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How to export a UserContext into the PRIDE XML Format


  • :!: Exporting a UserContext to PRIDE XML format is only available for MSIdb version D.4 (or later versions).
  • :!: In hEIDI versions v1.10.1, v1.11.0 and up to now (MSIdb E.1), the header of the generated PRIDE XML file is not totally achieved (contact info, experiment & sample details, protocol steps, etc.). The user will have to use PRIDE Converter to build another PRIDE XML file, from which he will only copy the meta-infos and paste them into the hEIDI generated PRIDE XML file.


  • Only visible typical proteins of each protein group will be exported

Main steps to export a UserContext to PRIDE XML format

  1. From a UserContext in hEIDI, launch the PRIDE XML Export to create a first PRIDE XML file (see details below)
    1. If necessary, a dialog will appear (see below), import spectra into MSIdb.
  2. From the PRIDE Converter wizard, create a second PRIDE XML file (see here)
  3. Copy the header from the second PRIDE XML file and paste it into the first PRIDE XML file (see below)
  4. Check your modified PRIDE XML file using PRIDE Inspector

1. Launch PRIDE XML Export from hEIDI

Follow these steps to generate a PRIDE XML file from a given context:

  • After having created or opened an hEIDI project, open your MSI session but :!: Don't forget to activate your hEIDI project.
  • Check the file exists in your hEIDI project (see next section)
  • Select the UserContext you want to export. It has to be grouped and saved to MSIdb.
  • Select MS Identifications > Context > Export > PRIDE XML
  • Enter a name for your PRIDE XML file and browse to the directory of your choice (default is to use the name of the selected UserContext with the .xml extension in the hEIDI project directory).
  • [WARNING] A dialog may appear if spectra are missing
    • Answer No to stop the PRIDE XML Export process (Ask the INFO Team to populate the MSIdb with missing spectra)
  • If PRIDE XML Export ended successfully, a dialog message is displayed at the end of the export process
  • A dialog appears to display the log file (see exportpridelog for more details)
  • :!: Open the resulting .xml Pride file out of hEIDI using any external text editor. Opening the file in the hEIDI environment may cause memory issue if the file size is too big

The '''' file

In the file you provide meta information about your experiment (title, description, contact info), your sample(s), the instrument, the protocol steps, etc.
The PRIDE XML Export fonctionnality will then parse properties from the file and create the appropriate header in the resulting XML file.

:!: Warning :!:

When you create a new hEIDI project, a default file is created.

Warning about reusing old hEIDI Project

:!: If you use an old hEIDI project (created with hEIDI version lower than v1.10.1), check:

  • A file exists under <HEIDI_PROJECT_DIR>\heidi.project\. If it doesn't exist, simply create an empty text file, named

How to modify the '''' file in hEIDI

  • On the left side of the hEIDI interface, select the Files tab (or select in the main menu bar Window→Files)
  • Expand the node corresponding to the hEIDI project you are working on. Finally, expand the heidi.project directory.
  • Double-click on the file to open it in the hEIDI editor view (you can also right-click on the and select Open, it will display the contents of this file in a tabular way)
  • Change the contents of the file
  • Don't forget to save your changes by selecting File→Save in the main menu bar

2. Use PRIDE Converter to create another XML file

See here to create a PRIDE XML file from a MASCOT DAT file.

3. Extract meta-info from PRIDE XML file (generated by PRIDE Converter) to update the PRIDE XML file generated by hEIDI

The purpose is to replace meta-information from the first PRIDE XML file (generated by hEIDI) with the more detailled meta-information of the second PRIDE XML file (generated by PRIDE Converter)

4. Check your PRIDE XML file using PRIDE Inspector

how_to/exportpride.txt · Last modified: 2013/01/28 08:05 by