Proteomics

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Proteotypic peptides for SARS-CoV-2 variant detection

ABSTRACT: The recent SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent in the coming months, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Liquid chromatography-mass spectrometry (LC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers become well-established. This study demonstrates the potential to establish SARS-CoV-2 peptide markers by examining amino-acid variant-containing tryptic peptides, their MS fragmentation intensities, and their detection sensitivity in MS experiments. We have synthesized model tryptic peptides from of SARS-CoV-2 variants beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time.

INSTRUMENT(S): Orbitrap Exploris 240

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

SUBMITTER: Kantaphon Suddhapas  

LAB HEAD: Aaron Timperman

PROVIDER: PXD033777 | Pride | 2022-10-12

REPOSITORIES: Pride

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Publications

Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.

Suddhapas Kantaphon K   Choi M Hannah MH   Shortreed Michael R MR   Timperman AaronT A  

Journal of proteome research 20220915 10

The SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent for the foreseeable future, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) offers an exciting alternative det  ...[more]

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