ABSTRACT
Here we describe a protocol for identifying metabolites in respiratory specimens of patients that are SARS-CoV-2 positive, SARS-CoV-2 negative, or H1N1 positive. This protocol provides step-by-step instructions on sample collection from patients, followed by metabolite extraction. We use ultra-high-pressure liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS) for data acquisition and describe the steps for data analysis. The protocol was standardized with specific customization for SARS-CoV-2-containing respiratory specimens. For complete details on the use and execution of this protocol, please refer to Maras et al. (2021).
Subject(s)
COVID-19/diagnosis , Chromatography, High Pressure Liquid/methods , Metabolomics/methods , COVID-19/metabolism , Computational Biology , Diagnostic Tests, Routine , Gene Expression Profiling , Genetic Techniques , Humans , Influenza A Virus, H1N1 Subtype/metabolism , Influenza A Virus, H1N1 Subtype/pathogenicity , Mass Spectrometry/methods , Metabolome , Reference Standards , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Specimen Handling/methodsABSTRACT
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).