Metal Salts for Molecular Ion Yield Enhancement in Organic Secondary Ion Mass Spectrometry: A Critical Assessment

Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study

In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.

Cluster-Induced Desorption/Ionization of Polystyrene: Desorption Mechanism and Effect of Polymer Chain Length on Desorption Probability

Soft cluster-induced desorption/ionization of polystyrene oligomers was investigated with respect to application in mass spectrometry. Clear peak progressions corresponding to intact polystyrene molecules were observed in the mass spectra, and no fragmentation was detected; efficient desorption was deduced from quartz crystal microbalance measurements. Molecular dynamics (MD) simulations of the process revealed that even in the case of the nonpolar polystyrene molecules cluster-induced desorption proceeds via dissolvation in the polar clusters. Experimentally, a significantly lower desorption efficiency was observed for polystyrene molecules with larger chain length. Taking into account MD simulations and further experiments with mixed samples consisting of long- and short-chain polystyrene oligomers, the reduced desorption efficiency for longer chain polystyrene molecules was attributed to a stronger entanglement of the larger polystyrene molecules.

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.

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.

Probing nanoparticles and nanoparticle-conjugated biomolecules using time-of-flight secondary ion mass spectrometry

Bio-conjugated nanoparticles have emerged as novel molecular probes in nano-biotechnology and nanomedicine and chemical analyses of their surfaces have become challenges. The time-of-flight (TOF) secondary ion mass spectrometry (SIMS) has been one of the most powerful surface characterization techniques for both nanoparticles and biomolecules. When combined with various nanoparticle-based signal enhancing strategies, TOF-SIMS can probe the functionalization of nanoparticles as well as their locations and interactions in biological systems. Especially, nanoparticle-based SIMS is an attractive approach for label-free drug screening because signal-enhancing nanoparticles can be designed to directly measure the enzyme activity. The chemical-specific imaging analysis using SIMS is also well suited to screen nanoparticles and nanoparticle-biomolecule conjugates in complex environments. This review presents some recent applications of nanoparticle-based TOF-SIMS to the chemical analysis of complex biological systems.

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.

Fullerenes, nanotubes, and graphite as matrices for collision mechanism in secondary ion mass spectrometry: determination of cyclodextrin

A technique for improving the sensitivity of high mass molecular analysis is described. Three carbon species, fullerenes, single walled carbon nanotubes, and highly ordered pyrolytic graphite are introduced as matrices for the secondary ion mass spectrometry analysis of cyclodextrin (C(42)H(70)O(35), 1134 u). The fullerene and nanotubes are deposited as single deposition, and 10, 20, or 30 deposition films and cyclodextrin is deposited on top. The cyclodextrin parent-like ions and two fragments were analyzed. A 30 deposition fullerene film enhanced the intensity of cationized cyclodextrin with Na by a factor of 37. While the C(6)H(11)O(5) fragment, corresponding to one glucopyranose unit, increased by a factor of 16. Although fragmentation on fullerene is not suppressed, the intensity is twice as low as the parent-like ion. Deprotonated cyclodextrin increases by 100× and its C(8)H(7)O fragment by 10×. While the fullerene matrix enhances secondary ion emission, the nanotubes matrix film generates a basically constant yield. Graphite gives rise to lower intensity peaks than either fullerene or nanotubes. Scanning electron microscopy and atomic force microscopy provide images of the fullerene and nanotubes deposition films revealing flat and web structured surfaces, respectively. A "colliding ball" model is presented to provide a plausible physical mechanism of parent-like ion enhancement using the fullerene matrix.

Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold

The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).

