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.     

High-resolution MALDI imaging mass spectrometry allows localization of peptide distributions at cellular length scales in pituitary tissue sections

Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) has been used to determine peptide distributions directly from rat, mouse and human pituitary tissue sections. Since these organs are small (10²–10³ μm) the spatial resolution of IMS is a key issue in molecular imaging of pituitary tissue sections. Here we show that high-resolution IMS allows localization of neuropeptide distributions within different cell clusters of a single organ of a pituitary tissue section. The sample preparation protocol does not result in analyte redistribution and is therefore applicable to IMS experiments at cellular length scales. The stigmatic imaging mass spectrometer used in this study produces selected-ion-count images with pixel sizes of 500 nm and a resolving power of 4 μm, yielding superior spatial detail compared to images obtained in microprobe imaging experiments. Furthermore, we show that with imaging mass spectrometry a distinction can be made between different mammalian tissue sections based on differences in the amino acid sequence of neuropeptides with the same function. This example demonstrates the power of IMS for label-free molecular imaging at relevant biological length scales.     

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.     

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.     

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.     

Attempts for molecular depth profiling directly on a rat brain tissue section using fullerene and bismuth cluster ion beams

The capabilities of time of flight secondary ion mass spectrometry (TOF-SIMS) have been recently greatly improved with the arrival in this field of polyatomic ion sources. This technique is now able to map at the micron scale intact organic molecules in a range of a thousand Daltons or more, at the surface of tissue samples. Nevertheless, this remains a surface analysis technique, and three-dimensional information on the molecular composition of the sample could not be obtained due to the damage undergone by the organic molecules during their irradiation. The situation changed slightly with the low damage and low penetration depth of the C₆₀ fullerene ion beams. Recent promising studies have shown the possibility of organic molecular depth profiling using this kind of beams onto model samples. This possibility has been tried out directly onto a rat brain tissue section, which is the most commonly used biological tissue model in TOF-SIMS imaging method developments. The tissue surface has been sputtered with a 10 keV energy fullerene ion beam, and surface analyses were done with a 25 keV Bi₃⁺ ion beam at regular time intervals. The total depth which was analysed was more than two microns, with total primary ion doses of more than 10¹⁶ ions cm⁻². Although not in contradiction with results previously published but with much lower doses, it is found that the molecular damage remains too large, thus making molecular imaging very difficult. In addition, most of the lipids, which are usually the main observable molecules in TOF-SIMS, are concentrated close to the sample surface in the first hundreds of nanometers.     

Solvent-free matrix dry-coating for MALDI imaging of phospholipids

A fast and simple, solvent-free matrix deposition protocol was developed for positive ionization mode phospholipid analysis in tissues. Finely ground 2,5-dihydroxybenzoic acid was deposited onto sagittal mouse brain sections using a dry-coating technique, in which solid matrix particles were filtered directly onto the tissue through a 20-microm stainless steel sieve. Phospholipid signals were obtained directly off these sections, allowing acquisition of high-resolution MS images. These images were compared to those from serial sections that were spray-coated with a thin-layer chromatography (TLC) reagent sprayer. Signals obtained from the dry matrix deposition method were comparable to those from spray-coated sections, producing identical localization patterns with a simpler and faster sample preparation with virtually no analyte delocalization. This approach was found to yield highly reproducible results, eliminating much of the variance caused by operator differences, and making it an attractive alternative to the currently used matrix application methods.     

Matrix pre‐coated targets for high throughput MALDI imaging of proteins

We have developed matrix pre‐coated targets for imaging proteins in thin tissue sections by matrix‐assisted laser desorption/ionization mass spectrometry. Gold covered microscope slides were coated with sinapinic acid (SA) in batches in advance and were shown to be stable for over 6 months when kept in the dark. The sample preparation protocol using these SA pre‐coated targets involves treatment with diisopropylethylamine (DIEA)‐H₂O vapor, transforming the matrix layer to a viscous ionic liquid. This SA‐DIEA ionic liquid layer extracts proteins and other analytes from tissue sections that are thaw mounted to this target. DIEA is removed by the immersion of the target into diluted acetic acid, allowing SA to co‐crystallize with extracted analytes directly on the target. Ion images (3–70 kDa) of sections of mouse brain and rat kidney at spatial resolution down to 10 µm were obtained. Use of pre‐coated slides greatly reduces sample preparation time for matrix‐assisted laser desorption/ionization imaging while providing high throughput, low cost and high spatial resolution images. Copyright © 2014 John Wiley & Sons, Ltd.     

