# MS data analysis with Search GUI and PeptideShaker
# Live Resources
Ihling et al present a protein MS-based ‘proof-of-principle’ method to detect SARS-CoV-2 virus proteins from gargle samples from COVID-19 patients. Their protocol consists of an acetone precipitation step, followed by tryptic digestion of gargle solution proteins, followed by MS analysis. In the original manuscript, the authors detect peptides from SARS-CoV-2 virus proteins and present evidence for their spectral annotation. This study is an initiative in developing a routine MS-based diagnostic method for COVID-19 patients.
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 nine 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.