Which is more important in bioimaging SIMS experiments-The sample preparation or the nature of the projectile?

Improvement of Lipid Detection in Mouse Brain and Human Uterine Tissue Sections Using In Situ Matrix Enhanced Secondary Ion Mass Spectrometry

The potential of mass spectrometry imaging, and especially ToF-SIMS 2D and 3D imaging, for submicrometer-scale, label-free molecular localization in biological tissues is undisputable. Nevertheless, sensitivity issues remain, especially when one wants to achieve the best lateral and vertical (nanometer-scale) resolution. In this study, the interest of in situ matrix transfer for tissue analysis with cluster ion beams (Bin+, Arn+) is explored in detail, using a series of six low molecular weight acidic (MALDI) matrices. After estimating the sensitivity enhancements for phosphatidylcholine (PC), an abundant lipid type present in almost any kind of cell membrane, the most promising matrices were softly transferred in situ on mouse brain and human uterine tissue samples using a 10 keV Ar3000+ cluster beam. Signal enhancements up to 1 order of magnitude for intact lipid signals were observed in both tissues under Bi5+ and Ar3000+ bombardment. The main findings of this study lie in the in-depth characterization of uterine tissue samples, the demonstration that the transferred matrices also improve signal efficiency in the negative ion polarity and that they perform as well when using Bin+ and Arn+ primary ions for analysis and imaging.

Improved ion imaging of slowly dried neurons and skin cells by graphene cover in time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful tool to obtain both chemical information and spatial distribution of specific molecules of interest on a specimen surface. However, since the focused ion beam requires ultrahigh vacuum conditions for desorption and ionization of analytes, proper specimen preparation, such as drying, freeze-drying, and frozen dehydration, is required for ToF-SIMS analysis. In particular, biological specimens with high moisture content generally have a problem of specimen deformation during the normal drying process for a vacuum environment. In this study, the authors propose a cellular specimen preparation method to improve the ion imaging of cells by reducing the deformation of specimens in ToF-SIMS analysis. When the cells on the slide substrate are completely covered with single-layer graphene, the ToF-SIMS imaging is improved by reduced cell deformation due to slow drying. In addition, the graphene encapsulation also induces a reduction in the yield of secondary ions, thereby suppressing the background ion spectra generated by the unwanted organic residues on the substrate, resulting in the improvement of ToF-SIMS imaging. The authors also found that adding plasma treatment to this sample preparation can further improve ion imaging of cells. After cell dehydration is completed, the covered graphene layer can be peeled off by air-plasma treatment and the unwanted organic residues on the substrate can be removed due to plasma cleaning, thereby much improving ion imaging of cells.

Preparation of cellular samples using graphene cover and air-plasma treatment for time-of-flight secondary ion mass spectrometry imaging

We report on sample preparation methods based on plasma treatment for an improvement of multiple molecular ion images of cellular membranes in the ToF-SIMS method. The air-plasma treatment of fixed cellular samples efficiently removed the organic residues of any solutions used during sample preparation and improved the quality of ToF-SIMS images due to the resulting clean surface. We also studied cell preparation methods that combine single-layer graphene covering with air-plasma treatment to achieve a synergistic effect that eliminates background spectra by organic impurities while minimizing morphological cell deformation in a vacuum environmental analysis. When the cellular sample on the glass substrate is completely covered with the single-layer graphene, the cells trapped between the graphene and the substrate can effectively reduce morphological deformation by slow-dehydration. After slow-dehydration of cells is completed inside the graphene-cover, the covered graphene layer can be peeled off by air-plasma treatment, and the unwanted organic residues on the surface of cells and substrate can also be removed by plasma cleaning, thereby much improving ion imaging of cells with the ToF-SIMS method. It is confirmed that the cell samples in which the graphene-cover was removed by air-plasma treatment maintained their morphology well in comparison with the rapid air-dried cells in atomic force microscopy (AFM) and ToF-SIMS images.

Cell preparation methods that combine a single-layer graphene cover with air-plasma treatment for improvement of ToF-SIMS imaging.