基于非负分解方法的质谱成像数据特征提取

质谱成像技术能够在同一个实验里无需标记手段而获得样品表面的分子信息及其分布信息,是当前质谱分析的热点.其分析所得数据量大且复杂,使其特征难以提取.多元统计分析方法,特别是主成分分析法已应用于质谱成像数据的压缩和特征提取.然而由于主成分分析常产生负的数据结果,其意义难以解释且不易分解为单一的特征.本研究开发出一种基于非负分解的质谱成像数据提取方法,能够提取单一的分子特征及其在样品上的分布特征,并将多个单一的特征分布通过红、绿、蓝三色叠加显示,获得轮廓直观的综合特征分布.应用本方法对小鼠脑组织切片质谱成像数据进行分析,可直观分解出灰质区域、白质区域和背景区域,相对主成分分析方法更直观且易于解释.应用本方法对在同一个样品靶上的人膀胱癌变组织和其相邻非癌变组织切片质谱成像数据进行分析,癌变与非癌变组织间差异清晰直观.本研究设计的质谱成像软件可由http://www.msimaging.net获取.     

Matrix-free mass spectrometric imaging using laser desorption ionisation Fourier transform ion cyclotron resonance mass spectrometry

Mass spectrometry imaging (MSI) is a powerful tool in metabolomics and proteomics for the spatial localization and identification of pharmaceuticals, metabolites, lipids, peptides and proteins in biological tissues. However, sample preparation remains a crucial variable in obtaining the most accurate distributions. Common washing steps used to remove salts, and solvent-based matrix application, allow analyte spreading to occur. Solvent-free matrix applications can reduce this risk, but increase the possibility of ionisation bias due to matrix adhesion to tissue sections. We report here the use of matrix-free MSI using laser desorption ionisation performed on a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. We used unprocessed tissue with no post-processing following thaw-mounting on matrix-assisted laser desorption ionisation (MALDI) indium-tin oxide (ITO) target plates. The identification and distribution of a range of phospholipids in mouse brain and kidney sections are presented and compared with previously published MALDI time-of-flight (TOF) MSI distributions.     

Optimization of automated matrix deposition for biomolecular mapping using a spotter

Imaging mass spectrometry using matrix-assisted laser desorption/ionization allows the detailed mapping of biomolecules directly from tissue. Matrix deposition is the key step for successful imaging. The appropriate concentration and deposition of matrix is critical for extraction, desorption, and ionization of molecules from tissue without losing molecular localization. The main challenge to meet these criteria is to deposit matrix droplets homogeneously on the tissue section. This work shows how a chemical inkjet printer was used for this purpose resulting in the imaging of phosphatidylcholines and sulfatides. The intricacies involved in effective matrix deposition are discussed.     

A simple DNA Characterization method using fiber-fluorescence in situ hybridization performed without DNA fragmentation

We performed high-resolution fluorescence imaging of lambda phage DNA molecules hybridized with fluorescent-labeled DNA and peptide nucleic acid probes. In this method, the target DNA and probe were mixed, rapidly denatured and then subjected to liquid hybridization conditions. The hybridized DNA sample was then spotted onto a nontreated glass substrate and subjected to molecular combing. The resultant continuous fluorescence signal of intact lambda DNA shows that the fluorescent-labeled probes bound to the predicted sites but in a pattern that was clearly different to the beads-on-a-string pattern typical for fiber-fluorescence in situ hybridization. The key changes to the conventional method are hybridization of the free target DNA in liquid and lowering the denaturation temperature. The method described here allows the rapid and direct visualization of the specific binding sites of intact DNA molecules without damaging the DNA fibers and causing fragmentation of the fluorescence signal. This technique should be a useful tool in studies of genetics and also large-scale DNA sequencing projects.     

