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Mass Spectrometer missing from MS Console - Solution 3 - WKB11456

Article number: 11456


  • The mass spectrometer is missing from the MS console.
  • The console only shows the ACQUITY.
  • Rebooting the PC does not resolve the issue.
  • May have an Unhandled Exception error: 


  • Xevo or Synapt G2 Mass Spectrometers
  • Any Waters Mass Spectrometer that should show up in the console


Corrupt xml files


  1. Exit MassLynx.
  2. Run the StopACQUITYProcesses.cmd from "C:\Program Files (x86)\Waters Instruments\Bin". 
  3. Navigate to C:\MassLynx\Intellistart\Configuration.
  4. Rename any of the xml files that are blank when opened. The usual culprit is UserCustomConfigurations.xml, but there could be more.
  5. Restart MassLynx. The deleted corrupted xml files should regenerate automatically. If not, repeat steps 1 through 3 and replace the corrupt xml files with files from another instrument. If you have no access to "good" xml files, contact Waters Technical Support at 1-888-292-8377. 


In one case it was reported the new files were found in  following location: C:\Users\administrators

This solution has also worked in cases where the MS was missing from the console but no Unhandled Exception error pop ups occurred.

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