I would rather negative punishment (removal of something good), than positive punishment (giving something unwanted - scary sounds).
My concern with the use of a shaker can, or any other startle-method, would be that you may create a negative association between the small dog and the scary stimulus. And wouldn't it be a shame to create a negative association for your dobe?
We have a yorkshire terrier and doberman living peacefully in the same house, and have not had to use anything scary, startling, or uncomfortable.
We encouraged Eva to play on the ground (rather than standing, bouncing, and running around) when she wanted to approach Maya (the yorkie). If she got up to bounce around, we simply took her by the collar (gently and calmly), and coaxed her back into her down position. Yes, we needed to repeat this several times throughout the day. It takes time, and calm, consistent responses.
Eva (as most dobes do) has a tendency to want to use her feet to swat and poke other dogs into playing with her (this pretty well never works, as most dogs just get pissed off). With the little one, every time we saw Eva use her feet, we would tell her "no feet", and move her paws away.
Throughout the first several months, the two were not allowed free time together unsupervised (not that we allowed a dober-pup free unsupervised time regardless), and all play was closely monitored. I spent a lot of time on the floor with the dogs at first, then sitting or standing very close by if I needed to interfeer.
If Eva was too riled up, and needed too many corrections, she would be put in a time-out. Time-outs were either 30-45seconds in the bathroom (door closed), behind a baby gate, or on the other end of the room (away from Maya).
After some time, when she was getting much better when interacting with Maya, if she did slip-up, we opted for a time-out, rather than any redirections. At that point, she wasn't being taught what to do anymore, she was being reminded that she didn't follow the rules. Does that make sense?
Large and small dogs need to learn how to interact appropriately with each other. Dobes can learn fairly easily how to play differently with small dogs, but you also need to be thinking about how to approach your little dog so that she can learn how to accept your big dog.
It sounds like they both need lots of positive reinforcement while interacting. Reinforce the dobe for not being obnoxious, and reinforce the peke for being around your dobe and tolerating play (which, if rewarded frequently enough with high-value reinforcement, should go from tolerance to actual enjoyment).
Good luck with the two of them. Just keep the sessions brief and calm, but do not give up on your pups. They can both learn better social manners with your consistency.