Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry,Journal of Proteome Research

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Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-11-12 , DOI: 10.1021/acs.jproteome.0c00369
Wenrong Chen ₁ , Xiaowen Liu _{1,

2}

Affiliation

In proteogenomic studies, genomic and transcriptomic variants are incorporated into customized protein databases for the identification of proteoforms, especially proteoforms with sample-specific variants. Most proteogenomic research has been focused on combining genomic or transcriptomic data with bottom-up mass spectrometry data. In the last decade, top-down mass spectrometry has attracted increasing attention because of its capacity to identify various proteoforms with alterations. However, top-down proteogenomics, in which genomic or transcriptomic data are combined with top-down mass spectrometry data, has not been widely adopted, and there is still a lack of software tools for top-down proteogenomic data analysis. In this paper, we introduce TopPG, a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events. Experiments on top-down proteogenomic data of DLD-1 colorectal cancer cells showed that TopPG coupled with database search confidently identified proteoforms with sample-specific alterations.

中文翻译：

结合 RNA-Seq 和自上而下质谱法进行蛋白质组鉴定

在蛋白质基因组学研究中，基因组和转录组变异被整合到定制的蛋白质数据库中，用于鉴定蛋白质型，尤其是具有样品特异性变异的蛋白质型。大多数蛋白质组学研究都集中在将基因组或转录组数据与自下而上的质谱数据相结合。在过去的十年中，自上而下的质谱法因其能够识别具有改变的各种蛋白质型的能力而引起了越来越多的关注。然而，自上而下的蛋白质基因组学，其中基因组或转录组数据与自上而下的质谱数据相结合，尚未被广泛采用，并且仍然缺乏用于自上而下的蛋白质基因组数据分析的软件工具。在本文中，我们介绍了 TopPG，一种蛋白质基因组学工具，用于生成具有遗传改变和选择性剪接事件的蛋白质组序列数据库。对 DLD-1 结肠直肠癌细胞自上而下的蛋白质组学数据的实验表明，TopPG 与数据库搜索相结合，可以自信地识别出具有样本特异性改变的蛋白质组。

更新日期：2021-01-01

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