37 research outputs found
Multivariate analysis of 3D ToF-SIMS images: method validation and application to cultured neuronal networks
No full textThis deposit contains the raw ToF-SIMS data of freeze-dried cells used in Van Nuffel, Sebastiaan, et al. "Multivariate analysis of 3D ToF-SIMS images: method validation and application to cultured neuronal networks." Analyst 141.1 (2016): 90-95
ToF-SIMS Parallel Imaging MS/MS of Lead Soaps in Embedded Paint Cross Sections
No full textToF-SIMS imaging datasets of multilayered paint cross sections, embedded in polypol resin. It contains a positive and negative polarity ToF-SIMS image of Sample 1, a positive polarity MS/MS image of Sample 2, and a positive polarity MS/MS image of Sample 3. TOF-SIMS analyses were performed on a PHI nanoTOF II instrument (Physical Electronics, Chanhassen, MN, USA) equipped with a 30keV Binq+ liquid metal ion gun (LMIG) used as an analysis beam, and an Ar gas cluster ion beam (GCIB; 10keV) for nondestructive sputter cleaning
TOF-SIMS Imaging of Biological Tissue Sections and Structural Determination Using Tandem MS
No full textOver the past couple of years, imaging mass spectrometry (IMS) has arisen as a powerful tool to answer research questions in the biomedical field. Imaging mass spectrometry allows for label-free chemical imaging by providing full molecular information. The IMS technique best positioned for cell and tissue analysis is time-of-flight secondary ion mass spectrometry (ToF-SIMS) because it has the best spatial resolution of all the molecular IMS techniques and can detect many biochemical species and especially lipids with high sensitivity. Because one must rely on the mass and isotopic pattern of an ion in combination with positive correlations with lower mass fragments to help identify its structure, one major problem during ToF-SIMS experiments is the ambiguity when assigning a molecule to a certain mass peak. The solution are instruments with tandem MS capabilities as was already the case for many MALDI-ToF instruments more than a decade ago. It has been a few years since instruments with this capability were introduced and a number of interesting publications have been produced highlighting the advantages in biological SIMS work. Here, we present a protocol describing how tandem MS can be used to elucidate the structure of unknown or ambiguous mass peaks in biological tissue samples observed during ToF-SIMS imaging based on our experiences.</p
Three-dimensional time-of-flight secondary ion mass spectrometry imaging of primary neuronal cell cultures
No full textTime-of-flight secondary ion mass spectrometry (ToF-SIMS) has proven its ability to characterise (in)organic surfaces, and is increasingly used for the characterisation of biological samples such as single cells. By combining ion imaging and molecular depth profiling it is possible to render 3D chemical images, which provides a novel, label-free way to investigate biological systems. Major challenges lie, however, in the development of data analysis tools and protocols that preserve the cell morphology. Here, we develop and employ such tools and protocols for the investigation of neuronal networks.
One of the reasons 3D ToF-SIMS imaging of cells is underused is the lack of powerful data analysis tools as 3D ToF-SIMS measurements generate very large data sets. To address this issue, we developed a method that allows the application of principal component analysis (PCA) to be expanded to large 3D images making 3D ToF-SIMS image processing of whole, intact cells and cellular networks with multivariate analysis now accessible on a routine basis. Using this method, we are able to separate cellular material from the substrate and can then correct z-offsets due to the cells' topography resulting in a more accurate surface heightmap. The method also facilitates differentiation between cellular components such as lipids and amino acids allowing the cell membrane, the cytoplasm and the extracellular matrix (ECM) to be easily distinguished from one another.
These developments permit us to investigate the intracellular localisation of specific native and non-native compounds label-free, not just in single cells but also in larger cellular networks. The visualisation of the cellular uptake of non-native compounds, namely fluorescent dyes, in primary rat cortical neurons and the chemical differentiation between cell types, namely primary rat cortical neurons and retinal pigment epithelium (RPE) cells, are presented as applications. Even though the dyes have distinct fragment ions in the high mass range, it was not possible to detect the fluorophores by 3D ToF-SIMS imaging of freeze-dried cells. However, it was possible to detect distinct differences in the kind of ions detected for freeze-dried primary rat cortical neurons and RPE cells albeit in the low mass range.
