Related Experiment Video
Updated: Jan 26, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
Published on: October 13, 2020
mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry
Charlie Bayne1,2, Brianna Hurysz3,4,5, David J Gonzalez4,5,6
1Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA. chbayne@health.ucsd.edu.
Background:
Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS) is a powerful method for determining the substrate specificity of proteolytic enzymes, which is essential for developing protease inhibitors, diagnostics, and protease-activated therapeutics. However, the complex datasets generated by MSP-MS pose significant analytical challenges and have limited accessibility for non-specialist users.
Results:
We developed mspms, a Bioconductor R package with an accompanying graphical interface, to streamline the analysis of MSP-MS data. Mspms standardizes workflows for data preparation, processing, statistical analysis, and visualization. The tool is designed for accessibility, serving advanced users through the R package and broader audiences through a web-based interface. We validated mspms using data from four well-characterized cathepsins (A-D), demonstrating that it reliably captures expected substrate specificities.
Conclusions:
mspms is the first publicly available, comprehensive platform for MSP-MS data analysis downstream of peptide identification and quantification. It integrates preprocessing, normalization, statistical testing, and visualization into a single, transparent, and user-friendly framework, making it a valuable resource for the protease research community. The package is distributed via Bioconductor, and a graphical interface is available online for interactive use.
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