To do what you need to do certainly possible, but will be difficult in that you will have to write the protocol drivers for the PPP connection yourself--though you might find a set of drivers someone else wrote. The good news is that the protocol is well documented:
http://www.ietf.org/rfc/rfc1331.txt
The bad news is that the referenced document is a decade old and there have been numerious extensions made to the original protocol. Hence, you will probibly need to get and understand the protocol in a fair amount of detail even if you get someone's drivers.
For more research into this do an Alta-Vista search for "point-to-point protocol" (including the quotation marks).
Note that the serial port doesn't know (or typically care) what the format of the
data passing through it is. So there really isn't any shifting between "modes" as such.
What instrument are you trying to talk to?
Mike...
mporter@arielcorp.com