I'm not quite sure I know exactly the right conditions to use, but you should be a little bit more specific as to how you plan on analyzing the peptides....
Are you just trying to verify them by size? Do you have an antibody probe?
I recently analyzed 10 kd proteins using PAGE. I made a 12% gel, and kept a good deal of space (maybe 3 cm) between the lowest MW marker and the bottom of the gel. I then stained with Coomassie.
My low weight proteins didn't take the coomassie stain very well, so I'll be trying silver stain later this week.
Thanks for suggestions. Well I do not know the exact size of peptides they are less than 2kda. They didn't appear on the 15%gel stained with coomassie. I thing should try tricine SDS page.