I guess it can:

You can select SQL query analyzer selection, sql server trace table, workload file.

The easiest way to run it over on an entire sp: type "exec sp..." into Query analizer, than run the tuning wizard for this section.

The problem is (or may be) that you have to specify the parameters of the sp. (A large sp's behavior could be very different depending on it parameters.)

I prefer to run a profiler and than run the sp with several different parameters (with the commonly used parameters), than run the tunning wizard on the trace table.

I hope it helps