{"doi":"10.1101/2020.05.27.119644","title":"Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry","abstract":"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 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":126818,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.916,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":298237,"name":"Xiaowen Liu","orcid":"0000-0003-4139-1127","position":1,"is_corresponding":false},{"id":574790,"name":"Wenrong Chen","orcid":"0000-0002-8052-604X","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-18T23:15:27.226519Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}