Proteins are released from cells by different secretory pathways. The secretory pathway via the ER-Golgi route - realized by a signal sequence - is referred to as “classical secretion”. In contrast, alternative secretory pathways were summarized as “unconventional protein secretion”. Until now, unconventional protein secretion was lacking attention due to the absence of detailed mechanistic insight and limited experimental access. However, there is a growing number of experimental data showing that a large proportion of secreted proteins is released by these alternative routes. Secretomics - the analysis of all secreted proteins of a cell population - offers the opportunity to gain more functional insight into unconventional protein secretion. Several pitfalls in secretome analysis starting with the analyzed cell model and sample preparation to data analysis have to be considered for detailed characterization of the secretome. Here, we highlight the investigation of secretomes by quantitative LC-MS/MS analysis and discuss pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis.

蛋白质通过不同的分泌途径从细胞中释放出来。通过信号序列实现的经由ER-高尔基体途径的分泌途径被称为“经典分泌”。相反，替代性分泌途径被概括为“非常规蛋白质分泌”。到目前为止，由于缺乏详细的机理研究和有限的实验途径，非常规蛋白质的分泌一直缺乏关注。但是，越来越多的实验数据表明，这些替代途径释放了很大一部分分泌的蛋白质。分泌组学-对细胞群所有分泌蛋白的分析-提供了获得更多功能性洞察非常规蛋白分泌的机会。从分泌物分析的细胞模型到样品制备再到数据分析，在分泌物组分析中有几个陷阱必须考虑，以便对分泌物组进行详细的表征。在这里，我们重点介绍了通过定量LC-MS / MS分析对分泌蛋白组的研究，并讨论了通过分泌蛋白组分析表征非常规分泌蛋白的陷阱和机遇。