ProSAP

ProSAP analyzes thermal shift assays to quantify proteome-wide protein stability changes and support drug–target identification using thermal proteome profiling (TPP), nonparametric analysis (NPARC), and isothermal shift assay (iTSA) methods.

Key Features:

• Integrated workflow: Five modules—data preprocessing, data visualization, TPP analysis, NPARC, and iTSA analysis—support processing from quantitative input tables to interpreted stability results.
• Input compatibility: Accepts proteomics quantitative tables generated by Proteome Discoverer and MaxQuant.
• Thermal proteome profiling (TPP) analysis: Implements TPP analysis to reduce false-positive target identification in thermal shift assays.
• Nonparametric analysis (NPARC): Includes NPARC as a flexible, parameter-free approach for detecting stability shifts.
• Isothermal shift assay (iTSA) analysis: Supports iTSA analysis using edgeR and DESeq2 and includes reported comparisons to t-test and Limma for target identification and ranking.

Scientific Applications:

• Drug–target identification: Identifies candidate drug targets by detecting proteome-wide stability changes upon treatment.
• Proteome-wide stability profiling: Quantifies and compares protein stability changes across conditions using thermal shift assays and TPP.
• Protein–ligand and protein–protein interaction studies: Assists in studying protein–ligand and protein–protein interactions at proteome scale through stability shifts.

Methodology:

Computational methods explicitly include data preprocessing, data visualization, thermal proteome profiling (TPP) analysis, nonparametric analysis (NPARC), and isothermal shift assay (iTSA) analysis using edgeR and DESeq2, with comparisons to t-test and Limma.