Reduce the matrix effect in biological tissue imaging using dynamic reactive ionization and gas cluster ion beams

Recent advances in mass spectrometry imaging of single cells

Mass spectrometry imaging (MSI) is a sensitive, specific, label-free imaging analysis technique that can simultaneously obtain the spatial distribution, relative content, and structural information of hundreds of biomolecules in cells and tissues, such as lipids, small drug molecules, peptides, proteins, and other compounds. The study of molecular mapping of single cells can reveal major scientific issues such as the activity pattern of living organisms, disease pathogenesis, drug-targeted therapy, and cellular heterogeneity. Applying MSI technology to the molecular mapping of single cells can provide new insights and ideas for the study of single-cell metabolomics. This review aims to provide an informative resource for those in the MSI community who are interested in single-cell imaging. Particularly, we discuss advances in imaging schemes and sample preparation, instrumentation improvements, data processing and analysis, and 3D MSI over the past few years that have allowed MSI to emerge as a powerful technique in the molecular imaging of single cells. Also, we highlight some of the most cutting-edge studies in single-cell MSI, demonstrating the future potential of single-cell MSI. Visualizing molecular distribution at the single-cell or even sub-cellular level can provide us with richer cell information, which strongly contributes to advancing research fields such as biomedicine, life sciences, pharmacodynamic testing, and metabolomics. At the end of the review, we summarize the current development of single-cell MSI technology and look into the future of this technology.

Using mass spectrometry imaging to visualize age-related subcellular disruption

Metabolic homeostasis balances the production and consumption of energetic molecules to maintain active, healthy cells. Cellular stress, which disrupts metabolism and leads to the loss of cellular homeostasis, is important in age-related diseases. We focus here on the role of organelle dysfunction in age-related diseases, including the roles of energy deficiencies, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, changes in metabolic flux in aging (e.g., Ca2+ and nicotinamide adenine dinucleotide), and alterations in the endoplasmic reticulum-mitochondria contact sites that regulate the trafficking of metabolites. Tools for single-cell resolution of metabolite pools and metabolic flux in animal models of aging and age-related diseases are urgently needed. High-resolution mass spectrometry imaging (MSI) provides a revolutionary approach for capturing the metabolic states of individual cells and cellular interactions without the dissociation of tissues. mass spectrometry imaging can be a powerful tool to elucidate the role of stress-induced cellular dysfunction in aging.

ToF-SIMS Depth Profiling of Metal, Metal Oxide, and Alloy Multilayers in Atmospheres of H2, C2H2, CO, and O2

The influence of the flooding gas during ToF-SIMS depth profiling was studied to reduce the matrix effect and improve the quality of the depth profiles. The profiles were measured on three multilayered samples prepared by PVD. They were composed of metal, metal oxide, and alloy layers. Dual-beam depth profiling was performed with 1 keV Cs⁺ and 1 keV O₂⁺ sputter beams and analyzed with a Bi⁺ primary beam. The novelty of this work was the application of H₂, C₂H₂, CO, and O₂ atmospheres during SIMS depth profiling. Negative cluster secondary ions, formed from sputtered metals/metal oxides and the flooding gases, were analyzed. A systematic comparison and evaluation of the ToF-SIMS depth profiles were performed regarding the matrix effect, ionization probability, chemical sensitivity, sputtering rate, and depth resolution. We found that depth profiling in the C₂H₂, CO, and O₂ atmospheres has some advantages over UHV depth profiling, but it still lacks some of the information needed for an unambiguous determination of multilayered structures. The ToF-SIMS depth profiles were significantly improved during H₂ flooding in terms of matrix-effect reduction. The structures of all the samples were clearly resolved while measuring the intensity of the M_nH_m^-, M_nO_m^-, M_nO_mH^-, and M_n^- cluster secondary ions. A further decrease in the matrix effect was obtained by normalization of the measured signals. The use of H₂ is proposed for the depth profiling of metal/metal oxide multilayers and alloys.

