Díez Paula, Droste Conrad, Dégano Rosa M, González-Muñoz María, Ibarrola Nieves, Pérez-Andrés Martín, Garin-Muga Alba, Segura Víctor, Marko-Varga Gyorgy, LaBaer Joshua, Orfao Alberto, Corrales Fernando J, De Las Rivas Javier, Fuentes Manuel
Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
J Proteome Res. 2015 Sep 4;14(9):3530-40. doi: 10.1021/acs.jproteome.5b00474. Epub 2015 Aug 5.
A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems.
可以开展一项关于人类细胞分子活性图谱的综合研究，以整合两种不同但互补的视角：转录组学和蛋白质组学。在基因组时代之后，蛋白质组学已成为一种强大的工具，可同时识别和表征细胞中数千种不同活性蛋白质的汇总情况。因此，以染色体为中心的人类蛋白质组计划（C-HPP）正在推动对人类蛋白质组进行全面表征，将高通量蛋白质组学与蛋白质编码基因全基因组表达谱数据相结合。在此，我们展示了使用纳升超高效液相色谱-线性离子阱-轨道阱Velos蛋白质组学平台对人类淋巴瘤B细胞系（拉莫斯细胞系）进行的完整蛋白质组分析，并结合了对同一细胞类型的深入转录组分析。数据可通过蛋白质组交换中心获取，标识符为PXD001933。蛋白质组学和转录组学数据集的整合显示，两种组学方法鉴定出的蛋白质有94%重叠。此外，蛋白质组图谱的功能富集分析表明，与B细胞的生物学和形态学特征直接相关的几种功能得到了富集。相应地，人类全基因组中约30%的蛋白质编码基因被鉴定为在拉莫斯细胞中表达（所有染色体上基因的稳定平均表达率为30%），这揭示了一种特定人类细胞类型中存在的蛋白质表达集的规模。此外，我们还报告了数据集中缺失蛋白质的鉴定情况，突出了该方法的强大功能。同时，还对neXtProt和UniProt数据库搜索结果进行了比较。总之，我们的转录组学和蛋白质组学实验分析提供了一份关于人类淋巴瘤B细胞类型表达蛋白质组的高覆盖率报告，清晰地洞察了表征这些细胞的生物学过程。通过这种方式，我们证明了结合组学方法对特定生物系统进行全面表征的有用性。
