A novel approach to elucidate the ionization mechanism for the [M + H]+ molecular ion of organic molecules is investigated by molecular depth profiling of isotopically enriched thin films. Using a model bi-layer film of phenylalanine (PHE) and PHE-D8, the results show formation of an [M + D]+ molecular ion for the non-enriched PHE molecule attributed to rearrangements of chemical damage due to successive primary ion impacts. The [M + D]+ ion is observed at the interface for 19.9nm in the enriched-on-top system and 9.9nm for the enriched-on-bottom system. This ion formation is direct evidence for dynamically created pre-formed ions as a result of chemical damage rearrangement induced by previous primary ion bombardment events.
SIMS; isotope; interface; deuterium; fundamentals; depth profile
A molecular multilayer stack composed of alternating Langmuir-Blodgett films was analyzed by ToF-SIMS imaging in combination with intermediate sputter erosion using a focused C60+ cluster ion beam. From the resulting dataset, depth profiles of any desired lateral portion of the analyzed field-of-view can be extracted in retrospect, allowing the influence of the gating area on the apparent depth resolution to be assessed. In a similar way, the observed degradation of depth resolution with increasing depth of the analyzed interface can be analyzed in order to determine the ‘intrinsic’ depth resolution of the method.
molecular depth profiling; 3D analysis; depth resolution; organic multilayer analysis
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 C60+ primary ion beam. Parameters associated with the depth profile such as depth resolution, uniformity of sputtering yield and topography are evaluated between 90 K 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 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 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.
The recent boom of energy storage and conversion devices, exploiting ionic liquids (ILs) to enhance the performance, requires an in-depth understanding of this new class of electrolytes in device operation conditions. One central question critical to device performance is how the mobile ions accumulate near charged electrodes. Here, we present the excess ion depth profiles of ILs in ionomer membrane actuators (Aquivion/1-butyl-2,3-dimethylimidazolium chloride (BMMI-Cl), 27 μm thick), characterized directly by Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) at liquid nitrogen temperature. Experimental results reveal that for the IL studied, cations and anions are accumulated at both electrodes. The large difference in the total volume occupied by the excess ions between the two electrodes cause the observed large bending actuation of the actuator. Hence we demonstrate that ToF-SIMS experiment provides great insights on the physics nature of ionic devices.
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; lipids; cluster sources; sample preparation; C60+QSTAR; J105 3D Chemical Imager and imaging mass spectrometry (IMS)
Time-of-flight Secondary ion mass spectrometry (ToF-SIMS) provides a method for the detection of native and exogenous compounds in biological samples on a cellular scale. Through the development of novel ion beams the amount of molecular signal available from the sample surface has been increased. Through the introduction of polyatomic ion beams, particularly C60, ToF-SIMS can now be used to monitor molecular signals as a function of depth as the sample is eroded thus proving the ability to generate 3D molecular images. Here we describe how this new capability has led to the development of novel instrumentation for 3D molecular imaging while also highlighting the importance of sample preparation and discuss the challenges that still need to be overcome to maximise the impact of the technique.
Time-of-flight secondary ion mass spectrometry and atomic force microscopy are employed to characterize a wedge-shaped crater eroded by a 40keV C60+ cluster ion beam on an organic film of Irganox 1010 doped with Irganox 3114 delta layers. From an examination of the resulting surface, the information about depth resolution, topography and erosion rate can be obtained as a function of crater depth for every depth in a single experiment. It is shown that when measurements are performed at liquid nitrogen temperature, a constant erosion rate and reduced bombardment induced surface roughness is observed. At room temperature, however, the erosion rate drops by ~1/3 during the removal of the 400 nm Irganox film and the roughness gradually increased to from 1 nm ~4 nm. From SIMS lateral images of the beveled crater and AFM topography results, depth resolution was further improved by employing glancing angles of incidence and lower primary ion beam energy. Sub-10 nm depth resolution was observed under the optimized conditions on a routine basis. In general, we show that the wedge-crater beveling is an important tool for elucidating the factors that are important for molecular depth profiling experiments.