Improvement of biomolecular analysis in thin films using in situ matrix enhanced secondary ion mass spectrometry

Sensitivity to molecular ions remains a limiting factor for high resolution imaging mass spectrometry of organic and biological materials. Here, we investigate a variant of matrix-enhanced secondary ion mass spectrometry in which the transfer of matrix molecules to the analyte sample is carried out in situ (in situ ME-SIMS). This approach is therefore compatible with both 2D and 3D imaging by SIMS. In this exploratory study, nanoscale matrix layers were sputter-transferred inside our time-of-flight (ToF)-SIMS to a series of thin films of biomolecules (proteins, sugars, lipids) adsorbed on silicon, and the resulting layers were analyzed and depth-profiled. For this purpose, matrix molecules were desorbed from a coated target (obtained by drop-casting or sublimation) using 10 keV Ar₃₀₀₀⁺ ion beam sputtering, followed by redeposition on a collector carrying the sample to be analyzed. After evaluating the quality of the transfer of six different matrices on bare Si collectors, α-cyano-4-hydroxycinnamic acid (CHCA) was selected for further experiments. The mass spectra and depth profiles obtained from the organic layer prior to and after the sputter-transfer of CHCA were compared, along with those obtained from regular ME-SIMS samples (dried droplets) and, finally, with MALDI data for the same matrix-analyte combinations. Signal amplification factors were calculated by dividing the integrated molecular intensities obtained with or without matrix transfer. While the amplification factors are between 0.5 and 2 for molecules already detected with high intensities in SIMS, such as cholesterol or human angiotensin, other compounds show very large integrated signal amplification, even above two orders of magnitude. This is the case for D-glucose and cardiolipin, for which the molecular ion intensity is low (or very low) under normal SIMS analysis conditions. For such low ionization probability compounds, the beneficial effect of the matrix is unquestionable. Test experiments on mouse brain tissue sections also indicate signal enhancement with the matrix, especially for high mass lipid ions.

Effect of energy per atom (E/n) on the Ar gas cluster ion beam (Ar-GCIB) and O2+ cosputter process

Gas cluster ion beam (GCIB) is a promising technique for preserving molecular structures during ion sputtering and successfully profiling biological and soft materials. However, although GCIB yields lower damage accumulation compared with C60+ and monoatomic ion beams, the inevitable alteration of the chemical structure can introduce artifacts into the resulting depth profile. To enhance the ionization yield and further mask damage, a low-energy O2+ (200-500 V) cosputter can be applied. While the energy per atom (E/n) of GCIB is known to be an important factor influencing the sputter process, the manner through which E/n affects the GCIB-O2+ cosputter process remains unclear. In this study, poly(ethylene terephthalate) (PET) was used as a model material to investigate the sputter process of 10-20 kV Ar1000-4000+ (E/n = 2.5-20 eV per atom) with and without O2+ cosputter at different energies and currents. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) with Bi32+ as the primary ion was used to examine surfaces sputtered at different fluences. The sputter craters were also measured by alpha-step and atomic force microscopy in quantitative imaging mode. The SIMS results showed that the steady-state cannot be obtained with E/n values of less than 5 eV per atom due to damage accumulation using single GCIB sputtering. With a moderate E/n value of 5-15 eV per atom, the steady-state can be obtained, but the ∼50% decay in intensity indicated that damage cannot be masked completely despite the higher sputter yield. Furthermore, the surface Young's modulus decreased with increasing E/n, suggesting that depolymerization occurred. At an E/n value of 20 eV per atom, a failed profile was obtained with rapidly decreased sputter rate and secondary ion intensity due to the ion-induced crosslink. With O2+ cosputtering and a moderate E/n value, the oxidized species generated by O2+ enhanced the ionization yield, which led to a higher ion intensity at steady-state in general. Because higher kinetic energy or current density of O2+ led to a larger interaction volume and more structural damage that suppressed molecular ion intensity, the enhancement from O2+ was most apparent with low-energy-high-current (200 V, 80 μA cm-2) or high-energy-low-current (500 V, 5 μA cm-2) O2+ cosputtering with 0.5 μA cm-2 GCIBs. In these cases, little or no intensity drop was observed at the steady-state.

