{"doi":"10.1002/pmic.70020","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 posttranslational modifications and sequence variations. In top-down tandem mass spectrometry (TD-MS/MS) experiments, multiple proteoforms are often co-fragmented, resulting in multiplexed TD-MS/MS spectra. Due to their increased complexity, compared to spectra from single proteoforms, multiplexed TD-MS/MS spectra present significant challenges 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 substantially increases the sensitivity and accuracy of proteoform identification in multiplexed TD-MS/MS spectral analysis compared to existing tools. SUMMARY: Top-down mass spectrometry (TDMS) is a powerful technique for analyzing intact proteoforms; however, identifying multiple co-fragmented proteoforms from multiplexed tandem mass spectrometry (MS/MS) spectra remains a significant challenge. In this paper, we introduce TopMPI, a new computational tool specifically designed to identify multiplexed TD-MS/MS spectra using a two-round database search strategy. Compared to existing tools, TopMPI significantly improves the sensitivity and accuracy of proteoform identification from multiplexed MS/MS spectra. The development of TopMPI enhances the identification of low abundance proteoforms in complex biological samples and increases the potential of TDMS for discovering proteoform biomarkers in disease studies.","journal":"PROTEOMICS","year":2025,"id":541957,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9572,"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":25,"raw_metadata":null,"created_at":"2026-07-19T02:52:51.593043Z","pmid":"40739704","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":[]}