# Proteomics analysis of naso-pharyngeal swabs samples from COVID-19 infected and non-infected individuals
# Live Resources
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.
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.
The COVID-19 positive patient samples detected peptides from SARS-CoV-2 proteins (see below). The Peptide search workflow yields 9 COV-2 peptides and the Peptide Validation workflow yields 10 COV-2 peptides.
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 as shown below.