Quantitative chemical imaging with multiplex stimulated Raman scattering microscopy

Stimulated Raman scattering (SRS) microscopy is a newly developed label-free chemical imaging technique that overcomes the speed limitation of confocal Raman microscopy while avoiding the nonresonant background problem of coherent anti-Stokes Raman scattering (CARS) microscopy. Previous demonstrations have been limited to single Raman band measurements. We present a novel modulation multiplexing approach that allows real-time detection of multiple species using the fast Fourier transform. We demonstrate the quantitative determination of chemical concentrations in a ternary mixture. Furthermore, two imaging applications are pursued: (1) quantitative determination of oil content as well as pigment and protein concentration in microalgae cultures; and (2) 3D high-resolution imaging of blood, lipids, and protein distribution in ex vivo mouse skin tissue. We believe that quantitative multiplex SRS uniquely combines the advantage of fast label-free imaging with the fingerprinting capability of Raman spectroscopy and enables numerous applications in lipid biology as well as biomedical imaging.     

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.     

Trace determination of gadolinium in biomedical samples by diode laser-based multi-step resonance ionization mass spectrometry

The application of high-resolution multi-step resonance ionization mass spectrometry (RIMS) to the trace determination of the rare earth element gadolinium is described. Utilizing three-step resonant excitation into an autoionizing level, both isobaric and isotopic selectivity of >10(7) were attained. An overall detection efficiency of approximately 10(-7) and an isotope specific detection limit of 1.5 x 10(9) atoms have been demonstrated. When targeting the major isotope (158)Gd, this corresponds to a total Gd detection limit of 1.6 pg. Additionally, linear response has been demonstrated over a dynamic range of six orders of magnitude. The method has been used to determine the Gd content in various normal and tumor tissue samples, taken from a laboratory mouse shortly after injection of gadolinium diethylenetriaminepentaacetic acid dimeglumine (Gd-DTPA), which is used as a contrast agent for magnetic resonance imaging (MRI). The RIMS results show Gd concentrations that vary by more than two orders of magnitude (0.07-11.5 microg mL(-1)) depending on the tissue type. This variability is similar to that observed in MRI scans that depict Gd-DTPA content in the mouse prior to dissection, and illustrates the potential for quantitative trace analysis in microsamples of biomedical materials.     

Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging

Negative ion desorption electrospray ionization (DESI) was used for the analysis of an ex vivo tissue sample set comprising primary colorectal adenocarcinoma samples and colorectal adenocarcinoma liver metastasis samples. Frozen sections (12 μm thick) were analyzed by means of DESI imaging mass spectrometry (IMS) with spatial resolution of 100 μm using a computer-controlled DESI imaging stage mounted on a high resolution Orbitrap mass spectrometer. DESI-IMS data were found to predominantly feature complex lipids, including phosphatidyl-inositols, phophatidyl-ethanolamines, phosphatidyl-serines, phosphatidyl-ethanolamine plasmalogens, phosphatidic acids, phosphatidyl-glycerols, ceramides, sphingolipids, and sulfatides among others. Molecular constituents were identified based on their exact mass and MS/MS fragmentation spectra. An identified set of molecules was found to be in good agreement with previously reported DESI imaging data. Different histological tissue types were found to yield characteristic mass spectrometric data in each individual section. Histological features were identified by comparison to hematoxylin-eosin stained neighboring sections. Ions specific to certain histological tissue types (connective tissue, smooth muscle, healthy mucosa, healthy liver parenchyma, and adenocarcinoma) were identified by semi-automated screening of data. While each section featured a number of tissue-specific species, no potential global biomarker was found in the full sample set for any of the tissue types. As an alternative approach, data were analyzed by principal component analysis (PCA) and linear discriminant analysis (LDA) which resulted in efficient separation of data points based on their histological types. A pixel-by-pixel tissue identification method was developed, featuring the PCA/LDA analysis of authentic data set, and localization of unknowns in the resulting 60D, histologically assigned LDA space. Novel approach was found to yield results which are in 95% agreement with the results of classical histology. KRAS mutation status was determined for each sample by standard molecular biology methods and a similar PCA/LDA approach was developed to assess the feasibility of the determination of this important parameter using solely DESI imaging data. Results showed that the mutant and wild-type samples fully separated. DESI-MS and molecular biology results were in agreement in 90% of the cases.     

