Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays

Performance improvements in DNA-modified surfaces required for microarray and biosensor applications rely on improved capabilities to accurately characterize the chemistry and structure of immobilized DNA molecules on micropatterned surfaces. Recent innovations in imaging X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) now permit more detailed studies of micropatterned surfaces. We have exploited the complementary information provided by imaging XPS and imaging TOF-SIMS to detail the chemical composition, spatial distribution, and hybridization efficiency of amine-terminated single-stranded DNA (ssDNA) bound to commercial polyacrylamide-based, amine-reactive microarray slides, immobilized in both macrospot and microarray diagnostic formats. Combinations of XPS imaging and small spot analysis were used to identify micropatterned DNA spots within printed DNA arrays on slide surfaces and quantify DNA elements within individual microarray spots for determination of probe immobilization and hybridization efficiencies. This represents the first report of imaging XPS of DNA immobilization and hybridization efficiencies for arrays fabricated on commercial microarray slides. Imaging TOF-SIMS provided distinct analytical data on the lateral distribution of DNA within single array microspots before and after target hybridization. Principal component analysis (PCA) applied to TOF-SIMS imaging datasets demonstrated that the combination of these two techniques provides information not readily observable in TOF-SIMS images alone, particularly in identifying species associated with array spot nonuniformities (e.g., "halo" or "donut" effects often observed in fluorescence images). Chemically specific spot images were compared to conventional fluorescence scanned images in microarrays to provide new information on spot-to-spot DNA variations that affect current diagnostic reliability, assay variance, and sensitivity.     

Structural effects in the analysis of supported lipid bilayers by time-of-flight secondary ion mass spectrometry

We contribute to the rapidly emerging interest in the application of time-of-flight secondary ion mass spectrometry (TOF-SIMS) for chemical analysis of biological materials by presenting a careful TOF-SIMS investigation of structurally different SiO2-supported phospholipid assemblies. Freeze-dried supported 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (POPC) bilayers, Langmuir-Blodgett POPC monolayers, and disordered thick POPC films were investigated. Compared with the two latter structures, the supported bilayer showed a strong (5-10 times) enhancement in the yield of both the molecular and the dimer ion peaks of POPC, suggesting that the molecular peak may be used as a sensitive indicator for changes in the membrane structure and, in particular, an indicator for the presence of bilayer structures in, e.g., cell and tissue samples. The detection efficiency and the useful lateral resolution indicate that a lateral resolution of around 100 nm can be obtained on all structures by imaging the phosphocholine ion at 184 u using Bi3+ primary ions. For the chemically specific molecular peak at 760 u, the measured detection efficiencies correspond to a useful lateral resolution of around 2 microm for the bilayer structure. The results are discussed in relation to recent dynamic SIMS (nano-SIMS) analysis of freeze-dried supported lipid bilayers, displaying similar or higher lateral resolution, but which in contrast to TOF-SIMS requires isotopic labeling of the analyzed lipids.     

Surface analysis of polyethyleneterephthalate by ESCA and TOF-SIMS

PET (poly(ethylene-terephthalate)) samples provided by different suppliers were investigated with the surface-sensitive methods as electron spectroscopy for chemical analysis (ESCA) and time-of-flight secondary ion mass spectrometry (TOF-SIMS). Analysis by means of ESCA provides chemical information from a near-surface region of roughly 6 nm. Specific ESCA data on chemical shifts and on the ratio between oxygen and carbon are compared with corresponding values expected for the molecular structure of bulk PET. In addition, direct chemical information on the molecular structure at the PET surface (essentially from the first two monolayers) has been obtained by TOF-SIMS. Especially, positive and negative TOF-SIMS mass spectra were analyzed in detail and assigned with respect to characteristic polymer fragment ions. Several polymer additives as well as some contaminations present at the PET surfaces could be identified with TOF-SIMS. Dependent on the PET supplier, antioxidants and lubricants such as Irgafos 168, octylstearate, octylpalmitate, octylarachidate and PDMS (polydimethylsiloxane) found at the sample surfaces give typical positive and negative ion fragments.     

