You could use iRefIndex. It integrates data from several protein-protein interaction databases. The last update was two years ago though. If you need to do it yourself, you need to map all interaction partners to the same reference gene or protein set. I typically map all interaction partners to EnsEMBL genes because I usually need gene level interactions and also this is easier than trying to identify protein isoforms across databases. If the latter is what you want, look at the method in the iRefIndex paper.

Ok, Thank you, This was really helpful