MSstatsPTM

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs), including summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Key Features:

• Multi-platform support: Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling workflows.
• PTM site quantification: Quantifies PTM sites (modified residues) and their corresponding proteins.
• Integration of quantification results: Integrates PTM site and protein-level quantification results.
• Summarization: Provides functions for data summarization.
• Abundance estimation: Estimates PTM site abundance.
• Differential analysis: Detects changes in PTMs across experimental conditions.

Scientific Applications:

• Post-translational modification analysis: Statistical characterization of PTMs in quantitative proteomics experiments.
• Multi-labeling workflow analysis: Analysis of PTM data from DDA, DIA, SRM, or TMT labeling experiments.
• Integrated PTM and protein quantification: Combined analysis of PTM site changes with corresponding protein abundance changes.

Methodology:

MSstatsPTM performs quantification of PTM sites (modified residues) and their corresponding proteins, integrates the quantification results, and applies statistical methods for summarization, abundance estimation, and detection of changes across experimental conditions.