Alizor |
Pathfinder Lost Omens, Rulebook Subscriber
Unless it says character level the ability would be determined by class level. In the case you describe the specialist abilities would be determined only by wizard levels. However as 3.5 material, the Master Specialist would need to be converted. I can't remember off the top of my head, but it wouldn't be too difficult to convert the PrC to include a progression of the original Specialist abilities.
Just remember while converting that you do need to take balance of the classes into account. If the master specialist barely gives anything up to start the class, then the reward over straight wizard shouldn't be too large. You "shouldn't have your cake and eat it too" effectively.