The current release of Mascot Distiller is version 2.6.2

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

Thermo Orbitrap Fusion Lumos data

There is a new version of Thermo MSFileReader available that fixes a scan hierarchy problem with some Orbitrap Fusion Lumos data. The symptom is that scans in the Mascot Distiller explorer tree are displayed in strict scan order, which means the parent child relationships of Survey, MS2 and MS3 scans are incorrect. If unsure whether this applies to your data, compare the scan hierarchy for the same raw file in Distiller and Xcalibur.

The fix is to download and install MSFileReader 3.1 SP4 from the Thermo software support site (requires registration). This will update XRawfile2_x64.dll from version to Note that Thermo no longer supports 32-bit Windows, and this update will only fix 64-bit Distiller.

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

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.

Windows Server 2003 SP2

Microsoft .NET installation will fail on Windows Server 2003 SP2 unless the Windows imaging component is installed. Before trying to install Distiller, download and install WIC using one of these links:

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.