Exosomes are extracellular vesicles derived from the endosomal compartment that are potentially involved in intercellular communication. Here, we found that frequently used biomarkers of exosomes are heterogeneous, and do not exhibit universal utility across different cell types. To uncover ubiquitous and abundant proteins, we used an unbiased and quantitative proteomic approach based on super-stable isotope labeling with amino acids in cell culture (super-SILAC), coupled to high-resolution mass spectrometry. In total, 1,212 proteins were quantified in the proteome of exosomes, irrespective of the cellular source or isolation method. A cohort of 22 proteins was universally enriched. Fifteen proteins were consistently depleted in the proteome of exosomes compared to cells. Among the enriched proteins, we identified biogenesis-related proteins, GTPases and membrane proteins, such as CD47 and ITGB1. The cohort of depleted proteins in exosomes was predominantly composed of nuclear proteins. We identified syntenin-1 as a consistently abundant protein in exosomes from different cellular origins. Syntenin-1 is also present in exosomes across different species and biofluids, highlighting its potential use as a putative universal biomarker of exosomes. Our study provides a comprehensive quantitative atlas of core proteins ubiquitous to exosomes that can serve as a resource for the scientific community.

外泌体是源自内体区室的细胞外囊泡，可能参与细胞间通讯。在这里，我们发现经常使用的外泌体生物标志物是异质的，并且在不同细胞类型中没有表现出通用性。为了发现普遍存在且丰富的蛋白质，我们使用了一种公正的定量蛋白质组学方法，该方法基于细胞培养物中氨基酸的超稳定同位素标记（super-SILAC），并结合高分辨率质谱法。无论细胞来源或分离方法如何，外泌体蛋白质组中总共对 1,212 种蛋白质进行了定量。一组 22 种蛋白质被普遍富集。与细胞相比，外泌体蛋白质组中有 15 种蛋白质持续缺失。在富集的蛋白质中，我们鉴定了生物发生相关的蛋白质、GTP酶和膜蛋白，例如CD47和ITGB1。外泌体中耗尽的蛋白质组主要由核蛋白组成。我们发现 Syntenin-1 是来自不同细胞来源的外泌体中一致丰富的蛋白质。 Syntenin-1 也存在于不同物种和生物体液的外泌体中，突显了其作为外泌体假定的通用生物标志物的潜在用途。我们的研究提供了外泌体中普遍存在的核心蛋白的全面定量图谱，可以作为科学界的资源。