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Updated: Jun 16, 2025
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Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins
Published on: August 31, 2017
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A Comprehensive Data Processing Pipeline for Phosphoproteomics in Viral Infection Studies
Sini Huuskonen1, Xiaonan Liu1, Kari Salokas1
1Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
Methods in Molecular Biology (Clifton, N.J.)
|June 14, 2025
Summary
This study details a method for analyzing cellular responses to viral infections using quantitative phosphoproteome analysis. It identifies key phosphorylation events to understand virus-host interactions and potential therapeutic targets.
Area of Science:
- Proteomics
- Virology
- Cellular Biology
Background:
- Phosphorylation is a critical posttranslational modification regulating cellular processes.
- Virus-host interactions heavily involve phosphorylation events.
- Understanding these events is key to combating viral infections.
Purpose of the Study:
- To establish a comprehensive methodology for quantitative global and phosphoproteome analysis of virus-infected cells.
- To develop a robust pipeline for identifying phosphorylation changes during viral infection.
- To uncover potential therapeutic targets and understand viral pathogenesis.
Main Methods:
- Cell lysis and protein sample preparation (reduction, alkylation, digestion, desalting).
- Phosphopeptide enrichment using CAE-Ti-IMAC microspheres.
- High-throughput Data-Independent Acquisition-Parallel Accumulation-Serial Fragmentation (DIA-PASEF) Mass Spectrometry (MS) analysis using TimsTOF Pro 2.
- Data processing and analysis using the DIA-NN program.
Main Results:
- Sensitive detection of phosphorylation events in virus-infected cells.
- Comprehensive profiling of phosphoproteome alterations.
- Identification of key pathways affected by viral infection.
Conclusions:
- The protocol provides a robust framework for studying viral infection mechanisms.
- It enables the identification of potential therapeutic targets for antiviral strategies.
- This approach aids in elucidating molecular mechanisms of viral pathogenesis and host immune evasion.
