Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Updating or migrating to Mascot Server 3.0

This page describes how to update your Mascot Server to version 3.0, upgrade your Mascot licence to use additional processors, and migrate a Mascot installation to new hardware. For the correct procedure, please choose from the options below. If none of these apply, please contact us.

Important: If you want to make a trial installation, do not register using your permanent Mascot 3.0 product key. Email support@matrixscience.com to request a 14 day temporary licence key.

  1. Updating to version 3.0 on the current hardware
  2. Upgrading Mascot Server to use additional processors
  3. Migrating to new hardware

Updating to version 3.0 on the current hardware

Linux

  1. Some configuration files may be replaced with factory default on updating Mascot, for example config/quantitation.xml and config/crosslinking.xml. Please make a backup of files in the config directory.
  2. The update procedure is described in Chapter 2 of the Installation & Setup Manual. This is manual.pdf in the Mascot installation package.
  3. The installation script will update config/mascot.dat by adding new options, but will retain all existing sequence database configuration settings and other options.
  4. Compare the other configuration files in config with the files you backed up, and restore any local changes you had made (for example, quantitation methods).
  5. If you are updating from Mascot 2.4 or earlier, see the note about local modifications to unimod.xml in technical support under Known Issues.

Windows

  1. Do not uninstall the old version of Mascot. Just run setup64.exe as described in Chapter 3 of the Installation & Setup Manual. This is manual.pdf in the Mascot installation package.
  2. If a configuration file from the previous version of Mascot was replaced with factory default, the Mascot installer moves it to a folder under the main Mascot folder called _install_backup.
  3. Compare the configuration files between config and _install_backup, and restore any local changes you had made (for example, quantitation methods).
  4. If you are updating from Mascot 2.4 or earlier, see the note about local modifications to unimod.xml in technical support under Known Issues.

Upgrading Mascot Server to use additional processors on the current hardware

  1. Go to your local Mascot home page and choose Database Status, Licence info, Register a new product key. Follow the instructions to register your upgrade key.
  2. After registering your new product key and downloading the licence file, go to the Database Status page and verify that the number of processors shows the correct, new value.
  3. The number of threads displayed for each active database should be -1, which means this setting is auto-determined. If the number of threads for a database has been specified as a fixed number, you may or may not wish to change this in view of having more processors available (Configuration Editor; Database Manager).

Additional steps if you have a Mascot Cluster:

  1. Stop the Mascot Service (Windows) or kill ms-monitor.exe (Linux).
  2. In the cluster section of config/mascot.dat, the number of processors in SubClusterSet 0 should be set to -1 (automatic). If it is a fixed number, you will need to change this to -1 or to the new number of processors.
  3. Edit config/nodelist.txt to change the numbers of processors on existing search nodes and/or add new definitions for additional search nodes.
  4. The operating system on each new search node must be configured exactly as described in Chapter 11 of the Installation & Setup Manual.
  5. Start the Mascot Service (Windows) or start ms-monitor.exe (Linux).

Migrating to new hardware

These steps are appropriate for:

  • Migrating Mascot Server 3.0 to new hardware
  • Migrating an older Mascot installation to new hardware, and updating to 3.0 at the same time

Preparation

The Mascot Server licence is locked to the hardware. Contact us in advance to request a 14-day temporary licence.

Download the Mascot Server 3.0 installation package. The link is normally sent by e-mail, or you may have received a paper booklet containing the link. Contact us if you cannot find the link.

Perform a clean installation on the new hardware

  1. Follow the instructions in Chapter 2 (Linux) or Chapter 3 (Windows) of the Installation & Setup Manual. This is manual.pdf in the Mascot installation package.

Ensure everything is working correctly in the clean installation

  1. Mascot Server ships with a copy of SwissProt. If you chose not to install it, enable it now: from your local Mascot home page, go to Configuration Editor then Database Manager; Enable predefined definition; SwissProt.
  2. Run a couple of test searches from a web browser on a different PC and make sure you can view the result reports. Fix any issues before proceeding.

