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.

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.

Enhancing Ion Signals and Improving Matrix Selection in Time-of-Flight Secondary Ion Mass Spectrometry with Microvolume Expansion Using Large Argon Clusters

The molecular environment has an important impact on the ionization mechanism in time-of-flight secondary ion mass spectrometry (ToF-SIMS). In complex samples, desorption/ionization, and thus the detection of a molecular signal, can be hampered by molecular entanglement, ionization-suppressive neighbors, or even an unfavorable sample substrate. Here, a method called microvolume expansion is developed to overcome these negative effects. Large argon clusters are able to transfer biomolecules from a target to a collector in vacuum. In this study, argon gas cluster ion beams (Arn+-GCIB with n centered around 3000 or 5000) are used to expand a microvolume from the sample to a collector, which is a material ideally enhancing the ionization yield. The collector is then analyzed using a liquid metal ion gun. The signal amplification factor corresponding to the expansion of phosphatidylcholine (PC) lipid on collectors partially covered with acidic matrices was evaluated as an initial proof of concept. In one experiment, the PC expansion on a pattern of four drop-casted matrix-assisted laser desorption/ionization matrices led to the selection of α-cyano-4-hydroxycinnamic (CHCA) as the optimal candidate for cationic PC detection. The ion signal is increased by at least three orders of magnitude when PC was expanded using 10 keV Ar3000+ and Ar5000+ on a sublimated layer of CHCA. Finally, the expansion of the gray matter of a mouse on different materials (Si, Au-coated Si, CHCA, and polyethylene) was achieved with varying degrees of success, demonstrating the potential of the method to further analyze complex and fragile biological assemblies.

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.

Method for Molecular Layer Deposition Using Gas Cluster Ion Beam Sputtering with Example Application In Situ Matrix-Enhanced Secondary Ion Mass Spectrometry

We introduce a technique for the directed transfer of molecules from an adjacent reservoir onto a sample surface inside the vacuum chamber of a ToF-SIMS instrument using gas cluster ion beam (GCIB) sputtering. An example application for in situ matrix-enhanced secondary ion mass spectrometry (ME SIMS) is provided. This protocol has attractive features since most modern SIMS instruments are equipped with a GCIB gun. No solvents are required that would delocalize analytes at the surface, and the transfer of matrix molecules can be interlaced with SIMS depth profiling and 3D imaging sputtering and analysis cycles, which is not possible with conventional ME SIMS strategies. The amount of molecular deposition can be finely tuned, which is important for such a surface sensitive technique as SIMS. To demonstrate the concept, we used 2,5-DHB as a matrix for the enhancement of three drug molecules embedded in a tissue homogenate. By automatic operation of sputter deposition and erosion (cleanup) cycles, depth profiling could be achieved with ME SIMS with good repeatability (<4% RSD). Furthermore, we explored several different matrix compounds, including α-CHCA and aqueous solutions of Brønsted acids (formic acid) and 3-nitrobenzonitrile, a volatile compound known to spontaneously produce ions. The latter two matrix compounds were applied at cryogenic measurement conditions, which extend the range of matrices applicable for ME SIMS. Enhancement ratios range from 2 to 13, depending on the analytes and matrix. The method works in principle, but enhancement ratios for the drug molecules are rather limited at this point. Further study and optimization is needed, and the technique introduced here provides a tool to perform systematic studies of matrix compounds and experimental conditions for their potential for signal enhancement in ME SIMS.

Single-cell omics analyses with single molecular detection: challenges and perspectives

The ultimate goal of single-cell analyses is to obtain the biomolecular content for each cell in unicellular and multicellular organisms at different points of their life cycle under variable environmental conditions. These require an assessment of: a) the total number of cells, b) the total number of cell types, and c) the complete and quantitative single molecular detection and identification for all classes of biopolymers, and organic and inorganic compounds, in each individual cell. For proteins, glycans, lipids, and metabolites, whose sequences cannot be amplified by copying as in the case of nucleic acids, the detection limit by mass spectrometry is about 10⁵ molecules. Therefore, proteomic, glycomic, lipidomic, and metabolomic analyses do not yet permit the assembly of the complete single-cell omes. The construction of novel nanoelectrophoretic arrays and nano in microarrays on a single 1-cm-diameter chip has shown proof of concept for a high throughput platform for parallel processing of thousands of individual cells. Combined with dynamic secondary ion mass spectrometry, with 3D scanning capability and lateral resolution of 50 nm, the sensitivity of single molecular quantification and identification for all classes of biomolecules could be reached. Further development and routine application of such technological and instrumentation solution would allow assembly of complete omes with a quantitative assessment of structural and functional cellular diversity at the molecular level.

Development of a Knudsen-type matrix coater for sample preparation for mass spectrometry imaging

The use of time-of-flight secondary ion mass spectrometry (SIMS) is of increasing interest for biological and medical applications due to its ability to provide chemical information on a submicrometer scale. However, the detection of larger biomolecules such as phospholipids and peptides is often inhibited by high fragmentation rates and low ionization efficiencies. One way to increase the secondary ion molecular yield is to chemically modify the surface using the matrix-enhanced SIMS approach, where an organic matrix is placed upon the surface. In this study, a Knudsen cell type matrix coater was developed in order to produce well-defined thicknesses of a matrix on a sample in order to study the effect of these matrix layers on the secondary ions. Using this technique, an order of magnitude enhancement of the useful ion yield for lipids was observed and clear enhancement of image contrast for lipids in brain tissue was demonstrated. The study shows that the layer thickness has a great influence on the emission of secondary ions, and therefore, its precise control is important for optimal yield enhancement.

Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS

Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix.