TOPPR

TOPPR provides a repository and analysis platform for proteolytic processing events in human and mouse proteins by aggregating published proteolytically processed sites and associated proteomics data.

Key Features:

• Fragmentation spectra visualization: Fragmentation mass spectra are displayed for each identified processing site with fragment ion annotations and search engine scores.
• Data retrieval methods: Retrieval supports listing substrates associated with specific cellular stimuli or assays; searching substrates by UniProtKB/Swiss-Prot accession number, entry name, or description; and conducting motif searches to find substrates matching a user-defined protease specificity profile.
• Analysis methods: Supports annotation of predicted secondary structures, known domains, and experimentally obtained 3D structures where available, and visualization of substrate orthologs and conserved sequence stretches using iceLogo visualization.
• Data scope and provenance: Contains thousands of published proteolytically processed sites for human and mouse proteins with comprehensive provenance information.

Scientific Applications:

• Protease specificity and substrate interaction analysis: Enables detailed investigation of protease specificity and substrate interactions using site-level data and motif searches.
• Comparative substrate analyses: Facilitates comparative analyses across substrates and orthologs, including identification of conserved sequence stretches with iceLogo.
• Structural and functional impact assessment: Supports analysis of structural and functional consequences of protein cleavage by integrating secondary structure, domain annotations, and available experimental 3D structures.

Methodology:

Computational methods include fragmentation mass spectrum annotation with fragment ion annotations and search engine scores, motif searches, predicted secondary structure and domain annotation, ortholog mapping, and iceLogo visualization.