It depends what you want to do. Isoelectric precipitation will separate your protein from carbohydrates, but it often leads to irreversible aggregation and denaturation of your protein. So, it is an effective way of removing contaminaiting proteins from a solution of carbohydrates, but it would not be ideal if you wanted to purify a sample of protein. A better choice for purifying protein from a mixture of carbohydrates would be to use ammonium sulfate precipitation. This works in the same way, but the it usually will not denature your protein.
So, if you want to purify the carbohydrates use isoelectric precipitation. If you want to purify the protein, go with the ammonium sulfate precipitation.