Time-of-flight secondary ion mass spectrometric analysis of the interface between bone and titanium implants

Implant healing into bone tissue is a process where the mature bone grows towards and eventually fuses with the implant. In this study we investigated implant healing during 4 weeks with focus on the implant-tissue interface. Our main interest was to study the mineralization process around the implant. Titanium discs were implanted in rat tibia for 2 and 4 weeks. After implantation cross sections of bone and implant were made using a low-speed saw equipped with a diamond wafering blade. One section from each sample was stained with basic fuchsin and micrographed by light microscopy (LM). The other section was analyzed with imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) using a Bi(3)(+) cluster ion source. This ion source has recently been shown to enable identification of high-mass hydroxyapatite (HA) fragment ions (m/z 291-653) in bone samples. The LM images were used to identify areas suitable for TOF-SIMS analysis. Three areas were selected for mass spectral analysis, corresponding to interface region, bone and soft tissue, from which positive ion spectra were recorded. In the areas identified as bone, high-mass HA fragments ions were found after both 2 and 4 weeks. In the soft tissue area, no high-mass ions were found after 4 weeks. However, after 2 weeks HA-related ions were identified in mineralized spots in areas defined as soft tissue. After 4 but not after 2 weeks, high-mass HA fragment ions were found in the interface region. In conclusion, differences were observed regarding mineralization between 2 and 4 weeks of implantation and between different regions surrounding the implants. Imaging TOF-SIMS analysis using a Bi(3)(+) cluster as ion source enables identification of high-mass HA fragment ions at implant-tissue interfaces in bone. This technique might therefore be useful for biocompatibility assessment and for studying the mineralization process at implant surfaces.     

Resonance ionization mass spectrometry of ion beam sputtered neutrals for element- and isotope-selective analysis of plutonium in micro-particles

Micro-particles containing actinides are of interest for risk assessments of contaminated areas, nuclear forensic analyses, and IAEA as well as Euratom safeguards programs. For their analysis, secondary ion mass spectrometry (SIMS) has been established as the state-of-the-art standard technique. In the case of actinide mixtures within the particles, however, SIMS suffers from isobaric interferences (e.g., ²³⁸U/²³⁸Pu, ²⁴¹Am/²⁴¹Pu). This can be eliminated by applying resonance ionization mass spectrometry which is based on stepwise resonant excitation and ionization of atoms with laser light, followed by mass spectrometric detection of the produced ions, combining high elemental selectivity with the analysis of isotopic compositions. This paper describes the instrumental modifications for coupling a commercial time-of-flight (TOF)-SIMS apparatus with three-step resonant post-ionization of the sputtered neutrals using a high-repetition-rate (kHz) Nd:YAG laser pumped tunable titanium:sapphire laser system. Spatially resolved ion images obtained from actinide-containing particles in TOF-SIMS mode demonstrate the capability for isotopic and spatial resolution. Results from three-step resonant post-ionization of bulk Gd and Pu samples successfully demonstrate the high elemental selectivity of this process.     

Chemical Analysis of Inorganic and Organic Surfaces and Thin Films by Static Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

By using mass spectrometry to analyze the atomic and molecular secondary ions that are emitted from a solid surface when bombarded with ions, one obtains detailed information about the chemical composition of the surface. A time-of-flight mass spectrometer is especially suitable for the analysis of secondary ions because of its high transmission, high mass resolution, and ability to detect ions of different masses simultaneously. By using a finely focused primary ion beam it is also possible to analyze microareas and generate surface images with a lateral resolution of 0.1 μm or less. Static time-of-flight secondary ion mass spectrometry (TOF-SIMS) allows monolayer imaging and local analysis of monolayers with high sensitivity, a wide mass range, high mass resolution, and high lateral resolution. Besides information on elements and isotopes, the technique yields direct information on the molecular level and can also be used to analyze surface species of high molecular mass that are thermally unstable and cannot be vaporized. The method can be applied to practically all types of materials and sample forms, including insulators in particular. In this article the basic principles of TOF-SIMS are explained, and its analytical capabilities for both large area and imaging applications are illustrated by examples. These include silicon surfaces (both uniform and structured), thermally unstable organic molecules on surfaces, synthetic polymers, and synthetically prepared molecular surface films, particles, and fibers. Emitted neutral particles can also be analyzed by postionization with a laser, and the possibilities of this technique are discussed.     

