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, de novo 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两种分析方案，对B淋巴母细胞系（B-lymphoblastoid cell line, BLCL1408-1038）的人类白细胞抗原（Human Leukocyte Antigen, HLA）I类与II类肽组进行解析。研究中分别分离HLA I类与II类分子，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 sequencing），并以通用蛋白质知识库（Universal Protein Resource, UniProt）的人类参考蛋白质组，以及2020年8月下载的GRCh38版本RefSeq非编码转录组作为参照，对肽段鉴定结果进行了优化校正。针对PEAKS-DB分析流程，本研究采用了UniProt人类参考蛋白质组与反向诱饵数据库（reversed decoy database）作为参照库。更多详细信息可参阅本团队的预印本：https://www.biorxiv.org/content/10.1101/2021.09.19.460988v1.abstract。