Ammonium trifluoroacetate is widely used as a reagent in organic synthesis, particularly in the preparation of peptides and other biomolecules. It serves as a buffer in liquid chromatography, especially in mass spectrometry, due to its volatility and compatibility with analytical instruments. Additionally, it is employed in the synthesis of fluorinated compounds, where it acts as a source of trifluoroacetate ions. Its ability to stabilize reactive intermediates makes it valuable in various chemical reactions, including those involving sensitive or complex molecules.