Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples

Arghya Banerjee; Medha Gayathri J Pai; Avinash Singh; Mehar Un Nissa; Sanjeeva Srivastava

doi:10.1016/j.xpro.2022.101177

Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples

STAR Protoc. 2022 Feb 2;3(1):101177. doi: 10.1016/j.xpro.2022.101177. eCollection 2022 Mar 18.

Authors

Arghya Banerjee¹, Medha Gayathri J Pai¹, Avinash Singh¹, Mehar Un Nissa¹, Sanjeeva Srivastava¹

Affiliation

¹ Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.

Abstract

With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold standard, it has several limitations; therefore, more complementary assays are required. This protocol describes how to identify SARS-CoV-2 protein from patients' nasopharyngeal swab samples. We first introduce the approach of label-free quantitative proteomics. We then detail target verification by triple quadrupole mass spectrometry (MS)-based targeted proteomics. For complete details on the use and execution of this profile, please refer to Bankar et al. (2021).

Keywords: Clinical Protocol; Health Sciences; Mass Spectrometry; Protein Biochemistry; Proteomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 / metabolism*
Female
Humans
Male
Nasopharynx / metabolism*
Nasopharynx / virology
Proteomics*
SARS-CoV-2 / metabolism*
Specimen Handling*
Tandem Mass Spectrometry*
Viral Proteins / metabolism*

Substances

Viral Proteins