Peps work with and without carbs. Personally I've been running a protocol called CPWO, or carbless post workout for about a week with great benefits. At any rate, to answer your question, it depends. In my case I use Isopure zero carb post-workout at the same time that I pin Modgrf-1/Ghrp-2 or Ipamorelin. Protein does not affect pulsation to any degree. Fats and, to a lesser degree, carbohydrates do. If you are going with the traditional approach of consuming protein AND carbs PWO then personally I would dose my GHRP/GHRH combo and then consume the protein and carbs 15 minutes later. This will only effect maximal pulsation in a minimal way and will ensure that your body has the raw materials that it needs to work with in order for hypertrophy to occour optimally.
This of course assumes that your prime goal is anabolism......