P4PP: A Universal Shotgun Proteomics Data Analysis Pipeline for Virus Identification

Area of Science:

• Virology
• Proteomics
• Bioinformatics

Background:

• Human viral infections pose a significant threat, necessitating advanced detection methods.
• Existing diagnostic tools may struggle with novel, mutated, or re-emerging viral threats.

Purpose of the Study:

• To develop and validate a data analysis approach for shotgun proteomic data to detect diverse virus species.
• To establish a comprehensive proteome database and pipeline for pandemic preparedness (P4PP).

Main Methods:

• Development of the P4PP pipeline and database (P4PP v01) for virus identification.
• Analysis of 174 mass spectrometry datasets from virus-infected and non-infected cell lines.
• Utilized discriminatory peptides for species-level virus identification.

Main Results:

• The P4PP pipeline successfully identified 1896 virus species across 32 families.
• 146 out of 160 virus-infected samples were correctly identified at the species level; 4 at the family level.
• Accurate subtyping of influenza A and SARS-CoV-2 was demonstrated with sufficient peptide data.

Conclusions:

• Shotgun proteomics combined with the P4PP approach can identify all virus types cultivated in cell lines.
• This agnostic virus proteome analysis has the potential to significantly enhance viral diagnostic laboratories' capabilities.
• The P4PP system offers improved preparedness against unexpected, mutated, or re-emerging viral pathogens.