You seem to be talking about timer triggered ADC. You can do this. It is discussed in the SAM manual in 43.6.5. You can connect basically any of the timers so long as they are in waveform mode. This could all be a bit tricky if you are new to the whole process but look at the DueTimer library (GitHub - ivanseidel/DueTimer: ⏳ Timer Library fully implemented for Arduino DUE) for an example of how to set up timers. You will likely have to provide some different settings but the code will show you how you set things up. You have to do this same type of thing to configure the ADC as well. The Arduino core is not going to help you out with any of this.