scholarly journals Spatially resolved chemical imaging of individual atmospheric particles using nanoscale imaging mass spectrometry: insight into particle origin and chemistry

2014 ◽  
Vol 6 (8) ◽  
pp. 2444-2451 ◽  
Author(s):  
Sutapa Ghosal ◽  
Peter K. Weber ◽  
Alexander Laskin
Keyword(s):  
Mass Spectrometry ◽  
Environmental Impact ◽  
Imaging Mass Spectrometry ◽  
Chemical Imaging ◽  
Atmospheric Particles ◽  
Spatially Resolved ◽  
Potential Environmental Impact ◽  
Nanoscale Imaging ◽  
Insight Into ◽  
Bulk Chemistry

Knowledge of the spatially resolved composition of atmospheric particles is essential for differentiating between their surface versus bulk chemistry and understanding particle reactivity and the potential environmental impact.

scholarly journals Automated Biomarker Candidate Discovery in Imaging Mass Spectrometry Data Through Spatially Localized Shapley Additive Explanations

2020 ◽  
Author(s):  
Leonoor E.M. Tideman ◽  
Lukasz G. Migas ◽  
Katerina V. Djambazova ◽  
Nathan Heath Patterson ◽  
Richard M. Caprioli ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Molecular Species ◽  
Imaging Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Decision Making Process ◽  
Spatial Specificity ◽  
The Relationship ◽  
Insight Into ◽  
Imaging Mass Spectrometry Data

AbstractThe search for molecular species that are differentially expressed between biological states is an important step towards discovering promising biomarker candidates. In imaging mass spectrometry (IMS), performing this search manually is often impractical due to the large size and high-dimensionality of IMS datasets. Instead, we propose an interpretable machine learning workflow that automatically identifies biomarker candidates by their mass-to-charge ratios, and that quantitatively estimates their relevance to recognizing a given biological class using Shapley additive explanations (SHAP). The task of biomarker candidate discovery is translated into a feature ranking problem: given a classification model that assigns pixels to different biological classes on the basis of their mass spectra, the molecular species that the model uses as features are ranked in descending order of relative predictive importance such that the top-ranking features have a higher likelihood of being useful biomarkers. Besides providing the user with an experiment-wide measure of a molecular species’ biomarker potential, our workflow delivers spatially localized explanations of the classification model’s decision-making process in the form of a novel representation called SHAP maps. SHAP maps deliver insight into the spatial specificity of biomarker candidates by highlighting in which regions of the tissue sample each feature provides discriminative information and in which regions it does not. SHAP maps also enable one to determine whether the relationship between a biomarker candidate and a biological state of interest is correlative or anticorrelative. Our automated approach to estimating a molecular species’ potential for characterizing a user-provided biological class, combined with the untargeted and multiplexed nature of IMS, allows for the rapid screening of thousands of molecular species and the obtention of a broader biomarker candidate shortlist than would be possible through targeted manual assessment. Our biomarker candidate discovery workflow is demonstrated on mouse-pup and rat kidney case studies.HighlightsOur workflow automates the discovery of biomarker candidates in imaging mass spectrometry data by using state-of-the-art machine learning methodology to produce a shortlist of molecular species that are differentially expressed with regards to a user-provided biological class.A model interpretability method called Shapley additive explanations (SHAP), with observational Shapley values, enables us to quantify the local and global predictive importance of molecular species with respect to recognizing a user-provided biological class.By providing spatially localized explanations for a classification model’s decision-making process, SHAP maps deliver insight into the spatial specificity of biomarker candidates and enable one to determine whether (and where) the relationship between a biomarker candidate and the class of interest is correlative or anticorrelative.

scholarly journals Electrochemistry at the Synapse

2019 ◽  
Vol 12 (1) ◽  
pp. 297-321 ◽  
Author(s):  
Mimi Shin ◽  
Ying Wang ◽  
Jason R. Borgus ◽  
B. Jill Venton
Keyword(s):  
Mass Spectrometry ◽  
Electrochemical Measurements ◽  
Chemical Information ◽  
Fast Scan Cyclic Voltammetry ◽  
Spatially Resolved ◽  
Future Challenges ◽  
Insight Into ◽  
Partial Release ◽  
Electrochemical Cytometry ◽  
Made In

