Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics.,Journal of Proteome Research

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Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2018-05-08 , DOI: 10.1021/acs.jproteome.8b00165
David J Clark ₁ , Yingwei Hu ₁ , William Bocik ₂ , Lijun Chen ₁ , Michael Schnaubelt ₁ , Rhonda Roberts ₂ , Punit Shah ₁ , Gordon Whiteley ₂ , Hui Zhang ₁

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Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance; however, inherent drawbacks of PDX-derived material, including extended time needed to grow tumors and high level of expertise needed, have resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but also NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference.

中文翻译：

NCI-7 细胞系组作为临床蛋白质组学参考材料的评估。

参考材料对于临床测试的可重复性基准测试至关重要，对于监测临床蛋白质组学实验室性能也至关重要。用于人类蛋白质组质谱分析的参考材料理想地包含足够的蛋白质以适当地代表人类蛋白质组，并且在不同批次的样品再生中表现出稳定的蛋白质组成。此前，临床蛋白质组肿瘤分析联盟 (CPTAC) 利用 PDX 衍生的比较参考 (CompRef) 材料对蛋白质组性能进行纵向评估；然而，PDX 衍生材料的固有缺点，包括生长肿瘤所需的时间较长和所需的高水平专业知识，导致人们努力寻找新的 CompRef 材料来源。在这项研究中，我们检查了使用七个癌细胞系组（NCI-7 细胞系组）作为人类蛋白质组质谱分析参考材料的效用。我们的结果表明，NCI-7 材料不仅适用于实验室样品制备方法的基准测试，而且 NCI-7 样品生成在全局水平和磷蛋白水平上均具有高度可重复性。此外，NCI-7 蛋白质组的预测基因组和实验覆盖范围表明 NCI-7 材料也可用作通用标准蛋白质组参考。

更新日期：2018-05-09

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