Salt effects on ion formation in desorption mass spectrometry: an investigation into the role of alkali chlorides on peak suppression in time-of-flight-secondary ion mass spectrometry

In secondary ion mass spectrometry, the molecular environment from which a sample is analyzed can influence ion formation, affecting the resulting data. With the recent surge in studies involving examination of biological specimens, a better understanding of constituents commonly found in biological matrixes is necessary. In this article we discuss results from an investigation directed at understanding the role of salts doped as alkali chlorides in a model biological environment, arginine. The data show that addition of salt to the model system causes ion suppression of all the major mass spectral peaks attributed to arginine, with KCl having the largest suppression effect. Potential causes for the suppression effects are briefly discussed in relation to collected data. These theories include sample degradation, formation of salt adduct peaks, and anion neutralization. Investigation of the arginine salt data in comparison with data collected from pure salt systems indicates that suppression of the positive secondary ions is likely caused by a neutralization process involving the salt counteranion, chloride. To address the suppression issue, various procedures were performed on the arginine films such as sample washing with a cleaning solution (ammonium formate, ethanol, water) and analysis of films in a frozen-hydrated state. We present data from the analysis of the frozen-hydrated samples that shows both an ion yield enhancement and a significant amelioration of the salt suppression effects when compared to the samples run under standard conditions, demonstrating that it is a helpful approach to dealing with salt suppression.

Cluster ion beam profiling of organics by secondary ion mass spectrometry--does sodium affect the molecular ion intensity at interfaces?

The use of cluster ion beam sputtering for depth profiling organic materials is of growing technological importance and is a very active area of research. At the 44th IUVSTA Workshop on "Sputtering and Ion Emission by Cluster Ion Beams", recent results were presented of a cluster ion beam depth profile of a thin organic molecular layer on a silicon wafer substrate. Those data showed that the intensity of molecular secondary ions is observed to increase at the interface and this was explained in terms of the higher stopping power in the substrate and a consequently higher sputtering yield and even higher secondary ion molecular sputtering yield. An alternative hypothesis was postulated in the workshop discussion which may be paraphrased as: "under primary ion bombardment of an organic layer, mobile ions such as sodium may migrate to the interface with the inorganic substrate and this enhancement of the sodium concentration increases the ionisation probability, so increasing the molecular ion yield observed at the interface". It is important to understand if measurement artefacts occur at interfaces for quantification as these are of great technological relevance - for example, the concentration of drug in a drug delivery system. Here, we evaluate the above hypothesis using a sample that exhibits regions of high and low sodium concentration at both the organic surface and the interface with the silicon wafer substrate. There is no evidence to support the hypothesis that the probability of molecular secondary ion ionisation is related to the sodium concentration at these levels.

Imaging mass spectrometry

Imaging mass spectrometry combines the chemical specificity and parallel detection of mass spectrometry with microscopic imaging capabilities. The ability to simultaneously obtain images from all analytes detected, from atomic to macromolecular ions, allows the analyst to probe the chemical organization of a sample and to correlate this with physical features. The sensitivity of the ionization step, sample preparation, the spatial resolution, and the speed of the technique are all important parameters that affect the type of information obtained. Recently, significant progress has been made in each of these steps for both secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) imaging of biological samples. Examples demonstrating localization of proteins in tumors, a reduction of lamellar phospholipids in the region binding two single celled organisms, and sub-cellular distributions of several biomolecules have all contributed to an increasing upsurge in interest in imaging mass spectrometry. Here we review many of the instrumental developments and methodological approaches responsible for this increased interest, compare and contrast the information provided by SIMS and MALDI imaging, and discuss future possibilities.

Asymmetric Synthesis of Mono- and Dinuclear Bis(dipyrrinato) Complexes

The diastereoselective syntheses of Zn(II) bis(dipyrrinato) helicates is reported, involving ligands templated by the incorporation of homochiral binol within the linker joining the two dipyrrinato units. The most diastereoselective formation of dinuclear bis(dipyrrinato) helicates to date is reported. The formation of either mononuclear or dinuclear helicates can be tuned by varying the length of the linker between the dipyrrinato units and by varying the complexation procedure. The neutral dipyrrinato helicates were readily analyzed by HPLC to ascertain diastereoselectivity, and circular dichroism studies revealed the helical nature of the complexes. The molar ellipticities of the helicates produced by diastereoselective complexation are very large in the visible region and typically correspond to binol moieties in the UV region. Extensive X-ray crystallographic investigations further confirmed the helicity of the mononuclear Zn(II) helicates and identified significant interlayer displacement and bending within crystals.

