High-Reactivity Matrices Increase the Sensitivity of Matrix Enhanced Secondary Ion Mass Spectrometry

High-Throughput Quantitative Analysis of Amino Acids in Freeze-Dried Drops Using Time-of-Flight Secondary Ion Mass Spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a promising analytical tool for molecular profiling in biological applications. However, its ultrahigh vacuum environment and matrix effects hamper the absolute quantitation of solution samples. Herein, we present a rapid high-throughput platform for quantitative ToF-SIMS analysis of amino acids in matrix deposits formed from freeze-dried solution drops through ice sublimation on a parylene film microarray substrate. Droplets of the amino acid solutions, which were mixed with stable isotope-labeled phenylalanine (F*) of high concentration (10 mM), were loaded on wells of the microarray, then frozen and evaporated slowly below the freezing point, forming continuous solid-phase F* matrix deposits. The amino acids (≤500 μM), adequately well dispersed throughout the F* matrix deposits on each well, were quantitatively analyzed by ToF-SIMS in a rapid and high-throughput fashion. The lower limit of quantitation reached below 10 μM.

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.

Influence of Matrix pKa on Molecular Ion Formation in Matrix-Enhanced Secondary-Ion Mass Spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is one of the most important techniques for chemical imaging of nanomaterials and biological samples with high lateral resolution. However, low ionization efficiency limits the detection of many molecules at low concentrations or in very small volumes. One promising approach to increasing the sensitivity of the technique is by the addition of a matrix that promotes ionization and desorption of important analyte molecules. This approach is known as matrix-enhanced secondary-ion mass spectrometry (ME-SIMS). We have investigated the effect of matrix acidity on molecular ion formation in three different biomolecules. A series of cinnamic acid based matrixes that vary in acidity was employed to systematically investigate the influence of matrix acidity on analyte ion formation. The positive ion signal for all three biomolecules showed a strong increase for more acidic matrixes. The most acidic matrix was then vapor-deposited onto mouse brain sections. This led to significant enhancement of lipid signals from the brain. This work indicates that proton donation plays an important role in the formation of molecular ions in ME-SIMS.

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.

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.

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.

Visualizing molecular distributions for biomaterials applications with mass spectrometry imaging: a review

Mass spectrometry imaging (MSI) is a rapidly emerging field that is continually finding applications in new and exciting areas. The ability of MSI to measure the spatial distribution of molecules at or near the surface of complex substrates makes it an ideal candidate for many applications, including those in the sphere of materials chemistry. Continual development and optimization of both ionization sources and analyzer technologies have resulted in a wide array of MSI tools available, both commercially available and custom-built, with each configuration possessing inherent strengths and limitations. Despite the unique potential of MSI over other chemical imaging methods, their potential and application to (bio)materials science remains in our view a largely underexplored avenue. This review will discuss these techniques enabling high parallel molecular detection, focusing on those with reported uses in (bio)materials chemistry applications and highlighted with select applications. Different technologies are presented in three main sections; secondary ion mass spectrometry (SIMS) imaging, matrix-assisted laser desorption ionization (MALDI) MSI, and emerging MSI technologies with potential for biomaterial analysis. The first two sections (SIMS and MALDI) discuss well-established methods that are continually evolving both in technological advancements and in experimental versatility. In the third section, relatively new and versatile technologies capable of performing measurements under ambient conditions will be introduced, with reported applications in materials chemistry or potential applications discussed. The aim of this review is to provide a concise resource for those interested in utilizing MSI for applications such as biomimetic materials, biological/synthetic material interfaces, polymer formulation and bulk property characterization, as well as the spatial and chemical distributions of nanoparticles, or any other molecular imaging application requiring broad chemical speciation.

Sequencing and Identification of Endogenous Neuropeptides with Matrix-Enhanced Secondary Ion Mass Spectrometry Tandem Mass Spectrometry

Matrix-enhanced secondary ion mass spectrometry (ME-SIMS) has overcome one of the biggest disadvantages of SIMS analysis by providing the ability to detect intact biomolecules at high spatial resolution. By increasing ionization efficiency and minimizing primary ion beam-induced fragmentation of analytes, ME-SIMS has proven useful for detection of numerous biorelevant species, now including peptides. We report here the first demonstration of tandem ME-SIMS for de novo sequencing of endogenous neuropeptides from tissue in situ (i.e., rat pituitary gland). The peptide ions were isolated for tandem MS analysis using a 1 Da mass isolation window, followed by collision-induced dissociation (CID) at 1.5 keV in a collision cell filled with argon gas, for confident identification of the detected peptide. Using this method, neuropeptides up to m/z 2000 were detected and sequenced from the posterior lobe of the rat pituitary gland. These results demonstrate the potential for ME-SIMS tandem MS development in bottom-up proteomics imaging at high-spatial resolution.

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

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.

An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue

We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS.

