The current release of Mascot Distiller is version 2.8.2

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 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.

On Windows Server, when the installer tries to enable the .NET framework 3.5 feature (required by CompassXtract), it can fail with the following error:
Windows Server roles and features cannot be automatically installed or uninstalled via the Windows Features Control Panel.

If you encounter this issue:

  • Cancel installation
  • Manually enable the .NET Framework 3.5 feature from the Add Roles and Features Wizard in Server Manager
  • Resume the Mascot Distiller installer.

Mascot Distiller stops working after Windows 10 update

A cumulative Windows 10 update can break the Visual C++ 2012 redistributable package shipped with Mascot Distiller. If either Mascot Distiller or Mascot Daemon stop working after completing a Windows Update, please go to Apps & Features in Control Panel, scroll down to Microsoft Visual C++ 2012 Redistributable and check the version shown for the x86 and the x64 packages.

If either one is not 11.0.61030, please try the following:

  1. Close Mascot Distiller and Mascot Daemon
  2. Download and install both the x86 and x64 versions of VC++ 2012 Redistributable Update 4 from here
  3. Restart Mascot Distiller

Errors in Python reports can cause incorrect output

We have identified the following errors in some of the Python reports shipped with all versions of Mascot Distiller 2.8:

  • If you select a multiple testing false discovery ratio correction method for the ANOVA plus clustering report, then incorrect protein descriptions in the table below the heatmap can be shown
  • If you run the hierarchical clustering report, the table headers below the heatmap are not shown in the clustered order
  • The Table Peptides report can display the correct peptide ratio information, but the incorrect protein ratio information
To fix these issues, please apply the following hotfix:
  1. Download
  2. Extract the contents of the zip in the Mascot Distiller\reports directory. By default you will find this at C:\Program Files\Matrix Science\Mascot Distiller\reports and you will need Administrator access to do this.
  3. Re-run the reports to confirm that the issue has been fixed