Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies.
Chen LiJerico RevoteSri H RamarathinamShan Zou ChungNathan Paul CroftKatherine E ScullZiyi HuangRochelle AyalaAsolina BraunNicole A MifsudPatricia T IllingPouya FaridiAnthony Wayne PurcellPublished in: Proteomics (2021)
SARS-CoV-2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS-CoV-2, identifying potential T cell epitopes derived from the SARS-CoV-2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS-CoV-2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user-friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide-HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.
Keyphrases
- sars cov
- ms ms
- respiratory syndrome coronavirus
- tandem mass spectrometry
- immune response
- high performance liquid chromatography
- ultra high performance liquid chromatography
- amino acid
- case control
- endothelial cells
- optical coherence tomography
- emergency department
- gas chromatography
- toll like receptor
- health information
- computed tomography
- risk assessment
- liquid chromatography tandem mass spectrometry
- coronavirus disease
- solid phase extraction
- mass spectrometry
- social media
- induced pluripotent stem cells
- binding protein