ReviewJournal of proteome research2023
Top-Down Proteomics and the Challenges of True Proteoform Characterization.
Review 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 53 papers.
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Who cites it
53 citing papers in PubMed.
- Development of a thiol-ene microfluidic chip for CE-MS of peptides and proteins.Analytical and bioanalytical chemistry · 2026Article
- The "2DE-Pattern" Database for Inventory of Proteoform Profiles: 2026 Upgrade and Update on Outcomes.Proteomes · 2026Article
- AMPK phosphorylation proceeds through hierarchical proteoform cascades revealed by integrated mass spectrometry.Science advances · 2026Article
- Beyond Protein Abundance: Proteoform Diversity and Phosphoproteome Remodeling in Maize (Proteomes · 2026Review
- ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Salivary protein macromolecules as diagnostic and therapeutic biomarkers linking oral health and neurodegenerative diseases-emerging mechanisms and future perspectives.Inflammopharmacology · 2026Review
- Nuclear Proteomics to Understand the Promotive Effect of Plant-Derived Smoke Solution on Wheat Under Salt Stress.Proteomes · 2026Article
- Deep Proteoform Sequencing with Top-Down Direct Mass Technology.bioRxiv : the preprint server for biology · 2026Article
- In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.Molecular & cellular proteomics : MCP · 2026Article
- Discovery of a sulfotyrosine-motif in the human TrkB extracellular domain required for agonist activation.bioRxiv : the preprint server for biology · 2026Article
- Native Top-Down Mass Spectrometry Combined with High-Resolution Charge Variant Analysis of Trastuzumab Originator and Biosimilars.Journal of the American Society for Mass Spectrometry · 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
- Top-Down Mass Spectrometry and Its Current Applications in Biomarker Discovery in Aging and Age-Related Diseases.International journal of molecular sciences · 2026Review
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Recent Developments and Applications of Capillary and Microchip Electrophoresis in Proteomics and Peptidomics (2023-2025).Journal of separation science · 2026Review
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- Top-Down Proteomics of Skinned Human Muscle Fibers Reveals Proteoform-Resolved Fiber-to-Fiber Variability.Journal of mass spectrometry : JMS · 2026Article
- Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down Mass Spectrometry.Analytical chemistry · 2026Article
- Protein Language Models: Applications and Perspectives.Journal of proteome research · 2026Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms) extracted from biological samples. True proteoform characterization requires that both the base protein sequence be defined and any mass shifts identified, ideally localizing their positions within the protein sequence. Being able to fully elucidate proteoform profiles lends insight into characterizing proteoform-unique roles, and is a crucial aspect of defining protein structure-function relationships and the specific roles of different (combinations of) protein modifications. However, defining and pinpointing protein post-translational modifications (PTMs) on intact proteins remains a challenge. Characterization of (heavily) modified proteins (>∼30 kDa) remains problematic, especially when they exist in a population of similarly modified, or kindred, proteoforms. This issue is compounded as the number of modifications increases, and thus the number of theoretical combinations. Here, we present our perspective on the challenges of analyzing kindred proteoform populations, focusing on annotation of protein modifications on an "average" protein. Furthermore, we discuss the technical requirements to obtain high quality fragmentation spectral data to robustly define site-specific PTMs, and the fact that this is tempered by the time requirements necessary to separate proteoforms in advance of mass spectrometry analysis.
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