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

Mascot Server version 2.2

Patch to 2.2.07 before updating unimod.xml

The error tolerant search in Mascot 2.2.06 and earlier has a limit of 1024 modifications. The number of specificities in Unimod has recently exceeded this limit. To avoid problems, ensure you update to 2.2.07 before downloading the latest unimod.xml. For Windows, the service pack can be downloaded from this page. For Linux and Solaris, email to

Installation Tips

Windows Vista: Mascot will run under all Windows Vista editions except for Starter and Home Basic. Before installing, refer to this important information concerning IIS7 configuration.

Windows Server 2008: Mascot will run under all Server 2008 editions except for Core. Before installing, refer to this important information concerning IIS7 configuration.

Windows 7: Mascot will run under all Windows 7 editions except for Starter and Home Basic. Before installing, refer to this important information concerning IIS7 configuration.

Installation troubleshooter for Windows version 2.2.01 only.

Windows update procedure

All version 2.2.x patches have been collected into a single executable file. This will update earlier 2.2.x versions to the latest revision. It will not update files from 2.1.x and earlier versions.

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. In most cases, this will only affect two files: (i) quantitation.xml, if you modified or added any quantitation methods, (ii) enzymes, if you modified or added any enzyme definitions.

  • 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. If your Microsoft Windows Installer is an out-of-date version, you will get the following error message: This patch package could not be opened. Contact the application vendor to verify that this is a valid Windows Installer patch package. (0×80070664). Usually, this will only be encountered on a system isolated from the Internet or where Windows Automatic Update is disabled. The fix is to update Windows Installer by downloading the Windows Installer 3.1 Redistributable from Microsoft.
  • After the patches have been installed you can delete the executable.
  • This self-extracting patch archive was created using 7-Zip, which is licensed under the GNU LGP Licence. The source code for 7-Zip can be downloaded here.

Available Fixes

  • 2191: Add /LARGEADDRESSAWARE flag for Windows
  • 2233: Installer fails to set permissions on all files
  • 2443: Progress reports are slightly off for NA searches with FRAMES
  • 2444: Various minor Configuration Editor bugs
  • 2447: Confusing error message from Daemon with security and Integra user
  • 2448: fails with Integra system user when security is enabled on Linux
  • 2452: More minor Configuration Editor bugs
  • 2454: mod_file should be re-written whenever a process changes it
  • 2457: Installer fails if IIS web site is bound to a specific interface or URL contains an IP address
  • 2458: Need to set correct permissions on unimod.xml and quantitation.xml
  • 2465: Mascot Daemon 2.2 no longer works with IIS integrated authentication (2.1 was OK)
  • 2466: Need to leak bytes in additional place for quant reports to keep connection alive
  • 2467: ms-monitor fails when shutting down under Windows with ms-lockmem enabled
  • 2471: PMF speed improvements
  • 2472: Multiple instances of too many ions error in mzData causes nph-mascot.exe to crash
  • 2473: Cannot have space in lcq_dta.exe path name in Daemon
  • 2477: Modifications defined locally in one spectrum being used for match in other spectra
  • 2478: Perl scripts outputting http headers with charset=ISO-8859-1. Should be utf-8
  • 2479: Matches being reported for invalid etags
  • 2481: Peptide view and master results might show different set of potential modifications fro error tolerant match when 13C>0
  • 2482: Speed improvements for etag searches
  • 2484: Export help not clear
  • 2485: takes a sessionID parameter, but doesn’t pass it on to ms-getseq.exe
  • 2486: New configuration file to support modification name aliases
  • 2487: Improve support for Vista
  • 2488: Installer needs to configure IIS 6 to enable cgi and x-cgi executables and Perl scripts
  • 2489: The Mascot paths in the registry now have a trailing slash.
  • 2494: Daemon fails to pass through Distiller error messages
  • 2497: Mysterious crash while writing results file for nucleic acid search
  • 2498: Improve error reporting in scripts when something goes wrong and a graphic is missing
  • 2506: URL arguments for quant formatting not being passed to export script
  • 2507: Problems with drag and drop to repeat a search in Daemon
  • 2511: MS/MS search speed improvements
  • 2512: primary_nl string could be incorrect if multiple peptide matches with identical scores
  • 2519: State of hide error tolerant checkbox not passed to protein view
  • 2520: Protein view and enzymes created by config editor are incompatible
  • 2522: Increase range of charge states available in lcq_dta_shell
  • 2524: Intermittent crash with integrated ET search and sequences with ambiguous residues
  • 2525: Not pulling new files for 2007 ASMS workshop
  • 2528: Could get memory overrun causing a repeat search to crash under Windows
  • 2529: Table of matches at bottom of peptide view doesn’t always agree with pop-up in master results
  • 2530: Scripts and parser had different upper limit on significance threshold
  • 2536: Added support for "Big" Mascot.
  • 2542: Fixed performance issue in "" resulting from fix for CR#2529.
  • 2543: Remove legacy uninstall entry for Mascot in “Add/Remove Programs”.
  • 2550: Isotope correction for multiplex quantitation was not implemented correctly.
  • 2551: Modified AB correction code in “”.
  • 2562: Protein View report returns an error for hits without any significant peptide matches.
  • 2563: Submitting a search from clients such as Mascot Distiller and Mascot Daemon results in spurious "Failed to lock file" messages in the error log.
  • 2572: Database maintenance utility corrupts a Windows group name that includes non-ASCII characters, which causes "SetEntriesInAcl" errors.
  • 2584: In cluster mode, automatic decoy search only performed decoy part on the first node.
  • 2592: Uninstall removes some potentially useful config files.
  • 2629: Rare crash on Windows cluster. No message in error log files
  • 2663: Crash with multiple subclusters
  • 2670: Error M00248 – Invalid taxonomy name class (authority |) and (unpublished name |)
  • 2673: Spurious ‘Too many modifications’ message for quantitation method
  • 2694: Can’t lock both SwissProt and NCBInr on Server 2003 (x64) cluster
  • 2697: Crash with average quantitation protocol and no variable mods.
  • 2735: MS/MS mzData file fails with out of memory if first spectrum is MS with ~ 8000 peaks
  • 2744: Test search fails with multiple sub cluster
  • 2751: Error M00251 – taxonomy indexes ignored when number of threads very large (> 20).
  • 2832: Can’t repair, update or remove Mascot 2.2 if Perl is upgraded to 5.10.
  • 2838: Error tolerant searches fail with new unimod.xml – too many mods.
  • P581: Intel Dunnington and Nehalem processors now supported on Linux