Protocol for global proteome, virome, and metaproteome profiling of respiratory specimen (VTM) in COVID-19 patient by LC-MS/MS-based analysis

STAR Protoc. 2022 Mar 18;3(1):101045. doi: 10.1016/j.xpro.2021.101045. Epub 2021 Nov 27.

Abstract

In this protocol, we describe global proteome profiling for the respiratory specimen of COVID-19 patients, patients suspected with COVID-19, and H1N1 patients. In this protocol, details for identifying host, viral, or bacterial proteome (Meta-proteome) are provided. Major steps of the protocol include virus inactivation, protein quantification and digestion, desalting of peptides, high-resolution mass spectrometry (HRMS)-based analysis, and downstream bioinformatics analysis. For complete details on the use and execution of this profile, please refer to Maras et al. (2021).

Keywords: Health Sciences; Mass Spectrometry; Proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 / metabolism
  • Chromatography, Liquid / methods
  • Computational Biology
  • Diagnostic Tests, Routine
  • Gene Expression Profiling
  • Genetic Techniques
  • Genome, Viral / genetics
  • Genomics / methods*
  • Humans
  • Influenza A Virus, H1N1 Subtype / metabolism
  • Influenza A Virus, H1N1 Subtype / pathogenicity
  • Peptides
  • Proteome
  • Proteomics / methods*
  • SARS-CoV-2 / metabolism
  • SARS-CoV-2 / pathogenicity
  • Specimen Handling / methods
  • Tandem Mass Spectrometry / methods
  • Virome / genetics
  • Virome / physiology

Substances

  • Peptides
  • Proteome