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Profiling SARS-CoV-2 Infection by High-Throughput Shotgun Proteomics
Lucia Grenga1, Duarte Gouveia1, Jean Armengaud2
1Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France.
Methods in Molecular Biology (Clifton, N.J.)
|May 13, 2022
Summary
Understanding SARS-CoV-2 infection requires mapping viral and host proteins. This study details a proteomics method to track these protein dynamics over time in infected cells.
Area of Science:
- Proteomics
- Virology
- Molecular Biology
Background:
- Understanding SARS-CoV-2 pathogenesis requires detailed knowledge of viral and host protein expression during infection.
- Current methods for protein analysis need optimization for complex biological samples like infected cell models.
Purpose of the Study:
- To establish a comprehensive proteomic profiling method for SARS-CoV-2-infected cell models.
- To analyze time-resolved proteomic changes induced by SARS-CoV-2 infection.
Main Methods:
- Sample preparation involving protein purification and tryptic digestion in the presence of detergents.
- Shotgun proteomics pipeline utilizing reverse-phase ultrahigh-performance liquid chromatography (RP-UHPLC) and high-resolution tandem mass spectrometry (HR-MS/MS).
- Bioinformatic analysis for peptide-spectrum matching against a combined viral and host protein database, including contaminants.
Main Results:
- Identification and quantification of thousands of viral and host peptides, enabling protein abundance inference.
- Characterization of dynamic changes in protein expression profiles throughout the course of SARS-CoV-2 infection.
- Distinguishing infection-specific proteomic alterations from background noise.
Conclusions:
- The described proteomics workflow provides a robust method for comprehensive SARS-CoV-2 infection profiling.
- This approach facilitates the deciphering of molecular mechanisms underlying viral pathogenesis.
- Time-resolved proteomic data offers critical insights into host-pathogen interactions during infection.
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