To obtain meaningful results, however, it is paramount that sample preparation does not induce significant physical or chemical changes. We present the first comprehensive comparison between large 3D ToF-SIMS images of freeze-dried and frozen-hydrated cells using PCA to facilitate the data analysis of these large data sets. A higher degree of colocalisation of the K+ signal with cell regions is observed for frozen-hydrated cells, which indicates a lower degree of membrane damage and migration of diffusible chemical species. Frozen-hydrated cell samples are therefore considered to best reflect the native cell state, but freeze-dried cell samples allow far easier sample handling. The mass spectrum of frozen-hydrated cellular material also has increased ion intensities for higher-mass fragments, which is an additional advantage, because the poor signal-to-noise ratio of molecular species with m/z > 200 is a major bottleneck in the advancement of ToF-SIMS imaging as a diagnostic tool
Three-dimensional time-of-flight secondary ion mass spectrometry imaging of primary neuronal cell cultures
Full text linkTime-of-flight secondary ion mass spectrometry (ToF-SIMS) has proven its ability to characterise (in)organic surfaces, and is increasingly used for the characterisation of biological samples such as single cells. By combining ion imaging and molecular depth profiling it is possible to render 3D chemical images, which provides a novel, label-free way to investigate biological systems. Major challenges lie, however, in the development of data analysis tools and protocols that preserve the cell morphology. Here, we develop and employ such tools and protocols for the investigation of neuronal networks. \ud
One of the reasons 3D ToF-SIMS imaging of cells is underused is the lack of powerful data analysis tools as 3D ToF-SIMS measurements generate very large data sets. To address this issue, we developed a method that allows the application of principal component analysis (PCA) to be expanded to large 3D images making 3D ToF-SIMS image processing of whole, intact cells and cellular networks with multivariate analysis now accessible on a routine basis. Using this method, we are able to separate cellular material from the substrate and can then correct z-offsets due to the cells' topography resulting in a more accurate surface heightmap. The method also facilitates differentiation between cellular components such as lipids and amino acids allowing the cell membrane, the cytoplasm and the extracellular matrix (ECM) to be easily distinguished from one another.\ud
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These developments permit us to investigate the intracellular localisation of specific native and non-native compounds label-free, not just in single cells but also in larger cellular networks. The visualisation of the cellular uptake of non-native compounds, namely fluorescent dyes, in primary rat cortical neurons and the chemical differentiation between cell types, namely primary rat cortical neurons and retinal pigment epithelium (RPE) cells, are presented as applications. Even though the dyes have distinct fragment ions in the high mass range, it was not possible to detect the fluorophores by 3D ToF-SIMS imaging of freeze-dried cells. However, it was possible to detect distinct differences in the kind of ions detected for freeze-dried primary rat cortical neurons and RPE cells albeit in the low mass range.\ud
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To obtain meaningful results, however, it is paramount that sample preparation does not induce significant physical or chemical changes. We present the first comprehensive comparison between large 3D ToF-SIMS images of freeze-dried and frozen-hydrated cells using PCA to facilitate the data analysis of these large data sets. A higher degree of colocalisation of the K+ signal with cell regions is observed for frozen-hydrated cells, which indicates a lower degree of membrane damage and migration of diffusible chemical species. Frozen-hydrated cell samples are therefore considered to best reflect the native cell state, but freeze-dried cell samples allow far easier sample handling. The mass spectrum of frozen-hydrated cellular material also has increased ion intensities for higher-mass fragments, which is an additional advantage, because the poor signal-to-noise ratio of molecular species with m/z > 200 is a major bottleneck in the advancement of ToF-SIMS imaging as a diagnostic tool
Experimental study of the organic ion intensity distribution in the ion imaging of coated polymer fibres with S-SIMS
No full textAbstract: Time-of-Flight Static Secondary Ion Mass Spectrometry excels in probing the molecular composition of the outer monolayer of flat samples with a lateral resolution in the sub-mu m range. However, the method faces significant methodological problems in the case of non-conducting samples with high topography or surface curvature, such as fibres, yarns or fabrics. Specifically, the useful secondary ion yield in a given spot on the fibre depends on the local incidence angle, the height above the earthed sample holder, the position relative to the axis of the mass analyser and the extent of the local surface charging. This study has focused on the empiric reduction of the useful ion yield variations observed in the ion images of fibres with diameter of 25 and 100 mu m. Up to now, most literature data consider the analysis of