Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , Pamplona 31008, Spain.
IdiSNA, Navarra Institute for Health Research , Pamplona 31008, Spain.
J Proteome Res. 2017 Dec 1;16(12):4374-4390. doi: 10.1021/acs.jproteome.7b00388. Epub 2017 Oct 11.
The Human Proteome Project (HPP) aims deciphering the complete map of the human proteome. In the past few years, significant efforts of the HPP teams have been dedicated to the experimental detection of the missing proteins, which lack reliable mass spectrometry evidence of their existence. In this endeavor, an in depth analysis of shotgun experiments might represent a valuable resource to select a biological matrix in design validation experiments. In this work, we used all the proteomic experiments from the NCI60 cell lines and applied an integrative approach based on the results obtained from Comet, Mascot, OMSSA, and X!Tandem. This workflow benefits from the complementarity of these search engines to increase the proteome coverage. Five missing proteins C-HPP guidelines compliant were identified, although further validation is needed. Moreover, 165 missing proteins were detected with only one unique peptide, and their functional analysis supported their participation in cellular pathways as was also proposed in other studies. Finally, we performed a combined analysis of the gene expression levels and the proteomic identifications from the common cell lines between the NCI60 and the CCLE project to suggest alternatives for further validation of missing protein observations.
人类蛋白质组计划（HPP）旨在破译人类蛋白质组的完整图谱。在过去的几年中，HPP 团队进行了大量努力，致力于实验检测缺失的蛋白质，这些蛋白质缺乏可靠的质谱证据证明其存在。在这一努力中，对鸟枪法实验的深入分析可能代表了选择设计验证实验中生物基质的有价值资源。在这项工作中，我们使用了 NCI60 细胞系的所有蛋白质组学实验，并应用了基于 Comet、Mascot、OMSSA 和 X!Tandem 结果的综合方法。这种工作流程受益于这些搜索引擎的互补性，以提高蛋白质组覆盖率。符合 C-HPP 指南的 5 种缺失蛋白被鉴定出来，尽管还需要进一步验证。此外，还检测到 165 种仅有一种独特肽的缺失蛋白，它们的功能分析支持它们参与细胞途径，这在其他研究中也有提出。最后，我们对 NCI60 和 CCLE 项目中常见细胞系的基因表达水平和蛋白质组鉴定进行了综合分析，为进一步验证缺失蛋白的观察结果提出了替代方案。
