI and shotgun lipidomics. We show herein that our method is capable of quantifying more than 50 different phosphatidylcholine and sphingomyelin species from single cells and can easily distinguish between cells of different lineages or cells treated with exogenous fatty acids. Moreover, our method can detect more subtle differences in the lipidome between cell lines of the same cancer type. Our approach can be run in parallel with other single-cell technologies to deliver near-complete, high-throughput multi-omics data on cells with a similar phenotype and has the capacity to significantly advance our current knowledge on cellular heterogeneity.

Applications of multivariate analysis and unsupervised machine learning to ToF-SIMS images of organic, bioorganic, and biological systems

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging offers a powerful, label-free method for exploring organic, bioorganic, and biological systems. The technique is capable of very high spatial resolution, while also producing an enormous amount of information about the chemical and molecular composition of a surface. However, this information is inherently complex, making interpretation and analysis of the vast amount of data produced by a single ToF-SIMS experiment a considerable challenge. Much research over the past few decades has focused on the application and development of multivariate analysis (MVA) and machine learning (ML) techniques that find meaningful patterns and relationships in these datasets. Here, we review the unsupervised algorithms—that is, algorithms that do not require ground truth labels—that have been applied to ToF-SIMS images, as well as other algorithms and approaches that have been used in the broader family of mass spectrometry imaging (MSI) techniques. We first give a nontechnical overview of several commonly used classes of unsupervised algorithms, such as matrix factorization, clustering, and nonlinear dimensionality reduction. We then review the application of unsupervised algorithms to various organic, bioorganic, and biological systems including cells and tissues, organic films, residues and coatings, and spatially structured systems such as polymer microarrays. We then cover several novel algorithms employed for other MSI techniques that have received little attention from ToF-SIMS imaging researchers. We conclude with a brief outline of potential future directions for the application of MVA and ML algorithms to ToF-SIMS images.

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.

Effective processing and evaluation of chemical imaging data with respect to morphological features of the zebrafish embryo

A workflow was developed and implemented in a software tool for the automated combination of spatially resolved laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) data and data on the morphology of the biological tissue. Making use of a recently published biological annotation software, FishImager automatically assigns the biological feature as regions of interest (ROIs) and overlays them with the quantitative LA-ICP-MS data. Furthermore, statistical tools including cluster algorithms can be applied to the elemental intensity data and directly compared with the ROIs. This is effectively visualized in heatmaps. This allows gaining statistical significance on distribution and co-localization patterns. Finally, the biological functions of the assigned ROIs can then be easily linked with elemental distributions. We demonstrate the versatility of FishImager with quantitative LA-ICP-MS data of the zebrafish embryo tissue. The distribution of natural elements and xenobiotics is analyzed and discussed. With the help of FishImager, it was possible to identify compartments affected by toxicity effects or biological mechanisms to eliminate the xenobiotic. The presented workflow can be used for clinical and ecotoxicological testing, for example. Ultimately, it is a tool to simplify and reproduce interpretations of imaging LA-ICP-MS data in many applications.

Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation

It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. Graphical Abstract.

Automated patterning and probing with multiple nanoscale tools for single-cell analysis

The nano-manipulation approach that combines Focused Ion Beam (FIB) milling and various imaging and probing techniques enables researchers to investigate the cellular structures in three dimensions. Such fusion approach, however, requires extensive effort on locating and examining randomly-distributed targets due to limited Field of View (FOV) when high magnification is desired. In the present study, we present the development that automates 'pattern and probe' particularly for single-cell analysis, achieved by computer aided tools including feature recognition and geometric planning algorithms. Scheduling of serial FOVs for imaging and probing of multiple cells was considered as a rectangle covering problem, and optimal or near-optimal solutions were obtained with the heuristics developed. FIB milling was then employed automatically followed by downstream analysis using Atomic Force Microscopy (AFM) to probe the cellular interior. Our strategy was applied to examine bacterial cells (Klebsiella pneumoniae) and achieved high efficiency with limited human interference. The developed algorithms can be easily adapted and integrated with different imaging platforms towards high-throughput imaging analysis of single cells.

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS

Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples—both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight–secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection.

IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples—both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.

Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of 'Superbugs'

Emergence of multidrug resistant Gram-negative bacteria has caused a global health crisis and last-line class of antibiotics such as polymyxins are increasingly used. The chemical composition at the cell surface plays a key role in antibiotic resistance. Unlike imaging the cellular ultrastructure with well-developed electron microscopy, the acquisition of a high-resolution chemical map of the bacterial surface still remains a technological challenge. In this study, we developed an atom probe tomography (APT) analysis approach to acquire mass spectra in the pulsed-voltage mode and reconstructed the 3D chemical distribution of atoms and molecules in the subcellular domain at the near-atomic scale. Using focused ion beam (FIB) milling together with micromanipulation, site-specific samples were retrieved from a single cell of Acinetobacter baumannii prepared as needle-shaped tips with end radii less than 60 nm, followed by a nanoscale coating of silver in the order of 10 nm. The significantly elevated conductivity provided by the metallic coating enabled successful and routine field evaporation of the biological material, with all the benefits of pulsed-voltage APT. In parallel with conventional cryo-TEM imaging, our novel approach was applied to investigate polymyxin-susceptible and -resistant strains of A. baumannii after treatment of polymyxin B. Acquired atom probe mass spectra from the cell envelope revealed characteristic fragments of phosphocholine from the polymyxin-susceptible strain, but limited signals from this molecule were detected in the polymyxin-resistant strain. This study promises unprecedented capacity for 3D nanoscale imaging and chemical mapping of bacterial cells at the ultimate 3D spatial resolution using APT.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Focused ion beams in biology

A quiet revolution is under way in technologies used for nanoscale cellular imaging. Focused ion beams, previously restricted to the materials sciences and semiconductor fields, are rapidly becoming powerful tools for ultrastructural imaging of biological samples. Cell and tissue architecture, as preserved in plastic-embedded resin or in plunge-frozen form, can be investigated in three dimensions by scanning electron microscopy imaging of freshly created surfaces that result from the progressive removal of material using a focused ion beam. The focused ion beam can also be used as a sculpting tool to create specific specimen shapes such as lamellae or needles that can be analyzed further by transmission electron microscopy or by methods that probe chemical composition. Here we provide an in-depth primer to the application of focused ion beams in biology, including a guide to the practical aspects of using the technology, as well as selected examples of its contribution to the generation of new insights into subcellular architecture and mechanisms underlying host-pathogen interactions.

Phytochemical profiling in single plant cell by high performance liquid chromatography-mass spectrometry

A simple and universal method was successfully established to profile and identify bioactive phytochemicals and common metabolites in the single plant cell by using high performance liquid chromatography coupled with high resolution electrospray ionization mass spectrometry.

Multidimensional characterisation of biomechanical structures by combining Atomic Force Microscopy and Focused Ion Beam: A study of the rat whisker

Understanding the heterogeneity of biological structures, particularly at the micro/nano scale can offer insights valuable for multidisciplinary research in tissue engineering and biomimicry designs. Here we propose to combine nanocharacterisation tools, particularly Focused Ion Beam (FIB) and Atomic Force Microscopy (AFM) for three dimensional mapping of mechanical modulus and chemical signatures. The prototype platform is applied to image and investigate the fundamental mechanics of the rat face whiskers, a high-acuity sensor used to gain detailed information about the world. Grazing angle FIB milling was first applied to expose the interior cross section of the rat whisker sample, followed by a "lift-out" method to retrieve and position the target sample for further analyses. AFM force spectroscopy measurements revealed a non-uniform pattern of elastic modulus across the cross section, with a range from 0.8GPa to 13.5GPa. The highest elastic modulus was found at the outer cuticle region of the whisker, and values gradually decreased towards the interior cortex and medulla regions. Elemental mapping with EDS confirmed that the interior of the rat whisker is dominated by C, O, N, S, Cl and K, with a significant change of elemental distribution close to the exterior cuticle region. Based on these data, a novel comprehensive three dimensional (3D) elastic modulus model was constructed, and stress distributions under realistic conditions were investigated with Finite Element Analysis (FEA). The simulations could well account for the passive whisker deflections, with calculated resonant frequency as well as force-deflection for the whiskers being in good agreement with reported experimental data. Limitations and further applications are discussed for the proposed FIB/AFM approach, which holds good promise as a unique platform to gain insights on various heterogeneous biomaterials and biomechanical systems.

Emerging technology: applications of Raman spectroscopy for prostate cancer

There is a need in prostate cancer diagnostics and research for a label-free imaging methodology that is nondestructive, rapid, objective, and uninfluenced by water. Raman spectroscopy provides a molecular signature, which can be scaled from micron-level regions of interest in cells to macroscopic areas of tissue. It can be used for applications ranging from in vivo or in vitro diagnostics to basic science laboratory testing. This work describes the fundamentals of Raman spectroscopy and complementary techniques including surface enhanced Raman scattering, resonance Raman spectroscopy, coherent anti-Stokes Raman spectroscopy, confocal Raman spectroscopy, stimulated Raman scattering, and spatially offset Raman spectroscopy. Clinical applications of Raman spectroscopy to prostate cancer will be discussed, including screening, biopsy, margin assessment, and monitoring of treatment efficacy. Laboratory applications including cell identification, culture monitoring, therapeutics development, and live imaging of cellular processes are discussed. Potential future avenues of research are described, with emphasis on multiplexing Raman spectroscopy with other modalities.

