A Comprehensive Data Processing Pipeline for Phosphoproteomics in Viral Infection Studies.

Sini Huuskonen, Xiaonan Liu, Kari Salokas, Antti Tuhkala, Salla Keskitalo, Markku Varjosalo

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

6 authors.

Sini HuuskonenInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.

Xiaonan LiuInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.

Kari SalokasInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.

Antti TuhkalaInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.

Salla KeskitaloInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.

Markku VarjosaloInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland. markku.varjosalo@helsinki.fi.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

This protocol outlines a comprehensive methodology for investigating cellular responses to viral infections through quantitative global and phosphoproteome analysis. Phosphorylation, a crucial posttranslational modification, regulates various cellular processes and plays a key role in virus-host interactions. To study the phosphorylation events, we have developed an analysis pipeline, and the subsequent steps detail sample preparation techniques for obtaining high-quality protein samples suitable for phosphoproteomic analysis. These include lysing virus-infected cells, processing protein samples through reduction, alkylation, digestion, and desalting, and enriching phosphopeptides using CAE-Ti-IMAC microspheres. High-throughput DIA-PASEF MS-analysis using TimsTOF Pro 2 facilitates sensitive detection of phosphorylation events, enabling a comprehensive understanding of viral infection, replication, and cytotoxicity in the host cell. The protocol also integrates the DIA-NN program for processing and analyzing MS data. Overall, this protocol provides a robust framework for identifying potential therapeutic targets within these altered pathways for elucidating the molecular mechanisms underlying viral pathogenesis and host immune evasion.

Indexed as

PhosphoproteinsProteomeProteomicsVirus DiseasesHost-Pathogen InteractionsHumansPhosphopeptidesPhosphorylationProtein Processing, Post-TranslationalPhosphopeptidesPhosphoproteinsProteomeDIA-PASEF MS-analysisPhosphopeptide enrichmentPhosphoproteomicsPhosphorylationPosttranslational modifications (PTMs)Protein kinasesSARS-CoV-2Viral infectionsVirus-host interactions

Identifiers

PMID40515996

DOI10.1038/s41592-019-0638-x

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.