Definition
Peptides carry charged groups, and in solid form those charges are balanced by counter-ions. Basic residues such as lysine, arginine and histidine, plus the free N-terminus, pair with anions: trifluoroacetate from synthesis and purification, or acetate and chloride after ion exchange. Counter-ions contribute to total powder mass, which is one reason net peptide content is below 100%, and they can influence solubility, hygroscopicity and behaviour in biological assays. Trifluoroacetate in particular has been reported to affect some cell-based readouts. The counter-ion is usually determined by ion chromatography, or by fluorine NMR for TFA. A complete certificate of analysis identifies the salt form so researchers can account for it in concentration calculations.