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I recently purchased a 50 gallon tank. Squirt is now about 3 inches.
The problem is when I but food that won't float like tuna or chicken in the tank he will follow it down about half way but then give up , therefore I end up with a beautiful collection of waste food at the bottom of the tank. I'm wondering is my tank too deep for him?

I don't think it's too deep, he just has to get used to going up and down.
Frankie and Ralph usually go down to the bottom of the tank and "forage" for pieces of sunken food after I've left the room, or in the morning if they're feeling a bit hungry.
Especially with things like tuna, I'm sure he'll figure out that if he wants that tasty morsel, he's going to have to go all the way to the bottom.
Try feeding him, then leaving. He might be so excited to see you (like most turtles are), that he's more intent on begging from you, instead of seeing that there's actually food around.

My turts are 3 inches and in a 50 gallon and they go up and down like elevators, so it's nothing to worry about. Ditto on what BullDog said.

If it's shredded tuna and chicken (like the stuff from the can), I stopped feeding that to my turtle because it's SO messy, it just goes all over. Rather, if you go and buy these little pouches of salmon (or tuna or chicken) over near those cans, it costs a little bit more, but then you can give them a chunk. My turtle takes the chunk from my fingers and swims away quickly with it in his mouth, like "MINE!!"

It's not that the water is too deep. He just has to get used to his surroundings.

In the meantime, if you want to feed him a piece of chicken as a treat, don't just toss it in the tank & wait for him to find it. Actually hold it up to his nose so he takes it from you. This will help ensure that he actually "eats" it and doesn't have to go looking for it.

Or you can feed him treats in a separate pan of water. I have been doing this with Sheba with great success over the last 18 yrs I have had her. It works great, and you never have to worry about a mess in the tank.