Metal-assisted secondary ion mass spectrometry using atomic (Ga+, In+) and fullerene projectiles

The advantages and drawbacks of using either monatomic or buckminsterfullerene primary ions for metal-assisted secondary ion mass spectrometry (MetA-SIMS) are investigated using a series of organic samples including additive molecules, polyolefins, and small peptides. Gold deposition is mostly performed by sputter-coating, and in some cases, the results are compared to those of thermal evaporation (already used in a previous article: Delcorte, A.; Médard, N.; Bertrand, P. Anal. Chem. 2002, 74, 4955). The microstructure of the gold-covered sample surfaces is assessed by scanning and transmission electron microscopies. The merits of the different sets of experimental conditions are established via the analysis of fragment and parent-like ion yields. For most of the analyzed samples, the highest yields of fragment and parent-like ions are already reached with the sole use of C60+ projectiles. Metallization of the sample does not lead to a significant additional enhancement. For polyethylene and polypropylene, however, gold metallization associated with Ga+/In+ projectiles appears to be the only way to observe large cationized, sample-specific chain segments (m/z approximately 1000-2000). A detailed study of the polypropylene mass spectra as a function of gold coverage shows that the dynamics of yield enhancement by metal nanoparticles is strongly dependent on the choice of the projectile, e.g., a pronounced increase with Ga+ and a slow decay with C60+. The cases of Irganox 1010, a polymer antioxidant, and leucine enkephalin, a small peptide, allow us to investigate the specific influence of the experimental conditions on the emission of parent(like) ions such as M+, (M + Na)+, and (M + Au)+. The results show a dependence on both the type of sample and the considered secondary ion. Using theoretical and experimental arguments, the discussion identifies some of the mechanisms underlying the general trends observed in the results. Guidelines concerning the choice of the experimental conditions for MetA-SIMS are provided.

Static secondary ion mass spectrometry for biological and biomedical research

Static secondary ion mass spectrometry (SSIMS) is a capable of providing detailed atomic and molecular characterization of the surface chemistry of biological and biomedical materials. The technique is particularly suited to the detection and imaging of small molecules such as membrane lipids, metabolites, and drugs. A limit of detection in the ppm range and spatial resolution <1 microm can be obtained. Recent progress in instrumental developments, notably cluster ion beams, and the application of multivariate data analysis protocols, promise further advances. This chapter presents a brief overview of the theory and instrumentation of static secondary ion mass spectrometry followed by examples of a range of biological and biomedical applications. Because of the ultrahigh vacuum requirements and extreme surface sensitivity of the technique, appropriate sample preparation and handling is essential. These protocols, and the analysis methodology required to ensure high-quality, reliable data are described.

Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging

To expand the role of high spatial resolution secondary ion mass spectrometry (SIMS) in biological studies, numerous developments have been reported in recent years for enhancing the molecular ion yield of high mass molecules. These include both surface modification, including matrix-enhanced SIMS and metal-assisted SIMS, and polyatomic primary ions. Using rat brain tissue sections and a bismuth primary ion gun able to produce atomic and polyatomic primary ions, we report here how the sensitivity enhancements provided by these developments are additive. Combined surface modification and polyatomic primary ions provided approximately 15.8 times more signal than using atomic primary ions on the raw sample, whereas surface modification and polyatomic primary ions yield approximately 3.8 and approximately 8.4 times more signal. This higher sensitivity is used to generate chemically specific images of higher mass biomolecules using a single molecular ion peak.

Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes

This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.