ArticleJournal of the American Society for Mass Spectrometry2017
Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope.
Article in Journal of the American Society for Mass Spectrometry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- A machine learning method for calculating highly localized protein stabilities.Nature communications · 2026Article
- Use of hydrogen deuterium exchange mass spectrometry in tandem with modern structural biology.The Biochemical journal · 2026Review
- HXMS: a standardized file format for HX-MS data.Bioinformatics (Oxford, England) · 2026Article
- HXMS: a standardized file format for HX/MS data.bioRxiv : the preprint server for biology · 2025Article
- Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles.bioRxiv : the preprint server for biology · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Using hydrogen-deuterium exchange mass spectrometry to characterize Mtr4 interactions with RNA.Methods in enzymology · 2022Article
- Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook.Frontiers in immunology · 2022Review
- The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX-MS, DSC, and nanoDSF.Protein science : a publication of the Protein Society · 2021Article
- Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Parallel Chemoselective Profiling for Mapping Protein Structure.Cell chemical biology · 2020Article
- Imidazolium Compounds as Internal Exchange Reporters for Hydrogen/Deuterium Exchange by Mass Spectrometry.Analytical chemistry · 2020Article
- Dynamics and Location of the Allosteric Midazolam Site in Cytochrome P4503A4 in Lipid Nanodiscs.Biochemistry · 2020Article
- Estimating Constraints for Protection Factors from HDX-MS Data.Biophysical journal · 2019Article
- High-Resolution HDX-MS of Cytochrome c Using Pepsin/Fungal Protease Type XIII Mixed Bed Column.Journal of the American Society for Mass Spectrometry · 2019Article
- Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry.Protein and peptide letters · 2019Review
- Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data.Journal of the American Society for Mass Spectrometry · 2018Article
- Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.Journal of the American Society for Mass Spectrometry · 2017Article
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Abstract
A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification. Graphical Abstract ᅟ.
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