Certain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolytic enzymes including RNases and proteases that may lead to degradation of RNA and proteins during sample processing. For such tumor tissues with RNA instability, RNAlater containing a high concentration of quaternary ammonium sulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a few studies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences the proteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensive analysis of the effect of RNAlater on the proteome and phosphoproteome using high-resolution mass spectrometry. PDAC tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was kept at - 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozen tissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptides of 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylation between the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneously activated pathways among the three patients that were not altered by RNAlater. These results indicate that the tissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies where preservation of intact DNA, RNA and proteins is prerequisite. Data from this study are available via ProteomeXchange with the identifier PXD010710.

中文翻译：

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全面的蛋白质组和磷酸化蛋白质组分析显示，RNAlater对蛋白质丰度和磷酸化的影响可忽略不计。

已知某些肿瘤（例如胰腺导管腺癌（PDAC））包含多种水解酶，包括RNase和蛋白酶，这些酶可能导致样品处理过程中RNA和蛋白质降解。对于具有RNA不稳定的此类肿瘤组织，经常使用含有高浓度季铵盐硫酸盐的RNAlater来变性RNA水解酶，以保护RNA免受水解。尽管已经进行了一些研究来确定RNAlater对DNA和RNA的作用，但是很大程度上未知RNAlater是否影响蛋白质组和磷酸化蛋白质组。在这项研究中，我们使用高分辨率质谱对RNAlater对蛋白质组和磷酸化蛋白质组的作用进行了系统，全面的分析。将来自三名患者的PDAC组织分别粉碎，将每位患者的组织粉分成两部分，其中一份在RNAlater中于4°C孵育24小时（RNAlater组织），而另一份则在-80°C（冷冻组织）。在RNAlater组织和冷冻组织上进行的全面定量分析实验，鉴定出了8,803个蛋白质组的99,136个不同的肽和16,436个磷酸位的17,345个磷肽。数据显示RNAlater组织和冷冻组织之间蛋白质和磷酸化均无明显的定量变化。此外，磷酸化蛋白质组数据显示了三位患者中被RNAlater改变的异质激活途径。这些结果表明，使用RNAlater进行组织保存的方法可以有效地用于PDAC组织进行蛋白质组学研究，其中完整的DNA，RNA和蛋白质的保存是必需的。这项研究的数据可通过ProteomeXchange获得，其标识符为PXD010710。