MSstatsShiny

MSstatsShiny performs statistical analysis of quantitative proteomics data by integrating the MSstats suite to enable relative quantification and hypothesis testing for LC-MS/MS bottom-up experiments.

Key Features:

• Integration with MSstats suite: Integrates MSstats, MSstatsTMT, and MSstatsPTM Bioconductor packages for downstream statistical analysis of proteomics data.
• Supported acquisition types: Supports label-free data-dependent acquisitions (DDAs), data-independent acquisitions (DIAs), and tandem mass tag (TMT)-based DDA workflows.
• Analysis levels: Quantifies and analyzes relative changes at the peptide, protein, and post-translational modification (PTM) levels.
• Reproducibility: Generates an R script that programmatically reproduces the analysis to support reproducible research.
• Data type handling: Processes quantitative data derived from bottom-up liquid chromatography–tandem mass spectrometry (LC-MS/MS) proteomics experiments.

Scientific Applications:

• Protein identification and quantification: Facilitates identification and quantification of proteins in complex biological mixtures derived from LC-MS/MS experiments.
• Comparative analysis: Enables statistical comparison of protein and PTM abundance changes between experimental conditions.
• Demonstration on public datasets: Applied to MassIVE datasets MSV000086623 and MSV000085565 for real-world proteomics analyses.

Methodology:

Implements the statistical methods provided by MSstats, MSstatsTMT, and MSstatsPTM for modeling and testing relative abundance changes in peptide, protein, and PTM-level quantitative LC-MS/MS data and can export an R script that reproduces the analysis.