# Proteomics analysis of naso-pharyngeal swabs samples from COVID-19 infected and non-infected individuals

# Live Resources

usegalaxy.eu
Input Negative data Input Negative data view view
Input Positive data Input Positive data view view
PXD020394 history PXD020394 history view view
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workflow workflow run run

# Description

Rivera et al performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis. Tryptic peptides obtained from five COVID-19 positive and five COVID-19 negative samples were analysed by LC-MS/MS using a Q-Exactive Plus mass spectrometer. The mass spectrometry (MS) data was made available via ProteomeXchange (PXD020394) so as to facilitate the use of MS-based approaches for COVID-19 diagnosis.

# Workflow

The Galaxy workflow includes RAW data conversion to MGF and mzML format. The MGF files are searched against the combined database of Human Uniprot proteome, contaminant proteins and SARS-Cov-2 proteins database using X!tandem, MSGF+, OMSSA search algorithms with SearchGUI and FDR and protein grouping using PeptideShaker. This resulted in detection of ten peptides from SARS-CoV-2 proteins. The detected peptides were searched against NCBInr to ascertain that these peptides were specific to SARS-CoV-2 proteins. The detected peptides were later subjected to analysis by PepQuery and Lorikeet to ascertain the quality of peptide identification.

# Results

The COVID-19 positive patient samples detected peptides from SARS-CoV-2 proteins (see below). COVID-19 negative samples also detected two peptides from COVID-19 proteins - however Lorikeet analysis showed that the spectral evidence for these peptides did not support the peptide-spectral-match.