Use of metabolic imaging to monitor heterogeneity of tumour response following therapeutic mTORC1/2 pathway inhibition.

The PI3K-mTOR-AKT pathway regulates tumour proliferation, gene expression and metabolism, but pathway inhibition induces heterogeneous feedback reactivation, limiting anti-tumour responses. Measuring heterogeneity of pathway inhibition in tissues using protein biomarker phosphorylation or location is challenging. An integrated multi-modal imaging workflow was developed to assess the heterogeneity of AZD2014 (mTORC1/2 inhibitor) response in a PTEN-null renal cancer model.

Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.

Chromosome conformation capture (3C) sequencing approaches, like Hi-C or micro-C, allow for an unbiased view of chromatin interactions. Most analysis methods rely on so-called interaction matrices, which are derived from counting read pairs in bins of fixed size. Here, we propose the Voronoi diagram, as implemented in Voronoi for chromosome conformation capture data visualization (v3c-viz) to visualize 3C data.

Screening of volatile organic compounds (VOCs) from liquid fungal cultures using ambient mass spectrometry.

The potential of fungi for use as biotechnological factories in the production of a range of valuable metabolites, such as enzymes, terpenes, and volatile aroma compounds, is high. Unlike other microorganisms, fungi mostly secrete secondary metabolites into the culture medium, allowing for easy extraction and analysis. To date, the most commonly used technique in the analysis of volatile organic compounds (VOCs) is gas chromatography, which is time and labour consuming.

Do Anti-tuberculosis Drugs Reach Their Target?─High-Resolution Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Provides Information on Drug Penetration into Necrotic Granulomas.

Tuberculosis (TB) is characterized by mycobacteria-harboring centrally necrotizing granulomas. The efficacy of anti-TB drugs depends on their ability to reach the bacteria in the center of these lesions. Therefore, we developed a mass spectrometry (MS) imaging workflow to evaluate drug penetration in tissue.

MALDI mass spectrometry imaging: From constituents in fresh food to ingredients, contaminants and additives in processed food.

Mass Spectrometry imaging (MS imaging) provides spatial information for a wide range of compound classes in different sample matrices. We used MS imaging to investigate the distribution of components in fresh and processed food, including meat, dairy and bakery products. The MS imaging workflow was optimized to cater to the specific properties and challenges of the individual samples.

Multi-modal molecular imaging maps the correlation between tumor microenvironments and nanomedicine distribution.

Gaining insight into the heterogeneity of nanoparticle drug distribution within tumors would improve both design and clinical translation of nanomedicines. There is little data showing the spatio-temporal behavior of nanomedicines in tissues as current methods are not able to provide a comprehensive view of the nanomedicine distribution, released drug or its effects in the context of a complex tissue microenvironment. A new experimental approach which integrates the molecular imaging and bioanalytical technologies MSI and IMC was developed to determine the biodistribution of total drug and drug metabolite delivered via PLA-PEG nanoparticles and to overlay this with imaging of the nanomedicine in the context of detailed tumor microenvironment markers.

An overview of image registration for aligning mass spectrometry imaging with clinically relevant imaging modalities.

Mass spectrometry imaging (MSI) is used in many aspects of clinical research, including pharmacokinetics, toxicology, personalised medicine, and surgical decision-making. Maximising its potential requires the spatial integration of MSI images with imaging data from existing clinical imaging modalities, such as histology and MRI. To ensure that the information is properly integrated, all contributing images must be accurately aligned.

Holistic Characterization of a Typhimurium Infection Model Using Integrated Molecular Imaging.

A more complete and holistic view on host-microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Typhimurium infection in the liver of a mouse model using the Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism.

Method to Investigate the Distribution of Water-Soluble Drug-Delivery Systems in Fresh Frozen Tissues Using Imaging Mass Cytometry.

Imaging mass cytometry (IMC) offers the opportunity to image metal- and heavy halogen-containing xenobiotics in a highly multiplexed experiment with other immunochemistry-based reagents to distinguish uptake into different tissue structures or cell types. However, in practice, many xenobiotics are not amenable to this analysis, as any compound which is not bound to the tissue matrix will delocalize during aqueous sample-processing steps required for IMC analysis. Here, we present a strategy to perform IMC experiments on a water-soluble polysarcosine-modified dendrimer drug-delivery system (S-Dends).

Deep Learning-Based Annotation Transfer between Molecular Imaging Modalities: An Automated Workflow for Multimodal Data Integration.

An ever-increasing array of imaging technologies are being used in the study of complex biological samples, each of which provides complementary, occasionally overlapping information at different length scales and spatial resolutions. It is important to understand the information provided by one technique in the context of the other to achieve a more holistic overview of such complex samples. One way to achieve this is to use annotations from one modality to investigate additional modalities.

MALDI-2 at Atmospheric Pressure-Parameter Optimization and First Imaging Experiments.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a powerful label-free technique for mapping the spatial distribution of biomolecules directly from tissue. However, like most other MSI techniques, it suffers from low ionization yields and ion suppression effects for biomolecules that might be of interest for a specific application at hand. Recently, a form of laser postionization was introduced (coined MALDI-2) that critically boosts the ion yield for many glyco- and phospholipids by several orders of magnitude and makes the detection of further biomolecular species possible.

Correlative Hyperspectral Imaging Using a Dimensionality-Reduction-Based Image Fusion Method.

Chemical imaging techniques are increasingly being used in combination to achieve a greater understanding of a sample. This is especially true in the case of mass spectrometry imaging (MSI), where the use of different ionization sources allows detection of different classes of molecules across a range of spatial resolutions. There has been significant recent effort in the development of data fusion algorithms that attempt to combine the benefits of multiple techniques, such that the output provides additional information that would have not been present or obvious from the individual techniques alone.

