Bioconductor Release 3.23 Chemoproteomics Updates #159
Description
Introduction
Proteomic experiments using liquid-chromatography mass spectrometry (LC-MS) are ever increasing in size and complexity. While advancing statistical methods for these experiments is crucial, equally important is the infrastructure to streamline use of these methods. The MSstats family of free open-source statistical software packages for MS-based proteomics is designed to handle a variety of biological questions and experimental designs. MSstats additionally supports a graphical user interface, MSstatsShiny, that streamlines reproducible data analysis without requiring programming expertise. Here, we present additions to MSstatsShiny to enhance the user experience. These include support for chemoproteomic experiments.
Methods
We look to integrate the package MSstatsResponse, which was specifically designed to support large-scale chemoproteomic experiments. We highlight these new extensions with multiple experiments with differing designs and complexity. We show that various analysis workflows previously requiring multiple packages and programming expertise can now be reproduced on a single interface, while reducing setup time and user error. We present dose response curve model fitting and visualizations that capture abundance patterns across dosage levels and report IC50 values with their confidence intervals for each protein. For future experiment planning, new power curve plots for chemoproteomic experiments illustrate how the number of doses and replicates per dose interact to determine statistical power. We lastly demonstrate dose response analysis, when integrated with interactive biological network visualizations, streamlines biological interpretation and uncovers hypotheses for future follow up experiments.
Timeline
Due 4/20/2026.
Datasets
We want to be able to use these case studies for the May Institute short course in May.
- Chemoproteomics dataset
- Selevsek timecourse dataset
- PTM time course dataset https://ood.explorer.northeastern.edu/pun/sys/dashboard/files/fs//projects/VitekLab/Projects/Talus/Talus_Project/PTM_Garrido/Figure6-processing.R
Developer Outcomes
- Ownership of statistical modeling UI and server code
- Ownership of sample size calculation UI and server code
- Ownership of dose response curve code
- Adaptability to handle updates regarding protein turnover & other similar experiments