Your question is very general. Also, biological processes are not 0 and 1. If you use form D amino acids in the design of the peptide, it will be more difficult to digest tissue enzymes.techniques like PEGylation can also be used to increase the duration of the peptide in the body.to test for the peptide in the mouse's body, you can use an ELISA test to detect the peptide in the serum or plasma and urine of the animal.
Well... you are assuming that destruction by proteases is a bad thing? Understand that ALL vaccine antigens needs to be "processed" intracellularly to be able to be presented correctly to stimulate T cells. I'm not that well verse in how much free proteases are outside of cells... but I'm going to assume VERY little. Otherwise, you will be destroying your own cells and secreted proteins, etc.
Anyway... most peptide vaccines don't work by themselves. The formulation includes other things that push for development of memory and antibody responses.
i'm have more experience on protein based vaccines that peptide based vaccines, however based on literature the PEGylation seems a possible approacch to extend the peptide timelife after imunization and this seems to be also due to protection that PEG may confer against protease digestion.
Attached you can find an article that seems to me interesting