Peppy

Peppy performs proteogenomic searches by generating peptide databases from genomic sequences and matching peptides to MS/MS spectra to identify novel proteins, annotate genes, and detect peptides unique to individual genomes.

Key Features:

• Automated peptide-database generation: Generates comprehensive peptide databases directly from input genomes and tracks peptide loci.
• Peptide–spectrum matching and scoring: Matches peptides to MS/MS spectra and assigns confidence values to peptide-spectrum matches.
• Decoy database generation and FDR control: Automatically generates decoy databases and performs target-decoy searches to estimate false discovery rates at user-defined thresholds.
• Multithreading and Java implementation: Implemented in Java with a fully multithreaded architecture for parallel processing across CPU cores.
• Scalability for large genomes: Optimizes computational efficiency and resource management to support proteogenomic searches on large genomes.

Scientific Applications:

• Novel protein discovery: Identification of novel proteins and aberrant protein forms from genomic-derived peptide databases and MS/MS data.
• Gene annotation: Support for annotating genes by mapping identified peptides back to genomic loci.
• Detection of individual-specific peptides: Detection of peptides unique to individual genomes and individual-specific peptide sequences for studies of genomic diversity.
• Biomarker and therapeutic target identification: Enabling discovery of biomarkers and potential therapeutic targets relevant to personalized medicine.

Methodology:

Generates a comprehensive peptide database from the input genome and tracks peptide loci, matches peptides to MS/MS spectra and assigns confidence values, and generates and searches decoy databases (target-decoy searches) to estimate false discovery rates; implemented in Java with fully multithreaded execution.