Welcome to HaDeX!

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

Citation

Puchala W, Burdukiewicz M, Kistowski M, Dabrowska KA, Badaczewska-Dawid AE, Cysewski D and Dadlez M (2019). HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data. R package version 1.0.

Funding

This work is supported by Foundation of Polish Science (TEAM TECH CORE FACILITY/2016-2/2 Mass Spectrometry of Biopharmaceuticals - improved methodologies for qualitative, quantitative and structural characterization of drugs, proteinaceous drug targets and diagnostic molecules).

Links



Upload your file. Otherwise you will see example data.

Currently HaDeX is limited to `cluster` files from DynamX 3.0 and 2.0

Accepted file extensions: .csv, .xsl, .xslx.

Supplied file should containt at least two repetitions of the measurement fot the uncertainty to be calculated.

If supplied file contains modificated peptides, maximal exchange control cannot be applied.

File status:
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Please be aware that loading data (including example file) may take a while. Be patient.

In order for program to behave correctly, please make sure supplied file fulfills following requirements:

Settings

Values chosen here are propagated into all of the tables for coherent results.





Select parameters for the plot.

Comparison plot parameters:

Choose time parameters:
Choose states for comparison:

Woods plot parameters:

Zoom:


Protein name

Reconstructed sequence




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Save chart (.svg)

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.


Select parameters for the plot.

Choose time parameters:
Choose peptide:




Select parameters for the plot.

The plot can be rendered only for relative experimental values.

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Save chart (.svg)

This function plots the change in the uncertainty of deuteration levels as a function of incubation time. The uncertainty is averaged over all peptides available at a given time point in a selected state. This chart has a double function: firstly, it allows checking if the measurement uncertainty is decreasing over time (which is the expected behaviour) and the second one helps to plan the appropriate incubation length for the tested protein (whether we obtain the desired data reliability values).



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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).


Choose items for report:


Elements chosen for report have the same parameters as chosen in panel e.g. axis range and title. Adjust parameters for plots as needed in the report.

Create report!

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