# Proteomic re-analysis of upper respiratory tract clinical samples

# Live Resources

Input data Input data view view
PXD025214 Positive sample history PXD025214 Positive sample history view view
PXD025214 Negative samplehistory PXD025214 Negative samplehistory view view
workflow workflow run run

# Description

Carvalho lab (opens new window) performed shotgun proteomics analysis of upper respiratory samples of patients. Data-dependent acquisition MS spectra were acquired using Q Exactive HF-X mass spectrometer coupled with an UltiMate 3000 Nano LC system via EASY-spray positive ion source.

# 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 PepQuery Validation workflow. This resulted in detection of 39 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 Lorikeet visualization to ascertain the quality of peptide identification.

# Results

We detected 39 COVID-19 peptides from all pooled samples in the upper respiratory tract datasets. We detected 39 SARS-CoV2 peptides from positive patients , 9 SARS-CoV2 peptides from negative patient samples. The peptides were subjected to BLAST-P andLorikeet analysis to ascertain the validity of peptide spectral matches. The validation of the spectral quality showed the presence of the peptides "MAGNGGDAALALLLLDR", "DGIIWVATEGALNTPK", "RGPEQTQGNFGDQELIR", and "IGMEVTPSGTWLTYTGAIK" in COVID-19 positive patients.