ArticleJournal of the American Society for Mass Spectrometry2018
Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses.
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 13 papers.
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Who cites it
13 citing papers in PubMed.
- Modulating pseudokinase conformation from the ATP-binding site.Structure (London, England : 1993) · 2026Article
- Structural heterogeneity and substrate engagement mechanism of the bacterial proteasome activator Bpa.Nature communications · 2026Article
- MultiPassMerger: Automated data processing for multipass cyclic ion mobility HDX-MS.Protein science : a publication of the Protein Society · 2025Article
- Mapping the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry.The Journal of biological chemistry · 2025Article
- Stability convergence in natural antibodies with ultra-long hypervariable loops.Communications biology · 2025Article
- Structural basis for allosteric modulation of M. tuberculosis proteasome core particle.Nature communications · 2025Article
- MgbioRxiv : the preprint server for biology · 2024Article
- Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications.Analytical chemistry · 2024Article
- Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein.Nature communications · 2023Article
- OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.Analytical chemistry · 2023Article
- Fundamentals of HDX-MS.Essays in biochemistry · 2023Review
- Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies.Analytical chemistry · 2023Article
- Article
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Authors and funding
2 authors.
Funding
Abstract
Hydrogen deuterium exchange measured by mass spectrometry (HDX-MS) is a commonly used technique for studying the structural dynamics of proteins in solution. The first part of any bottom-up HDX-MS experiment is to identify the peptides generated from a digestion step. This requires manual inspection of the identified peptides to determine their use for HDX-MS analysis, which is a time-consuming task. Throughout the literature, there have been different approaches for removing peptides that do not yield quantifiable HDX information. This includes using validity scores from the software used in the generation of the peptide map and that the peptide should be found in two out of three technical replicate experiments. Here, we analyze the previously available methods for filtering the identified peptides in regard to their ability to predict whether a peptide will provide quantifiable HDX-MS data or not. We also present a new score-based system relying on a combination of MS/MS parameters that offers an improved method for separating quantifiable peptides from the nonquantifiable. Using this score-based method reduces the number of peptide spectra that needs to be manually inspected and thereby the time spent curating HDX-MS data. Graphical Abstract ᅟ.
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Registered trials
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.