The SH-SY5Y cell line is often used as a surrogate for neurons in cell-based studies. This cell line is frequently differentiated with all-trans retinoic acid (ATRA) over a 7-day period, which confers neuron-like properties to the cells. However, no analysis of proteome remodeling has followed the progress of this transition. Here, we quantitatively profiled over 9400 proteins across a 7-day treatment with retinoic acid using state-of-the-art mass spectrometry-based proteomics technologies, including FAIMS, real-time database searching, and TMTpro16 sample multiplexing. Gene ontology analysis revealed that categories with the highest increases in protein abundance were related to the plasma membrane/extracellular space. To showcase our data set, we surveyed the protein abundance profiles linked to neurofilament bundle assembly, neuron projections, and neuronal cell body formation. These proteins exhibited increases in abundance level, yet we observed multiple patterns among the queried proteins. The data presented represent a rich resource for investigating temporal protein abundance changes in SH-SY5Y cells differentiated with retinoic acid. Moreover, the sample preparation and data acquisition strategies used here can be readily applied to any analogous cell line differentiation analysis.

中文翻译：

---

使用 FAIMS 和实时搜索对 SH-SY5Y 与视黄酸分化的时间蛋白质组学分析

SH-SY5Y 细胞系通常用作基于细胞的研究中神经元的替代品。这种细胞系经常用全反式分化视黄酸 (ATRA) 持续 7 天，赋予细胞类似神经元的特性。然而，没有蛋白质组重构的分析跟随这种转变的进展。在这里，我们使用最先进的基于质谱的蛋白质组学技术（包括 FAIMS、实时数据库搜索和 TMTpro16 样本多路复用）对 7 天的视黄酸处理中的 9400 多种蛋白质进行了定量分析。基因本体分析显示，蛋白质丰度增加最多的类别与质膜/细胞外空间有关。为了展示我们的数据集，我们调查了与神经丝束组装、神经元投射和神经元细胞体形成相关的蛋白质丰度概况。这些蛋白质表现出丰度水平的增加，然而，我们在查询的蛋白质中观察到了多种模式。所提供的数据代表了研究用视黄酸分化的 SH-SY5Y 细胞的时间蛋白质丰度变化的丰富资源。此外，这里使用的样品制备和数据采集策略可以很容易地应用于任何类似的细胞系分化分析。