fibres positioned along or perpendicular to the projection of the projectile beam in the plane of the sample surface because these specific geometries facilitate the interpretation of the ion images. However, it has been discovered that the diagonal orientation of the fibre in the field-of-view largely reduces the ion yield variations for fibres with a small diameter (25 mu m). The situation is different for fibres with a diameter of 100 mu m. In that case, the ion images contain no secondary ion counts for the pixels referring to a significant part of the fibre. In particular, the resulting lack of delineation between the shadow zone in the front of the fibre and the boundary of the fibre hampers the practical use of the ion images A fourfold decrease of the extraction voltage or a 20% increase of the distance between sample holder and extraction electrode is found to improve the detection of secondary ions from the part of the fibre facing towards the impinging primary ion beam. These observations have been tentatively related to the mass analyser acceptance and its dependence on the delicate balance between conflicting effects such as field strength and curvature of the field lines, secondary ion emission angle and initial kinetic energy and difference in local surface potential due to the position in the extraction field and charge build-up during analysis. (C) 2013 Elsevier B. V. All rights reserved
ToF-SIMS spectra of historical inorganic pigments:Natural and synthetic ultramarine blues and smalt in both polarities
No full textTime-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly used to analyze cultural heritage materials because it can simultaneously detect organic and inorganic materials while mapping them on a surface. The precise identification of a pigment in a specific layer of a painting or of remaining color on a statue can inform about the technique used or the time of manufacture as well as expose possible forgeries when anachronistic ingredients are identified. Reference spectra are required to confidently identify a given pigment using ToF-SIMS. This paper focuses on four blue pigments manufactured following historical recipes: two natural ground and processed lapis lazuli pigments, one synthetic ultramarine pigment, and the blue-colored ground cobalt glass pigment smalt. The positive and negative polarity ToF-SIMS reference spectra using a Bi3+ primary ion species are presented. Differentiating these family of pigments is of interest as they have similar compositions but are used in very different contexts. It is particularly noteworthy that the two natural lapis lazuli pigments can be distinguished from the synthetic counterpart ultramarine using ToF-SIMS
Tof-SIMS spectra of historical inorganic pigments
No full textInternational audienceCultural Heritage materials, like historical paintings, are complex heterogeneous objects comprising multiple microstructures with various organic and inorganic natural or synthetic materials. Additionally, they often have aged within uncontrolled environments, sometimes over centuries. Mass spectrometry imaging techniques are helpful to investigate the resulting heterogeneous microstructures, providing additional knowledge on artwork's nature and state of preservation. ToF-SIMS has growing relevance, as it offers the possibility to simultaneously detect and map both organic and inorganic materials on the micrometric scale
Transferable Mass Spectrometry Methods: Examination of Authenticity in Artwork
Full text linkThis chapter discusses the use of mass spectrometry for the authentication of artwork and its transferability to forensics. The general process for art authentication is first discussed. An overview of the main mass spectrometry techniques that are currently used for art authentication is provided, along with commentary on the associated sample preparation and the data that can be obtained. Five examples of real authentication cases, where mass spectrometry techniques were used, are reported with the lessons learnt from them. Finally, the potential for the use of these analytical techniques during criminal prosecutions involving art is discussed, while also highlighting the numerous challenges that one may encounter
Tof-SIMS spectra of historical inorganic pigments:Calcium white pigments in both polarities
No full textTime-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly used to analyze cultural heritage materials because it can simultaneously detect organic and inorganic materials while mapping them on a surface. The precise identification of a pigment in a specific layer of a painting or of remaining color on a statue can inform about the technique used or the time of manufacture as well as expose possible forgeries when anachronistic ingredients are identified. Reference spectra are required to confidently identify a given pigment using ToF-SIMS. This database focuses on six white pigments made from calcium-rich natural or synthetized materials, prepared following traditional processes. Such pigments are frequently found in the preparation layers, namely, "ground," separating the support from the observable paint layers, and providing a smooth surface to hold the paint on while preventing its absorption by the substrate. Differentiating between these pigments is helpful to better describe the painting practice. Here, ToF-SIMS reference spectra using a Bi-3(+) primary ion species are presented for both polarities
