Delaware Valley Mass Spectrometry Discussion Group

Mass Spectrometry Imaging (MSI) is a powerful technology that allows scientists to visualize the spatial distribution of molecules such as biomarkers and metabolites. Here I will describe our efforts to create tools for MSI analysis guided by principles of open-access and ease of use, starting with an R Shiny app called MSI.EAGLE. This app was developed using the R Shiny web application framework and builds on top of the Cardinal package for R. This is designed to be an open-source, flexible tool to implement new methods while also being easy to use for researchers with diverse backgrounds and skill sets. MSI.EAGLE has a modular structure that makes it easy to customize and collaborate on its development. It features a user-friendly interface that allows researchers to perform tasks such as segmentation using Uniform Manifold Approximation Projection (UMAP), background segmentation/removal from tissues, and phenotype assignment based on periodic frequencies of pixels in x/y or based on manual parameters.

I will describe a specific application of MSI.EAGLE in a workflow for custom micro-well surface design suitable for desorption electrospray ionization (DESI-MS). This application serves to address a demand for cheap and rapid mass spectrometry testing of biofluids. The workflow consists of three steps: customizing PARAFILM surfaces using 3D printed molds; spotting samples using high-throughput robotics on the Opentrons platform; and analyzing data using MSI.EAGLE. This system allows researchers to access custom surface design workflows and perform high-throughput analyses in a cost-effective manner.