The Influence of MS Imaging Parameters on UV-MALDI Desorption and Ion Yield.

Ultraviolet matrix-assisted laser desorption/ionization mass spectrometry imaging (UV-MALDI MSI) is a widely used technique for imaging molecular distributions within biological systems. While much work exists concerning desorption in UV-MALDI MS, the effects of commonly varied parameters for imaging applications (repetition rate, use of continuous raster mode and raster speed), which determine spatial resolution and limits of detection for the technique, remain largely unknown. We use multiple surface characterization modalities to obtain quantitative measurements of material desorption and analyte ion yield in thin film model systems of two matrix compounds, arising from different UV-MALDI MSI sampling conditions.

Error-Free Data Visualization and Processing through imzML and mzML Validation.

Open data formats are key to facilitating data processing, sharing, and integration. The imzML format ( http://imzml.org/ ) has drastically improved these aspects of mass spectrometry imaging data.

Two-Phase and Graph-Based Clustering Methods for Accurate and Efficient Segmentation of Large Mass Spectrometry Images.

Clustering is widely used in MSI to segment anatomical features and differentiate tissue types, but existing approaches are both CPU and memory-intensive, limiting their application to small, single data sets. We propose a new approach that uses a graph-based algorithm with a two-phase sampling method that overcomes this limitation. We demonstrate the algorithm on a range of sample types and show that it can segment anatomical features that are not identified using commonly employed algorithms in MSI, and we validate our results on synthetic MSI data.

Raster-Mode Continuous-Flow Liquid Microjunction Mass Spectrometry Imaging of Proteins in Thin Tissue Sections.

Mass spectrometry imaging by use of continuous-flow liquid microjunction sampling at discrete locations (array mode) has previously been demonstrated. In this Letter, we demonstrate continuous-flow liquid microjunction mass spectrometry imaging of proteins from thin tissue sections in raster mode and discuss advantages (a 10-fold reduction in analysis time) and challenges (suitable solvent systems, data interpretation) of the approach. Visualization of data is nontrivial, requiring correlation of solvent-flow, mass spectral data acquisition rate, data quality, and liquid microjunction sampling area.

Analysis of Urine, Oral fluid and Fingerprints by Liquid Extraction Surface Analysis Coupled to High Resolution MS and MS/MS - Opportunities for Forensic and Biomedical Science.

Liquid Extraction Surface Analysis (LESA) is a new, high throughput tool for ambient mass spectrometry. A solvent droplet is deposited from a pipette tip onto a surface and maintains contact with both the surface and the pipette tip for a few seconds before being re-aspirated. The technique is particularly suited to the analysis of trace materials on surfaces due to its high sensitivity and low volume of sample removal.

Testing for Multivariate Normality in Mass Spectrometry Imaging Data: A Robust Statistical Approach for Clustering Evaluation and the Generation of Synthetic Mass Spectrometry Imaging Data Sets.

Spatial clustering is a powerful tool in mass spectrometry imaging (MSI) and has been demonstrated to be capable of differentiating tumor types, visualizing intratumor heterogeneity, and segmenting anatomical structures. Several clustering methods have been applied to mass spectrometry imaging data, but a principled comparison and evaluation of different clustering techniques presents a significant challenge. We propose that testing whether the data has a multivariate normal distribution within clusters can be used to evaluate the performance when using algorithms that assume normality in the data, such as k-means clustering.

SpectralAnalysis: Software for the Masses.

The amount of data produced by spectral imaging techniques, such as mass spectrometry imaging, is rapidly increasing as technology and instrumentation advances. This, combined with an increasingly multimodal approach to analytical science, presents a significant challenge in the handling of large data from multiple sources. Here, we present software that can be used through the entire analysis workflow, from raw data through preprocessing (including a wide range of methods for smoothing, baseline correction, normalization, and image generation) to multivariate analysis (for example, memory efficient principal component analysis (PCA), non-negative matrix factorization (NMF), maximum autocorrelation factor (MAF), and probabilistic latent semantic analysis (PLSA)), for data sets acquired from single experiments to large multi-instrument, multimodality, and multicenter studies.

MALDI Imaging of Liquid Extraction Surface Analysis Sampled Tissue.

Combined mass spectrometry imaging methods in which two different techniques are executed on the same sample have recently been reported for a number of sample types. Such an approach can be used to examine the sampling effects of the first technique with a second, higher resolution method and also combines the advantages of each technique for a more complete analysis. In this work matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) was used to study the effects of liquid extraction surface analysis (LESA) sampling on mouse brain tissue.

LESA FAIMS Mass Spectrometry for the Spatial Profiling of Proteins from Tissue.

We have shown previously that coupling of high field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility, with liquid extraction surface analysis (LESA) mass spectrometry of tissue results in significant improvements in the resulting protein mass spectra. Here, we demonstrate LESA FAIMS mass spectrometry imaging of proteins in sections of mouse brain and liver tissue. The results are compared with LESA mass spectrometry images obtained in the absence of FAIMS.

Probing the Relationship Between Detected Ion Intensity, Laser Fluence, and Beam Profile in Thin Film and Tissue in MALDI MSI.

Matrix assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) is increasingly widely used to provide information regarding molecular location within tissue samples. The nature of the photon distribution within the irradiated region, the laser beam profile, and fluence, will significantly affect the form and abundance of the detected ions. Previous studies into these phenomena have focused on circular-core optic fibers or Gaussian beam profiles irradiating dried droplet preparations, where peptides were employed as the analyte of interest.