The current release of Mascot Distiller is version 2.8.0

If you are using an earlier version, you should download and install this free update.

The functionality contained in optional toolboxes will only be enabled if included in your licence. Please contact sales@matrixscience.com for information about licence upgrades.

Known Issues

Scaling issues with application level Windows scaling

There is a known issue if Windows is set to scale the Mascot Distiller Workstation GUI using ‘application’ level scaling. The symptoms are that the text on the explorer trees is too large and the spectrum or chromatogram graphics are outside the boundaries of their enclosing windows. To solve this issue:

  • Ensure that ‘High DPI scaling’ setting for MascotDistiller.exe is not set to ‘Application’
  • If you are connecting to the workstation with Mascot Distiller installed via a remote desktop connection, ensure that scaling is not set in the display settings on the remote system. Scaling should only be set on the client PC
  • If Mascot Distiller is running on a VMWare hosted virtual machine, ensure that the Display scaling ‘Automatically adjust user interface size in the virtual machine’ option is unchecked in the settings for the virtual machine in VMWare Tools

Batch automation using Mascot Daemon 2.4 and earlier

If you are using Mascot Distiller as a data import filter in Mascot Daemon 2.4 or earlier, you need to run the Daemon ‘service’ component on the desktop. Otherwise, it may run out of resources. Details of how to make this change are in the Daemon help under In depth; Mascot Daemon Service. Briefly:

  • Exit Mascot Daemon
  • Select the entry for the Mascot Daemon Service in the Windows services control panel, right-click, and choose Properties
  • Stop the service and set the startup type to disabled
  • When Mascot Daemon is next launched, it will be unable to start the service and will display an error message
  • Choose ignore

Exporting ion mobility values in peak lists using Mascot Daemon batch automation

If you are using Mascot Distiller as a data import filter in Mascot Daemon and you need to export ion mobility values in the generated MGF file, you need to enable a setting using the following procedure:

  • Log into Windows as a user with Administrator privileges
  • Type ‘cmd’ into the Windows search bar
  • Right click over ‘Command Prompt’ and click ‘Run as Administrator’
  • Navigate to the directory containing MascotDistiller.exe (by default this will be C:\Program Files\Matrix Science\Mascot Distiller)
  • Run the following command:
    • MascotDistiller.exe -batch -daemonMGFIonMobilityParam 1

Bruker CompassXtract

Clean installations of certain 64-bit editions of Windows may be missing a Windows library required by Bruker CompassXtract. The symptoms are that the Bruker provider is unavailable in Distiller and you get error messages about msvcr71.dll being missing when Mascot Daemon starts up. The fix is to download msvcr71.dll and copy it to C:\Program Files (x86)\Bruker Daltonik\CompassXtract

Occasionally, when updating CompassXtract, the installation fails with error number 1935. The fix is to run a Windows registry cleaner, such as the one from Auslogics.

Error when opening Bruker XMASS/XTOF files

When creating or opening project files from Bruker XMASS/XTOF datasets, Mascot Distiller can fail with an error similar to the following:

Unable to open data source. (Something unexpected happened.)
This occurs because two required files are missing from the 64-bit MDRO installation. If you encounter this, you can fix the issue using the following procedure:

  1. Close Mascot Distiller
  2. Copy the following two files from “C:\Program Files (x86)\Common Files\Matrix Science\MDRO” to a temporary location on your hard disk:
    • FlexVariableTable.xml
    • ICRVariableTable.xml
  3. Move the copies of FlexVariableTable.xml and ICRVariableTable.xml you have just made into “C:\Program Files\Common Files\Matrix Science\MDRO”. You will be prompted for Administrator access to do this
  4. Restart Mascot Distiller. You should now be able to open Bruker XMASS/XTOF datasets

Mascot Server Updates

Mascot Server 2.2

To perform quantitation using the Average or Replicate protocols, Mascot Server must be patched to 2.2.06 or later. Details can be found on the Mascot Server support page.

If you plan to use the Quantitation Toolbox, you can download an updated copy of quantitation.xml for your Mascot Server. (Right click the link and choose Save As.) This file is similar to the one in use on this site, has more methods than the original file, and some settings for earlier methods have been updated. Do not copy this file onto a Mascot 2.3 system; the file shipped with Mascot 2.3 is a later version.

Mascot Server 2.0

If you wish to use Mascot Distiller 2.x with Mascot Server 2.0, certain files on the server must be updated. Note that these updates are for Mascot Server 2.0 only. Mascot Distiller 2.x cannot be used with Mascot Server 1.9 or earlier.

Updates can be downloaded using the following links. The Perl scripts should be copied to the Mascot cgi directory, while ms-searchcontrol.exe goes into the Mascot bin directory. For Unix, the files need to be un-tarred and you may need to change ownership and permissions to make the files executable by CGI processes.