Selenium (Se), as an essential trace element, plays crucial roles in many organisms including humans. The biological functions of selenium are mainly mediated by selenoproteins, a unique class of selenium-containing proteins in which selenium is inserted in the form of selenocysteine. Due to their low abundance and uneven tissue distribution, detection of selenoproteins within proteomes is very challenging, and therefore functional studies of these proteins are limited. In this study, we developed a computational method, named as selenium-encoded isotopic signature targeted profiling (SESTAR), which utilizes the distinct natural isotopic distribution of selenium to assist detection of trace selenium-containing signals from shotgun-proteomic data. SESTAR can detect femtomole quantities of synthetic selenopeptides in a benchmark test and dramatically improved detection of native selenoproteins from tissue proteomes in a targeted profiling mode. By applying SESTAR to screen publicly available datasets from Human Proteome Map, we provide a comprehensive picture of selenoprotein distributions in human primary hematopoietic cells and tissues. We further demonstrated that SESTAR can aid chemical-proteomic strategies to identify additional selenoprotein targets of RSL3, a canonical inducer of cell ferroptosis. We believe SESTAR not only serves as a powerful tool for global profiling of native selenoproteomes, but can also work seamlessly with chemical-proteomic profiling strategies to enhance identification of target proteins, post-translational modifications, or protein–protein interactions.

中文翻译：

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硒编码同位素签名靶向分析

硒（Se）作为必需的微量元素，在包括人类在内的许多生物中都起着至关重要的作用。硒的生物学功能主要由硒蛋白介导，硒蛋白是一类独特的含硒蛋白，硒以硒代半胱氨酸的形式插入其中。由于它们的丰度低和组织分布不均匀，蛋白质组内硒蛋白的检测非常具有挑战性，因此对这些蛋白的功能研究受到限制。在这项研究中，我们开发了一种计算方法，称为硒编码同位素特征标记靶向分析（SESTAR），该方法利用硒的独特天然同位素分布来协助从shot弹枪蛋白质组学数据中检测痕量含硒信号。SESTAR可以在基准测试中检测出飞摩尔数量的合成硒肽，并以靶向分析模式显着改善了从组织蛋白质组中检测天然硒蛋白的能力。通过应用SESTAR筛选人类蛋白质组图的公开可用数据集，我们提供了人类原代造血细胞和组织中硒蛋白分布的全面图像。我们进一步证明SESTAR可以辅助化学蛋白质组学策略来鉴定RSL3（细胞肥大症的典型诱导剂）的其他硒蛋白靶标。我们相信SESTAR不仅可以作为一种功能强大的工具来对天然硒蛋白质组进行全球概况分析，而且还可以与化学蛋白质组概况分析策略无缝协作，以增强对目标蛋白质，翻译后修饰或蛋白质与蛋白质相互作用的识别。