Fractions containing the peptide will be collected and lyophilized. The actual purity obviously depends on how conservatively the fractions are pooled. Users need to specify what level of purity is required. Even after lyophilization, peptides retain significant amounts of water. The water content of a given peptide powder varies depending on the sequence of the peptide, storage conditions, handling, and other factors.
Some peptides are very hygroscopic.
The presence of counter-ions cannot be avoided because of ion pairing. The exact concentration of the peptide in the crude product can be determined by amino acid analysis using a small aliquot from the crude peptide solution. The volume of this aliquot must be accurately measured and recorded because this value is necessary for calculating the concentration of the stock-solution. The extent of coupling will be estimated by amino acid analysis. The extent of peptide coupling will be determined by amino acid analysis.