Proteomic re-analysis of nasopharyngeal swab samples from COVID-19 patients

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Description

Bankar et.al (opens new window) performed proteomics study on nasopharyngeal swab samples from COVID-19 patients sample. This study was performed to identify a panel of host proteins which could serve as biomarkers of severity prediction .Data-dependent acquisition MS spectra were acquired using Orbitrap-Fusion mass spectrometer.

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 35 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 35 COVID-19 peptides in the nasopharyngeal swab samples. The peptides were subjected to BLAST-P and Lorikeet analysis to ascertain the validity of peptide spectral matches. Our results validated the presence of peptide "DGIIWVATEGALNTPK" with good spectral quality.