Mass Spectrometry Imaging Data Analysis with ShinyCardinal

Given the rapid growth and improvement in both mass spectrometry imaging (MSI) techniques and its applications, there is a critical need for the development of efficient and comprehensive computational tools for MSI data analysis. As such, we introduce ShinyCardinal, an open-source and vendor-neutral software that covers all step in MSI data analysis. It leverages the R package Cardinal to enhance its functionalities by introducing several additional important features, such as removal of background noises and matrix peaks, deisotoping, absolute quantification, network analysis, and metabolite identification. ShinyCardinal is built as a desktop application (https://shinycardinal.sourceforge.io) with a conveniently designed graphic user interface to provide users a stable, consistent, and user-friendly data analysis framework. The versatility and capabilities of ShinyCardinal is demonstrated with nine MSI datasets acquired from different platforms.