High-resolution,imaging TOF-SIMS: novel applications in medical research

The use of high-resolution, imaging TOF-SIMS is described and examples are made to demonstrate the application of the method in medical research. Cytochemistry by TOF-SIMS is shown by localization of diacylglycerol (DG) in cryostat sections of hyaline cartilage and by localization of corticosterone in cryostat sections of the adrenal gland cortex. Quantitative measurements and comparison of groups is shown by comparing the lipid content of adipose tissue from two mouse strains, transgenic mouse expressing the FOXC2 gene and wild-type controls. Finally, biopsies made for histopathological diagnosis of infantile reversible cytochrome c oxidase deficiency myopathy were analyzed in order to define the chemical content of areas showing a pathological structure in the light microscope. The use of high-resolution, imaging TOF-SIMS in medical research allows analysis of intact tissue and probe-free localization of specific target molecules in cells and tissues. The TOF-SIMS analysis is not dependent on penetration of reagents into the sample and also independent of probe reactivity such as cross-reactivity or background staining. The TOF-SIMS method can be made quantitative and allows for analysis of specific target molecules in defined tissue compartments.     

Molecular imaging of lipids in cells and tissues

The distribution pattern of lipid species in biological tissues was analyzed with imaging mass spectrometry (TOF-SIMS; time-of-flight secondary ion mass spectrometry). The first application shows distribution of a glycosphingolipid, the galactosylceramide-sulfate (sulfatide) with different hydrocarbon chain lengths and the fatty acids palmitate and oleate in rat cerebellum. Sulfatides were seen localized in regions suggested as paranodal areas of rat cerebellar white matter as well as in the granular layer, with highest concentrations at the borders of the white matter. Different distribution patterns could be shown for the fatty acid C16:0 palmitate and C18:1 oleate in rat cerebellum, which seem to origin partly from the hydrocarbon chains of phosphatidylcholine. Results were shown for two different tissue preparation methods, which were plunge-freezing and cryostat sectioning as well as high-pressure freezing, freeze-fracturing and freeze-drying.The second application shows TOF-SIMS analysis on a biological trial of choleratoxin treatment in mouse intestine. The effect of cholera toxin on lipids in the intestinal epithelium was shown by comparing control and cholera toxin treated mouse intestine samples. A significant increase of the cholesterol concentration was seen after treatment. Cholesterol was mainly localized to the brush border of enterocytes of the intestinal villi, which could be explained by the presence of cholesterol-rich lipid rafts present on the microvilli or by relations to cholesterol uptake. After cholera toxin exposure, cholesterol was seen increased in the nuclei of enterocytes and apparently in the interstitium of the villi.We find that imaging TOF-SIMS is a powerful tool for studies of lipid distributions in cells and tissues, enabling the elucidation of their role in cell function and biology.     

Adlayers of dimannoside thiols on gold: surface chemical analysis

Carbohydrate films on gold based on dimannoside thiols (DMT) were prepared, and a complementary surface chemical analysis was performed in detail by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), near-edge X-ray absorption fine structure (NEXAFS), FT-IR, and contact angle measurements in order to verify formation of ω-carbohydrate-functionalized alkylthiol films. XPS (C 1s, O 1s, and S 2p) reveals information on carbohydrate specific alkoxy (C-O) and acetal moieties (O-C-O) as well as thiolate species attached to gold. Angle-resolved synchrotron XPS was used for chemical speciation at ultimate surface sensitivity. Angle-resolved XPS analysis suggests the presence of an excess top layer composed of unbound sulfur components combined with alkyl moieties. Further support for DMT attachment on Au is given by ToF-SIMS and FT-IR analysis. Carbon and oxygen K-edge NEXAFS spectra were interpreted by applying the building block model supported by comparison to data of 1-undecanethiol, poly(vinyl alcohol), and polyoxymethylene. No linear dichroism effect was observed in the angle-resolved C K-edge NEXAFS.     

