MVP_A

MVP_A visualizes and integrates proteogenomic data by combining genomic sequencing with mass spectrometry-based proteomics to enable interactive peptide-level and genome-coordinate exploration.

Key Features:

• mzSQLite input: Uses SQLite databases in the mzSQLite custom datatype encapsulating mass spectrometry-based peptide identification information, variant annotation tables, and coding sequence tables.
• Galaxy API integration: Interacts with the Galaxy API to read mzSQLite inputs and send filtered peptide data back to Galaxy for further analysis.
• Peptide filtering: Provides interactive filtering of peptides based on sequence criteria and data quality metrics.
• Annotated MS and protein visualization: Displays annotated peptide MS data and protein-level information mapped to genomic coordinates.
• IGVjs integration: Integrates Integrated Genomics Viewer JavaScript (IGVjs) to visualize peptides alongside corresponding transcript and genomic coding sequences.
• Data export and sharing: Enables saving and sharing of processed data and visualizations via Galaxy.
• Extensibility: Supports addition of new proteogenomic visualization functionalities.

Scientific Applications:

• Proteogenomic dataset exploration: Exploration and interpretation of combined genomic sequencing and mass spectrometry-based proteomics datasets.
• Variant peptide analysis: Annotation and inspection of variant peptides using variant annotation tables and mapped coding sequences.
• Peptide quality control: Filtering peptide identifications by sequence criteria and data quality metrics for QC and downstream processing.
• Integrative visualization: Visualizing peptides in genomic context alongside transcripts and coding sequences using IGVjs.
• Downstream workflow integration: Exporting filtered peptide sets back to Galaxy for integration with other 'omic tools and analyses.

Methodology:

Implemented as an HTML plugin primarily using JavaScript, leveraging the Galaxy API, consuming mzSQLite SQLite databases containing peptide identifications, variant annotation tables, and coding sequence tables, integrating IGVjs for genome-context visualization, and enabling export of filtered peptide data back to Galaxy.