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

Live Resources

usegalaxy.eu

Description

Cardozo et al (opens new window) 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