Detection of ZrO₂ Nanoparticles in Lung Tissue Sections by Time-of-Flight Secondary Ion Mass Spectrometry and Ion Beam Microscopy

The increasing use of nanoparticles (NP) in commercial products requires elaborated techniques to detect NP in the tissue of exposed organisms. However, due to the low amount of material, the detection and exact localization of NP within tissue sections is demanding. In this respect, Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) and Ion Beam Microscopy (IBM) are promising techniques, because they both offer sub-micron lateral resolutions along with high sensitivities. Here, we compare the performance of the non-material-consumptive IBM and material-consumptive ToF-SIMS for the detection of ZrO₂ NP (primary size 9–10 nm) in rat lung tissue. Unfixed or methanol-fixed air-dried cryo-sections were subjected to IBM using proton beam scanning or to three-dimensional ToF-SIMS (3D ToF-SIMS) using either oxygen or argon gas cluster ion beams for complete sample sputtering. Some sample sites were analyzed first by IBM and subsequently by 3D ToF-SIMS, to compare results from exactly the same site. Both techniques revealed that ZrO₂ NP particles occurred mostly agglomerated in phagocytic cells with only small quantities being associated to the lung epithelium, with Zr, S, and P colocalized within the same biological structures. However, while IBM provided quantitative information on element distribution, 3D ToF-SIMS delivered a higher lateral resolution and a lower limit of detection under these conditions. We, therefore, conclude that 3D ToF-SIMS, although not yet a quantitative technique, is a highly valuable tool for the detection of NP in biological tissue.

Storage of cell samples for ToF-SIMS experiments-How to maintain sample integrity

In order to obtain comparable and reproducible results from time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of biological cells, the influence of sample preparation and storage has to be carefully considered. It has been previously shown that the impact of the chosen preparation routine is crucial. In continuation of this work, the impact of storage needs to be addressed, as besides the fact that degradation will unavoidably take place, the effects of different storage procedures in combination with specific sample preparations remain largely unknown. Therefore, this work examines different wet (buffer, water, and alcohol) and dry (air-dried, freeze-dried, and critical-point-dried) storage procedures on human mesenchymal stem cell cultures. All cell samples were analyzed by ToF-SIMS immediately after preparation and after a storage period of 4 weeks. The obtained spectra were compared by principal component analysis with lipid- and amino acid-related signals known from the literature. In all dry storage procedures, notable degradation effects were observed, especially for lipid-, but also for amino acid-signal intensities. This leads to the conclusion that dried samples are to some extent easier to handle, yet the procedure is not the optimal storage solution. Degradation proceeds faster, which is possibly caused by oxidation reactions and cleaving enzymes that might still be active. Just as well, wet stored samples in alcohol struggle with decreased signal intensities from lipids and amino acids after storage. Compared to that, the wet stored samples in a buffered or pure aqueous environment revealed no degradation effects after 4 weeks. However, this storage bears a higher risk of fungi/bacterial contamination, as sterile conditions are typically not maintained. Thus, regular solution change is recommended for optimized storage conditions. Not directly exposing the samples to air, wet storage seems to minimize oxidation effects, and hence, buffer or water storage with regular renewal of the solution is recommended for short storage periods.

Bioanalytics in Quantitive (Bio)imaging/Mapping of Metallic Elements in Biological Samples

The aim of this article is to describe selected analytical techniques and their applications in the quantitative mapping/(bio)imaging of metals in biological samples. This work presents the advantages and disadvantages as well as the appropriate methods of scope for research. Distribution of metals in biological samples is currently one of the most important issues in physiology, toxicology, pharmacology, and other disciplines where functional information about the distribution of metals is essential. This issue is a subject of research in (bio)imaging/mapping studies, which use a variety of analytical techniques for the identification and determination of metallic elements. Increased interest in analytical techniques enabling the (bio)imaging of metals in a variety of biological material has been observed more recently. Measuring the distribution of trace metals in tissues after a drug dose or ingestion of poison-containing metals allows for the studying of pathomechanisms and the pathophysiology of various diseases and disorders related to the management of metals in human and animal systems.

Correlating microscopy techniques and ToF-SIMS analysis of fully grown mammalian oocytes

An innovative protocol for the 2D-molecular thin film analysis applying ToF-SIMS, SEM, AFM and optical microscopy imaging of fully grown mice oocytes is described.

