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

Mascot Server version 2.5

Updating and upgrading procedures

Known Issues

Database Manager

Database Manager cannot download Fasta files generated by Uniprot database queries, such as Uniprot proteomes. The work-around is to download the Fasta file manually, as described here. Note that downloads of the full Swiss-Prot or Trembl databases are not affected. Also note that you should not attempt to enable any of the predefined Uniprot proteome databases, because the downloaded file will contain all Uniprot entries, not just those specified in the query.

Perl 5.8 or 5.10

With Perl versions 5.8 or 5.10, if a predefined database definition is enabled in Database Manager but the download is cancelled, it is possible to get the following fatal error:

Cannot handle date (00, 00, 00, 01, 0, 2070) at ../bin/modules/Util/ line 91

If you encounter this error, the fix is to update to the ActivePerl included on the Mascot Server 2.5 program CD. After updating Perl on Windows, locate Mascot Server in the programs and features section of the Windows control panel and choose Repair. Instructions for installing ActivePerl on Linux can be found on page 6 of the manual. You will also need to follow steps 1 and 2 (only) of the Installation Script, as described on page 10 in the manual, to create a new soft link for the Mascot Parser Perl module.


The list of modifications used by Mascot is taken from Unimod by downloading the database contents in XML format (unimod.xml). In Mascot 2.4 and earlier, if you wanted to change a modification or add a new one, this could be done using the Mascot Configuration Editor or, if you were very brave, by editing unimod.xml. The unsatisfactory aspect of this was that any changes were lost if you downloaded a fresh copy of unimod.xml.

This has been improved in 2.5 by saving all changes to a separate file and merging this with the downloaded file to create the working copy of unimod.xml. The Modifications module of the Configuration Editor has a button (Check Unimod) which looks to see whether a newer unimod.xml file is available. If so, you can choose to download it. The downloaded file is re-named to master.xml and saved to the mascot/config/unimod directory. Any local changes you make using the Configuration Editor are saved to a separate file called usermod.xml in the same directory. When the Mascot Monitor service sees that either file has changed, it merges the two files to create a new unimod.xml in the mascot/config directory. (Note that this means you should never edit or update unimod.xml … your changes could disappear at any time.)

If you are updating to Mascot 2.5 from Mascot 2.4 or earlier, and only have a small number of changes to your local list of modifications, the easiest solution is to re-enter them one final time using the Configuration Editor. If you have a large number of changes, rename your old unimod.xml file to usermod.xml and copy it to mascot/config/unimod, over-writing the existing file. A few seconds later, a new unimod.xml will be created automatically in mascot/config. The only time this won’t work is if you had edited unimod.xml to create a new entry in the elements or mod_bricks sections. If this is the case, please contact support for guidance.

One glitch: when updating from 2.5.0 to 2.5.1, the Windows service pack will replace the existing usermod.xml with a clean file. So, you may need to recover the previous usermod.xml by copying it from _install_backup\config\unimod to config\unimod

Distiller multi-file quantitation when Mascot Server runs in cluster mode

There is an issue when all of the following apply:

  • Mascot Server 2.5 is running in cluster mode
  • You create a memory efficient, multi-file project
  • You perform quantitation

Under these conditions, only the quantitation results from one of the files are reported. The fix is to increase SplitNumberOfQueries in the Options section of mascot.dat to a large value, e.g. 1000000. This will make large searches slightly slower because some of the improvements introduced in 2.5 for cluster mode are bypassed. Remember to undo this change and revert SplitNumberOfQueries to 1000 when a fix is released (bug 12059).

Installation Tips

Windows Vista and later: It is essential that IIS is correctly configured before installing Perl or Mascot. Refer to Chapter 3 of the Mascot Server Installation & Setup Manual for details.

Windows update procedure

All version 2.5.x patches have been collected into a single executable file. This will update earlier 2.5.x versions to the latest revision. It will not update version 2.4 or earlier to version 2.5.