The angular distribution of intact organic molecules desorbed by energetic C60 primary ions was probed both experimentally and with molecular dynamics computer simulations. For benzo[a]pyrene, the angular distribution of intact molecules is observed to peak at off-normal angles. Molecular dynamics computer simulations on a similar system show the mechanism of desorption involves fast deposition of energy followed by fluid-flow and effusive-type emission of intact molecules. The off-normal peak in the angular distribution is shown to arise from emission of intact molecules from the rim of a crater formed during the cluster impact. This signature is unique for molecules because fragmentation processes remove molecules that would otherwise eject at directions near-normal to the surface.
angular distribution; fluid-flow desorption; effusive desorption; C60 sputtering; molecular dynamics computer simulations; tof-snms; photoionization
An organic delta layer system made of alternating Langmuir Blodgett multilayers of barium arachidate (AA) and barium dimyristoyl phosphatidate (DMPA) was constructed to elucidate the factors that control depth resolution in molecular depth profile experiments. More specifically, one or several bilayers of DMPA (4.4 nm) were embedded in relatively thick (51 to 105 nm) multilayer stacks of AA, resulting in a well-defined delta-layer model system closely resembling a biological membrane. 3-D imaging ToF-SIMS depth profile analysis was performed on this system using a focused buckminsterfullerene (C60) cluster ion beam. The delta layer depth response function measured in these experiments exhibits similar features as those determined in inorganic depth profiling, namely an asymmetric shape with quasi-exponential leading and trailing edges and a central Gaussian peak. The effects of sample temperature, primary ion kinetic energy and incident angle on the depth resolution were investigated. While the information depth of the acquired SIMS spectra was found to be temperature independent, the depth resolution was found to be significantly improved at low temperature. Ion induced mixing is proposed to be largely responsible for the broadening, rather than topography, as determined by AFM, therefore depth resolution can be optimized using lower kinetic energy, glancing angle and liquid nitrogen temperature.
molecular depth profiling; SIMS; delta layer; buckminsterfullerene (C60)
Imaging TOF-SIMS now has the potential to provide spatially resolved chemical information for a wide variety of molecules in biological tissue and single cells. Although early studies focused on low molecular weight fragment ions, the advent of polyatomic primary ion sources has opened detection schemes to a much wider range of molecules with molecular weights extending to greater than 1000 Da. In this regard, a number of workers have reported the distribution of drug molecules and of metabolites under various conditions. Here we discuss a number of challenges facing this field given the new measurement paradigms. Very different sample preparation measurement considerations emerge as the desired spatial resolution approaches 1 micron. At values above 1 micron, freeze drying methods appear to be successful and there are enough molecules in the probe area to detect higher mass species directly. For example, we have detected the molecular ion of more than 50 different lipids in brain tissue and in a lawn of cells, using ms/ms techniques to assign structure. Characterization of single cells becomes much more challenging, however, since there are many fewer molecules available for detection, and sample pretreatment to enhance ionization can move molecules around, reducing the effective lateral resolution. For these systems, preparation of frozen hydrated samples appears to be the best way to avoid artifacts. Moreover, since polyatomic projectiles now allow molecular depth profiling, use of frozen hydrated samples is the only way to preserve 3-dimensional structure of cells. Currently, using a conventional high performance imaging TOF-SIMS system, the sensitivity is on the limit of being able to detect the higher mass molecular ions. Several examples will be given to illustrate each of the above issues. The prospects for improving the sensitivity of this type of imaging will also be discussed.
A C60+ 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 C60+ 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.
Secondary ion mass spectrometry and atomic force microscopy are employed to characterize a wedge-shaped crater eroded by 40 keV C60+ bombardment of a 395-nm thin film of Irganox 1010 doped with four delta layers of Irganox 3114. The wedge structure creates a laterally magnified cross section of the film. From an examination of the resulting surface, information about depth resolution, topography and erosion rate can be obtained as a function of crater depth in a single experiment. This protocol provides a straightforward way to determine the parameters necessary to characterize molecular depth profiles, and to obtain an accurate depth scale for erosion experiments.
