ProtyQuant

ProtyQuant processes multiple label-free shotgun proteomics datasets to perform peptide-spectrum matching, protein inference, and label-free quantification for comparative proteomics.

Key Features:

• Compatibility with TPP: Reads pepXML files generated by various search engines for integration with the Trans-Proteomic Pipeline.
• Peptide-spectrum matching: Handles peptide-spectrum matching inputs from pepXML for downstream inference and quantification.
• PIPQ modifications: Uses peptide probabilities (PIPQ modifications) for protein inference and quantification to improve sensitivity and linearity.
• Accumulated peptide probabilities (app): Utilizes app for protein probability estimation and quantification tasks.
• Protein inference algorithms: Implements Multiple Counting, Equal Division, and Linear Programming algorithms for peptide-to-protein assignment.
• Output format: Produces human-readable plain text tables for downstream analysis.

Scientific Applications:

• Label-free Quantification: Enhances detection and quantification of proteins with reported superior sensitivity and linearity compared to ProteinProphet.

Methodology:

Reads pepXML inputs and performs peptide-spectrum matching, protein inference, and quantification by employing Multiple Counting, Equal Division, and Linear Programming for peptide-to-protein assignment while using peptide probabilities (PIPQ modifications) and accumulated peptide probabilities (app) for protein probability estimation and quantification.