MEMHDX: Mixed Effects Models for HDX-MS analysis
developed by Stevenn Volant & Veronique Hourdel (Institut Pasteur)
contact us at: memhdx [at] pasteur.fr
This tool allows users to perfom an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters and of HDX Workbench http://hdx.florida.scripps.edu/hdx_workbench/Home.html . Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.
Example of MEMHDX results
How to use MEMHDX
MEMHDX workflow: A .csv file containing deuterium uptake values for all identified peptides is exported after raw data extraction and analysis by dedicated HDX-MS software (e.g., DynamX). The .csv file is uploaded to MEMHDX where a linear mixed-effects model is applied to statistically validate the dataset. Main results are displayed on a 'Logit representation' (for data clustering and validation) and visualized using a global summary plot and the 3D structure, where available. A user-friendly ShinyInterface facilitates the use of the application.
Statistical Analysis of HDX-MS Experiments
1. To begin your analysis
MEMHDX requires a .csv file (with comma as separator). This file MUST contain the following variables:
Start: Peptide Start position on the protein
End: Peptide End position on the protein
Sequence: Peptide Sequence
State: Name of the conditions (n=2)
Exposure: Value of the exposure time (min)
Replicate: Replicate number (n >= 3)
z : Peptide charge
Center: Centroid m/z value
MaxUptake: Maximum number of exchangeable amide hydrogens
2. Select your file
3. Options
4. Perform analysis
MEMHDX publications
If you are using MEMHDX for your HDX-MS Analyses, please cite the article below:
Article
-Bioinformatics
MEMHDX: An interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets.,
Hourdel V, Volant S, O'Brien DP, Chenal A, Chamot-Rooke J, Dillies MA, Brier S, 2016 Jul 13, full text
Posters & Presentations
- ASMS, 2015:
Probing Conformational Changes Occurring at the Calmodulin Interface upon Adenylate Cyclase Binding Using a Fully Automated HDX-MS Workflow
Darragh P. O'Brien, Stevenn Volant, Véronique Hourdel, Marilyne Davi, Marie-Agnès Dillies, Daniel Ladant, Julia Chamot-Rooke, Alexandre Chenal and Sébastien Brier
- JOBIM, 2015:
A novel statistical approach and R package to analyse HDX-MS of protein-protein interactions
Stevenn Volant, Véronique Hourdel, Darragh P. O'Brien, Sébastien Brier and Marie-Agnès Dillies
What's new in MEMHDX
february 22nd 2017
HDX Workbench can now export a .csv file compatible with MEMHDX.
august 30th 2016
Biological Threshold: The "Biological Threshold" is now considered as a global parameter by MEMHDX and used in the Logit Plot.
july 29th 2016
Global overview tab: A "Global Overview" tab has been added to assess and visualize the precision across all replicates independent of either the condition, number of peptides or labeling time.
Biological threshold: A “Biological Threshold” has been added in the "Global visualization" tab. This parameter allows the identification of statistically significant peptides displaying Fractional Uptake Difference values below the user-defined threshold (default value sets to 2%).