Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

Investigations of missing proteins (MPs) are being endorsed by many bioanalytical strategies. We proposed that proteogenomics of testis tissue was a feasible approach to identify more MPs because testis tissues have higher gene expression levels. Here we combined proteomics and transcriptomics to survey gene expression in human testis tissues from three post-mortem individuals. Proteins were extracted and separated with glycine- and tricine-SDS-PAGE. A total of 9597 protein groups were identified; of these, 166 protein groups were listed as MPs, including 138 groups (83.1%) with transcriptional evidence. A total of 2948 proteins are designated as MPs, and 5.6% of these were identified in this study. The high incidence of MPs in testis tissue indicates that this is a rich resource for MPs. Functional category analysis revealed that the biological processes that testis MPs are mainly involved in are sexual reproduction and spermatogenesis. Some of the MPs are potentially involved in tumorgenesis in other tissues. Therefore, this proteogenomics analysis of individual testis tissues provides convincing evidence of the discovery of MPs. All mass spectrometry data from this study have been deposited in the ProteomeXchange (data set identifier PXD002179).缺失蛋白（missing proteins, MPs）的相关研究正得到众多生物分析策略的支持。我们提出，利用睾丸组织的蛋白质基因组学（proteogenomics）是鉴定更多缺失蛋白的可行途径，因为睾丸组织的基因表达水平更高。本研究结合蛋白质组学与转录组学，对3名遗体捐献者的人类睾丸组织基因表达情况进行了调研。研究人员提取蛋白质后，采用甘氨酸-SDS聚丙烯酰胺凝胶电泳（glycine-SDS-PAGE）与tricine-SDS聚丙烯酰胺凝胶电泳（tricine-SDS-PAGE）进行分离。最终共鉴定得到9597个蛋白质组，其中166个被归类为缺失蛋白，包含138个（占比83.1%）带有转录组学证据的蛋白质组。目前已有2948个蛋白质被标注为缺失蛋白，其中5.6%在本研究中被成功鉴定。缺失蛋白在睾丸组织中的高检出率表明，睾丸组织是发掘缺失蛋白的优质资源库。功能分类分析结果显示，睾丸缺失蛋白主要参与的生物学过程包括有性生殖与精子发生。部分缺失蛋白可能参与其他组织的肿瘤发生过程。因此，本研究针对单一个体睾丸组织开展的蛋白质基因组学分析，为缺失蛋白的发现提供了有力佐证。本研究产生的所有质谱数据已提交至蛋白质组交换数据库（ProteomeXchange），数据集标识符为PXD002179。