C-O Bond Dissociation and Induced Chemical Ionization Using High Energy (CO2)n+ Gas Cluster Ion Beam

A gas cluster ion beam (GCIB) source, consisting of CO₂ clusters and operating with kinetic energies of up to 60 keV, has been developed for the high resolution and high sensitivity imaging of intact biomolecules. The CO₂ molecule is an excellent molecule to employ in a GCIB source due to its relative stability and improved focusing capabilities, especially when compared to the conventionally employed Ar cluster source. Here we report on experiments aimed to examine the behavior of CO₂ clusters as they impact a surface under a variety of conditions. Clusters of (CO₂)_n⁺ (n = 2000~10,000) with varying sizes and kinetic energies were employed to interrogate both an organic and inorganic surface. The results show that C-O bond dissociation did not occur when the energy per molecule is less than 5 eV/n, but that oxygen adducts were seen in increasing intensity as the energy is above 5 eV/n, particularly, drastic enhancement up to 100 times of oxygen adducts was observed on Au surface. For Irganox 1010, an organic surface, oxygen containing adducts were observed with moderate signal enhancement. Molecular dynamics computer simulations were employed to test the hypothesis that the C-O bond is broken at high values of eV/n. These calculations show that C-O bond dissociation occurs at eV/n values less than the C-O bond energy (8.3 eV) by interaction with surface topological features. In general, the experiments suggest that the projectiles containing oxygen can enhance the ionization efficiency of surface molecules via chemically induced processes, and that CO₂ can be an effective cluster ion source for SIMS experiments. Graphical Abstract.

Quantifying SIMS of Organic Mixtures and Depth Profiles-Characterizing Matrix Effects of Fragment Ions

Sets of matrix factors, Ξ, are reported for the first time for secondary ions in secondary ion mass spectrometry for several binary organic systems. These show the interplay of the effects of ion velocity, fragment chemistry, and the secondary ion point of origin. Matrix factors are reported for negative ions for Irganox 1010 with FMOC or Irganox 1098 and, for both positive and negative ions, with Ir(ppy)2(acac). For Irganox 1010/FMOC, the Ξ values for Irganox 1010 fall with m/z, whereas those for FMOC rise. For m/z < 250, Ξ scales very approximately with (m/z)^0.5, supporting a dependence on the ion velocity at low mass. Low-mass ions generally have low matrix factors but |Ξ| may still exceed 0.5 for m/z < 50. Analysis of ion sequences with addition or loss of a hydrogen atom shows that the Ξ values for Irganox 1010 and FMOC ions change by - 0.026 and 0.24 per hydrogen atom, respectively, arising from the changing charge transfer rate constant. This effect adds to that of velocity and may be associated with the nine times more hydrogen atoms in the Irganox 1010 molecule than in FMOC. For Irganox 1098/Irganox 1010, the molecular similarity leads to small |Ξ|, except for the pseudo molecular ions where the behavior follows Irganox 1010/FMOC. For Ir(ppy)2(acac)/Irganox 1010, the positive secondary ions show twice the matrix effects of negative ions. These data provide the first overall assessment of matrix factors in organic mixtures necessary for improved understanding for quantification and the precise localization of species. Graphical Abstract ᅟ.

The influence of polyatomic primary ion chemistry on matrix effects in secondary ion mass spectrometry analysis

RATIONALE

The application of mass spectrometry imaging techniques to determine two- (2D) and three- (3D) dimensional chemical distribution ideally provides uniform, high sensitivity to multiple components and reliable quantification. These criteria are typically not met due to variations in sensitivity due to the chemistry of the analyte and surrounding surface chemistry. Here we explore the influence of projectile beam chemistry and sample chemistry in time-of-flight secondary ion mass spectrometry (TOF-SIMS). To the authors' knowledge this is the first time the combined effects of projectile chemistry and sample environment on the quantitative determination of mixed samples have been systematically studied.

METHODS

Secondary ion yields of lipid and amino acid mixtures were measured under 20 keV C₆₀ , Ar_n , and (H₂ O)_n cluster ion bombardment (n = 2000 or 4000) using TOF-SIMS. Ion suppression/enhancement effects were studied in dry sample films and in trehalose and water ice matrices.