Note: If the service pack needs to replace any configuration files or Perl scripts that you have modified, it will move your modified file to a Mascot sub-directory called _install_backup. Inspect any files placed in this directory to see whether you wish to merge your changes into the updated files.

  • Locate your original Mascot installation CD, which may be required during the update
  • On the Mascot Server PC, as a user with Administrator privileges, click on the appropriate download link and either choose Run or Save the file to your local hard drive and then execute it.
    x86 for 32 bit Windows: MascotServer_SvcPack_2_5_1.exe (14 Mb)
    x64 for 64 bit Windows: MascotServer_x64_SvcPack_2_5_1.exe (23 Mb)
  • After the patches have been installed you can delete the executable.

Linux update procedure

All version 2.5.x patches have been collected into a single archive. This will update earlier 2.5.x versions to the latest revision. It will not update version 2.4 or earlier to version 2.5.

  • Check that there are no searches running on the server
  • Kill ms-monitor.exe
  • Download the archive to /usr/local/mascot (or to wherever Mascot is installed)
    mascot_2_5_01_patch_x86_64-linux.tar.bz2 (124 Mb)
  • Unpack the files, replacing those from the earlier version, (the –backup option creates backups of the files that are overwritten)
    tar -jx --backup -f mascot_2_5_01_patch_x86_64-linux.tar.bz2
  • Ensure that the ownership of the files matches the user ID that your web server is configured to use. The .tar file has been created using root:root. The required ID when Apache is installed from a RedHat RPM will be apache:apache, and when installed on Ubuntu or Debian, it will be www-data:www-data
    find . -user root | xargs chown apache:apache
  • Start ms-monitor.exe

