ArticleBioinformatics (Oxford, England)2024
HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- HaDeX2: multi-dimensional analysis of hydrogen-deuterium exchange mass spectrometry data.Bioinformatics (Oxford, England) · 2026Article
- HydroBot: Software for Interactive Hydrogen/Deuterium-Exchange Mass Spectrometry Multistate Analysis.Journal of the American Society for Mass Spectrometry · 2026Article
- Disorder with consequence: Phosphorylation sites in HSPB5 yield distinct structural outcomes.bioRxiv : the preprint server for biology · 2025Article
- Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A framework for automated multimodal HDX-MS analysis.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
summaryHydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) is a powerful protein characterization technique that provides insights into protein dynamics and flexibility at the peptide level. However, analyzing HDX-MS data presents a significant challenge due to the wealth of information it generates. Each experiment produces data for hundreds of peptides, often measured in triplicate across multiple time points. Comparisons between different protein states create distinct datasets containing thousands of peptides that require matching, rigorous statistical evaluation, and visualization. Our open-source R package, HDXBoxeR, is a comprehensive tool designed to facilitate statistical analysis and comparison of multiple sets among samples and time points for different protein states, along with data visualization. AVAILABILITY AND IMPLEMENTATION: HDXBoxeR is accessible as the R package (https://cran.r-project.org/web//packages/HDXBoxeR) and GitHub: mkajano/HDXBoxeR.
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Identifiers
What Socratic holds
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 Socratic graph.