ProteoViz

ProteoViz analyzes and visualizes phosphoproteomics data from mass spectrometry to support interpretation of phosphorylation events at protein and modified peptide levels.

Key Features:

• Normalization and Differential Expression Analysis: R scripts perform normalization and differential expression analysis of proteomics data to identify significant changes in phosphorylation.
• Identification of Sequence Motifs and Kinases: Identifies sequence motifs and associated kinases within phosphoproteomic datasets and links them to phosphorylated peptides.
• Gene Set Enrichment Pathways: Facilitates gene set enrichment analysis connecting significant phosphosites to biological pathways.
• Interactive Visualization Plots: Generates interactive visualization plots for exploration of proteins and phosphorylated peptides.
• Integration with Existing Databases: Links phosphosites with sequence motifs and pathways and enables integration of outputs with external databases.

Scientific Applications:

• Cellular signaling and protein regulation: Supports analysis of phosphorylation-mediated signaling and regulation of protein function.
• Cancer and translational studies: Applicable to phosphoproteomic experiments such as kinase inhibitor treatments in lymphoma cell lines to investigate disease mechanisms and cancer biology.

Methodology:

R scripts normalize raw proteomics data and perform differential expression analysis to identify phosphorylation changes, then identify sequence motifs and kinases, perform gene set enrichment linking phosphosites to pathways, and generate visualization plots.