PepMapViz

PepMapViz enables import, mapping, and comparative analysis of peptide data from mass spectrometry tools, with visualization of peptide clusters for immunogenicity prediction and protein modification exploration.

Key Features:

• Multi-tool peptide import: Imports peptide data output from multiple popular mass spectrometry analysis tools.
• Peptide-to-protein mapping: Maps peptides to their parent protein sequences.
• Protein domain and modification highlighting: Highlights protein domains and modifications in a linearized format.
• Comparative visualization: Enables comparative visualization across multiple experimental conditions.
• Immunogenicity prediction visualization: Visualizes MHC-presented peptide clusters in different antibody regions to predict potential immunogenicity of antibody-based therapies.
• Cross-software result comparison: Aids in visualization of cross-software mass spectrometry results at the peptide level for specific proteins.
• Post-translational modification coverage analysis: Visualizes post-translational modification coverage across different experimental conditions.

Scientific Applications:

• Immunogenicity prediction: Visualizes peptide clusters in antibody regions to predict potential immunogenicity of antibody-based therapies.
• Post-translational modification analysis: Explores protein modifications and post-translational modification coverage across experimental conditions.
• Cross-software mass spectrometry validation: Compares mass spectrometry results at the peptide level across different software tools for specific proteins.
• Protein domain characterization: Displays domain details in a linearized format mapped to peptide positions.

Methodology:

PepMapViz is implemented in R and maps peptides to parent protein sequences with domain and modification highlighting.