ArticleBioinformatics (Oxford, England)2020
HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A closely related pair of superoxide dismutase isozymes from Staphylococcus aureus show distinct stabilities and proton-exchange dynamics.The Journal of biological chemistry · 2026Article
- 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
- Dynamics and structural features of the eEF1A1 and eEF1A2 paralogs.Nucleic acids research · 2025Article
- HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data.Journal of proteome research · 2025Article
- Kingfisher: An open-sourced web-based platform for the analysis of hydrogen exchange mass spectrometry data.Protein science : a publication of the Protein Society · 2025Article
- The molecular properties of the bHLH TCF4 protein as an intrinsically disordered hub transcription factor.Cell communication and signaling : CCS · 2025Article
- Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.Chemical reviews · 2024Review
- HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states.Bioinformatics (Oxford, England) · 2024Article
- Deciphering the dual nature of nesfatin-1: a tale of zinc ion's Janus-faced influence.Cell communication and signaling : CCS · 2024Article
- Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B.Molecular cell · 2024Article
- Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein.Journal of molecular biology · 2023Article
- OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.Analytical chemistry · 2023Article
- Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A heterotypic assembly mechanism regulates CHIP E3 ligase activity.The EMBO journal · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Dynamics of protein kinases and pseudokinases by HDX-MS.Methods in enzymology · 2022Article
- protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data.Bioinformatics advances · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationHydrogen-deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites addressing emerging standards in data analysis.
resultsWe propose HaDeX, a novel tool for processing, analysis and visualization of HDX-MS experiments. HaDeX supports a reproducible analytical process, including data exploration, quality control and generation of publication-quality figures. AVAILABILITY AND IMPLEMENTATION: HaDeX is available primarily as a web-server (http://mslab-ibb.pl/shiny/HaDeX/), but its all functionalities are also accessible as the R package (https://CRAN.R-project.org/package=HaDeX) and standalone software (https://sourceforge.net/projects/HaDeX/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.