How do you make sure that no salts are left in your preparations after purification and precipitation?

We QC our products by 31P NMR which reveals inorganic phosphate salt. This is usually the salt of most concern for enzymologists since it is an inhibitor of many polymerases. For other salts, the lambda max and epsilon values of the modified nucleoside are used to make sure the optical density matches the actual dry weight. The concentration of NTP in the final solution is determined spectrally. This spectra is not affected by the salt form of the triphosphate, assuring we deliver accurate quantities of our NTPs, based on the molecular weight of the free acid form.