# Proteomics analysis of respiratory tract samples from CoviD-19 infected patients

# Live Resources

usegalaxy.eu
Input data Input data view view
PXD019119 history PXD019119 history view view
workflow workflow run run

# Description

Cardozo et al collected bottom-up mass spectrometry (MS) data on respiratory tract samples from ten COVID-19 positive patient samples. Data-dependent acquisition MS spectra were acquired using hybrid quadrupole-Orbitrap tandem mass spectrometry. The MS data was used to generate a spectral library of targeted COVID-19 peptides for targeted MS assay for clinical samples.

# 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 71 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

We detected 71 COVID-19 peptides from all pooled samples in the respiratory tract datasets. The peptides were subjected to BLAST-P and Lorikeet analysis to ascertain the validity of peptide spectral matches.

Pool 18 Pool 34 Pool 38 Pool 47 Pool 51
COVID-19 Peptides 12 60 21 59 40