SmartPhos

SmartPhos streamlines phosphoproteomics data analysis through pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut.

Key Features:

• Pre-processing: Performs normalization, normalization correction, transformation, imputation, and batch effect correction on phosphoproteomics data.
• Quality Control and Visualization: Implements PCA and heatmap generation for exploratory data analysis.
• Differential Analysis: Supports differential expression analysis and time-series clustering.
• Functional Inference: Performs gene set enrichment analysis and kinase activity inference.

Scientific Applications:

• Phosphoproteomics Data Analysis: Processes and analyzes phosphoproteomics datasets from MaxQuant and Spectronaut search engines.
• Temporal Phosphorylation Dynamics: Enables time-series clustering to study phosphorylation changes over time.
• Kinase Signaling Research: Infers kinase activity from phosphoproteomics data to investigate signaling pathway regulation.

Methodology:

SmartPhos implements normalization, normalization correction, transformation, imputation, batch effect correction, PCA, heatmap visualization, differential expression analysis, time-series clustering, gene set enrichment analysis, and kinase activity inference.