ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data

Area of Science:

• Biochemistry
• Pharmacology
• Bioinformatics

Background:

• Cellular Thermal Shift Assay (CETSA) is vital for drug-target identification.
• Statistical analysis is critical for interpreting CETSA results and drawing conclusions.
• Existing tools may lack comprehensive analysis methods or user-friendliness.

Purpose of the Study:

• Introduce ProSAP (Protein Stability Analysis Pod), an open-source software.
• Provide multiple statistical analysis methods for thermal proteome profiling (TPP) and related assays.
• Evaluate the performance of ProSAP and compare different analytical algorithms.

Main Methods:

• Developed ProSAP, a cross-platform, user-friendly software tool.
• Implemented methods for TPP analysis, nonparametric analysis (NPA), proteome integral solubility alteration, and isothermal shift assay (iTSA).
• Tested ProSAP using multiple datasets and compared algorithm performance.

Main Results:

• TPP analysis demonstrated higher accuracy with fewer false positive targets compared to NPA methods.
• NPA methods offer flexibility and are parameter-free.
• For iTSA, edgeR and DESeq2 identified more true targets than t-test and Limma, though ranking performance was similar across methods.

Conclusions:

• ProSAP provides a versatile platform for analyzing protein thermal stability data.
• The choice of statistical method impacts accuracy and target identification in CETSA-based studies.
• ProSAP software is accessible for researchers in drug discovery and target identification.