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Trypsin/P was set as the enzyme parameter, a maximum of 2 missed cleavage was allowed, carbamidomethylation was set as a fixed modification and methionine N-terminal excision and oxidation were set as variable modifications with a maximum of 2 allowed per peptide

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Possible artefacts arising from the artificiality of such assays can be explored by comparing results from pseudovirus (clonal) infection of cell lines with those from authentic replicating (quasispecies) virus infection of primary cells