Here's when Optimus assigns Thomas to protect the Matrix, Blue Ruby and Black Pearl in Thomas' Place as a Prime.
Optimus Prime: Thomas.
Thomas: Yes, Optimus?
Optimus Prime: I knew that Tirek has returned.
Optimus Prime: The Princesses sent Mako and Spencer to spy on Tirek earlier and Mako found out Tirek's plans.
Princess Luna: He wishes to use the Matrix of Leadership to bring back Megatrain's army.
Thomas: So what are we gonna do?
Optimus Prime: That is why you must protect the Matrix.
Optimus Prime: Cause Tirek will want to get the Matrix With Ernie by his side, they will rule the world and the universe.
Thomas: Can't someone else do it?
Optimus Prime: No Thomas, you have to do it. Only a Prime can take the Matrix.
Princess Celestia: Tirek doesn't know that you're a Prime, so you have to do it.
Optimus Prime: But you must also protect the Blue Ruby and the Black Pearl as well.
Thomas: I thought Tirek couldn't steal magic anymore.
Princess Celestia: He can't but we can't risk him receiving the most powerful gems in the world.
Optimus Prime: So what will it be Thomas? [he takes the Matrix out of his chest]
Thomas: I'll do it!
Optimus Prime; Now, Listen to me Thomas, do not let Tirek and Ernie have the Matrix or the gems for anything! Even if it means making a sacrifice.The world will be doomed if you do so. Understand?
Thomas: I understand.
Optimus Prime: Good. [he place the Matrix and gems into Thomas]
[Thomas soon puffs away]
[With Ernie and Tirek]
Tirek: [sniffs] It's Canterlot. We're getting close.
Ernie: Once we ge the Matrix the universe is ours!