Latest applications of 3D ToF-SIMS bio-imaging

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a rapidly developing technique for the characterization of a wide range of materials. Recently, advances in instrumentation and sample preparation approaches have provided the ability to perform 3D molecular imaging experiments. Polyatomic ion beams, such as C60, and gas cluster ion beams, often Arn (n = 500-4000), substantially reduce the subsurface damage accumulation associated with continued bombardment of organic samples with atomic beams. In this review, the capabilities of the technique are discussed and examples of the 3D imaging approach for the analysis of model membrane systems, plant single cell, and tissue samples are presented. Ongoing challenges for 3D ToF-SIMS imaging are also discussed along with recent developments that might offer improved 3D imaging prospects in the near future.

Effects of plasma-generated nitrogen functionalities on the upregulation of osteogenesis of bone marrow-derived mesenchymal stem cells

A tertiary amine constructed controllably by plasma technology possesses the optimal capability to promote BMSC osteogenesis.

In situ probing the interior of single bacterial cells at nanometer scale

We report a novel approach to probe the interior of single bacterial cells at nanometre resolution by combining focused ion beam (FIB) and atomic force microscopy (AFM). After removing layers of pre-defined thickness in the order of 100 nm on the target bacterial cells with FIB milling, AFM of different modes can be employed to probe the cellular interior under both ambient and aqueous environments. Our initial investigations focused on the surface topology induced by FIB milling and the hydration effects on AFM measurements, followed by assessment of the sample protocols. With fine-tuning of the process parameters, in situ AFM probing beneath the bacterial cell wall was achieved for the first time. We further demonstrate the proposed method by performing a spatial mapping of intracellular elasticity and chemistry of the multi-drug resistant strain Klebsiella pneumoniae cells prior to and after it was exposed to the 'last-line' antibiotic polymyxin B. Our results revealed increased stiffness occurring in both surface and interior regions of the treated cells, suggesting loss of integrity of the outer membrane from polymyxin treatments. In addition, the hydrophobicity measurement using a functionalized AFM tip was able to highlight the evident hydrophobic portion of the cell such as the regions containing cell membrane. We expect that the proposed FIB-AFM platform will help in gaining deeper insights of bacteria-drug interactions to develop potential strategies for combating multi-drug resistance.

Three-Dimensional Imaging of Viral Infections

Three-dimensional (3D) imaging technologies are beginning to have significant impact in the field of virology, as they are helping us understand how viruses take control of cells. In this article we review several methodologies for 3D imaging of cells and show how these technologies are contributing to the study of viral infections and the characterization of specialized structures formed in virus-infected cells. We include 3D reconstruction by transmission electron microscopy (TEM) using serial sections, electron tomography, and focused ion beam scanning electron microscopy (FIB-SEM). We summarize from these methods selected contributions to our understanding of viral entry, replication, morphogenesis, egress and propagation, and changes in the spatial architecture of virus-infected cells. In combination with live-cell imaging, correlative microscopy, and new techniques for molecular mapping in situ, the availability of these methods for 3D imaging is expected to provide deeper insights into understanding the structural and dynamic aspects of viral infection.

Single cell analysis with probe ESI-mass spectrometry: detection of metabolites at cellular and subcellular levels

Molecular analysis at cellular and subcellular levels, whether on selected molecules or at the metabolomics scale, is still a challenge now. Here we propose a method based on probe ESI mass spectrometry (PESI-MS) for single cell analysis. Detection of metabolites at cellular and subcellular levels was successfully achieved. In our work, tungsten probes with a tip diameter of about 1 μm were directly inserted into live cells to enrich metabolites. Then the enriched metabolites were directly desorbed/ionized from the tip of the probe for mass spectrometry (MS) detection. The direct desorption/ionization of the enriched metabolites from the tip of the probe greatly improved the sensitivity by a factor of about 30 fold compared to those methods that eluted the enriched analytes into a liquid phase for subsequent MS detection. We applied the PESI-MS to the detection of metabolites in single Allium cepa cells. Different kinds of metabolites, including 6 fructans, 4 lipids, and 8 flavone derivatives in single cells, have been successfully detected. Significant metabolite diversity was observed among different cells types of A. cepa bulb and different subcellular compartments of the same cell. We found that the inner epidermal cells had about 20 fold more fructans than the outer epidermal cells, while the outer epidermal cells had more lipids. We expected that PESI-MS might be a candidate in the future studies of single cell "omics".