Mass spectrometric imaging is a powerful tool to interrogate biological complexity. One such technique, ToF-SIMS imaging, has been successfully utilized for sub-cellular imaging of cell membrane components. In order for this technique to provide insight into biological processes, it is critical to characterize the figures of merit. Because a SIMS instrument counts individual events, the precision of the measurement is controlled by counting statistics. As the analysis area decreases, the number of molecules available for analysis diminishes. This becomes critical when imaging sub-cellular features; it limits the information obtainable, resulting in images with only a few counts of interest per pixel. Many features observed in low intensity images are artifacts of counting statistics, making validation of these features crucial to arriving at accurate conclusions. With ToF-SIMS imaging, the experimentally attainable spatial resolution is a function of the molecule of interest, sample matrix, concentration, primary ion, instrument transmission, and spot size of the primary ion beam. A model, based on Poisson statistics, has been developed to validate SIMS imaging data when signal is limited. This model can be used to estimate the effective spatial resolution and limits of detection prior to analysis, making it a powerful tool for tailoring future investigations. In addition, the model allows comparison of pixel-to-pixel intensity and can be used to validate the significance of observed image features. The implications and capabilities of the model are demonstrated by imaging the cell membrane of resting RBL-2H3 mast cells.
Time-of-flight secondary ion mass spectrometry is utilized to characterize the response of Langmuir–Blodgett (LB) multilayers under the bombardment by buckminsterfullerene primary ions. The LB multilayers are formed by barium arachidate and barium dimyristoyl phosphatidate on a Si substrate. The unique sputtering properties of the C60 ion beam result in successful molecular depth profiling of both the single component and multilayers of alternating chemical composition. At cryogenic (liquid nitrogen) temperatures, the high mass signals of both molecules remain stable under sputtering, while at room temperature, they gradually decrease with primary ion dose. The low temperature also leads to a higher average sputter yield of molecules. Depth resolution varies from 20 to 50 nm and can be reduced further by lowering the primary ion energy or by using glancing angles of incidence of the primary ion beam.
This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C60, exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining the molecular specificity of mass spectrometry. When the beams are microfocused to a spot on the sample, bioimaging experiments in two and three dimensions are feasible. We describe emerging theoretical models that allow the energy-deposition process to be understood on an atomic and molecular basis. Moreover, experiments on model systems are described that allow protocols for imaging on biological materials to be implemented. Finally, we present recent applications of imaging to biological tissue and single cells to illustrate the future directions of this methodology.
secondary ion mass spectrometry; bioimaging; molecular depth profiling; three-dimensional molecular imaging; C60; molecular dynamics
Sputter depth profiling of organic films while maintaining the molecular integrity of the sample has long been deemed impossible because of the accumulation of ion bombardment-induced chemical damage. Only recently, it was found that this problem can be greatly reduced if cluster ion beams are used for sputter erosion. For organic samples, carbon cluster ions appear to be particularly well suited for such a task. Analysis of available data reveals that a projectile appears to be more effective as the number of carbon atoms in the cluster is increased, leaving fullerene ions as the most promising candidates to date. Using a commercially available, highly focused C60q+ cluster ion beam, we demonstrate the versatility of the technique for depth profiling various organic films deposited on a silicon substrate and elucidate the dependence of the results on properties such as projectile ion impact energy and angle, and sample temperature. Moreover, examples are shown where the technique is applied to organic multilayer structures in order to investigate the depth resolution across film-film interfaces. These model experiments allow collection of valuable information on how cluster impact molecular depth profiling works and how to understand and optimize the depth resolution achieved using this technique.
