ArticleJournal of proteome research2021
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry.
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 36 papers.
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Who cites it
36 citing papers in PubMed.
- Proteoform analysis by mass spectrometry reveals post-translational processing of legumins and vicilins in chickpeas (Cicer arietinum L.).Analytical and bioanalytical chemistry · 2026Article
- Extensive Backbone Cleavage Coverage of Intact Proteoforms in a Mass Range of 10-70 kDa by Integrating Electron, Collision, and Photon-Based Fragmentation Techniques during an Electrophoretic Time Scale.Journal of the American Society for Mass Spectrometry · 2026Article
- Uncovering the covalent inhibitors of SARS-CoV-2 MJournal of pharmaceutical analysis · 2026Article
- Determination of Thermochemical Barriers in Multiple-Collision-Induced Dissociation Experiments on Gas-Phase Protein Complexes.Journal of the American Chemical Society · 2025Article
- Hyphenation of Trapped Ion Mobility to Two-Dimensional Mass Spectrometry for Protein Analysis in Complex Biomixtures.Journal of the American Society for Mass Spectrometry · 2025Article
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
- Dissecting Hidden Liraglutide Oligomerization Pathways via Direct Mass Technology, Electron-Capture Dissociation, and Molecular Dynamics.Analytical chemistry · 2025Article
- Mass spectrometry structural analysis of intrinsically disordered phosphoproteins.International journal of mass spectrometry · 2025Article
- Top-Down and Middle-Down Mass Spectrometry of Antibodies.Molecular & cellular proteomics : MCP · 2025Review
- Tracking proteasome degradation: A cross-organ analysis via intact degradomics mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.Journal of the American Society for Mass Spectrometry · 2025Article
- Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS.The Analyst · 2024Article
- Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications.Analytical methods : advancing methods and applications · 2024Review
- Panda-UV Unlocks Deeper Protein Characterization with Internal Fragments in Ultraviolet Photodissociation Mass Spectrometry.Analytical chemistry · 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
- Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies.Journal of the American Society for Mass Spectrometry · 2024Article
- Improved characterization of trastuzumab deruxtecan with PTCR and internal fragments implemented in middle-down MS workflows.Analytical and bioanalytical chemistry · 2024Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Characterization of Molecular Tweezer Binding on α-Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation Inhibition.Journal of the American Society for Mass Spectrometry · 2023Article
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Authors and funding
6 authors.
Funding
Abstract
Top-down mass spectrometry (TD-MS) of peptides and proteins results in product ions that can be correlated to polypeptide sequence. Fragments can either be terminal fragments, which contain either the N- or the C-terminus, or internal fragments that contain neither termini. Normally, only terminal fragments are assigned due to the computational difficulties of assigning internal fragments. Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complementary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum. Data are available via the MassIVE community resource with the identifiers MSV000086788 and MSV000086789.
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