Rebooting computer: G6530B QTOF

Not entirely sure what you mean by "smart shutdown", but rebooting the PC doesn´t affect the QTOF at all. There is a computer with an operating system in the instrument, the SmartCard, so the QTOF can run on it´s own without being permanently controlled by an external PC. However, shutting down the so-called engines (software proceses) is still something I would do before rebooting.

Shutting down acquition completly is a two step process- closing the User Interface (MH Acq) and closing the MH Acq Engines (rocket in the icon panel on the botttom right of the screen).  You can right click on the rocket and select shutdown engines.

If you are referring to the Shutdown SmartCard utility, I would only run this before power cycling the MS or maybe as part of troubleshooting. 

Thanks for your advice! Sorry I meant as operate SmartCard before rebooting.

I was confused some people operate SmartCard before rebooting, and some people don't.

Appreciate your help!

Thank you for giving me some details. Appreciate your help!