MhcVizPipe

MhcVizPipe visualizes and evaluates mass spectrometry-based immunopeptidomic datasets to assess peptide presentation by MHC class I and II, binding motifs, and enrichment.

Key Features:

• Integration with prediction and clustering tools: Integrates outputs from NetMHCpan, NetMHCIIpan, and GibbsCluster for analysis of MHC class I and II ligand datasets.
• Report generation (HTML): Produces organized visual reports in HTML format summarizing peptide-level and motif-level results.
• Quality assessment and enrichment analysis: Computes rapid assessments of dataset quality and specific peptide enrichment metrics for immunopeptidomic samples.
• Binding motif and non-canonical peptide analysis: Identifies expected and unexpected binding motifs and supports analysis of non-canonical MHC peptides.
• Support for evaluation of experimental protocols and species: Facilitates assessment of sample preparation protocols and antibody-based MHC peptide isolation across mouse and human samples.

Scientific Applications:

• Dataset quality control: Rapidly assess the quality of mass spectrometry-derived immunopeptidomic datasets.
• Peptide–MHC interaction analysis: Characterize peptide binding to MHC class I and II using NetMHCpan/NetMHCIIpan-derived predictions.
• Motif discovery: Detect and visualize MHC binding motifs, including unexpected motifs.
• Non-canonical peptide characterization: Support analysis and reporting of non-canonical MHC peptides.
• Protocol and reagent evaluation: Compare enrichment and recovery related to sample preparation protocols and MHC peptide isolation antibodies in mouse and human studies.

Methodology:

MhcVizPipe integrates outputs from NetMHCpan, NetMHCIIpan, and GibbsCluster with mass spectrometry-derived peptide lists to generate HTML visual reports and quality/enrichment summaries.