Transfer configuration files

  1. If Mascot Security was enabled on the old system, copy across:
    • mascot/config/security_options.xml
    • mascot/config/user.xml
    • mascot/config/group.xml
    Then enable Mascot Security (Chapter 12 of the Installation & Setup manual).
  2. Other files in mascot/config that you may have modified are:
    • crosslinking.xml (if migrating from 2.7 or later)
    • enzymes
    • fragmentation_rules
    • library_mod_aliases (if migrating from 2.6 or later)
    • ML_adapters.toml (if migrating from 3.0 or later)
    • quantitation.xml
    • taxonomy
    • unimod/usermod.xml (if migrating from 2.5 or later)
    • unimod/usermod_xl.xml (if migrating from 2.7 or later)
    • unimod/specificity_visibility.* (if migrating from 2.5 or later)
    Use a good text editor or diff (Linux) or fc (Windows) to compare the old and new versions before copying any old configuration files to the new system.
  3. Note: If you are migrating from Mascot 2.4 or earlier, any local modifications you have made to unimod.xml are not preserved.

Transfer old searches (optional)

  1. Copy all your search result files from the old system to the new system: directories matching mascot/data/2* (for example, mascot/data/20240630). Do not copy mascot/data/test, mascot/data/cache or mascot/data/F*.*.
  2. Copy over mascot/data/mascot.job, replacing the file on the new system (this file contains the last job number).
  3. Copy over the search log mascot/logs/searches.log, replacing the file on the new system.
  4. Check you can open old search results using the links in the search log.

Transfer sequence databases (optional)

If you had only a few, mostly public databases active on your old server, it is easiest to enable them from the predefined database definitions in Database Manager on the new server. Doing this means that the configurations will be kept up-to-date automatically, and makes it easy to schedule automatic updating of the database files.

If you had a large number of active databases on your old server that you had configured manually, the instructions for migrating them are below. The instructions apply if you are migrating from Mascot Server 2.4 or later. When migrating from Mascot Server 2.3 or earlier, please contact us for assistance.

  1. Copy the sequence database directories and files to the new server. By default, these are stored in mascot/sequence but may have been stored in different path(s) on the old server.
  2. Compare the dates of the files in the mascot/taxonomy directory. If the files on the old server are newer than those on the new server, copy these files across to mascot/taxonomy.
  3. Copy across Database Manager configuration:
    • config/db_manager/public plus all the files it contains
    • config/db_manager/global.conf (if it exists)
    • config/db_manager/configuration.xml (replace this file if it exists)
  4. Open config/mascot.dat on the old server and scroll down to the Cron section. Copy all command lines containing dbman_add_task.pl to the Cron section of mascot.dat on the new system. (These lines define scheduled database updates, if any are active.)
  5. If the Mascot installation path is different on the new server, or if any path to a sequence database has changed, edit the following configuration files.
    • Before editing any file, make a backup in some other directory.
    • Check the Cron section in config/mascot.dat, and fix the paths to dbman_add_task.pl and dbman_process_tasks.pl to point to the corresponding scripts in the new server.
    • In config/db_manager/global.conf (if it exists), change the setting sequence directory under [default directories] to point to the new default sequence directory.
    • In config/db_manager/configuration.xml, do a global search and replace from the old sequence directory to the new sequence directory. The elements to target are msgd:current_path and msgd:incoming_path under msgd:databases. If you’ve set up sequence databases outside the Mascot sequence directory, you need to manually inspect the paths under msgd:databases and edit as necessary.
    • In config/db_manager/configuration.xml, do a global search and replace from the old UniGene directory to the new UniGene directory. The elements to target are msgd:path under msgd:unigene_entries.
    • In config/db_manager/configuration.xml, delete the lines starting from <msgd:mascot_dat_md5> and ending with </msgd:mascot_dat_md5>, including these tags.
  6. Go to your local Mascot home page, Configuration Editor, Database Manager. It will detect that configuration.xml doesn’t match mascot.dat anymore. Click on Fix mascot.dat. The list of databases should now match between the old and new servers.
  7. If you are migrating from Mascot Server 2.8 or earlier, then all the databases will be recompressed, because the index file format has changed in Mascot Server 3.0. Wait until the last database has finished compressing and all databases are online.

Register the permanent licence

  1. Contact us when you are ready to move the licence permanently to the new system. We will send you a unique replacement key.
  2. If updating from Mascot Server 2.3 or earlier: Copy the old licence file config/mascot.license from the old server to the mascot/config directory on the new server. Then register your replacement key.
  3. If updating from Mascot Server 2.4 or later: Register the replacement key normally.
  4. Finally, Mascot must be deleted or uninstalled from the old system.