Mit sidney pacific mail forward1/1/2023 ![]() ![]() Sheet 12: Coverage estimates for the alleles in the two profiled cell lines (A549 and HEK293T) per HLA locus and per HLA). For TMT time course experiments, peptides were filtered for quantitative values and TMT ratios to the 24h time point were median normalized. Sheet 3-11: Peptide identifications from HLA-I immunoprecipitation experiments in A549 and HEK293T cells ± SARS-CoV-2 after filtering for contaminants and length 8-11. For binding prediction using HLAthena, residues were considered unmodified columns show the most likely HLA allele a peptide is bound to in the respective cell line as well as the percentile binding rank. Mit sidney pacific mail forward manual#“x” denotes identification in individual experiments, “T” in TMT experiments, “-” indicates that the peptide was detected but did not pass FDR correction in that sample, confidence level in identification was evaluated based on Spectrum Mill Score, after manual inspection of MS/MS spectra and comparison to synthetic peptide spectra for available peptides (Y: validated by synthetic peptide, N/A: synthetic peptide not available). Cysteines were detected in their carbamidomethylated or cysteinylated modification state, methionines were oxidized. HLA-I peptidomics and allele coverage in A549 and HEK293T cells, related to Figures 1, 2, 3, 4, 5, and 7 Sheet 1: Legend for Table, Sheet 2: HLA-I bound peptide sequences from SARS-CoV-2 proteins identified in both A549 and HEK293T cells. ![]()
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