Time-of-flight secondary ion mass spectrometry in the helium ion microscope

Advances in mass spectrometry imaging for spatial cancer metabolomics

Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.

Quantitative nanoscale imaging using transmission He ion channelling contrast: Proof-of-concept and application to study isolated crystalline defects

A newly developed microscope prototype, namely npSCOPE, consisting of a Gas Field Ion Source (GFIS) column and a position sensitive Delay-line Detector (DLD) was used to perform Scanning Transmission Ion Microscopy (STIM) using keV He+ ions. One experiment used 25 keV ions and a second experiment used 30 keV ions. STIM imaging of a 50 nm thick free-standing gold membrane exhibited excellent contrast due to ion channelling and revealed rich microstructural features including isolated nanoscale twin bands which matched well with the contrast in the conventional ion-induced Secondary Electron (SE) imaging mode. Transmission Kikuchi Diffraction (TKD) and Backscattered Electron (BSE) imaging were performed on the same areas to correlate and confirm the microstructural features observed in STIM. Monte Carlo simulations of the ion and electron trajectories were performed with parameters similar to the experimental conditions to derive insights related to beam broadening and its effect in the degradation of transmission image resolution. For the experimental conditions used, STIM imaging showed a lateral resolution close to30 nm. Dark twin bands in bright grains as well as bright twin bands in dark grains were observed in STIM. Some of the twin bands were invisible in STIM. For the specific experimental conditions used, the ion transmission efficiency across a particular twin band was found to decrease by a factor of 2.8. Surprisingly, some grains showed contrast reversal when the Field of View (FOV) was changed indicating the sensitivity of the channelling contrast to even small changes in illumination conditions. These observations are discussed using ion channelling conditions and crystallographic orientations of the grains and twin bands. This study demonstrates for the first time the potential of STIM imaging using keV He+ ions to quantitatively investigate channelling in nanoscale structures including isolated crystalline defects.

npSCOPE: A New Multimodal Instrument for In Situ Correlative Analysis of Nanoparticles

Over the last few decades, nanoparticles have become a key element in a number of scientific and technological fields, spanning from materials science to life sciences. The characterization of nanoparticles or samples containing nanoparticles, in terms of morphology, chemical composition, and other parameters, typically involves investigations with various analytical tools, requiring complex workflows and extending the duration of such studies to several days or even weeks. Here, we report on the development of a new unique in situ correlative instrument, allowing us to answer questions about the shape, size, size distribution, and chemical composition of the nanoparticles using a single probe. Combining various microscopic and analytical capabilities in one single instrument allows a considerable increase in flexibility and a reduction in the duration of such complex investigations. The new instrument is based on focused ion beam microscopy technology using a gas field ion source as a key enabler and combining it with specifically developed secondary ion mass spectrometry and scanning transmission ion microscopy technology. We will present the underlying concept, the instrument and its main components, and proof-of-concept studies performed on this novel instrument. For this purpose, different pure titanium dioxide nanoparticle samples were investigated. Furthermore, the distribution and localization of the nanoparticles in biological model systems were studied. Our results demonstrate the performance and usefulness of the instrument for nanoparticle investigations, paving the way for a number of future applications, in particular, nanotoxicological research.

Highest resolution chemical imaging based on secondary ion mass spectrometry performed on the helium ion microscope

This paper is a review on the combination between Helium Ion Microscopy (HIM) and Secondary Ion Mass Spectrometry (SIMS), which is a recently developed technique that is of particular relevance in the context of the quest for high-resolution high-sensitivity nano-analytical solutions. We start by giving an overview on the HIM-SIMS concept and the underlying fundamental principles of both HIM and SIMS. We then present and discuss instrumental aspects of the HIM and SIMS techniques, highlighting the advantage of the integrated HIM-SIMS instrument. We give an overview on the performance characteristics of the HIM-SIMS technique, which is capable of producing elemental SIMS maps with lateral resolution below 20 nm, approaching the physical resolution limits, while maintaining a sub-nanometric resolution in the secondary electron microscopy mode. In addition, we showcase different strategies and methods allowing to take profit of both capabilities of the HIM-SIMS instrument (high-resolution imaging using secondary electrons and mass filtered secondary sons) in a correlative approach. Since its development HIM-SIMS has been successfully applied to a large variety of scientific and technological topics. Here, we will present and summarise recent applications of nanoscale imaging in materials research, life sciences and geology.