Phosphatidylethanolamine-induced cholesterol domains chemically identified with mass spectrometric imaging

Coexisting liquid phases of model membrane systems are chemically identified using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS). The systems studied were Langmuir-Blodgett (LB) model membranes of cholesterol (CH) with two different phospholipids, one a major component in the outer plasma membrane bilayer leaflet (dipalmitoylphosphatidylcholine (PC)) and the other a major component in the inner leaflet (dipalmitoylphosphatidylethanolamine (PE)). Binary mixtures of CH with each of the phospholipids were investigated, as well as a ternary system. A single homogeneous phase is evident for PC/CH, whereas both systems containing PE show lateral heterogeneity with phospholipid-rich and CH-rich regions. The interaction between CH and the two phospholipids differs due to the disparity between the phospholipid headgroups. Imaging TOF-SIMS offers a novel opportunity to chemically identify and differentiate the specific membrane locations of CH and phospholipid in membrane regions without the use of fluorescent dyes. This unique imaging method has been used to demonstrate the formation of micrometer-size CH domains in phosphatidylethanolamine-rich systems and is further evidence suggesting that CH may facilitate transport and signaling across the two leaflets of the plasma membrane.     

Localization of sphingomyelin in cholesterol domains by imaging mass spectrometry

The location of each lipid in a palmitoyloleoylphosphatidylcholine/18:0 sphingomyelin/cholesterol monolayer system is laterally resolved using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) without the necessity of adding fluorescent labels. This system of coexisting immiscible liquid phases shows cholesterol domains with sizes and shapes comparable to those in the fluorescence microscopy literature. The results show that SM localizes with cholesterol and that palmitoyloleoylphosphatidylcholine is excluded. Moreover, the segregation is not complete, and there is a small amount of both phospholipids distributed throughout.     

TOF-SIMS analysis of structured surfaces biofunctionalized by a one-step coupling of a spacer-linked GRGDS peptide

Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) was applied to validate GRGDS peptide patterned surfaces. The structuring of the surfaces included several steps: micro contact printing (μCP), chemical etching and aminofunctionalization followed by chemical coupling of spacer-linked GRGDS peptides via an isothiocyanate anchor. TOF-SIMS analysis of characteristic ions and molecular fragments with a lateral resolution of 100 nm allowed proving the change in chemical properties of the surface with each step during the structuring process. We found that the application of polydimethylsiloxane as stamp material resulted in the contamination of the surface with this polymer. TOF-SIMS investigations, however, also showed that during the preparation process the contaminations were removed and do not influence the bio functionality of the surface patterns. The results of the surface analysis carried out with TOF-SIMS were confirmed by complementary cell adhesion experiments with murine fibroblasts. As a result, specific cell adhesion restricted to GRGDS peptide functionalized areas was obvious by the formation of focal adhesion contacts in the fibroblasts. Thus, TOF-SIMS is the method of choice in chemical characterization of surfaces in structuring and functionalization processes, because it offers the opportunity to follow surface contamination during the preparation process and to assess the influence of the contamination on the applicability of the final substrate.     

