Identification and Imaging of Prostaglandin Isomers Utilizing MS3 Product Ions and Silver Cationization

Spatial metabolomics platform combining mass spectrometry imaging and in-depth chemical characterization with capillary electrophoresis

Spatial metabolomics offers the combination of molecular identification and localization. As a tool for spatial metabolomics, mass spectrometry imaging (MSI) can provide detailed information on localization. However, molecular annotation with MSI is challenging due to the lack of separation prior to mass spectrometric analysis. Contrarily, surface sampling capillary electrophoresis mass spectrometry (SS-CE-MS) provides detailed molecular information, although the size of the sampling sites is modest. Here, we describe a platform for spatial metabolomics where MSI using pneumatically assisted nanospray desorption electrospray ionization (PA-nano-DESI) is combined with SS-CE-MS to gain both in-depth chemical information and spatial localization from thin tissue sections. We present the workflow, including the user-friendly setup and switching between the techniques, compare the obtained data, and demonstrate a quantitative approach when using the platform for spatial metabolomics of ischemic stroke.

Pneumatically Assisted Microfluidic Probe for Enhanced Mass Spectrometry Imaging Performance

A pneumatically assisted microfluidic probe (MFP) with two microfluidic channels has been developed for nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) of biological samples. This design simplifies the experimental setup, making it independent of the vacuum suction at the mass spectrometer inlet. The implementation of pneumatically assisted solvent flow through the probe enables stable, high solvent flow rates required to maintain a consistent liquid bridge during high-throughput MSI experiments. This approach addresses challenges associated with using MFP nano-DESI probes on mass spectrometers that have limited vacuum suction and the operation of MFPs with small microfluidic channels. We demonstrate the robustness of the pneumatically assisted MFP with 30 μm channels, which cannot be used for high-throughput MSI experiments without pneumatic assistance, by successfully imaging five mouse brain tissue sections without interruptions.

imzML Writer: An Easy-to-Use Python Pipeline for Conversion of Continuously Acquired Raw Mass Spectrometry Imaging Data to imzML Format

Mass spectrometry imaging (MSI) is a technique that uncovers the contextual distribution of biomolecules in tissue. This involves collecting large data sets with information-rich mass spectra in each pixel. To streamline image processing and interpretation, the MSI community has developed toolboxes for image preprocessing, segmentation, statistical analysis, and visualization. These generally require data to be input as imzML files, an Extensible Markup Language file with vocabulary for mass spectrometry and imaging-specific parameters. While commercial systems (e.g., MALDI) come with proprietary file converters, to our knowledge, no open-access user-friendly converters exist for continuously acquired imaging data (e.g., nano-DESI, DESI). Here, we present imzML Writer, an easy-to-use Python application with a graphical user interface to convert data from vendor format into pixel-aligned imzML files. We package this application with imzML Scout, allowing visualization of the resulting file(s) and batch export of ion images across a range of image and data formats (e.g., PNG, TIF, CSV). To demonstrate the utility of files generated by imzML Writer, we processed nano-DESI data with popular tools such as Cardinal MSI and METASPACE. Overall, this work provides a simple open-access tool for emerging MSI modality users to access advanced MSI processing tools reliant on imzML format. ImzML Writer is available as a distributable Python package via pip or as a standalone program for Mac and PC at https://github.com/VIU-Metabolomics/imzML_Writer.

The Octadecanoids: Synthesis and Bioactivity of 18-Carbon Oxygenated Fatty Acids in Mammals, Bacteria, and Fungi

The octadecanoids are a broad class of lipids consisting of the oxygenated products of 18-carbon fatty acids. Originally referring to production of the phytohormone jasmonic acid, the octadecanoid pathway has been expanded to include products of all 18-carbon fatty acids. Octadecanoids are formed biosynthetically in mammals via cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) activity, as well as nonenzymatically by photo- and autoxidation mechanisms. While octadecanoids are well-known mediators in plants, their role in the regulation of mammalian biological processes has been generally neglected. However, there have been significant advancements in recognizing the importance of these compounds in mammals and their involvement in the mediation of inflammation, nociception, and cell proliferation, as well as in immuno- and tissue modulation, coagulation processes, hormone regulation, and skin barrier formation. More recently, the gut microbiome has been shown to be a significant source of octadecanoid biosynthesis, providing additional biosynthetic routes including hydratase activity (e.g., CLA-HY, FA-HY1, FA-HY2). In this review, we summarize the current field of octadecanoids, propose standardized nomenclature, provide details of octadecanoid preparation and measurement, summarize the phase-I metabolic pathway of octadecanoid formation in mammals, bacteria, and fungi, and describe their biological activity in relation to mammalian pathophysiology as well as their potential use as biomarkers of health and disease.

