Unipept visualizations

Unipept visualizations visualizes metaproteome biodiversity and taxonomic composition using tryptic peptide information from shotgun mass spectrometry (MS/MS) mapped to UniProtKB.

Key Features:

• Tryptic peptide input: Uses tryptic peptide information derived from shotgun mass spectrometry (MS/MS) experiments as the primary data for analysis.
• Efficient index-based retrieval: Employs an efficient index structure to retrieve all occurrences of a tryptic peptide within UniProtKB records.
• Lowest common ancestor (LCA) taxon-specificity analysis: Applies an LCA approach to determine peptide taxonomic specificity, remaining robust to taxonomic misarrangements, misidentifications, and annotation inaccuracies.
• Visualization types: Generates treemaps, sunburst charts, and treeview visualizations to represent taxonomic composition and biodiversity.
• Multipeptide analysis: Performs multipeptide analysis to assess sample biodiversity by considering multiple peptides simultaneously.
• Scalability for metaproteomics: Designed to handle extensive metaproteomics datasets typical of shotgun MS/MS studies.

Scientific Applications:

• Metaproteome biodiversity studies: Investigates biodiversity and taxonomic composition in metaproteome samples, including bacterial phyllosphere and human gut microbiomes.
• Reanalysis of public datasets: Enables reanalysis of publicly available shotgun MS/MS datasets to uncover taxonomic and biodiversity insights.

Methodology:

Integrates tryptic peptide data from shotgun MS/MS with an index linked to UniProtKB records, applies a lowest common ancestor (LCA) algorithm for taxonomic assignment, and generates treemap, sunburst, and treeview visualizations.