Before exporting a given UserContext to PRIDE XML file, check if the MSI database need to be populated with spectrum details.

Since hEIDI 1.11.1, this functionality is no more available from the hEIDI GUI, but has to be executed (outside from hEIDI, see bellow) [by your system administrator].

• Download Paloma-<version>.zip and unzip to <Paloma-install> directory.
• Go to <Paloma-install>/ and run : java -Djava.library.path=./lib -Xms512m -Xmx1024m -classpath .\paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder <option>
  • In -Xmx option you can specify more memory depending on your system (amount of memory and 32bits or 64bits) : -Xmx4000m …
  • Option are described if no parameter is specified in command line… Nevertheless, here they are : -u <user> -p <password> -url <dbURL> -m <root> [-d <driver>] -cid <context_id> where
    • <user> : user for DB connection
    • <password> : password for DB connection
    • <dbURL> : url to DB such as jdbc:postgresql:/ / <server_name>/<DB_Name>
    • <root> : Path to mascot data files
    • <driver> : Optional, default is Postgresql driver (org.postgresql.Driver)
    • <context_id> : Context ID to get spectra for

Since hEIDI 1.11.1, this functionality is no more available. Should be reintegrated …

• After having created or opened an hEIDI project, open your MSI session but Don't forget to activate your hEIDI project.
• Check, in Windows Explorer, you have mapped a drive to the Mascot data folder (\\cp-mascot\data) and you are connected to that folder.
• Select a UserContext. It has to be grouped and saved to MSIdb.
• Select the menu MS Identifications→Database Update→Populate with spectra
• A dialog will appear on the screen to indicate if spectrum details are missing for this UserContext
• Check the Mascot data root path. You can use \\cp-mascot\data or the corresponding Drive Letter you have set up in Windows Explorer, for example Y:.

• If spectrum details are missing, click on Ok, populate MSIdb with missing spectra, else click on Do nothing & Close this window
• In case you have clicked Yes, a message will appear when process is finished