Tutorial 6: File conversion for HDExaminer

In version 2.3.1, we added a facility to Deuteros that expanded its analysis to HDExaminer files. A web-based Colab notebook is also available.

This (short) tutorial will cover how to convert HDExaminer files into the DynamX cluster format for input into Deuteros, as well as explain how the conversion is done for transparency.

Converting files in Deuteros

1. Navigate to the File Conversion tab in Deuteros.
2. Press browse and navigate to the HDExaminer file.
3. If the Current Format and New Format are not HDExaminer and DynamX (Cluster), set them to these values.
4. Press Convert and Done! should be displayed. The converted file is placed in the same directory as the HDExaminer file, with the _dynamx.csv suffix.
5. In the Data Import box, Browse to the new _dynamx.csv file and import as usual. Give the following settings for import:

6. Clicking on an imported peptide will generate the kinetics plot for the peptide.

HDExaminer vs DynamX Cluster format

HDExaminer file is a 36-column file that contains replicate-level data for peptides in their different experimental states. In contrast, the DynamX Cluster file has 15 columns, but also contains replicate-level data.

Most columns in The HDExaminer file are not necessary to generate a Cluster-like format. Below shows the mapping between HDExaminer and DynamX Cluster columns:

Cluster Col	HDExaminer Col	Calculation
Protein	Protein	As is
Start	Start	As is
End	End	As is
Sequence	Sequence	As is
Modification		Leave empty
Fragment		Leave empty
MaxUptake		Calculate from sequence: (n_res-n_pro-1)
MHP		'Exp Cent' - '# Deut'
State	Protein State	As is
Exposure	Deut Time	Remove trailing 's'
File	Experiment	As is
z	Charge	As is
RT	Search RT	As is
Inten	Max Inty	As is
Center	Exp Cent	As is