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.

本研究采用SMSNet与PEAKS-DB对B淋巴母细胞系（BLCL1408-1038）的I类与II类人类白细胞抗原（HLA）肽组进行分析。实验中分别对I类与II类HLA进行分离并单独开展分析。针对SMSNet分析流程，本研究实施了从头测序（de novo），并针对通用蛋白质资源数据库（UniProt）参考人类蛋白质组以及2020年8月下载的GRCh38 RefSeq非编码转录组对肽段鉴定结果进行精细化校正。针对PEAKS-DB分析流程，则采用通用蛋白质资源数据库（UniProt）参考人类蛋白质组与反向诱饵数据库完成肽段鉴定。更多详细信息可参阅本团队的预印本文章：https://www.biorxiv.org/content/10.1101/2021.09.19.460988v1.abstract。