Why is trifluoroacetic acid (TFA) the preferred acid for the sample pre-treatment and elution solvent?
TFA is commonly used as an ion-pairing agent in peptide and protein analysis for sample cleanup as well as high performance liquid chromatography (HPLC) applications. In an acidic environment, any basic residues on the peptide will form a positive charge. The negative counter ion in the acid will then pair with the positively charged base. Using a counter ion with a small organic chain, like TFA, will increase the hydrophobicity of the peptide and increase the affinity of the peptide for the hydrophobic stationary phase.
