Inflect

Inflect analyzes Thermal Proteome Profiling (TPP) and Chemical-Protein Interaction by Thermal Shift Assay (CETSA) proteomics abundance data to calculate protein melt temperatures (T_m) and relative melt shifts for identifying protein stability changes.

Key Features:

• T_m and melt shift calculation: Calculates protein melt temperatures (T_m) and relative melt shifts from proteomics abundance data.
• Melt curve generation: Generates detailed melt curves for each protein that meets specified filtering criteria.
• Data matrix output: Produces a data matrix compatible with downstream analytical packages such as UpsetR for replicate comparisons.
• Workflow evaluation and sensitivity analysis: Evaluates how individual calculation steps influence the final list of stabilized or destabilized proteins to assess analytical sensitivity.
• TPP and CETSA data processing: Processes Thermal Proteome Profiling (TPP) and CETSA proteomics abundance datasets.
• R implementation: Implemented in R for computational analysis.
• Analysis optimization: Derives an optimized analysis workflow based on assessment of calculation step impacts to improve identification sensitivity.

Scientific Applications:

• Protein–ligand interaction analysis: Identifies protein–ligand interactions via thermal stabilization or destabilization signatures.
• Protein stability mapping: Maps protein stability changes within cellular environments using TPP and CETSA datasets.
• Signaling pathway investigation: Provides stability-based evidence to probe biological signaling pathways.
• Drug discovery and target identification: Supports drug discovery by detecting proteins whose thermal stability shifts upon ligand binding.

Methodology:

Calculates protein T_m and relative melt shifts from proteomics abundance data, generates per-protein melt curves subject to filtering criteria, produces data matrices compatible with UpsetR for replicate comparison, and evaluates the influence of individual calculation steps to derive an optimized analysis workflow.