Pep2Graph

Pep2Graph analyzes proteolytic cleavages from PROTOMAP gel-based mass spectrometry data by mapping peptide sequence coverage and in-gel migration shifts to identify proteolytic events.

Key Features:

• Integration with PROTOMAP: Processes PROTOMAP mass spectrometry-based proteomics data to detect proteolysis-associated changes in protein migration within gels.
• Two-dimensional peptographs: Generates peptographs that combine in-gel migration position with peptide sequence coverage for visual interpretation of cleavage patterns.
• Correlation with spectral counts: Associates peptide sequence positions with mass spectrometry spectral counts to support identification of cleavage sites.
• Detection of migration shifts: Identifies shifts in protein in-gel migration indicative of proteolytic processing.
• Integration of peptide sequence information: Incorporates peptide sequence mappings from in-gel proteomics to relate observed fragments to proteolytic events.

Scientific Applications:

• Protease cleavage mapping: Identification and mapping of proteolytic cleavage events from gel-based mass spectrometry data.
• Study of protease-regulated processes: Analysis of how proteolysis affects cellular functions such as DNA replication, transcription, cell proliferation, differentiation, migration, and apoptosis.
• Investigation of disease mechanisms: Comparative analysis of proteolytic events in physiological and pathological contexts to inform potential therapeutic targets.

Methodology:

Collects PROTOMAP mass spectrometry proteomics data, processes it to identify shifts in protein in-gel migration indicative of proteolysis, integrates peptide sequence mappings and spectral counts, and presents results as two-dimensional peptographs.