Internal Energy Distribution of Secondary Ions Under Argon and Bismuth Cluster Bombardments: "Soft" Versus "Hard" Desorption-Ionization Process

Suppressing Lithium Migration in a Carbon Fiber Negative Electrode During Atom Probe Tomography Analysis

Carbon fibers can play dual roles, carrying mechanical load and hosting lithium (Li) simultaneously in multifunctional devices called structural batteries. It is essential to gain a detailed understanding on the interaction between Li and carbon fibers on the nanoscale. Atom probe tomography (APT) can potentially reveal individual Li and C atoms. However, lithiated carbon fibers experience massive Li migration once exposed to the electric field in the APT instrument. We show that a few nanometers of a chromium (Cr) coating on APT specimens can shield the electric field and suppress the massive Li migration. The related effects of the Cr coating, such as introduction of oxygen, enhanced mass resolving power of the mass spectrum, and increased portion of single hits, are also discussed.

Molecular Dynamics Simulations of Soft and Reactive Landing of Proteins Desorbed by Argon Cluster Bombardment

Reactive molecular dynamics (MD) simulations were conducted to investigate the soft and reactive landing of hyperthermal velocity proteins transferred to a vacuum using large argon clusters. Experimentally, the interaction of argon cluster ion beams (Ar1000-5000+) with a target biofilm was previously used in such a manner to transfer lysozymes onto a collector with the retention of their bioactivity, paving the way to a new solvent-free method for complex biosurface nanofabrication. However, the experiments did not give access to a microscopic view of the interactions needed for their full understanding, which can be provided by the MD model. Our reactive force field simulations clarify the landing mechanisms of the lysozymes and their fragments on collectors with different natures (gold- and hydrogen-terminated graphite). The results highlight the conditions of soft and reactive landing on rigid surfaces, the effects of the protein structure, energy, and incidence angle before landing, and the adhesion forces with the collector substrate. Many of the obtained results can be generalized to other soft and reactive landing approaches used for biomolecules such as electrospray ionization and matrix-assisted laser desorption ionization.

Gas Cluster Ion Beam-Assisted Deposition for Fabricating Dry Multilayers Containing Enzyme and Substrate with On-Demand Release

Gas cluster ion beam (GCIB)-assisted deposition is used to build multilayered protein-based structures. In this process, Ar3000-5000+ clusters bombard and sputter molecules from a reservoir (target) to a collector, an operation that can be sequentially repeated with multiple targets. The process occurs under a vacuum, making it adequate for further sample conservation in the dry state, since many proteins do not have long-term storage stability in the aqueous state. First of all, the stability in time and versatility in terms of molecule selection are demonstrated with the fabrication of peptide multilayers featuring a clear separation. Then, lysozyme and trypsin are used as protein models to show that the activity remaining on the collector after deposition is linearly proportional to the argon ion dose. The energy per atom (E/n) of the Ar clusters is a parameter that was also changed for lysozyme deposition, and its increase negatively affects activity. The intact detection of larger protein molecules by SDS-PAGE gel electrophoresis and a bioassay (trypsin at ≈25 kDa and glucose oxidase (GOx) at ≈80 kDa) is demonstrated. Finally, GOx and horseradish peroxidase, two proteins involved in the same enzymatic cascade, are successively deposited on β-d-glucose to build an on-demand release material in which the enzymes and the substrate (β-d-glucose) are combined in a dry trilayer, and the reaction occurs only upon reintroduction in aqueous medium.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

Matrix-Enhanced SIMS: The Influence of Primary Ion Species and Cluster Size on Ion Yield and Ion Yield Enhancement of Lipids

