# Proteomic re-analysis of upper respiratory tract clinical samples
# Live Resources
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.
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.
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.