ArticleNature methods2024
Influence of different sample preparation approaches on proteoform identification by top-down proteomics.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 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
- Modulating proteoform charge states and signal intensities in LC-MS using a nanoflow sheath liquid interface.Analytical and bioanalytical chemistry · 2026Article
- A Draft Map of E. coli Proteoforms.Analytical chemistry · 2026Article
- Top-Down versus Bottom-Up Proteomics in Highly Sensitive LC-MS-Based Profiling of Limited Samples.Analytical chemistry · 2026Article
- Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions.Foods (Basel, Switzerland) · 2026Review
- Article
- Differential protein network and biological functions atlas from multi-tissue proteomics in patients with depression.Molecular psychiatry · 2026Article
- Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction.bioRxiv : the preprint server for biology · 2026Article
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Quantitative Mapping of NHS Ester-Protein Reactivity Using Native Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2026Article
- Improved High-Throughput Platform for In-Cell Fast Photochemical Oxidation of Proteins via an AutomatedJournal of the American Society for Mass Spectrometry · 2026Article
- Recent Developments and Applications of Capillary and Microchip Electrophoresis in Proteomics and Peptidomics (2023-2025).Journal of separation science · 2026Review
- Intact Proteoform Analysis by Capillary Electrophoresis-Mass Spectrometry. Are We There Yet?Angewandte Chemie (International ed. in English) · 2026Article
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Characterization of Cytokine Treatment on Human Pancreatic Islets by Top-Down Proteomics.Proteomics · 2025Article
- Article
- Comparative Analysis of Proteoform Clean-Up Methods for In-Depth Top-Down Proteomics.Proteomics · 2025Article
- Top-Down Proteomics: Why and When?Proteomics · 2025Article
- Article
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Top-down proteomics using mass spectrometry facilitates the identification of intact proteoforms, that is, all molecular forms of proteins. Multiple past advances have lead to the development of numerous sample preparation workflows. Here we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction and alkylation, proteoform enrichment, purification and fractionation. We found that all steps in sample preparation influence the subset of proteoforms identified (for example, their number, confidence, physicochemical properties and artificially generated modifications). The various sample preparation strategies resulted in complementary identifications, substantially increasing the proteome coverage. Overall, we identified 13,975 proteoforms from 2,720 proteins of human Caco-2 cells. The results presented can serve as suggestions for designing and adapting top-down proteomics sample preparation strategies to particular research questions. Moreover, we expect that the sampling bias and modifications identified at the intact protein level will also be useful in improving bottom-up proteomics approaches.
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