Proteomic re-analysis of bronchoalveolar lavage fluid in COVID-19 patients

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Description

Zeng lab (opens new window) collected bottom-up mass spectrometry (MS) data on bronchoalveolar lavage fluid in COVID-19 positive patient samples with respiratory failure. Data-dependent acquisition MS spectra were acquired using Q Exactive HF-X mass spectrometer coupled with an EASY-nLC 1200 system and a nano-electrospray 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 88 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.

Our Database search workflow did not detect any SARS-CoV2 peptides from both positive and negative samples.

Results

We detected 36 COVID-19 peptides from all pooled samples in the respiratory tract datasets, We detected 25 SARS-CoV2 peptides from positive patients , 11 SARS-CoV2 peptides from negative patient samples. The peptides were subjected to BLAST-P andLorikeet analysis to ascertain the validity of peptide spectral matches.