SQuAPP

SQuAPP performs integrative quantitative analysis of protein, peptide, and post-translational modification (PTM) datasets to detect protein-level-independent modulation of modifications and support comparative proteomic interpretation.

Key Features:

• Workflow-based processing: Implements a structured workflow encompassing quality control, pre-processing, statistical analysis, and visualization of quantitative proteomics data.
• Multi-level data integration: Handles protein, peptide, and PTM datasets simultaneously to enable combined analysis across molecular levels.
• PTM-level modulation detection: Identifies protein-level-independent modulation of modifications and assesses dynamic interactions among different PTMs.
• Parallel dataset processing: Supports parallel processing of protein, peptide, and PTM datasets for comprehensive examination and interpretation.

Scientific Applications:

• PTM-focused proteomics: Analysis of modulation of the proteome by PTMs such as phosphorylation and proteolytic processing.
• Integrative proteomic interpretation: Uncovering intricate relationships within proteomic data through combined protein, peptide, and PTM analysis.

Methodology:

Processes quantitative proteomics data through quality control, pre-processing, statistical analysis, and parallel analysis of protein, peptide, and PTM datasets.