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Compared to free amino acids, protein amino acids in mushroom have gained little attention. No studies have investigated mushroom protein hydrolysis kinetics; moreover, investigation into cooking impact on protein amino acids is scarce. This study aimed to 1) examine the hydrolysis time-scheme of mushroom protein amino acids in order to investigate the hydrolysis method using a mushroom matrix; and 2) investigate the impact of cooking on protein amino acids within two groups: white and crimini mushrooms with a roasting cooking method and portobello and shiitake mushrooms with sautéing and roasting methods. For Aim 1, mushroom powder was hydrolyzed at 2, 4, 12, 24, 48, 72, and 96 hr. The results showed logical hydrolysis progression. For Aim 2, whole mushroom samples were hydrolyzed with the traditional 24 hr 6N acid hydrolysis. Protein amino acids in the hydrolysates were then quantified via EZ:Faast derivatization and ensuing GC-MS analysis. Significant cooking method and mushroom type interactions were observed for 66.7–81.8% of the 21–22 amino acids detected, confounding direct comparison of the two cooking methods. All total and most (66.7–100%) individual protein amino acids significantly decreased upon cooking for all samples. Met was the most limiting essential amino acid in all samples, but it was subject to oxidation-induced variance. The second most limiting amino acid, His, did not significantly differ between sautéing and roasting cooking methods. This study adds knowledge regarding mushroom's protein amino acid profile and how cooking methods affect the profile.