Imaging fibrinogen adsorbed on noble metal surfaces with scanning tunneling microscopy: correlation of images with electron spectroscopy for chemical analysis, secondary ion mass spectrometry, and radiolabeling studies

Fibrinogen adsorption on gold and platinum surfaces has been studied with electron spectroscopy for chemical analysis (ESCA), secondary ion mass spectrometry (SIMS), ¹²⁵I labeling, and scanning tunneling microscopy (STM). Stable images of single molecules have been obtained, but are rare. ESCA, SIMS, and labeling studies confirm that absorbed fibrinogen is present on samples at monolayer and submonolayer coverages even when STM images show only a bare substrate. Imaging is more reproducible at high coverages at which single molecules cannot be resolved. Possible explanations for the failure of STM to observe adsorbed fibrinogen molecules are discussed.     

Surface analysis of polymer materials by secondary ion mass spectrometry

Atomic as well as molecular secondary ions are emitted from the uppermost monolayer of a solid during ion bombardment. Mass analysis of these positive and negative secondary ions supplies detailed information on the chemical composition of the bombarded surface. High mass range (> 10,000 u), high mass resolution (m/Δm > 10,000), accurate mass determination (ppm range) and high sensitivity (ppm of a monolayer) are achieved by applying time-of-flight (TOF) mass analyzers. TOF-SIMS has been successfully applied to a wide variety of polymer materials, including polymer blends, chemically or plasma modified surfaces, and plasma polymerization layers. Detailed information on the composition of repeat units, endgroups, oligomer distributions, additives, as well as surface contaminants can be obtained. Basic concepts of TOF-SIMS will be described and typical analytical examples for the characterization of polymer materials will be presented.     

Structural analysis of secondary ions by post-source decay in time-of-flight secondary ion mass spectrometry

Tandem mass spectrometry measurements have been achieved using time-of-flight secondary ion mass spectrometry (TOF-SIMS) and a post source decay (PSD)-like method. The performance of the method has been demonstrated on model molecules with well-known fragmentation pathways. Several lipids have been fragmented including the phosphocholine ion, phosphatidylcholines, cholesterol and vitamin E. Pure samples were analyzed, and the results compared with those obtained with the same compounds on a quadrupole-TOF hybrid mass spectrometer. Then, the structures of some lipids which are currently observed in the TOF-SIMS imaging of mammalian tissue sections were verified.     

Rapid identification of trimethyl and triethyl amines using sulphonic acidic ionic liquids: A time-of-flight secondary ion mass spectrometry study of fragmentation reactions

The time-of-flight secondary ion mass spectrometry (TOF-SIMS) has emerged as a powerful tool for the unswerving detection of biomolecules, in particular, proteins and peptides. To date, there is very little information available on the direct determination of trimethyl/triethyl amines using TOF-SIMS. One major hurdle in this regard is an ultrahigh vacuum system, usually needed in TOF-SIMS, which hampers its usability to trimethyl/triethyl amines owing to their high evaporation rate. We designed an efficient and sensitive protocol for rapid identification and sensitive determination of tertiaryalkyl amines using TOF-SIMS. The amines were derivatized by reaction with 1,4-butane sultone and sulphuric acid sequentially to afford the corresponding sulphonic acidic ionic liquids (ILs). The TOF-SIMS analysis of these task-specific ILs (TSILs) was carried out in both positive and negative polarity. The positive ion mass spectra of TSILs showed sharp fragmented peaks for tertiaryalkyl amines at typical level and up to 10 ppm. The possible mechanism for different fragmentation pathways in positive polarity was discussed.     

Photoresists comparative analysis using soft X-ray synchrotron radiation and time-of-flight mass spectrometry

Positive photoresists are widely used in lithographic process for the fabrication of relief components. When exposed to UV radiation they suffer chemical reactions modifying their chemical and physical properties. Aiming to follow molecular modifications among two different photoresists unexposed and previously exposed to ultraviolet light we have employed spectroscopic techniques coupled with mass spectrometry in the study of the AZ-1518 and AZ-4620 photoresists. The photon stimulated ion desorption (PSID) technique following the S K-edge NEXAFS spectrum was employed at the brazilian synchrotron light source (LNLS), during single-bunch operation and using time-of-flight mass spectrometry (TOF-MS) for ion analysis. NEXAFS and PSID mass spectra on both AZ-1518 and AZ-4620 photoresists (unexposed and exposed) were obtained and relative desorption ion yield curves determined for the main fragments as a function of the photon energy. They present marked different PSID spectra. Fragments related to the photochemical decomposition of the AZ-1518 photoresist could be clearly identified differently from the AZ-4620. Studies on the hardness of both photoresists were performed using O₂ plasma reactive ion etching (RIE) technique, analyzed by scanning electron microscopy (SEM) and used to explain different desorption yields in the PSID spectra. These results show that the PSID technique is adequate to investigate structural changes in molecular level in different unexposed and exposed photoresists, which is crucial for improving our knowledge about the breakup process.     

