Mascot Daemon Support

It is important to upgrade Mascot Daemon whenever you upgrade Mascot Server, so that the first two fields of the Mascot Daemon version number match those of the Mascot Server. The third field of the version number is the patch level, and this does not need to match.

Known Issues

• The majority of reported problems concern accessing files on remote machines. Mascot Daemon 2.0 and later runs as a service, which logs on to Windows using the Local System account. This user account does not have network privileges, so cannot access remote files. The fix is to change the service logon to a more privileged user, as described in the topic In Depth, Mascot Daemon Service in the Mascot Daemon on-line help.
• If you uninstall Mascot Daemon, and then re-install in a different path, it will fail to launch correctly and you will get the message "Failed to start Mascot Daemon Service". This is because the original installation path is still present in certain registry entries. (Note that you may not see this message until you next re-boot the PC).
  1. Choose OK, then Cancel, to exit Mascot Daemon.
  2. Ensure the Windows Control Panel Services Applet is not running.
  3. The fix requires a Microsoft utility, sc.exe, which can be found on your Mascot server, in the mascot/cluster/Windows_NT directory. It can also be found on the Mascot installation CD, in mascot.tar (Unix) or \unpacked\cluster\Windows_NT (Windows). Copy this file to the Daemon PC, and execute it at a command prompt by entering the following:
     sc delete MascotDaemonService
     It should return [SC] Delete Service SUCCESS.
  4. From the Windows Start menu, choose Run, enter regedit, and choose OK. If the following key exists, then delete it. (It should not exist, unless the Services Applet was running during the previous step): HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\MascotDaemonService
     WARNING: Editing the registry may render your computer unusable.
  5. You should then be able to launch Mascot Daemon and enter the URL of the local Mascot server.

Version 2.1.x

All Mascot Daemon version 2.1.x patches have been collected into a single executable file. This will update version 2.1.x to 2.1.06, but will not update files from earlier versions.

Available Fixes

• 1948: Print window for task report fails to update when selected task changes
• 2034: External processes appear to be lost if dialog closed and re-opened
• 2037: Negative ion support
• 2044: Raw file path not included in scan title when processing with Distiller
• 2054: Misleading error message when Mascot server URL incorrect
• 2065: Parameter editor fails to clear mod selections when loading parameter file
• 2076: Cannot handle paths containing double byte characters
• 2079: Fails to allow for electron mass when importing DTA files
• 2097: Browse for folder dialog cannot browse below domain level
• 2106: Cannot process *.t2d files using Data Explorer
• 2120: Run Voyager macro seems to be broken in Data Explorer 3.5
• 2130: Automation error from Integra Daemon when using Distiller
• 2132: Additional updates for Distiller 2.0 and Mascot 2.1.02
• 2133: Daemon service has memory leak (2.1.03 only)
• 2142: Repeat at interval mode of follow-up is broken.
• 2144: Pause/Cancel/Resume buttons apply to wrong tasks after a task is deleted
• 2186: Status tab may display an old task label when a new task is added
• 2203: Change default setting for "Save Distiller project" to true
• 2208: Parameters editor tab: instrument combo box not disabled when MS/MS unchecked
• 2213: File not found error if using import filter and task name has trailing space(s)
• 2227: Distiller 2.0 import will process wrong scan range if scan numbers are not consecutive in data file

Update procedure

1. Download and save the update program MascotDaemon_20060321.exe (904 kB) to the PC running Mascot Daemon.
2. If running, exit Mascot Daemon
3. As a user with Administrator privileges, start the update program.
4. Verify that the Mascot Daemon application directory has been correctly identified.
5. Choose to apply the patches.
6. After the patches have been installed you can delete the update program.

Notes

• After installing Mascot Daemon, you must run it at least once before trying to install the update patch. This is to ensure the Mascot Daemon service is created

Version 2.0.x

All Mascot Daemon version 2.0.x patches have been collected into a single executable file. This will update version 2.0.00 to 2.0.05, but will not update files from earlier versions.

Available Fixes

• 1670, 1672: Drag & drop onto follower task should not require data to be re-imported
• 1684: Analyst import only worked for MS/MS data
• 1718: Missing backslash for data files selected from non-drive root, local shares
• 1725: Drag & drop onto follower task fails if original data file was directory structure
• 1741: Couldn't switch between HTTP/1.0 and HTTP/1.1
• 1744: Cannot run as unprivileged user
• 1767: Save intermediate peak lists from data import filters to disk
• 1802: Restored <localuser> tag
• 1805: Double backslash for data files selected from drive root folder in multi-file selection

Update procedure

1. Download and save the update program MascotDaemon_20040825.exe (541 kb) to the PC running Mascot Daemon.
2. As a user with Administrator privileges, start the update program.
3. Verify that the Mascot Daemon application directory has been correctly identified.
4. Choose to apply the patches.
5. After the patches have been installed you can delete the update program.
6. When Mascot Daemon is next run, you will be warned that the task database must be updated. Only Microsoft Access (Jet) databases can be updated automatically. If you are using a different provider, you will need to update the database manually. Add a new field to the Mascot_Daemon_Files table: peak_list, nullable, varchar(255) or varchar2(255)

Notes

• The fix to enable import of Analyst MS data for a peptide mass fingerprint using mascot.dll requires the "script" to be version 1.6b10 or later. This can be downloaded from the Analyst help page
• All peak lists created by Mascot Daemon are now saved to MGF files. That is, peak lists created by any data import filter except for Masslynx sample list. Files are saved in a directory tree, with a default root of <application directory>\mgf. A different location can be specified in the Preferences dialog.
• For each task, a unique directory is created using the task ID and name (e.g. "34 Untitled"). Hence, task names must now conform to windows file name restrictions, (\/:*?"<>| are illegal). Each peak list will be named <modified data file path>.mgf. The data file name alone is not sufficient because a task can have multiple data files with the same name. If the original data file was \\fred\c$\xcalibur\bill.raw, the peak list will be ~~fred~c$~xcalibur~bill.raw.mgf
• The peak list files created by a task will be deleted automatically if and when the task is deleted. You can delete them manually if you wish, outside of Mascot Daemon. If a deleted file is required by Mascot Daemon, (can only happen as result of drag & drop), this will generate an error message.
• To repeat a search interactively against a different database without re-importing the data file, either (i) drag & drop the result file onto the new task, or (ii) create a new task to search the cached peak list explicitly (no import filter). You cannot just clone the task and then re-run it because there is nothing to prevent the import filter options being changed.