Effects of a proton-conducting ionic liquid on secondary ion formation in time-of-flight secondary ion mass spectrometry

RATIONALE

A protic ionic liquid, diethylmethylammonium trifluoromethanesulfonate ([dema][TfO]), has low vapor pressure and high protonic conductivity even at room temperature. Since [dema][TfO] has a mobile proton in its salt structure, its primary beam is expected to enhance the formation of protonated molecular ions. However, mass spectrometric characteristics of [dema][TfO] are not well known. In order to develop an ionic-liquid primary beam source, it is necessary to investigate such characteristics.

METHODS

The first time-of-flight secondary ion mass spectrometry (TOF-SIMS) experiment using an Ar(+) primary ion beam was performed to analyze two samples: a neat [dema][TfO] sample and a mixed sample of arginine and [dema][TfO]. Beam characteristics of [dema][TfO] generated by vacuum electrospray were investigated using an apparatus for measuring transient responses of a beam current. The second TOF-SIMS experiment using a [dema][TfO] primary beam was performed to analyze three samples: arginine, a mixture of arginine and [dema][TfO], and poly(ethylene glycol) (PEG300).

RESULTS

The [dema][TfO] primary beam was useful in generating protonated arginine; however, it was not helpful in detecting PEG300. The results were explained by considering gas-phase basicities and proton affinities of analytes and [dema][TfO] constituents. Projectile energy per nucleon of the [dema][TfO] beam was examined; it would be necessary to reduce m/z values of ionic-liquid charged droplets. In addition, a screening method was proposed to select ionic liquids suitable for primary ion beams.

CONCLUSIONS

Since [dema][TfO] can act as a proton source, its primary beam can effectively generate protonated secondary ions of analytes. Consequently, proton-conducting ionic liquids such as [dema][TfO] are expected to have great potentials as primary ion beams in TOF-SIMS.

Three-dimensional nanoscale molecular imaging by extreme ultraviolet laser ablation mass spectrometry

Analytical probes capable of mapping molecular composition at the nanoscale are of critical importance to materials research, biology and medicine. Mass spectral imaging makes it possible to visualize the spatial organization of multiple molecular components at a sample's surface. However, it is challenging for mass spectral imaging to map molecular composition in three dimensions (3D) with submicron resolution. Here we describe a mass spectral imaging method that exploits the high 3D localization of absorbed extreme ultraviolet laser light and its fundamentally distinct interaction with matter to determine molecular composition from a volume as small as 50 zl in a single laser shot. Molecular imaging with a lateral resolution of 75 nm and a depth resolution of 20 nm is demonstrated. These results open opportunities to visualize chemical composition and chemical changes in 3D at the nanoscale.

Investigations Into the Interactions of a MALDI Matrix with Organic Thin Films Using C60+ SIMS Depth Profiling

Molecular depth profiling of multilayer organic films is now an established protocol for cluster secondary ion mass spectrometry (SIMS). This unique capability is exploited here to study the ionization mechanism associated with matrix-enhanced SIMS and possibly matrix assisted laser desorption/ionization (MALDI). Successful depth profiling experiments were performed on model bi-layer systems using 2,5-dihydroxybenzoic acid (DHB) as the matrix with dipalmitoylphosphatidylcholine (DPPC) or phenylalanine (PHE). The interaction between the matrix and organic analyte is monitored at the interface of the films. Tri-layer films with D2O as a thin-film sandwiched between the matrix and organic layers are also investigated to determine what role, if any, water plays during ionization. The results show successful depth profiles when taken at 90K. Mixing is observed at the interfaces of the films due to primary ion bombardment, but this mixing does not recreate the conditions necessary for ionization enhancement.

Secondary ion mass spectrometry imaging of biological cells and tissues

Secondary ion mass spectrometry (SIMS) is capable of providing detailed atomic and molecular characterization of the surface chemistry of (bio)molecular samples. It is one of a range of mass spectrometry imaging techniques that combine the high sensitivity and specificity of mass spectrometry with the capability to view the distribution of analytes within solid samples. The technique is particularly suited to the detection and imaging of small molecules such as lipids and other metabolites. A limit of detection in the ppm range and spatial resolution <1 μm can be obtained. Recent progress in instrumental developments, including new cluster ion beams, the implementation of tandem mass spectrometry (MS/MS), and the application of multivariate data analysis protocols promise further advances. This chapter presents a brief overview of the technique and methodology of SIMS using exemplar studies of biological cells and tissue.

Microscope mode secondary ion mass spectrometry imaging with a Timepix detector

In-vacuum active pixel detectors enable high sensitivity, highly parallel time- and space-resolved detection of ions from complex surfaces. For the first time, a Timepix detector assembly was combined with a secondary ion mass spectrometer for microscope mode secondary ion mass spectrometry (SIMS) imaging. Time resolved images from various benchmark samples demonstrate the imaging capabilities of the detector system. The main advantages of the active pixel detector are the higher signal-to-noise ratio and parallel acquisition of arrival time and position. Microscope mode SIMS imaging of biomolecules is demonstrated from tissue sections with the Timepix detector.