AlphaMap

AlphaMap maps identified peptides and post-translational modifications onto protein sequences to integrate experimental proteomics data with UniProt sequence annotations for visual exploratory analysis.

Key Features:

• Integration with Sequence Annotations: Maps identified peptides and post-translational modifications from proteomic datasets to their corresponding protein sequences and incorporates UniProt annotations.
• Visualization Capabilities: Generates publication-quality, customizable visualizations of peptide-level mappings and sequence annotations.
• Proteolytic Cleavage Site Highlighting: Highlights expected proteolytic cleavage sites on protein sequences relative to identified peptides.
• Dataset Integration: Synthesizes experimental information across proteomic datasets with publicly available sequence annotations.
• Customization: Allows tailoring of displayed annotations and visual parameters to specific research questions.
• Python package integration: Provides a Python package for incorporation into analysis workflows.

Scientific Applications:

• Sequence-level annotation of proteomics data: Contextualizes peptide and PTM identifications by mapping them onto UniProt-annotated protein sequences.
• PTM identification and localization: Aids identification and visualization of post-translational modifications within protein sequences.
• Protease cleavage and peptide coverage analysis: Assesses expected proteolytic cleavage sites and peptide coverage across protein sequences.
• Exploratory and hypothesis-driven analysis: Facilitates visual exploration to generate and test hypotheses about protein function and regulation.

Methodology:

Maps proteomic peptides and post-translational modifications to protein sequences, overlays annotations from UniProt, and highlights expected proteolytic cleavage sites.