1. Did you change the residue count in the apes window? I think default is 100. That will determine expected peak count. However, you can also try adjusting contour level. Just delete all the peaks (pa - Del) and try again. And, you may want to delete selected peaks after apes as they are notified as probable noise. So, be careful not to lose selection right after apes run.

2. How many peaks do you have? If you dont have so many peaks, you can arbitrarily assign a few peaks and use guesses intensively. I did not develop any tool for 2D NOESY but I will keep that in mind there is a request.

Cheers,

Woonghee