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Rapid Identification of Pathogens01:25

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

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Identification of Nucleolar Factors During HIV-1 Replication Through Rev Immunoprecipitation and Mass Spectrometry
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P4PP: A Universal Shotgun Proteomics Data Analysis Pipeline for Virus Identification.

Armand Paauw1, Evgeni Levin2, Ingrid A I Voskamp-Visser1

  • 1Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, Rijswijk, the Netherlands.

Molecular & Cellular Proteomics : MCP
|May 31, 2025
PubMed
Summary

A new proteomic data analysis pipeline (P4PP) identifies 1896 virus species, including human infectious viruses. This method enhances viral diagnostics for emerging and mutated viruses.

Keywords:
P4PP pipelinepandemic preparednesspeptidesproteomicsvirus identification

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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.