ArticleProteomics2025
Proteoform Identification Using Multiplexed Top-Down Mass Spectra.
Article in Proteomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
4 citing papers in PubMed.
- Proton Transfer Charge Reduction Enables Isobaric Labeling-Based Proteoform Quantification of Overlapping Signals in Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2026Article
- Proteoform Identification Using Multiplexed Top-Down Mass Spectra.Proteomics · 2025Article
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
- TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification.Analytical chemistry · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.