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This work aimed to validate a method for the quantification of free amino acids in cheese whey protein concentrate and cheese whey protein hydrolysate via gas chromatography coupled with mass spectrometry (GC–MS). For this, free amino acid analysis was carried out with deproteinisation, where the efficiencies of acetonitrile and trichloroacetic acid were compared, prior to derivatisation with N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide before GC–MS analysis. The results demonstrated that using trichloroacetic acid enabled the determination of 13 free amino acids (l -alanine, l -valine, l -leucine, l -isoleucine, l -proline, l -methionine, l -serine, l -phenylalanine, l -aspartic acid, l -glutamic acid, l -lysine, l -tyrosine, and l -cystine) in cheese whey protein concentrate and hydrolysate. The method was validated in terms of recovery (85–105%), limits of detection (0.03–0.77 μg mL−1), and limits of quantification (0.09–2.56 μg mL−1). This GC–MS methodology can be used in food laboratories for the quantification of some free amino acids, including branched-chain amino acids, in solid dairy products. [ABSTRACT FROM AUTHOR]