ArticleJournal of proteome research2021
Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2025Article
- Electron Capture Dissociation for Discovery Top-Down Proteomics of Peptides and Small Proteins on Chromatographic Time Scales.Journal of the American Society for Mass Spectrometry · 2025Article
- Improved Annotation of Internal Fragments via Trapped-Ion Mobility Enhanced Top-Down Sequencing of Protein Ions.Journal of mass spectrometry : JMS · 2025Article
- Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications.Analytical methods : advancing methods and applications · 2024Review
- Tracking Inhibition of Human Small C-Terminal Domain Phosphatase 1 Using 193 nm Ultraviolet Photodissociation Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Spectral averaging with outlier rejection algorithms to increase identifications in top-down proteomics.Proteomics · 2024Article
- Native Capillary Electrophoresis-Mass Spectrometry of Near 1 MDa Non-Covalent GroEL/GroES/Substrate Protein Complexes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Internal Fragments Enhance Middle-Down Mass Spectrometry Structural Characterization of Monoclonal Antibodies and Antibody-Drug Conjugates.Analytical chemistry · 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
- Added Value of Internal Fragments for Top-Down Mass Spectrometry of Intact Monoclonal Antibodies and Antibody-Drug Conjugates.Analytical chemistry · 2023Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
A large fraction of observed fragment ion intensity remains unidentified in top-down proteomics. The elucidation of these unknown fragment ions could enable researchers to identify additional proteoforms and reduce proteoform ambiguity in their analyses. Internal fragment ions have received considerable attention as a major source of these unidentified fragment ions. Internal fragments are product ions that contain neither protein terminus, in contrast with terminal ions that contain a single terminus. There are many more possible internal fragments than terminal fragments, and the resulting computational complexity has historically limited the application of internal fragment ions to low-complexity samples containing only one or a few proteins of interest. We implemented internal fragment ion functionality in MetaMorpheus to allow the proteome-wide annotation of internal fragment ions. MetaMorpheus first uses terminal fragment ions to identify putative proteoforms and then employs internal fragment ions to disambiguate similar proteoforms. In the analysis of mammalian cell lysates, we found that MetaMorpheus could disambiguate over half of its previously ambiguous proteoforms while also providing up to a 7% increase in proteoform-spectrum matches identified at a 1% false discovery rate.
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