Introduction to time-of-flight secondary ion mass spectrometry application in chromatographic analysis

New on-line analytical system coupling thin layer chromatography (TLC) and high selective identification unit-time of flight secondary ion mass spectrometry (TOF-SIMS) is introduced in this article. Chromatographic mixture separation and analyte surface deposition followed with surface TOF-SIMS analysis on-line allows to identify the analytes at trace and ultratrace levels. The selected analytes with different detectability and identification possibility were analysed in this hyphenated unit (Methyl Red indicator, Terpinolen and Giberrelic acid). Here, the chromatographic thin layer plays a universal role: separation unit, analyte depositing surface and TOF-SIMS interface, finally. Two depositing substrates and TOF-SIMS compatible interfaces were tested in above-mentioned interfacing unit: modified aluminium backed chromatographic thin layer and monolithic silica thin layer. The sets of positive and negative ions TOF-SIMS spectra obtained from different SIMS modes of analysis were used for analyte identification purposes. SIMS enables analyte detection with high mass resolution at the concentration level that is not achieved by other methods.     

Tandem mass spectrometric analysis of (13)C-containing ions from a mixture of homologous peptides differing by one mass unit at a residue

Tandem mass spectrometry of a mixture of two peptides that differ from each other by a single mass unit due to mutation is presented. The mutant beta-globin of hemoglobin Hoshida is present along with the normal counterpart, and the amino acid substitution of glutamine for glutamic acid is located within tryptic peptide T5 of M(r) 2057. 9. The mass of the mutated peptide is 1 u lower. In the isotopic cluster for the doubly charged ion of the peptide T5, the resolved ion with mass of 1030.0 represents the normal peptide with 93 (12)C atoms and the mutated one with 92 (12)C and one (13)C atoms. Collision-induced dissociation (CID) of this composite ion identified the mutation by presenting a key fragment derived from the (12)C-only mutant peptide, as reported in a previous study. Similarly, when an ion containing multiple (13)C atoms was selected as a precursor for CID, the mutation could be identified, even in large fragments, by a marked change in the shape of the isotopic cluster for the consecutive product ions. This study demonstrates the merit of selecting a resolved ion rather than the whole isotopic cluster as a precursor in the CID measurements of large peptides or proteins for characterizing heterozygous mutations.     

Chemical microcharacterization of ultrathin iodide conversion layers and adsorbed thiocyanate surface layers on silver halide microcrystals with time-of-flight SIMS.

The technique of imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) and dual beam depth profiling has been used to study the composition of the surface of tabular silver halide microcrystals. Analysis of individual microcrystals with a size well below 1 microm from a given emulsion is possible. The method is successfully applied for the characterization of silver halide microcrystals with subpercent global iodide concentrations confined in surface layers with a thickness below 5 nm. The developed TOF-SIMS analytical procedure is explicitly demonstrated for the molecular imaging of adsorbed thiocyanate layers (SCN) at crystal surfaces of individual crystals and for the differentiation of iodide conversion layers synthesized with KI and with AgI micrates (nanocrystals with a size between 10 and 50 nm). It can be concluded that TOF-SIMS as a microanalytical, surface-sensitive technique has some unique properties over other analytical techniques for the study of complex structured surface layers of silver halide microcrystals. This offers valuable information to support the synthesis of future photographic emulsions.