Molecular depth profiling; Cluster SIMS; Carbon clusters; Cluster ion beams
The early stages of C60 bombardment of octane and octatetraene crystals are modeled using molecular dynamics simulations with incident energies of 5-20 keV. Using the AIREBO potential, which allows for chemical reactions in hydrocarbon molecules, we are able to investigate how the projectile energy is partitioned into changes in potential and kinetic energy as well as how much energy flows into reacted molecules and internal energy. Several animations have been included to illustrate the bombardment process. The results show that the material near the edge of the crater can be ejected with low internal energies and that ejected molecules maintain their internal energies in the plume, in contrast to a collisional cooling mechanism previously proposed. In addition, a single C60 bombardment was able to create many free and reacted H atoms which may aid in the ionization of molecules upon subsequent bombardment events.
Biological membrane fusion is crucial to numerous cellular events, including sexual reproduction and exocytosis. Here, mass spectrometry images demonstrate that the low-curvature lipid phosphatidylcholine is diminished in the membrane regions between fusing Tetrahymena, where a multitude of highly curved fusion pores exist. Additionally, mass spectra and principal component analysis indicate that the fusion region contains elevated amounts of 2-aminoethylphosphonolipid, a high-curvature lipid. This evidence suggests that biological fusion involves and might in fact be driven by a heterogeneous redistribution of lipids at the fusion site.
A hybrid quadrupole orthogonal time-of-flight mass spectrometer optimized for MALDI and electrospray ionization has been equipped with a C60 cluster ion source. This configuration is shown to exhibit a number of characteristics that improve the performance of traditional time-of-flight secondary ion mass spectrometry (SIMS) experiments for the analysis of complex organic materials, and potentially, for chemical imaging. Specifically, the primary ion beam is operated as a continuous rather than a pulsed beam, resulting in up to 4 orders of magnitude greater ion fluence on the target. The secondary ions are extracted at very low voltage into 8 millitorr of N2 gas introduced for collisional focusing and cooling purposes. This extraction configuration is shown to yield secondary ions that rapidly lose memory of the mechanism of their birth, yielding tandem mass spectra that are identical for SIMS and MALDI. With implementation of ion trapping, the extraction efficiency is shown to be equivalent to that found in traditional TOF-SIMS machines. Examples are given, for a variety of substrates that illustrate mass resolution of 12,000–15,600 with mass range for inorganic compounds to m/z 40,000. Preliminary chemical mapping experiments show that with added sensitivity, imaging in the MS/MS mode of operation is straightforward. In general, the combination of MALDI and SIMS is shown to add capabilities to each technique, providing a robust platform for TOF-SIMS experiments that already exists in a large number of laboratories.
Molecular depth profiling of organic overlayers was performed using a mass selected C60 ion beam in conjunction with time-of-flight (TOF-SIMS) mass spectrometry. The characteristics of sputter depth profiles acquired for a 300-nm Trehalose film on silicon were studied as a function of the kinetic impact energy of the projectile ions. The results are interpreted in terms of a simple model describing the balance between sputter erosion and ion induced chemical damage. It is shown that the efficiency of the projectile to clean up the fragmentation debris produced by its own impact represents a key parameter governing the success of molecular depth profile analysis.
Sample preparation is central to acquiring meaningful molecule-specific images with SIMS, especially when submicron lateral resolution is involved. The issue is to maintain the distribution of target molecules while attempting to introduce biological cells or tissue into the high vacuum environment of the mass spectrometer. Here we compare freeze-drying, freeze-etching, freeze-fracture and trehalose vitrification as possible strategies for these experiments. The results show that the prospects for successful imaging experiments are greatly improved with all of these methods when using cluster ion bombardment, particularly C60+ ions, not only due to increased sensitivity of this projectiles, but also since it removes contamination overlayers without insult to the underlying chemistry. The emergence of 3-dimensional imaging capabilities also suggests that sample preparation should not perturb the 3-dimensional morphology of the cell, a situation not generally possible during freeze-drying. Hence, sample preparation and projectile type are strongly coupled parameters for bioimaging with mass spectrometry.
