Protein quality, as determined by the PDCAAS method, is a measure of a protein's ability to provide adequate levels of essential amino acids for human needs. PDCAAS is calculated using an amino acid profile and true digestibility of a food protein. Soy protein is recognized as a high quality plant protein, but published PDCAAS values may vary based on the soy protein ingredient as well as the reproducibility and accuracy of the testing methods. Comparison of PDCAAS values for four differently processed soy ingredients, including three isolated soy proteins (ISP) and one soy protein concentrate (SPC), was made using two different laboratories with evaluation of the impact of the reproducibility and accuracy of amino acid profiles. PDCAAS calculations, using amino acid values from one laboratory, yielded a truncated PDCAAS of 1.00 for all four ingredients, while a second laboratory provided statistically significantly lower scores (0.95-1.00). We conclude that analytical method error can be a significant contributor to PDCAAS differences and can be mitigated by the application of amino acid nitrogen recovery correction factors.