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Chen W, Liu X. Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. J Proteome Res. 2020;20(1):261-269doi: 10.1021/acs.jproteome.0c00369.
Chen, W., & Liu, X. (2021). Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. Journal of proteome research, 20(1), 261-269. https://doi.org/10.1021/acs.jproteome.0c00369
Chen, Wenrong, and Liu, Xiaowen. "Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry." Journal of proteome research vol. 20,1 (2021): 261-269. doi: https://doi.org/10.1021/acs.jproteome.0c00369
Chen W, Liu X. Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. J Proteome Res. 2021 Jan 01;20(1):261-269. doi: 10.1021/acs.jproteome.0c00369. Epub 2020 Nov 12. PMID: 33183009; PMCID: PMC7775893.
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J Proteome Res. 2021 Jan 01;20(1):261-269. doi: 10.1021/acs.jproteome.0c00369. Epub 2020 Nov 12.

Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.

Journal of proteome research

Wenrong Chen, Xiaowen Liu

Affiliations

  1. Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States.
  2. Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.

PMID: 33183009 PMCID: PMC7775893 DOI: 10.1021/acs.jproteome.0c00369

Abstract

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.

Keywords: RNA-seq; proteogenomics; top-down mass spectrometry

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