Pepshell

Pepshell visualizes and analyzes mass spectrometry-based conformational proteomics data to characterize protein conformational changes and dynamics.

Key Features:

• Mass spectrometry support: Handles data derived from limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labeling experiments.
• Peptide-level visualization: Displays identified peptides mapped to protein sequences and structural contexts.
• Comparative analysis: Compares datasets across experimental conditions such as varying proteolysis times or protein binding to different substrates or inhibitors.
• Conformational characterization: Enables detection and interpretation of protein conformational changes and dynamics related to post-translational modifications, cofactors, and molecular interactions.

Scientific Applications:

• Structural biology: Characterizes protein dynamics to inform understanding of protein function.
• Post-translational modification analysis: Investigates how modifications alter protein conformation and dynamics.
• Interaction studies: Assesses conformational effects of binding to cofactors, substrates, or inhibitors.
• Comparative proteomics: Evaluates differences across time courses or experimental conditions in conformational proteomics experiments.

Methodology:

Processes mass spectrometry-derived datasets from limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labeling, visualizes identified peptides at sequence and structural levels, and performs comparative analyses across experimental conditions.