Electrochemical measurements of neurotransmitters provide insight into the dynamics of neurotransmission. In this review, we describe the development of electrochemical measurements of neurotransmitters and how they started with extrasynaptic measurements but now are pushing toward synaptic measurements. Traditionally, biosensors or fast-scan cyclic voltammetry have monitored extrasynaptic levels of neurotransmitters, such as dopamine, serotonin, adenosine, glutamate, and acetylcholine. Amperometry and electrochemical cytometry techniques have revealed mechanisms of exocytosis, suggesting partial release. Advances in nanoelectrodes now allow spatially resolved, electrochemical measurements in a synapse, which is only 20–100 nm wide. Synaptic measurements of dopamine and acetylcholine have been made. In this article, electrochemical measurements are also compared to optical imaging and mass spectrometry measurements, and while these other techniques provide enhanced spatial or chemical information, electrochemistry is best at monitoring real-time neurotransmission. Future challenges include combining electrochemistry with these other techniques in order to facilitate multisite and multianalyte monitoring.

Atmospheric Pressure Sampling for Laser Ablation Based Nanoscale Imaging Mass Spectrometry: Ions or Neutrals?

2010 ◽  
Vol 115 (4) ◽  
pp. 1006-1013 ◽  
Author(s):  
Liang Zhu ◽  
Johannes Stadler ◽  
Thomas A. Schmitz ◽  
Frank Krumeich ◽  
Renato Zenobi
Keyword(s):  
Mass Spectrometry ◽  
Laser Ablation ◽  
Atmospheric Pressure ◽  
Imaging Mass Spectrometry ◽  
Nanoscale Imaging

scholarly journals Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

Microbiology ◽  
2011 ◽  
Vol 157 (9) ◽  
pp. 2485-2492 ◽  
Author(s):  
David J. Gonzalez ◽  
Nina M. Haste ◽  
Andrew Hollands ◽  
Tinya C. Fleming ◽  
Matthew Hamby ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Staphylococcus Aureus ◽  
Bacillus Subtilis ◽  
Imaging Mass Spectrometry ◽  
Life Forms ◽  
Microbial Competition ◽  
Metabolic Output ◽  
Antibiotic Discovery ◽  
And Staphylococcus Aureus ◽  
Insight Into

Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery.

scholarly journals Helium Ion Microscopy with Secondary Ion Mass Spectrometry (HIM-SIMS) for the analysis and quantitation of polyolefins

2020 ◽  
Author(s):  
Olga S Ovchinnikova ◽  
Nikolay Borodinov ◽  
Artem A Trofimov ◽  
Stephen T King ◽  
Matthias Lorenz ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Detection System ◽  
Chemical Imaging ◽  
Daily Lives ◽  
Spatially Resolved ◽  
Helium Ion ◽  
Ion Mass Spectrometry ◽  
Chemical Technique ◽  
Secondary Ion

Petroleum based polyolefin plastics makeup a large part of the multicomponent/multiphase plastics we use in our daily lives.  Multiple plastics are often compounded, laminated or coextruded in these multicomponent systems creating multiple phases and interfaces of varying strengths. Significant opportunity exists in developing strategies for enhancing interfacial properties as well as facilitating disposal of polyolefin plastics by upcycling of polymeric products for reuse. Thus, interfaces and chemically distinct phases in these materials need to be probed structurally and chemically at the relevant length scales. To date, chemical imaging of polymer and polymer blends has been primarily accomplished using time-of-flight secondary ion mass spectrometry (ToF-SIMS) to directly visualize the distribution of components in a complex material with spatial resolution ranging from 100 nm to 5μm. However, in many cases this resolution falls far short of visualizing interfaces directly. To overcome these limitations recent work has focused on developing a SIMS detection system based on the helium ion microscope (HIM) enabling chemical imaging to ~14 nm. Here, we utilize the HIM-SIMS for quantitative differentiation between the olefin-based polymers of polyethylene (PE) and polypropylene (PP). We illustrate both quantitative analysis for separating PE and PP using specific mass fragment ratios as well as demonstrate spatially resolved imaging of phase separated domains within PE thin films with ~14 nm chemical and ~2 nm morphological spatial resolutions. Overall, we demonstrate HIM-SIMS as a multimodal chemical technique for imaging and quantification of polyolefin interfaces, that could be more broadly applied to the analysis of multicomponent/multiphase polymeric systems.

