Protocol for global proteome, virome, and metaproteome profiling of respiratory specimen (VTM) in COVID-19 patient by LC-MS/MS-based analysis
Gaurav Tripathi, Nupur Sharma, Vasundhra Bindal, Manisha Yadav, Babu Mathew, Shvetank Sharma, Ekta Gupta, Jaswinder Singh Maras, Shiv Kumar Sarin
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).
Topics & Concepts
ProteomeHuman viromeCoronavirus disease 2019 (COVID-19)Computational biologyProtocol (science)Profiling (computer programming)BioinformaticsChemistryMetagenomicsBiologyMedicineComputer sciencePathologyBiochemistryGeneDiseaseInfectious disease (medical specialty)Operating systemAlternative medicineRespiratory viral infections researchMetabolomics and Mass Spectrometry StudiesSARS-CoV-2 detection and testing