pepFunk

pepFunk performs peptide-centric functional analysis of metaproteomic data from the human gut microbiome to improve functional assignment and pathway enrichment at the peptide level.

Key Features:

• Peptide-centric workflow: Focuses analysis on peptides rather than proteins to retain information and reduce ambiguity in peptide-to-protein mapping.
• Curated peptide database: Uses a peptide database curated specifically for human gut microbiome studies to improve computational efficiency.
• KEGG integration: Maps peptides to KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations to enable pathway-level enrichment analysis.
• GSVA adaptation: Applies Gene Set Variation Analysis (GSVA) adapted for peptide-level data to assess pathway activity variation.
• Shared-peptide handling: Explicitly addresses peptides shared among multiple proteins arising from enzymatic digestion to reduce assignment errors.
• Enhanced pathway detection: Demonstrates improved identification of enriched KEGG pathways compared to conventional protein-centric methods.

Scientific Applications:

• Metaproteomic functional profiling: Functional characterization of human gut microbiome samples at the peptide level.
• Pathway enrichment analysis: Identification of enriched KEGG pathways from peptide-level data.
• Statistical functional comparison: Increased statistical power for differential functional analyses using peptide-centric approaches with GSVA.
• Ambiguity resolution: Reduction of functional assignment ambiguity caused by peptides shared among multiple proteins.

Methodology:

Implements a peptide-centric workflow using a curated human gut microbiome peptide database, integrates KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations for pathway mapping, adapts Gene Set Variation Analysis (GSVA) for peptide data, and explicitly accounts for peptides shared among proteins due to enzymatic digestion.