GCMS won't start run without pushing the "Start" button on GC

My computer recently crashed and we lost all of our old files including our previous methods and data. We were using an older version of Chemstation (Saphire). We just got a new computer and MassHunter program set up through Agilent and the tech assisted us in making our method.

I was starting to run my first calibration with the new program and I seem to be having issues with starting the run, I set up a 12 sequence run, I can hear my headspace sampler sampling and setting up the run, the GC gets ready and the MS is awaiting the sample but when the sample should be going to the GC, the headspace sampler reads "Sequence aborted: external not ready" and the run stops. If I push the start button on the GC the sample continues as it should but the sequence does not continue.

Any suggestions? I was thinking maybe I'm missing a step in the program since we're basically starting from scratch.


I have a 7697A Headspace Sampler, 7890A GC, and 5975C VL MSD. And, as I said, we just had MassHunter installed.



  • Hello,

    when a sequence has been started:
    * observe GC:

       => is the pre-run LED permanently on?
       => is the pre-run LED flashing? (wait, or more than 2-5min: use GC status button for details)
       => if pre-run LED is permanently OFF:
                a) what is the status of the option "prep run on manual request"?
                      in: (menu) Instrument > GC configuration > (tab) configuration => checkbox: PrepRun on Manual Request

                b) what happens to the HS SEQ./sampler when the button preprun (1x) on the GC is pressed?

    * STATUS button on the GC : is there any indication of unready?


    * if the above points do not provide clear information:
          - method orientation, if old data files are available:
                the .D folder always contains a method "print" (as acqmeth.txt).
          - which start remote devices are connected to the GC APG port?
          - create LOG file collection after next error => (menu) Help > Gather diagnostic files

          - activate the GC status screen inside ACQ Masshunter:



    regards, M

  • Thanks for all the info!


    - The Pre Run light was off, I checked the status on the GC and the "Auto prep run" was off, I also checked the GC configuration tab in MassHunter and this showed that the "Prep run on manual request" was off as well.

    - When the Prep Run button is pressed on the GC, the HS sampler proceeds with the first sample which is then analyzed by the GCMS. After this first sample the run stops and sequence is aborted.

    - The Status on the GC shows that the system is ready.


    After this I played around with a few things, I checked the "Prep run on manual request" box in MassHunter, this allowed me to run my first sample without having to press the "Start" or "Prep Run" buttons on the GC, but after the first sample the sequence was halted again. When the second sample was ready to inject into the GC, the run time for the first sample was not yet complete, then the HS sampler aborted the sequence. I watched the GC Status Screen and while the first sample was running the GC ready state was "ready" and once the sequence was aborted the status screen read "GC ready state: not ready; Host: Not ready; Oven: temperature not ready"

  • jdevon,
    comment on the GC internal auto-prep run: it should never be activated when using Agilent software for GC control. In other words: if the GC internal autopreprun=on is used, there might even be some disturbances in the SW process.

    start remote cable:
    if the HS sampler is waiting for an GC unready & HS starts when the GC is ready again (even after pressing the prep-run button), then the cable is most likely OK.


    "prep run on manual request (PROMR) checkbox:
    * the previous test: press the GC "pre run button" & the HS sampler will continue => for me this indicates that the PROMR function must be activated inside Masshunter (GC driver)
    * note: the PROMR must not always be activated automatically, because there are Agilent sampler drivers that send a PrepRun to the GC automatically.
    * PROMR: is actually a global ACQ parameter but after changing it, the method/all methods must be saved/converted!!
    * PROMR is permanently deactivated after a PC reinstallation, from GC driver 3.x version on.


    So I would recommend the following test:
    * use one method for several HS vials/runs in one SEQ (after PROMR was activated)
    * for these test purposes it is recommended to use the method as "test-name" temporarily
    * if now all vials have been processed correctly:
       ~ the change PROMR is correct
       ~ PROMR should be used for all methods
       ~ additionally i would now use a test SEQ which contains more than one method.

    if the sampler should not continue its tasks, the GC status should be monitored:
      a) on the GC: Status button
      b) ACQ Software: GC status info
      c) Status LEDs on the GC (must light up permanently)
          Ready? Pre Run LED ?

  • Perhaps some info about the expected sequence of events would be helpful.


    1) The data system should prepare itself for a run started by a device other than the GC to start. (For the 7697, if you have the proper cable, that does not include setting "Prep run on manual request".) This happens when you start the sequence in MassHunter.

    2) The GC must be ready.

    3) The headspace sampler ("HS") finishes heating the vial and doing early preparation.

    4) The HS signals to the GC to prepare via the remote cable. This causes the PreRun light on the GC to come on. The Not Ready light on the GC may also come on. The GC may have to adjust pneumatics to become ready in the prepared state.

    5) Once the GC has become ready again, the HS injects and starts the run via the remote cable.

    6) The HS has a "GC cycle time" setting. That time must be long enough so that the GC can complete its run and become ready again in the "GC cycle time" interval, including getting zone temperatures back to the initial settings. The HS schedules its operations so that it will look for the GC to be ready for the next injection after the GC cycle time has elapsed after the previous run start.


    From reading your description, I'm wondering (1) whether you have the right part number for the remote cable so that the HS can signal to the GC that it is time for it to prepare, and (2) whether there is a setting in the HS that controls whether it signals to the GC when it is time to prepare. Also, it sounds like you don't have the GC cycle time set long enough so that the GC run is complete when the HS is ready to start the next run, much less long enough to let the GC become ready again after the run completes before the HS has the next sample ready.


    I hope this helps.

  • hello ,

    since i would like to learn from the ideas of all the authors:

    did anything help?

  • I apologize for not getting back to you sooner.

    It turns out that the issue was that the GC method was running too long for the time sequence that the sampler was set on. The sampler was wanting to inject before the GC was ready causing the sampler to abort the sequence.  All I had to do was shorten the GC method timeframe.


    Thanks for your time and help!

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