How to export a UserContext into the PRIDE XML Format

Warning:

• 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.

Note:

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

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

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 runDescriptor.properties 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

In the runDescriptor.properties 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 runDescriptor.properties file and create the appropriate header in the resulting XML file.

Warning

• This feature is in progress, so we highky recommand to use the PRIDE Converter instead of using ''runDescriptor.properties'' file, in order to easily create a full detailled header for your PRIDE XML file. Nevertheless, if you want to learn more about using the runDescriptor.properties file, click here for more details about filling in this file)
  

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

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

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

• 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 runDescriptor.properties file to open it in the hEIDI editor view (you can also right-click on the runDescriptor.properties 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

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

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)