Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.
复制标题
DOI：
10.1074/mcp.m111.014050
复制
发表时间：
2012-03
期刊：
影响因子：
--
通讯作者：
Mann M
中科院分区：
文献类型：
--
作者：
Geiger T;Wehner A;Schaab C;Cox J;Mann M
对哺乳动物细胞系进行深入的蛋白质组学分析将产生一份生物研究中最常用系统的组成部分清单。基于质谱的蛋白质组学可以以全局和无偏的方式识别和定量蛋白质，并且可以突出在这些系统之间改变的细胞过程。我们使用LTQ-Orbitrap系列质谱仪分析了11种人类细胞系，该质谱仪具有“高场”Orbitrap质量分析仪，具有改进的分辨率和测序速度。我们总共鉴定了11，731种蛋白质，平均每个细胞系中有10，361 ± 120种蛋白质。这种非常高的蛋白质组覆盖率使得能够分析广泛的过程和功能。尽管细胞系的起源不同，但我们的定量结果显示，表达的蛋白质具有惊人的高相似性。然而，蛋白质组的这种全局相似性并不意味着11个细胞系中单个蛋白质的表达水平相等，因为我们发现其中约三分之二的表达水平存在显著差异。低丰度和高丰度蛋白质的细胞表达水平的变异性是相似的，甚至许多具有家庭角色的最高表达蛋白质在细胞之间也显示出显著差异。代谢途径，具有高冗余度，表现出可变的表达，而基本的细胞功能，如基础转录机制变化少得多。我们利用这些细胞系蛋白质组的知识，构建一个广泛覆盖的“超级SILAC”定量标准。连同随附的论文（Schaab，C. MCP 2012，PMID：22301388），这些数据可用于获得细胞系蛋白质组内和跨细胞系蛋白质组的目的蛋白质的参考表达谱。
Deep proteomic analysis of mammalian cell lines would yield an inventory of the building blocks of the most commonly used systems in biological research. Mass spectrometry-based proteomics can identify and quantify proteins in a global and unbiased manner and can highlight the cellular processes that are altered between such systems. We analyzed 11 human cell lines using an LTQ-Orbitrap family mass spectrometer with a “high field” Orbitrap mass analyzer with improved resolution and sequencing speed. We identified a total of 11,731 proteins, and on average 10,361 ± 120 proteins in each cell line. This very high proteome coverage enabled analysis of a broad range of processes and functions. Despite the distinct origins of the cell lines, our quantitative results showed surprisingly high similarity in terms of expressed proteins. Nevertheless, this global similarity of the proteomes did not imply equal expression levels of individual proteins across the 11 cell lines, as we found significant differences in expression levels for an estimated two-third of them. The variability in cellular expression levels was similar for low and high abundance proteins, and even many of the most highly expressed proteins with household roles showed significant differences between cells. Metabolic pathways, which have high redundancy, exhibited variable expression, whereas basic cellular functions such as the basal transcription machinery varied much less. We harness knowledge of these cell line proteomes for the construction of a broad coverage “super-SILAC” quantification standard. Together with the accompanying paper (Schaab, C. MCP 2012, PMID: 22301388) these data can be used to obtain reference expression profiles for proteins of interest both within and across cell line proteomes.