A vast number of human cell lines are available for cell culture model‐based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH‐SY5Y, and SVGp12. A mass spectrometry‐based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth is used. To this end, this strategy leverages TMTpro16‐based sample multiplexing, high‐field asymmetric ion mobility spectrometry, and real‐time database searching. The data show that the differences in the relative protein abundance profiles reflect cell line diversity. The authors also determine several hundred proteins to be highly enriched for a given cell line, and perform gene ontology and pathway analysis on these cell line‐enriched proteins. An R Shiny application is designed to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection for addressing a given scientific inquiry or for improving an experimental design.

中文翻译：

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使用高场不对称离子迁移谱和实时数据库搜索对八种人类细胞系进行基于等压标记的蛋白质分析

大量人类细胞系可用于基于细胞培养模型的研究，因此由于细胞系选择，结果可能存在差异。为了研究这个概念，作者确定了一组八种不同但普遍研究的人类细胞系的相对蛋白质丰度谱。该面板包括 HAP1、HEK293T、HeLa、HepG2、Jurkat、Panc1、SH-SY5Y 和 SVGp12。使用基于质谱的蛋白质组学工作流程，旨在提高定量准确性，同时保持分析深度。为此，该策略利用了基于 TMTpro16 的样品多路复用、高场不对称离子迁移谱和实时数据库搜索。数据显示相对蛋白质丰度曲线的差异反映了细胞系的多样性。作者还确定了给定细胞系高度富集的数百种蛋白质，并对这些富含细胞系的蛋白质进行基因本体和通路分析。R Shiny 应用程序旨在查询蛋白质丰度概况并检索具有相似模式的蛋白质。此处使用的工作流程可应用于其他细胞系，以帮助选择细胞系以解决给定的科学调查或改进实验设计。