Assessment of different sample preparation routes for mass spectrometric monitoring and imaging of lipids in bone cells via ToF-SIMS

In ToF-SIMS analysis, the experimental outcome from cell experiments is to a great extent influenced by the sample preparation routine. In order to better judge this critical influence in the case of lipid analysis, a detailed comparison of different sample preparation routines is performed-aiming at an optimized preparation routine for systematic lipid imaging of cell cultures. For this purpose, human mesenchymal stem cells were analyzed: (a) as chemically fixed, (b) freeze-dried, and (c) frozen-hydrated. For chemical fixation, different fixatives, i.e., glutaraldehyde, paraformaldehyde, and a mixture of both, were tested with different postfixative handling procedures like storage in phosphate buffered saline, water or critical point drying. Furthermore, secondary lipid fixation via osmium tetroxide was taken into account and the effect of an ascending alcohol series with and without this secondary lipid fixation was evaluated. Concerning freeze-drying, three different postprocessing possibilities were examined. One can be considered as a pure cryofixation technique while the other two routes were based on chemical fixation. Cryofixation methods known from literature, i.e., freeze-fracturing and simple frozen-hydrated preparation, were also evaluated to complete the comparison of sample preparation techniques. Subsequent data evaluation of SIMS spectra in both, positive and negative, ion mode was performed via principal component analysis by use of peak sets representative for lipids. For freeze-fracturing, these experiments revealed poor reproducibility making this preparation route unsuitable for systematic investigations and statistic data evaluation. Freeze-drying after cryofixation showed improved reproducibility and well preserved lipid contents while the other freeze-drying procedures showed drawbacks in one of these criteria. In comparison, chemical fixation techniques via glutar- and/or paraformaldehyde proved most suitable in terms of reproducibility and preserved lipid contents, while alcohol and osmium treatment led to the extraction of lipids and are therefore not recommended.

ToF-SIMS of tissues: "lessons learned" from mice and women

The ability to image cells and tissues with chemical and molecular specificity could greatly expand our understanding of biological processes. The subcellular resolution mass spectral imaging capability of time of flight secondary ion mass spectrometry (ToF-SIMS) has the potential to acquire chemically detailed images. However, the complexities of biological systems combined with the sensitivity of ToF-SIMS require careful planning of experimental methods. Tissue sample preparation methods of formalin fixation followed by paraffin embedding (FFPE) and OCT embedding are compared. Results show that the FFPE can potentially be used as a tissue sample preparation protocol for ToF-SIMS analysis if a cluster ion pre-sputter is used prior to analysis and if nonlipid related tissue features are the features of interest. In contrast, embedding tissue in OCT minimizes contamination and maintains lipid signals. Various data acquisition methodologies and analysis options are discussed and compared using mouse breast and diaphragm muscle tissue. Methodologies for acquiring ToF-SIMS 2D images are highlighted along with applications of multivariate analysis to better identify specific features in a tissue sections when compared to H&E images of serial sections. Identification of tissue features is necessary for researchers to visualize a molecular map that correlates with specific biological features or functions. Finally, lessons learned from sample preparation, data acquisition, and data analysis methods developed using mouse models are applied to a preliminary analysis of human breast tumor tissue sections.

TOF-SIMS 3D imaging of native and non-native species within HeLa cells

In this study, a non-native chemical species, bromodeoxyuridine (BrdU), was imaged within single HeLa cells using time-of-flight secondary ion mass spectrometry (TOF-SIMS). z-corrected 3D images were reconstructed that accurately portray the distribution of intracellular BrdU as well as other intracellular structures. The BrdU was localized to the nucleus of cells, whereas structures composed of CxHyOz(-) species were located in bundles on the periphery of cells. The CxHyOz(-) subcellular features had a spatial resolution at or slightly below a micrometer (900 nm), as defined by the distance between the 16% and 84% intensities in a line scan across the edge of the features. Additionally, important parameters influencing the quality of the HeLa cell 3D images were investigated. Atomic force microscopy measurements revealed that the HeLa cells were sputtered at a rate of approximately 4 nm per 10(13) C60(+) ions/cm(2) at 10 keV and a 45° incident angle. Optimal 3D images were acquired using a Bi3(+) liquid metal ion gun operating in the simultaneous high mass and spatial resolution mode.

Characterization of sample preparation methods of NIH/3T3 fibroblasts for ToF-SIMS analysis

The information that is obtained from single cells during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis is influenced by the method that was used to prepare the cells. The removal of extracellular media before analysis is necessary, but the rinsing technique should not damage the plasma membrane of the cell. The presence of intracellular salts reduced the secondary ion yield an average of 2.6-fold during Bi3 (+)/C60 (++) depth profiles. Chemical fixation followed by rinsing removed a majority of the intracellular salts, "recovering" the positive secondary ion yields. The formaldehyde-fixation process removed a majority of the intracellular Cl(-), but other key anions were not removed in significant amounts. The data presented here is consistent the anion neutralization mechanism largely responsible for the lower ion yields. All of the organic secondary ions that were detected in the freeze-dried cells were also detected in the formaldehyde-fixed cells, suggesting that the fixation process did not remove any molecular species to an extent that is detectable by ToF-SIMS. Compared to freeze dried cells, well preserved, frozen-hydrated cells showed little increase, or a decreased yield, for most low mass ions, but an increased yield for larger mass fragments. This is consistent with a reduced damage cross section at cryogenic analysis temperatures, although proton donation from water and reduction the salt effects in the presence of water likely also play roles. Numerous ions detected from the frozen-hydrated cells were not detected from the freeze dried cells, however many of these ions were attributed to chemical combinations of water, salts and the ammonium acetate rinsing solution.

