ArticleAnalytical chemistry2023
TopFD: A Proteoform Feature Detection Tool for Top-Down Proteomics.
Article in Analytical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- ProteoformTracker: an interactive tool for planning proteoform detectability in top-down and middle-down proteomics.bioRxiv : the preprint server for biology · 2026Article
- A Draft Map of E. coli Proteoforms.Analytical chemistry · 2026Article
- Native Multidimensional Protein Complex Identification and Topology Characterization (Native MudPIT).Analytical chemistry · 2026Article
- Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona.Nature communications · 2026Article
- Advancing the Reproducibility and Repeatability of Capillary Zone Electrophoresis-Mass Spectrometry-Based Top-Down Proteomics by an Improved Capillary Coating Procedure.Journal of proteome research · 2026Article
- Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction.bioRxiv : the preprint server for biology · 2026Article
- Top-Down Mass Spectrometry and Its Current Applications in Biomarker Discovery in Aging and Age-Related Diseases.International journal of molecular sciences · 2026Review
- Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD.Clinical proteomics · 2026Review
- Article
- Quantitative Mapping of NHS Ester-Protein Reactivity Using Native Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2026Article
- Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas.Nature protocols · 2026Review
- Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down Mass Spectrometry.Analytical chemistry · 2026Article
- Intact Proteoform Analysis by Capillary Electrophoresis-Mass Spectrometry. Are We There Yet?Angewandte Chemie (International ed. in English) · 2026Article
- Characterization of the Intact Proteomic Profile of Senescent-Associated Secretory Phenotype by Top-Down Mass Spectrometry.Analytical chemistry · 2025Article
- Quantitative Top-Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells.Proteomics · 2025Article
- Proteoform Identification Using Multiplexed Top-Down Mass Spectra.Proteomics · 2025Article
- Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle-Down, and De Novo Bottom-Up Mass Spectrometry.Molecular & cellular proteomics : MCP · 2025Article
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
- Modification of human metallothioneins by garlic organosulfur compounds, allicin and ajoene: direct effect on zinc homeostasis with relevance to immune regulation.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2025Article
- Fast and Accurate Charge State Deconvolution of Protein Mass Spectra.Analytical chemistry · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
Top-down liquid chromatography-mass spectrometry (LC-MS) analyzes intact proteoforms and generates mass spectra containing peaks of proteoforms with various isotopic compositions, charge states, and retention times. An essential step in top-down MS data analysis is proteoform feature detection, which aims to group these peaks into peak sets (features), each containing all peaks of a proteoform. Accurate protein feature detection enhances the accuracy in MS-based proteoform identification and quantification. Here, we present TopFD, a software tool for top-down MS feature detection that integrates algorithms for proteoform feature detection, feature boundary refinement, and machine learning models for proteoform feature evaluation. We performed extensive benchmarking of TopFD, ProMex, FlashDeconv, and Xtract using seven top-down MS data sets and demonstrated that TopFD outperforms other tools in feature accuracy, reproducibility, and feature abundance reproducibility.
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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.