Data for "Catching the Wave: Detection and verification of variant SARS-CoV-2 peptides in clinical samples collected during infection waves from diverse geographical locations"

The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a major health crisis worldwide with its continuously emerging new strains resulting in new viral variants that drive “waves” of infection. PCR or antigen detection assays have been routinely used to detect clinical infections, however, the emergence of these newer strains has presented challenges in detection. One of the alternatives has been to detect and characterize variant-specific peptide sequences from viral proteins using mass spectrometry (MS)-based methods. MS methods can potentially help in both diagnostics and vaccine development, by understanding the dynamic changes in the viral proteome associated with specific strains and infection waves. In this study, we have developed an accessible, flexible, and shareable bioinformatics Galaxy workflow to detect variant-specific peptide sequences from MS data derived from the clinical samples. We demonstrate the utility of the workflow by characterizing published clinical data from across the world during various pandemic waves. From our analysis, we could detect and rigorously verify peptides specific to the Gamma (P.1), Delta (B.1.617.2, AY.4, AY.4.2), and Omicron (XE, B.1.1.529, BA.1, BA.2, BA.3, BA.4) variants and their associated phylogenetic lineages. We anticipate the study presented here will enable others seeking to use MS-based methods to monitor the status of the SARS-CoV-2 landscape as the pandemic progresses.