A method and system for adapting communication protocol between a host computer system and a peripheral computer system depending on the transport infrastructure used, so that communication can be optimized and/or customized to the transport mechanism used. A connection between the two computer systems is made. This connection is via one transport mechanism out of many possible transport mechanisms, such as a serial cradle, networked cradle, modem, cellular wireless, radio frequency, infrared, Internet, etc. The host computer system recognizes which transport mechanism is being used and determines the communication protocol based on the transport mechanism. For example, if the transport mechanism is low bandwidth wireless, the communication protocol may call for data encryption for security and data compression for economy. The communication protocol can be optimized for other parameters, such as authentication of the user attempting data transfer, and restriction on the data set to be transferred. The host system and peripheral computer then communicate using the determined protocol. In one embodiment, the parameters of the communication protocols may be updated by the user of the peripheral computer to affect only that user. In another embodiment, the parameters of communication protocols may be updated by a system administrator and affect all users of that system.