Welcome to HaDeX!
Thank you for using our tool.
Questions/feature requests/commercial applications: hadex@ibb.waw.pl
This is the development version of the application and may not be working correctly yet. The official version will be available soon.
About
The HaDeX web server relies on functions from the HaDeX R package. For more information check our documentation.
Authors and contributors
Citation
Puchała, W., Burdukiewicz, M., Kistowski, M., Dąbrowska, K.A., Badaczewska-Dawid, A.E., Cysewski, D., and Dadlez, M. (2020). HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments. Bioinformatics 36, 4516–4518 (10.1093/bioinformatics/btaa587).
Upload your file. Otherwise, you will see the example data.
Currently HaDeX is limited to `cluster` files from DynamX 3.0 or 2.0 and `tables` file from HDeXaminer. The supplied file should contain at least two repetitions of the measurement for the uncertainty to be calculated. If the supplied file contains modified peptides, maximal exchange control cannot be applied.
Please be aware that loading data (including example file) may take a while. Thank you for the patience.
File status:
If the file contains both modified and unmodified version of a peptide, they are treated as different ones.
For the program to behave correctly, please make sure supplied file fulfills all requirements. Requirements can be displayed by clicking the button.
Upload settings
Values chosen here are propagated into all of the tabs for coherent results.
Select the parameters:
File from HDeXaminer detected!
Some of the information from the data file requires your confirmation. For the additional information on how the data from HDeXaminer is processed, check the requirements above. Keep in mind that the MHP value is generated based on the peptide sequence and therefore, may differ from actual value in case of the modifications.Select parameters for the plot
Select time parameters
Comparison plot parameters
Woods plot parameters
Differential plot presents the uptake difference between State 1 and State 2.
Test
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
The empty values (e.q. `Frac DU`) mean there was not sufficient data for this peptide. Abbreviations from the table: DU - deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Import data for HDX Viewer
Feature under construction
The first amino acid of the peptide is omitted.
Create fileThe empty values (e.q. `Frac Diff DU`) mean there was not sufficient data for this peptide. There is a possibility that the measurement result is available for only one state of the peptide. Abbreviations from the table: Diff DU - differential deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
States
Volcano plot presents the uptake difference between State 1 and State 2.
Displayed values:
Timepoints
Test
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
For more information see about hybrid testing see: Hageman, T. S. & Weis, D. D. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 91, 8008–8016 (2019).
Save chart (.svg)Select parameters for the plot
State
Timepoints
Visualization
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
The empty values (e.q. `Frac DU`) means there was not sufficient data for this peptide. Abbreviations from the table: DU - deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Test
Visualization
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
The empty values (e.q. `Frac DU`) mean there was not sufficient data for this peptide.
Save chart (.svg)The table presents data from the chosen x plot range. The empty values (e.q. `Frac Diff DU`) mean there was not sufficient data for this peptide. There is a possibility that the measurement result is available for only one state of the peptide. Abbreviations from the table: Diff DU - differential deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
State
Timepoints
Visualization
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
Abbreviations from the table: DU - deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
States
Differential plot presents the uptake difference [Da] between State 1 and State 2.
Timepoints
Test
Visualization
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
The table presents data from the chosen x plot range. Abbreviations from the table: Diff DU - differential deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
Timepoints
Choose time parameters:
State
Peptide
Choose peptide:
Visualization
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
Download uptake curves for all peptides in selected form, based on the parameters from the Settings panel. Preparing the plots may take a while.
Download the zipped folder with separate files:
Download folderSelect parameters for the plot
States
Differential uptake curve presents the difference between two biological states.
Timepoints
Choose time parameters:
Peptide
Choose peptide:
Visualization
Test
Zoom
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
Download uptake curves for all peptides in selected form, based on the parameters from the Settings panel. Preparing the plots may take a while.
Download the zipped folder with separate files:
Download folderSelect parameters for the plot
Page under construction!
Currently plot works on default parameters as an example.
Abbreviations from the table: DU - deuterium uptake, Frac - fractional, Theo - theoretical, U(value) - uncertainty of value.
Select parameters for the plot
Select parameters:
Select parameters for the plot
States
Manhattan plot presents the t-Student test results for difference between two biological states.
t-Student Test
Time points
The axis ticks have the same size as the axis label. The legend text size is the same as the x axis label.
Select parameters for the plot
States
Timepoints
Select parameters for the plot
Select parameters:
Parameters for measurements plot:
Sequence
Visualization for mass uptake curve
Zoom
The axis ticks have the same size as the axis label.
Protein name
Reconstructed sequence
Source: Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105-132.
This table was adapted from the HDX Data Summary (Masson, G.R., Burke, J.E., Ahn, N.G., Anand, G.S., Borchers, C., Brier, S., Bou-Assaf, G.M., Engen, J.R., Englander, S.W., Faber, J., et al. (2019). Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 16, 595–602).
Select elements for the raport
Elements chosen for report have the same parameters as chosen in suitable panels e.g. axis range, plot title or theoretical maximal exchange control. Adjust parameters as needed in the report.
Create report!
About
The HaDeX web server relies on functions from the HaDeX R package. For more information check our documentation.
Authors and contributors
Citation
Puchała, W., Burdukiewicz, M., Kistowski, M., Dąbrowska, K.A., Badaczewska-Dawid, A.E., Cysewski, D., and Dadlez, M. (2020). HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments. Bioinformatics 36, 4516–4518 (10.1093/bioinformatics/btaa587).
Resources
If you are interested to dig more into the world of HDX-MS, please see the following:
List of resources
Manually curated lists of software, publications and other resources related to the analysis of HDX-MS data. It is community-maintained and new items are added when noticed. It is a valuable resorce to explore HDX-MS and what is done by the scientists from different labs.
List can be found here.
Feel free to fork the repository and add things you found valuable that are missing from the list.
powerHaDeX
The R-packages that allows super-fast isotopic envelopes simulations based on the algorithm by Zhong-Yuan Kan due to the usage of Markov chains. The functionalities of the package are will be available soon in a form of a GUI.
Repository is available here.