Time-of-flight secondary ion mass spectrometry is one of the most promising techniques for label-free analysis of biomolecules with nanoscale spatial resolution. However, high-resolution imaging of larger biomolecules such as phospholipids and peptides is often hampered by low yields of molecular ions. Matrix-enhanced SIMS (ME-SIMS), in which an organic matrix is added to the sample, is one promising approach to enhancing the ion yield for biomolecules. Optimizing this approach has, however, been challenging because the processes involved in increasing the ion yield in ME-SIMS are not yet fully understood. In this work, the matrix α-cyano-4-hydroxycinnamic acid (HCCA) has been combined with cluster primary ion analysis to better understand the roles of proton donation and reduced fragmentation on lipid molecule ion yield. A model system consisting of 1:100 mol ratio dipalmitoylphosphatidylcholine (DPPC) in HCCA as well as an HCCA-coated mouse brain cryosection have been studied using a range of Bi and Ar cluster ions. Although the molecular ion yield increased with an increase in cluster ion size, the enhancement of the signals from intact lipid molecules decreased with an increase in cluster ion size for both the model system and the mouse brain. Additionally, in both systems, protonated molecular ions were significantly more enhanced than sodium and potassium cationized molecules for all of the primary ions utilized. For the model system, the DPPC molecular ion yield was increased by more than an order of magnitude for all of the primary ions studied, and fragmentation of DPPC was dramatically reduced. However, on the brain sample, even though the HCCA matrix reduced DPPC fragmentation for all of the primary ions studied, the matrix coating suppressed the ion yield for some lipids when the larger cluster primary ions were employed. This indicated insufficient migration of the lipids into the matrix coating, so that dilution by the matrix overpowered the enhancement effect. This study provides strong evidence that the HCCA matrix both enhances protonation and reduces fragmentation. For imaging applications, the ability of the analytes to migrate to the surface of the matrix coating is also a critical factor for useful signal enhancement. This work demonstrates that the HCCA matrix provides a softer desorption environment when using Bi cluster ions than that obtained using the large gas cluster ions studied alone, indicating the potential for improved high spatial resolution imaging with ME-SIMS.

Time-of-flight secondary ion mass spectrometry imaging in cultural heritage: A focus on old paintings

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging is a surface analysis technique that identifies and spatially resolves the chemical composition of a sample with a lateral resolution of less than 1 μm. Depth analyses can also be performed over thicknesses of several microns. In the case of a painting cross section, for example, TOF-SIMS can identify the organic composition, by detecting molecular ions and fragments of binders, as well as the mineral composition of most of the pigments. Importantly, the technique is almost not destructive and is therefore increasingly used in cultural heritage research such as the analysis of painting samples, especially old paintings. In this review, state of the art of TOF-SIMS analysis methods will be described with a particular focus on tuning the instruments for the analysis of painting cross sections and with several examples from the literature showing the added value of this technique when studying cultural heritage samples.

(CO2)n+, (H2O)n+, and (H2O)n+ (CO2) gas cluster ion beam secondary ion mass spectrometry: analysis of lipid extracts, cells, and Alzheimer's model mouse brain tissue

This work assesses the potential of new water cluster-based ion beams for improving the capabilities of secondary ion mass spectrometry (SIMS) for in situ lipidomics. The effect of water clusters was compared to carbon dioxide clusters, along with the effect of using pure water clusters compared to mixed water and carbon dioxide clusters. A signal increase was found when using pure water clusters. However, when analyzing cells, a more substantial signal increase was found in positive ion mode when the water clusters also contained carbon dioxide, suggesting that additional reactions are in play. The effects of using a water primary ion beam on a more complex sample were investigated by analyzing brain tissue from an Alzheimer’s disease transgenic mouse model. The results indicate that the ToF-SIMS results are approaching those from MALDI as ToF-SIMS was able to image lyso-phosphocholine (LPC) lipids, a lipid class that for a long time has eluded detection during SIMS analyses. Gangliosides, sulfatides, and cholesterol were also imaged.

Comparison of internal energy distributions generated by supercritical fluid chromatography versus liquid chromatography hyphenated with electrospray high resolution mass spectrometry

The internal energy distributions of thermometer ions dissolved in supercritical and liquid solvents and produced in the gas phase by electrospray (ESI) were measured and compared by the survival yield method. The influence of different chromatographic conditions such as the nature of solvents, the composition of the mobile phase, the pressure of the back pressure regulator was studied for supercritical fluid chromatography (SFC) whereas the influence of the composition and of the flow rate of the mobile phase was investigated for liquid chromatography (LC). The MS instrumental parameters were studied in parallel for SFC and LC showing that the drying gas temperature and the fragmentor voltage affected the internal energy distribution, whereas the capillary voltage did not modify the internal energy distribution. A comparison of the internal energy distributions generated by SFC and LC was carried out leading to conclude that SFC led to higher internal energy, i.e. more in-source fragment ions, than LC.

