How-to populate MSI database with spectrum details

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].

To import spectrum detail for a specified context using Paloma tool, you need to have the context id. This property is accessible in Context property sheet. View in accessproperties page.

• Download Paloma-<version>.zip and unzip to <Paloma-install> directory. (Download is available at the following FTP site : ftp://ftp.cea.fr/pub/edyp/heidi)
• In command prompt (Run → Cmd), go to <Paloma-install>/ and run :

  java -Djava.library.path=./lib -Xms512m  -Xmx1024m  -classpath ./paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder [OPTIONS]

  • -Xmx option allow you to specify amount of memory to use for yhios process. Depending on your system (amount of memory and 32bits or 64bits), you can set more memory : -Xmx4000m for example
  • OPTIONS 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
• You can verify there were no error by opening paloma-<user>.log from <Paloma-install> directory. This file contains lots of information, for debug purpose.
  • Search for any “ERROR ” string to verify no error occurs.
  • You can also see how many mascot dat file were parsed.

Look for entry such has

         INFO SpectrumEntriesSearch - The selected context contains 2,686 species and 2,686 spectrum are needed
         INFO SpectrumEntriesSearch - Paloma - SpectrumEntriesSearch - identify 44 dat files
         INFO SpectrumEntriesSearch -  .... featuring 2686 peptides
         INFO SpectrumMatchFeeder - Paloma - SpectrumMatchFeeder - will parse 44 dat files 

• You will also see “44” entry like Parser dat file : XXXXX. Each followed by Parser dat file DONE

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