Mass spectrometry imaging with high resolution in mass and space

Mass spectrometry (MS) imaging links molecular information and the spatial distribution of analytes within a sample. In contrast to most histochemical techniques, mass spectrometry imaging can differentiate molecular modifications and does not require labeling of targeted compounds. We have recently introduced the first mass spectrometry imaging method that provides highly specific molecular information (high resolution and accuracy in mass) at cellular dimensions (high resolution in space). This method is based on a matrix-assisted laser desorption/ionization (MALDI) imaging source working at atmospheric pressure which is coupled to an orbital trapping mass spectrometer. Here, we present a number of application examples and demonstrate the benefit of ‘mass spectrometry imaging with high resolution in mass and space.’ Phospholipids, peptides and drug compounds were imaged in a number of tissue samples at a spatial resolution of 5–10 μm. Proteins were analyzed after on-tissue tryptic digestion at 50-μm resolution. Additional applications include the analysis of single cells and of human lung carcinoma tissue as well as the first MALDI imaging measurement of tissue at 3 μm pixel size. MS image analysis for all these experiments showed excellent correlation with histological staining evaluation. The high mass resolution (R = 30,000) and mass accuracy (typically 1 ppm) proved to be essential for specific image generation and reliable identification of analytes in tissue samples. The ability to combine the required high-quality mass analysis with spatial resolution in the range of single cells is a unique feature of our method. With that, it has the potential to supplement classical histochemical protocols and to provide new insights about molecular processes on the cellular level.

Correlated imaging--a grand challenge in chemical analysis

Correlated chemical imaging is an emerging strategy for acquisition of images by combining information from multiplexed measurement platforms to track, visualize, and interpret in situ changes in the structure, organization, and activities of interesting chemical systems, frequently spanning multiple decades in space and time. Acquiring and correlating information from complementary imaging experiments has the potential to expose complex chemical behavior in ways that are simply not available from single methods applied in isolation, thereby greatly amplifying the information gathering power of imaging experiments. However, in order to correlate image information across platforms, a number of issues must be addressed. First, signals are obtained from disparate experiments with fundamentally different figures of merit, including pixel size, spatial resolution, dynamic range, and acquisition rates. In addition, images are often acquired on different instruments in different locations, so the sample must be registered spatially so that the same area of the sample landscape is addressed. The signals acquired must be correlated in both spatial and temporal domains, and the resulting information has to be presented in a way that is readily understood. These requirements pose special challenges for image cross-correlation that go well beyond those posed in single technique imaging approaches. The special opportunities and challenges that attend correlated imaging are explored by specific reference to correlated mass spectrometric and Raman imaging, a topic of substantial and growing interest.

The effect of high vacuum on the mechanical properties and bioactivity of collagen fibril matrices

The extracellular matrix (ECM) environment plays a critical role in organism development and disease. Surface sensitive microscopy techniques for studying the structural and chemical properties of ECMs are often performed in high vacuum (HV) environments. In this report, we examine the affect HV conditions have on the bioactivity and mechanical properties of type I collagen fibrillar matrices. We find that HV exposure has an unappreciable affect on the cell spreading response and mechanical properties of these collagen fibril matrices. Conversely, low vacuum environments cause fibrils to become mechanically rigid as indicated by force microscopy, resulting in greater cell spreading. Time-of-flight secondary ion mass spectrometry results show no noticeable spectral differences between HV-treated and dehydrated matrices. While previous reports have shown that HV can denature proteins in monolayers, these observations indicate that HV-exposure does not mechanically or biochemically alter collagen in its supramolecular configuration. These results may have implication for complex ECM matrices such as decellularized scaffolds.

Technologies for detecting metals in single cells

In order to fully understand the metallomics of an organism, it is essential to know how much metal is present in each cell and, ideally, to know both the spatial and chemical distributions of each metal (i.e., where within the cell is a metal found, and in what chemical form). No single technique provides all of this information. This chapter reviews the various methods that can be used and the strengths and weaknesses of each.