Direct Analysis of Ion-Induced Peptide Fragmentation in Secondary-Ion Mass Spectrometry

Primary-ion-induced fragmentation in organic molecules can strongly influence the results in secondary-ion mass spectrometry (SIMS) of organic and biomolecular samples. In order to characterize this ion-induced fragmentation, oligopeptide samples irradiated in SIMS experiments were investigated by means of desorption/ionization induced by neutral SO₂ clusters (DINeC). The latter is a nondestructive desorption method for mass spectrometry of biomolecules, which gives direct access to the fragments induced in the sample. Comparison of TOF-SIMS and DINeC mass spectra revealed qualitative differences between the fragments, which remain in the sample and the fragments sputtered during ion bombardment. The fragmentation strength and its spatial distribution were found to be quantitatively different for Bi₁⁺, Bi₃⁺, and Ar₁₀₀₀⁺ primary ions, leading to different distributions of the degree of fragmentation in the samples as directly measured by means of DINeC depth profiles.

Cryogenic OrbiSIMS Localizes Semi-Volatile Molecules in Biological Tissues

OrbiSIMS is a recently developed instrument for label-free imaging of chemicals with micron spatial resolution and high mass resolution. We report a cryogenic workflow for OrbiSIMS (Cryo-OrbiSIMS) that improves chemical detection of lipids and other biomolecules in tissues. Cryo-OrbiSIMS boosts ionization yield and decreases ion-beam induced fragmentation, greatly improving the detection of biomolecules such as triacylglycerides. It also increases chemical coverage to include molecules with intermediate or high vapor pressures, such as free fatty acids and semi-volatile organic compounds (SVOCs). We find that Cryo-OrbiSIMS reveals the hitherto unknown localization patterns of SVOCs with high spatial and chemical resolution in diverse plant, animal, and human tissues. We also show that Cryo-OrbiSIMS can be combined with genetic analysis to identify enzymes regulating SVOC metabolism. Cryo-OrbiSIMS is applicable to high resolution imaging of a wide variety of non-volatile and semi-volatile molecules across many areas of biomedicine.

Large cluster ions: soft local probes and tools for organic and bio surfaces

Ionised cluster beams have been produced and employed for thin film deposition and surface processing for half a century. In the last two decades, kiloelectronvolt cluster ions have also proved to be outstanding for surface characterisation by secondary ion mass spectrometry (SIMS), because their sputter and ion yields are enhanced in a non-linear fashion with respect to monoatomic projectiles, with a resulting step change of sensitivity for analysis and imaging. In particular, large gas cluster ion beams, or GCIB, have now become a reference in organic surface and thin film analysis using SIMS and X-ray photoelectron spectroscopy (XPS). The reason is that they induce soft molecular desorption and offer the opportunity to conduct damageless depth-profiling and 3D molecular imaging of the most sensitive organic electronics and biological samples, with a nanoscale depth resolution. In line with these recent developments, the present review focuses on rather weakly-bound, light-element cluster ions, such as noble or other gas clusters, and water or alcohol nanodroplets (excluding clusters made of metals, inorganic salts or ionic liquids) and their interaction with surfaces (essentially, but not exclusively, organic). The scope of this article encompasses three aspects. The first one is the fundamentals of large cluster impacts with surfaces, using the wealth of information provided by molecular dynamics simulations and experimental observations. The second focus is on recent applications of large cluster ion beams in surface characterisation, including mass spectrometric analysis and 2D localisation of large molecules, molecular depth-profiling and 3D molecular imaging. Finally, the perspective explores cutting edge developments, involving (i) new types of clusters with a chemistry designed to enhance performance for mass spectrometry imaging, (ii) the use of cluster fragment ion backscattering to locally retrieve physical surface properties and (iii) the fabrication of new biosurface and thin film architectures, where large cluster ion beams are used as tools to transfer biomolecules in vacuo from a target reservoir to any collector substrate.