Bio-imaging with the helium-ion microscope: A review

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

Scanning transmission imaging in the helium ion microscope using a microchannel plate with a delay line detector

A detection system based on a microchannel plate with a delay line readout structure has been developed to perform scanning transmission ion microscopy (STIM) in the helium ion microscope (HIM). This system is an improvement over other existing approaches since it combines the information of the scanning beam position on the sample with the position (scattering angle) and time of the transmission events. Various imaging modes, such as bright field and dark field or the direct image of the transmitted signal, can be created by post-processing the collected STIM data. Furthermore, the detector has high spatial and temporal resolution, is sensitive to both ions and neutral particles over a wide energy range, and shows robustness against ion beam-induced damage. A special in-vacuum movable support gives the possibility of moving the detector vertically, placing the detector closer to the sample for the detection of high-angle scattering events, or moving it down to increase the angular resolution and distance for time-of-flight measurements. With this new system, we show composition-dependent contrast for amorphous materials and the contrast difference between small-angle and high-angle scattering signals. We also detect channeling-related contrast on polycrystalline silicon, thallium chloride nanocrystals, and single-crystalline silicon by comparing the signal transmitted at different directions for the same data set.

Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine

Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.

Visualization and Chemical Characterization of the Cathode Electrolyte Interphase Using He-Ion Microscopy and In Situ Time-of-Flight Secondary Ion Mass Spectrometry

Unstable cathode electrolyte interphase (CEI) formation increases degradation in high voltage Li-ion battery materials. Few techniques couple characterization of nano-scale CEI layers on the macroscale with in situ chemical characterization, and thus, information on how the underlying microstructure affects CEI formation is lost. Here, the process of CEI formation in a high voltage cathode material, LiCoPO₄, has been investigated for the first time using helium ion microscopy (HIM) and in situ time-of-flight (ToF) secondary ion mass spectrometry (SIMS). The combination of HIM and Ne-ion ToF-SIMS has been used to correlate the cycle-dependent morphology of the CEI layer on LiCoPO₄ with a local cathode microstructure, including position, thickness, and chemistry. HIM imaging identified partial dissolution of the CEI layer on discharge resulting in in-homogenous CEI coverage on larger LiCoPO₄ agglomerates. Ne-ion ToF-SIMS characterization identified oxyfluorophosphates from HF attack by the electrolyte and a Li-rich surface region. Variable thickness of the CEI layer coupled with inactive Li on the surface of LiCoPO₄ electrodes contributes to severe degradation over the course of 10 cycles. The HIM-SIMS technique has potential to further investigate the effect of microstructures on CEI formation in cathode materials or solid electrolyte interphase formation in anodes, thus aiding future electrode development.

Channeling effects in gold nanoclusters under He ion irradiation: insights from molecular dynamics simulations

The interpretation of helium ion microscopy (HIM) images of crystalline metal clusters requires microscopic understanding of the effects of He ion irradiation on the system, including energy deposition and associated heating, as well as channeling patterns. While channeling in bulk metals has been studied at length, there is no quantitative data for small clusters. We carry out molecular dynamics simulations to investigate the behavior of gold nanoparticles with diameters of 5-15 nm under 30 keV He ion irradiation. We show that impacts of the ions can give rise to substantial heating of the clusters through deposition of energy into electronic degrees of freedom, but it does not affect channeling, as clusters cool down between consecutive impact of the ions under typical imaging conditions. At the same time, high temperatures and small cluster sizes should give rise to fast annealing of defects so that the system remains crystalline. Our results show that ion-channeling occurs not only in the principal low-index, but also in the intermediate directions. The strengths of different channels are specified, and their correlations with sputtering-yield and damage production is discussed, along with size-dependence of these properties. The effects of planar defects, such as stacking faults on channeling were also investigated. Finally, we discuss the implications of our results for the analysis of HIM images of metal clusters.

Stationary beam full-field transmission helium ion microscopy using sub-50 keV He+: Projected images and intensity patterns

A dedicated transmission helium ion microscope (THIM) for sub-50 keV helium has been constructed to investigate ion scattering processes and contrast mechanisms, aiding the development of new imaging and analysis modalities. Unlike a commercial helium ion microscope (HIM), the in-house built instrument allows full flexibility in experimental configuration. Here, we report projection imaging and intensity patterns obtained from powder and bulk crystalline samples using stationary broad-beam as well as convergent-beam illumination conditions in THIM. The He⁺ ions formed unexpected spot patterns in the far field for MgO, BN and NaCl powder samples, but not for Au-coated MgO. The origin of the spot patterns in these samples was investigated. Surface diffraction of ions was excluded as a possible cause because the recorded scattering angles do not correspond to the predicted Bragg angles. Complementary secondary electron (SE) imaging in the HIM revealed that these samples charge significantly under He⁺ ion irradiation. The spot patterns obtained in the THIM experiments are explained as artefacts related to sample charging. The results presented here indicate that factors other than channeling, blocking and surface diffraction of ions have an impact on the final intensity distribution in the far field. Hence, the different processes contributing to the final intensities will need to be understood in order to decouple and study the relevant ion-beam scattering and deflection phenomena.