CPFP

CPFP analyzes shotgun mass-spectrometry proteomics data to identify, validate, and quantify peptides and proteins from LC-MS/MS datasets.

Key Features:

• Multi-engine peptide identification: Employs multiple search engines to perform peptide identification from LC-MS/MS spectra.
• Result integration and validation: Combines outputs from different search engines and applies validation procedures to improve identification confidence using state-of-the-art techniques.
• Protein and peptide quantitation: Performs quantitation of peptides and proteins derived from LC-MS/MS data.
• Scalability and cluster execution: Supports execution of jobs on compute clusters to scale analyses for high-throughput datasets.
• Shotgun LC-MS/MS support: Targets shotgun mass-spectrometry workflows typical of proteomics experiments.

Scientific Applications:

• Proteomics core facility workflows: Standardizes identification, validation, and quantitation workflows used by proteomics core facilities.
• High-throughput proteomics: Processes large-scale LC-MS/MS datasets for high-throughput proteomic studies.
• Peptide and protein characterization: Supports discovery, identification, validation, and quantitation of peptides and proteins from complex biological samples.

Methodology:

Peptide identification using multiple search engines; aggregation of search outputs for validation; peptide and protein quantitation; and optional cluster execution of jobs for scalability.