Is 6230 TOF safe pumped down, but without TOF electronics turned off?

Recently, after a pump down and HV conditioning sequence, TOF electronics shut off without any obvious error. Seems to have been software related, but I don't want to keep attempting to condition the electronics in order to troubleshoot. This happened during COVID-19 lab shutdown. Is it okay to leave it in this state (Vac+N2 on, but TOF electronics off) for extended periods? Or should the HV electronics be conditioned and the entire instrument left in Standby? I can't find any relevant resources on this.


My understanding is that as long as the internal electronics are protected under vacuum, they should be fine on or off.

  • HI lcomb,

    How long was the TOF pumping before you tried to condition electronics? Did the TOF icon go red?  What do you consider extended time? As long as you know you will have good clean uninterrupted N2 and uninterrupted power you should be ok.

  • Using the Diagnostic program, I set the instrument to pump down and do subsequent 8 hour HV conditioning (per the manual) in order to bring the instrument up in standby. The instrument had down just fine overnight and the vacuum was at the levels specified in the manual, but yes the TOF light is red.


    There is no anticipated change in N2 and power currently which is why we were intending to leave it in Standby for the foreseeable future. Extended time would be 6 weeks (anticipating no research in this time), but I of course have access and can do maintenance on the instrument or shut it down completely if necessary.

  • Sorry, meant to say: it pumped down just fine, vac at good levels, but the HV conditioning seemed to not have worked and the TOF light is red.

  • Hi,

    When you were doing the High Voltage conditioning, did you also check 10kV portion. This is not available in Acq B.09 or higher.



  • As long as you are positive that there will be no interruption to the nitrogen and electrical supplies, you can leave the system in standby. 


    The thinking on the HV conditioning has evolved over time.  As Mitch mentioned, the 10kV conditioning is still available in older versions of QTOF Diagnostics, but it should never be used.  Currently, the only time we recommend to perform conditioning is at install, or when service has been performed in the stage 5 vacuum region (detector replaced, flight tube removed, etc.)  The HV conditioning has been removed from the PM checklist as it is no longer recommended after venting to clean ion optics.


    Here are the shutdown instructions we've been sending customers.  This is for the QTOF but it applies to TOF as well.




    1. If you have an uninterrupted drying gas source (N2 generator) we recommend that you put the system into Standby.  However, if there is a possibility of power interruptions or gas shutoff (e.g. air feed into the N2 generator) we recommend completely powering off the instrument as described in the steps below document.


    1. If you have an interrupted drying gas source (dewars) we recommend venting the system following the procedures below. Please note the importance of waiting for the vent to complete (turbos spin down), and running the Smartcard shutdown script before powering off at the front button.


    Shutdown/Vent Procedure for 6530, 6545, 6545XT, 6550, 6560 (NOT 6546)

    1. Place system into Standby
    2. Wait 30 minutes for source to cool off.
    3. Select Vent in MS Tab of QTOF
    4. Wait 30 minutes after starting vent
    5. Check vacuum in MS actuals screen (760 torr is atmosphere)
    6. Run SmartCard shutdown script
    7. Go to main power switch on QTOF and switch to OFF
    8. After vent is complete, Source should be COLD. Remove spray shield, place Thick GC rubber septum inside spray shield and place back onto system.
    9. Turn off the power to the PC and monitors
    10. Turn down pressure on N2 Gas lines to 0 psi and turn valve off
    11. Disconnect the nitrogen line between the valve and the filters
    12. Cap the nitrogen tube going to the filters with a Swagelok cap
    13. Unplug the power cords from the system


    Hope this helps!

  • Thanks for the help,

    What I failed to mention in my poorly worded initial post is that the issue was trying to bring our instrument up in standby. I had vented it, thinking we would store it this way for some time. After having done so, I was informed from our Agilent rep that its better to leave it in standby. Since I had only just vented it, I decided (maybe mistakenly) that it was better I bring the instrument back up in standby as our building has constant N2 supply and we are anticipating no change in power supply. I followed the manual to do so, selecting pump down and 8 hour HV conditioning in the diagnostic window (instrument is only a few months old, so I'm not familiar with the 10kV process you are referencing). I left the instrument overnight to do this. The following morning, the pump down was successful but it appeared the TOF electronics had not come online or anything. I attempted the HV conditioning again and this time it worked, the light changed to yellow, the values looked fine, etc. I then went to open the data acquisition program, which wouldn't connect for some reason and the TOF electronics turned off at this point. Since then, I have been afraid to meddle to much as I have minimal experience with these instruments. So currently, vacuum levels are good, but light is red because the TOF electronics themselves are off (Showing "Not Ready" in diagnostic panel).

  • For some reason the 6230s will stay in an 'insufficient high vacuum' error state for a few minutes after being powered on/power cycled and Acquisition is open.  Generally this state will clear in a few minutes.  You can also try to manually clear the error in QTOF Diagnostics using the button in the lower right hand corner:

    Also, if Diag is configured so that you can access the SC Readbacks tab, you can query the instrument to see what the error message is.  Go to the SC Readbacks tab, then click on run state:

    Any error should be shown.  Please let me know what you find.

  • Problem resolved! Thanks!


    I clicked "Run State" and it showed a fault in communicating with the TOF. I clicked the "Recover Fault" button and the fault cleared. I think the instrument has been fine and in standby this whole time, but for whatever reason the fault problem in communicating with the instrument was showing it as off.

    After clearing the fault, everything immediately was reading as it should in the diagnostics window for standby and the light changed back to yellow. The acquisition software also opened without a hitch.

  • Great!  Thanks for reporting back.

  • This question has been marked as assumed answered.

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