Proofing can be two things: with regard to yeast, it is mixing your yeast, yeast food, and warm water and letting it sit somewhere warm for about 10 minutes so that the yeast has a chance to fully activate.
With regard to the dough, it is letting the finished and shaped dough sit somewhere warm for about an hour so that the yeast inside has a chance to work its magic and your loaf rises.
I've tried this a couple times recently as a loaf instead of rolls (sans bread machine) and it works well. I upped the quanitity of all ingredients by about 50%, increased bake time a little bit to get into the middle of the loaf, and it comes out tasty and sliceable. I've also done a carraway rye and a pumpernickel version.
The carraway version is easy, I just grind up a tabelspoon of carraway seeds with the flax, then add another tablespoon of whole seeds in with the dough as I knead.
The pumpernickel involves the two tablespoons of carraway seed (one ground, one whole) as well as two tablespoons of decaf instant coffee and two tablespoons of cocoa powder. This one was really phenomenal, great pumpernickel taste, and the heavier flavor of the pumpernickel bread masked and LC taste to the bread at all.
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