Imaging mass spectrometry in neuroscience

Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging.

Image and Spectral Processing for ToF-SIMS Analysis of Biological Materials

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) instruments can rapidly produce large complex data sets. Within each spectrum, there can be hundreds of peaks. A typical 256×256 pixel image contains 65,536 spectra. If this is extended to a 3D image, the number of spectra in a given data set can reach the millions. The challenge becomes how to process these large data sets while taking into account the changes and differences between all the peaks in the spectra. This is particularly challenging for biological materials that all contain the same types of proteins and lipids, just in varying concentrations and spatial distributions. This data analysis challenge is further complicated by the limitations in the ion yield of higher mass, more chemically specific species, and potentially by the processing power of typical computers. Herein we briefly discuss analysis methodologies including univariate analysis, multivariate analysis (MVA) methods, and some of the limitations of ToF-SIMS analysis of biological materials.

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.

ToF-SIMS imaging and depth profiling of HeLa cells treated with bromodeoxyuridine

Time of flight secondary ion mass spectrometry 2D images and molecular depth profiles of human HeLa cells treated with bromodeoxyuridine (BrdU) were acquired in the dual beam mode (Bi(3) (+) analysis beam, C(60) (+) etching beam). Several preparation protocols were investigated and were compared to a simple wash-and-dry method. The feasibility of using C(60) to clean the samples prior to imaging with Bi was also investigated quantitatively by calibrating full depth profiles of the cells using atomic force microscopy. BrdU was used as a marker for the cell nucleus, facilitating identification and localization of sub-cellular features during depth profiling. Results show that C(60) can be used to remove the surface contamination and to access different layers within the cells for 2D imaging. For a 1 nA, 10 keV C(60) (+) beam incident at 45° and rastered over a 500 × 500 μm(2) area, ~1 nm of biological material was sputtered every second. Our results show that HeLa cells were completely removed after etching with 1.3×10(15) C(60) (+) ions per cm(2), giving an average etching rate of 3.9 nm for every 10(13) C(60) per cm(2) at 10 keV and 45° incidence.

Nanotome cluster bombardment to recover spatial chemistry after preparation of biological samples for SIMS imaging

A C(60)(+) cluster ion projectile is employed for sputter cleaning biological surfaces to reveal spatio-chemical information obscured by contamination overlayers. This protocol is used as a supplemental sample preparation method for time of flight secondary ion mass spectrometry (ToF-SIMS) imaging of frozen and freeze-dried biological materials. Following the removal of nanometers of material from the surface using sputter cleaning, a frozen-patterned cholesterol film and a freeze-dried tissue sample were analyzed using ToF-SIMS imaging. In both experiments, the chemical information was maintained after the sputter dose, due to the minimal chemical damage caused by C(60)(+) bombardment. The damage to the surface produced by freeze-drying the tissue sample was found to have a greater effect on the loss of cholesterol signal than the sputter-induced damage. In addition to maintaining the chemical information, sputtering is not found to alter the spatial distribution of molecules on the surface. This approach removes artifacts that might obscure the surface chemistry of the sample and are common to many biological sample preparation schemes for ToF-SIMS imaging.

Lipid detection, identification, and imaging single cells with SIMS

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) can be utilized to map the distribution of various molecules on a surface with submicrometer resolution. Many of its biological applications have been in the study of membrane lipids, such as phospholipids and cholesterol. For these studies, the effectiveness of chemical mapping is limited by low signal intensity from various biomolecules. Because of the high-energy nature of the SIMS ionization process, many molecules are identified by detection of characteristic fragments. Cluster ion sources are able to increase ionization, leading to increased information collected from a surface. In this chapter, we highlight the utility of SIMS to image lipids at single cells. Particularly, we will describe sample preparation, data collection, and the analysis of lipids for two systems; rat oligodendrocytes and Tetrahymena thermophila. SIMS spectra yield information regarding lipid identity and concentration across cell surface.