MSstatsShiny

MSstatsShiny provides a point and click end-to-end statistical analysis pipeline for proteomics experiments integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM.

Key Features:

• Multi-acquisition support: MSstatsShiny analyzes data-dependent acquisitions (DDA) that are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions.
• Post-translational modification analysis: MSstatsShiny supports experiments targeting post-translational modifications (PTMs) through integration with MSstatsPTM.
• Reproducible analysis generation: MSstatsShiny automatically saves user selections and builds an R script that recreates their analysis.

Scientific Applications:

• Label-free proteomics: MSstatsShiny performs statistical analysis of label-free DDA proteomics data.
• TMT-based proteomics: MSstatsShiny performs statistical analysis of tandem mass tag (TMT)-based quantitative proteomics data.
• PTM-focused studies: MSstatsShiny enables statistical analysis of experiments targeting post-translational modifications.
• Targeted proteomics: MSstatsShiny analyzes selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) data.
• Data-independent acquisition: MSstatsShiny supports statistical analysis of DIA proteomics data.

Methodology:

MSstatsShiny integrates with the R packages MSstats, MSstatsTMT, and MSstatsPTM to perform statistical analysis.