RESULTS

The extent of the matrix effects and the secondary ion yield were found to depend on the chemistry of the primary ion beam and (for C₆₀ , Ar_n ) on the nature of the sample matrix. Under (H₂ O)_n bombardment the sample matrix had negligible effect on the analysis.

CONCLUSIONS

Compared with C₆₀ and Ar_n , water-containing cluster projectiles enhanced the sensitivity of TOF-SIMS determination of the chosen analytes and reduced the effect of signal suppression/enhancement in multicomponent samples and in different sample matrices. One possible explanation for this is that the (H₂ O)₄₀₀₀ projectile initiates on impact a nanoscale matrix environment that is very similar to that in frozen-hydrated samples in terms of the resulting ionisation effects. The competition between analytes for protons and the effect of the sample matrix are reduced with water-containing cluster projectiles. These chemically reactive projectile beams have improved characteristics for quantitative chemical imaging by TOF-SIMS compared with their non-reactive counterparts.

Gas Cluster Ion Beams for Secondary Ion Mass Spectrometry

Gas cluster ion beams (GCIBs) provide new opportunities for bioimaging and molecular depth profiling with secondary ion mass spectrometry (SIMS). These beams, consisting of clusters containing thousands of particles, initiate desorption of target molecules with high yield and minimal fragmentation. This review emphasizes the unique opportunities for implementing these sources, especially for bioimaging applications. Theoretical aspects of the cluster ion/solid interaction are developed to maximize conditions for successful mass spectrometry. In addition, the history of how GCIBs have become practical laboratory tools is reviewed. Special emphasis is placed on the versatility of these sources, as size, kinetic energy, and chemical composition can be varied easily to maximize lateral resolution, hopefully to less than 1 micron, and to maximize ionization efficiency. Recent examples of bioimaging applications are also presented.

Reducing the Matrix Effect in Organic Cluster SIMS Using Dynamic Reactive Ionization

Dynamic reactive ionization (DRI) utilizes a reactive molecule, HCl, which is doped into an Ar cluster projectile and activated to produce protons at the bombardment site on the cold sample surface with the presence of water. The methodology has been shown to enhance the ionization of protonated molecular ions and to reduce salt suppression in complex biomatrices. In this study, we further examine the possibility of obtaining improved quantitation with DRI during depth profiling of thin films. Using a trehalose film as a model system, we are able to define optimal DRI conditions for depth profiling. Next, the strategy is applied to a multilayer system consisting of the polymer antioxidants Irganox 1098 and 1010. These binary mixtures have demonstrated large matrix effects, making quantitative SIMS measurement not feasible. Systematic comparisons of depth profiling of this multilayer film between directly using GCIB, and under DRI conditions, show that the latter enhances protonated ions for both components by 4- to ~15-fold, resulting in uniform depth profiling in positive ion mode and almost no matrix effect in negative ion mode. The methodology offers a new strategy to tackle the matrix effect and should lead to improved quantitative measurement using SIMS. Graphical Abstract ᅟ.

CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry

The emergence of argon-based gas cluster ion beams for SIMS experiments opens new possibilities for molecular depth profiling and 3D chemical imaging. These beams generally leave less surface chemical damage and yield mass spectra with reduced fragmentation compared with smaller cluster projectiles. For nanoscale bioimaging applications, however, limited sensitivity due to low ionization probability and technical challenges of beam focusing remain problematic. The use of gas cluster ion beams based upon systems other than argon offer an opportunity to resolve these difficulties. Here we report on the prospects of employing CO2 as a simple alternative to argon. Ionization efficiency, chemical damage, sputter rate, and beam focus are investigated on model compounds using a series of CO2 and Ar cluster projectiles (cluster size 1000-5000) with the same mass. The results show that the two projectiles are very similar in each of these aspects. Computer simulations comparing the impact of Ar2000 and (CO2)2000 on an organic target also confirm that the CO2 molecules in the cluster projectile remain intact, acting as a single particle of m/z 44. The imaging resolution employing CO2 cluster projectiles is improved by more than a factor of two. The advantage of CO2 versus Ar is also related to the increased stability which, in addition, facilitates the operation of the gas cluster ion beams (GCIB) system at lower backing pressure. Graphical Abstract ᅟ.