A peripheral is something like a UART or a TIMER pin.
Essentially, each pin can have one of three functions:
GPIO (PIO Controller) Example: PA0
Peripheral A (varies depending on pin.) Example: CAN TX0
Peripheral B (varies depending on pin.) Example: PWML3
There's a big table in chapter 9 ("Perpipherals") (page 40 in my datasheet) listing all the possibilities for each port pin.