Prowl first mentioned that Processor over matter is a technique that a trained Cyber-Ninja can use. Although he never finished his actual training, he was able to use it to break out of his Stasis cuffs and save Optimus Prime.
When Prowl and the others were in stasis cuffs and about to see Optimus die, Prowl said that Processor over matter could help get out and hummed until it got him out just in time to get Prime loose of his cuffs. (Bumblebee hated the humming). He later used the technique in order to free Sari Sumdac from the overpowering energy of the AllSpark key but failed. He also tried Processor Over Matter on Omega Supreme in order to free the giant Autobot from Megatron's control.
finally having a flashback Prowl remembered how Yoketron told him how Processor over matter helped him see Prowl even with his hologram projector disguising him. He then took all Prowls upgrades away. When he escaped from Lockdown's ship Prowl used Processor over Matter to pick up the score board in the stadium off of Liar Starscream and Sentinel. This amazed Jazz who apparently never learned "P over M" even though he did finish his training. he then told Prowl that Yoketron would be proud to see him wear his helmet.
Whilst trapped inside Soundwave's virtual reality, Prowl made use of the Processor Over Matter technique to escape the reality and returned to the real world... sadly, Soundwave just knocked him out and plugged him in again.
In the episode "Endgame, Part II" Prowl and Jazz attempted to use Processor over matter to gather all of the scattered allspark fragents(one of which was in Starscream's head keeping him online) so they could use their power to creat a shield around the self-destructing Omega Supreme Clone to keep it from destroying the city(and supposedly everything within a 100 mile radius as said by Starscream). They gathered a large number of fragments but they still didn't have enough power to create the shield. Dispite Jazz's pleas Prowl sarificed his own spark to add enough power to create the shield. Optimus was caught in the shield while fighting Megatron. Megatron had pinned him to the shield, happy that at least he knew he would die taking Optimus Prime with him. At the last second what appeared to be Prowl's ghost(or his essence) appeared in the shield and took Optimus out of the shield out of the shield as the bomb went off, saving him.