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How to start up or pump down a powered down mass spectrometer - WKB1049

Article number: 1049


Take a fully powered-down system and get it pumping and into Operate.

Start up a QTof from complete shutdown.


  • MassLynx 4.1
  • Q-Tof Premier
  • LCT Premier
  • Synapt
  • Synapt G2
  • Synapt G2 S
  • Synapt G2 Si
  • Xevo QTof
  • Xevo G2 QTof
  • Xevo G2 S QTof
  • Xevo G2 XS QTof


  1. Power-on the host PC and then log into Windows.
  2. Power-on the LC and let it initialize. 
  3. Make sure the vacuum override switch is in the Auto position. This is the upper toggle switch on XEVO instruments, and is mounted above the four power switches on Synapt and QTOF P instruments. On an LCT P it is located inside the instrument on the power module and cannot be accessed without removing the covers. Powering on the instrument with the vacuum override switch in the Override position will cause the vacuum pumps too start immediately and without the programmed delay sequence, and can damage the pumps. 
  4. For a Synapt, QTof P, or LCT P: flip the vacuum and then the electronics breaker, wait a minute, and then flip the epc and aux breakers. For a Xevo, make sure the MS power cord is plugged in and both toggle switches on the back (middle-bottom) are in the up position.
  5. Wait 5 minutes, or until the white/purple light stops flashing on the Synapt G2/S/Si.
  6. Go into MassLynx and open the tune page.
  7. From the tune page, pump the instrument down using vacuum (from the top drop-down menu in the middle of the tune page) and select pump. The MS will pump down faster if the isolation valve is closed and the argon or CID/trap gas is on. Be sure to open it before going into Operate mode. For a G2/S/Si QTof, pump down from the MS console by selecting Operate. This method is better than pumping from the tune page because it puts the instrument into Operate once the vacuum is good; Be sure to open the ion block isolation valve once the system has been pumping for a 20 to 30 minutes.
  8. If you are not pumping down using the console, open the isolation valve and put the instrument into Operate mode once the Tof vacuum is less than 1.2e-6 mBar.
  9. For a Q-Tof Premier, Synapt G1, or LCT Premier, the MCPs must be conditioned.
  10. Once the MS has been in Operate for an hour, you can calibrate. If the system was vented for a while (days), it is best to wait until the mass spectrometer is close to the previous vacuum before calibrating.


To vent and shut down the instrument, see Article # 1047 - How to shut down my QTof.

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