COVID-19 analysis on usegalaxy.★

# Proteomics analysis of COVID-19 lung tissues

# Live Resources

usegalaxy.eu
Input data Input data view view
PXD018094 normal history PXD018094 normal history view view
PXD018094 infected history PXD018094 infected history view view
workflow workflow run run

# Description

Leng et al (opens new window) performed MS/MS analysis to characterize molecular mechanisms underlying COVID-19 pathogenesis in fresh lung tissues obtained from newly deceased patients with COVID-19 pneumonia.

# 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 peptides from SARS-CoV-2 proteins in both positive and negative patients. 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 Lorikeet analysis to ascertain the quality of peptide identification. However, when we ran the database searching workflow on the RAW files, we did not find any COVID-19 peptides.

# Results

The COVID-19 positive patient samples detected 16 SARS-CoV-2 peptides and we also detected 26 peptides from negative samples.

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