{"doi":"10.1101/2025.02.05.636727","title":"Proteoform identification using multiplexed top-down mass spectra","abstract":"Top-down mass spectrometry (TDMS) is the method of choice for analyzing intact proteoforms, as well as their post-translational modifications and sequence variations. In TDMS experiments, multiple proteoforms are often co-fragmented in tandem mass spectrometry (MS/MS) analysis, resulting in multiplexed TD-MS/MS spectra. Since multiplexed TD-MS/MS spectra are more complex than common spectra generated from single proteoforms, these spectra pose a significant challenge for proteoform identification and quantification. Here we present TopMPI, a new computational tool specifically designed for the identification of multiplexed TD-MS/MS spectra. Experimental results demonstrate that TopMPI significantly increases proteoform identifications and reduces identification errors in multiplexed TD-MS/MS spectral analysis compared to existing tools.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":557282,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"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":0.9573,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1281738,"name":"Xingzhao Xiong","orcid":"0000-0002-9384-4573","position":1,"is_corresponding":false},{"id":298237,"name":"Xiaowen Liu","orcid":"0000-0003-4139-1127","position":2,"is_corresponding":false},{"id":1431080,"name":"Zhige Wang","orcid":null,"position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:17.435961Z","pmid":"39975217","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":[]}