mspms: A Comprehensive R Package and Graphic Interface for Multiplex Substrate Profiling by Mass Spectrometry Analysis

Abstract

Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS) is a powerful method for determining the substrate specificity of proteolytic enzymes, knowledge key for developing protease inhibitors, diagnostics, and protease-activated therapeutics. However, the complex datasets generated by MSP-MS pose significant analytical challenges. To address this, we developed mspms, a Bioconductor R package complemented by an intuitive graphical interface. Mspms streamlines MSP-MS data analysis by standardizing workflows for data preparation, processing, statistical analysis, and visualization. Designed for accessibility, it serves both advanced users via the R package and broader audiences through the web interface. We validated mspms by profiling the substrate specificity of four well-characterized cathepsins (A-D), demonstrating its ability to reliably capture expected substrate specificities. As the first publicly available platform for MSP-MS data analysis, mspms delivers comprehensive functionality, transparency, and ease of use, making it a valuable resource for the protease research community. Access to mspms is available through the Bioconductor project at https://bioconductor.org/packages/mspms, and a graphic interface is available at https://gonzalezlab.shinyapps.io/mspms_shiny/. Author SummaryWe developed mspms, an easy-to-use tool that helps researchers analyze data from a proteomics technique called Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS). This software improves on previous methods of analyzing MSP-MS data, which required the user to navigate a confusing mix of R scripts, manual manipulation of spreadsheets, and third-party tools--an approach that was daunting for collaborators and new graduate students alike. Mspms streamlines the process, enabling faster, more reliable, and reproducible data analysis. We tested the tool using well-known proteases and found that it accurately identifies their known targets. As the first comprehensive tool for MSP-MS analysis, mspms makes this method approachable to a wider audience. Its available for free through the Bioconductor project at https://bioconductor.org/packages/mspms, and a graphical interface is available at https://gonzalezlab.shinyapps.io/mspms_shiny/.