Before injecting a sample to the MS there are a few steps to prepare the instrumentation.

Start Up

  • If using the LC, turn on each componant of the LC (towers on the left).  The LC is comprised of the degasser, pumps, mixers, columns, auto sampler and the diode array detector (DAD).
  • Depending on which program was used last the MS may not be configured to “talk” with the LC.  Ensure this connection by right clicking the Voyager Engine Launcher.
    Launcher icon

    Launcher icon

  • Turn Engine off by left clicking Shutdown Engine. The icon will turn red.
  • Open Instrument Configuration from the desk top.
  • Make sure that the Mass Spectrometer box is checked, Agilent 6200 series Time of Flight is selected and if using the LC components check the Agilent LC Systems Access box.  Click OK.
  • Return to the rocket shaped Voyager Engine Launcher button, right click icon and then left click Start Engine. Now that the engines are on the date can be shared between instruments.  Note: If there is an error it is usually due to the LC components not being turned on.  
  • Next click Data Acquisition, a red monitor shaped icon on the bottom left of the screen. This is where you can calibrate or tune the MS to your needs and manage your sample method.
    Data Acquisition Icon (in red)

    Data Acquisition Icon (in red)

  • Turn instruments on with green On button.


  • Before adding samples it is often beneficial to run a tune program.  In the upper left hand corner of the screen is a context box.  It can be set to Acquisition or Tune.  Select Tune.  The instrument status bar will indicate when the each component is ready to operate. There should be five instruments listed: HiP Sampler, Binary Pump, Column Comp., DAD and TOF.  The DAD needs time to warm up, but it is not advised to avoid this delay by leaving it on because the bulb may wear out prematurely.
  • Ensure that the Ion Source matches the one being used in this case it is Dual AJS ESI, select Ion Polarity for either positive or negative.
  • Check that the tune mix in the MS is appropriate for your tune, there is a high concentration mix labeled + tune 100% for a positive ion application and a lower concentration mix, labeled negative tune mix.
  • The MS needs to be told which bottle your calibration mix is in, double check that the bottle selected in Calibrant Bottle matches your tune mix.  Generally this is B.
    Reference on the left, and calibration bottle on the right.

    Reference on the left, and calibration bottle on the right.

  • If the LC’s pump is on switch the LC Stream to Waste while tuning.
  • In the center box click on the autotune tab, select positive or negative (depending on your needs) and a tune program such as Quick Tune, or Check Tune.
  •   Select Start Autotune.
  • Select Tune Report, and then Print.
  • This printed copy can be added to the binder beside the printer and the file saved.  Each new tune file overwrites to preceding one.