How would I neutralize a PEP (Phosphoenolpyruvic) acid?
For our work, we also need to make 100 mM PEP and we neutralize it using KOH. Traditionally, using Na+ based salts isn't ideal for biological assays so K+ salts are better for our applications.

Alternatively, if you're adding the PEP to a different solution, you can buffer the reaction solution. While the Phosphate does have a good amount of buffering capacity, effective concentrations of the molecule will be low so you ultimately won't be adding much.