SMSNet and PEAKS-DB identification from HLA peptidomics of B-lymphoblastoid cell line (BLCL1408-1038, PXD028088)

SMSNet and PEAKS-DB analysis of HLA class I and class II peptidomes of B-lymphoblastoid cell line (BLCL1408-1038). HLA class I and class II were isolated and analyzed separately. For SMSNet, <i>de novo</i> sequencing was performed and the identifications were refined against UniProt reference human proteome and a GRCh38 RefSeq non-coding transcriptome (downloaded August 2020). For PEAKS-DB, the UniProt reference human proteome and reversed decoy database was used. More information can be found in our preprint at https://www.biorxiv.org/content/10.1101/2021.09.19.460988v1.abstract.