ArticleBioinformatics (Oxford, England)2016
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- HydroBot: Software for Interactive Hydrogen/Deuterium-Exchange Mass Spectrometry Multistate Analysis.Journal of the American Society for Mass Spectrometry · 2026Article
- Segmented filamentous bacteria undergo a structural transition at their adhesive tip during unicellular to filament development.Nature communications · 2025Article
- Deciphering molecular determinants of GPBAR1-Gs protein interactions by HDX-MS and cryo-EM.Scientific reports · 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
- Neurofilament Light Chain under the Lens of Structural Mass Spectrometry.ACS chemical neuroscience · 2025Article
- Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.Chemical reviews · 2024Review
- Strategies for Top-Down Hydrogen Deuterium Exchange-Mass Spectrometry: A Mini Review and Perspective.Journal of mass spectrometry : JMS · 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
- Membranes prime the RapGEF EPAC1 to transduce cAMP signaling.Nature communications · 2023Article
- OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.Analytical chemistry · 2023Article
- The Deuterium Calculator: An Open-Source Tool for Hydrogen-Deuterium Exchange Mass Spectrometry Analysis.Journal of proteome research · 2023Article
- Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping.Frontiers in analytical science · 2023Article
- Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium.BMC biology · 2022Article
- Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry.Communications biology · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics.Frontiers in molecular biosciences · 2022Review
- HD-eXplosion: visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering.Bioinformatics (Oxford, England) · 2021Article
- Discovery of a cooperative mode of inhibiting RIPK1 kinase.Cell discovery · 2021Article
- Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry.Bioinformatics (Oxford, England) · 2021Article
- The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity.Nature communications · 2021Article
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7 authors.
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Abstract
motivationWith the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation.
resultsWe introduce a web application and a new R-package named 'MEMHDX' to help users analyze, validate and visualize large HDX-MS datasets. MEMHDX is composed of two elements. A statistical tool aids in the validation of the results by applying a mixed-effects model for each peptide, in each experimental condition, and at each time point, taking into account the time dependency of the HDX reaction and number of independent replicates. Two adjusted P-values are generated per peptide, one for the 'Change in dynamics' and one for the 'Magnitude of ΔD', and are used to classify the data by means of a 'Logit' representation. A user-friendly interface developed with Shiny by RStudio facilitates the use of the package. This interactive tool allows the user to easily and rapidly validate, visualize and compare the relative deuterium incorporation on the amino acid sequence and 3D structure, providing both spatial and temporal information. AVAILABILITY AND IMPLEMENTATION: MEMHDX is freely available as a web tool at the project home page http://memhdx.c3bi.pasteur.fr CONTACT: marie-agnes.dillies@pasteur.fr or sebastien.brier@pasteur.frSupplementary information: Supplementary data is available at Bioinformatics online.
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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.