TY - JOUR T1 - Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry JF - bioRxiv DO - 10.1101/2020.05.27.119644 SP - 2020.05.27.119644 AU - Wenrong Chen AU - Xiaowen Liu Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/05/28/2020.05.27.119644.abstract N2 - 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 still lack of software tools for top-down proteogenomic data analysis. In this paper, we introduce TopPG, a proteogenomic tool for identifying proteoforms with genetic alterations and alternative splicing events. Experiments on top-down proteogenomic data of DLD-1 colorectal cancer cells showed that TopPG can confidently identify proteoforms with sample-specific alterations.Competing Interest StatementThe authors have declared no competing interest. ER -