ArticleBioinformatics (Oxford, England)2017
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Proteoform Identification Using Multiplexed Top-Down Mass Spectra.Proteomics · 2025Article
- Finding coexisting combinations of posttranslational modifications with HomMTM spectra.Briefings in bioinformatics · 2025Article
- ResNeXt-Based Rescoring Model for Proteoform Characterization in Top-Down Mass Spectra.Interdisciplinary sciences, computational life sciences · 2025Article
- Proteoform identification and quantification based on alignment graphs.Bioinformatics (Oxford, England) · 2024Article
- Recent Contributions of Proteomics to Our Understanding of Reversible NJournal of proteome research · 2024Review
- Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra.Bioinformatics (Oxford, England) · 2024Article
- Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Top-Down Proteomics and the Challenges of True Proteoform Characterization.Journal of proteome research · 2023Review
- Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations.Journal of proteome research · 2023Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.Journal of proteome research · 2023Article
- Evaluation of Machine Learning Models for Proteoform Retention and Migration Time Prediction in Top-Down Mass Spectrometry.Journal of proteome research · 2022Article
- Top-Down Mass Spectrometry Data Analysis Using TopPIC Suite.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization.Journal of the American Society for Mass Spectrometry · 2021Article
- Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN.Proteomes · 2021Article
- Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.Journal of proteome research · 2021Article
- TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation.PEARC20 : Practice and Experience in Advanced Research Computing 2020 : Catch the wave : July 27-31, 2020, Portland, Or Virtual Conference. Practice and Experience in Advanced Research Computing (Conference) (2020 : Online) · 2020Article
- In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates.Biochemical Society transactions · 2020Review
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6 authors.
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Abstract
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. Availability and implementation: http://proteomics.informatics.iupui.edu/software/topmg/. Contact: xwliu@iupui.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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