Expanding Spatial Metabolomics Coverage with Lithium-Doped Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging

Spatial metabolomics has emerged as a powerful tool capable of revealing metabolic gradients throughout complex heterogeneous tissues. While mass spectrometry imaging (MSI) technologies designed to generate spatial metabolomic data have improved significantly over time, metabolite coverage is still a significant limitation. It is possible to achieve deeper metabolite coverage by imaging in positive and negative polarities or imaging several serial sections with different targeted biomolecular classes. However, this significantly increases the number of tissue samples required for biological studies and reduces the capacity for larger sample cohorts. Herein, we introduce lithium-doped nanospray desorption electrospray ionization (nano-DESI) as a simple and robust method to increase spatial metabolomics coverage, which is achieved through enhancements to ionization efficiencies in positive ion mode for metabolites and lipids lacking basic moieties, and improved structurally diagnostic tandem mass spectra for [M + Li]+ adducts. Specifically, signal intensities were found to be enhanced by 10-1000× for 96 compounds including small molecule metabolites, fatty acids, neutral lipids (e.g., diacylglycerols, DAG), and phospholipids when lithium was added to the ESI solvent. In addition, proof-of-principle results reveal that lithium-doped nano-DESI MSI was able to comprehensively visualize metabolites and lipids in the prostaglandin (PG) biosynthetic pathway with PG isomeric resolution in an ovarian tumor section. These data show colocalization of fatty acid (FA) 20:4 containing DAGs, FA 20:4 monoacylglycerols (MAGs), and FA 20:4 with PGE2 and disparate localizations of PGD2. Overall, this study describes a simple and powerful approach to more comprehensively probe the spatial metabolome with MSI.

Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging (nano-DESI MSI): A Tutorial Review

Nanospray desorption electrospray ionization (nano-DESI) is a liquid-based ambient mass spectrometry imaging (MSI) technique that enables visualization of analyte distributions in biological samples down to cellular-level spatial resolution. Since its inception, significant advancements have been made to the nano-DESI experimental platform to facilitate molecular imaging with high throughput, deep molecular coverage, and spatial resolution better than 10 μm. The molecular selectivity of nano-DESI MSI has been enhanced using new data acquisition strategies, the development of separation and online derivatization approaches for isobar separation and isomer-selective imaging, and the optimization of the working solvent composition to improve analyte extraction and ionization efficiency. Furthermore, nano-DESI MSI research has underscored the importance of matrix effects and established normalization methods for accurately measuring concentration gradients in complex biological samples. This tutorial offers a comprehensive guide to nano-DESI experiments, detailing fundamental principles and data acquisition and processing methods and discussing essential operational parameters.

Mass spectrometry imaging for spatially resolved multi-omics molecular mapping

The recent upswing in the integration of spatial multi-omics for conducting multidimensional information measurements is opening a new chapter in biological research. Mapping the landscape of various biomolecules including metabolites, proteins, nucleic acids, etc., and even deciphering their functional interactions and pathways is believed to provide a more holistic and nuanced exploration of the molecular intricacies within living systems. Mass spectrometry imaging (MSI) stands as a forefront technique for spatially mapping the metabolome, lipidome, and proteome within diverse tissue and cell samples. In this review, we offer a systematic survey delineating different MSI techniques for spatially resolved multi-omics analysis, elucidating their principles, capabilities, and limitations. Particularly, we focus on the advancements in methodologies aimed at augmenting the molecular sensitivity and specificity of MSI; and depict the burgeoning integration of MSI-based spatial metabolomics, lipidomics, and proteomics, encompassing the synergy with other imaging modalities. Furthermore, we offer speculative insights into the potential trajectory of MSI technology in the future.

Hardware and software solutions for implementing nanospray desorption electrospray ionization (nano-DESI) sources on commercial mass spectrometers

Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization mass spectrometry imaging (MSI) approach that enables spatial mapping of biological and environmental samples with high spatial resolution and throughput. Because nano-DESI has not yet been commercialized, researchers develop their own sources and interface them with different commercial mass spectrometers. Previously, several protocols focusing on the fabrication of nano-DESI probes have been reported. In this tutorial, we discuss different hardware requirements for coupling the nano-DESI source to commercial mass spectrometers, such as the safety interlock, inlet extension, and contact closure. In addition, we describe the structure of our custom software for controlling the nano-DESI MSI platform and provide detailed instructions for its usage. With this tutorial, interested researchers should be able to implement nano-DESI experiments in their labs.

Lipid Isobar and Isomer Imaging Using Nanospray Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry

Mass spectrometry imaging (MSI) is widely used for examining the spatial distributions of molecules in biological samples. Conventional MSI approaches, in which molecules extracted from the sample are distinguished based on their mass-to-charge ratio, cannot distinguish between isomeric species and some closely spaced isobars. To facilitate isobar separation, MSI is typically performed using high-resolution mass spectrometers. Nevertheless, the complexity of the mixture of biomolecules observed in each pixel of the image presents a challenge, even for modern mass spectrometers with the highest resolving power. Herein, we implement nanospray desorption electrospray ionization (nano-DESI) MSI on a triple quadrupole (QqQ) mass spectrometer for the spatial mapping of isobaric and isomeric species in biological tissues. We use multiple reaction monitoring acquisition mode (MRM) with unit mass resolution to demonstrate the performance of this new platform by imaging lipids in mouse brain and rat kidney tissues. We demonstrate that imaging in MRM mode may be used to distinguish between isobaric phospholipids requiring a mass resolving power of 3,800,000. Additionally, we have been able to image eicosanoid isomers, a largely unexplored class of signaling molecules present in tissues at low concentrations, in rat kidney tissue. This new capability substantially enhances the specificity and selectivity of MSI, enabling spatial localization of species that remain unresolved in conventional MSI experiments.