HaDeX

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 (2020). HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data. Bioinformatics, 10.1093/bioinformatics/btaa587.

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) and Narodowe Centrum Nauki (Preludium Bis 1 2019/35/O/NZ2/03745 Wysokorozdzielcza analiza danych z eksperymentów wymiany proton-deuter monitorowanych spektrometrią mas).

Settings

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

Choose protein:

Choose maximal exchange control for chosen protein:

Choose D20 concentration [%]:

Move sequence start:

Correct sequence length:

Select parameters for the plot.

Theoretical calculations

Choose values type:

relative

absolute

Comparison plot parameters:

Choose time parameters:

CHOSEN

OUT

Choose states for comparison:

CD160

CD160VEM

Woods plot parameters:

State 1

State 2

Confidence limit 1:

Confidence limit 2:

Zoom:

Choose y range for comparison plot:

Choose y range for Woods plot:

Choose x range for both plots:

Comparison plot title:

Comparison plot axis x label:

Comparison plot axis y label:

Woods plot title:

Woods plot axis x label:

Woods plot axis y label:

Comparison plot
Data

Save chart (.svg)

Woods plot
Data

Save chart (.svg)

Peptide Coverage
Data

Save chart (.svg)

Position Frequency
Data

Save chart (.svg)

Protein name

Reconstructed sequence

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.

Theoretical calculations

Choose values type:

relative

absolute

Choose time parameters:

OUT

Choose peptide:

Choose y range for the plot:

Uptake curve title:

Uptake curve axis x label:

Uptake curve axis y label:

Uptake curve
Data

Save chart (.svg)

Select parameters for the plot.

The plot can be rendered only for relative experimental values.

Choose in time:

Choose time:

State 1

State 2

Quality control plot
Data

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).

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).

Welcome to HaDeX!

Thank you for using our tool.

Questions/feature requests/commercial applications: hadex@ibb.waw.pl

About

Authors

Citation

Funding

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:

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

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.

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.

Welcome to HaDeX website!

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