Welcome to HaDeX GUI!
Thank you for using our tool.
Questions/feature requests/commercial applications: hadex@ibb.waw.pl
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).
Funding
This project is part of 2019/35/O/NZ2/03745 grant from National Science Centre in Poland and originated within the TEAM TECH programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM TECH CORE FACILITY/2016-2/2).
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:
For the program to behave correctly, please make sure supplied file fulfills all requirements.
Show requirements
Upload settings
Values chosen here are propagated into all of the tabs for coherent results.
Select the parameters:
Upload structure file!
If available, upload the pdb file with protein structure. Uptake data shown on the supplied structure is placed in the `Hires` part.Select parameters for the plot
Common settings
Calculation
Timepoints
Comparison Plot settings
States
Colors
Woods Plot settings
States
Differential plot presents the uptake difference between State 1 and State 2.
Test
Visualization
Adjustment settings
Ranges
Labels
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. 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.
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
Calculation
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Test
Subregion
Visualization
Ranges
Labels
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. 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
Calculation
State
Timepoints
Visualization
Labels
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. 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
Calculation
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Test
Visualization
Labels
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. 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
Calculation
State
Timepoints
Visualization
Labels
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. 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
Calculation
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Test
Visualization
Labels
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. 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
Calculation
States
Timepoints
Peptide
Select peptide:
Visualization
Ranges
Labels
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. 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
Calculation
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Peptide
Select peptide:
Visualization
Test
Ranges
Labels
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. 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
Select parameters for the plot
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Test
Visualization
Labels
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. 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
State
Timepoints
Visualization
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
Calculation
State
Timepoints
Selected exposure above will be presented on the structure, if supplied.
Select parameters for the plot
Calculation
States
Differential plot presents the uptake difference between State 1 and State 2.
Timepoints
Selected exposure above will be presented on the structure, if supplied.
Select parameters for the plot
State
Timepoints
Peptide
Select peptide:
Visualization
Ranges
Labels
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
Visualization
Select parameters for the plot
State
Subregion
Select parameters for the plot
Variable
State
Timepoints
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 to include in the report
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 reportAbout
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).
Funding
This project is part of 2019/35/O/NZ2/03745 grant from National Science Centre in Poland and originated within the TEAM TECH programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM TECH CORE FACILITY/2016-2/2).
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.