Assuming you mean machine quilting -
Unless you have a persnickety machine, you can use just about anything for quilting! I think it's best to keep a cotton thread in the bobbin, but some people use specialty threads there, too.
An embroidery needle might work better with some threads to prevent fraying.
Some battings might work better than others (preventing fraying, again).
I think I would restrict the use of non-cotton threads to decorative quilts, because bed quilts need to be washable and get more handling. I like to make sure my bed quilts are very durable. Cotton seems a better choice for that.