Thanks for the multiple responses. I think the TSA agent did violate protocol in how she approached me, did not provide proper explanation, did not discuss how I would be patted down, how baby would be patted down, etc. She was also unprofessional when she criticized the fact that I didn't have a stroller or a car seat (neither of which are required).

If a pat down was necessary since I had unopened formula (and since I've flown out of PBI before with unopened formula I don't think it was necessary, as they have previously tested it w/o opening it, by taking the overlay off [but not breaking the cap seal] and putting it in a machine) then explain what you are doing in a professional manner and go through the standard speech. In this instance I probably would have opted for private screening as there might have been a place for my baby as I did not want a stranger touching her.

Yes, I lost my cool, but frankly I was glad several people heard what was going on. Three people later came up to me in the boarding area to express their own outrage, one woman said she really wanted to say something to the agent or offer to hold the baby but was afraid to.