ArticleJournal of the American Society for Mass Spectrometry2018
The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics.
Article in Journal of the American Society for Mass Spectrometry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Combinatorial Probabilities of Multiple Fragmentation Events Explain Polypeptide MS/MS Intensity Distribution, Overrepresentation of Smaller Fragments, and Missing Middle of Top-Down MS.Rapid communications in mass spectrometry : RCM · 2026Article
- A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2025Article
- A Fast Neural Network for Isotopic Charge State Assignment.Journal of the American Chemical Society · 2025Article
- Photolysis of the peptide bond at 193 and 222 nm.The Journal of chemical physics · 2025Article
- Panda-UV Unlocks Deeper Protein Characterization with Internal Fragments in Ultraviolet Photodissociation Mass Spectrometry.Analytical chemistry · 2024Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Improved characterization of trastuzumab deruxtecan with PTCR and internal fragments implemented in middle-down MS workflows.Analytical and bioanalytical chemistry · 2024Article
- Diagnostic utility of N-terminal TMPP labels for unambiguous identification of clipped sites in therapeutic proteins.Scientific reports · 2023Article
- Spacer Fidelity Assessments of Guide RNA by Top-Down Mass Spectrometry.ACS central science · 2023Article
- Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling.Journal of proteome research · 2023Article
- Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins.The Analyst · 2022Article
- Deciphering combinatorial post-translational modifications by top-down mass spectrometry.Current opinion in chemical biology · 2022Review
- Towards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometry.Analytica chimica acta · 2022Article
- Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.Journal of proteome research · 2021Article
- Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation.Journal of the American Society for Mass Spectrometry · 2021Article
- Improved Sequence Analysis of Intact Proteins by Parallel Ion Parking during Electron Transfer Dissociation.Analytical chemistry · 2021Article
- Internal Fragments Generated from Different Top-Down Mass Spectrometry Fragmentation Methods Extend Protein Sequence Coverage.Journal of the American Society for Mass Spectrometry · 2021Article
- ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry.Journal of proteome research · 2021Article
- Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2020Article
- Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. Graphical abstract ᅟ.
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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.