ArticleJournal of proteome research2023
Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.
Article in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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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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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Properties, Origin, and Consistency of Truncated Proteoforms Across Top-Down Proteomic Studies.Molecular & cellular proteomics : MCP · 2025Pooled it
- Deep Proteoform Sequencing with Top-Down Direct Mass Technology.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
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Robust Real-Time Sperm Tracking with Identity Reassignment Using Extended Kalman Filtering.Sensors (Basel, Switzerland) · 2025Article
- Top-Down and Middle-Down Mass Spectrometry of Antibodies.Molecular & cellular proteomics : MCP · 2025Review
- A Fast Neural Network for Isotopic Charge State Assignment.Journal of the American Chemical Society · 2025Article
- PEPPI-MS: gel-based sample pre-fractionation for deep top-down and middle-down proteomics.Nature protocols · 2025Review
- Spatial top-down proteomics for the functional characterization of human kidney.Clinical proteomics · 2025Article
- Review
- Immunoaffinity Intact Top-Down Mass Spectrometry for Quantification of Neuron-Specific Enolase Gamma, a Low-Abundance Protein Biomarker.Analytical chemistry · 2025Article
- Influence of different sample preparation approaches on proteoform identification by top-down proteomics.Nature methods · 2024Article
- pyMS-Vis, an Open-Source Python Application for Visualizing and Investigating Deconvoluted Top-Down Mass Spectrometric Experiments: A Histone Proteoform Case Study.Analytical chemistry · 2024Article
- Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications.Analytical methods : advancing methods and applications · 2024Review
- Spatial top-down proteomics for the functional characterization of human kidney.bioRxiv : the preprint server for biology · 2024Article
- Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience.Proteomes · 2024Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Top-Down Proteomics and the Challenges of True Proteoform Characterization.Journal of proteome research · 2023Review
- High-Throughput Deconvolution of Native Protein Mass Spectrometry Imaging Data Sets for Mass Domain Analysis.Analytical chemistry · 2023Article
- Unraveling Posttranslational Modification Complexity: Advances in Quantitative Histone Proteoform Mass Spectrometry.Mass spectrometry reviewsReview
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Authors and funding
15 authors.
Funding
Abstract
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate. We evaluated deconvolution engines (ThermoFisher Xtract, Bruker AutoMSn, Matrix Science Mascot Distiller, TopFD, and FLASHDeconv) in both ThermoFisher Orbitrap-class and Bruker maXis Q-TOF data (PXD033208) to produce consistent precursor charges and mass determinations. Finally, we sought post-translational modifications (PTMs) in proteoforms from bovine milk (PXD031744) and human ovarian tissue. Contemporary identification workflows produce excellent PrSM yields, although approximately half of all identified proteoforms from these four pipelines were specific to only one workflow. Deconvolution algorithms disagree on precursor masses and charges, contributing to identification variability. Detection of PTMs is inconsistent among algorithms. In bovine milk, 18% of PrSMs produced by pTop and TopMG were singly phosphorylated, but this percentage fell to 1% for one algorithm. Applying multiple search engines produces more comprehensive assessments of experiments. Top-down algorithms would benefit from greater interoperability.
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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.