Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry
dc.contributor.author | Chen, Wenrong | |
dc.contributor.author | Liu, Xiaowen | |
dc.contributor.department | BioHealth Informatics, School of Informatics and Computing | en_US |
dc.date.accessioned | 2023-04-20T14:29:11Z | |
dc.date.available | 2023-04-20T14:29:11Z | |
dc.date.issued | 2021 | |
dc.description.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. | en_US |
dc.eprint.version | Author's manuscript | en_US |
dc.identifier.citation | Chen W, Liu X. Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. J Proteome Res. 2021;20(1):261-269. doi:10.1021/acs.jproteome.0c00369 | en_US |
dc.identifier.uri | https://hdl.handle.net/1805/32533 | |
dc.language.iso | en_US | en_US |
dc.publisher | American Chemical Society | en_US |
dc.relation.isversionof | 10.1021/acs.jproteome.0c00369 | en_US |
dc.relation.journal | Journal of Proteome Research | en_US |
dc.rights | Publisher Policy | en_US |
dc.source | PMC | en_US |
dc.subject | Proteogenomics | en_US |
dc.subject | Top-down mass spectrometry | en_US |
dc.subject | RNA-seq | en_US |
dc.title | Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry | en_US |
dc.type | Article | en_US |