How long is your peptide? How much do you have it?

Depending of this two questions:

LC-MS, NMR, 20% acrylamide SDS-PAGE, size-exclusion FPLC can be applied. Please feel free to ask, if I'm not a specialist in the technique for you, we will find someone knows more than both of us;)

Hi Jan

my peptide is 16 to 18 residue long. I have few mg of my each peptide. Except LC-MS i am not familiar with other techniques.

Except LC-MS other techniques are useless for your experiment :) You should see both substrate and products.

Please check before how to remove pepsin. Other issue I’m afraid are their self-digestion products (like in case of trypsin?). This you should check carefully.

several parallel digestion experiments, time dependent (0h, 2h, 4h to 1 day), followed by lyophilization and LC/MS/MS analysis

The stability of peptide can be checked by incubating peptide with pepsin  at optimal temperature