Multivariate analysis of ToF-SIMS data from multicomponent systems: the why, when, and how

The use of multivariate analysis (MVA) methods in the processing of time-of-flight secondary ion mass spectrometry (ToF-SIMS) data has become increasingly more common. MVA presents a powerful set of tools to aid the user in processing data from complex, multicomponent surfaces such as biological materials and biosensors. When properly used, MVA can help the user identify the major sources of differences within a sample or between samples, determine where certain compounds exist on a sample, or verify the presence of compounds that have been engineered into the surface. Of all the MVA methods, principal component analysis (PCA) is the most commonly used and forms an excellent starting point for the application of many of the other methods employed to process ToF-SIMS data. Herein we discuss the application of PCA and other MVA methods to multicomponent ToF-SIMS data and provide guidelines on their application and use.

Single cell matrix-assisted laser desorption/ionization mass spectrometry imaging

Application of mass spectrometry imaging (MS imaging) analysis to single cells was so far restricted either by spatial resolution in the case of matrix-assisted laser desorption/ionization (MALDI) or by mass resolution/mass range in the case of secondary ion mass spectrometry (SIMS). In this study we demonstrate for the first time the combination of high spatial resolution (7 μm pixel), high mass accuracy (<3 ppm rms), and high mass resolution (R = 100,000 at m/z = 200) in the same MS imaging measurement of single cells. HeLa cells were grown directly on indium tin oxide (ITO) coated glass slides. A dedicated sample preparation protocol was developed including fixation with glutaraldehyde and matrix coating with a pneumatic spraying device. Mass spectrometry imaging measurements with 7 μm pixel size were performed with a high resolution atmospheric-pressure matrix-assisted laser desorption/ionization (AP-MALDI) imaging source attached to an Exactive Orbitrap mass spectrometer. Selected ion images were generated with a bin width of Δm/z = ±0.005. Selected ion images and optical fluorescence images of HeLa cells showed excellent correlation. Examples demonstrate that a lower mass resolution and a lower spatial resolution would result in a significant loss of information. High mass accuracy measurements of better than 3 ppm (root-mean-square) under imaging conditions provide confident identification of imaged compounds. Numerous compounds including small metabolites such as adenine, guanine, and cholesterol as well as different lipid classes such as phosphatidylcholine, sphingomyelin, diglycerides, and triglycerides were detected and identified based on a mass spectrum acquired from an individual spot of 7 μm in diameter. These measurements provide molecularly specific images of larger metabolites (phospholipids) in native single cells. The developed method can be used for a wide range of detailed investigations of metabolic changes in single cells.

Automated correlation and classification of secondary ion mass spectrometry images using a k-means cluster method

We present a novel method for correlating and classifying ion-specific time-of-flight secondary ion mass spectrometry (ToF-SIMS) images within a multispectral dataset by grouping images with similar pixel intensity distributions. Binary centroid images are created by employing a k-means-based custom algorithm. Centroid images are compared to grayscale SIMS images using a newly developed correlation method that assigns the SIMS images to classes that have similar spatial (rather than spectral) patterns. Image features of both large and small spatial extent are identified without the need for image pre-processing, such as normalization or fixed-range mass-binning. A subsequent classification step tracks the class assignment of SIMS images over multiple iterations of increasing n classes per iteration, providing information about groups of images that have similar chemistry. Details are discussed while presenting data acquired with ToF-SIMS on a model sample of laser-printed inks. This approach can lead to the identification of distinct ion-specific chemistries for mass spectral imaging by ToF-SIMS, as well as matrix-assisted laser desorption ionization (MALDI), and desorption electrospray ionization (DESI).

Chemical mapping of mammalian cells by atom probe tomography

In atom probe tomography (APT), a technique that has been used to determine 3D maps of ion compositions of metals and semiconductors at sub-nanometer resolutions, controlled emissions of ions can be induced from needle-shaped specimens in the vicinity of a strong electric field. Detection of these ions in the plane of a position sensitive detector provides two-dimensional compositional information while the sequence of ion arrival at the detector provides information in the third dimension. Here we explore the use of APT technology for imaging biological specimens. We demonstrate that it is possible to obtain 3D spatial distributions of cellular ions and metabolites from unstained, freeze-dried mammalian cells. Multiple peaks were reliably obtained in the mass spectrum from tips with diameters of ~50 nm and heights of ~200 nm, with mass-to-charge ratios (m/z) ranging from 1 to 80. Peaks at m/z 12, 23, 28 and 39, corresponding to carbon, sodium, carbonyl and potassium ions respectively, showed distinct patterns of spatial distribution within the cell. Our studies establish that APT could become a powerful tool for mapping the sub-cellular distribution of atomic species, such as labeled metabolites, at 3D spatial resolutions as high as ~1 nm.

Mass spectrometry imaging and profiling of single cells

Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies-secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption/ionization mass spectrometry (MALDI MS)-are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enables new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling.