Hey,
I don't know what Pro Tools is capable of doing, but I'm sure that it can sync to something called MTC (MIDI Time Code).
1. Set up the the MPC to transmit MTC as the master.
2. Set up Pro Tools to receive MTC as the slave.
3. Connect a MIDI cable from the MPC MIDI out and plug it into the MIDI in on your computer...I don't know if the Digi001 has a MIDI port, if it doesn't you will have to buy a MIDI interface to install onto your computer.
4. Hit play on the MPC.
When you hit play, the MPC will send MTC down the MIDI cable and into Pro Tools. The MTC essentially says, "Hi, I'm a sequencer and I'm sending some timing messages so that we work together at the same speed".
When Pro Tools hears the MTC from the MIDI cable, it says, "Hi, I'm Pro Tools and I can hear the timing messages you're sending me, let's work together at the same speed".
If everything is set up correctly, Pro Tools should start recording audio from the audio inputs of the Digi001...
If this is too much of a pain, you could simply just hit record in Pro Tools, then play on the MPC and record it freely...one of the benefits of an editor like Pro Tools is that you can graphically move the audio tracks around so that they line up.
Feel free to ask of you have any more questions,
Nick