Taken from the Encyclopizza dough troubleshooting guidehttp://www.correllconcepts.com/Encyclopizza/07_Dough_trouble-shooting/07_dough-crust_trouble-shooting.htm#_Toc533730480
31 - Crust forms bubbles during baking
Dough under-proofed (i.e., under-risen)
Use more-risen dough for making pizza. See the previous section on Under-risen Dough Balls. Also, read the chapter on Dough Management.
Use less-risen dough for making pizza. See the previous section on Over-risen Dough Balls. Also, read the chapter on Dough Management.
High percentage of water in dough formula
Reduce the water portion in the dough formula by 2 to 4 percent of flour weight. This can help reduce the presence of super-large (pita-bread style) bubbles.
COMMENT: Most bubbling problems are caused by under-proofed dough. For top quality crust, the recommended way to reduce bubbling is use optimally proofed dough—neither under-risen nor over-risen. However sometimes that’s not always possible. In emergency cases, when dough is under-proofed, perforate the rolled dough using a dough docker. However, docking has the effect of creating a very flat crust. So unless you desire a flat crust, docking should only be used as a last resort. Other methods of (possibly) reducing bubbles include (a) assembling the pizza with the soft bottom side of the dough facing up, and (b) using a slightly longer bake time and lower temperature. Because crust bubbling is a universal concern among pizzerias, the following special discussion is provided.
Discussion: Crust Bubbling
Dough/crust bubbling is a problem that has plagued pizzerias for decades. Of course, not all pizzerias consider it a problem. Some actually like bubbles because they feel their customers like them. However, many operators abhor bubbles, especially the large kind that move cheese and toppings off an entire slice or, worse yet, off half the pizza.
To eliminate bubbles it helps to know what happens during baking. Here’s how it works. Dough contains thousand of air cells created during fermentation or proofing. These air cells are separated from one another by cell walls. At the onset of baking, the air cells expand slightly due to a burst of yeast activity, a process called oven spring. Following oven spring, the starch in the cell walls gelatinizes, or absorbs surrounding moisture. Gelatinization, in turn, causes the protein (i.e., gluten) in the cell walls to lose moisture. The reduction of moisture in the protein causes it to retract and become less elastic. This results in pinpoint holes forming in the cell walls. Following that, the protein coagulates and, thereby, firms up—giving the crust its firm cellular structure. Following coagulation, steam develops in the cells and vents out the pinpoint holes and, eventually, out the top of the crust. To see evidence of where steam vents out the top of the crust, scrape away the cheese and sauce from a properly proofed, properly baked pizza and you’ll see many small holes in the top of the crust, which served as steam vents.
For the pinpoint holes to form in the cell walls, the walls must be of the proper thickness and contain the proper amount of moisture. When dough is improperly proofed—that is, either under-risen or over-risen—the cell walls are of the “wrong” thickness. In under-proofed dough they are too thick. In over-proofed dough they are too thin.
When holes fail to form in the cell walls, the steam generated during baking cannot dissipate properly from the cells. As a result, it builds up within each cell, forcing the cell upward and eventually ripping the cell walls. In effect, instead of dissipating through an open cellular network and out the top of the crust, as happens with properly proofed dough, the steam rips open the cellular structure in a chain reaction—rupturing one cell wall after another and, eventually, forming one large cell.
There’s a difference between bubbles formed from under-proofing versus over-proofing. Bubbles from under-proofing tend to be flat but large in diameter. If unpopped, they can blow up an entire pizza. This is the process by which pita or pocket bread is made. Bubbles from over-proofing tend to be high but smaller in diameter. They rise up like little ping-pong balls and eventually form a hole at the top, at which time they stop expanding. They almost always burn. Most pizza bubbling problems are of the under-proofed type.
To resolve a bubbling problem, dough fermentation must be adjusted accordingly. To stop bubbling caused by under-proofed dough, increase the amount of fermentation. To stop bubbling caused by over-proofed dough, reduce the amount of fermentation.
In addition to proper proofing, it has been found that reducing the amount of water in a dough formula can help with reducing bubbling when dealing with the under-proofed type. The reduction in moisture aids in creating the pinpoint holes in the cells walls.
EDIY (2/1/2013): For an alternative to the Correll link, see http://web.archive.org/web/20040602213637/http://correllconcepts.com/Encyclopizza/07_Dough_trouble-shooting/07_dough-crust_trouble-shooting.htm