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两种分析流程，对B淋巴母细胞系BLCL1408-1038的I类、II类人类白细胞抗原（Human Leukocyte Antigen, HLA）肽组开展分析。研究人员对该细胞系的I类与II类人类白细胞抗原分别进行了分离与分析。针对SMSNet分析流程，本研究实施了从头测序（de novo sequencing），并以UniProt参考人类蛋白质组与2020年8月下载的GRCh38 RefSeq非编码转录组作为参考库，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UniProt参考人类蛋白质组与反向诱饵数据库（reversed decoy database）作为分析依据。更多详细信息可参阅本团队于bioRxiv发布的预印本：https://www.biorxiv.org/content/10.1101/2021.09.19.460988v1.abstract。