Trifluoroacetic acid (TFA) is widely used as a reagent and solvent in organic synthesis. It is particularly effective in deprotection reactions, such as the removal of Boc (tert-butoxycarbonyl) protecting groups from amines in peptide synthesis. Due to its strong acidity and volatility, TFA is easily removed after reaction completion, making it ideal for purification processes.

It serves as a catalyst in esterifications, alkylations, and other acid-promoted transformations. In chromatography, TFA is commonly used as an ion-pairing agent in reversed-phase HPLC for the separation of peptides and proteins, improving peak resolution and sample recovery.

TFA is also employed in the preparation of trifluoroacetyl derivatives of organic compounds, which are useful intermediates in pharmaceutical and agrochemical manufacturing. Its ability to stabilize certain reactive intermediates makes it valuable in the synthesis of fluorinated compounds, which often exhibit enhanced biological activity and metabolic stability.

In materials science, TFA is used in the production of fluoropolymers and electronic chemicals, including precursors for liquid crystals and semiconductors. It is also utilized in etching and cleaning processes in the electronics industry due to its corrosive nature and solubility properties.