scholarly journals Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul D. Piehowski ◽  
Ying Zhu ◽  
Lisa M. Bramer ◽  
Kelly G. Stratton ◽  
Rui Zhao ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Spatial Distribution ◽  
Spatial Resolution ◽  
A Priori ◽  
Imaging Mass Spectrometry ◽  
Biological Tissues ◽  
Label Free ◽  
Tissue Sections ◽  
Spatially Resolved ◽  
Tissue Surfaces

AbstractBiological tissues exhibit complex spatial heterogeneity that directs the functions of multicellular organisms. Quantifying protein expression is essential for elucidating processes within complex biological assemblies. Imaging mass spectrometry (IMS) is a powerful emerging tool for mapping the spatial distribution of metabolites and lipids across tissue surfaces, but technical challenges have limited the application of IMS to the analysis of proteomes. Methods for probing the spatial distribution of the proteome have generally relied on the use of labels and/or antibodies, which limits multiplexing and requires a priori knowledge of protein targets. Past efforts to make spatially resolved proteome measurements across tissues have had limited spatial resolution and proteome coverage and have relied on manual workflows. Here, we demonstrate an automated approach to imaging that utilizes label-free nanoproteomics to analyze tissue voxels, generating quantitative cell-type-specific images for >2000 proteins with 100-µm spatial resolution across mouse uterine tissue sections preparing for blastocyst implantation.

Multimodal chemical imaging of a single brain tissue section using ToF-SIMS, MALDI-ToF and immuno/histochemical staining

The Analyst ◽  
2021 ◽  
Author(s):  
Ibrahim Kaya ◽  
Eva Jennische ◽  
Stefan Lange ◽  
Per Malmberg
Keyword(s):  
Mass Spectrometry ◽  
Brain Tissue ◽  
Tissue Section ◽  
Imaging Mass Spectrometry ◽  
Chemical Imaging ◽  
Histochemical Staining ◽  
Maldi Tof ◽  
Tof Sims ◽  
Brain Tissue Section

ToF-SIMS and/or MALDI-ToF imaging mass spectrometry of a single brain tissue section followed by classical- or immuno- histochemical staining.

scholarly journals Localization of the Lens Intermediate Filament Switch by Imaging Mass Spectrometry

2020 ◽  
Author(s):  
Zhen Wang ◽  
Daniel J. Ryan ◽  
Kevin L Schey
Keyword(s):  
Mass Spectrometry ◽  
Intermediate Filament ◽  
Imaging Mass Spectrometry ◽  
Enzymatic Digestion ◽  
Cytoskeletal Proteins ◽  
Spatially Resolved ◽  
Narrow Region ◽  
Molecular Features ◽  
Maldi Ims ◽  
High Concentrations

AbstractImaging mass spectrometry (IMS) enables targeted and untargeted visualization of the spatial localization of molecules in tissues with great specificity. The lens is a unique tissue that contains fiber cells corresponding to various stages of differentiation that are packed in a highly spatial order. The application of IMS to lens tissue localizes molecular features that are spatially related to the fiber cell organization. Such spatially resolved molecular information assists our understanding of lens structure and physiology; however, protein IMS studies are typically limited to abundant, soluble, low molecular weight proteins. In this study, a method was developed for imaging low solubility cytoskeletal proteins in the lens; a tissue that is filled with high concentrations of soluble crystallins. Optimized tissue washes combined with on-tissue enzymatic digestion allowed successful imaging of peptides corresponding to known lens cytoskeletal proteins. The resulting peptide signals facilitated segmentation of the bovine lens into molecularly distinct regions. A sharp intermediate filament transition from vimentin to lens-specific beaded filament proteins was detected in the lens cortex. MALDI IMS also revealed the region where posttranslational myristoylation of filensin occurs and the results indicate that truncation and myristoylation of filensin starts soon after filensin expression increased in the inner cortex. From intermediate filament switch to filensin truncation and myristoylation, multiple remarkable changes occur in the narrow region of lens cortex. MALDI images delineated the boundaries of distinct lens regions that will guide further proteomic and interactomic studies.

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