Influence of molecular environment on the analysis of phospholipids by time-of-flight secondary ion mass spectrometry

Understanding the influence of molecular environment on phospholipids is important in time-of-flight secondary ion mass spectrometry (TOF-SIMS) studies of complex systems such as cellular membranes. Varying the molecular environment of model membrane Langmuir-Blodgett (LB) films is shown to affect the TOF-SIMS signal of the phospholipids in the films. The molecular environment of a LB film of dipalmitoylphosphatidylcholine (DPPC) is changed by varying the film density, varying the sample substrate, and the addition of cholesterol. An increase in film density results in a decrease in the headgroup fragment ion signal at a mass-to-charge ratio of 184 (phosphocholine). Varying the sample substrate increases the secondary ion yield of phosphocholine as does the addition of proton-donating molecules such as cholesterol to the DPPC LB film. Switching from a model system of DPPC and cholesterol to one of dipalmitoylphosphatidylethanolamine (DPPE) and cholesterol demonstrates the ability of cholesterol to also mask the phospholipid headgroup ion signal. TOF-SIMS studies of simplistic phospholipid LB model membrane systems demonstrate the potential use of these systems in TOF-SIMS analysis of cells.     

MALDI tissue imaging: from biomarker discovery to clinical applications

Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for the generation of multidimensional spatial expression maps of biomolecules directly from a tissue section. From a clinical proteomics perspective, this method correlates molecular detail to histopathological changes found in patient-derived tissues, enhancing the ability to identify candidates for disease biomarkers. The unbiased analysis and spatial mapping of a variety of molecules directly from clinical tissue sections can be achieved through this method. Conversely, targeted IMS, by the incorporation of laser-reactive molecular tags onto antibodies, aptamers, and other affinity molecules, enables analysis of specific molecules or a class of molecules. In addition to exploring tissue during biomarker discovery, the integration of MALDI-IMS methods into existing clinical pathology laboratory practices could prove beneficial to diagnostics. Querying tissue for the expression of specific biomarkers in a biopsy is a critical component in clinical decision-making and such markers are a major goal of translational research. An important challenge in cancer diagnostics will be to assay multiple parameters in a single slide when tissue quantities are limited. The development of multiplexed assays that maximize the yield of information from a small biopsy will help meet a critical challenge to current biomarker research. This review focuses on the use of MALDI-IMS in biomarker discovery and its potential as a clinical diagnostic tool with specific reference to our application of this technology to prostate cancer.     

Protein identification by accurate mass matrix-assisted laser desorption/ionization imaging of tryptic peptides

The spatial distribution of proteins in tissue sections can be used to identify potential markers for pathological processes. Tissue sections are often subjected to enzymatic digestion before matrix‐assisted laser desorption/ionization (MALDI) imaging. This study is targeted at improving the on‐tissue identification of tryptic peptides by accurate mass measurements and complementary off‐line liquid chromatography coupled to electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) analysis. Two adjacent mouse brain sections were analyzed in parallel. The first section was spotted with trypsin and analyzed by MALDI imaging. Direct on‐tissue MS/MS experiments of this section resulted in the identification of 14 peptides (originating from 4 proteins). The second tissue section was homogenized, fractionated by ultracentrifugation and digested with trypsin prior to LC/ESI‐MS/MS analysis. The number of identified peptides was increased to 153 (corresponding to 106 proteins) by matching imaged mass peaks to peptides which were identified in these LC/ESI‐MS/MS experiments. All results (including MALDI imaging data) were based on accurate mass measurements (RMS <2 ppm) and allow a confident identification of tryptic peptides. Measurements based on lower accuracy would have led to ambiguous or misleading results. MS images of identified peptides were generated with a bin width (mass range used for image generation) of Δm/z = 0.01. The application of accurate mass measurements and additional LC/MS measurements increased both the quality and the number of peptide identifications. The advantages of this approach for the analysis of biological tissue sections are demonstrated and discussed in detail. Results indicate that accurate mass measurements are needed for confident identification and specific image generation of tryptic peptides in tissue sections. Copyright © 2011 John Wiley & Sons, Ltd.     

Gangliosides' analysis by MALDI-ion mobility MS

The combination of ion mobility with matrix-assisted laser desorption/ionization allows for the rapid separation and analysis of biomolecules in complex mixtures (such as tissue sections and cellular extracts), as isobaric lipid, peptide, and oligonucleotide molecular ions are pre-separated in the mobility cell before mass analysis. In this study, MALDI-IM MS is used to analyze gangliosides, a class of complex glycosphingolipids that has different degrees of sialylation. Both GD1a and GD1b, structural isomers, were studied to see the effects on gas-phase structure depending upon the localization of the sialic acids. A total ganglioside extract from mouse brain was also analyzed to measure the effectiveness of ion mobility to separate out the different ganglioside species in a complex mixture.