Fixes included in this patch

  • 5652: Windows 2003, 2008, 7: ForkForUnixApache is unreliable
  • 10966: Add option to create results cache files and report progress to ms-searchcontrol.exe and
  • 11333: PercolatorMinQueries default value is too low.
  • 11354: Exporting as Mascot DAT fails if InterFileBasePath has lowercase drive letter
  • 11476: Test in enzyme editor cannot cope with CR in sequence
  • 11523: Report Builder sometimes fails to load
  • 11543: Security misbehaves when user is web authenticated
  • 11771: Update mzTab export output to 1.0
  • 11783: Update mzIdentML controlled vocabulary to 3.64
  • 11784: Fix the back button in the search form
  • 11806: Mark p-values and standard deviation for protein quant with weighted average unavailable
  • 11825: ms_inputquery and ms_searchparams are slow when called frequently
  • 11826: Allow non-alphanumeric characters in ratio names in Report Builder
  • 11842: Intermittent crash on all OS. Occurs most often on Linux multi-core systems.
  • 11843: Too many open files when database is not memory mapped
  • 11845: Some new/delete operations occurring in search threads. Can affect memory performance.
  • 11846: Test search printout missing from manual
  • 11847: Default amino acid configuration assigns J as (Iso)leucine.
  • 11848: Database file .nam not moved to old directory after upgrade.
  • 11851: With guest account enabled, user name and email not passed through
  • 11853: Selected mods are not passed through to the search when using admin account
  • 11854: Mascot crash if using taxonomy filter with non memory mapped db.
  • 11855: Negative elapsed time in search status if server hardware clock is out of sync.
  • 11856: Modification stats missing ET mods
  • 11857: ET pass not finding match found in first pass
  • 11858: Windows installer should always now set ForkForUnixApache to 0
  • 11860: DB Manager needs to check perl paths in cron section of mascot.dat
  • 11861: Using a very long filename crashes monitor at the end of the test search.
  • 11862: Searching the unassigned list on for an existing Mr(calc) highlights the entries but gives an error message saying it wasn’t found
  • 11863, 11891: Full name not loaded from master.xml for 4AcAllylGal due to ‘alpha’ character, Linux only.
  • 11872: Strong match missing from error tolerant search.
  • 11873: Not all ions labelled correctly in when using local modification
  • 11875: Use of uninitialized value’ when searching fixed mods in Unassigned tab
  • 11877: Export to XML formats sometimes fails under Perl 5.8 and Perl 5.10
  • 11880: Show tooltip when standard deviation or p-value is not available
  • 11881: nph-mascot.exe should return fatal error if search submitted and ms-monitor.exe not running
  • 11882: ms-status.exe Show=MS_STATUSXML can report errors using invalid XML
  • 11883, 11915: Allow normalisation to selected peptides or proteins for summed intensities
  • 11884: Sort order of available columns in Report builder
  • 11885: Attempting to call function matrix_science::ms_peptidesummary::getPeptide before createSummary() has completed
  • 11888: Support VS 2013 in Parser
  • 11890: Multiline FILE section in mime input from Proteome Discoverer causes error in cluster mode
  • 11892: Specificities visibility in configuration editor not allowing for multiple sites of the same name that differ by position.
  • 11895: Doubly charged fragments not labelled on new MS/MS graphic
  • 11896: Query-level modifications: neutral losses in Unimod section should be sorted by mass
  • 11898: Be more robust against invalid proxy URLs
  • 11899: findSpecGroup() sorts modification sites incorrectly
  • 11900: DB Manager throws fatal error when unpacking taxdump.tar.gz in Perl 5.18
  • 11901: New progress doesn’t refresh if connection is lost
  • 11907: Quantitation parser functions should allow a peptide to be excluded if it matches more than one component
  • 11914: Don’t allow FASTA filepaths longer than 255 characters
  • 11924: Multiline error messages in search status are shown as one line
  • 11925: Warn if accession contains white space
  • 11929: Setting user type to Web Authentication actually sets it to Agent String
  • 11933: Descriptions not displayed for report clustered using UniGene
  • 11936: doesn’t accept sessionID URL argument
  • 11937: Implementation of ms_peptidesummary::willCreateCache function that doesn’t require a ms_mascotresfile object
  • 11938: Crash with lots of local mods
  • 11943: emPAI values too high for searches with query level varmods
  • 11945: AA substitutions are being listed in and the search form
  • 11951: SVG Spectrum Viewer fragment annotation lines should be black
  • 11952: Make nph-mascot.exe output the percolator .pip file
  • 11959: ms_mascotresfile::getRepeatSearchString() needs to be faster
  • 11960: Open cache files for writing as soon as possible to reduce potential problems with multiple processes trying to create at the same time
  • 11965: Vanilla search crashes against mus_EST database
  • 11977: Add boolean parameter to loadPepMatchesForProteinFromCache to control whether the entire protein family is loaded
  • 11981: Need to be able to set masses of J, O and U to 0. Confusing if you delete the definition for Pyrrolysine in the config editor, still get O=237.147727
  • 11989: version parse rule for EBI EST not working
  • 12006: Search form in IE8 or earlier: ‘Can’t move focus to the control because it is invisible, not enabled, or of a type that does not accept the focus’
  • 12008: Top down searches fail with error M00454 if security is disabled
  • 12012: Deep recursion on subroutine ‘DBManager::Workhorse::CLI::_GET_request_filepath’ at ../bin/modules/DBManager/Workhorse/ line 3821.
  • 12013: Modification specificities comparison not allowing for multiple sites that differ by position
  • 12014: Modification used to obtain match is not listed in result file
  • 12017: Database Manager accepts \\w in parse rule and interprets it as a character class
  • 12030: Divide by zero in get_ms_mascotresults_params()
  • 12038: bool getAveragePeptideIntensity of ms_ms1quantitation doesn’t work from Java
  • 12040: Mascot crash. Running Swissprot test search on Windows 2012 Server in cluster mode.
  • 12044: Recreate default usermod.xml if missing.