Bioimaging; Cluster SIMS; Freeze-fracture; Freeze-etching; C60; Vitrification
The effect of incident angle on the quality of SIMS molecular depth profiling using C60+ was investigated. Cholesterol films of ~300 nm thickness on Si were employed as a model and were eroded using 40 keV C60+ at an incident angle of 40° and 73° with respect to the surface normal. The erosion process was characterized by determining at each angle the relative amount of chemical damage, the total sputtering yield of cholesterol molecules, and the interface width between the film and the Si substrate. The results show that there is less molecule damage at an angle of incidence of 73° and that the total sputtering yield is largest at an angle of incidence of 40°. The measurements suggest reduced damage is not necessarily dependent upon enhanced yields and that depositing the incident energy nearer the surface by using glancing angles is most important. The interface width parameter supports this idea by indicating that at the 73° incident angle, C60+ produces a smaller altered layer depth. Overall, the results show that 73° incidence is the better angle for molecular depth profiling using 40 keV C60+.
SIMS; C60+; Incident angle; Molecular depth profiling
Molecular depth profiling and three-dimensional imaging using cluster projectiles and SIMS have become a prominent tool for organic and biological materials characterization. To further explore the fundamental features of cluster bombardment of organic materials, especially depth resolution and differential sputtering, we have developed a reproducible and robust model system consisting of Langmuir–Blodgett (LB) multilayer films. Molecular depth profiles were acquired, using a 40-keV C60+ probe, with LB films chemically alternating between barium arachidate and barium dimyristoyl phosphatidate. The chemical structures were successfully resolved as a function of depth. The molecular ion signals were better preserved when the experiment was performed under cryogenic conditions than at room temperature. A novel method was used to convert the scale of fluence into depth which facilitated quantitative measurement of the interface width. Furthermore, the LB films were imaged as a function of depth. The reconstruction of the SIMS images correctly represented the original chemical structure of the film. It also provided useful information about interface mixing and edge effects during sputtering.
Molecular depth profiling; 3D imaging; Langmuir; Blodgett films; Multilayers; Cluster beam; SIMS
We report the use of SIMS imaging to quantify the relative difference in the amount of lipid between two sections, the plasma membrane and the cytoplasm, of single cells from two different populations. Cells were each labeled with lipophillic dyes, frozen, fractured and analyzed in a ToF-SIMS mass spectrometer equipped with a 40 keV C60+ ion source. In addition to identifying cells from separate populations, the lipophilic dyes can be used as a marker for the outer leaflet of the cell membrane and therefore as a depth finder. Here, we show that it is possible to compare the amount of lipids with particular headgroups in the cell membrane of a treated cell to the membrane of a control cell. Following erosion of the cell membranes, the amount of the two specific lipid head groups in the cytoplasm of the treated cell can be compared to those lipids in a control cell. Here we take the first step in this experimental design and display the ability to analyze multiple sections of frozen cells following a single fracture.
Single cell; cluster; C60; SIMS
Primordial germ cells (PGCs) are the embryonic precursors of the sperm and eggs. Environmental or genetic defects that alter PGC development can impair fertility or cause formation of germ cell tumors.
We demonstrate a novel role for cholesterol during germ cell migration in mice. Cholesterol was measured in living tissue dissected from mouse embryos and was found to accumulate within the developing gonads as germ cells migrate to colonize these structures. Cholesterol synthesis was blocked in culture by inhibiting the activity of HMG CoA reductase (HMGCR) resulting in germ cell survival and migration defects. These defects were rescued by co-addition of isoprenoids and cholesterol, but neither compound alone was sufficient. In contrast, loss of the last or penultimate enzyme in cholesterol biosynthesis did not alter PGC numbers or position in vivo. However embryos that lack these enzymes do not exhibit cholesterol defects at the stage at which PGCs are migrating. This demonstrates that during gestation, the cholesterol required for PGC migration can be supplied maternally.
In the mouse, cholesterol is required for PGC survival and motility. It may act cell-autonomously by regulating clustering of growth factor receptors within PGCs or non cell-autonomously by controlling release of growth factors required for PGC guidance and survival.