While the Instrument Method Wizard lets you specify Smart Startup procedures and Smart Shutdown procedures, these only apply to the LC part of the setup. To shut down your MS instrument via the Chromeleon CDS software at the end of a sequence, you must end the sequence with an injection that runs a short instrument method that is dedicated specifically to shutting down the MS instrument.

Procedure

  1. In the MS part of the shutdown instrument method, define a full-MS scan acquisition that is sufficiently short, for example, 1 minute.
  2. In the LC part, define a gradient that ultimately turns off the eluent flow all the way down to 0 mL/min.
  3. If the previous method ran at an elevated temperature, configure the LC part of the shutdown instrument method to return the column to room temperature.
  4. To specify that the shutdown instrument method turns the MS instrument into Standby mode, open the Instrument Method Script Editor.
  5. Just before the Stop Run command, insert the delay command and set its value to 10 seconds.
  6. After the delay, insert the operatingmode command from the MSDevice category and set its value to Standby.
  7. Save this as a separate instrument method and assign it to a dedicated shutdown injection at the end of a sequence, when you want the entire system to shut down.